Effect of maternal exercises on biophysical fetal and maternal parameters: a transversal study

PubMed Central

dos Santos, Caroline Mombaque; dos Santos, Wendel Mombaque; Gallarreta, Francisco Maximiliano Pancich; Pigatto, Camila; Portela, Luiz Osório Cruz; de Morais, Edson Nunes

2016-01-01

ABSTRACT Objective To evaluate the acute effects of maternal and fetal hemodynamic responses in pregnant women submitted to fetal Doppler and an aerobic physical exercise test according to the degree of effort during the activity and the impact on the well-being. Methods Transversal study with low risk pregnant women, obtained by convenience sample with gestational age between 26 to 34 weeks. The participants carry out a progressive exercise test. Results After the exercise session, reduced resistance (p=0.02) and pulsatility indices (p=0.01) were identified in the umbilical artery; however, other Doppler parameters analyzed, in addition to cardiotocography and fetal biophysical profile did not achieve significant change. Maternal parameters obtained linear growth with activity, but it was not possible to establish a standard with the Borg scale, and oxygen saturation remained stable. Conclusion A short submaximal exercise had little effect on placental blood flow after exercise in pregnancies without complications, corroborating that healthy fetus maintains homeostasis even in situations that alter maternal hemodynamics. PMID:28076590

Evaluating Machine Learning Regression Algorithms for Operational Retrieval of Biophysical Parameters: Opportunities for Sentinel

NASA Astrophysics Data System (ADS)

Verrelst, Jochem; Rivera, J. P.; Alonso, L.; Guanter, L.; Moreno, J.

2012-04-01

ESA’s upcoming satellites Sentinel-2 (S2) and Sentinel-3 (S3) aim to ensure continuity for Landsat 5/7, SPOT- 5, SPOT-Vegetation and Envisat MERIS observations by providing superspectral images of high spatial and temporal resolution. S2 and S3 will deliver near real-time operational products with a high accuracy for land monitoring. This unprecedented data availability leads to an urgent need for developing robust and accurate retrieval methods. Machine learning regression algorithms could be powerful candidates for the estimation of biophysical parameters from satellite reflectance measurements because of their ability to perform adaptive, nonlinear data fitting. By using data from the ESA-led field campaign SPARC (Barrax, Spain), it was recently found [1] that Gaussian processes regression (GPR) outperformed competitive machine learning algorithms such as neural networks, support vector regression) and kernel ridge regression both in terms of accuracy and computational speed. For various Sentinel configurations (S2-10m, S2- 20m, S2-60m and S3-300m) three important biophysical parameters were estimated: leaf chlorophyll content (Chl), leaf area index (LAI) and fractional vegetation cover (FVC). GPR was the only method that reached the 10% precision required by end users in the estimation of Chl. In view of implementing the regressor into operational monitoring applications, here the portability of locally trained GPR models to other images was evaluated. The associated confidence maps proved to be a good indicator for evaluating the robustness of the trained models. Consistent retrievals were obtained across the different images, particularly over agricultural sites. To make the method suitable for operational use, however, the poorer confidences over bare soil areas suggest that the training dataset should be expanded with inputs from various land cover types.

Quantifying the thermal heat requirement of Brassica in assessing biophysical parameters under semi-arid microenvironments

NASA Astrophysics Data System (ADS)

Adak, Tarun; Chakravarty, N. V. K.

2010-07-01

Evaluation of the thermal heat requirement of Brassica spp. across agro-ecological regions is required in order to understand the further effects of climate change. Spatio-temporal changes in hydrothermal regimes are likely to affect the physiological growth pattern of the crop, which in turn will affect economic yields and crop quality. Such information is helpful in developing crop simulation models to describe the differential thermal regimes that prevail at different phenophases of the crop. Thus, the current lack of quantitative information on the thermal heat requirement of Brassica crops under debranched microenvironments prompted the present study, which set out to examine the response of biophysical parameters [leaf area index (LAI), dry biomass production, seed yield and oil content] to modified microenvironments. Following 2 years of field experiments on Typic Ustocrepts soils under semi-arid climatic conditions, it was concluded that the Brassica crop is significantly responsive to microenvironment modification. A highly significant and curvilinear relationship was observed between LAI and dry biomass production with accumulated heat units, with thermal accumulation explaining ≥80% of the variation in LAI and dry biomass production. It was further observed that the economic seed yield and oil content, which are a function of the prevailing weather conditions, were significantly responsive to the heat units accumulated from sowing to 50% physiological maturity. Linear regression analysis showed that growing degree days (GDD) could indicate 60-70% variation in seed yield and oil content, probably because of the significant response to differential thermal microenvironments. The present study illustrates the statistically strong and significant response of biophysical parameters of Brassica spp. to microenvironment modification in semi-arid regions of northern India.

Chapter 5 - Development of biophysical gradient layers for the LANDFIRE Prototype Project

Treesearch

Lisa Holsinger; Robert E. Keane; Russell Parsons; Eva Karau

2006-01-01

Distributions of plant species are generally continuous, gradually changing across landscapes and blending into each other due to the influence of, and interactions between, a complex array of biophysical gradients (Whittaker 1967; 1975). Key biophysical gradients for understanding vegetation distributions include moisture, temperature, evaporative demand, nutrient...

Contactless diagnostics of biophysical parameters of skin and blood on the basis of approximating functions for radiation fluxes scattered by skin

NASA Astrophysics Data System (ADS)

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

2014-03-01

Approximating expressions are derived to calculate spectral and spatial characteristics of diffuse reflection of light from a two-layer medium mimicking human skin. The effectiveness of the use of these expressions in the optical diagnosis of skin biophysical parameters (tissue scattering parameters, concentration of melanin in the epidermis, concentration of total haemoglobin and bilirubin in the tissues of the dermis) and content of haemoglobin derivatives in blood (oxy-, deoxy-, met-, carboxy- and sulfhaemoglobin) is analysed numerically. The methods are proposed to determine in realtime these parameters without contact of the measuring instrument with the patient's body.

Biophysics of protein evolution and evolutionary protein biophysics

PubMed Central

Sikosek, Tobias; Chan, Hue Sun

2014-01-01

The study of molecular evolution at the level of protein-coding genes often entails comparing large datasets of sequences to infer their evolutionary relationships. Despite the importance of a protein's structure and conformational dynamics to its function and thus its fitness, common phylogenetic methods embody minimal biophysical knowledge of proteins. To underscore the biophysical constraints on natural selection, we survey effects of protein mutations, highlighting the physical basis for marginal stability of natural globular proteins and how requirement for kinetic stability and avoidance of misfolding and misinteractions might have affected protein evolution. The biophysical underpinnings of these effects have been addressed by models with an explicit coarse-grained spatial representation of the polypeptide chain. Sequence–structure mappings based on such models are powerful conceptual tools that rationalize mutational robustness, evolvability, epistasis, promiscuous function performed by ‘hidden’ conformational states, resolution of adaptive conflicts and conformational switches in the evolution from one protein fold to another. Recently, protein biophysics has been applied to derive more accurate evolutionary accounts of sequence data. Methods have also been developed to exploit sequence-based evolutionary information to predict biophysical behaviours of proteins. The success of these approaches demonstrates a deep synergy between the fields of protein biophysics and protein evolution. PMID:25165599

Biophysics of olfaction

NASA Astrophysics Data System (ADS)

Marques Simoes de Souza, Fabio; Antunes, Gabriela

2007-03-01

The majority of the biophysical models of olfaction have been focused on the electrical properties of the system, which is justified by the relative facility of recording the electrical activity of the olfactory cells. However, depending on the level of detail utilized, a biophysical model can explore molecular, cellular and network phenomena. This review presents the state of the art of the biophysical approach to understanding olfaction. The reader is introduced to the principal problems involving the study of olfaction and guided gradually to comprehend why it is important to develop biophysical models to investigate olfaction. A large number of representative biophysical efforts in olfaction, their main contributions, the trends for the next generations of biophysical models and the improvements that may be explored by future biophysicists of olfaction have been reviewed.

Mesoscale, Radiometrically Referenced, Multi-Temporal Hyperspectral Data for Co2 Leak Detection by Locating Spatial Variation of Biophysically Relevant Parameters

NASA Astrophysics Data System (ADS)

McCann, Cooper Patrick

Low-cost flight-based hyperspectral imaging systems have the potential to provide valuable information for ecosystem and environmental studies as well as aide in land management and land health monitoring. This thesis describes (1) a bootstrap method of producing mesoscale, radiometrically-referenced hyperspectral data using the Landsat surface reflectance (LaSRC) data product as a reference target, (2) biophysically relevant basis functions to model the reflectance spectra, (3) an unsupervised classification technique based on natural histogram splitting of these biophysically relevant parameters, and (4) local and multi-temporal anomaly detection. The bootstrap method extends standard processing techniques to remove uneven illumination conditions between flight passes, allowing the creation of radiometrically self-consistent data. Through selective spectral and spatial resampling, LaSRC data is used as a radiometric reference target. Advantages of the bootstrap method include the need for minimal site access, no ancillary instrumentation, and automated data processing. Data from a flight on 06/02/2016 is compared with concurrently collected ground based reflectance spectra as a means of validation achieving an average error of 2.74%. Fitting reflectance spectra using basis functions, based on biophysically relevant spectral features, allows both noise and data reductions while shifting information from spectral bands to biophysical features. Histogram splitting is used to determine a clustering based on natural splittings of these fit parameters. The Indian Pines reference data enabled comparisons of the efficacy of this technique to established techniques. The splitting technique is shown to be an improvement over the ISODATA clustering technique with an overall accuracy of 34.3/19.0% before merging and 40.9/39.2% after merging. This improvement is also seen as an improvement of kappa before/after merging of 24.8/30.5 for the histogram splitting technique

Biophysics of NASA radiation quality factors.

PubMed

Cucinotta, Francis A

2015-09-01

NASA has implemented new radiation quality factors (QFs) for projecting cancer risks from space radiation exposures to astronauts. The NASA QFs are based on particle track structure concepts with parameters derived from available radiobiology data, and NASA introduces distinct QFs for solid cancer and leukaemia risk estimates. The NASA model was reviewed by the US National Research Council and approved for use by NASA for risk assessment for International Space Station missions and trade studies of future exploration missions to Mars and other destinations. A key feature of the NASA QFs is to represent the uncertainty in the QF assessments and evaluate the importance of the QF uncertainty to overall uncertainties in cancer risk projections. In this article, the biophysical basis for the probability distribution functions representing QF uncertainties was reviewed, and approaches needed to reduce uncertainties were discussed. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Dynamic causal modelling: a critical review of the biophysical and statistical foundations.

PubMed

Daunizeau, J; David, O; Stephan, K E

2011-09-15

The goal of dynamic causal modelling (DCM) of neuroimaging data is to study experimentally induced changes in functional integration among brain regions. This requires (i) biophysically plausible and physiologically interpretable models of neuronal network dynamics that can predict distributed brain responses to experimental stimuli and (ii) efficient statistical methods for parameter estimation and model comparison. These two key components of DCM have been the focus of more than thirty methodological articles since the seminal work of Friston and colleagues published in 2003. In this paper, we provide a critical review of the current state-of-the-art of DCM. We inspect the properties of DCM in relation to the most common neuroimaging modalities (fMRI and EEG/MEG) and the specificity of inference on neural systems that can be made from these data. We then discuss both the plausibility of the underlying biophysical models and the robustness of the statistical inversion techniques. Finally, we discuss potential extensions of the current DCM framework, such as stochastic DCMs, plastic DCMs and field DCMs. Copyright © 2009 Elsevier Inc. All rights reserved.

Retrieval of biophysical parameters with AVIRIS and ISM: The Landes Forest, south west France

NASA Technical Reports Server (NTRS)

Zagolski, F.; Gastellu-Etchegorry, J. P.; Mougin, E.; Giordano, G.; Marty, G.; Letoan, T.; Beaudoin, A.

1992-01-01

The first steps of an experiment for investigating the capability of airborne spectrometer data for retrieval of biophysical parameters of vegetation, especially water conditions are presented. Airborne Visible/Infrared Imaging Spectrometer (AVIRIS) and ISM data were acquired in the frame of the 1991 NASA/JPL and CNES campaigns on the Landes, South west France, a large and flat forest area with mainly maritime pines. In-situ measurements were completed at that time; i.e. reflectance spectra, atmospheric profiles, sampling for further laboratory analyses of elements concentrations (lignin, water, cellulose, nitrogen,...). All information was integrated in an already existing data base (age, LAI, DBH, understory cover,...). A methodology was designed for (1) obtaining geometrically and atmospherically corrected reflectance data, (2) registering all available information, and (3) analyzing these multi-source informations. Our objective is to conduct comparative studies with simulation reflectance models, and to improve these models, especially in the MIR.

Biophysical mechanism of differential growth during gravitropism

NASA Technical Reports Server (NTRS)

Cosgrove, D.

1984-01-01

A research project is described the goal of which is to determine the mechanism of gravitropic curvature in plant stems at the biophysical and the cellular level. The reorientation of plant organs under the influence of gravity is due to differential growth of the upper and lower sides of the organ. The rate of plant cell enlargement is governed by four biophysical parameters: (1) the extensibility of the cell wall; (2) the minimum stress in the cell wall required for wall expansion (the "yield threshold'); (3) the osmotic pressure difference between the cell contents and the water source; and (4) the hydraulic conductivity of the pathway for water uptake. Gravitropic response must involve differential alteration of one or more of these four parameters on the two sides of the growing organ. Each of these factors will be examined to assess the role it plays in gravitropism.

Hyperspectral measurements for estimating biophysical parameters and CO2 exchanges in a rice field

NASA Astrophysics Data System (ADS)

Rossini, M.; Migliavacca, M.; Meroni, M.; Manca, G.; Cogliati, S.; Busetto, L.; Picchi, V.; Galvagno, M.; Colombo, R.; Seufert, G.

2009-04-01

The objective of this work was to monitor the main biophysical and structural parameters as well as the CO2 exchanges between atmosphere and a terrestrial ecosystem from remote and high spectral resolution spectroradiometric measurements. Estimation of photosynthetic rate or gross primary productivity from remotely sensed data is based on the light use efficiency model (LUE), which states that carbon exchange is a function of the photosynthetically active radiation absorbed by vegetation (APAR) and the radiation use efficiency (ɛ) which represents the conversion efficiency of energy to fixed carbon. Hyperspectral data were used in this study in order to derived both the APAR of green vegetation and the ɛ term. The experimental site was a rice paddy field in North Italy equipped with an Eddy Covariance (EC) flux measurement tower (Castellaro IES-JRC site). Intensive field campaigns were conducted during summer 2007 and 2008. In each sampling day, canopy optical properties, canopy structure, biophysical and ecophysiological parameters were measured. EC fluxes were calculated with a time step of 30 minutes according to EUROFLUX methodology. Measured half-hourly net ecosystem exchange (NEE) was partitioned to derive half hourly gross ecosystem production (GEP). Canopy reflectance spectra were collected under clear sky conditions using two portable spectrometers (HR4000, OceanOptics, USA) characterised by different spectral resolutions. A spectrometer characterised by a Full Width at Half Maximum (FWHM) of 0.13 nm was used to estimate steady-state fluorescence (F) and a second one with a FWHM of 2.8 nm was used for the computation of traditional vegetation indices (e.g. NVDI, Normalized Difference Vegetation Index and SAVI, Soil Adjusted Vegetation Index) and PRI (Photochemical Reflectance Index, Gamon et al. 1992). F was estimated by exploiting a variation of the Fraunhofer Line Depth (FLD) principle (Plascyk 1975): the spectral fitting method described in Meroni

Biotic games and cloud experimentation as novel media for biophysics education

NASA Astrophysics Data System (ADS)

Riedel-Kruse, Ingmar; Blikstein, Paulo

2014-03-01

First-hand, open-ended experimentation is key for effective formal and informal biophysics education. We developed, tested and assessed multiple new platforms that enable students and children to directly interact with and learn about microscopic biophysical processes: (1) Biotic games that enable local and online play using galvano- and photo-tactic stimulation of micro-swimmers, illustrating concepts such as biased random walks, Low Reynolds number hydrodynamics, and Brownian motion; (2) an undergraduate course where students learn optics, electronics, micro-fluidics, real time image analysis, and instrument control by building biotic games; and (3) a graduate class on the biophysics of multi-cellular systems that contains a cloud experimentation lab enabling students to execute open-ended chemotaxis experiments on slimemolds online, analyze their data, and build biophysical models. Our work aims to generate the equivalent excitement and educational impact for biophysics as robotics and video games have had for mechatronics and computer science, respectively. We also discuss how scaled-up cloud experimentation systems can support MOOCs with true lab components and life-science research in general.

Non-invasive diagnostics of several structural and biophysical parameters of skin cover by spectral light reflectance

NASA Astrophysics Data System (ADS)

Ivanov, Arkady P.; Barun, Vladimir V.

2007-05-01

A calculation scheme and an algorithm to simultaneously diagnose several structural and biophysical parameters of skin by reflected light are constructed in the paper. The procedure is based the fact that, after absorption and scattering, light reflected by tissue contains information on its optically active chromophores and structure. The problem on isolating the desired parameters is a spectroscopic one under multiple scattering conditions. The latter considerably complicates the solution of the problem and requires the elaboration of an approach that is specific to the object studied. The procedure presented in the paper is based on spectral tissue model properties proposed earlier and engineering methods for solving the radiative transfer equation. The desired parameters are melanin and blood volume fractions, f and c, epidermis thickness d, mean diameter D of capillaries, and blood oxygenation degree S. Spectral diffuse reflectance R(λ) of skin over the range of 400 to 850 nm was calculated as a first stage. Then the sensitivity of R(λ) to the above parameters was studied to optimize the algorithm by wavelengths and to propose an experimental scheme for diagnostics. It is shown that blood volume fraction and f*d product can be rather surely determined by the reflected green -- red light. One can find f and d separately as well as D by the blue reflectance. The last stage is the derivation of S at about 600 nm.

Biophysics of α-Synuclein Membrane Interactions

PubMed Central

Pfefferkorn, Candace M.; Jiang, Zhiping; Lee, Jennifer C.

2011-01-01

Membrane proteins participate in nearly all cellular processes; however, because of experimental limitations, their characterization lags far behind that of soluble proteins. Peripheral membrane proteins are particularly challenging to study because of their inherent propensity to adopt multiple and/or transient conformations in solution and upon membrane association. In this review, we summarize useful biophysical techniques for the study of peripheral membrane proteins and their application in the characterization of the membrane interactions of the natively unfolded and Parkinson’s disease (PD) related protein, α-synuclein (α-syn). We give particular focus to studies that have led to the current understanding of membrane-bound α-syn structure and the elucidation of specific membrane properties that affect α-syn-membrane binding. Finally, we discuss biophysical evidence supporting a key role for membranes and α-syn in PD pathogenesis. PMID:21819966

Cell biology, biophysics, and mechanobiology: From the basics to Clinics.

PubMed

Zeng, Y

2017-04-29

Cell biology, biomechanics and biophysics are the key subjects that guide our understanding in diverse areas of tissue growth, development, remodeling and homeostasis. Novel discoveries such as molecular mechanism, and mechanobiological mechanism in cell biology, biomechanics and biophysics play essential roles in our understanding of the pathogenesis of various human diseases, as well as in designing the treatment of these diseases. In addition, studies in these areas will also facilitate early diagnostics of human diseases, such as cardiovascular diseases and cancer. In this special issue, we collected 10 original research articles and 1 review...

Radiation dosimetry and biophysical models of space radiation effects

NASA Technical Reports Server (NTRS)

Cucinotta, Francis A.; Wu, Honglu; Shavers, Mark R.; George, Kerry

2003-01-01

Estimating the biological risks from space radiation remains a difficult problem because of the many radiation types including protons, heavy ions, and secondary neutrons, and the absence of epidemiology data for these radiation types. Developing useful biophysical parameters or models that relate energy deposition by space particles to the probabilities of biological outcomes is a complex problem. Physical measurements of space radiation include the absorbed dose, dose equivalent, and linear energy transfer (LET) spectra. In contrast to conventional dosimetric methods, models of radiation track structure provide descriptions of energy deposition events in biomolecules, cells, or tissues, which can be used to develop biophysical models of radiation risks. In this paper, we address the biophysical description of heavy particle tracks in the context of the interpretation of both space radiation dosimetry and radiobiology data, which may provide insights into new approaches to these problems.

Molecular and Cellular Biophysics

NASA Astrophysics Data System (ADS)

Jackson, Meyer B.

2006-01-01

Molecular and Cellular Biophysics provides advanced undergraduate and graduate students with a foundation in the basic concepts of biophysics. Students who have taken physical chemistry and calculus courses will find this book an accessible and valuable aid in learning how these concepts can be used in biological research. The text provides a rigorous treatment of the fundamental theories in biophysics and illustrates their application with examples. Conformational transitions of proteins are studied first using thermodynamics, and subsequently with kinetics. Allosteric theory is developed as the synthesis of conformational transitions and association reactions. Basic ideas of thermodynamics and kinetics are applied to topics such as protein folding, enzyme catalysis and ion channel permeation. These concepts are then used as the building blocks in a treatment of membrane excitability. Through these examples, students will gain an understanding of the general importance and broad applicability of biophysical principles to biological problems. Offers a unique synthesis of concepts across a wide range of biophysical topics Provides a rigorous theoretical treatment, alongside applications in biological systems Author has been teaching biophysics for nearly 25 years

A new tower-based hyperspectral system for the estimation of CO2 fluxes and biophysical parameters in a subalpine grassland ecosystem

NASA Astrophysics Data System (ADS)

Vescovo, L.; Gianelle, D.; Marcolla, B.; Zaldei, A.; Sakowska, K.

2013-12-01

Linking optical remote sensing with carbon fluxes and biophysical parameters is critical to exploit spatial and temporal extensive information useful for validating model simulations at different scales. Proximal sensing is fundamental to quantify and understand the seasonal dynamics of ecosystems and to upscale the observations carried out at the ground level. In this study, we present the results from an ongoing research project at the FLUXNET eddy covariance site of Monte Bondone (Italy). The site is located at 1550 m a.s.l. on a mountain plateau in the Italian Alps (Viote del Monte Bondone). The area is managed as an extensively-managed meadow, cut once a year, and dominated by Nardus stricta and Festuca nigrescens. The climate of this area is sub-continental (warm and wet summer), with precipitation peaks in spring and autumn. A new hyperspectral system (WhiteRef Box, developed by Fondazione Edmund Mach in collaboration with the Institute of Biometeorology, CNR, Italy) based on the ASD FieldSpec spectrometer (spectral range 350-2500 nm, resolution ~3 nm at 700 nm) was designed to acquire continuous radiometric measurements. The system was installed on the eddy covariance tower at a height of 6 m, with a field of view of 25°. To obtain reflectance values, white panel radiance spectra and canopy radiance spectra were collected every 5 minutes between 10:00 a.m. and 1:00 p.m. (solar time) during the growing season of 2013. In addition, measurements of biophysical parameters such as above-ground biomass, fraction of Absorbed Photosynthetically Active Radiation (fAPAR), Plant Area Index, Canopy Chlorophyll Content, Canopy Water Content and Green Herbage Ratio were performed at weekly intervals within the spectrometer footprint (~5 m2). In this work, we present some preliminary results regarding the potential of spectral vegetation indices - based on VNIR and SWIR spectral bands- for capturing seasonal trends of CO2 fluxes as well as vegetation biophysical

Biophysics of α-synuclein membrane interactions.

PubMed

Pfefferkorn, Candace M; Jiang, Zhiping; Lee, Jennifer C

2012-02-01

Membrane proteins participate in nearly all cellular processes; however, because of experimental limitations, their characterization lags far behind that of soluble proteins. Peripheral membrane proteins are particularly challenging to study because of their inherent propensity to adopt multiple and/or transient conformations in solution and upon membrane association. In this review, we summarize useful biophysical techniques for the study of peripheral membrane proteins and their application in the characterization of the membrane interactions of the natively unfolded and Parkinson's disease (PD) related protein, α-synuclein (α-syn). We give particular focus to studies that have led to the current understanding of membrane-bound α-syn structure and the elucidation of specific membrane properties that affect α-syn-membrane binding. Finally, we discuss biophysical evidence supporting a key role for membranes and α-syn in PD pathogenesis. This article is part of a Special Issue entitled: Membrane protein structure and function. Copyright © 2011. Published by Elsevier B.V.

Senegalese land surface change analysis and biophysical parameter estimation using NOAA AVHRR spectral data

NASA Technical Reports Server (NTRS)

Vukovich, Fred M.; Toll, David L.; Kennard, Ruth L.

1989-01-01

Surface biophysical estimates were derived from analysis of NOAA Advanced Very High Spectral Resolution (AVHRR) spectral data of the Senegalese area of west Africa. The parameters derived were of solar albedo, spectral visible and near-infrared band reflectance, spectral vegetative index, and ground temperature. Wet and dry linked AVHRR scenes from 1981 through 1985 in Senegal were analyzed for a semi-wet southerly site near Tambacounda and a predominantly dry northerly site near Podor. Related problems were studied to convert satellite derived radiance to biophysical estimates of the land surface. Problems studied were associated with sensor miscalibration, atmospheric and aerosol spatial variability, surface anisotropy of reflected radiation, narrow satellite band reflectance to broad solar band conversion, and ground emissivity correction. The middle-infrared reflectance was approximated with a visible AVHRR reflectance for improving solar albedo estimates. In addition, the spectral composition of solar irradiance (direct and diffuse radiation) between major spectral regions (i.e., ultraviolet, visible, near-infrared, and middle-infrared) was found to be insensitive to changes in the clear sky atmospheric optical depth in the narrow band to solar band conversion procedure. Solar albedo derived estimates for both sites were not found to change markedly with significant antecedent precipitation events or correspondingly from increases in green leaf vegetation density. The bright soil/substrate contributed to a high albedo for the dry related scenes, whereas the high internal leaf reflectance in green vegetation canopies in the near-infrared contributed to high solar albedo for the wet related scenes. The relationship between solar albedo and ground temperature was poor, indicating the solar albedo has little control of the ground temperature. The normalized difference vegetation index (NDVI) and the derived visible reflectance were more sensitive to antecedent

New horizons in Biophysics

PubMed Central

2011-01-01

This editorial celebrates the re-launch of PMC Biophysics previously published by PhysMath Central, in its new format as BMC Biophysics published by BioMed Central with an expanded scope and Editorial Board. BMC Biophysics will fill its own niche in the BMC series alongside complementary companion journals including BMC Bioinformatics, BMC Medical Physics, BMC Structural Biology and BMC Systems Biology. PMID:21595996

Biophysical applications of neutron Compton scattering

NASA Astrophysics Data System (ADS)

Wanderlingh, U. N.; Albergamo, F.; Hayward, R. L.; Middendorf, H. D.

Neutron Compton scattering (NCS) can be applied to measuring nuclear momentum distributions and potential parameters in molecules of biophysical interest. We discuss the analysis of NCS spectra from peptide models, focusing on the characterisation of the amide proton dynamics in terms of the width of the H-bond potential well, its Laplacian, and the mean kinetic energy of the proton. The Sears expansion is used to quantify deviations from the high-Q limit (impulse approximation), and line-shape asymmetry parameters are evaluated in terms of Hermite polynomials. Results on NCS from selectively deuterated acetanilide are used to illustrate this approach.

Assimilation of Biophysical Neuronal Dynamics in Neuromorphic VLSI.

PubMed

Wang, Jun; Breen, Daniel; Akinin, Abraham; Broccard, Frederic; Abarbanel, Henry D I; Cauwenberghs, Gert

2017-12-01

Representing the biophysics of neuronal dynamics and behavior offers a principled analysis-by-synthesis approach toward understanding mechanisms of nervous system functions. We report on a set of procedures assimilating and emulating neurobiological data on a neuromorphic very large scale integrated (VLSI) circuit. The analog VLSI chip, NeuroDyn, features 384 digitally programmable parameters specifying for 4 generalized Hodgkin-Huxley neurons coupled through 12 conductance-based chemical synapses. The parameters also describe reversal potentials, maximal conductances, and spline regressed kinetic functions for ion channel gating variables. In one set of experiments, we assimilated membrane potential recorded from one of the neurons on the chip to the model structure upon which NeuroDyn was designed using the known current input sequence. We arrived at the programmed parameters except for model errors due to analog imperfections in the chip fabrication. In a related set of experiments, we replicated songbird individual neuron dynamics on NeuroDyn by estimating and configuring parameters extracted using data assimilation from intracellular neural recordings. Faithful emulation of detailed biophysical neural dynamics will enable the use of NeuroDyn as a tool to probe electrical and molecular properties of functional neural circuits. Neuroscience applications include studying the relationship between molecular properties of neurons and the emergence of different spike patterns or different brain behaviors. Clinical applications include studying and predicting effects of neuromodulators or neurodegenerative diseases on ion channel kinetics.

The Biophysics of Infection.

PubMed

Leake, Mark C

2016-01-01

Our understanding of the processes involved in infection has grown enormously in the past decade due in part to emerging methods of biophysics. This new insight has been enabled through advances in interdisciplinary experimental technologies and theoretical methods at the cutting-edge interface of the life and physical sciences. For example, this has involved several state-of-the-art biophysical tools used in conjunction with molecular and cell biology approaches, which enable investigation of infection in living cells. There are also new, emerging interfacial science tools which enable significant improvements to the resolution of quantitative measurements both in space and time. These include single-molecule biophysics methods and super-resolution microscopy approaches. These new technological tools in particular have underpinned much new understanding of dynamic processes of infection at a molecular length scale. Also, there are many valuable advances made recently in theoretical approaches of biophysics which enable advances in predictive modelling to generate new understanding of infection. Here, I discuss these advances, and take stock on our knowledge of the biophysics of infection and discuss where future advances may lead.

Quantum-Sequencing: Biophysics of quantum tunneling through nucleic acids

NASA Astrophysics Data System (ADS)

Casamada Ribot, Josep; Chatterjee, Anushree; Nagpal, Prashant

2014-03-01

Tunneling microscopy and spectroscopy has extensively been used in physical surface sciences to study quantum tunneling to measure electronic local density of states of nanomaterials and to characterize adsorbed species. Quantum-Sequencing (Q-Seq) is a new method based on tunneling microscopy for electronic sequencing of single molecule of nucleic acids. A major goal of third-generation sequencing technologies is to develop a fast, reliable, enzyme-free single-molecule sequencing method. Here, we present the unique ``electronic fingerprints'' for all nucleotides on DNA and RNA using Q-Seq along their intrinsic biophysical parameters. We have analyzed tunneling spectra for the nucleotides at different pH conditions and analyzed the HOMO, LUMO and energy gap for all of them. In addition we show a number of biophysical parameters to further characterize all nucleobases (electron and hole transition voltage and energy barriers). These results highlight the robustness of Q-Seq as a technique for next-generation sequencing.

Biophysical aspects of using liposomes as delivery vehicles.

PubMed

Ulrich, Anne S

2002-04-01

Liposomes are used as biocompatible carriers of drugs, peptides, proteins, plasmic DNA, antisense oligonucleotides or ribozymes, for pharmaceutical, cosmetic, and biochemical purposes. The enormous versatility in particle size and in the physical parameters of the lipids affords an attractive potential for constructing tailor-made vehicles for a wide range of applications. Some of the recent literature will be reviewed here and presented from a biophysical point of view, thus providing a background for the more specialized articles in this special issue on liposome technology. Different properties (size, colloidal behavior, phase transitions, and polymorphism) of diverse lipid formulations (liposomes, lipoplexes, cubic phases, emulsions, and solid lipid nanoparticles) for distinct applications (parenteral, transdermal, pulmonary, and oral administration) will be rationalized in terms of common structural, thermodynamic and kinetic parameters of the lipids. This general biophysical basis helps to understand pharmaceutically relevant aspects such as liposome stability during storage and towards serum, the biodistribution and specific targeting of cargo, and how to trigger drug release and membrane fusion. Methods for the preparation and characterization of liposomal formulations in vitro will be outlined, too.

Biophysical and physicochemical methods differentiate highly ligand-efficient human D-amino acid oxidase inhibitors.

PubMed

Lange, Jos H M; Venhorst, Jennifer; van Dongen, Maria J P; Frankena, Jurjen; Bassissi, Firas; de Bruin, Natasja M W J; den Besten, Cathaline; de Beer, Stephanie B A; Oostenbrink, Chris; Markova, Natalia; Kruse, Chris G

2011-10-01

Many early drug research efforts are too reductionist thereby not delivering key parameters such as kinetics and thermodynamics of target-ligand binding. A set of human D-Amino Acid Oxidase (DAAO) inhibitors 1-6 was applied to demonstrate the impact of key biophysical techniques and physicochemical methods in the differentiation of chemical entities that cannot be adequately distinguished on the basis of their normalized potency (ligand efficiency) values. The resulting biophysical and physicochemical data were related to relevant pharmacodynamic and pharmacokinetic properties. Surface Plasmon Resonance data indicated prolonged target-ligand residence times for 5 and 6 as compared to 1-4, based on the observed k(off) values. The Isothermal Titration Calorimetry-derived thermodynamic binding profiles of 1-6 to the DAAO enzyme revealed favorable contributions of both ΔH and ΔS to their ΔG values. Surprisingly, the thermodynamic binding profile of 3 elicited a substantially higher favorable contribution of ΔH to ΔG in comparison with the structurally closely related fused bicyclic acid 4. Molecular dynamics simulations and free energy calculations of 1, 3, and 4 led to novel insights into the thermodynamic properties of the binding process at an atomic level and in the different thermodynamic signatures of 3 and 4. The presented holistic approach is anticipated to facilitate the identification of compounds with best-in-class properties at an early research stage. Copyright © 2011 Elsevier Masson SAS. All rights reserved.

Biophysical Neural Spiking, Bursting, and Excitability Dynamics in Reconfigurable Analog VLSI.

PubMed

Yu, T; Sejnowski, T J; Cauwenberghs, G

2011-10-01

We study a range of neural dynamics under variations in biophysical parameters underlying extended Morris-Lecar and Hodgkin-Huxley models in three gating variables. The extended models are implemented in NeuroDyn, a four neuron, twelve synapse continuous-time analog VLSI programmable neural emulation platform with generalized channel kinetics and biophysical membrane dynamics. The dynamics exhibit a wide range of time scales extending beyond 100 ms neglected in typical silicon models of tonic spiking neurons. Circuit simulations and measurements show transition from tonic spiking to tonic bursting dynamics through variation of a single conductance parameter governing calcium recovery. We similarly demonstrate transition from graded to all-or-none neural excitability in the onset of spiking dynamics through the variation of channel kinetic parameters governing the speed of potassium activation. Other combinations of variations in conductance and channel kinetic parameters give rise to phasic spiking and spike frequency adaptation dynamics. The NeuroDyn chip consumes 1.29 mW and occupies 3 mm × 3 mm in 0.5 μm CMOS, supporting emerging developments in neuromorphic silicon-neuron interfaces.

Biophysics of the Senses

NASA Astrophysics Data System (ADS)

Presley, Tennille D.

2016-12-01

Biophysics of the Senses connects fundamental properties of physics to biological systems, relating them directly to the human body. It includes discussions of the role of charges and free radicals in disease and homeostasis, how aspects of mechanics impact normal body functions, human bioelectricity and circuitry, forces within the body, and biophysical sensory mechanisms. This is an exciting view of how sensory aspects of biophysics are utilized in everyday life for students who are curious but struggle with the connection between biology and physics.

Classification of high-resolution multi-swath hyperspectral data using Landsat 8 surface reflectance data as a calibration target and a novel histogram based unsupervised classification technique to determine natural classes from biophysically relevant fit parameters

NASA Astrophysics Data System (ADS)

McCann, C.; Repasky, K. S.; Morin, M.; Lawrence, R. L.; Powell, S. L.

2016-12-01

Compact, cost-effective, flight-based hyperspectral imaging systems can provide scientifically relevant data over large areas for a variety of applications such as ecosystem studies, precision agriculture, and land management. To fully realize this capability, unsupervised classification techniques based on radiometrically-calibrated data that cluster based on biophysical similarity rather than simply spectral similarity are needed. An automated technique to produce high-resolution, large-area, radiometrically-calibrated hyperspectral data sets based on the Landsat surface reflectance data product as a calibration target was developed and applied to three subsequent years of data covering approximately 1850 hectares. The radiometrically-calibrated data allows inter-comparison of the temporal series. Advantages of the radiometric calibration technique include the need for minimal site access, no ancillary instrumentation, and automated processing. Fitting the reflectance spectra of each pixel using a set of biophysically relevant basis functions reduces the data from 80 spectral bands to 9 parameters providing noise reduction and data compression. Examination of histograms of these parameters allows for determination of natural splitting into biophysical similar clusters. This method creates clusters that are similar in terms of biophysical parameters, not simply spectral proximity. Furthermore, this method can be applied to other data sets, such as urban scenes, by developing other physically meaningful basis functions. The ability to use hyperspectral imaging for a variety of important applications requires the development of data processing techniques that can be automated. The radiometric-calibration combined with the histogram based unsupervised classification technique presented here provide one potential avenue for managing big-data associated with hyperspectral imaging.

A multivariate analysis of biophysical parameters of tallgrass prairie among land management practices and years

USGS Publications Warehouse

Griffith, J.A.; Price, K.P.; Martinko, E.A.

2001-01-01

Six treatments of eastern Kansas tallgrass prairie - native prairie, hayed, mowed, grazed, burned and untreated - were studied to examine the biophysical effects of land management practices on grasslands. On each treatment, measurements of plant biomass, leaf area index, plant cover, leaf moisture and soil moisture were collected. In addition, measurements were taken of the Normalized Difference Vegetation Index (NDVI), which is derived from spectral reflectance measurements. Measurements were taken in mid-June, mid-July and late summer of 1990 and 1991. Multivariate analysis of variance was used to determine whether there were differences in the set of variables among treatments and years. Follow-up tests included univariate t-tests to determine which variables were contributing to any significant difference. Results showed a significant difference (p < 0.0005) among treatments in the composite of parameters during each of the months sampled. In most treatment types, there was a significant difference between years within each month. The univariate tests showed, however, that only some variables, primarily soil moisture, were contributing to this difference. We conclude that biomass and % plant cover show the best potential to serve as long-term indicators of grassland condition as they generally were sensitive to effects of different land management practices but not to yearly change in weather conditions. NDVI was insensitive to precipitation differences between years in July for most treatments, but was not in the native prairie. Choice of sampling time is important for these parameters to serve effectively as indicators.

Cellular biophysical markers of hydroxyurea treatment in sickle cell disease

NASA Astrophysics Data System (ADS)

So, Peter T. C.; Hosseini, Poorya; Abidi, Sabia Z.; Du, E.; Papageorgiou, Dimitrios P.; Park, YongKeun; Higgins, John; Kato, Gregory J.; Suresh, Subra; Dao, Ming; Yaqoob, Zahid

2017-04-01

Using a common-path interferometric technique, we measure biomechanical and morphological properties of individual red blood cells in SCD patients as a function of cell density, and investigate the correlation of these biophysical properties with drug intake as well as other clinically measured parameters.

Parameter Estimation with Almost No Public Communication for Continuous-Variable Quantum Key Distribution

NASA Astrophysics Data System (ADS)

Lupo, Cosmo; Ottaviani, Carlo; Papanastasiou, Panagiotis; Pirandola, Stefano

2018-06-01

One crucial step in any quantum key distribution (QKD) scheme is parameter estimation. In a typical QKD protocol the users have to sacrifice part of their raw data to estimate the parameters of the communication channel as, for example, the error rate. This introduces a trade-off between the secret key rate and the accuracy of parameter estimation in the finite-size regime. Here we show that continuous-variable QKD is not subject to this constraint as the whole raw keys can be used for both parameter estimation and secret key generation, without compromising the security. First, we show that this property holds for measurement-device-independent (MDI) protocols, as a consequence of the fact that in a MDI protocol the correlations between Alice and Bob are postselected by the measurement performed by an untrusted relay. This result is then extended beyond the MDI framework by exploiting the fact that MDI protocols can simulate device-dependent one-way QKD with arbitrarily high precision.

Biophysical effects on temperature and precipitation due to land cover change

NASA Astrophysics Data System (ADS)

Perugini, Lucia; Caporaso, Luca; Marconi, Sergio; Cescatti, Alessandro; Quesada, Benjamin; de Noblet-Ducoudré, Nathalie; House, Johanna I.; Arneth, Almut

2017-05-01

Anthropogenic land cover changes (LCC) affect regional and global climate through biophysical variations of the surface energy budget mediated by albedo, evapotranspiration, and roughness. This change in surface energy budget may exacerbate or counteract biogeochemical greenhouse gas effects of LCC, with a large body of emerging assessments being produced, sometimes apparently contradictory. We reviewed the existing scientific literature with the objective to provide an overview of the state-of-the-knowledge of the biophysical LCC climate effects, in support of the assessment of mitigation/adaptation land policies. Out of the published studies that were analyzed, 28 papers fulfilled the eligibility criteria, providing surface air temperature and/or precipitation change with respect to LCC regionally and/or globally. We provide a synthesis of the signal, magnitude and uncertainty of temperature and precipitation changes in response to LCC biophysical effects by climate region (boreal/temperate/tropical) and by key land cover transitions. Model results indicate that a modification of biophysical processes at the land surface has a strong regional climate effect, and non-negligible global impact on temperature. Simulations experiments of large-scale (i.e. complete) regional deforestation lead to a mean reduction in precipitation in all regions, while air surface temperature increases in the tropics and decreases in boreal regions. The net global climate effects of regional deforestation are less certain. There is an overall consensus in the model experiments that the average global biophysical climate response to complete global deforestation is atmospheric cooling and drying. Observed estimates of temperature change following deforestation indicate a smaller effect than model-based regional estimates in boreal regions, comparable results in the tropics, and contrasting results in temperate regions. Regional/local biophysical effects following LCC are important for

[Influence of accessories mixing ratio on sludge biophysical co-drying].

PubMed

Yang, Jin-Long; Du, Qiong; Li, Dong; Han, Rong; Zhao, Yan; Wang, Hong-Tao

2011-08-01

Parameters (temperature, water content and so on) in the process of sludge biophysical co-drying were studied in self-made biophysical co-drying reactor. The sludge: tree bark: recycled sludge was set as 7: 3: 0.5, 9: 3: 0.5, 12: 3: 0.5 respectively. The results suggested that sludge temperature first increased then decreased along with drying time, water content decreased in the first 96 h, then had no obvious variability. While sludge: tree bark: recycled sludge was 9: 3: 0.5, the temperature of sludge spiraling, received to max 67 degrees C at 48 h under three different accessories mixture ratio, and was kept for 72 h above 55 degrees C, then spiraling, the final water content of sludge decreased from 74.1% to 61.8%, received the optimal water content removing rate 43.5%. Accessories mixing ratio had important influence on the process of sludge biophysical co-drying, sludge with proper mixing ratio can modify the structure of sludge, improve sludge permeability, arouse and keep microorganic activity, which will enhance sludge temperature and strengthen water content removal rate.

Biophysical Discovery through the Lens of a Computational Microscope

NASA Astrophysics Data System (ADS)

Amaro, Rommie

With exascale computing power on the horizon, improvements in the underlying algorithms and available structural experimental data are enabling new paradigms for chemical discovery. My work has provided key insights for the systematic incorporation of structural information resulting from state-of-the-art biophysical simulations into protocols for inhibitor and drug discovery. We have shown that many disease targets have druggable pockets that are otherwise ``hidden'' in high resolution x-ray structures, and that this is a common theme across a wide range of targets in different disease areas. We continue to push the limits of computational biophysical modeling by expanding the time and length scales accessible to molecular simulation. My sights are set on, ultimately, the development of detailed physical models of cells, as the fundamental unit of life, and two recent achievements highlight our efforts in this arena. First is the development of a molecular and Brownian dynamics multi-scale modeling framework, which allows us to investigate drug binding kinetics in addition to thermodynamics. In parallel, we have made significant progress developing new tools to extend molecular structure to cellular environments. Collectively, these achievements are enabling the investigation of the chemical and biophysical nature of cells at unprecedented scales.

Temporal analysis of vegetation indices related to biophysical parameters using Sentinel 2A images to estimate maize production

NASA Astrophysics Data System (ADS)

Macedo, Lucas Saran; Kawakubo, Fernando Shinji

2017-10-01

Agricultural production is one of the most important Brazilian economic activities accounting for about 21,5% of total Gross Domestic Product. In this scenario, the use of satellite images for estimating biophysical parameters along the phenological development of agricultural crops allows the conclusion about the sanity of planting and helps the projection on design production trends. The objective of this study is to analyze the temporal patterns and variation of six vegetion indexes obtained from the bands of Sentinel 2A satellite, associated with greenness (NDVI and ClRE), senescence (mARI and PSRI) and water content (DSWI and NDWI) to estimate maize production. The temporal pattern of the indices was analyzed in function of productivity data collected in-situ. The results obtained evidenced the importance of the SWIR and Red Edge ranges with Pearson correlation values of the temporal mean for NDWI 0.88 and 0.76 for CLRE.

A semisupervised support vector regression method to estimate biophysical parameters from remotely sensed images

NASA Astrophysics Data System (ADS)

Castelletti, Davide; Demir, Begüm; Bruzzone, Lorenzo

2014-10-01

This paper presents a novel semisupervised learning (SSL) technique defined in the context of ɛ-insensitive support vector regression (SVR) to estimate biophysical parameters from remotely sensed images. The proposed SSL method aims to mitigate the problems of small-sized biased training sets without collecting any additional samples with reference measures. This is achieved on the basis of two consecutive steps. The first step is devoted to inject additional priors information in the learning phase of the SVR in order to adapt the importance of each training sample according to distribution of the unlabeled samples. To this end, a weight is initially associated to each training sample based on a novel strategy that defines higher weights for the samples located in the high density regions of the feature space while giving reduced weights to those that fall into the low density regions of the feature space. Then, in order to exploit different weights for training samples in the learning phase of the SVR, we introduce a weighted SVR (WSVR) algorithm. The second step is devoted to jointly exploit labeled and informative unlabeled samples for further improving the definition of the WSVR learning function. To this end, the most informative unlabeled samples that have an expected accurate target values are initially selected according to a novel strategy that relies on the distribution of the unlabeled samples in the feature space and on the WSVR function estimated at the first step. Then, we introduce a restructured WSVR algorithm that jointly uses labeled and unlabeled samples in the learning phase of the WSVR algorithm and tunes their importance by different values of regularization parameters. Experimental results obtained for the estimation of single-tree stem volume show the effectiveness of the proposed SSL method.

Turboelectric Aircraft Drive Key Performance Parameters and Functional Requirements

NASA Technical Reports Server (NTRS)

Jansen, Ralph H.; Brown, Gerald V.; Felder, James L.; Duffy, Kirsten P.

2016-01-01

The purpose of this paper is to propose specific power and efficiency as the key performance parameters for a turboelectric aircraft power system and investigate their impact on the overall aircraft. Key functional requirements are identified that impact the power system design. Breguet range equations for a base aircraft and a turboelectric aircraft are found. The benefits and costs that may result from the turboelectric system are enumerated. A break-even analysis is conducted to find the minimum allowable electric drive specific power and efficiency that can preserve the range, initial weight, operating empty weight, and payload weight of the base aircraft.

Turboelectric Aircraft Drive Key Performance Parameters and Functional Requirements

NASA Technical Reports Server (NTRS)

Jansen, Ralph; Brown, Gerald V.; Felder, James L.; Duffy, Kirsten P.

2015-01-01

The purpose of this presentation is to propose specific power and efficiency as the key performance parameters for a turboelectric aircraft power system and investigate their impact on the overall aircraft. Key functional requirements are identified that impact the power system design. Breguet range equations for a base aircraft and a turboelectric aircraft are found. The benefits and costs that may result from the turboelectric system are enumerated. A break-even analysis is conducted to find the minimum allowable electric drive specific power and efficiency that can preserve the range, initial weight, operating empty weight, and payload weight of the base aircraft.

Turboelectric Aircraft Drive Key Performance Parameters and Functional Requirements

NASA Technical Reports Server (NTRS)

Jansen, Ralph H.; Brown, Gerald V.; Felder, James L.; Duffy, Kirsten P.

2015-01-01

The purpose of this paper is to propose specific power and efficiency as the key performance parameters for a turboelectric aircraft power system and investigate their impact on the overall aircraft. Key functional requirements are identified that impact the power system design. Breguet range equations for a base aircraft and a turboelectric aircraft are found. The benefits and costs that may result from the turboelectric system are enumerated. A break-even analysis is conducted to find the minimum allowable electric drive specific power and efficiency that can preserve the range, initial weight, operating empty weight, and payload weight of the base aircraft.

Single Nucleobase Identification Using Biophysical Signatures from Nanoelectronic Quantum Tunneling.

PubMed

Korshoj, Lee E; Afsari, Sepideh; Khan, Sajida; Chatterjee, Anushree; Nagpal, Prashant

2017-03-01

Nanoelectronic DNA sequencing can provide an important alternative to sequencing-by-synthesis by reducing sample preparation time, cost, and complexity as a high-throughput next-generation technique with accurate single-molecule identification. However, sample noise and signature overlap continue to prevent high-resolution and accurate sequencing results. Probing the molecular orbitals of chemically distinct DNA nucleobases offers a path for facile sequence identification, but molecular entropy (from nucleotide conformations) makes such identification difficult when relying only on the energies of lowest-unoccupied and highest-occupied molecular orbitals (LUMO and HOMO). Here, nine biophysical parameters are developed to better characterize molecular orbitals of individual nucleobases, intended for single-molecule DNA sequencing using quantum tunneling of charges. For this analysis, theoretical models for quantum tunneling are combined with transition voltage spectroscopy to obtain measurable parameters unique to the molecule within an electronic junction. Scanning tunneling spectroscopy is then used to measure these nine biophysical parameters for DNA nucleotides, and a modified machine learning algorithm identified nucleobases. The new parameters significantly improve base calling over merely using LUMO and HOMO frontier orbital energies. Furthermore, high accuracies for identifying DNA nucleobases were observed at different pH conditions. These results have significant implications for developing a robust and accurate high-throughput nanoelectronic DNA sequencing technique. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Unravel biophysical factors on river water quality response in Chilean Central-Southern watersheds.

PubMed

Yevenes, Mariela A; Arumí, José L; Farías, Laura

2016-05-01

Identifying the key anthropogenic (land uses) and natural (topography and climate) biophysical drivers affecting river water quality is essential for efficient management of water resources. We tested the hypothesis that water quality can be predicted by different biophysical factors. Multivariate statistics based on a geographical information system (GIS) were used to explore the influence of factors (i.e., precipitation, topography, and land uses) on water quality (i.e., nitrate (NO 3 (-)), phosphate (PO 4 (3-)), silicate (Si(OH)4), dissolved oxygen (DO), suspended solids (TSS), biological oxygen demand (DO), temperature (T), conductivity (EC), and pH) for two consecutive years in the Itata and Biobío river watersheds, Central Chile (36° 00' and 38° 30'). The results showed that (NO 3 (-)), (PO 4 (3-)), Si(OH)4, TSS, EC, and DO were higher during rainy season (austral fall, winter, and spring), whereas BOD and temperature were higher during dry season. The spatial variation of these parameters in both watersheds was related to land use, topography (e.g., soil moisture, soil hydrological group, and erodability), and precipitation. Soil hydrological group and soil moisture were the strongest explanatory predictors for PO 4 (3-) , Si(OH)4 and EC in the river, followed by land use such as agriculture for NO 3 (-) and DO and silviculture for TSS and Si(OH)4. High-resolution water leaching and runoff maps allowed us to identify agriculture areas with major probability of water leaching and higher probability of runoff in silviculture areas. Moreover, redundancy analysis (RDA) revealed that land uses (agriculture and silviculture) explained in 60 % the river water quality variation. Our finding highlights the vulnerability of Chilean river waters to different biophysical drivers, rather than climate conditions alone, which is amplified by human-induced degradation.

Detection and isolation of cell-derived microparticles are compromised by protein complexes resulting from shared biophysical parameters.

PubMed

György, Bence; Módos, Károly; Pállinger, Eva; Pálóczi, Krisztina; Pásztói, Mária; Misják, Petra; Deli, Mária A; Sipos, Aron; Szalai, Anikó; Voszka, István; Polgár, Anna; Tóth, Kálmán; Csete, Mária; Nagy, György; Gay, Steffen; Falus, András; Kittel, Agnes; Buzás, Edit I

2011-01-27

Numerous diseases, recently reported to associate with elevated microvesicle/microparticle (MP) counts, have also long been known to be characterized by accelerated immune complex (IC) formation. The goal of this study was to investigate the potential overlap between parameters of protein complexes (eg, ICs or avidin-biotin complexes) and MPs, which might perturb detection and/or isolation of MPs. In this work, after comprehensive characterization of MPs by electron microscopy, atomic force microscopy, dynamic light-scattering analysis, and flow cytometry, for the first time, we drive attention to the fact that protein complexes, especially insoluble ICs, overlap in biophysical properties (size, light scattering, and sedimentation) with MPs. This, in turn, affects MP quantification by flow cytometry and purification by differential centrifugation, especially in diseases in which IC formation is common, including not only autoimmune diseases, but also hematologic disorders, infections, and cancer. These data may necessitate reevaluation of certain published data on patient-derived MPs and contribute to correct the clinical laboratory assessment of the presence and biologic functions of MPs in health and disease.

Key parameters controlling the performance of catalytic motors

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

Esplandiu, Maria J.; Afshar Farniya, Ali; Reguera, David, E-mail: dreguera@ub.edu

2016-03-28

The development of autonomous micro/nanomotors driven by self-generated chemical gradients is a topic of high interest given their potential impact in medicine and environmental remediation. Although impressive functionalities of these devices have been demonstrated, a detailed understanding of the propulsion mechanism is still lacking. In this work, we perform a comprehensive numerical analysis of the key parameters governing the actuation of bimetallic catalytic micropumps. We show that the fluid motion is driven by self-generated electro-osmosis where the electric field originates by a proton current rather than by a lateral charge asymmetry inside the double layer. Hence, the surface potential andmore » the electric field are the key parameters for setting the pumping strength and directionality. The proton flux that generates the electric field stems from the proton gradient induced by the electrochemical reactions taken place at the pump. Surprisingly the electric field and consequently the fluid flow are mainly controlled by the ionic strength and not by the conductivity of the solution, as one could have expected. We have also analyzed the influence of the chemical fuel concentration, electrochemical reaction rates, and size of the metallic structures for an optimized pump performance. Our findings cast light on the complex chemomechanical actuation of catalytic motors and provide important clues for the search, design, and optimization of novel catalytic actuators.« less

Key parameters controlling the performance of catalytic motors.

PubMed

Esplandiu, Maria J; Afshar Farniya, Ali; Reguera, David

2016-03-28

The development of autonomous micro/nanomotors driven by self-generated chemical gradients is a topic of high interest given their potential impact in medicine and environmental remediation. Although impressive functionalities of these devices have been demonstrated, a detailed understanding of the propulsion mechanism is still lacking. In this work, we perform a comprehensive numerical analysis of the key parameters governing the actuation of bimetallic catalytic micropumps. We show that the fluid motion is driven by self-generated electro-osmosis where the electric field originates by a proton current rather than by a lateral charge asymmetry inside the double layer. Hence, the surface potential and the electric field are the key parameters for setting the pumping strength and directionality. The proton flux that generates the electric field stems from the proton gradient induced by the electrochemical reactions taken place at the pump. Surprisingly the electric field and consequently the fluid flow are mainly controlled by the ionic strength and not by the conductivity of the solution, as one could have expected. We have also analyzed the influence of the chemical fuel concentration, electrochemical reaction rates, and size of the metallic structures for an optimized pump performance. Our findings cast light on the complex chemomechanical actuation of catalytic motors and provide important clues for the search, design, and optimization of novel catalytic actuators.

Commentary on “Biophysical Economics” and Evolving Areas

NASA Astrophysics Data System (ADS)

Flomenbom, Ophir; Coban, Gul Unal; Adigüzel, Yekbun

2016-07-01

In this Issue, papers in the area of socio-econo-physics and biophysical economics are presented. We have recently introduced socio-econo-physics and biophysical economics in Biophysical Reviews and Letters (BRL), yet saw 3 to 4 relevant papers just in these most recent three quarters. In this commentary, we therefore would like to elaborate on the topics of socio-econo-physics and biophysical economics and to introduce these concepts to the readers of BRL and the biophysical community of science, with the purpose of supporting many more publications here in BRL, in this evolving area.

Engineered biomaterial and biophysical stimulation as combinatorial strategies to address prosthetic infection by pathogenic bacteria.

PubMed

Boda, Sunil Kumar; Basu, Bikramjit

2017-10-01

A plethora of antimicrobial strategies are being developed to address prosthetic infection. The currently available methods for implant infection treatment include the use of antibiotics and revision surgery. Among the bacterial strains, Staphylococcus species pose significant challenges particularly, with regard to hospital acquired infections. In order to combat such life threatening infectious diseases, researchers have developed implantable biomaterials incorporating nanoparticles, antimicrobial reinforcements, surface coatings, slippery/non-adhesive and contact killing surfaces. This review discusses a few of the biomaterial and biophysical antimicrobial strategies, which are in the developmental stage and actively being pursued by several research groups. The clinical efficacy of biophysical stimulation methods such as ultrasound, electric and magnetic field treatments against prosthetic infection depends critically on the stimulation protocol and parameters of the treatment modality. A common thread among the three biophysical stimulation methods is the mechanism of bactericidal action, which is centered on biophysical rupture of bacterial membranes, the generation of reactive oxygen species (ROS) and bacterial membrane depolarization evoked by the interference of essential ion-transport. Although the extent of antimicrobial effect, normally achieved through biophysical stimulation protocol is insufficient to warrant therapeutic application, a combination of antibiotic/ROS inducing agents and biophysical stimulation methods can elicit a clinically relevant reduction in viable bacterial numbers. In this review, we present a detailed account of both the biomaterial and biophysical approaches for achieving maximum bacterial inactivation. Summarizing, the biophysical stimulation methods in a combinatorial manner with material based strategies can be a more potent solution to control bacterial infections. © 2016 Wiley Periodicals, Inc. J Biomed Mater Res Part B

Historical and Critical Review on Biophysical Economics

NASA Astrophysics Data System (ADS)

Adigüzel, Yekbun

2016-07-01

Biophysical economics is initiated with the long history of the relation of economics with ecological basis and biophysical perspectives of the physiocrats. It inherently has social, economic, biological, environmental, natural, physical, and scientific grounds. Biological entities in economy like the resources, consumers, populations, and parts of production systems, etc. could all be dealt by biophysical economics. Considering this wide scope, current work is a “biophysical economics at a glance” rather than a comprehensive review of the full range of topics that may just be adequately covered in a book-length work. However, the sense of its wide range of applications is aimed to be provided to the reader in this work. Here, modern approaches and biophysical growth theory are presented after the long history and an overview of the concepts in biophysical economics. Examples of the recent studies are provided at the end with discussions. This review is also related to the work by Cleveland, “Biophysical Economics: From Physiocracy to Ecological Economics and Industrial Ecology” [C. J. Cleveland, in Advances in Bioeconomics and Sustainability: Essay in Honor of Nicholas Gerogescu-Roegen, eds. J. Gowdy and K. Mayumi (Edward Elgar Publishing, Cheltenham, England, 1999), pp. 125-154.]. Relevant parts include critics and comments on the presented concepts in a parallelized fashion with the Cleveland’s work.

Cellular biophysics during freezing of rat and mouse sperm predicts post-thaw motility.

PubMed

Hagiwara, Mie; Choi, Jeung Hwan; Devireddy, Ramachandra V; Roberts, Kenneth P; Wolkers, Willem F; Makhlouf, Antoine; Bischof, John C

2009-10-01

Though cryopreservation of mouse sperm yields good survival and motility after thawing, cryopreservation of rat sperm remains a challenge. This study was designed to evaluate the biophysics (membrane permeability) of rat in comparison to mouse to better understand the cooling rate response that contributes to cryopreservation success or failure in these two sperm types. In order to extract subzero membrane hydraulic permeability in the presence of ice, a differential scanning calorimeter (DSC) method was used. By analyzing rat and mouse sperm frozen at 5 degrees C/min and 20 degrees C/min, heat release signatures characteristic of each sperm type were obtained and correlated to cellular dehydration. The dehydration response was then fit to a model of cellular water transport (dehydration) by adjusting cell-specific biophysical (membrane hydraulic permeability) parameters L(pg) and E(Lp). A "combined fit" (to 5 degrees C/min and 20 degrees C/min data) for rat sperm in Biggers-Whitten-Whittingham media yielded L(pg) = 0.007 microm min(-1) atm(-1) and E(Lp) = 17.8 kcal/mol, and in egg yolk cryopreservation media yielded L(pg) = 0.005 microm min(-1) atm(-1) and E(Lp) = 14.3 kcal/mol. These parameters, especially the activation energy, were found to be lower than previously published parameters for mouse sperm. In addition, the biophysical responses in mouse and rat sperm were shown to depend on the constituents of the cryopreservation media, in particular egg yolk and glycerol. Using these parameters, optimal cooling rates for cryopreservation were predicted for each sperm based on a criteria of 5%-15% normalized cell water at -30 degrees C during freezing in cryopreservation media. These predicted rates range from 53 degrees C/min to 70 degrees C/min and from 28 degrees C/min to 36 degrees C/min in rat and mouse, respectively. These predictions were validated by comparison to experimentally determined cryopreservation outcomes, in this case based on motility. Maximum

Biophysics of cadherin adhesion.

PubMed

Leckband, Deborah; Sivasankar, Sanjeevi

2012-01-01

Since the identification of cadherins and the publication of the first crystal structures, the mechanism of cadherin adhesion, and the underlying structural basis have been studied with a number of different experimental techniques, different classical cadherin subtypes, and cadherin fragments. Earlier studies based on biophysical measurements and structure determinations resulted in seemingly contradictory findings regarding cadherin adhesion. However, recent experimental data increasingly reveal parallels between structures, solution binding data, and adhesion-based biophysical measurements that are beginning to both reconcile apparent differences and generate a more comprehensive model of cadherin-mediated cell adhesion. This chapter summarizes the functional, structural, and biophysical findings relevant to cadherin junction assembly and adhesion. We emphasize emerging parallels between findings obtained with different experimental approaches. Although none of the current models accounts for all of the available experimental and structural data, this chapter discusses possible origins of apparent discrepancies, highlights remaining gaps in current knowledge, and proposes challenges for further study.

Pathological levels of glucosylceramide change the biophysical properties of artificial and cell membranes.

PubMed

Varela, Ana R P; Ventura, Ana E; Carreira, Ana C; Fedorov, Aleksander; Futerman, Anthony H; Prieto, Manuel; Silva, Liana C

2016-12-21

Glucosylceramide (GlcCer) plays an active role in the regulation of various cellular events. Moreover, GlcCer is also a key modulator of membrane biophysical properties, which might be linked to the mechanism of its biological action. In order to understand the biophysical implications of GlcCer on membranes of living cells, we first studied the effect of GlcCer on artificial membranes containing 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), sphingomyelin (SM) and cholesterol (Chol). Using an array of biophysical methods, we demonstrate that at lower GlcCer/Chol ratios, GlcCer stabilizes SM/Chol-enriched liquid-ordered domains. However, upon decreasing the Chol content, GlcCer significantly increased membrane order through the formation of gel domains. Changes in pH disturbed the packing properties of GlcCer-containing membranes, leading to an increase in membrane fluidity and reduced membrane electronegativity. To address the biophysical impact of GlcCer in biological membranes, studies were performed in wild type and in fibroblasts treated with conduritol-B-epoxide (CBE), which causes intracellular GlcCer accumulation, and in fibroblasts from patients with type I Gaucher disease (GD). Decreased membrane fluidity was observed in cells containing higher levels of GlcCer, such as in CBE-treated and GD cells. Together, we demonstrate that elevated GlcCer levels change the biophysical properties of cellular membranes, which might compromise membrane-associated cellular events and be of relevance for understanding the pathology of diseases, such as GD, in which GlcCer accumulates at high levels.

Biophysical Micromixer

PubMed Central

Wang, Chin-Tsan; Hu, Yuh-Chung; Hu, Tzu-Yang

2009-01-01

In this study a biophysical passive micromixer with channel anamorphosis in a space of 370 μm, which is shorter than traditional passive micromixers, could be created by mimicing features of vascular flow networks and executed with Reynolds numbers ranging from 1 to 90. Split and recombination (SAR) was the main mixing method for enhancing the convection effect and promoting the mixing performance in the biophysical channel. The 2D numerical results reveal that good mixing efficiency of the mixer was possible, with εmixing = 0.876 at Reynolds number ration Rer = 0.85. Generally speaking, increasing the Reynolds number will enhance the mixing. In addition, the sidewall effect will influence the mixing performance and an optimal mixing performance with εmixing = 0.803 will occur at an aspect ratio of AR = 2. These findings will be useful for enhancing mixing performance for passive micromixers. PMID:22346704

Biophysical micromixer.

PubMed

Wang, Chin-Tsan; Hu, Yuh-Chung; Hu, Tzu-Yang

2009-01-01

In this study a biophysical passive micromixer with channel anamorphosis in a space of 370 μm, which is shorter than traditional passive micromixers, could be created by mimicing features of vascular flow networks and executed with Reynolds numbers ranging from 1 to 90. Split and recombination (SAR) was the main mixing method for enhancing the convection effect and promoting the mixing performance in the biophysical channel. The 2D numerical results reveal that good mixing efficiency of the mixer was possible, with ε(mixing) = 0.876 at Reynolds number ration Re(r) = 0.85. Generally speaking, increasing the Reynolds number will enhance the mixing. In addition, the sidewall effect will influence the mixing performance and an optimal mixing performance with ε(mixing) = 0.803 will occur at an aspect ratio of AR = 2. These findings will be useful for enhancing mixing performance for passive micromixers.

Estimation of biophysical properties of upland Sitka spruce (Picea sitchensis) plantations

NASA Technical Reports Server (NTRS)

Green, Robert M.

1993-01-01

It is widely accepted that estimates of forest above-ground biomass are required as inputs to forest ecosystem models, and that SAR data have the potential to provide such information. This study describes relationships between polarimetric radar backscatter and key biophysical properties of a coniferous plantation in upland central Wales, U.K. Over the test site, topography was relatively complex and was expected to influence the amount of radar backscatter.

Unusual biophysics of intrinsically disordered proteins.

PubMed

Uversky, Vladimir N

2013-05-01

Research of a past decade and a half leaves no doubt that complete understanding of protein functionality requires close consideration of the fact that many functional proteins do not have well-folded structures. These intrinsically disordered proteins (IDPs) and proteins with intrinsically disordered protein regions (IDPRs) are highly abundant in nature and play a number of crucial roles in a living cell. Their functions, which are typically associated with a wide range of intermolecular interactions where IDPs possess remarkable binding promiscuity, complement functional repertoire of ordered proteins. All this requires a close attention to the peculiarities of biophysics of these proteins. In this review, some key biophysical features of IDPs are covered. In addition to the peculiar sequence characteristics of IDPs these biophysical features include sequential, structural, and spatiotemporal heterogeneity of IDPs; their rough and relatively flat energy landscapes; their ability to undergo both induced folding and induced unfolding; the ability to interact specifically with structurally unrelated partners; the ability to gain different structures at binding to different partners; and the ability to keep essential amount of disorder even in the bound form. IDPs are also characterized by the "turned-out" response to the changes in their environment, where they gain some structure under conditions resulting in denaturation or even unfolding of ordered proteins. It is proposed that the heterogeneous spatiotemporal structure of IDPs/IDPRs can be described as a set of foldons, inducible foldons, semi-foldons, non-foldons, and unfoldons. They may lose their function when folded, and activation of some IDPs is associated with the awaking of the dormant disorder. It is possible that IDPs represent the "edge of chaos" systems which operate in a region between order and complete randomness or chaos, where the complexity is maximal. This article is part of a Special Issue

Biophysical and Economic Uncertainty in the Analysis of Poverty Impacts of Climate Change

NASA Astrophysics Data System (ADS)

Hertel, T. W.; Lobell, D. B.; Verma, M.

2011-12-01

This paper seeks to understand the main sources of uncertainty in assessing the impacts of climate change on agricultural output, international trade, and poverty. We incorporate biophysical uncertainty by sampling from a distribution of global climate model predictions for temperature and precipitation for 2050. The implications of these realizations for crop yields around the globe are estimated using the recently published statistical crop yield functions provided by Lobell, Schlenker and Costa-Roberts (2011). By comparing these yields to those predicted under current climate, we obtain the likely change in crop yields owing to climate change. The economic uncertainty in our analysis relates to the response of the global economic system to these biophysical shocks. We use a modified version of the GTAP model to elicit the impact of the biophysical shocks on global patterns of production, consumption, trade and poverty. Uncertainty in these responses is reflected in the econometrically estimated parameters governing the responsiveness of international trade, consumption, production (and hence the intensive margin of supply response), and factor supplies (which govern the extensive margin of supply response). We sample from the distributions of these parameters as specified by Hertel et al. (2007) and Keeney and Hertel (2009). We find that, even though it is difficult to predict where in the world agricultural crops will be favorably affected by climate change, the responses of economic variables, including output and exports can be far more robust (Table 1). This is due to the fact that supply and demand decisions depend on relative prices, and relative prices depend on productivity changes relative to other crops in a given region, or relative to similar crops in other parts of the world. We also find that uncertainty in poverty impacts of climate change appears to be almost entirely driven by biophysical uncertainty.

Estimation efficiency of usage satellite derived and modelled biophysical products for yield forecasting

NASA Astrophysics Data System (ADS)

Kolotii, Andrii; Kussul, Nataliia; Skakun, Sergii; Shelestov, Andrii; Ostapenko, Vadim; Oliinyk, Tamara

2015-04-01

Efficient and timely crop monitoring and yield forecasting are important tasks for ensuring of stability and sustainable economic development [1]. As winter crops pay prominent role in agriculture of Ukraine - the main focus of this study is concentrated on winter wheat. In our previous research [2, 3] it was shown that usage of biophysical parameters of crops such as FAPAR (derived from Geoland-2 portal as for SPOT Vegetation data) is far more efficient for crop yield forecasting to NDVI derived from MODIS data - for available data. In our current work efficiency of usage such biophysical parameters as LAI, FAPAR, FCOVER (derived from SPOT Vegetation and PROBA-V data at resolution of 1 km and simulated within WOFOST model) and NDVI product (derived from MODIS) for winter wheat monitoring and yield forecasting is estimated. As the part of crop monitoring workflow (vegetation anomaly detection, vegetation indexes and products analysis) and yield forecasting SPIRITS tool developed by JRC is used. Statistics extraction is done for landcover maps created in SRI within FP-7 SIGMA project. Efficiency of usage satellite based and modelled with WOFOST model biophysical products is estimated. [1] N. Kussul, S. Skakun, A. Shelestov, O. Kussul, "Sensor Web approach to Flood Monitoring and Risk Assessment", in: IGARSS 2013, 21-26 July 2013, Melbourne, Australia, pp. 815-818. [2] F. Kogan, N. Kussul, T. Adamenko, S. Skakun, O. Kravchenko, O. Kryvobok, A. Shelestov, A. Kolotii, O. Kussul, and A. Lavrenyuk, "Winter wheat yield forecasting in Ukraine based on Earth observation, meteorological data and biophysical models," International Journal of Applied Earth Observation and Geoinformation, vol. 23, pp. 192-203, 2013. [3] Kussul O., Kussul N., Skakun S., Kravchenko O., Shelestov A., Kolotii A, "Assessment of relative efficiency of using MODIS data to winter wheat yield forecasting in Ukraine", in: IGARSS 2013, 21-26 July 2013, Melbourne, Australia, pp. 3235 - 3238.

Biophysical Aspects of Spindle Evolution

NASA Astrophysics Data System (ADS)

Farhadifar, Reza; Baer, Charlie; Needleman, Daniel

2011-03-01

The continual propagation of genetic material from one generation to the next is one of the most basic characteristics of all organisms. In eukaryotes, DNA is segregated into the two daughter cells by a highly dynamic, self-organizing structure called the mitotic spindle. Mitotic spindles can show remarkable variability between tissues and organisms, but there is currently little understanding of the biophysical and evolutionary basis of this diversity. We are studying how spontaneous mutations modify cell division during nematode development. By comparing the mutational variation - the raw material of evolution - with the variation present in nature, we are investigating how the mitotic spindle is shaped over the course of evolution. This combination of quantitative genetics and cellular biophysics gives insight into how the structure and dynamics of the spindle is formed through selection, drift, and biophysical constraints.

Calculations of key magnetospheric parameters using the isotropic and anisotropic SPSU global MHD code

NASA Astrophysics Data System (ADS)

Samsonov, Andrey; Gordeev, Evgeny; Sergeev, Victor

2017-04-01

As it was recently suggested (e.g., Gordeev et al., 2015), the global magnetospheric configuration can be characterized by a set of key parameters, such as the magnetopause distance at the subsolar point and on the terminator plane, the magnetic field in the magnetotail lobe and the plasma sheet thermal pressure, the cross polar cap electric potential drop and the total field-aligned current. For given solar wind conditions, the values of these parameters can be obtained from both empirical models and global MHD simulations. We validate the recently developed global MHD code SPSU-16 using the key magnetospheric parameters mentioned above. The code SPSU-16 can calculate both the isotropic and anisotropic MHD equations. In the anisotropic version, we use the modified double-adiabatic equations in which the T⊥/T∥ (the ratio of perpendicular to parallel thermal pressures) has been bounded from above by the mirror and ion-cyclotron thresholds and from below by the firehose threshold. The results of validation for the SPSU-16 code well agree with the previously published results of other global codes. Some key parameters coincide in the isotropic and anisotropic MHD simulations, but some are different.

Partially Turboelectric Aircraft Drive Key Performance Parameters

NASA Technical Reports Server (NTRS)

Jansen, Ralph H.; Duffy, Kirsten P.; Brown, Gerald V.

2017-01-01

The purpose of this paper is to propose electric drive specific power, electric drive efficiency, and electrical propulsion fraction as the key performance parameters for a partially turboelectric aircraft power system and to investigate their impact on the overall aircraft performance. Breguet range equations for a base conventional turbofan aircraft and a partially turboelectric aircraft are found. The benefits and costs that may result from the partially turboelectric system are enumerated. A break even analysis is conducted to find the minimum allowable electric drive specific power and efficiency, for a given electrical propulsion fraction, that can preserve the range, fuel weight, operating empty weight, and payload weight of the conventional aircraft. Current and future power system performance is compared to the required performance to determine the potential benefit.

Biophysical model of bacterial cell interactions with nanopatterned cicada wing surfaces.

PubMed

Pogodin, Sergey; Hasan, Jafar; Baulin, Vladimir A; Webb, Hayden K; Truong, Vi Khanh; Phong Nguyen, The Hong; Boshkovikj, Veselin; Fluke, Christopher J; Watson, Gregory S; Watson, Jolanta A; Crawford, Russell J; Ivanova, Elena P

2013-02-19

The nanopattern on the surface of Clanger cicada (Psaltoda claripennis) wings represents the first example of a new class of biomaterials that can kill bacteria on contact based solely on their physical surface structure. The wings provide a model for the development of novel functional surfaces that possess an increased resistance to bacterial contamination and infection. We propose a biophysical model of the interactions between bacterial cells and cicada wing surface structures, and show that mechanical properties, in particular cell rigidity, are key factors in determining bacterial resistance/sensitivity to the bactericidal nature of the wing surface. We confirmed this experimentally by decreasing the rigidity of surface-resistant strains through microwave irradiation of the cells, which renders them susceptible to the wing effects. Our findings demonstrate the potential benefits of incorporating cicada wing nanopatterns into the design of antibacterial nanomaterials. Copyright © 2013 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Biophysical Intervention Strategies.

ERIC Educational Resources Information Center

Benson, Scott

1987-01-01

Biophysical interventions as part of an ecological approach to intervention with handicapped children include psychotropic medications (neuroleptics, antidepressants, stimulants, minor tranquilizers and sedatives, lithium); nutritional agents (sugar, vitamins, food allergies); and physical therapies (patterning, optometric training). (DB)

Desert plains classification based on Geomorphometrical parameters (Case study: Aghda, Yazd)

NASA Astrophysics Data System (ADS)

Tazeh, mahdi; Kalantari, Saeideh

2013-04-01

This research focuses on plains. There are several tremendous methods and classification which presented for plain classification. One of The natural resource based classification which is mostly using in Iran, classified plains into three types, Erosional Pediment, Denudation Pediment Aggradational Piedmont. The qualitative and quantitative factors to differentiate them from each other are also used appropriately. In this study effective Geomorphometrical parameters in differentiate landforms were applied for plain. Geomorphometrical parameters are calculable and can be extracted using mathematical equations and the corresponding relations on digital elevation model. Geomorphometrical parameters used in this study included Percent of Slope, Plan Curvature, Profile Curvature, Minimum Curvature, the Maximum Curvature, Cross sectional Curvature, Longitudinal Curvature and Gaussian Curvature. The results indicated that the most important affecting Geomorphometrical parameters for plain and desert classifications includes: Percent of Slope, Minimum Curvature, Profile Curvature, and Longitudinal Curvature. Key Words: Plain, Geomorphometry, Classification, Biophysical, Yazd Khezarabad.

Foreword for Special Issue on Environmental Biophysics

USDA-ARS?s Scientific Manuscript database

This special issue on Environmental Biophysics is presented in honor of Dr. John Norman. Over the past four decades, Dr. Norman has dedicated himself to building bridges between disparate scientific disciplines for a better understanding and prediction of biophysical interactions. The consummate i...

Program review. Challenges and opportunities for training the next generation of biophysicists: perspectives of the directors of the Molecular Biophysics Training Program at Northwestern University.

PubMed

Neuhaus, Francis; Widom, Jonathan; MacDonald, Robert; Jardetzky, Theodore; Radhakrishnan, Ishwar

2008-04-01

Molecular biophysics is a broad, diverse, and dynamic field that has presented a variety of unique challenges and opportunities for training future generations of investigators. Having been or currently being intimately associated with the Molecular Biophysics Training Program at Northwestern, we present our perspectives on various issues that we have encountered over the years. We propose no cookie-cutter solutions, as there is no consensus on what constitutes the "ideal" program. However, there is uniformity in opinion on some key issues that might be useful to those interested in establishing a biophysics training program.

Systems Biophysics of Gene Expression

PubMed Central

Vilar, Jose M.G.; Saiz, Leonor

2013-01-01

Gene expression is a process central to any form of life. It involves multiple temporal and functional scales that extend from specific protein-DNA interactions to the coordinated regulation of multiple genes in response to intracellular and extracellular changes. This diversity in scales poses fundamental challenges to the use of traditional approaches to fully understand even the simplest gene expression systems. Recent advances in computational systems biophysics have provided promising avenues to reliably integrate the molecular detail of biophysical process into the system behavior. Here, we review recent advances in the description of gene regulation as a system of biophysical processes that extend from specific protein-DNA interactions to the combinatorial assembly of nucleoprotein complexes. There is now basic mechanistic understanding on how promoters controlled by multiple, local and distal, DNA binding sites for transcription factors can actively control transcriptional noise, cell-to-cell variability, and other properties of gene regulation, including precision and flexibility of the transcriptional responses. PMID:23790365

Channel-parameter estimation for satellite-to-submarine continuous-variable quantum key distribution

NASA Astrophysics Data System (ADS)

Guo, Ying; Xie, Cailang; Huang, Peng; Li, Jiawei; Zhang, Ling; Huang, Duan; Zeng, Guihua

2018-05-01

This paper deals with a channel-parameter estimation for continuous-variable quantum key distribution (CV-QKD) over a satellite-to-submarine link. In particular, we focus on the channel transmittances and the excess noise which are affected by atmospheric turbulence, surface roughness, zenith angle of the satellite, wind speed, submarine depth, etc. The estimation method is based on proposed algorithms and is applied to low-Earth orbits using the Monte Carlo approach. For light at 550 nm with a repetition frequency of 1 MHz, the effects of the estimated parameters on the performance of the CV-QKD system are assessed by a simulation by comparing the secret key bit rate in the daytime and at night. Our results show the feasibility of satellite-to-submarine CV-QKD, providing an unconditionally secure approach to achieve global networks for underwater communications.

Key parameters design of an aerial target detection system on a space-based platform

NASA Astrophysics Data System (ADS)

Zhu, Hanlu; Li, Yejin; Hu, Tingliang; Rao, Peng

2018-02-01

To ensure flight safety of an aerial aircraft and avoid recurrence of aircraft collisions, a method of multi-information fusion is proposed to design the key parameter to realize aircraft target detection on a space-based platform. The key parameters of a detection wave band and spatial resolution using the target-background absolute contrast, target-background relative contrast, and signal-to-clutter ratio were determined. This study also presented the signal-to-interference ratio for analyzing system performance. Key parameters are obtained through the simulation of a specific aircraft. And the simulation results show that the boundary ground sampling distance is 30 and 35 m in the mid- wavelength infrared (MWIR) and long-wavelength infrared (LWIR) bands for most aircraft detection, and the most reasonable detection wavebands is 3.4 to 4.2 μm and 4.35 to 4.5 μm in the MWIR bands, and 9.2 to 9.8 μm in the LWIR bands. We also found that the direction of detection has a great impact on the detection efficiency, especially in MWIR bands.

Project support of practical training in biophysics.

PubMed

Mornstein, V; Vlk, D; Forytkova, L

2006-01-01

The Department of Biophysics ensures practical training in biophysics and related subjects for students of medical and health study programmes. Demonstrations of medical technology are an important part of this training. Teaching for Faculty of Sciences in biophysical study programmes becomes also very important. Some lectures and demonstrations of technology are involved, but the practical trainig is missing. About 1 mil. CZK for additional laboratory equipment was obtained from the HEIDF project No. 1866/ 2005 "The demonstration and measuring technology for education in medical biophysics and radiological physics" for measuring system DEWETRON for high frequency signal analysis, Fluke Ti30 IR camera, PM 9000B patient monitor, ARSENAL AF 1 fluorescence microscope, and Nikon Coolpix 4500 digital camera with accessories for microphotography. At the present time, further financial resources are being provided by a development project of Ministry of Education "Inter-university co-operation in biomedical technology and engineering using top technologies" in total amount of almost 5 mil CZK, whereas over 2 mil CZK from this project are reserved for student laboratory equipment. The main goal of this project is to ensure the participation of Medical Faculty in educational co-operation in the biomedical technology and engineering, namely with the Faculty of Electrical Engineering and Communication (FEEC), Brno University of Technology. There will be taught those areas of biophysics which are not covered by FEEC, thus forming a separate subject "General Biophysics". The following instruments will be installed: UV-VIS spectrophotometers, rotation viscometers, tensiometers, microscopes with digital image processing, cooled centrifuge, optical benches, and some smaller instruments for practical measurements.

Mapping of Biophysical Parameters of Rice Agriculture System from Hyperspectral Imagery

NASA Astrophysics Data System (ADS)

Moharana, Shreedevi; Duta, Subashisa

2017-04-01

difference infrared index (NDII) predictive models demonstrated the spatial variability of leaf water content from 40 percentage to 90 percentage in the same rice agriculture system which has a good agreement with observed in-situ leaf water measurements. The spatial information of these parameters will be useful for crop nutrient management and yield forecasting, and will serve as inputs to various crop-forecasting models for developing a precision rice agriculture system. Key words: Rice agriculture system, nitrogen, chlorophyll, leaf water content, vegetation index

Raman biophysical markers in skin cancer diagnosis.

PubMed

Feng, Xu; Moy, Austin J; Nguyen, Hieu T M; Zhang, Yao; Zhang, Jason; Fox, Matthew C; Sebastian, Katherine R; Reichenberg, Jason S; Markey, Mia K; Tunnell, James W

2018-05-01

Raman spectroscopy (RS) has demonstrated great potential for in vivo cancer screening; however, the biophysical changes that occur for specific diagnoses remain unclear. We recently developed an inverse biophysical skin cancer model to address this issue. Here, we presented the first demonstration of in vivo melanoma and nonmelanoma skin cancer (NMSC) detection based on this model. We fit the model to our previous clinical dataset and extracted the concentration of eight Raman active components in 100 lesions in 65 patients diagnosed with malignant melanoma (MM), dysplastic nevi (DN), basal cell carcinoma, squamous cell carcinoma, and actinic keratosis. We then used logistic regression and leave-one-lesion-out cross validation to determine the diagnostically relevant model components. Our results showed that the biophysical model captures the diagnostic power of the previously used statistical classification model while also providing the skin's biophysical composition. In addition, collagen and triolein were the most relevant biomarkers to represent the spectral variances between MM and DN, and between NMSC and normal tissue. Our work demonstrates the ability of RS to reveal the biophysical basis for accurate diagnosis of different skin cancers, which may eventually lead to a reduction in the number of unnecessary excisional skin biopsies performed. (2018) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE).

Live-cell mass profiling: an emerging approach in quantitative biophysics.

PubMed

Zangle, Thomas A; Teitell, Michael A

2014-12-01

Cell mass, volume and growth rate are tightly controlled biophysical parameters in cellular development and homeostasis, and pathological cell growth defines cancer in metazoans. The first measurements of cell mass were made in the 1950s, but only recently have advances in computer science and microfabrication spurred the rapid development of precision mass-quantifying approaches. Here we discuss available techniques for quantifying the mass of single live cells with an emphasis on relative features, capabilities and drawbacks for different applications.

Effect of maternal exercises on biophysical fetal and maternal parameters: a transversal study.

PubMed

Santos, Caroline Mombaque Dos; Santos, Wendel Mombaque Dos; Gallarreta, Francisco Maximiliano Pancich; Pigatto, Camila; Portela, Luiz Osório Cruz; Morais, Edson Nunes de

2016-01-01

To evaluate the acute effects of maternal and fetal hemodynamic responses in pregnant women submitted to fetal Doppler and an aerobic physical exercise test according to the degree of effort during the activity and the impact on the well-being. Transversal study with low risk pregnant women, obtained by convenience sample with gestational age between 26 to 34 weeks. The participants carry out a progressive exercise test. After the exercise session, reduced resistance (p=0.02) and pulsatility indices (p=0.01) were identified in the umbilical artery; however, other Doppler parameters analyzed, in addition to cardiotocography and fetal biophysical profile did not achieve significant change. Maternal parameters obtained linear growth with activity, but it was not possible to establish a standard with the Borg scale, and oxygen saturation remained stable. A short submaximal exercise had little effect on placental blood flow after exercise in pregnancies without complications, corroborating that healthy fetus maintains homeostasis even in situations that alter maternal hemodynamics. Avaliar os efeitos agudos de respostas hemodinâmicas maternas e fetais em gestantes submetidas a Doppler fetal e a um teste de exercício físico aeróbio, de acordo com o grau de esforço durante a atividade e o impacto sobre o bem-estar. Estudo transversal desenvolvido com gestantes de baixo risco, por amostra de conveniência com idade gestacional entre 26 e 34 semanas. As participantes realizam um teste de esforço progressivo. Na artéria umbilical, após sessão de exercício físico, identificou-se a redução do índice de resistência (p=0,02) e do índice de pulsatilidade (p=0,01), mas os demais parâmetros Doppler analisados, além da cardiotocografia e do perfil biofísico fetal, não obtiveram alteração significativa. Os parâmetros maternos obtiveram crescimento linear com a atividade, mas não foi possível estabelecer padrão com a escala de Borg, e a saturação de oxig

Program Review Challenges and Opportunities for Training the Next Generation of Biophysicists: Perspectives of the Directors of the Molecular Biophysics Training Program at Northwestern University

PubMed Central

Neuhaus, Francis; Widom, Jonathan; MacDonald, Robert; Jardetzky, Theodore; Radhakrishnan, Ishwar

2009-01-01

Molecular biophysics is a broad, diverse, and dynamic field that has presented a variety of unique challenges and opportunities for training future generations of investigators. Having been or currently being intimately associated with the Molecular Biophysics Training Program at Northwestern, we present our perspectives on various issues that we have encountered over the years. We propose no cookie-cutter solutions, as there is no consensus on what constitutes the “ideal” program. However, there is uniformity in opinion on some key issues that might be useful to those interested in establishing a biophysics training program. PMID:18293401

Biophysics: for HTS hit validation, chemical lead optimization, and beyond.

PubMed

Genick, Christine C; Wright, S Kirk

2017-09-01

There are many challenges to the drug discovery process, including the complexity of the target, its interactions, and how these factors play a role in causing the disease. Traditionally, biophysics has been used for hit validation and chemical lead optimization. With its increased throughput and sensitivity, biophysics is now being applied earlier in this process to empower target characterization and hit finding. Areas covered: In this article, the authors provide an overview of how biophysics can be utilized to assess the quality of the reagents used in screening assays, to validate potential tool compounds, to test the integrity of screening assays, and to create follow-up strategies for compound characterization. They also briefly discuss the utilization of different biophysical methods in hit validation to help avoid the resource consuming pitfalls caused by the lack of hit overlap between biophysical methods. Expert opinion: The use of biophysics early on in the drug discovery process has proven crucial to identifying and characterizing targets of complex nature. It also has enabled the identification and classification of small molecules which interact in an allosteric or covalent manner with the target. By applying biophysics in this manner and at the early stages of this process, the chances of finding chemical leads with novel mechanisms of action are increased. In the future, focused screens with biophysics as a primary readout will become increasingly common.

Method of determining forest production from remotely sensed forest parameters

DOEpatents

Corey, J.C.; Mackey, H.E. Jr.

1987-08-31

A method of determining forest production entirely from remotely sensed data in which remotely sensed multispectral scanner (MSS) data on forest 5 composition is combined with remotely sensed radar imaging data on forest stand biophysical parameters to provide a measure of forest production. A high correlation has been found to exist between the remotely sensed radar imaging data and on site measurements of biophysical 10 parameters such as stand height, diameter at breast height, total tree height, mean area per tree, and timber stand volume.

Trends in Biophysical Research and Their Implications for Medical Libraries

PubMed Central

Chen, Ching-chih

1973-01-01

This is a statistical survey of the trends in biophysical research as reflected by papers presented at four Biophysical Society (BPS) annual meetings between 1958 and 1972 and by the funding sources of the reported projects. The study reveals that biophysical research has grown quite substantially, particularly since 1968. Although biophysics is truly interdisciplinary, since 1968 there has been more pronounced emphasis on biomedically oriented problems and a tendency toward more specific and more highly specialized problems. Between 1958 and 1972, most biophysicists were academic researchers, 50% of whom were biomedical scientists. Over three quarters of the ongoing biophysical research projects during this period were supported by governmental agencies, and among them, the National Institutes of Health was the largest single funding source. PMID:4573970

Predicting the Presence of Scyphozoan Jellyfish in the Gulf of Mexico Using a Biophysical Model

NASA Astrophysics Data System (ADS)

Aleksa, K. T.; Nero, R. W.; Wiggert, J. D.; Graham, W. M.

2016-02-01

The study and quantification of jellyfish (cnidarian medusae and ctenophores) is difficult due to their fragile body plan and a composition similar to their environment. The development of a predictive biophysical jellyfish model would be the first of its kind for the Gulf of Mexico and could provide assistance in ecological research and human interactions. In this study, the collection data of two scyphozoan medusae, Chrysaora quinquecirrha and Aurelia spp., were extracted from SEAMAP trawling surveys and were used to determine biophysical predictors for the presence of large jellyfish medusae in the Gulf of Mexico. Both in situ and remote sensing measurements from 2003 to 2013 were obtained. Logistic regressions were then applied to 27 biophysical parameters derived from these data to explore and determine significant predictors for the presence of medusae. Significant predictors identified by this analysis included water temperature, chlorophyll a, turbidity, distance from shore, and salinity. Future application for this model include foraging assessment of gelatinous predators as well as possible near real time monitoring of the distribution and movement of these medusae in the Gulf of Mexico.

A predictive biophysical model of translational coupling to coordinate and control protein expression in bacterial operons

PubMed Central

Tian, Tian; Salis, Howard M.

2015-01-01

Natural and engineered genetic systems require the coordinated expression of proteins. In bacteria, translational coupling provides a genetically encoded mechanism to control expression level ratios within multi-cistronic operons. We have developed a sequence-to-function biophysical model of translational coupling to predict expression level ratios in natural operons and to design synthetic operons with desired expression level ratios. To quantitatively measure ribosome re-initiation rates, we designed and characterized 22 bi-cistronic operon variants with systematically modified intergenic distances and upstream translation rates. We then derived a thermodynamic free energy model to calculate de novo initiation rates as a result of ribosome-assisted unfolding of intergenic RNA structures. The complete biophysical model has only five free parameters, but was able to accurately predict downstream translation rates for 120 synthetic bi-cistronic and tri-cistronic operons with rationally designed intergenic regions and systematically increased upstream translation rates. The biophysical model also accurately predicted the translation rates of the nine protein atp operon, compared to ribosome profiling measurements. Altogether, the biophysical model quantitatively predicts how translational coupling controls protein expression levels in synthetic and natural bacterial operons, providing a deeper understanding of an important post-transcriptional regulatory mechanism and offering the ability to rationally engineer operons with desired behaviors. PMID:26117546

Space Biophysics: Accomplishments, Trends, Challenges

NASA Technical Reports Server (NTRS)

Smith, Jeffrey D.

2015-01-01

Physics and biology are inextricably linked. All the chemical and biological processes of life are dutifully bound to follow the rules and laws of physics. In space, these physical laws seem to turn on their head and biological systems, from microbes to humans, adapt and evolve in myriad ways to cope with the changed physical influences of the space environment. Gravity is the most prominent change in space that influences biology. In microgravity, the physical processes of sedimentation, density-driven convective flow, influence of surface tension and fluid pressure profoundly influence biology at the molecular and cellular level as well as at the whole-body level. Gravity sensing mechanisms are altered, structural and functional components of biology (such as bone and muscle) are reduced and changes in the way fluids and gasses behave also drive the way microbial systems and biofilms grow as well as the way plants and animals adapt. The radiation environment also effects life in space. Solar particle events and high energy cosmic radiation can cause serious damage to DNA and other biomolecules. The results can cause mutation, cellular damage or death, leading to health consequences of acute radiation damage or long-term health consequences such as increased cancer risk. Space Biophysics is the study and utilization of physical changes in space that cause changes in biological systems. The unique physical environment in space has been used successfully to grow high-quality protein crystals and 3D tissue cultures that could not be grown in the presence of unidirectional gravitational acceleration here on Earth. All biological processes that change in space have their root in a biophysical alteration due to microgravity and/or the radiation environment of space. In order to fully-understand the risks to human health in space and to fully-understand how humans, plants, animals and microbes can safely and effectively travel and eventually live for long periods beyond

Acupuncture-Based Biophysical Frontiers of Complementary Medicine

DTIC Science & Technology

2001-10-28

cf. Fig. 1, an evolutionary older type of intercell communications , transporting ionic electrical signals between excitable cells, whose conductivity...traditional psychology: Biophysical bases of psychosomatic disorders and transpersonal stress reprogramming", in Basic and Clinical Aspects of the Theory...biophysical basis of transpersonal transcendental phenomena", Int. J. Appl. Sci. & Computat, vol. 7, pp. 174-187, 2000 [also presented at Int. Conf

The biophysics of neuronal growth

NASA Astrophysics Data System (ADS)

Franze, Kristian; Guck, Jochen

2010-09-01

For a long time, neuroscience has focused on biochemical, molecular biological and electrophysiological aspects of neuronal physiology and pathology. However, there is a growing body of evidence indicating the importance of physical stimuli for neuronal growth and development. In this review we briefly summarize the historical background of neurobiophysics and give an overview over the current understanding of neuronal growth from a physics perspective. We show how biophysics has so far contributed to a better understanding of neuronal growth and discuss current inconsistencies. Finally, we speculate how biophysics may contribute to the successful treatment of lesions to the central nervous system, which have been considered incurable until very recently.

Effective connectivity: Influence, causality and biophysical modeling

PubMed Central

Valdes-Sosa, Pedro A.; Roebroeck, Alard; Daunizeau, Jean; Friston, Karl

2011-01-01

This is the final paper in a Comments and Controversies series dedicated to “The identification of interacting networks in the brain using fMRI: Model selection, causality and deconvolution”. We argue that discovering effective connectivity depends critically on state-space models with biophysically informed observation and state equations. These models have to be endowed with priors on unknown parameters and afford checks for model Identifiability. We consider the similarities and differences among Dynamic Causal Modeling, Granger Causal Modeling and other approaches. We establish links between past and current statistical causal modeling, in terms of Bayesian dependency graphs and Wiener–Akaike–Granger–Schweder influence measures. We show that some of the challenges faced in this field have promising solutions and speculate on future developments. PMID:21477655

Biophysical regulation of stem cell differentiation.

PubMed

Govey, Peter M; Loiselle, Alayna E; Donahue, Henry J

2013-06-01

Bone adaptation to its mechanical environment, from embryonic through adult life, is thought to be the product of increased osteoblastic differentiation from mesenchymal stem cells. In parallel with tissue-scale loading, these heterogeneous populations of multipotent stem cells are subject to a variety of biophysical cues within their native microenvironments. Bone marrow-derived mesenchymal stem cells-the most broadly studied source of osteoblastic progenitors-undergo osteoblastic differentiation in vitro in response to biophysical signals, including hydrostatic pressure, fluid flow and accompanying shear stress, substrate strain and stiffness, substrate topography, and electromagnetic fields. Furthermore, stem cells may be subject to indirect regulation by mechano-sensing osteocytes positioned to more readily detect these same loading-induced signals within the bone matrix. Such paracrine and juxtacrine regulation of differentiation by osteocytes occurs in vitro. Further studies are needed to confirm both direct and indirect mechanisms of biophysical regulation within the in vivo stem cell niche.

Large scale in vivo recordings to study neuronal biophysics.

PubMed

Giocomo, Lisa M

2015-06-01

Over the last several years, technological advances have enabled researchers to more readily observe single-cell membrane biophysics in awake, behaving animals. Studies utilizing these technologies have provided important insights into the mechanisms generating functional neural codes in both sensory and non-sensory cortical circuits. Crucial for a deeper understanding of how membrane biophysics control circuit dynamics however, is a continued effort to move toward large scale studies of membrane biophysics, in terms of the numbers of neurons and ion channels examined. Future work faces a number of theoretical and technical challenges on this front but recent technological developments hold great promise for a larger scale understanding of how membrane biophysics contribute to circuit coding and computation. Copyright © 2014 Elsevier Ltd. All rights reserved.

Vegetation controls on the biophysical surface properties at global scale

NASA Astrophysics Data System (ADS)

Forzieri, Giovanni; Cescatti, Alessandro

2016-04-01

Leaf area index (LAI) plays an important role in determining resistances to heat, moisture and momentum exchanges between the land surface and atmosphere. Exploring how variations in LAI may induce changes in the surface energy balance is a key to understanding vegetation-climate interactions and for predicting biophysical climate impacts associated to changes in land cover. To this end, we analyzed remote sensing-observed dynamics in LAI, surface energy fluxes and climate drivers at global scale. We investigated the link between interannual variability of LAI and the components of the surface energy budget under diverse climate gradients. Results show that a 25% increase in annual LAI may induce up to 2% increase in available surface energy, as consequence of higher short wave absorption due to reduced albedos, up to 20% increase and 10% decrease in latent and sensible heat, respectively, leading to a decrease of the Bowen ratio in densely vegetated canopies. Opposite patterns are found for a reduction in LAI of similar magnitude. Such changes are strongly modulated by concurrent year-to-year variations and climatological means of air temperature, precipitation and snow cover as well as by land cover-specific physiological processes. Boreal and semi-arid regions appear to be mostly exposed to large changes in biophysical surface processes induced by interannual fluctuations in LAI. The combination of the emergent patters translates into variations in the long-wave outgoing radiation that reflect the surface warming/cooling associated to LAI changes. These findings provide a deeper understanding of the vegetation control on biophysical surface properties and define a set of observational-based diagnostics of LAI-dependent land surface-atmosphere interactions.

The application of multiple biophysical cues to engineer functional neocartilage for treatment of osteoarthritis. Part I: cellular response.

PubMed

Brady, Mariea A; Waldman, Stephen D; Ethier, C Ross

2015-02-01

Osteoarthritis (OA) is a complex disease of the joint for which current treatments are unsatisfactory, thus motivating development of tissue engineering (TE)-based therapies. To date, TE strategies have had some success, developing replacement tissue constructs with biochemical properties approaching that of native cartilage. However, poor biomechanical properties and limited postimplantation integration with surrounding tissue are major shortcomings that need to be addressed. Functional tissue engineering strategies that apply physiologically relevant biophysical cues provide a platform to improve TE constructs before implantation. In the previous decade, new experimental and theoretical findings in cartilage biomechanics and electromechanics have emerged, resulting in an increased understanding of the complex interplay of multiple biophysical cues in the extracellular matrix of the tissue. The effect of biophysical stimulation on cartilage, and the resulting chondrocyte-mediated biosynthesis, remodeling, degradation, and repair, has, therefore, been extensively explored by the TE community. This article compares and contrasts the cellular response of chondrocytes to multiple biophysical stimuli, and may be read in conjunction with its companion paper that compares and contrasts the subsequent intracellular signal transduction cascades. Mechanical, magnetic, and electrical stimuli promote proliferation, differentiation, and maturation of chondrocytes within established dose parameters or "biological windows." This knowledge will provide a framework for ongoing studies incorporating multiple biophysical cues in TE functional neocartilage for treatment of OA.

The application of multiple biophysical cues to engineer functional neocartilage for treatment of osteoarthritis. Part II: signal transduction.

PubMed

Brady, Mariea A; Waldman, Stephen D; Ethier, C Ross

2015-02-01

The unique mechanoelectrochemical environment of cartilage has motivated researchers to investigate the effect of multiple biophysical cues, including mechanical, magnetic, and electrical stimulation, on chondrocyte biology. It is well established that biophysical stimuli promote chondrocyte proliferation, differentiation, and maturation within "biological windows" of defined dose parameters, including mode, frequency, magnitude, and duration of stimuli (see companion review Part I: Cellular Response). However, the underlying molecular mechanisms and signal transduction pathways activated in response to multiple biophysical stimuli remain to be elucidated. Understanding the mechanisms of biophysical signal transduction will deepen knowledge of tissue organogenesis, remodeling, and regeneration and aiding in the treatment of pathologies such as osteoarthritis. Further, this knowledge will provide the tissue engineer with a potent toolset to manipulate and control cell fate and subsequently develop functional replacement cartilage. The aim of this article is to review chondrocyte signal transduction pathways in response to mechanical, magnetic, and electrical cues. Signal transduction does not occur along a single pathway; rather a number of parallel pathways appear to be activated, with calcium signaling apparently common to all three types of stimuli, though there are different modes of activation. Current tissue engineering strategies, such as the development of "smart" functionalized biomaterials that enable the delivery of growth factors or integration of conjugated nanoparticles, may further benefit from targeting known signal transduction pathways in combination with external biophysical cues.

BIOPHYSICAL ASSESSMENTS: WHO CARES?

EPA Science Inventory

An initial statement of this discussion topic was "are ecological economic studies without explicit biophysical assessments fraudulent?" -- implying that such studies were at least misleading, if not intentionally deceitful. To a person trained in the physical/biological sciences...

Bio-physical modeling of time-resolved forward scattering by Listeria colonies

NASA Astrophysics Data System (ADS)

Bae, Euiwon; Banada, Padmapriya P.; Bhunia, Arun K.; Hirleman, E. Daniel

2006-10-01

We have developed a detection system and associated protocol based on optical forward scattering where the bacterial colonies of various species and strains growing on solid nutrient surfaces produced unique scatter signatures. The aim of the present investigation was to develop a bio-physical model for the relevant phenomena. In particular, we considered time-varying macroscopic morphological properties of the growing colonies and modeled the scattering using scalar diffraction theory. For the present work we performed detailed studies with three species of Listeria; L. innocua, L. monocytogenes, and L. ivanovii. The baseline experiments involved cultures grown on brain heart infusion (BHI) agar and the scatter images were captured every six hours for an incubation period of 42 hours. The morphologies of the colonies were studied by phase contrast microscopy, including measurement of the diameter of the colony. Growth curves, represented by colony diameter as a function of time, were compared with the time-evolution of scattering signatures. Similar studies were carried out with L. monocytogenes grown on different substrates. Non-dimensionalizing incubation time in terms of the time to reach stationary phase was effective in reducing the dimensionality of the model. Bio-physical properties of the colony such as diameter, bacteria density variation, surface curvature/profile, and transmission coefficient are important parameters in predicting the features of the forward scattering signatures. These parameters are included in a baseline model that treats the colony as a concentric structure with radial variations in phase modulation. In some cases azimuthal variations and random phase inclusions were included as well. The end result is a protocol (growth media, incubation time and conditions) that produces reproducible and distinguishable scatter patterns for a variety of harmful food borne pathogens in a short period of time. Further, the bio-physical model we

The role of tissue microstructure and water exchange in biophysical modelling of diffusion in white matter.

PubMed

Nilsson, Markus; van Westen, Danielle; Ståhlberg, Freddy; Sundgren, Pia C; Lätt, Jimmy

2013-08-01

Biophysical models that describe the outcome of white matter diffusion MRI experiments have various degrees of complexity. While the simplest models assume equal-sized and parallel axons, more elaborate ones may include distributions of axon diameters and axonal orientation dispersions. These microstructural features can be inferred from diffusion-weighted signal attenuation curves by solving an inverse problem, validated in several Monte Carlo simulation studies. Model development has been paralleled by microscopy studies of the microstructure of excised and fixed nerves, confirming that axon diameter estimates from diffusion measurements agree with those from microscopy. However, results obtained in vivo are less conclusive. For example, the amount of slowly diffusing water is lower than expected, and the diffusion-encoded signal is apparently insensitive to diffusion time variations, contrary to what may be expected. Recent understandings of the resolution limit in diffusion MRI, the rate of water exchange, and the presence of microscopic axonal undulation and axonal orientation dispersions may, however, explain such apparent contradictions. Knowledge of the effects of biophysical mechanisms on water diffusion in tissue can be used to predict the outcome of diffusion tensor imaging (DTI) and of diffusion kurtosis imaging (DKI) studies. Alterations of DTI or DKI parameters found in studies of pathologies such as ischemic stroke can thus be compared with those predicted by modelling. Observations in agreement with the predictions strengthen the credibility of biophysical models; those in disagreement could provide clues of how to improve them. DKI is particularly suited for this purpose; it is performed using higher b-values than DTI, and thus carries more information about the tissue microstructure. The purpose of this review is to provide an update on the current understanding of how various properties of the tissue microstructure and the rate of water exchange

A comparison of biophysical characterization techniques in predicting monoclonal antibody stability.

PubMed

Thiagarajan, Geetha; Semple, Andrew; James, Jose K; Cheung, Jason K; Shameem, Mohammed

2016-01-01

With the rapid growth of biopharmaceutical product development, knowledge of therapeutic protein stability has become increasingly important. We evaluated assays that measure solution-mediated interactions and key molecular characteristics of 9 formulated monoclonal antibody (mAb) therapeutics, to predict their stability behavior. Colloidal interactions, self-association propensity and conformational stability were measured using effective surface charge via zeta potential, diffusion interaction parameter (kD) and differential scanning calorimetry (DSC), respectively. The molecular features of all 9 mAbs were compared to their stability at accelerated (25°C and 40°C) and long-term storage conditions (2-8°C) as measured by size exclusion chromatography. At accelerated storage conditions, the majority of the mAbs in this study degraded via fragmentation rather than aggregation. Our results show that colloidal stability, self-association propensity and conformational characteristics (exposed tryptophan) provide reasonable prediction of accelerated stability, with limited predictive value at 2-8°C stability. While no correlations to stability behavior were observed with onset-of-melting temperatures or domain unfolding temperatures, by DSC, melting of the Fab domain with the CH2 domain suggests lower stability at stressed conditions. The relevance of identifying appropriate biophysical assays based on the primary degradation pathways is discussed.

Assessing sustainable biophysical human-nature connectedness at regional scales

NASA Astrophysics Data System (ADS)

Dorninger, Christian; Abson, David J.; Fischer, Joern; von Wehrden, Henrik

2017-05-01

Humans are biophysically connected to the biosphere through the flows of materials and energy appropriated from ecosystems. While this connection is fundamental for human well-being, many modern societies have—for better or worse—disconnected themselves from the natural productivity of their immediate regional environment. In this paper, we conceptualize the biophysical human-nature connectedness of land use systems at regional scales. We distinguish two mechanisms by which primordial connectedness of people to regional ecosystems has been circumvented via the use of external inputs. First, ‘biospheric disconnection’ refers to people drawing on non-renewable minerals from outside the biosphere (e.g. fossils, metals and other minerals). Second, ‘spatial disconnection’ arises from the imports and exports of biomass products and imported mineral resources used to extract and process ecological goods. Both mechanisms allow for greater regional resource use than would be possible otherwise, but both pose challenges for sustainability, for example, through waste generation, depletion of non-renewable resources and environmental burden shifting to distant regions. In contrast, biophysically reconnected land use systems may provide renewed opportunities for inhabitants to develop an awareness of their impacts and fundamental reliance on ecosystems. To better understand the causes, consequences, and possible remedies related to biophysical disconnectedness, new quantitative methods to assess the extent of regional biophysical human-nature connectedness are needed. To this end, we propose a new methodological framework that can be applied to assess biophysical human-nature connectedness in any region of the world.

Prediction of Geomagnetic Activity and Key Parameters in High-Latitude Ionosphere-Basic Elements

NASA Technical Reports Server (NTRS)

Lyatsky, W.; Khazanov, G. V.

2007-01-01

Prediction of geomagnetic activity and related events in the Earth's magnetosphere and ionosphere is an important task of the Space Weather program. Prediction reliability is dependent on the prediction method and elements included in the prediction scheme. Two main elements are a suitable geomagnetic activity index and coupling function -- the combination of solar wind parameters providing the best correlation between upstream solar wind data and geomagnetic activity. The appropriate choice of these two elements is imperative for any reliable prediction model. The purpose of this work was to elaborate on these two elements -- the appropriate geomagnetic activity index and the coupling function -- and investigate the opportunity to improve the reliability of the prediction of geomagnetic activity and other events in the Earth's magnetosphere. The new polar magnetic index of geomagnetic activity and the new version of the coupling function lead to a significant increase in the reliability of predicting the geomagnetic activity and some key parameters, such as cross-polar cap voltage and total Joule heating in high-latitude ionosphere, which play a very important role in the development of geomagnetic and other activity in the Earth s magnetosphere, and are widely used as key input parameters in modeling magnetospheric, ionospheric, and thermospheric processes.

Dynamic analysis of modified transcutaneous lower blepharoplasty based on biochemical and biophysical principles.

PubMed

Liao, Chuh-Kai; Tsai, Feng-Chou; Fong, Tsorng-Harn; Huang, Chin-Ju; Shen, Yi-Chin; Ku, Yuan-Hao; Su, Ching-Hua

2013-12-01

In this study, we analyzed the key parameters of modified transcutaneous lower blepharoplasty based on multidisciplinary principles (biochemical findings and biophysical wrinkling theory). A total of 408 female patients received our subciliary lower blepharoplasty between March 2002 and January 2010. The severity of the eyebags (dynamic wrinkle numbers and prolapse) was evaluated through preoperative and postoperative photography, whereas the excised lower eyelid skin specimens from 56 patients were investigated with hematoxylin and eosin staining. The modified techniques produced significant improvements in the severity of eyebags in all age groups (P < 0.001). Poor surgical outcome was found to correlate significantly with preoperative dynamic wrinkle numbers (P < 0.001). Age, dynamic wrinkle numbers, and prolapse correlated significantly with dermal fiber density (P = 0.004, 0.000, and 0.000, respectively) but not epidermal, rete ridge, and dermal thickness or the number of rete ridges. In conclusion, modified transcutaneous lower blepharoplasty provides significant improvement to dynamic wrinkles and prolapse in the eyebags. Periorbital aging progressively disturbs the dermal compactness (fiber density) until the structure can no longer hold its integrity at the critical age (around the age of 40).

Biophysics and systems biology.

PubMed

Noble, Denis

2010-03-13

Biophysics at the systems level, as distinct from molecular biophysics, acquired its most famous paradigm in the work of Hodgkin and Huxley, who integrated their equations for the nerve impulse in 1952. Their approach has since been extended to other organs of the body, notably including the heart. The modern field of computational biology has expanded rapidly during the first decade of the twenty-first century and, through its contribution to what is now called systems biology, it is set to revise many of the fundamental principles of biology, including the relations between genotypes and phenotypes. Evolutionary theory, in particular, will require re-assessment. To succeed in this, computational and systems biology will need to develop the theoretical framework required to deal with multilevel interactions. While computational power is necessary, and is forthcoming, it is not sufficient. We will also require mathematical insight, perhaps of a nature we have not yet identified. This article is therefore also a challenge to mathematicians to develop such insights.

Biophysics and systems biology

PubMed Central

Noble, Denis

2010-01-01

Biophysics at the systems level, as distinct from molecular biophysics, acquired its most famous paradigm in the work of Hodgkin and Huxley, who integrated their equations for the nerve impulse in 1952. Their approach has since been extended to other organs of the body, notably including the heart. The modern field of computational biology has expanded rapidly during the first decade of the twenty-first century and, through its contribution to what is now called systems biology, it is set to revise many of the fundamental principles of biology, including the relations between genotypes and phenotypes. Evolutionary theory, in particular, will require re-assessment. To succeed in this, computational and systems biology will need to develop the theoretical framework required to deal with multilevel interactions. While computational power is necessary, and is forthcoming, it is not sufficient. We will also require mathematical insight, perhaps of a nature we have not yet identified. This article is therefore also a challenge to mathematicians to develop such insights. PMID:20123750

The role of bio-physical cohesive substrates on sediment winnowing and bedform development

NASA Astrophysics Data System (ADS)

Ye, Leiping; Parsons, Daniel; Manning, Andrew

2017-04-01

Existing sediment transport and bedform size predictions for natural open-channel flows in many environments are seriously impeded by a lack of process-based knowledge concerning the dynamics of complex bed sediment mixtures comprising cohesionless sand and biologically-active cohesive muds. A series of flume experiments (14 experimental runs) with different substrate mixtures of sand-clay-EPS (Extracellular Polymeric Substance) are combined with a detailed estuarine field survey (Dee estuary, NW England) to investigate the development of bedform morphologies and characteristics of suspended sediment over bio-physical cohesive substrates. The experimental results indicate that winnowing and sediment sorting can occur pervasively in bio-physical cohesive sediment - flow systems. Importantly however, the evolution of the bed and bedform dynamics, and hence turbulence production, is significantly reduced as bed substrate cohesivity increases. The estuarine subtidal zone survey also revealed that the bio-physical cohesion provided by both the clay and microorganism fractions in the bed plays a significant role in controlling the interactions between bed substrate and sediment suspension, deposition and bedform generation. The work will be presented here concludes by outlining the need to extend and revisit the effects of cohesivity in morphodynamic systems and the sets of parameters presently used in numerical modelling, particularly in the context of the impact of climate change on estuarine and coastal systems.

Biophysical Approaches for Oral Wound Healing: Emphasis on Photobiomodulation

PubMed Central

Khan, Imran; Arany, Praveen

2015-01-01

Significance: Oral wounds can lead to significant pain and discomfort as well as affect overall general health due to poor diet and inadequate nutrition. Besides many biological and pharmaceutical methods being investigated, there is growing interest in exploring various biophysical devices that utilize electric, magnetic, ultrasound, pressure, and light energy. Recent Advances: Significant insight into mechanisms of these biophysical devices could provide a clear rationale for their clinical use. Preclinical studies are essential precursors in determining physiological mechanisms and elucidation of causal pathways. This will lead to development of safe and effective therapeutic protocols for clinical wound management. Critical Issues: Identification of precise events initiated by biophysical devices, specifically photobiomodulation—the major focus of this review, offers promising avenues in improving oral wound management. The primary phase responses initiated by the interventions that distinctly contribute to the therapeutic response must be clearly delineated from secondary phase responses. The latter events are a consequence of the wound healing process and must not be confused with causal mechanisms. Future Direction: Clinical adoption of these biophysical devices needs robust and efficacious protocols that can be developed by well-designed preclinical and clinical studies. Elucidation of the precise molecular mechanisms of these biophysical approaches could determine optimization of their applications for predictive oral wound care. PMID:26634185

Ultrasound—biophysics mechanisms†

PubMed Central

O'Brien, William D.

2007-01-01

Ultrasonic biophysics is the study of mechanisms responsible for how ultrasound and biological materials interact. Ultrasound-induced bioeffect or risk studies focus on issues related to the effects of ultrasound on biological materials. On the other hand, when biological materials affect the ultrasonic wave, this can be viewed as the basis for diagnostic ultrasound. Thus, an understanding of the interaction of ultrasound with tissue provides the scientific basis for image production and risk assessment. Relative to the bioeffect or risk studies, that is, the biophysical mechanisms by which ultrasound affects biological materials, ultrasound-induced bioeffects are generally separated into thermal and nonthermal mechanisms. Ultrasonic dosimetry is concerned with the quantitative determination of ultrasonic energy interaction with biological materials. Whenever ultrasonic energy is propagated into an attenuating material such as tissue, the amplitude of the wave decreases with distance. This attenuation is due to either absorption or scattering. Absorption is a mechanism that represents that portion of ultrasonic wave that is converted into heat, and scattering can be thought of as that portion of the wave, which changes direction. Because the medium can absorb energy to produce heat, a temperature rise may occur as long as the rate of heat production is greater than the rate of heat removal. Current interest with thermally mediated ultrasound-induced bioeffects has focused on the thermal isoeffect concept. The non-thermal mechanism that has received the most attention is acoustically generated cavitation wherein ultrasonic energy by cavitation bubbles is concentrated. Acoustic cavitation, in a broad sense, refers to ultrasonically induced bubble activity occurring in a biological material that contains pre-existing gaseous inclusions. Cavitation-related mechanisms include radiation force, microstreaming, shock waves, free radicals, microjets and strain. It is more

Delineating Biophysical Environments of the Sunda Banda Seascape, Indonesia

PubMed Central

Wang, Mingshu; Ahmadia, Gabby N.; Chollett, Iliana; Huang, Charles; Fox, Helen; Wijonarno, Anton; Madden, Marguerite

2015-01-01

The Sunda Banda Seascape (SBS), located in the center of the Coral Triangle, is a global center of marine biodiversity and a conservation priority. We proposed the first biophysical environmental delineation of the SBS using globally available satellite remote sensing and model-assimilated data to categorize this area into unique and meaningful biophysical classes. Specifically, the SBS was partitioned into eight biophysical classes characterized by similar sea surface temperature, chlorophyll a concentration, currents, and salinity patterns. Areas within each class were expected to have similar habitat types and ecosystem functions. Our work supplemented prevailing global marine management schemes by focusing in on a regional scale with finer spatial resolution. It also provided a baseline for academic research, ecological assessments and will facilitate marine spatial planning and conservation activities in the area. In addition, the framework and methods of delineating biophysical environments we presented can be expanded throughout the whole Coral Triangle to support research and conservation activities in this important region. PMID:25648170

Measuring Two Key Parameters of H3 Color Centers in Diamond

NASA Technical Reports Server (NTRS)

Roberts, W. Thomas

2005-01-01

A method of measuring two key parameters of H3 color centers in diamond has been created as part of a continuing effort to develop tunable, continuous-wave, visible lasers that would utilize diamond as the lasing medium. (An H3 color center in a diamond crystal lattice comprises two nitrogen atoms substituted for two carbon atoms bonded to a third carbon atom. H3 color centers can be induced artificially; they also occur naturally. If present in sufficient density, they impart a yellow hue.) The method may also be applicable to the corresponding parameters of other candidate lasing media. One of the parameters is the number density of color centers, which is needed for designing an efficient laser. The other parameter is an optical-absorption cross section, which, as explained below, is needed for determining the number density. The present method represents an improvement over prior methods in which optical-absorption measurements have been used to determine absorption cross sections or number densities. Heretofore, in order to determine a number density from such measurements, it has been necessary to know the applicable absorption cross section; alternatively, to determine the absorption cross section from such measurements, it has been necessary to know the number density. If, as in this case, both the number density and the absorption cross section are initially unknown, then it is impossible to determine either parameter in the absence of additional information.

Establishing the Capability of a 1D SVAT Modelling Scheme in Predicting Key Biophysical Vegetation Characterisation Parameters

NASA Astrophysics Data System (ADS)

Ireland, Gareth; Petropoulos, George P.; Carlson, Toby N.; Purdy, Sarah

2015-04-01

Sensitivity analysis (SA) consists of an integral and important validatory check of a computer simulation model before it is used to perform any kind of analysis. In the present work, we present the results from a SA performed on the SimSphere Soil Vegetation Atmosphere Transfer (SVAT) model utilising a cutting edge and robust Global Sensitivity Analysis (GSA) approach, based on the use of the Gaussian Emulation Machine for Sensitivity Analysis (GEM-SA) tool. The sensitivity of the following model outputs was evaluated: the ambient CO2 concentration and the rate of CO2 uptake by the plant, the ambient O3 concentration, the flux of O3 from the air to the plant/soil boundary, and the flux of O3 taken up by the plant alone. The most sensitive model inputs for the majority of model outputs were related to the structural properties of vegetation, namely, the Leaf Area Index, Fractional Vegetation Cover, Cuticle Resistance and Vegetation Height. External CO2 in the leaf and the O3 concentration in the air input parameters also exhibited significant influence on model outputs. This work presents a very important step towards an all-inclusive evaluation of SimSphere. Indeed, results from this study contribute decisively towards establishing its capability as a useful teaching and research tool in modelling Earth's land surface interactions. This is of considerable importance in the light of the rapidly expanding use of this model worldwide, which also includes research conducted by various Space Agencies examining its synergistic use with Earth Observation data towards the development of operational products at a global scale. This research was supported by the European Commission Marie Curie Re-Integration Grant "TRANSFORM-EO". SimSphere is currently maintained and freely distributed by the Department of Geography and Earth Sciences at Aberystwyth University (http://www.aber.ac.uk/simsphere). Keywords: CO2 flux, ambient CO2, O3 flux, SimSphere, Gaussian process emulators

Single Particle Orientation and Rotational Tracking (SPORT) in biophysical studies

NASA Astrophysics Data System (ADS)

Gu, Yan; Ha, Ji Won; Augspurger, Ashley E.; Chen, Kuangcai; Zhu, Shaobin; Fang, Ning

2013-10-01

The single particle orientation and rotational tracking (SPORT) techniques have seen rapid development in the past 5 years. Recent technical advances have greatly expanded the applicability of SPORT in biophysical studies. In this feature article, we survey the current development of SPORT and discuss its potential applications in biophysics, including cellular membrane processes and intracellular transport.The single particle orientation and rotational tracking (SPORT) techniques have seen rapid development in the past 5 years. Recent technical advances have greatly expanded the applicability of SPORT in biophysical studies. In this feature article, we survey the current development of SPORT and discuss its potential applications in biophysics, including cellular membrane processes and intracellular transport. Electronic supplementary information (ESI) available: Three supplementary movies and an experimental section. See DOI: 10.1039/c3nr02254d

Evaluating landscape health: Integrating societal goals and biophysical process

USGS Publications Warehouse

Rapport, D.J.; Gaudet, C.; Karr, J.R.; Baron, Jill S.; Bohlen, C.; Jackson, W.; Jones, Bruce; Naiman, R.J.; Norton, B.; Pollock, M. M.

1998-01-01

Evaluating landscape change requires the integration of the social and natural sciences. The social sciences contribute to articulating societal values that govern landscape change, while the natural sciences contribute to understanding the biophysical processes that are influenced by human activity and result in ecological change. Building upon Aldo Leopold's criteria for landscape health, the roles of societal values and biophysical processes in shaping the landscape are explored. A framework is developed for indicators of landscape health and integrity. Indicators of integrity are useful in measuring biological condition relative to the condition in landscapes largely unaffected by human activity, while indicators of health are useful in evaluating changes in highly modified landscapes. Integrating societal goals and biophysical processes requires identification of ecological services to be sustained within a given landscape. It also requires the proper choice of temporal and spatial scales. Societal values are based upon inter-generational concerns at regional scales (e.g. soil and ground water quality). Assessing the health and integrity of the environment at the landscape scale over a period of decades best integrates societal values with underlying biophysical processes. These principles are illustrated in two contrasting case studies: (1) the South Platte River study demonstrates the role of complex biophysical processes acting at a distance; and (2) the Kissimmee River study illustrates the critical importance of social, cultural and economic concerns in the design of remedial action plans. In both studies, however, interactions between the social and the biophysical governed the landscape outcomes. The legacy of evolution and the legacy of culture requires integration for the purpose of effectively coping with environmental change.

The Research and Implementation of Vehicle Bluetooth Hands-free Devices Key Parameters Downloading Algorithm

NASA Astrophysics Data System (ADS)

Zhang, Xiao-bo; Wang, Zhi-xue; Li, Jian-xin; Ma, Jian-hui; Li, Yang; Li, Yan-qiang

In order to facilitate Bluetooth function realization and information can be effectively tracked in the process of production, the vehicle Bluetooth hands-free devices need to download such key parameters as Bluetooth address, CVC license and base plate numbers, etc. Therefore, it is the aim to search simple and effective methods to download parameters for each vehicle Bluetooth hands-free device, and to control and record the use of parameters. In this paper, by means of Bluetooth Serial Peripheral Interface programmer device, the parallel port is switched to SPI. The first step is to download parameters is simulating SPI with the parallel port. To perform SPI function, operating the parallel port in accordance with the SPI timing. The next step is to achieve SPI data transceiver functions according to the programming parameters of options. Utilizing the new method, downloading parameters is fast and accurate. It fully meets vehicle Bluetooth hands-free devices production requirements. In the production line, it has played a large role.

Effect of the Key Mixture Parameters on Shrinkage of Reactive Powder Concrete

PubMed Central

Zubair, Ahmed

2014-01-01

Reactive powder concrete (RPC) mixtures are reported to have excellent mechanical and durability characteristics. However, such concrete mixtures having high amount of cementitious materials may have high early shrinkage causing cracking of concrete. In the present work, an attempt has been made to study the simultaneous effects of three key mixture parameters on shrinkage of the RPC mixtures. Considering three different levels of the three key mixture factors, a total of 27 mixtures of RPC were prepared according to 33 factorial experiment design. The specimens belonging to all 27 mixtures were monitored for shrinkage at different ages over a total period of 90 days. The test results were plotted to observe the variation of shrinkage with time and to see the effects of the key mixture factors. The experimental data pertaining to 90-day shrinkage were used to conduct analysis of variance to identify significance of each factor and to obtain an empirical equation correlating the shrinkage of RPC with the three key mixture factors. The rate of development of shrinkage at early ages was higher. The water to binder ratio was found to be the most prominent factor followed by cement content with the least effect of silica fume content. PMID:25050395

Effect of the key mixture parameters on shrinkage of reactive powder concrete.

PubMed

Ahmad, Shamsad; Zubair, Ahmed; Maslehuddin, Mohammed

2014-01-01

Reactive powder concrete (RPC) mixtures are reported to have excellent mechanical and durability characteristics. However, such concrete mixtures having high amount of cementitious materials may have high early shrinkage causing cracking of concrete. In the present work, an attempt has been made to study the simultaneous effects of three key mixture parameters on shrinkage of the RPC mixtures. Considering three different levels of the three key mixture factors, a total of 27 mixtures of RPC were prepared according to 3(3) factorial experiment design. The specimens belonging to all 27 mixtures were monitored for shrinkage at different ages over a total period of 90 days. The test results were plotted to observe the variation of shrinkage with time and to see the effects of the key mixture factors. The experimental data pertaining to 90-day shrinkage were used to conduct analysis of variance to identify significance of each factor and to obtain an empirical equation correlating the shrinkage of RPC with the three key mixture factors. The rate of development of shrinkage at early ages was higher. The water to binder ratio was found to be the most prominent factor followed by cement content with the least effect of silica fume content.

Bio-physical characterisation of polynyas as a key foraging habitat for juvenile male southern elephant seals (Mirounga leonina) in Prydz Bay, East Antarctica

PubMed Central

Bestley, Sophie; Corney, Stuart; Welsford, Dirk; Labrousse, Sara; Sumner, Michael; Hindell, Mark

2017-01-01

Antarctic coastal polynyas are persistent open water areas in the sea ice zone, and regions of high biological productivity thought to be important foraging habitat for marine predators. This study quantified southern elephant seal (Mirounga leonina) habitat use within and around the polynyas of the Prydz Bay region (63°E– 88°E) in East Antarctica, and examined the bio-physical characteristics structuring polynyas as foraging habitat. Output from a climatological regional ocean model was used to provide context for in situ temperature-salinity vertical profiles collected by tagged elephant seals and to characterise the physical properties structuring polynyas. Biological properties were explored using remotely-sensed surface chlorophyll (Chl-a) and, qualitatively, historical fish assemblage data. Spatially gridded residence time of seals was examined in relation to habitat characteristics using generalized additive mixed models. The results showed clear polynya usage during early autumn and increasingly concentrated usage during early winter. Bathymetry, Chl-a, surface net heat flux (representing polynya location), and bottom temperature were identified as significant bio-physical predictors of the spatio-temporal habitat usage. The findings from this study confirm that the most important marine habitats for juvenile male southern elephant seals within Prydz Bay region are polynyas. A hypothesis exists regarding the seasonal evolution of primary productivity, coupling from surface to subsurface productivity and supporting elevated rates of secondary production in the upper water column during summer-autumn. An advancement to this hypothesis is proposed here, whereby this bio-physical coupling is likely to extend throughout the water column as it becomes fully convected during autumn-winter, to also promote pelagic-benthic linkages important for benthic foraging within polynyas. PMID:28902905

Biophysical regulation of Chlamydia pneumoniae-infected monocyte recruitment to atherosclerotic foci

NASA Astrophysics Data System (ADS)

Evani, Shankar J.; Ramasubramanian, Anand K.

2016-01-01

Chlamydia pneumoniae infection is implicated in atherosclerosis although the contributory mechanisms are poorly understood. We hypothesize that C. pneumoniae infection favors the recruitment of monocytes to atherosclerotic foci by altering monocyte biophysics. Primary, fresh human monocytes were infected with C. pneumoniae for 8 h, and the interactions between monocytes and E-selectin or aortic endothelium under flow were characterized by video microscopy and image analysis. The distribution of membrane lipid rafts and adhesion receptors were analyzed by imaging flow cytometry. Infected cells rolled on E-selectin and endothelial surfaces, and this rolling was slower, steady and uniform compared to uninfected cells. Infection decreases cholesterol levels, increases membrane fluidity, disrupts lipid rafts, and redistributes CD44, which is the primary mediator of rolling interactions. Together, these changes translate to higher firm adhesion of infected monocytes on endothelium, which is enhanced in the presence of LDL. Uninfected monocytes treated with LDL or left untreated were used as baseline control. Our results demonstrate that the membrane biophysical changes due to infection and hyperlipidemia are one of the key mechanisms by which C. pneumoniae can exacerbate atherosclerotic pathology. These findings provide a framework to characterize the role of ‘infectious burden’ in the development and progression of atherosclerosis.

Biophysical impacts of climate-smart agriculture in the Midwest United States.

PubMed

Bagley, Justin E; Miller, Jesse; Bernacchi, Carl J

2015-09-01

The potential impacts of climate change in the Midwest United States present unprecedented challenges to regional agriculture. In response to these challenges, a variety of climate-smart agricultural methodologies have been proposed to retain or improve crop yields, reduce agricultural greenhouse gas emissions, retain soil quality and increase climate resilience of agricultural systems. One component that is commonly neglected when assessing the environmental impacts of climate-smart agriculture is the biophysical impacts, where changes in ecosystem fluxes and storage of moisture and energy lead to perturbations in local climate and water availability. Using a combination of observational data and an agroecosystem model, a series of climate-smart agricultural scenarios were assessed to determine the biophysical impacts these techniques have in the Midwest United States. The first scenario extended the growing season for existing crops using future temperature and CO2 concentrations. The second scenario examined the biophysical impacts of no-till agriculture and the impacts of annually retaining crop debris. Finally, the third scenario evaluated the potential impacts that the adoption of perennial cultivars had on biophysical quantities. Each of these scenarios was found to have significant biophysical impacts. However, the timing and magnitude of the biophysical impacts differed between scenarios. © 2014 John Wiley & Sons Ltd.

Personalized Instruction with Bootstrap Tutors in an Introductory Biophysics Course

ERIC Educational Resources Information Center

Roper, L. David

1974-01-01

Discusses the conduct of an introductory biophysics course with a personalized instruction by using tutors selected from the students themselves. Included are three tables of text contents, a sample of a terminal questionnaire, and a list of biophysics references. (CC)

Biophysical model of ion transport across human respiratory epithelia allows quantification of ion permeabilities.

PubMed

Garcia, Guilherme J M; Boucher, Richard C; Elston, Timothy C

2013-02-05

Lung health and normal mucus clearance depend on adequate hydration of airway surfaces. Because transepithelial osmotic gradients drive water flows, sufficient hydration of the airway surface liquid depends on a balance between ion secretion and absorption by respiratory epithelia. In vitro experiments using cultures of primary human nasal epithelia and human bronchial epithelia have established many of the biophysical processes involved in airway surface liquid homeostasis. Most experimental studies, however, have focused on the apical membrane, despite the fact that ion transport across respiratory epithelia involves both cellular and paracellular pathways. In fact, the ion permeabilities of the basolateral membrane and paracellular pathway remain largely unknown. Here we use a biophysical model for water and ion transport to quantify ion permeabilities of all pathways (apical, basolateral, paracellular) in human nasal epithelia cultures using experimental (Ussing Chamber and microelectrode) data reported in the literature. We derive analytical formulas for the steady-state short-circuit current and membrane potential, which are for polarized epithelia the equivalent of the Goldman-Hodgkin-Katz equation for single isolated cells. These relations allow parameter estimation to be performed efficiently. By providing a method to quantify all the ion permeabilities of respiratory epithelia, the model may aid us in understanding the physiology that regulates normal airway surface hydration. Copyright © 2013 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Analysis of MODIS 250 m Time Series Product for LULC Classification and Retrieval of Crop Biophysical Parameter

NASA Astrophysics Data System (ADS)

Verma, A. K.; Garg, P. K.; Prasad, K. S. H.; Dadhwal, V. K.

2016-12-01

Agriculture is a backbone of Indian economy, providing livelihood to about 70% of the population. The primary objective of this research is to investigate the general applicability of time-series MODIS 250m Normalized difference vegetation index (NDVI) and Enhanced vegetation index (EVI) data for various Land use/Land cover (LULC) classification. The other objective is the retrieval of crop biophysical parameter using MODIS 250m resolution data. The Uttar Pradesh state of India is selected for this research work. A field study of 38 farms was conducted during entire crop season of the year 2015 to evaluate the applicability of MODIS 8-day, 250m resolution composite images for assessment of crop condition. The spectroradiometer is used for ground reflectance and the AccuPAR LP-80 Ceptometer is used to measure the agricultural crops Leaf Area Index (LAI). The AccuPAR measures Photosynthetically Active Radiation (PAR) and can invert these readings to give LAI for plant canopy. Ground-based canopy reflectance and LAI were used to calibrate a radiative transfer model to create look-up table (LUT) that was used to simulate LAI. The seasonal trend of MODIS-derived LAI was used to find crop parameter by adjusting the LAI simulated from climate-based crop yield model. Cloud free MODIS images of 250m resolution (16 day composite period) were downloaded using LP-DAAC website over a period of 12 months (Jan to Dec 2015). MODIS both the VI products were found to have sufficient spectral, spatial and temporal resolution to detect unique signatures for each class (water, fallow land, urban, dense vegetation, orchard, sugarcane and other crops). Ground truth data were collected using JUNO GPS. Multi-temporal VI signatures for vegetation classes were consistent with its general phenological characteristic and were spectrally separable at some point during the growing season. The MODIS NDVI and EVI multi-temporal images tracked similar seasonal responses for all croplands and were

Sequential weighted Wiener estimation for extraction of key tissue parameters in color imaging: a phantom study

NASA Astrophysics Data System (ADS)

Chen, Shuo; Lin, Xiaoqian; Zhu, Caigang; Liu, Quan

2014-12-01

Key tissue parameters, e.g., total hemoglobin concentration and tissue oxygenation, are important biomarkers in clinical diagnosis for various diseases. Although point measurement techniques based on diffuse reflectance spectroscopy can accurately recover these tissue parameters, they are not suitable for the examination of a large tissue region due to slow data acquisition. The previous imaging studies have shown that hemoglobin concentration and oxygenation can be estimated from color measurements with the assumption of known scattering properties, which is impractical in clinical applications. To overcome this limitation and speed-up image processing, we propose a method of sequential weighted Wiener estimation (WE) to quickly extract key tissue parameters, including total hemoglobin concentration (CtHb), hemoglobin oxygenation (StO2), scatterer density (α), and scattering power (β), from wide-band color measurements. This method takes advantage of the fact that each parameter is sensitive to the color measurements in a different way and attempts to maximize the contribution of those color measurements likely to generate correct results in WE. The method was evaluated on skin phantoms with varying CtHb, StO2, and scattering properties. The results demonstrate excellent agreement between the estimated tissue parameters and the corresponding reference values. Compared with traditional WE, the sequential weighted WE shows significant improvement in the estimation accuracy. This method could be used to monitor tissue parameters in an imaging setup in real time.

Biophysics of molecular gastronomy.

PubMed

Brenner, Michael P; Sörensen, Pia M

2015-03-26

Chefs and scientists exploring biophysical processes have given rise to molecular gastronomy. In this Commentary, we describe how a scientific understanding of recipes and techniques facilitates the development of new textures and expands the flavor palette. The new dishes that result engage our senses in unexpected ways. PAPERCLIP. Copyright © 2015 Elsevier Inc. All rights reserved.

Using a Functional Simulation of Crisis Management to Test the C2 Agility Model Parameters on Key Performance Variables

DTIC Science & Technology

2013-06-01

1 18th ICCRTS Using a Functional Simulation of Crisis Management to Test the C2 Agility Model Parameters on Key Performance Variables...AND SUBTITLE Using a Functional Simulation of Crisis Management to Test the C2 Agility Model Parameters on Key Performance Variables 5a. CONTRACT...command in crisis management. C2 Agility Model Agility can be conceptualized at a number of different levels; for instance at the team

Ultrafast fluorescence spectroscopy via upconversion applications to biophysics.

PubMed

Xu, Jianhua; Knutson, Jay R

2008-01-01

This chapter reviews basic concepts of nonlinear fluorescence upconversion, a technique whose temporal resolution is essentially limited only by the pulse width of the ultrafast laser. Design aspects for upconversion spectrophotofluorometers are discussed, and a recently developed system is described. We discuss applications in biophysics, particularly the measurement of time-resolved fluorescence spectra of proteins (with subpicosecond time resolution). Application of this technique to biophysical problems such as dynamics of tryptophan, peptides, proteins, and nucleic acids is reviewed.

Preface: Special Topic on Single-Molecule Biophysics

NASA Astrophysics Data System (ADS)

Makarov, Dmitrii E.; Schuler, Benjamin

2018-03-01

Single-molecule measurements are now almost routinely used to study biological systems and processes. The scope of this special topic emphasizes the physics side of single-molecule observations, with the goal of highlighting new developments in physical techniques as well as conceptual insights that single-molecule measurements bring to biophysics. This issue also comprises recent advances in theoretical physical models of single-molecule phenomena, interpretation of single-molecule signals, and fundamental areas of statistical mechanics that are related to single-molecule observations. A particular goal is to illustrate the increasing synergy between theory, simulation, and experiment in single-molecule biophysics.

Constructing Precisely Computing Networks with Biophysical Spiking Neurons.

PubMed

Schwemmer, Michael A; Fairhall, Adrienne L; Denéve, Sophie; Shea-Brown, Eric T

2015-07-15

While spike timing has been shown to carry detailed stimulus information at the sensory periphery, its possible role in network computation is less clear. Most models of computation by neural networks are based on population firing rates. In equivalent spiking implementations, firing is assumed to be random such that averaging across populations of neurons recovers the rate-based approach. Recently, however, Denéve and colleagues have suggested that the spiking behavior of neurons may be fundamental to how neuronal networks compute, with precise spike timing determined by each neuron's contribution to producing the desired output (Boerlin and Denéve, 2011; Boerlin et al., 2013). By postulating that each neuron fires to reduce the error in the network's output, it was demonstrated that linear computations can be performed by networks of integrate-and-fire neurons that communicate through instantaneous synapses. This left open, however, the possibility that realistic networks, with conductance-based neurons with subthreshold nonlinearity and the slower timescales of biophysical synapses, may not fit into this framework. Here, we show how the spike-based approach can be extended to biophysically plausible networks. We then show that our network reproduces a number of key features of cortical networks including irregular and Poisson-like spike times and a tight balance between excitation and inhibition. Lastly, we discuss how the behavior of our model scales with network size or with the number of neurons "recorded" from a larger computing network. These results significantly increase the biological plausibility of the spike-based approach to network computation. We derive a network of neurons with standard spike-generating currents and synapses with realistic timescales that computes based upon the principle that the precise timing of each spike is important for the computation. We then show that our network reproduces a number of key features of cortical networks

Determination of key parameters of vector multifractal vector fields

NASA Astrophysics Data System (ADS)

Schertzer, D. J. M.; Tchiguirinskaia, I.

2017-12-01

For too long time, multifractal analyses and simulations have been restricted to scalar-valued fields (Schertzer and Tchiguirinskaia, 2017a,b). For instance, the wind velocity multifractality has been mostly analysed in terms of scalar structure functions and with the scalar energy flux. This restriction has had the unfortunate consequences that multifractals were applicable to their full extent in geophysics, whereas it has inspired them. Indeed a key question in geophysics is the complexity of the interactions between various fields or they components. Nevertheless, sophisticated methods have been developed to determine the key parameters of scalar valued fields. In this communication, we first present the vector extensions of the universal multifractal analysis techniques to multifractals whose generator belong to a Levy-Clifford algebra (Schertzer and Tchiguirinskaia, 2015). We point out further extensions noting the increased complexity. For instance, the (scalar) index of multifractality becomes a matrice. Schertzer, D. and Tchiguirinskaia, I. (2015) `Multifractal vector fields and stochastic Clifford algebra', Chaos: An Interdisciplinary Journal of Nonlinear Science, 25(12), p. 123127. doi: 10.1063/1.4937364. Schertzer, D. and Tchiguirinskaia, I. (2017) `An Introduction to Multifractals and Scale Symmetry Groups', in Ghanbarian, B. and Hunt, A. (eds) Fractals: Concepts and Applications in Geosciences. CRC Press, p. (in press). Schertzer, D. and Tchiguirinskaia, I. (2017b) `Pandora Box of Multifractals: Barely Open ?', in Tsonis, A. A. (ed.) 30 Years of Nonlinear Dynamics in Geophysics. Berlin: Springer, p. (in press).

Parameter optimization in biased decoy-state quantum key distribution with both source errors and statistical fluctuations

NASA Astrophysics Data System (ADS)

Zhu, Jian-Rong; Li, Jian; Zhang, Chun-Mei; Wang, Qin

2017-10-01

The decoy-state method has been widely used in commercial quantum key distribution (QKD) systems. In view of the practical decoy-state QKD with both source errors and statistical fluctuations, we propose a universal model of full parameter optimization in biased decoy-state QKD with phase-randomized sources. Besides, we adopt this model to carry out simulations of two widely used sources: weak coherent source (WCS) and heralded single-photon source (HSPS). Results show that full parameter optimization can significantly improve not only the secure transmission distance but also the final key generation rate. And when taking source errors and statistical fluctuations into account, the performance of decoy-state QKD using HSPS suffered less than that of decoy-state QKD using WCS.

Ultrafast Fluorescence Spectroscopy via Upconversion: Applications to Biophysics

PubMed Central

Xu, Jianhua; Knutson, Jay R.

2012-01-01

This chapter reviews basic concepts of nonlinear fluorescence upconversion, a technique whose temporal resolution is essentially limited only by the pulse width of the ultrafast laser. Design aspects for upconversion spectrophotofluorometers are discussed, and a recently developed system is described. We discuss applications in biophysics, particularly the measurement of time-resolved fluorescence spectra of proteins (with subpicosecond time resolution). Application of this technique to biophysical problems such as dynamics of tryptophan, peptides, proteins, and nucleic acids is reviewed. PMID:19152860

Comparison of biophysical factors influencing on emphysema quantification with low-dose CT

NASA Astrophysics Data System (ADS)

Heo, Chang Yong; Kim, Jong Hyo

2014-03-01

Emphysema Index(EI) measurements in MDCT is known to be influenced by various biophysical factors such as total lung volume, and body size. We investigated the association of the four biophysical factors with emphysema index in low-dose MDCT. In particular, we attempted to identify a potentially stronger biophysical factor than total lung volume. A total of 400 low-dose MDCT volumes taken at 120kVp, 40mAs, 1mm thickness, and B30f reconstruction kernel were used. The lungs, airways, and pulmonary vessels were automatically segmented, and two Emphysema Indices, relative area below -950HU(RA950) and 15th percentile(Perc15), were extracted from the segmented lungs. The biophysical factors such as total lung volume(TLV), mode of lung attenuation(ModLA), effective body diameter(EBD), and the water equivalent body diameter(WBD) were estimated from the segmented lung and body area. The association of biophysical factors with emphysema indices were evaluated by correlation coefficients. The mean emphysema indices were 8.3±5.5(%) in RA950, and -930±18(HU) in Perc15. The estimates of biophysical factors were 4.7±1.0(L) in TLV, -901±21(HU) in ModLA, 26.9±2.2(cm) in EBD, and 25.9±2.6(cm) in WBD. The correlation coefficients of biophysical factors with RA950 were 0.73 in TLV, 0.94 in ModLA, 0.31 in EBD, and 0.18 WBD, the ones with Perc15 were 0.74 in TLV, 0.98 in ModLA, 0.29 in EBD, and 0.15 WBD. Study results revealed that two biophysical factors, TLV and ModLA, mostly affects the emphysema indices. In particular, the ModLA exhibited strongest correlation of 0.98 with Perc15, which indicating the ModLA is the most significant confounding biophysical factor in emphysema indices measurement.

Temporal measurement and analysis of high-resolution spectral signatures of plants and relationships to biophysical characteristics

NASA Astrophysics Data System (ADS)

Bostater, Charles R., Jr.; Rebbman, Jan; Hall, Carlton; Provancha, Mark; Vieglais, David

1995-11-01

Measurements of temporal reflectance signatures as a function of growing season for sand live oak (Quercus geminata), myrtle oak (Q. myrtifolia, and saw palmetto (Serenoa repens) were collected during a two year study period. Canopy level spectral reflectance signatures, as a function of 252 channels between 368 and 1115 nm, were collected using near nadir viewing geometry and a consistent sun illumination angle. Leaf level reflectance measurements were made in the laboratory using a halogen light source and an environmental optics chamber with a barium sulfate reflectance coating. Spectral measurements were related to several biophysical measurements utilizing optimal passive ambient correlation spectroscopy (OPACS) technique. Biophysical parameters included percent moisture, water potential (MPa), total chlorophyll, and total Kjeldahl nitrogen. Quantitative data processing techniques were used to determine optimal bands based on the utilization of a second order derivative or inflection estimator. An optical cleanup procedure was then employed that computes the double inflection ratio (DIR) spectra for all possible three band combinations normalized to the previously computed optimal bands. These results demonstrate a unique approach to the analysis of high spectral resolution reflectance signatures for estimation of several biophysical measures of plants at the leaf and canopy level from optimally selected bands or bandwidths.

Key Parameters for Operator Diagnosis of BWR Plant Condition during a Severe Accident

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

Clayton, Dwight A.; Poore, III, Willis P.

2015-01-01

The objective of this research is to examine the key information needed from nuclear power plant instrumentation to guide severe accident management and mitigation for boiling water reactor (BWR) designs (specifically, a BWR/4-Mark I), estimate environmental conditions that the instrumentation will experience during a severe accident, and identify potential gaps in existing instrumentation that may require further research and development. This report notes the key parameters that instrumentation needs to measure to help operators respond to severe accidents. A follow-up report will assess severe accident environmental conditions as estimated by severe accident simulation model analysis for a specific US BWR/4-Markmore » I plant for those instrumentation systems considered most important for accident management purposes.« less

Predictors of cerebral microembolization during phased radiofrequency ablation of atrial fibrillation: analysis of biophysical parameters from the ablation generator.

PubMed

Nagy-Balo, Edina; Kiss, Alexandra; Condie, Catherine; Stewart, Mark; Edes, Istvan; Csanadi, Zoltan

2014-06-01

Pulmonary vein isolation with phased radiofrequency current and use of a pulmonary vein ablation catheter (PVAC) has recently been associated with a high incidence of clinically silent brain infarcts on diffusion-weighted magnetic resonance imaging and a high microembolic signal (MES) count detected by transcranial Doppler. The purpose of this study was to investigate the potential correlation between different biophysical parameters of energy delivery (ED) and MES generation during PVAC ablation. MES counts during consecutive PVAC ablations were recorded for each ED and time stamped for correlation with temperature, power, and impedance data from the GENius 14.4 generator. Additionally, catheter-tissue contact was characterized by the template deviation score, calculated by comparing the temperature curve with an ideal template representing good contact, and by the respiratory contact failure score, to quantify temperature variations indicative of intermittent contact due to respiration. A total of 834 EDs during 48 PVAC ablations were analyzed. A significant increase in MES count was associated with a lower average temperature, a temperature integral over 62°C, a higher average power, the total energy delivered, higher respiration and template deviation scores (P <.0001), and simultaneous ED to the most proximal and distal poles of the PVAC (P <.0001). MES generation during ablation is related to different indicators of poor electrode-tissue contact, the total power delivered, and the interaction between the most distal and the most proximal electrodes. Copyright © 2014. Published by Elsevier Inc.

Crop Damage by Primates: Quantifying the Key Parameters of Crop-Raiding Events

PubMed Central

Wallace, Graham E.; Hill, Catherine M.

2012-01-01

Human-wildlife conflict often arises from crop-raiding, and insights regarding which aspects of raiding events determine crop loss are essential when developing and evaluating deterrents. However, because accounts of crop-raiding behaviour are frequently indirect, these parameters are rarely quantified or explicitly linked to crop damage. Using systematic observations of the behaviour of non-human primates on farms in western Uganda, this research identifies number of individuals raiding and duration of raid as the primary parameters determining crop loss. Secondary factors include distance travelled onto farm, age composition of the raiding group, and whether raids are in series. Regression models accounted for greater proportions of variation in crop loss when increasingly crop and species specific. Parameter values varied across primate species, probably reflecting differences in raiding tactics or perceptions of risk, and thereby providing indices of how comfortable primates are on-farm. Median raiding-group sizes were markedly smaller than the typical sizes of social groups. The research suggests that key parameters of raiding events can be used to measure the behavioural impacts of deterrents to raiding. Furthermore, farmers will benefit most from methods that discourage raiding by multiple individuals, reduce the size of raiding groups, or decrease the amount of time primates are on-farm. This study demonstrates the importance of directly relating crop loss to the parameters of raiding events, using systematic observations of the behaviour of multiple primate species. PMID:23056378

Resilience of Key Biological Parameters of the Senegalese Flat Sardinella to Overfishing and Climate Change.

PubMed

Ba, Kamarel; Thiaw, Modou; Lazar, Najih; Sarr, Alassane; Brochier, Timothée; Ndiaye, Ismaïla; Faye, Alioune; Sadio, Oumar; Panfili, Jacques; Thiaw, Omar Thiom; Brehmer, Patrice

2016-01-01

The stock of the Senegalese flat sardinella, Sardinella maderensis, is highly exploited in Senegal, West Africa. Its growth and reproduction parameters are key biological indicators for improving fisheries management. This study reviewed these parameters using landing data from small-scale fisheries in Senegal and literature information dated back more than 25 years. Age was estimated using length-frequency data to calculate growth parameters and assess the growth performance index. With global climate change there has been an increase in the average sea surface temperature along the Senegalese coast but the length-weight parameters, sex ratio, size at first sexual maturity, period of reproduction and condition factor of S. maderensis have not changed significantly. The above parameters of S. maderensis have hardly changed, despite high exploitation and fluctuations in environmental conditions that affect the early development phases of small pelagic fish in West Africa. This lack of plasticity of the species regarding of the biological parameters studied should be considered when planning relevant fishery management plans.

Nanodiscs in Membrane Biochemistry and Biophysics.

PubMed

Denisov, Ilia G; Sligar, Stephen G

2017-03-22

Membrane proteins play a most important part in metabolism, signaling, cell motility, transport, development, and many other biochemical and biophysical processes which constitute fundamentals of life on the molecular level. Detailed understanding of these processes is necessary for the progress of life sciences and biomedical applications. Nanodiscs provide a new and powerful tool for a broad spectrum of biochemical and biophysical studies of membrane proteins and are commonly acknowledged as an optimal membrane mimetic system that provides control over size, composition, and specific functional modifications on the nanometer scale. In this review we attempted to combine a comprehensive list of various applications of nanodisc technology with systematic analysis of the most attractive features of this system and advantages provided by nanodiscs for structural and mechanistic studies of membrane proteins.

Applications of Biophysics in High-Throughput Screening Hit Validation.

PubMed

Genick, Christine Clougherty; Barlier, Danielle; Monna, Dominique; Brunner, Reto; Bé, Céline; Scheufler, Clemens; Ottl, Johannes

2014-06-01

For approximately a decade, biophysical methods have been used to validate positive hits selected from high-throughput screening (HTS) campaigns with the goal to verify binding interactions using label-free assays. By applying label-free readouts, screen artifacts created by compound interference and fluorescence are discovered, enabling further characterization of the hits for their target specificity and selectivity. The use of several biophysical methods to extract this type of high-content information is required to prevent the promotion of false positives to the next level of hit validation and to select the best candidates for further chemical optimization. The typical technologies applied in this arena include dynamic light scattering, turbidometry, resonance waveguide, surface plasmon resonance, differential scanning fluorimetry, mass spectrometry, and others. Each technology can provide different types of information to enable the characterization of the binding interaction. Thus, these technologies can be incorporated in a hit-validation strategy not only according to the profile of chemical matter that is desired by the medicinal chemists, but also in a manner that is in agreement with the target protein's amenability to the screening format. Here, we present the results of screening strategies using biophysics with the objective to evaluate the approaches, discuss the advantages and challenges, and summarize the benefits in reference to lead discovery. In summary, the biophysics screens presented here demonstrated various hit rates from a list of ~2000 preselected, IC50-validated hits from HTS (an IC50 is the inhibitor concentration at which 50% inhibition of activity is observed). There are several lessons learned from these biophysical screens, which will be discussed in this article. © 2014 Society for Laboratory Automation and Screening.

Interleukin-10 reorganizes the cytoskeleton of mature dendritic cells leading to their impaired biophysical properties and motilities.

PubMed

Xu, Xiaoli; Liu, Xianmei; Long, Jinhua; Hu, Zuquan; Zheng, Qinni; Zhang, Chunlin; Li, Long; Wang, Yun; Jia, Yi; Qiu, Wei; Zhou, Jing; Yao, Weijuan; Zeng, Zhu

2017-01-01

Interlukin-10 (IL-10) is an immunomodulatory cytokine which predominantly induces immune-tolerance. It has been also identified as a major cytokine in the tumor microenvironment that markedly mediates tumor immune escape. Previous studies on the roles of IL-10 in tumor immunosuppression mainly focus on its biochemical effects. But the effects of IL-10 on the biophysical characteristics of immune cells are ill-defined. Dendritic cells (DCs) are the most potent antigen-presenting cells and play a key role in the anti-tumor immune response. IL-10 can affect the immune regulatory functions of DCs in various ways. In this study, we aim to explore the effects of IL-10 on the biophysical functions of mature DCs (mDCs). mDCs were treated with different concentrations of IL-10 and their biophysical characteristics were identified. The results showed that the biophysical properties of mDCs, including electrophoresis mobility, osmotic fragility and deformability, as well as their motilities, were impaired by IL-10. Meanwhile, the cytoskeleton (F-actin) of mDCs was reorganized by IL-10. IL-10 caused the alternations in the expressions of fasin1 and profilin1 as well as the phosphorylation of cofilin1 in a concentration-dependent fashion. Moreover, Fourier transformed infrared resonance data showed that IL-10 made the status of gene transcription and metabolic turnover of mDCs more active. These results demonstrate a new aspect of IL-10's actions on the immune system and represent one of the mechanisms for immune escape of tumors. It may provide a valuable clue to optimize and improve the efficiency of DC-based immunotherapy against cancer.

Comparisons of MODIS vegetation index products with biophysical and flux tower measurements

NASA Astrophysics Data System (ADS)

Sirikul, Natthanich

Vegetation indices (VI) play an important role in studies of global climate and biogeochemical cycles, and are also positively related to many biophysical parameters and satellite products, such as leaf area index (LAI), gross primary production (GPP), land surface water index (LSWI) and land surface temperature (LST). In this study we found that VI's had strong relationships with some biophysical products, such as gross primary production, yet were less well correlated with biophysical structural parameters, such as leaf area index. The relationships between MODIS VI's and biophysical field measured LAI showed poor correlation at semi-arid land and broadleaf forest land cover type whereas cropland showed stronger correlations than the other vegetation types. In addition, the relationship between the enhanced vegetation index (EVI)-LAI and normalized difference vegetation index (NDVI)-LAI did not show significant differences. Comparisons of the relationships between the EVI and NDVI with tower-measured GPP from 11 flux towers in North America, showed that MODIS EVI had much stronger relationships with tower-GPP than did NDVI, and EVI was better correlated with the seasonal dynamics of GPP than was NDVI. In addition, there were no significant differences among the 1x1, 3x3 and 7x7 pixel sample sizes. The comparisons of VIs from the 3 MODIS products from which VI's are generated (Standard VI (MOD13)), Nadir Adjusted Surface Reflectance (NBAR (MOD43)), and Surface Reflectance (MOD09)), showed that MODIS NBAR-EVI (MOD43) was best correlated with GPP compared with the other VI products. In addition, the MODIS VI - tower GPP relationships were significantly improved using NBAR-EVI over the more complex canopy structures, such as the broadleaf and needleleaf forests. The relationship of tower-GPP with other MODIS products would be useful in more thorough characterization of some land cover types in which the VI's have encountered problems. The land surface temperature

Single Particle Orientation and Rotational Tracking (SPORT) in biophysical studies

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

Gu, Yan; Ha, Ji Won; Augspurger, Ashley E.

The single particle orientation and rotational tracking (SPORT) techniques have seen rapid development in the past 5 years. Recent technical advances have greatly expanded the applicability of SPORT in biophysical studies. In this feature article, we survey the current development of SPORT and discuss its potential applications in biophysics, including cellular membrane processes and intracellular transport.

Perspective: Quantum mechanical methods in biochemistry and biophysics.

PubMed

Cui, Qiang

2016-10-14

In this perspective article, I discuss several research topics relevant to quantum mechanical (QM) methods in biophysical and biochemical applications. Due to the immense complexity of biological problems, the key is to develop methods that are able to strike the proper balance of computational efficiency and accuracy for the problem of interest. Therefore, in addition to the development of novel ab initio and density functional theory based QM methods for the study of reactive events that involve complex motifs such as transition metal clusters in metalloenzymes, it is equally important to develop inexpensive QM methods and advanced classical or quantal force fields to describe different physicochemical properties of biomolecules and their behaviors in complex environments. Maintaining a solid connection of these more approximate methods with rigorous QM methods is essential to their transferability and robustness. Comparison to diverse experimental observables helps validate computational models and mechanistic hypotheses as well as driving further development of computational methodologies.

Biophysical Regulation of Cell Behavior—Cross Talk between Substrate Stiffness and Nanotopography

PubMed Central

Yang, Yong; Wang, Kai; Gu, Xiaosong; Leong, Kam W.

2017-01-01

The stiffness and nanotopographical characteristics of the extracellular matrix (ECM) influence numerous developmental, physiological, and pathological processes in vivo. These biophysical cues have therefore been applied to modulate almost all aspects of cell behavior, from cell adhesion and spreading to proliferation and differentiation. Delineation of the biophysical modulation of cell behavior is critical to the rational design of new biomaterials, implants, and medical devices. The effects of stiffness and topographical cues on cell behavior have previously been reviewed, respectively; however, the interwoven effects of stiffness and nanotopographical cues on cell behavior have not been well described, despite similarities in phenotypic manifestations. Herein, we first review the effects of substrate stiffness and nanotopography on cell behavior, and then focus on intracellular transmission of the biophysical signals from integrins to nucleus. Attempts are made to connect extracellular regulation of cell behavior with the biophysical cues. We then discuss the challenges in dissecting the biophysical regulation of cell behavior and in translating the mechanistic understanding of these cues to tissue engineering and regenerative medicine. PMID:29071164

Indigenous community health and climate change: integrating biophysical and social science indicators

USGS Publications Warehouse

Donatuto, Jamie; Grossman, Eric E.; Konovsky, John; Grossman, Sarah; Campbell, Larry W.

2014-01-01

This article describes a pilot study evaluating the sensitivity of Indigenous community health to climate change impacts on Salish Sea shorelines (Washington State, United States and British Columbia, Canada). Current climate change assessments omit key community health concerns, which are vital to successful adaptation plans, particularly for Indigenous communities. Descriptive scaling techniques, employed in facilitated workshops with two Indigenous communities, tested the efficacy of ranking six key indicators of community health in relation to projected impacts to shellfish habitat and shoreline archaeological sites stemming from changes in the biophysical environment. Findings demonstrate that: when shellfish habitat and archaeological resources are impacted, so is Indigenous community health; not all community health indicators are equally impacted; and, the community health indicators of highest concern are not necessarily the same indicators most likely to be impacted. Based on the findings and feedback from community participants, exploratory trials were successful; Indigenous-specific health indicators may be useful to Indigenous communities who are assessing climate change sensitivities and creating adaptation plans.

Biophysical characterization of α-synuclein and its controversial structure

PubMed Central

Alderson, T Reid; Markley, John L

2013-01-01

α-synuclein, a presynaptic protein of poorly defined function, constitutes the main component of Parkinson disease-associated Lewy bodies. Extensive biophysical investigations have provided evidence that isolated α-synuclein is an intrinsically disordered protein (IDP) in vitro. Subsequently serving as a model IDP in numerous studies, α-synuclein has aided in the development of many technologies used to characterize IDPs and arguably represents the most thoroughly analyzed IDP to date. Recent reports, however, have challenged the disordered nature of α-synuclein inside cells and have instead proposed a physiologically relevant helical tetramer. Despite α-synuclein’s rich biophysical history, a single coherent picture has not yet emerged concerning its in vivo structure, dynamics, and physiological role(s). We present herein a review of the biophysical discoveries, developments, and models pertinent to the characterization of α-synuclein’s structure and analysis of the native tetramer controversy. PMID:24634806

A Bayesian Framework for Coupled Estimation of Key Unknown Parameters of Land Water and Energy Balance Equations

NASA Astrophysics Data System (ADS)

Farhadi, L.; Abdolghafoorian, A.

2015-12-01

The land surface is a key component of climate system. It controls the partitioning of available energy at the surface between sensible and latent heat, and partitioning of available water between evaporation and runoff. Water and energy cycle are intrinsically coupled through evaporation, which represents a heat exchange as latent heat flux. Accurate estimation of fluxes of heat and moisture are of significant importance in many fields such as hydrology, climatology and meteorology. In this study we develop and apply a Bayesian framework for estimating the key unknown parameters of terrestrial water and energy balance equations (i.e. moisture and heat diffusion) and their uncertainty in land surface models. These equations are coupled through flux of evaporation. The estimation system is based on the adjoint method for solving a least-squares optimization problem. The cost function consists of aggregated errors on state (i.e. moisture and temperature) with respect to observation and parameters estimation with respect to prior values over the entire assimilation period. This cost function is minimized with respect to parameters to identify models of sensible heat, latent heat/evaporation and drainage and runoff. Inverse of Hessian of the cost function is an approximation of the posterior uncertainty of parameter estimates. Uncertainty of estimated fluxes is estimated by propagating the uncertainty for linear and nonlinear function of key parameters through the method of First Order Second Moment (FOSM). Uncertainty analysis is used in this method to guide the formulation of a well-posed estimation problem. Accuracy of the method is assessed at point scale using surface energy and water fluxes generated by the Simultaneous Heat and Water (SHAW) model at the selected AmeriFlux stations. This method can be applied to diverse climates and land surface conditions with different spatial scales, using remotely sensed measurements of surface moisture and temperature states

Guidance for Large-scale Implementation of Alternate Wetting and Drying: A Biophysical Suitability Assessment

NASA Astrophysics Data System (ADS)

Sander, B. O.; Wassmann, R.; Nelson, A.; Palao, L.; Wollenberg, E.; Ishitani, M.

2014-12-01

The alternate wetting and drying (AWD) technology for rice production does not only save 15-30% of irrigation water, it also reduces methane emissions by up to 70%. AWD is defined by periodic drying and re-flooding of a rice field. Due to its high mitigation potential and its simplicity to execute this practice AWD has gained a lot of attention in recent years. The Climate and Clean Air Coalition (CCAC) has put AWD high on its agenda and funds a project to guide implementation of this technology in Vietnam, Bangladesh and Colombia. One crucial activity is a biophysical suitability assessment for AWD in the three countries. For this, we analyzed rainfall and soil data as well as potential evapotranspiration to assess if the water balance allows practicing AWD or if precipitation is too high for rice fields to fall dry. In my talk I will outline key factors for a successful large-scale implementation of AWD with a focus on the biophysical suitability assessment. The seasonal suitability maps that we generated highlight priority areas for AWD implementation and guide policy makers to informed decisions about meaningful investments in infrastructure and extension work.

Entropy generation in biophysical systems

NASA Astrophysics Data System (ADS)

Lucia, U.; Maino, G.

2013-03-01

Recently, in theoretical biology and in biophysical engineering the entropy production has been verified to approach asymptotically its maximum rate, by using the probability of individual elementary modes distributed in accordance with the Boltzmann distribution. The basis of this approach is the hypothesis that the entropy production rate is maximum at the stationary state. In the present work, this hypothesis is explained and motivated, starting from the entropy generation analysis. This latter quantity is obtained from the entropy balance for open systems considering the lifetime of the natural real process. The Lagrangian formalism is introduced in order to develop an analytical approach to the thermodynamic analysis of the open irreversible systems. The stationary conditions of the open systems are thus obtained in relation to the entropy generation and the least action principle. Consequently, the considered hypothesis is analytically proved and it represents an original basic approach in theoretical and mathematical biology and also in biophysical engineering. It is worth remarking that the present results show that entropy generation not only increases but increases as fast as possible.

Building biophysics in mid-century China: the University of Science and Technology of China.

PubMed

Luk, Yi Lai Christine

2015-01-01

Biophysics has been either an independent discipline or an element of another discipline in the United States, but it has always been recognized as a stand-alone discipline in the People's Republic of China (PRC) since 1949. To inquire into this apparent divergence, this paper investigates the formational history of biophysics in China by examining the early institutional history of one of the best-known and prestigious science and technology universities in the PRC, the University of Science and Technology of China (USTC). By showing how the university and its biophysics program co-evolved with national priorities from the school's founding in 1958 to the eve of the Cultural Revolution in 1966, the purpose of this paper is to assess the development of a scientific discipline in the context of national demands and institutional politics. Specific materials for analysis include the school's admission policies, curricula, students' dissertations, and research program. To further contextualize the institutional setting of Chinese biophysics, this paper begins with a general history of proto-biophysical institutions in China during the Nationalist-Communist transitional years. This paper could be of interest to historians wanting to know more about the origin of the biophysics profession in China, and in particular how research areas that constitute biophysics changed in tandem with socio-political contingencies.

Can biophysical properties of submersed macrophytes be determined by remote sensing?

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

Malthus, T.J.; Ciraolo, G.; La Loggia, G.

1997-06-01

This paper details the development of a computationally efficient Monte Carlo simulation program to model photon transport through submersed plant canopies, with emphasis on Seagrass communities. The model incorporates three components: the transmission of photons through a water column of varying depth and turbidity; the interaction of photons within a submersed plant canopy of varying biomass; and interactions with the bottom substrate. The three components of the model are discussed. Simulations were performed based on measured parameters for Posidonia oceanica and compared to measured subsurface reflectance spectra made over comparable seagrass communities in Sicilian coastal waters. It is shown thatmore » the output is realistic. Further simulations are undertaken to investigate the effect of depth and turbidity of the overlying water column. Both sets of results indicate the rapid loss of canopy signal as depth increases and water column phytoplankton concentrations increase. The implications for the development of algorithms for the estimation of submersed canopy biophysical parameters are briefly discussed.« less

A systemic study on key parameters affecting nanocomposite coatings on magnesium substrates.

PubMed

Johnson, Ian; Wang, Sebo Michelle; Silken, Christine; Liu, Huinan

2016-05-01

Nanocomposite coatings offer multiple functions simultaneously to improve the interfacial properties of magnesium (Mg) alloys for skeletal implant applications, e.g., controlling the degradation rate of Mg substrates, improving bone cell functions, and providing drug delivery capability. However, the effective service time of nanocomposite coatings may be limited due to their early delamination from the Mg-based substrates. Therefore, the objective of this study was to address the delamination issue of nanocomposite coatings, improve the coating properties for reducing the degradation of Mg-based substrates, and thus improve their cytocompatibility with bone marrow derived mesenchymal stem cells (BMSCs). The surface conditions of the substrates, polymer component type of the nanocomposite coatings, and post-deposition processing are the key parameters that contribute to the efficacy of the nanocomposite coatings in regulating substrate degradation and bone cell responses. Specifically, the effects of metallic surface versus alkaline heat-treated hydroxide surface of the substrates on coating quality were investigated. For the nanocomposite coatings, nanophase hydroxyapatite (nHA) was dispersed in three types of biodegradable polymers, i.e., poly(lactic-co-glycolic acid) (PLGA), poly(l-lactic acid) (PLLA), or poly(caprolactone) (PCL) to determine which polymer component could provide integrated properties for slowest Mg degradation. The nanocomposite coatings with or without post-deposition processing, i.e., melting, annealing, were compared to determine which processing route improved the properties of the nanocomposite coatings most significantly. The results showed that optimizing the coating processes addressed the delamination issue. The melted then annealed nHA/PCL coating on the metallic Mg substrates showed the slowest degradation and the best coating adhesion, among all the combinations of conditions studied; and, it improved the adhesion density of BMSCs

Teaching wave phenomena via biophysical applications

NASA Astrophysics Data System (ADS)

Reich, Daniel; Robbins, Mark; Leheny, Robert; Wonnell, Steven

2014-03-01

Over the past several years we have developed a two-semester second-year physics course sequence for students in the biosciences, tailored in part to the needs of undergraduate biophysics majors. One semester, ``Biological Physics,'' is based on the book of that name by P. Nelson. This talk will focus largely on the other semester, ``Wave Phenomena with Biophysical Applications,'' where we provide a novel introduction to the physics of waves, primarily through the study of experimental probes used in the biosciences that depend on the interaction of electromagnetic radiation with matter. Topic covered include: Fourier analysis, sound and hearing, diffraction - culminating in an analysis of x-ray fiber diffraction and its use in the determination of the structure of DNA - geometrical and physical optics, the physics of modern light microscopy, NMR and MRI. Laboratory exercises tailored to this course will also be described.

A biophysical basis for patchy mortality during heat waves.

PubMed

Mislan, K A S; Wethey, David S

2015-04-01

Extreme heat events cause patchy mortality in many habitats. We examine biophysical mechanisms responsible for patchy mortality in beds of the competitively dominant ecosystem engineer, the marine mussel Mytilus californianus, on the west coast of the United States. We used a biophysical model to predict daily fluctuations in body temperature at sites from southern California to Washington and used results of laboratory experiments on thermal tolerance to determine mortality rates from body temperature. In our model, we varied the rate of thermal conduction within mussel beds and found that this factor can account for large differences in body temperature and consequent mortality during heat waves. Mussel beds provide structural habitat for other species and increase local biodiversity, but, as sessile organisms, they are particularly vulnerable to extreme weather conditions. Identifying critical biophysical mechanisms related to mortality and ecological performance will improve our ability to predict the effects of climate change on these vulnerable ecosystems.

Social versus biophysical availability of wood in the northern United States

Treesearch

Brett J. Butler; Ma Zhao; David B. Kittredge; Paul Catanzaro

2010-01-01

The availability of wood, be it harvested for sawlogs, pulpwood, biomass, or other products, is constrained by social and biophysical factors. Knowing the difference between social and biophysical availability is important for understanding what can realistically be extracted. This study focuses on the wood located in family forests across the northern United States....

Daytime Changes of Skin Biophysical Characteristics: A Study of Hydration, Transepidermal Water Loss, pH, Sebum, Elasticity, Erythema, and Color Index on Middle Eastern Skin.

PubMed

Firooz, Alireza; Zartab, Hamed; Sadr, Bardia; Bagherpour, Leili Naraghi; Masoudi, Aidin; Fanian, Ferial; Dowlati, Yahya; Ehsani, Amir Hooshang; Samadi, Aniseh

2016-01-01

The exposure of skin to ultraviolet radiation and temperature differs significantly during the day. It is reasonable that biophysical parameters of human skin have periodic daily fluctuation. The objective of this study was to study the fluctuations of various biophysical characteristics of Middle Eastern skin in standardized experimental conditions. Seven biophysical parameters of skin including stratum corneum hydration, transepidermal water loss, pH, sebum, elasticity, skin color, and erythema index were measured at three time points (8 a.m., 12 p.m. and 4 p.m.) on the forearm of 12 healthy participants (mean age of 28.4 years) without any ongoing skin disease using the CK MPA 580 device in standard temperature and humidity conditions. A significant difference was observed between means of skin color index at 8 a.m. (175.42 ± 13.92) and 4 p.m. (164.44 ± 13.72, P = 0.025), between the pH at 8 a.m. (5.72 ± 0.48) and 4 p.m. (5.33 ± 0.55, P = 0.001) and pH at 12 p.m. (5.60 ± 0.48) and 4 p.m. (5.33 ± 0.55, P = 0.001). Other comparisons between the means of these parameters at different time points resulted in nonsignificant P values. There are daytime changes in skin color index and pH. Skin color index might be higher and cutaneous pH more basic in the early morning compared to later of the day.

A Multi-Sensor Approach to Enhance the Prediction of Mangrove Biophysical Characteristics in Chilika Lagoon and Bhitarkanika Wildlife Sanctuary, Odisha, India

NASA Astrophysics Data System (ADS)

Kumar, A.; Bledsoe, R.; Mishra, D. R.; Cameron, C.; Dahal, S.; Remillard, C.; Stone, A.; Stupp, P.

2017-12-01

Mangroves, one of the most productive ecosystems on Earth, play a major role in coastal ecosystem processes from mitigating erosion to acting as a barrier against tidal and storm surges associated with tropical cyclones. India has about 5 % of the world's mangrove vegetation, and over half of which is found along the east coast of the country. Chilika Lagoon and Bhitarkanika Wildlife Sanctuary are Ramsar sites of international wetland importance, situated in the state of Odisha along the east coast of India. Chilika Lagoon holds three small, but distinct mangrove patches, while Bhitarkanika Wildlife Sanctuary has several large, dense patches of mangroves. There is growing concern for the effective management and conservation of these mangrove forests. This study demonstrated the use of a suite of satellite data (Terra, Landsat, and Sentinel-1) for meeting the following objectives: 1. Derive a long-term spatio-temporal phenological maps of the biophysical parameters (chlorophyll, leaf area index, gross primary productivity, and evapotranspiration); 2. Analyze long-term spatio-temporal variability of physical and meteorological parameters; 3. Document decadal changes in mangroves area estimates starting from 1995 to 2017 using Landsat and radar data. The time series developed in this study revealed a phenological pattern for mangrove biophysical characteristics. Historical analysis of land cover maps indicated decrease in dense mangrove area and increase in open mangrove area and fragmentation. The results of this study will be used as an efficient biophysical mapping and monitoring protocol for mangrove forests in restoration decision-making.

Using the ARTMO toolbox for automated retrieval of biophysical parameters through radiative transfer model inversion: Optimizing LUT-based inversion

NASA Astrophysics Data System (ADS)

Verrelst, J.; Rivera, J. P.; Leonenko, G.; Alonso, L.; Moreno, J.

2012-04-01

Radiative transfer (RT) modeling plays a key role for earth observation (EO) because it is needed to design EO instruments and to develop and test inversion algorithms. The inversion of a RT model is considered as a successful approach for the retrieval of biophysical parameters because of being physically-based and generally applicable. However, to the broader community this approach is considered as laborious because of its many processing steps and expert knowledge is required to realize precise model parameterization. We have recently developed a radiative transfer toolbox ARTMO (Automated Radiative Transfer Models Operator) with the purpose of providing in a graphical user interface (GUI) essential models and tools required for terrestrial EO applications such as model inversion. In short, the toolbox allows the user: i) to choose between various plant leaf and canopy RT models (e.g. models from the PROSPECT and SAIL family, FLIGHT), ii) to choose between spectral band settings of various air- and space-borne sensors or defining own sensor settings, iii) to simulate a massive amount of spectra based on a look up table (LUT) approach and storing it in a relational database, iv) to plot spectra of multiple models and compare them with measured spectra, and finally, v) to run model inversion against optical imagery given several cost options and accuracy estimates. In this work ARTMO was used to tackle some well-known problems related to model inversion. According to Hadamard conditions, mathematical models of physical phenomena are mathematically invertible if the solution of the inverse problem to be solved exists, is unique and depends continuously on data. This assumption is not always met because of the large number of unknowns and different strategies have been proposed to overcome this problem. Several of these strategies have been implemented in ARTMO and were here analyzed to optimize the inversion performance. Data came from the SPARC-2003 dataset

Human and biophysical factors influencing modern fire disturbance in northern Wisconsin

Treesearch

Brian R. Sturtevant; David T. Cleland

2007-01-01

Humans cause most wildfires in northern Wisconsin, but interactions between human and biophysical variables affecting fire starts and size are not well understood. We applied classification tree analyses to a 16-year fire database from northern Wisconsin to evaluate the relative importance of human v. biophysical variables affecting fire occurrence within (1) all cover...

A dataset mapping the potential biophysical effects of vegetation cover change

NASA Astrophysics Data System (ADS)

Duveiller, Gregory; Hooker, Josh; Cescatti, Alessandro

2018-02-01

Changing the vegetation cover of the Earth has impacts on the biophysical properties of the surface and ultimately on the local climate. Depending on the specific type of vegetation change and on the background climate, the resulting competing biophysical processes can have a net warming or cooling effect, which can further vary both spatially and seasonally. Due to uncertain climate impacts and the lack of robust observations, biophysical effects are not yet considered in land-based climate policies. Here we present a dataset based on satellite remote sensing observations that provides the potential changes i) of the full surface energy balance, ii) at global scale, and iii) for multiple vegetation transitions, as would now be required for the comprehensive evaluation of land based mitigation plans. We anticipate that this dataset will provide valuable information to benchmark Earth system models, to assess future scenarios of land cover change and to develop the monitoring, reporting and verification guidelines required for the implementation of mitigation plans that account for biophysical land processes.

A dataset mapping the potential biophysical effects of vegetation cover change

PubMed Central

Duveiller, Gregory; Hooker, Josh; Cescatti, Alessandro

2018-01-01

Changing the vegetation cover of the Earth has impacts on the biophysical properties of the surface and ultimately on the local climate. Depending on the specific type of vegetation change and on the background climate, the resulting competing biophysical processes can have a net warming or cooling effect, which can further vary both spatially and seasonally. Due to uncertain climate impacts and the lack of robust observations, biophysical effects are not yet considered in land-based climate policies. Here we present a dataset based on satellite remote sensing observations that provides the potential changes i) of the full surface energy balance, ii) at global scale, and iii) for multiple vegetation transitions, as would now be required for the comprehensive evaluation of land based mitigation plans. We anticipate that this dataset will provide valuable information to benchmark Earth system models, to assess future scenarios of land cover change and to develop the monitoring, reporting and verification guidelines required for the implementation of mitigation plans that account for biophysical land processes. PMID:29461538

Stakeholder analysis and social-biophysical interdependencies for common pool resource management: La Brava Wetland (Argentina) as a case study.

PubMed

Romanelli, Asunción; Massone, Héctor E; Escalante, Alicia H

2011-09-01

This article gives an account of the implementation of a stakeholder analysis framework at La Brava Wetland Basin, Argentina, in a common-pool resource (CPR) management context. Firstly, the context in which the stakeholder framework was implemented is described. Secondly, a four-step methodology is applied: (1) stakeholder identification, (2) stakeholder differentiation-categorization, (3) investigation of stakeholders' relationships, and (4) analysis of social-biophysical interdependencies. This methodology classifies stakeholders according to their level of influence on the system and their potential in the conservation of natural resources. The main influential stakeholders are La Brava Village residents and tourism-related entrepreneurs who are empowered to make the more important decisions within the planning process of the ecosystem. While these key players are seen as facilitators of change, there are other groups (residents of the inner basin and fishermen) which are seen mainly as key blockers. The applied methodology for the Stakeholder Analysis and the evaluation of social-biophysical interdependencies carried out in this article can be seen as an encouraging example for other experts in natural sciences to learn and use these methods developed in social sciences. Major difficulties and some recommendations of applying this method in the practice by non-experts are discussed.

Validation of Global EO Biophysical Products at JECAM Test Site in Ukraine

NASA Astrophysics Data System (ADS)

Skakun, Sergii; Kussul, Nataliia; Kravchenko, Oleksiy; Basarab, Ruslan; Ostapenko, Vadym; Yailymov, Bohdan; Shelestov, Andrii; Kolotii, Andrii; Mironov, Andrii

Efficient global agriculture monitoring requires appropriate validation of Earth observation (EO) products for different regions and cropping system. This problem is addressed within the Joint Experiment of Crop Assessment and Monitoring (JECAM) initiative which aims to develop monitoring and reporting protocols and best practices for a variety of global agricultural systems. Ukraine is actively involved into JECAM, and a JECAM Ukraine test site was officially established in 2011. The following problems are being solved within JECAM Ukraine: (i) crop identification and crop area estimation [1]; (ii) crop yield forecasting [2]; (iii) EO products validation. The following case study regions were selected for these purposes: (i) the whole Kyiv oblast (28,000 sq. km) indented for crop mapping and acreage estimation; (ii) intensive observation sub-site in Pshenichne which is a research farm from the National University of Life and Environmental Sciences of Ukraine and indented for crop biophysical parameters estimation; (iii) Lviv region for rape-seed identification and crop rotation control; (iv) Crimea region for crop damage assessment due to droughts, and illegial field detection. In 2013, Ukrainian JECAM test site was selected as one of the “Champion User” for the ESA Sentinel-2 for Agriculture project. The test site was observed with SPOT-4 and RapidEye satellites every 5 days. The collected images are then used to simulate Sentinel-2 images for agriculture purposes. JECAM Ukraine is responsible for collecting ground observation data for validation purposes, and is involved in providing user requirements for Sentinel-2 agriculture related products. In particular, three field campaigns to characterize the vegetation biophysical parameters at the Pshenichne test site were carried out: First campaign - 14th to 17th of May 2013; second campaign - 12th to 15th of June 2013; third campaign - 14th to 17th of July 2013. Digital Hemispheric Photographs (DHP) images were

Characterizing Woody Vegetation Spectral and Structural Parameters with a 3-D Scene Model

NASA Astrophysics Data System (ADS)

Qin, W.; Yang, L.

2004-05-01

Quantification of structural and biophysical parameters of woody vegetation is of great significance in understanding vegetation condition, dynamics and functionality. Such information over a landscape scale is crucial for global and regional land cover characterization, global carbon-cycle research, forest resource inventories, and fire fuel estimation. While great efforts and progress have been made in mapping general land cover types over large area, at present, the ability to quantify regional woody vegetation structural and biophysical parameters is limited. One approach to address this research issue is through an integration of physically based 3-D scene model with multiangle and multispectral remote sensing data and in-situ measurements. The first step of this work is to model woody vegetation structure and its radiation regime using a physically based 3-D scene model and field data, before a robust operational algorithm can be developed for retrieval of important woody vegetation structural/biophysical parameters. In this study, we use an advanced 3-D scene model recently developed by Qin and Gerstl (2000), based on L-systems and radiosity theories. This 3-D scene model has been successfully applied to semi-arid shrubland to study structure and radiation regime at a regional scale. We apply this 3-D scene model to a more complicated and heterogeneous forest environment dominated by deciduous and coniferous trees. The data used in this study are from a field campaign conducted by NASA in a portion of the Superior National Forest (SNF) near Ely, Minnesota during the summers of 1983 and 1984, and supplement data collected during our revisit to the same area of SNF in summer of 2003. The model is first validated with reflectance measurements at different scales (ground observations, helicopter, aircraft, and satellite). Then its ability to characterize the structural and spectral parameters of the forest scene is evaluated. Based on the results from this study

Key Performance Parameter Driven Technology Goals for Electric Machines and Power Systems

NASA Technical Reports Server (NTRS)

Bowman, Cheryl; Jansen, Ralph; Brown, Gerald; Duffy, Kirsten; Trudell, Jeffrey

2015-01-01

Transitioning aviation to low carbon propulsion is one of the crucial strategic research thrust and is a driver in the search for alternative propulsion system for advanced aircraft configurations. This work requires multidisciplinary skills coming from multiple entities. The feasibility of scaling up various electric drive system technologies to meet the requirements of a large commercial transport is discussed in terms of key parameters. Functional requirements are identified that impact the power system design. A breakeven analysis is presented to find the minimum allowable electric drive specific power and efficiency that can preserve the range, initial weight, operating empty weight, and payload weight of the base aircraft.

Improving land surface parameter retrieval by integrating plant traits priors in the MULTIPLY data assimilation platform

NASA Astrophysics Data System (ADS)

Corbin, A. E.; Timmermans, J.; Hauser, L.; Bodegom, P. V.; Soudzilovskaia, N. A.

2017-12-01

There is a growing demand for accurate land surface parameterization from remote sensing (RS) observations. This demand has not been satisfied, because most estimation schemes apply 1) a single-sensor single-scale approach, and 2) require specific key-variables to be `guessed'. This is because of the relevant observational information required to accurately retrieve parameters of interest. Consequently, many schemes assume specific variables to be constant or not present; subsequently leading to more uncertainty. In this aspect, the MULTIscale SENTINEL land surface information retrieval Platform (MULTIPLY) was created. MULTIPLY couples a variety of RS sources with Radiative Transfer Models (RTM) over varying spectral ranges using data-assimilation to estimate geophysical parameters. In addition, MULTIPLY also uses prior information about the land surface to constrain the retrieval problem. This research aims to improve the retrieval of plant biophysical parameters through the use of priors of biophysical parameters/plant traits. Of particular interest are traits (physical, morphological or chemical trait) affecting individual performance and fitness of species. Plant traits that are able to be retrieved via RS and with RTMs include traits such as leaf-pigments, leaf water, LAI, phenols, C/N, etc. In-situ data for plant traits that are retrievable via RS techniques were collected for a meta-analysis from databases such as TRY, Ecosis, and individual collaborators. Of particular interest are the following traits: chlorophyll, carotenoids, anthocyanins, phenols, leaf water, and LAI. ANOVA statistics were generated for each traits according to species, plant functional groups (such as evergreens, grasses, etc.), and the trait itself. Afterwards, traits were also compared using covariance matrices. Using these as priors, MULTIPLY was is used to retrieve several plant traits in two validation sites in the Netherlands (Speulderbos) and in Finland (Sodankylä). Initial

Turbulence study in the vicinity of piano key weir: relevance, instrumentation, parameters and methods

NASA Astrophysics Data System (ADS)

Tiwari, Harinarayan; Sharma, Nayan

2017-05-01

This research paper focuses on the need of turbulence, instruments reliable to capture turbulence, different turbulence parameters and some advance methodology which can decompose various turbulence structures at different levels near hydraulic structures. Small-scale turbulence research has valid prospects in open channel flow. The relevance of the study is amplified as we introduce any hydraulic structure in the channel which disturbs the natural flow and creates discontinuity. To recover this discontinuity, the piano key weir (PKW) might be used with sloped keys. Constraints of empirical results in the vicinity of PKW necessitate extensive laboratory experiments with fair and reliable instrumentation techniques. Acoustic Doppler velocimeter was established to be best suited within range of some limitations using principal component analysis. Wavelet analysis is proposed to decompose the underlying turbulence structure in a better way.

Replacing natural wetlands with stormwater management facilities: Biophysical and perceived social values.

PubMed

Rooney, R C; Foote, L; Krogman, N; Pattison, J K; Wilson, M J; Bayley, S E

2015-04-15

Urban expansion replaces wetlands of natural origin with artificial stormwater management facilities. The literature suggests that efforts to mimic natural wetlands in the design of stormwater facilities can expand the provision of ecosystem services. Policy developments seek to capitalize on these improvements, encouraging developers to build stormwater wetlands in place of stormwater ponds; however, few have compared the biophysical values and social perceptions of these created wetlands to those of the natural wetlands they are replacing. We compared four types of wetlands: natural references sites, natural wetlands impacted by agriculture, created stormwater wetlands, and created stormwater ponds. We anticipated that they would exhibit a gradient in biodiversity, ecological integrity, chemical and hydrologic stress. We further anticipated that perceived values would mirror measured biophysical values. We found higher biophysical values associated with wetlands of natural origin (both reference and agriculturally impacted). The biophysical values of stormwater wetlands and stormwater ponds were lower and indistinguishable from one another. The perceived wetland values assessed by the public differed from the observed biophysical values. This has important policy implications, as the public are not likely to perceive the loss of values associated with the replacement of natural wetlands with created stormwater management facilities. We conclude that 1) agriculturally impacted wetlands provide biophysical values equivalent to those of natural wetlands, meaning that land use alone is not a great predictor of wetland value; 2) stormwater wetlands are not a substantive improvement over stormwater ponds, relative to wetlands of natural origin; 3) stormwater wetlands are poor mimics of natural wetlands, likely due to fundamental distinctions in terms of basin morphology, temporal variation in hydrology, ground water connectivity, and landscape position; 4) these

Biophysics and Thermodynamics: The Scientific Building Blocks of Bio-inspired Drug Delivery Nano Systems.

PubMed

Demetzos, Costas

2015-06-01

Biophysics and thermodynamics are considered as the scientific milestones for investigating the properties of materials. The relationship between the changes of temperature with the biophysical variables of biomaterials is important in the process of the development of drug delivery systems. Biophysics is a challenge sector of physics and should be used complementary with the biochemistry in order to discover new and promising technological platforms (i.e., drug delivery systems) and to disclose the 'silence functionality' of bio-inspired biological and artificial membranes. Thermal analysis and biophysical approaches in pharmaceuticals present reliable and versatile tools for their characterization and for the successful development of pharmaceutical products. The metastable phases of self-assembled nanostructures such as liposomes should be taken into consideration because they represent the thermal events can affect the functionality of advanced drug delivery nano systems. In conclusion, biophysics and thermodynamics are characterized as the building blocks for design and development of bio-inspired drug delivery systems.

Drought propagation and its relation with catchment biophysical characteristics

NASA Astrophysics Data System (ADS)

Alvarez-Garreton, C. D.; Lara, A.; Garreaud, R. D.

2016-12-01

Droughts propagate in the hydrological cycle from meteorological to soil moisture to hydrological droughts. To understand the drivers of this process is of paramount importance since the economic and societal impacts in water resources are directly related with hydrological droughts (and not with meteorological droughts, which have been most studied). This research analyses drought characteristics over a large region and identify its main exogenous (climate forcing) and endogenous (biophysical characteristics such as land cover type and topography) explanatory factors. The study region is Chile, which covers seven major climatic subtypes according to Köppen system, it has unique geographic characteristics, very sharp topography and a wide range of landscapes and vegetation conditions. Meteorological and hydrological droughts (deficit in precipitation and streamflow, respectively) are characterized by their durations and standardized deficit volumes using a variable threshold method, over 300 representative catchments (located between 27°S and 50°S). To quantify the propagation from meteorological to hydrological drought, we propose a novel drought attenuation index (DAI), calculated as the ratio between the meteorological drought severity slope and the hydrological drought severity slope. DAI varies from zero (catchment that attenuates completely a meteorological drought) to one (the meteorological drought is fully propagated through the hydrological cycle). This novel index provides key (and comparable) information about drought propagation over a wide range of different catchments, which has been highlighted as a major research gap. Similar drought indicators across the wide range of catchments are then linked with catchment biophysical characteristics. A thorough compilation of land cover information (including the percentage of native forests, grass land, urban and industrial areas, glaciers, water bodies and no vegetated areas), catchment physical

Software for Teaching Physiology and Biophysics.

ERIC Educational Resources Information Center

Weiss, Thomas F.; And Others

1992-01-01

Describes a software library developed to teach biophysics and physiology undergraduates that includes software on (1) the Hodgkin-Huxley model for excitation of action potentials in electrically excitable cells; (2) a random-walk model of diffusion; (3) single voltage-gated ion channels; (4) steady-state chemically mediated transport; and (5)…

Biophysical influence of coumarin 35 on bovine serum albumin: Spectroscopic study

NASA Astrophysics Data System (ADS)

Bayraktutan, Tuğba; Onganer, Yavuz

2017-01-01

The binding mechanism and protein-fluorescence probe interactions between bovine serum albumin (BSA) and coumarin 35 (C35) was investigated by using UV-Vis absorption and fluorescence spectroscopies since they remain major research topics in biophysics. The spectroscopic data indicated that a fluorescence quenching process for BSA-C35 system was occurred. The fluorescence quenching processes were analyzed using Stern-Volmer method. In this regard, Stern-Volmer quenching constants (KSV) and binding constants were calculated at different temperatures. The distance r between BSA (donor) and C35 (acceptor) was determined by exploiting fluorescence resonance energy transfer (FRET) method. Synchronous fluorescence spectra were also studied to observe information about conformational changes. Moreover, thermodynamics parameters were calculated for better understanding of interactions and conformational changes of the system.

Mapping technological and biophysical capacities of watersheds to regulate floods

USGS Publications Warehouse

Mogollón, Beatriz; Villamagna, Amy M.; Frimpong, Emmanuel A.; Angermeier, Paul

2016-01-01

Flood regulation is a widely valued and studied service provided by watersheds. Flood regulation benefits people directly by decreasing the socio-economic costs of flooding and indirectly by its positive impacts on cultural (e.g., fishing) and provisioning (e.g., water supply) ecosystem services. Like other regulating ecosystem services (e.g., pollination, water purification), flood regulation is often enhanced or replaced by technology, but the relative efficacy of natural versus technological features in controlling floods has scarcely been examined. In an effort to assess flood regulation capacity for selected urban watersheds in the southeastern United States, we: (1) used long-term flood records to assess relative influence of technological and biophysical indicators on flood magnitude and duration, (2) compared the widely used runoff curve number (RCN) approach for assessing the biophysical capacity to regulate floods to an alternative approach that acknowledges land cover and soil properties separately, and (3) mapped technological and biophysical flood regulation capacities based on indicator importance-values derived for flood magnitude and duration. We found that watersheds with high biophysical (via the alternative approach) and technological capacities lengthened the duration and lowered the peak of floods. We found the RCN approach yielded results opposite that expected, possibly because it confounds soil and land cover processes, particularly in urban landscapes, while our alternative approach coherently separates these processes. Mapping biophysical (via the alternative approach) and technological capacities revealed great differences among watersheds. Our study improves on previous mapping of flood regulation by (1) incorporating technological capacity, (2) providing high spatial resolution (i.e., 10-m pixel) maps of watershed capacities, and (3) deriving importance-values for selected landscape indicators. By accounting for technology that enhances

Covariance of biophysical data with digital topograpic and land use maps over the FIFE site

NASA Technical Reports Server (NTRS)

Davis, F. W.; Schimel, D. S.; Friedl, M. A.; Michaelsen, J. C.; Kittel, T. G. F.; Dubayah, R.; Dozier, J.

1992-01-01

This paper discusses the biophysical stratification of the FIFE site, implementation of the stratification utilizing geographic information system methods, and validation of the stratification with respect to field measurements of biomass, Bowen ratio, soil moisture, and the greenness vegetation index (GVI) derived from TM satellite data. Maps of burning and topographic position were significantly associated with variation in GVI, biomass, and Bowen ratio. The stratified design did not significantly alter the estimated site-wide means for surface climate parameters but accounted for between 25 and 45 percent of the sample variance depending on the variable.

Hemagglutinin-Mediated Membrane Fusion: A Biophysical Perspective.

PubMed

Boonstra, Sander; Blijleven, Jelle S; Roos, Wouter H; Onck, Patrick R; van der Giessen, Erik; van Oijen, Antoine M

2018-05-20

Influenza hemagglutinin (HA) is a viral membrane protein responsible for the initial steps of the entry of influenza virus into the host cell. It mediates binding of the virus particle to the host-cell membrane and catalyzes fusion of the viral membrane with that of the host. HA is therefore a major target in the development of antiviral strategies. The fusion of two membranes involves high activation barriers and proceeds through several intermediate states. Here, we provide a biophysical description of the membrane fusion process, relating its kinetic and thermodynamic properties to the large conformational changes taking place in HA and placing these in the context of multiple HA proteins working together to mediate fusion. Furthermore, we highlight the role of novel single-particle experiments and computational approaches in understanding the fusion process and their complementarity with other biophysical approaches.

Daytime Changes of Skin Biophysical Characteristics: A Study of Hydration, Transepidermal Water Loss, pH, Sebum, Elasticity, Erythema, and Color Index on Middle Eastern Skin

PubMed Central

Firooz, Alireza; Zartab, Hamed; Sadr, Bardia; Bagherpour, Leili Naraghi; Masoudi, Aidin; Fanian, Ferial; Dowlati, Yahya; Ehsani, Amir Hooshang; Samadi, Aniseh

2016-01-01

Background: The exposure of skin to ultraviolet radiation and temperature differs significantly during the day. It is reasonable that biophysical parameters of human skin have periodic daily fluctuation. The objective of this study was to study the fluctuations of various biophysical characteristics of Middle Eastern skin in standardized experimental conditions. Materials and Methods: Seven biophysical parameters of skin including stratum corneum hydration, transepidermal water loss, pH, sebum, elasticity, skin color, and erythema index were measured at three time points (8 a.m., 12 p.m. and 4 p.m.) on the forearm of 12 healthy participants (mean age of 28.4 years) without any ongoing skin disease using the CK MPA 580 device in standard temperature and humidity conditions. Results: A significant difference was observed between means of skin color index at 8 a.m. (175.42 ± 13.92) and 4 p.m. (164.44 ± 13.72, P = 0.025), between the pH at 8 a.m. (5.72 ± 0.48) and 4 p.m. (5.33 ± 0.55, P = 0.001) and pH at 12 p.m. (5.60 ± 0.48) and 4 p.m. (5.33 ± 0.55, P = 0.001). Other comparisons between the means of these parameters at different time points resulted in nonsignificant P values. Conclusion: There are daytime changes in skin color index and pH. Skin color index might be higher and cutaneous pH more basic in the early morning compared to later of the day. PMID:27904203

How gene order is influenced by the biophysics of transcription regulation

PubMed Central

Kolesov, Grigory; Wunderlich, Zeba; Laikova, Olga N.; Gelfand, Mikhail S.; Mirny, Leonid A.

2007-01-01

What are the forces that shape the structure of prokaryotic genomes: the order of genes, their proximity, and their orientation? Coregulation and coordinated horizontal gene transfer are believed to promote the proximity of functionally related genes and the formation of operons. However, forces that influence the structure of the genome beyond the level of a single operon remain unknown. Here, we show that the biophysical mechanism by which regulatory proteins search for their sites on DNA can impose constraints on genome structure. Using simulations, we demonstrate that rapid and reliable gene regulation requires that the transcription factor (TF) gene be close to the site on DNA the TF has to bind, thus promoting the colocalization of TF genes and their targets on the genome. We use parameters that have been measured in recent experiments to estimate the relevant length and times scales of this process and demonstrate that the search for a cognate site may be prohibitively slow if a TF has a low copy number and is not colocalized. We also analyze TFs and their sites in a number of bacterial genomes, confirm that they are colocalized significantly more often than expected, and show that this observation cannot be attributed to the pressure for coregulation or formation of selfish gene clusters, thus supporting the role of the biophysical constraint in shaping the structure of prokaryotic genomes. Our results demonstrate how spatial organization can influence timing and noise in gene expression. PMID:17709750

Dealing with the Challenges of Teaching Molecular Biophysics to Biochemistry Majors through an Heuristics-Based Approach

ERIC Educational Resources Information Center

Castanho, Miguel A. R. B.

2002-01-01

The main distinction between the overlapping fields of molecular biophysics and biochemistry resides in their different approaches to the same problems. Molecular biophysics makes more use of physical techniques and focuses on quantitative data. This difference encounters two difficult pedagogical challenges when teaching molecular biophysics to…

Italian biophysics and SIBPA speed-up the pace towards the long and winding road of the interdisciplinary science.

PubMed

Giacomazza, Daniela; Musio, Carlo

2016-01-01

This Special Issue of Biophysical Chemistry presents a selection of the contributions presented at the XXII National Congress of the Italian Society of Pure and Applied Biophysics (i.e., SIBPA, Società Italiana di Biofisica Pura ed Applicata) held on September 2014 in Palermo, Italy. Topics cover all biophysical disciplines, from molecular to cellular, to integrative biophysics giving a comprehensive view of the inter- and multi-disciplinary approach of modern biophysics. SIBPA, which turned 40 in 2013, continues to grow and attract interest.

Canopy-scale biophysical controls of transpiration and evaporation in the Amazon Basin

NASA Astrophysics Data System (ADS)

Mallick, Kaniska; Trebs, Ivonne; Boegh, Eva; Giustarini, Laura; Schlerf, Martin; Drewry, Darren T.; Hoffmann, Lucien; von Randow, Celso; Kruijt, Bart; Araùjo, Alessandro; Saleska, Scott; Ehleringer, James R.; Domingues, Tomas F.; Ometto, Jean Pierre H. B.; Nobre, Antonio D.; Leal de Moraes, Osvaldo Luiz; Hayek, Matthew; Munger, J. William; Wofsy, Steven C.

2016-10-01

Canopy and aerodynamic conductances (gC and gA) are two of the key land surface biophysical variables that control the land surface response of land surface schemes in climate models. Their representation is crucial for predicting transpiration (λET) and evaporation (λEE) flux components of the terrestrial latent heat flux (λE), which has important implications for global climate change and water resource management. By physical integration of radiometric surface temperature (TR) into an integrated framework of the Penman-Monteith and Shuttleworth-Wallace models, we present a novel approach to directly quantify the canopy-scale biophysical controls on λET and λEE over multiple plant functional types (PFTs) in the Amazon Basin. Combining data from six LBA (Large-scale Biosphere-Atmosphere Experiment in Amazonia) eddy covariance tower sites and a TR-driven physically based modeling approach, we identified the canopy-scale feedback-response mechanism between gC, λET, and atmospheric vapor pressure deficit (DA), without using any leaf-scale empirical parameterizations for the modeling. The TR-based model shows minor biophysical control on λET during the wet (rainy) seasons where λET becomes predominantly radiation driven and net radiation (RN) determines 75 to 80 % of the variances of λET. However, biophysical control on λET is dramatically increased during the dry seasons, and particularly the 2005 drought year, explaining 50 to 65 % of the variances of λET, and indicates λET to be substantially soil moisture driven during the rainfall deficit phase. Despite substantial differences in gA between forests and pastures, very similar canopy-atmosphere "coupling" was found in these two biomes due to soil moisture-induced decrease in gC in the pasture. This revealed the pragmatic aspect of the TR-driven model behavior that exhibits a high sensitivity of gC to per unit change in wetness as opposed to gA that is marginally sensitive to surface wetness variability

Optical vortices as potential indicators of biophysical dynamics

NASA Astrophysics Data System (ADS)

Majumdar, Anindya; Kirkpatrick, Sean J.

2017-03-01

Laser speckle patterns are granular patterns produced as a result of random interference of light waves. Optical vortices (OVs) are phase singularities in such speckle fields, characterized by zero intensity and an undefined phase. Decorrelation of the speckle fields causes these OVs to move in both time and space. In this work, a variety of parameters of these OVs have been studied. The speckle fields were simulated to undergo three distinct decorrelation behaviors- Gaussian, Lorentzian and constant decorrelations. Different decorrelation behaviors represent different dynamics. For example, Lorentzian and Gaussian decorrelations represent Brownian and ordered motions, respectively. Typical dynamical systems in biophysics are generally argued to be a combination of these. For each of the decorrelation behaviors under study, the vortex trails were tracked while varying the rate of decorrelation. Parameters such as the decorrelation length, average trail length and the deviation of the vortices as they traversed in the speckle field, were studied. Empirical studies were also performed to define the distinction between trails arising from different speckle decorrelation behaviors. The initial studies under stationary speckle fields were followed up by similar studies on shifting fields. A new idea to employ Poincaŕe plots in speckle analysis has also been introduced. Our studies indicate that tracking OVs can be a potential method to study cell and tissue dynamics.

Biophysical Variables Retrieval Over Russian Winter Wheat Fields Using Medium Resolution

NASA Astrophysics Data System (ADS)

d'Andrimont, Raphael; Waldner, Francois; Bartalev, Sergey; Plotnikov, Dmitry; Kleschenko, Alexander; Virchenko, Oleg; de Wit, Allard; Roerink, Gerbert; Defourny, Pierre

2013-12-01

Winter wheat production in the Russian Federation represents one of the sources of uncertainty for the international commodity market. In particular, adverse weather conditions may induce winter kill resulting in large yields' losses. Improving the monitoring of winter- wheat in Russia with a focus on winter-kill damage and its impacts on yield is thus a key challenge.This paper presents the methods and the results of the biophysical variables retrieval on a daily basis as an input for crop growth modeling at parcel level over a 10-years period (2003-2012) in the Russian context. The field campaigns carried out on 2 sites in the Tula region from 2010 to 2012 shows that it is possible to characterize the spatial and temporal variability at pixel, field and regional scale using medium resolution sensors (MODIS) over Russian fields.

Full-waveform and discrete-return lidar in salt marsh environments: An assessment of biophysical parameters, vertical uncertatinty, and nonparametric dem correction

NASA Astrophysics Data System (ADS)

Rogers, Jeffrey N.

High-resolution and high-accuracy elevation data sets of coastal salt marsh environments are necessary to support restoration and other management initiatives, such as adaptation to sea level rise. Lidar (light detection and ranging) data may serve this need by enabling efficient acquisition of detailed elevation data from an airborne platform. However, previous research has revealed that lidar data tend to have lower vertical accuracy (i.e., greater uncertainty) in salt marshes than in other environments. The increase in vertical uncertainty in lidar data of salt marshes can be attributed primarily to low, dense-growing salt marsh vegetation. Unfortunately, this increased vertical uncertainty often renders lidar-derived digital elevation models (DEM) ineffective for analysis of topographic features controlling tidal inundation frequency and ecology. This study aims to address these challenges by providing a detailed assessment of the factors influencing lidar-derived elevation uncertainty in marshes. The information gained from this assessment is then used to: 1) test the ability to predict marsh vegetation biophysical parameters from lidar-derived metrics, and 2) develop a method for improving salt marsh DEM accuracy. Discrete-return and full-waveform lidar, along with RTK GNSS (Real-time Kinematic Global Navigation Satellite System) reference data, were acquired for four salt marsh systems characterized by four major taxa (Spartina alterniflora, Spartina patens, Distichlis spicata, and Salicornia spp.) on Cape Cod, Massachusetts. These data were used to: 1) develop an innovative combination of full-waveform lidar and field methods to assess the vertical distribution of aboveground biomass as well as its light blocking properties; 2) investigate lidar elevation bias and standard deviation using varying interpolation and filtering methods; 3) evaluate the effects of seasonality (temporal differences between peak growth and senescent conditions) using lidar data

Advances in magnetic tweezers for single molecule and cell biophysics.

PubMed

Kilinc, Devrim; Lee, Gil U

2014-01-01

Magnetic tweezers (MTW) enable highly accurate forces to be transduced to molecules to study mechanotransduction at the molecular or cellular level. We review recent MTW studies in single molecule and cell biophysics that demonstrate the flexibility of this technique. We also discuss technical advances in the method on several fronts, i.e., from novel approaches for the measurement of torque to multiplexed biophysical assays. Finally, we describe multi-component nanorods with enhanced optical and magnetic properties and discuss their potential as future MTW probes.

Biophysical behavior of Scomberoides commersonianus skin collagen.

PubMed

Kolli, Nagamalleswari; Joseph, K Thomas; Ramasami, T

2002-06-01

Some biophysical characteristics of the skin collagen from Scomberoides commersonianus were measured and compared to those of rat tail tendon. Stress-strain data indicate that the strain at break as well as the tensile strength of the fish skin without scales increased significantly. The maximum tension in case of rat skin is at least a factor of two higher than that observed in fish skin. The much lower hydrothermal isometric tension measurements observed in fish skin are attributable to a lesser number of heat stable crosslinks. Stress relaxation measurements in the fish skin indicate that more than one relaxation process may be involved in the stabilization of collagenous matrix. The observed differences in the biophysical behavior of fish skin may well arise from combination of changes in extent of hydroxylation of proline in collagen synthesis, hydrogen bond network and fibril orientation as compared to rat tail tendon.

Estimating the biophysical properties of neurons with intracellular calcium dynamics.

PubMed

Ye, Jingxin; Rozdeba, Paul J; Morone, Uriel I; Daou, Arij; Abarbanel, Henry D I

2014-06-01

We investigate the dynamics of a conductance-based neuron model coupled to a model of intracellular calcium uptake and release by the endoplasmic reticulum. The intracellular calcium dynamics occur on a time scale that is orders of magnitude slower than voltage spiking behavior. Coupling these mechanisms sets the stage for the appearance of chaotic dynamics, which we observe within certain ranges of model parameter values. We then explore the question of whether one can, using observed voltage data alone, estimate the states and parameters of the voltage plus calcium (V+Ca) dynamics model. We find the answer is negative. Indeed, we show that voltage plus another observed quantity must be known to allow the estimation to be accurate. We show that observing both the voltage time course V(t) and the intracellular Ca time course will permit accurate estimation, and from the estimated model state, accurate prediction after observations are completed. This sets the stage for how one will be able to use a more detailed model of V+Ca dynamics in neuron activity in the analysis of experimental data on individual neurons as well as functional networks in which the nodes (neurons) have these biophysical properties.

Estimating the biophysical properties of neurons with intracellular calcium dynamics

NASA Astrophysics Data System (ADS)

Ye, Jingxin; Rozdeba, Paul J.; Morone, Uriel I.; Daou, Arij; Abarbanel, Henry D. I.

2014-06-01

We investigate the dynamics of a conductance-based neuron model coupled to a model of intracellular calcium uptake and release by the endoplasmic reticulum. The intracellular calcium dynamics occur on a time scale that is orders of magnitude slower than voltage spiking behavior. Coupling these mechanisms sets the stage for the appearance of chaotic dynamics, which we observe within certain ranges of model parameter values. We then explore the question of whether one can, using observed voltage data alone, estimate the states and parameters of the voltage plus calcium (V+Ca) dynamics model. We find the answer is negative. Indeed, we show that voltage plus another observed quantity must be known to allow the estimation to be accurate. We show that observing both the voltage time course V (t) and the intracellular Ca time course will permit accurate estimation, and from the estimated model state, accurate prediction after observations are completed. This sets the stage for how one will be able to use a more detailed model of V+Ca dynamics in neuron activity in the analysis of experimental data on individual neurons as well as functional networks in which the nodes (neurons) have these biophysical properties.

A key factor to the spin parameter of uniformly rotating compact stars: crust structure

NASA Astrophysics Data System (ADS)

Qi, Bin; Zhang, Nai-Bo; Sun, Bao-Yuan; Wang, Shou-Yu; Gao, Jian-Hua

2016-04-01

We study the dimensionless spin parameter j ≡ cJ/(GM2) of different kinds of uniformly rotating compact stars, including traditional neutron stars, hyperonic neutron stars and hybrid stars, based on relativistic mean field theory and the MIT bag model. It is found that jmax ˜ 0.7, which had been suggested in traditional neutron stars, is sustained for hyperonic neutron stars and hybrid stars with M > 0.5 M⊙. Not the interior but rather the crust structure of the stars is a key factor to determine jmax for three kinds of selected compact stars. Furthermore, a universal formula j = 0.63(f/fK) - 0.42(f/fK)2 + 0.48(f/fK)3 is suggested to determine the spin parameter at any rotational frequency f smaller than the Keplerian frequency fK.

Inversion of radiation data in biophysics

NASA Technical Reports Server (NTRS)

Twersky, V.

1972-01-01

Topics in biophysics are summarized in which radiation data inversion problems occur. The topics fall into two main categories. The first relates to information acquired about the distance environment through seeing, hearing, etc. The second relates to the use of electromagnetic, acoustic, or other radiation for diagnostic purposes, either at a bulk or a molecular level.

Dark energy and key physical parameters of clusters of galaxies

NASA Astrophysics Data System (ADS)

Bisnovatyi-Kogan, G. S.; Chernin, A. D.

2012-04-01

We study physics of clusters of galaxies embedded in the cosmic dark energy background. Under the assumption that dark energy is described by the cosmological constant, we show that the dynamical effects of dark energy are strong in clusters like the Virgo cluster. Specifically, the key physical parameters of the dark mater halos in clusters are determined by dark energy: (1) the halo cut-off radius is practically, if not exactly, equal to the zero-gravity radius at which the dark matter gravity is balanced by the dark energy antigravity; (2) the halo averaged density is equal to two densities of dark energy; (3) the halo edge (cut-off) density is the dark energy density with a numerical factor of the unity order slightly depending on the halo profile. The cluster gravitational potential well in which the particles of the dark halo (as well as galaxies and intracluster plasma) move is strongly affected by dark energy: the maximum of the potential is located at the zero-gravity radius of the cluster.

River bank burrowing by invasive crayfish: Spatial distribution, biophysical controls and biogeomorphic significance.

PubMed

Faller, Matej; Harvey, Gemma L; Henshaw, Alexander J; Bertoldi, Walter; Bruno, Maria Cristina; England, Judy

2016-11-01

Invasive species generate significant global environmental and economic costs and represent a particularly potent threat to freshwater systems. The biogeomorphic impacts of invasive aquatic and riparian species on river processes and landforms remain largely unquantified, but have the potential to generate significant sediment management issues within invaded catchments. Several species of invasive (non-native) crayfish are known to burrow into river banks and visual evidence of river bank damage is generating public concern and media attention. Despite this, there is a paucity of understanding of burrow distribution, biophysical controls and the potential significance of this problem beyond a small number of local studies at heavily impacted sites. This paper presents the first multi-catchment analysis of this phenomenon, combining existing data on biophysical river properties and invasive crayfish observations with purpose-designed field surveys across 103 river reaches to derive key trends. Crayfish burrows were observed on the majority of reaches, but burrowing tended to be patchy in spatial distribution, concentrated in a small proportion (<10%) of the length of rivers surveyed. Burrow distribution was better explained by local bank biophysical properties than by reach-scale properties, and burrowed banks were more likely to be characterised by cohesive bank material, steeper bank profiles with large areas of bare bank face, often on outer bend locations. Burrow excavation alone has delivered a considerable amount of sediment to invaded river systems in the surveyed sites (3tkm(-1) impacted bank) and this represents a minimum contribution and certainly an underestimate of the absolute yield (submerged burrows were not recorded). Furthermore, burrowing was associated with bank profiles that were either actively eroding or exposed to fluvial action and/or mass failure processes, providing the first quantitative evidence that invasive crayfish may cause or

International Solar-Terrestrial Program Key Parameter Visualization Tool Data: USA_NASA_DDF_ISTP_KP_0139

NASA Technical Reports Server (NTRS)

Ocuna, M. H.; Ogilvie, K. W.; Baker, D. N.; Curtis, S. A.; Fairfield, D. H.; Mish, W. H.

1999-01-01

The Global Geospace Science Program (GGS) is designed to improve greatly the understanding of the flow of energy, mass and momentum in the solar-terrestrial environment with particular emphasis on "Geospace". The Global Geospace Science Program is the US contribution to the International Solar-Terrestrial Physics (ISTP) Science Initiative. This CD-ROM issue describes the WIND and POLAR spacecraft, the scientific experiments carried onboard, the Theoretical and Ground Based investigations which constitute the US Global Geospace Science Program and the ISTP Data Systems which support the data acquisition and analysis effort. The International Solar-Terrestrial Physics Program (ISTP) Key Parameter Visualization Tool (KPVT), provided on the CD-ROM, was developed at the ISTP Science Planning and Operations Facility (SPOF). The KPVT is a generic software package for visualizing the key parameter data produced from all ISTP missions, interactively and simultaneously. The tool is designed to facilitate correlative displays of ISTP data from multiple spacecraft and instruments, and thus the selection of candidate events and data quality control. The software, written in IDL, includes a graphical/widget user interface, and runs on many platforms, including various UNIX workstations, Alpha/Open VMS, Macintosh (680x0 and PowerPC), and PC/Windows NT, Windows 3.1, and Windows 95.

International Solar-Terrestrial Program Key Parameter Visualization Tool Data: USA_NASA_DDF_ISTP_KP_0192

NASA Technical Reports Server (NTRS)

Ocuna, M. H.; Ogilvie, K. W.; Baker, D. N.; Curtis, S. A.; Fairfield, D. H.; Mish, W. H.

2001-01-01

The Global Geospace Science Program (GGS) is designed to improve greatly the understanding of the flow of energy, mass and momentum in the solar-terrestrial environment with particular emphasis on "Geospace". The Global Geospace Science Program is the US contribution to the International Solar-Terrestrial Physics (ISTP) Science Initiative. This CD-ROM issue describes the WIND and POLAR spacecraft, the scientific experiments carried onboard, the Theoretical and Ground Based investigations which constitute the US Global Geospace Science Program and the ISTP Data Systems which support the data acquisition and analysis effort. The International Solar-Terrestrial Physics Program (ISTP) Key Parameter Visualization Tool (KPVT), provided on the CD-ROM, was developed at the ISTP Science Planning and Operations Facility (SPOF). The KPVT is a generic software package for visualizing the key parameter data produced from all ISTP missions, interactively and simultaneously. The tool is designed to facilitate correlative displays of ISTP data from multiple spacecraft and instruments, and thus the selection of candidate events and data quality control. The software, written in IDL, includes a graphical/widget user interface, and runs on many platforms, including various UNIX workstations, Alpha/Open VMS, Macintosh (680x0 and PowerPC), and PC/Windows NT, Windows 3.1, and Windows 95.

Effect of ambient light on the time needed to complete a fetal biophysical profile: A randomized controlled trial.

PubMed

Said, Heather M; Gupta, Shweta; Vricella, Laura K; Wand, Katy; Nguyen, Thinh; Gross, Gilad

2017-10-01

The objective of this study is to determine whether ambient light serves as a fetal stimulus to decrease the amount of time needed to complete a biophysical profile. This is a randomized controlled trial of singleton gestations undergoing a biophysical profile. Patients were randomized to either ambient light or a darkened room. The primary outcome was the time needed to complete the biophysical profile. Secondary outcomes included total and individual component biophysical profile scores and scores less than 8. A subgroup analysis of different maternal body mass indices was also performed. 357 biophysical profile studies were analyzed. 182 studies were performed with ambient light and 175 were performed in a darkened room. There was no difference in the median time needed to complete the biophysical profile based on exposure to ambient light (6.1min in darkened room versus 6.6min with ambient light; P=0.73). No difference was found in total or individual component biophysical profile scores. Subgroup analysis by maternal body mass index did not demonstrate shorter study times with ambient light exposure in women who were normal weight, overweight or obese. Ambient light exposure did not decrease the time needed to complete the biophysical profile. There was no evidence that ambient light altered fetal behavior observed during the biophysical profile. Copyright © 2017 Elsevier B.V. All rights reserved.

Synthetic Biology: Engineering Living Systems from Biophysical Principles.

PubMed

Bartley, Bryan A; Kim, Kyung; Medley, J Kyle; Sauro, Herbert M

2017-03-28

Synthetic biology was founded as a biophysical discipline that sought explanations for the origins of life from chemical and physical first principles. Modern synthetic biology has been reinvented as an engineering discipline to design new organisms as well as to better understand fundamental biological mechanisms. However, success is still largely limited to the laboratory and transformative applications of synthetic biology are still in their infancy. Here, we review six principles of living systems and how they compare and contrast with engineered systems. We cite specific examples from the synthetic biology literature that illustrate these principles and speculate on their implications for further study. To fully realize the promise of synthetic biology, we must be aware of life's unique properties. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Biophysical Model of Ion Transport across Human Respiratory Epithelia Allows Quantification of Ion Permeabilities

PubMed Central

Garcia, Guilherme J.M.; Boucher, Richard C.; Elston, Timothy C.

2013-01-01

Lung health and normal mucus clearance depend on adequate hydration of airway surfaces. Because transepithelial osmotic gradients drive water flows, sufficient hydration of the airway surface liquid depends on a balance between ion secretion and absorption by respiratory epithelia. In vitro experiments using cultures of primary human nasal epithelia and human bronchial epithelia have established many of the biophysical processes involved in airway surface liquid homeostasis. Most experimental studies, however, have focused on the apical membrane, despite the fact that ion transport across respiratory epithelia involves both cellular and paracellular pathways. In fact, the ion permeabilities of the basolateral membrane and paracellular pathway remain largely unknown. Here we use a biophysical model for water and ion transport to quantify ion permeabilities of all pathways (apical, basolateral, paracellular) in human nasal epithelia cultures using experimental (Ussing Chamber and microelectrode) data reported in the literature. We derive analytical formulas for the steady-state short-circuit current and membrane potential, which are for polarized epithelia the equivalent of the Goldman-Hodgkin-Katz equation for single isolated cells. These relations allow parameter estimation to be performed efficiently. By providing a method to quantify all the ion permeabilities of respiratory epithelia, the model may aid us in understanding the physiology that regulates normal airway surface hydration. PMID:23442922

[Biophysics of single molecules].

PubMed

Serdiuk, I N; Deriusheva, E I

2011-01-01

The modern methods of research of biological molecules whose application led to the development of a new field of science, biophysics of single molecules, are reviewed. The measurement of the characteristics of single molecules enables one to reveal their individual features, and it is just for this reason that much more information can be obtained from one molecule than from the entire ensample of molecules. The high sensitivity of the methods considered in detail makes it possible to come close to the solution of the basic problem of practical importance, namely, the determination of the nucleotide sequence of a single DNA molecule.

Biophysical interactions between plant and soil: theory and practice

NASA Astrophysics Data System (ADS)

van der Ploeg, Martine

2016-04-01

Vegetation plays an essential role in the hydrological cycle, as it regulates the water flux to the atmosphere through evapotranspiration, while it is dependent on adequate water supply. Vegetation shapes the land surface by changing infiltration characteristics as a result of root growth, and controls soil moisture storage, which in turn affect runoff characteristics and groundwater recharge. Vegetation and the underlying geology are in constant interaction, wherein water plays a key role. The resilience of the coupled vegetation-soil system critically depends on its sensitivity to environmental changes. Models are a useful tool to explore interaction and feedbacks between vegetation, soil and landscape. Plants respond biochemically to their environment, while the models used for hydrology are often based on physical interactions. Gene-expression and genotype adaptation may complicate our modelling efforts in for example climate change impacts. Combination of new techniques to assess soil and plant properties facilitates assessment of biophysical interactions. This poster will review these techniques and compare the obtained insights of soil-plant relationships with the current modeling approaches.

Program review. The Interdisciplinary Biophysics Graduate Program at the University of Michigan.

PubMed

Gafni, Ari; Walter, Nils G

2008-04-01

The Michigan Biophysics Graduate Program (MBGP) was established in 1949, making it one of the first such programs in the world. The intellectual base of the program was significantly broadened in the 1980 when faculty members from a number of other units on campus were invited to join. Currently over forty faculty members from a variety of disciplines participate as mentors for the Ph.D. students enrolled in the MBGP providing our students with rich opportunities for academic learning and research. The MBGP has two main objectives: 1) to provide graduate students with both the intellectual and technical training in modern biophysics, 2) to sensitize our students to the power and unique opportunities of interdisciplinary work and thinking so as to train them to conduct research that crosses the boundaries between the biological and physical sciences. The program offers students opportunities to conduct research in a variety of areas of contemporary biophysics including structural biology, single molecule spectroscopy, spectroscopy and its applications, computational biology, membrane biophysics, neurobiophysics and enzymology. The MBGP offers a balanced curriculum that aims to provide our students with a strong academic base and, at the same time, accommodate their different academic backgrounds. Judging its past performance through the success of its former students, the MBGP has been highly successful, and there is every reason to believe that strong training in the biophysical sciences, as provided by the MBGP, will become even more valuable in the future both in the academic and the industrial settings. in the academic and the industrial settings.

Some behavioral aspects of energy descent: how a biophysical psychology might help people transition through the lean times ahead

PubMed Central

De Young, Raymond

2014-01-01

We may soon face biophysical limits to perpetual growth. Energy supplies may tighten and then begin a long slow descent while defensive expenditures rise to address problems caused by past resource consumption. The outcome may be significant changes in daily routines at the individual and community level. It is difficult to know when this scenario might begin to unfold but it clearly would constitute a new behavioral context, one that the behavioral sciences least attends to. Even if one posits a less dramatic scenario, people may still need to make many urgent and perhaps unsettling transitions. And while a robust response would be needed, it is not at all clear what should be the details of that response. Since it is likely that no single response will fix things everywhere, for all people or for all time, it would be useful to conduct many social experiments. Indeed, a culture of small experiments should be fostered which, at the individual and small group level, can be described as behavioral entrepreneurship. This may have begun, hidden in plain sight, but more social experiments are needed. To be of help, it may be useful to both package behavioral insights in a way that is practitioner-oriented and grounded in biophysical trends and to propose a few key questions that need attention. This paper begins the process of developing a biophysical psychology, incomplete as it is at this early stage. PMID:25404926

Some behavioral aspects of energy descent: how a biophysical psychology might help people transition through the lean times ahead.

PubMed

De Young, Raymond

2014-01-01

We may soon face biophysical limits to perpetual growth. Energy supplies may tighten and then begin a long slow descent while defensive expenditures rise to address problems caused by past resource consumption. The outcome may be significant changes in daily routines at the individual and community level. It is difficult to know when this scenario might begin to unfold but it clearly would constitute a new behavioral context, one that the behavioral sciences least attends to. Even if one posits a less dramatic scenario, people may still need to make many urgent and perhaps unsettling transitions. And while a robust response would be needed, it is not at all clear what should be the details of that response. Since it is likely that no single response will fix things everywhere, for all people or for all time, it would be useful to conduct many social experiments. Indeed, a culture of small experiments should be fostered which, at the individual and small group level, can be described as behavioral entrepreneurship. This may have begun, hidden in plain sight, but more social experiments are needed. To be of help, it may be useful to both package behavioral insights in a way that is practitioner-oriented and grounded in biophysical trends and to propose a few key questions that need attention. This paper begins the process of developing a biophysical psychology, incomplete as it is at this early stage.

The biophysics of renal sympathetic denervation using radiofrequency energy.

PubMed

Patel, Hitesh C; Dhillon, Paramdeep S; Mahfoud, Felix; Lindsay, Alistair C; Hayward, Carl; Ernst, Sabine; Lyon, Alexander R; Rosen, Stuart D; di Mario, Carlo

2014-05-01

Renal sympathetic denervation is currently performed in the treatment of resistant hypertension by interventionists who otherwise do not typically use radiofrequency (RF) energy ablation in their clinical practice. Adequate RF lesion formation is dependent upon good electrode-tissue contact, power delivery, electrode-tissue interface temperature, target-tissue impedance and the size of the catheter's active electrode. There is significant interplay between these variables and hence an appreciation of the biophysical determinants of RF lesion formation is required to provide effective and safe clinical care to our patients. In this review article, we summarize the biophysics of RF ablation and explain why and how complications of renal sympathetic denervation may occur and discuss methods to minimise them.

Raman spectroscopy reveals biophysical markers in skin cancer surgical margins

NASA Astrophysics Data System (ADS)

Feng, Xu; Moy, Austin J.; Nguyen, Hieu T. M.; Zhang, Yao; Fox, Matthew C.; Sebastian, Katherine R.; Reichenberg, Jason S.; Markey, Mia K.; Tunnell, James W.

2018-02-01

The recurrence rate of nonmelanoma skin cancer is highly related to the residual tumor after surgery. Although tissueconserving surgery, such as Mohs surgery, is a standard method for the treatment of nonmelanoma skin cancer, they are limited by lengthy and costly frozen-section histopathology. Raman spectroscopy (RS) is proving to be an objective, sensitive, and non-destructive tool for detecting skin cancer. Previous studies demonstrated the high sensitivity of RS in detecting tumor margins of basal cell carcinoma (BCC). However, those studies rely on statistical classification models and do not elucidate the skin biophysical composition. As a result, we aim to discover the biophysical differences between BCC and primary normal skin structures (including epidermis, dermis, hair follicle, sebaceous gland and fat). We obtained freshly resected ex vivo skin samples from fresh resection specimens from 14 patients undergoing Mohs surgery. Raman images were acquired from regions containing one or more structures using a custom built 830nm confocal Raman microscope. The spectra were grouped using K-means clustering analysis and annotated as either BCC or each of the five normal structures by comparing with the histopathology image of the serial section. The spectral data were then fit by a previously established biophysical model with eight primary skin constituents. Our results show that BCC has significant differences in the fit coefficients of nucleus, collagen, triolein, keratin and elastin compared with normal structures. Our study reveals RS has the potential to detect biophysical changes in resection margins, and supports the development of diagnostic algorithms for future intraoperative implementation of RS during Mohs surgery.

Chief, Structural Biophysics Laboratory | Center for Cancer Research

Cancer.gov

The SBL Chief is expected to establish a strong research program in structural biology/biophysics in addition to providing leadership of the SBL and the structural biology community in the NCI Intramural Program.  Applicants should hold a Ph.D., M.D./Ph.D., or equivalent doctoral degree in a relevant discipline, and should possess outstanding communication skills and documented leadership experience.  Tenured faculty or industrial scientists of equivalent rank with a demonstrated commitment to structural biophysics should apply.  Salary will be commensurate with experience and accomplishments.  This position is not restricted to U.S. citizens. A full civil service package of benefits (including health insurance, life insurance, and retirement) is available. This position is subject to a background investigation.  The NIH is dedicated to building a diverse community in its training and employment programs.

An In Situ and In Silico Evaluation of Biophysical Effects of 27 MHz Electromagnetic Whole Body Humans Exposure Expressed by the Limb Current

PubMed Central

2017-01-01

Objectives The aim was to evaluate correlations between biophysical effects of 27 MHz electromagnetic field exposure in humans (limb induced current (LIC)) and (1) parameters of affecting heterogeneous electric field and (2) body anthropometric properties, in order to improve the evaluation of electromagnetic environmental hazards. Methods Biophysical effects of exposure were studied in situ by measurements of LIC in 24 volunteers (at the ankle) standing near radio communication rod antenna and in silico in 4 numerical body phantoms exposed near a model of antenna. Results Strong, positive, statistically significant correlations were found in all exposure scenarios between LIC and body volume index (body height multiplied by mass) (r > 0.7; p < 0.001). The most informative exposure parameters, with respect to the evaluation of electromagnetic hazards by measurements (i.e., the ones strongest correlated with LIC), were found to be the value of electric field (unperturbed field, in the absence of body) in front of the chest (50 cm from body axis) or the maximum value in space occupied by human. Such parameters were not analysed in previous studies. Conclusions Exposed person's body volume and electric field strength in front of the chest determine LIC in studied exposure scenarios, but their wider applicability needs further studies. PMID:28758119

Biophysics of Mitosis

PubMed Central

McIntosh, J. Richard; Molodtsov, Maxim I.; Ataullakhanov, Fazly I.

2015-01-01

Mitosis is the process by which eukaryotic cells organize and segregate their chromosomes in preparation for cell division. It is accomplished by a cellular machine composed largely of microtubules and their associated proteins. This article reviews literature on mitosis from a biophysical point of view, drawing attention to the assembly and motility processes required to do this complex job with precision. Work from both the recent and the older literature is integrated into a description of relevant biological events and the experiments that probe their mechanisms. Theoretical work on specific subprocesses is also reviewed. Our goal is to provide a document that will expose biophysicists to the fascination of this quite amazing process and provide them with a good background from which they can pursue their own research interests in the subject. PMID:22321376

In vivo evaluation of some biophysical parameters of the facial skin of Indian subjects living in Mumbai. Part II: Variability with age and gender.

PubMed

Colomb, L; Flament, F; Wagle, A; Idelcaid, Y; Agrawal, D

2018-04-01

A previously published work explored the diversity of some biophysical parameters (colour, elasticity, sebum production, skin microrelief, etc.) of the skin of 1204 Indian women, differently aged, living in four Indian cities (Chennai, Delhi, Kolkata and Mumbai). The present work aimed at completing such research by focusing on possible gender-related differences in the same skin parameters, between Indian men and women living in the same Indian city (Mumbai). A total of 297 Indian men, differently aged (18-70y), were recruited in Mumbai, completing the panel of 303 women who were previously recruited in this same city. The same instrumental measurements of facial skin colour and its homogeneity, its mechanical properties, the sebum production, skin pores size, skin relief, etc. as in the previous work, were conducted. Overall, the facial skin colour shows a darker complexion in men as compared to women, on forehead, ocular region, lips, chin and cheek. The skin colour unevenness, which increases with age, was found higher in men, as compared to women. At comparable age, women and men present a same density of skin pores, whereas those of men appear larger, up to 55y. The deepness of Crow's feet wrinkles does not significantly differ between genders. A lesser extensibility was found on the cheeks of men. In men, the sebum production was found significantly higher than that of women at ages above 40y. This work indicates some commonly shared age-related skin features between women and men from Mumbai, despite slight different characteristics such as skin pigmentation, forehead/cheek colour contrast, mechanical properties and sebum production. © 2018 Society of Cosmetic Scientists and the Société Française de Cosmétologie.

Achievements and challenges in structural bioinformatics and computational biophysics.

PubMed

Samish, Ilan; Bourne, Philip E; Najmanovich, Rafael J

2015-01-01

The field of structural bioinformatics and computational biophysics has undergone a revolution in the last 10 years. Developments that are captured annually through the 3DSIG meeting, upon which this article reflects. An increase in the accessible data, computational resources and methodology has resulted in an increase in the size and resolution of studied systems and the complexity of the questions amenable to research. Concomitantly, the parameterization and efficiency of the methods have markedly improved along with their cross-validation with other computational and experimental results. The field exhibits an ever-increasing integration with biochemistry, biophysics and other disciplines. In this article, we discuss recent achievements along with current challenges within the field. © The Author 2014. Published by Oxford University Press.

Achievements and challenges in structural bioinformatics and computational biophysics

PubMed Central

Samish, Ilan; Bourne, Philip E.; Najmanovich, Rafael J.

2015-01-01

Motivation: The field of structural bioinformatics and computational biophysics has undergone a revolution in the last 10 years. Developments that are captured annually through the 3DSIG meeting, upon which this article reflects. Results: An increase in the accessible data, computational resources and methodology has resulted in an increase in the size and resolution of studied systems and the complexity of the questions amenable to research. Concomitantly, the parameterization and efficiency of the methods have markedly improved along with their cross-validation with other computational and experimental results. Conclusion: The field exhibits an ever-increasing integration with biochemistry, biophysics and other disciplines. In this article, we discuss recent achievements along with current challenges within the field. Contact: Rafael.Najmanovich@USherbrooke.ca PMID:25488929

Direct Scaling of Leaf-Resolving Biophysical Models from Leaves to Canopies

NASA Astrophysics Data System (ADS)

Bailey, B.; Mahaffee, W.; Hernandez Ochoa, M.

2017-12-01

Recent advances in the development of biophysical models and high-performance computing have enabled rapid increases in the level of detail that can be represented by simulations of plant systems. However, increasingly detailed models typically require increasingly detailed inputs, which can be a challenge to accurately specify. In this work, we explore the use of terrestrial LiDAR scanning data to accurately specify geometric inputs for high-resolution biophysical models that enables direct up-scaling of leaf-level biophysical processes. Terrestrial LiDAR scans generate "clouds" of millions of points that map out the geometric structure of the area of interest. However, points alone are often not particularly useful in generating geometric model inputs, as additional data processing techniques are required to provide necessary information regarding vegetation structure. A new method was developed that directly reconstructs as many leaves as possible that are in view of the LiDAR instrument, and uses a statistical backfilling technique to ensure that the overall leaf area and orientation distribution matches that of the actual vegetation being measured. This detailed structural data is used to provide inputs for leaf-resolving models of radiation, microclimate, evapotranspiration, and photosynthesis. Model complexity is afforded by utilizing graphics processing units (GPUs), which allows for simulations that resolve scales ranging from leaves to canopies. The model system was used to explore how heterogeneity in canopy architecture at various scales affects scaling of biophysical processes from leaves to canopies.

Chromosome aberrations and cell death by ionizing radiation: Evolution of a biophysical model

NASA Astrophysics Data System (ADS)

Ballarini, Francesca; Carante, Mario P.

2016-11-01

The manuscript summarizes and discusses the various versions of a radiation damage biophysical model, implemented as a Monte Carlo simulation code, originally developed for chromosome aberrations and subsequently extended to cell death. This extended version has been called BIANCA (BIophysical ANalysis of Cell death and chromosome Aberrations). According to the basic assumptions, complex double-strand breaks (called ;Cluster Lesions;, or CLs) produce independent chromosome free-ends, mis-rejoining within a threshold distance d (or un-rejoining) leads to chromosome aberrations, and ;lethal aberrations; (i.e., dicentrics plus rings plus large deletions) lead to clonogenic cell death. The mean number of CLs per Gy and per cell is an adjustable parameter. While in BIANCA the threshold distance d was the second parameter, in a subsequent version, called BIANCA II, d has been fixed as the mean distance between two adjacent interphase chromosome territories, and a new parameter, f, has been introduced to represent the chromosome free-end un-rejoining probability. Simulated dose-response curves for chromosome aberrations and cell survival obtained by the various model versions were compared with literature experimental data. Such comparisons provided indications on some open questions, including the role of energy deposition clustering at the nm and the μm level, the probability for a chromosome free-end to remain un-rejoined, and the relationship between chromosome aberrations and cell death. Although both BIANCA and BIANCA II provided cell survival curves in general agreement with human and hamster fibroblast survival data, BIANCA II allowed for a better reproduction of dicentrics, rings and deletions considered separately. Furthermore, the approach adopted in BIANCA II for d is more consistent with estimates reported in the literature. After testing against aberration and survival data, BIANCA II was applied to investigate the depth-dependence of the radiation

Characterising the biophysical properties of normal and hyperkeratotic foot skin.

PubMed

Hashmi, Farina; Nester, Christopher; Wright, Ciaran; Newton, Veronica; Lam, Sharon

2015-01-01

Plantar foot skin exhibits unique biophysical properties that are distinct from skin on other areas of the body. This paper characterises, using non-invasive methods, the biophysical properties of foot skin in healthy and pathological states including xerosis, heel fissures, calluses and corns. Ninety three people participated. Skin hydration, elasticity, collagen and elastin fibre organisation and surface texture was measured from plantar calluses, corns, fissured heel skin and xerotic heel skin. Previously published criteria were applied to classify the severity of each skin lesion and differences in the biophysical properties compared between each classification. Calluses, corns, xerotic heel skin and heel fissures had significantly lower levels of hydration; less elasticity and greater surface texture than unaffected skin sites (p < 0.01). Some evidence was found for a positive correlation between hydration and elasticity data (r ≤ 0.65) at hyperkeratotic sites. Significant differences in skin properties (with the exception of texture) were noted between different classifications of skin lesion. This study provides benchmark data for healthy and different severities of pathological foot skin. These data have applications ranging from monitoring the quality of foot skin, to measuring the efficacy of therapeutic interventions.

International Solar-Terrestrial Program Key Parameter Visualization Tool Data: USA_NASA_DDF_ISTP_IM_KP_0185

NASA Technical Reports Server (NTRS)

Ocuna, M. H.; Ogilvie, K. W.; Baker, D. N.; Curtis, S. A.; Fairfield, D. H.; Mish, W. H.

2000-01-01

The Global Geospace Science Program (GGS) is designed to improve greatly the understanding of the flow of energy, mass and momentum in the solar-terrestrial environment with particular emphasis on "Geospace". The Global Geospace Science Program is the US contribution to the International Solar-Terrestrial Physics (ISTP) Science Initiative. This CD-ROM issue describes the WIND and POLAR spacecraft, the scientific experiments carried onboard, the Theoretical and Ground Based investigations which constitute the US Global Geospace Science Program and the ISTP Data Systems which support the data acquisition and analysis effort. The International Solar-Terrestrial Physics Program (ISTP) Key Parameter Visualization Tool (KPVT), provided on the CD-ROM, was developed at the ISTP Science Planning and Operations Facility (SPOF). The KPVT is a generic software package for visualizing the key parameter data produced from all ISTP missions, interactively and simultaneously. The tool is designed to facilitate correlative displays of ISTP data from multiple spacecraft and instruments, and thus the selection of candidate events and data quality control. The software, written in IDL, includes a graphical/widget user interface, and runs on many platforms, including various UNIX workstations, Alpha/Open VMS, Macintosh (680x0 and PowerPC), and PC/Windows NT, Windows 3.1, and Windows 95.

International Solar-Terrestrial Program Key Parameter Visualization Tool Data: USA_NASA_DDF_ISTP_IM_KP_0161

NASA Technical Reports Server (NTRS)

Ocuna, M. H.; Ogilvie, K. W.; Baker, D. N.; Curtis, S. A.; Fairfield, D. H.; Mish, W. H.

2000-01-01

The Global Geospace Science Program (GGS) is designed to improve greatly the understanding of the flow of energy, mass and momentum in the solar-terrestrial environment with particular emphasis on "Geospace". The Global Geospace Science Program is the US contribution to the International Solar-Terrestrial Physics (ISTP) Science Initiative. This CD-ROM issue describes the WIND and POLAR spacecraft, the scientific experiments carried onboard, the Theoretical and Ground Based investigations which constitute the US Global Geospace Science Program and the ISTP Data Systems which support the data acquisition and analysis effort. The International Solar-Terrestrial Physics Program (ISTP) Key Parameter Visualization Tool (KPVT), provided on the CD-ROM, was developed at the ISTP Science Planning and Operations Facility (SPOF). The KPVT is a generic software package for visualizing the key parameter data produced from all ISTP missions, interactively and simultaneously. The tool is designed to facilitate correlative displays of ISTP data from multiple spacecraft and instruments, and thus the selection of candidate events and data quality control. The software, written in IDL, includes a graphical/widget user interface, and runs on many platforms, including various UNIX workstations, Alpha/Open VMS, Macintosh (680x0 and PowerPC), and PC/Windows NT, Windows 3.1, and Windows 95.

Microfluidic cell-phoresis enabling high-throughput analysis of red blood cell deformability and biophysical screening of antimalarial drugs.

PubMed

Santoso, Aline T; Deng, Xiaoyan; Lee, Jeong-Hyun; Matthews, Kerryn; Duffy, Simon P; Islamzada, Emel; McFaul, Sarah M; Myrand-Lapierre, Marie-Eve; Ma, Hongshen

2015-12-07

Changes in red blood cell (RBC) deformability are associated with the pathology of many diseases and could potentially be used to evaluate disease status and treatment efficacy. We developed a simple, sensitive, and multiplexed RBC deformability assay based on the spatial dispersion of single cells in structured microchannels. This mechanism is analogous to gel electrophoresis, but instead of transporting molecules through nano-structured material to measure their length, RBCs are transported through micro-structured material to measure their deformability. After transport, the spatial distribution of cells provides a readout similar to intensity bands in gel electrophoresis, enabling simultaneous measurement on multiple samples. We used this approach to study the biophysical signatures of falciparum malaria, for which we demonstrate label-free and calibration-free detection of ring-stage infection, as well as in vitro assessment of antimalarial drug efficacy. We show that clinical antimalarial drugs universally reduce the deformability of RBCs infected by Plasmodium falciparum and that recently discovered PfATP4 inhibitors, known to induce host-mediated parasite clearance, display a distinct biophysical signature. Our process captures key advantages from gel electrophoresis, including image-based readout and multiplexing, to provide a functional screen for new antimalarials and adjunctive agents.

Benchtop Technologies for Circulating Tumor Cells Separation Based on Biophysical Properties

PubMed Central

Low, Wan Shi; Wan Abas, Wan Abu Bakar

2015-01-01

Circulating tumor cells (CTCs) are tumor cells that have detached from primary tumor site and are transported via the circulation system. The importance of CTCs as prognostic biomarker is leveraged when multiple studies found that patient with cutoff of 5 CTCs per 7.5 mL blood has poor survival rate. Despite its clinical relevance, the isolation and characterization of CTCs can be quite challenging due to their large morphological variability and the rare presence of CTCs within the blood. Numerous methods have been employed and discussed in the literature for CTCs separation. In this paper, we will focus on label free CTCs isolation methods, in which the biophysical and biomechanical properties of cells (e.g., size, deformability, and electricity) are exploited for CTCs detection. To assess the present state of various isolation methods, key performance metrics such as capture efficiency, cell viability, and throughput will be reported. Finally, we discuss the challenges and future perspectives of CTC isolation technologies. PMID:25977918

Benchtop technologies for circulating tumor cells separation based on biophysical properties.

PubMed

Low, Wan Shi; Wan Abas, Wan Abu Bakar

2015-01-01

Circulating tumor cells (CTCs) are tumor cells that have detached from primary tumor site and are transported via the circulation system. The importance of CTCs as prognostic biomarker is leveraged when multiple studies found that patient with cutoff of 5 CTCs per 7.5 mL blood has poor survival rate. Despite its clinical relevance, the isolation and characterization of CTCs can be quite challenging due to their large morphological variability and the rare presence of CTCs within the blood. Numerous methods have been employed and discussed in the literature for CTCs separation. In this paper, we will focus on label free CTCs isolation methods, in which the biophysical and biomechanical properties of cells (e.g., size, deformability, and electricity) are exploited for CTCs detection. To assess the present state of various isolation methods, key performance metrics such as capture efficiency, cell viability, and throughput will be reported. Finally, we discuss the challenges and future perspectives of CTC isolation technologies.

Biochemical and Biophysical Cues in Matrix Design for Chronic and Diabetic Wound Treatment

PubMed Central

Xiao, Yun; Ahadian, Samad

2017-01-01

Progress in biomaterial science and engineering and increasing knowledge in cell biology have enabled us to develop functional biomaterials providing appropriate biochemical and biophysical cues for tissue regeneration applications. Tissue regeneration is particularly important to treat chronic wounds of people with diabetes. Understanding and controlling the cellular microenvironment of the wound tissue are important to improve the wound healing process. In this study, we review different biochemical (e.g., growth factors, peptides, DNA, and RNA) and biophysical (e.g., topographical guidance, pressure, electrical stimulation, and pulsed electromagnetic field) cues providing a functional and instructive acellular matrix to heal diabetic chronic wounds. The biochemical and biophysical signals generally regulate cell–matrix interactions and cell behavior and function inducing the tissue regeneration for chronic wounds. Some technologies and devices have already been developed and used in the clinic employing biochemical and biophysical cues for wound healing applications. These technologies can be integrated with smart biomaterials to deliver therapeutic agents to the wound tissue in a precise and controllable manner. This review provides useful guidance in understanding molecular mechanisms and signals in the healing of diabetic chronic wounds and in designing instructive biomaterials to treat them. PMID:27405960

A Biophysical Modeling Framework for Assessing the Environmental Impact of Biofuel Production

NASA Astrophysics Data System (ADS)

Zhang, X.; Izaurradle, C.; Manowitz, D.; West, T. O.; Post, W. M.; Thomson, A. M.; Nichols, J.; Bandaru, V.; Williams, J. R.

2009-12-01

Long-term sustainability of a biofuel economy necessitates environmentally friendly biofuel production systems. We describe a biophysical modeling framework developed to understand and quantify the environmental value and impact (e.g. water balance, nutrients balance, carbon balance, and soil quality) of different biomass cropping systems. This modeling framework consists of three major components: 1) a Geographic Information System (GIS) based data processing system, 2) a spatially-explicit biophysical modeling approach, and 3) a user friendly information distribution system. First, we developed a GIS to manage the large amount of geospatial data (e.g. climate, land use, soil, and hydrograhy) and extract input information for the biophysical model. Second, the Environmental Policy Integrated Climate (EPIC) biophysical model is used to predict the impact of various cropping systems and management intensities on productivity, water balance, and biogeochemical variables. Finally, a geo-database is developed to distribute the results of ecosystem service variables (e.g. net primary productivity, soil carbon balance, soil erosion, nitrogen and phosphorus losses, and N2O fluxes) simulated by EPIC for each spatial modeling unit online using PostgreSQL. We applied this framework in a Regional Intensive Management Area (RIMA) of 9 counties in Michigan. A total of 4,833 spatial units with relatively homogeneous biophysical properties were derived using SSURGO, Crop Data Layer, County, and 10-digit watershed boundaries. For each unit, EPIC was executed from 1980 to 2003 under 54 cropping scenarios (eg. corn, switchgrass, and hybrid poplar). The simulation results were compared with historical crop yields from USDA NASS. Spatial mapping of the results show high variability among different cropping scenarios in terms of the simulated ecosystem services variables. Overall, the framework developed in this study enables the incorporation of environmental factors into economic and

Quantifying Key Climate Parameter Uncertainties Using an Earth System Model with a Dynamic 3D Ocean

NASA Astrophysics Data System (ADS)

Olson, R.; Sriver, R. L.; Goes, M. P.; Urban, N.; Matthews, D.; Haran, M.; Keller, K.

2011-12-01

Climate projections hinge critically on uncertain climate model parameters such as climate sensitivity, vertical ocean diffusivity and anthropogenic sulfate aerosol forcings. Climate sensitivity is defined as the equilibrium global mean temperature response to a doubling of atmospheric CO2 concentrations. Vertical ocean diffusivity parameterizes sub-grid scale ocean vertical mixing processes. These parameters are typically estimated using Intermediate Complexity Earth System Models (EMICs) that lack a full 3D representation of the oceans, thereby neglecting the effects of mixing on ocean dynamics and meridional overturning. We improve on these studies by employing an EMIC with a dynamic 3D ocean model to estimate these parameters. We carry out historical climate simulations with the University of Victoria Earth System Climate Model (UVic ESCM) varying parameters that affect climate sensitivity, vertical ocean mixing, and effects of anthropogenic sulfate aerosols. We use a Bayesian approach whereby the likelihood of each parameter combination depends on how well the model simulates surface air temperature and upper ocean heat content. We use a Gaussian process emulator to interpolate the model output to an arbitrary parameter setting. We use Markov Chain Monte Carlo method to estimate the posterior probability distribution function (pdf) of these parameters. We explore the sensitivity of the results to prior assumptions about the parameters. In addition, we estimate the relative skill of different observations to constrain the parameters. We quantify the uncertainty in parameter estimates stemming from climate variability, model and observational errors. We explore the sensitivity of key decision-relevant climate projections to these parameters. We find that climate sensitivity and vertical ocean diffusivity estimates are consistent with previously published results. The climate sensitivity pdf is strongly affected by the prior assumptions, and by the scaling

Photophysical Study of Novel Perylene Analogues for Biophysical Applications

NASA Astrophysics Data System (ADS)

Palos-Chávez, Jorge; Penick, Mark; Negrete, George; Brancaleon, Lorenzo

2011-03-01

Perylene and perylene derivatives have been shown to be useful in a variety of photoinitiated applications, such as molecular dyes, organic solar cells, etc. Recently we started the characterization of novel 3,9-perylene analogues which could potentially lead to the synthesis of novel molecules with improved ability to separate charges. We have characterized the basic photophysical properties of these molecules, and we are currently investigating the photochemistry that leads to photoproducts in chlorinated compounds. Spectroscopic measurements show the substantial changes in photophysical parameters consistent with the conversion of the original compounds into photoproducts. SEM and AFM imaging show that these photoproducts form ordered particles. Mass spectrometry studies have confirmed the presence of these photoproducts as well. Additional studies are underway concerning the use of these novel perylene analogues in binding to biological structures such as proteins. It is hoped that these compounds will prove useful for biophysical applications, specifically in studying the manipulation of protein conformation via physical methods. Supported by NIH/NIGMS MBRS RISE GM-60655.

Biophysical regulation of epigenetic state and cell reprogramming

NASA Astrophysics Data System (ADS)

Downing, Timothy L.; Soto, Jennifer; Morez, Constant; Houssin, Timothee; Fritz, Ashley; Yuan, Falei; Chu, Julia; Patel, Shyam; Schaffer, David V.; Li, Song

2013-12-01

Biochemical factors can help reprogram somatic cells into pluripotent stem cells, yet the role of biophysical factors during reprogramming is unknown. Here, we show that biophysical cues, in the form of parallel microgrooves on the surface of cell-adhesive substrates, can replace the effects of small-molecule epigenetic modifiers and significantly improve reprogramming efficiency. The mechanism relies on the mechanomodulation of the cells’ epigenetic state. Specifically, decreased histone deacetylase activity and upregulation of the expression of WD repeat domain 5 (WDR5)—a subunit of H3 methyltranferase—by microgrooved surfaces lead to increased histone H3 acetylation and methylation. We also show that microtopography promotes a mesenchymal-to-epithelial transition in adult fibroblasts. Nanofibrous scaffolds with aligned fibre orientation produce effects similar to those produced by microgrooves, suggesting that changes in cell morphology may be responsible for modulation of the epigenetic state. These findings have important implications in cell biology and in the optimization of biomaterials for cell-engineering applications.

Investigating the Martian Ionospheric Conductivity Using MAVEN Key Parameter Data

NASA Astrophysics Data System (ADS)

Aleryani, O.; Raftery, C. L.; Fillingim, M. O.; Fogle, A. L.; Dunn, P.; McFadden, J. P.; Connerney, J. E. P.; Mahaffy, P. R.; Ergun, R. E.; Andersson, L.

2015-12-01

Since the Viking orbiters and landers in 1976, the Martian atmospheric composition has scarcely been investigated. New data from the Mars Atmosphere and Volatile EvolutioN (MAVEN) mission, launched in 2013, allows for a thorough study of the electrically conductive nature of the Martian ionosphere. Determinations of the electrical conductivity will be made using in-situ atmospheric and ionospheric measurements, rather than scientific models for the first time. The objective of this project is to calculate the conductivity of the Martian atmosphere, whenever possible, throughout the trajectory of the MAVEN spacecraft. MAVEN instrumentation used includes the Neutral Gas and Ion Mass Spectrometer (NGIMS) for neutral species density, the Suprathermal and Thermal Ion Compositions (STATIC) for ion composition, temperature and density, the Magnetometer (MAG) for the magnetic field strength and the Langmuir Probe and Waves (LPW) for electron temperature and density. MAVEN key parameter data are used for these calculations. We compare our results with previous, model-based estimates of the conductivity. These results will allow us to quantify the flow of atmospheric electric currents which can be analyzed further for a deeper understanding of the Martian ionospheric electrodynamics, bringing us closer to understanding the mystery of the loss of the Martian atmosphere.

Systems biology of cellular membranes: a convergence with biophysics.

PubMed

Chabanon, Morgan; Stachowiak, Jeanne C; Rangamani, Padmini

2017-09-01

Systems biology and systems medicine have played an important role in the last two decades in shaping our understanding of biological processes. While systems biology is synonymous with network maps and '-omics' approaches, it is not often associated with mechanical processes. Here, we make the case for considering the mechanical and geometrical aspects of biological membranes as a key step in pushing the frontiers of systems biology of cellular membranes forward. We begin by introducing the basic components of cellular membranes, and highlight their dynamical aspects. We then survey the functions of the plasma membrane and the endomembrane system in signaling, and discuss the role and origin of membrane curvature in these diverse cellular processes. We further give an overview of the experimental and modeling approaches to study membrane phenomena. We close with a perspective on the converging futures of systems biology and membrane biophysics, invoking the need to include physical variables such as location and geometry in the study of cellular membranes. WIREs Syst Biol Med 2017, 9:e1386. doi: 10.1002/wsbm.1386 For further resources related to this article, please visit the WIREs website. © 2017 Wiley Periodicals, Inc.

Biophysical models of protein evolution: Understanding the patterns of evolutionary sequence divergence

PubMed Central

Echave, Julian; Wilke, Claus O.

2018-01-01

For decades, rates of protein evolution have been interpreted in terms of the vague concept of “functional importance”. Slowly evolving proteins or sites within proteins were assumed to be more functionally important and thus subject to stronger selection pressure. More recently, biophysical models of protein evolution, which combine evolutionary theory with protein biophysics, have completely revolutionized our view of the forces that shape sequence divergence. Slowly evolving proteins have been found to evolve slowly because of selection against toxic misfolding and misinteractions, linking their rate of evolution primarily to their abundance. Similarly, most slowly evolving sites in proteins are not directly involved in function, but mutating them has large impacts on protein structure and stability. Here, we review the studies of the emergent field of biophysical protein evolution that have shaped our current understanding of sequence divergence patterns. We also propose future research directions to develop this nascent field. PMID:28301766

Screening of the aerodynamic and biophysical properties of barley malt

NASA Astrophysics Data System (ADS)

Ghodsvali, Alireza; Farzaneh, Vahid; Bakhshabadi, Hamid; Zare, Zahra; Karami, Zahra; Mokhtarian, Mohsen; Carvalho, Isabel. S.

2016-10-01

An understanding of the aerodynamic and biophysical properties of barley malt is necessary for the appropriate design of equipment for the handling, shipping, dehydration, grading, sorting and warehousing of this strategic crop. Malting is a complex biotechnological process that includes steeping; germination and finally, the dehydration of cereal grains under controlled temperature and humidity conditions. In this investigation, the biophysical properties of barley malt were predicted using two models of artificial neural networks as well as response surface methodology. Stepping time and germination time were selected as the independent variables and 1 000 kernel weight, kernel density and terminal velocity were selected as the dependent variables (responses). The obtained outcomes showed that the artificial neural network model, with a logarithmic sigmoid activation function, presents more precise results than the response surface model in the prediction of the aerodynamic and biophysical properties of produced barley malt. This model presented the best result with 8 nodes in the hidden layer and significant correlation coefficient values of 0.783, 0.767 and 0.991 were obtained for responses one thousand kernel weight, kernel density, and terminal velocity, respectively. The outcomes indicated that this novel technique could be successfully applied in quantitative and qualitative monitoring within the malting process.

Measuring (bio)physical tree properties using accelerometers

NASA Astrophysics Data System (ADS)

van Emmerik, Tim; Steele-Dunne, Susan; Hut, Rolf; Gentine, Pierre; Selker, John; van de Giesen, Nick

2017-04-01

Trees play a crucial role in the water, carbon and nitrogen cycle on local, regional and global scales. Understanding the exchange of heat, water, and CO2 between trees and the atmosphere is important to assess the impact of drought, deforestation and climate change. Unfortunately, ground measurements of tree dynamics are often expensive, or difficult due to challenging environments. We demonstrate the potential of measuring (bio)physical properties of trees using robust and affordable acceleration sensors. Tree sway is dependent on e.g. mass and wind energy absorption of the tree. By measuring tree acceleration we can relate the tree motion to external loads (e.g. precipitation), and tree (bio)physical properties (e.g. mass). Using five months of acceleration data of 19 trees in the Brazilian Amazon, we show that the frequency spectrum of tree sway is related to mass, precipitation, and canopy drag. This presentation aims to show the concept of using accelerometers to measure tree dynamics, and we acknowledge that the presented example applications is not an exhaustive list. Further analyses are the scope of current research, and we hope to inspire others to explore additional applications.

Sequentially distant but structurally similar proteins exhibit fold specific patterns based on their biophysical properties.

PubMed

Rajendran, Senthilnathan; Jothi, Arunachalam

2018-05-16

The Three-dimensional structure of a protein depends on the interaction between their amino acid residues. These interactions are in turn influenced by various biophysical properties of the amino acids. There are several examples of proteins that share the same fold but are very dissimilar at the sequence level. For proteins to share a common fold some crucial interactions should be maintained despite insignificant sequence similarity. Since the interactions are because of the biophysical properties of the amino acids, we should be able to detect descriptive patterns for folds at such a property level. In this line, the main focus of our research is to analyze such proteins and to characterize them in terms of their biophysical properties. Protein structures with sequence similarity lesser than 40% were selected for ten different subfolds from three different mainfolds (according to CATH classification) and were used for this analysis. We used the normalized values of the 49 physio-chemical, energetic and conformational properties of amino acids. We characterize the folds based on the average biophysical property values. We also observed a fold specific correlational behavior of biophysical properties despite a very low sequence similarity in our data. We further trained three different binary classification models (Naive Bayes-NB, Support Vector Machines-SVM and Bayesian Generalized Linear Model-BGLM) which could discriminate mainfold based on the biophysical properties. We also show that among the three generated models, the BGLM classifier model was able to discriminate protein sequences coming under all beta category with 81.43% accuracy and all alpha, alpha-beta proteins with 83.37% accuracy. Copyright © 2018 Elsevier Ltd. All rights reserved.

Institutional Factors Affecting Biophysical Outcomes in Forest Management

ERIC Educational Resources Information Center

Coleman, Eric A.

2009-01-01

Although there is considerable interest in the impact of diverse policies affecting the biophysical outcomes in forests, gaining a substantial sample over time of forests under different institutional arrangements has been difficult. This article analyzes data from 46 forests located in six countries over time. In forests where policies have been…

Use of passive UAS imaging to measure biophysical parameters in a southern Rocky Mountain subalpine forest

NASA Astrophysics Data System (ADS)

Caldwell, M. K.; Sloan, J.; Mladinich, C. S.; Wessman, C. A.

2013-12-01

Unmanned Aerial Systems (UAS) can provide detailed, fine spatial resolution imagery for ecological uses not otherwise obtainable through standard methods. The use of UAS imagery for ecology is a rapidly -evolving field, where the study of forest landscape ecology can be augmented using UAS imagery to scale and validate biophysical data from field measurements to spaceborne observations. High resolution imagery provided by UAS (30 cm2 pixels) offers detailed canopy cover and forest structure data in a time efficient and inexpensive manner. Using a GoPro Hero2 (2 mm focal length) camera mounted in the nose cone of a Raven unmanned system, we collected aerial and thermal data monthly during the summer 2013, over two subalpine forests in the Southern Rocky Mountains in Colorado. These forests are dominated by lodgepole pine (Pinus ponderosae) and have experienced insect-driven (primarily mountain pine beetle; MPB, Dendroctonus ponderosae) mortality. Objectives of this study include observations of forest health variables such as canopy water content (CWC) from thermal imagery and leaf area index (LAI), biomass and forest productivity from the Normalized Difference Vegetation Index (NDVI) from UAS imagery. Observations were, validated with ground measurements. Images were processed using a combination of AgiSoft Photoscan professional software and ENVI remote imaging software. We utilized the software Leaf Area Index Calculator (LAIC) developed by Córcoles et al. (2013) for calculating LAI from digital images and modified to conform to leaf area of needle-leaf trees as in Chen and Cihlar (1996) . LAIC uses a K-means cluster analysis to decipher the RGB levels for each pixel and distinguish between green aboveground vegetation and other materials, and project leaf area per unit of ground surface area (i.e. half total needle surface area per unit area). Preliminary LAIC UAS data shows summer average LAI was 3.8 in the most dense forest stands and 2.95 in less dense

The bio-physics of condensation of divalent cations into the bacterial wall has implications for growth of Gram-positive bacteria.

PubMed

Rauch, Cyril; Cherkaoui, Mohammed; Egan, Sharon; Leigh, James

2017-02-01

The anionic-polyelectrolyte nature of the wall of Gram-positive bacteria has long been suspected to be involved in homeostasis of essential cations and bacterial growth. A better understanding of the coupling between the biophysics and the biology of the wall is essential to understand some key features at play in ion-homeostasis in this living system. We consider the wall as a polyelectrolyte gel and balance the long-range electrostatic repulsion within this structure against the penalty entropy required to condense cations around wall polyelectrolytes. The resulting equations define how cations interact physically with the wall and the characteristic time required for a cation to leave the wall and enter into the bacterium to enable its usage for bacterial metabolism and growth. The model was challenged against experimental data regarding growth of Gram-positive bacteria in the presence of varying concentration of divalent ions. The model explains qualitatively and quantitatively how divalent cations interact with the wall as well as how the biophysical properties of the wall impact on bacterial growth (in particular the initiation of bacterial growth). The interplay between polymer biophysics and the biology of Gram positive bacteria is defined for the first time as a new set of variables that contribute to the kinetics of bacterial growth. Providing an understanding of how bacteria capture essential metal cations in way that does not follow usual binding laws has implications when considering the control of such organisms and their ability to survive and grow in extreme environments. Crown Copyright © 2016. Published by Elsevier B.V. All rights reserved.

Teaching biophysics. Strategies for recruiting and retaining minorities in physics and biophysics.

PubMed Central

Tanaka, J C; Gladney, L D

1993-01-01

Several strategies directed toward increasing the participation of minority students in physics and biophysics are presented. Since the number of minority students entering college with an interest in science and mathematics must be increased if we expect to see more students graduating in science, several programs aimed at increasing the level of instruction of physics and biology in urban middle schools and high schools are outlined. We also describe approaches designed to increase the retention of science major during the freshman core physics course where many potential science majors are lost. Increasing the number of minority students at the PhD level will rely increasingly on partnerships between research universities and historically black colleges and universities (HBCUs) and several programs already in effect are given as examples of such linkages. PMID:8369460

Biophysical, morphological, canopy optical property, and productivity data from the Superior National Forest

NASA Technical Reports Server (NTRS)

Hall, F. G.; Huemmrich, K. F.; Strebel, D. E.; Goetz, S. J.; Nickeson, J. E.; Woods, K. D.

1992-01-01

Described here are the results of a NASA field experiment conducted in the Superior National Forest near Ely, Minnesota, during the summers of 1983 and 1984. The purpose of the experiment was to examine the use of remote sensing to provide measurements of biophysical parameters in the boreal forests. Leaf area index, biomass, net primary productivity, canopy coverage, overstory and understory species composition data are reported for about 60 sites, representing a range of stand density and age for aspen and spruce. Leaf, needle, and bark high-resolution spectral reflectance and transmittance data are reported for the major boreal forest species. Canopy bidirectional reflectance measurements are provided from a helicopter-mounted Barnes Multiband Modular Radiometer (MMR) and the Thematic Mapper Simulator (TMS) on the NASA C-130 aircraft.

Integrating machine learning to achieve an automatic parameter prediction for practical continuous-variable quantum key distribution

NASA Astrophysics Data System (ADS)

Liu, Weiqi; Huang, Peng; Peng, Jinye; Fan, Jianping; Zeng, Guihua

2018-02-01

For supporting practical quantum key distribution (QKD), it is critical to stabilize the physical parameters of signals, e.g., the intensity, phase, and polarization of the laser signals, so that such QKD systems can achieve better performance and practical security. In this paper, an approach is developed by integrating a support vector regression (SVR) model to optimize the performance and practical security of the QKD system. First, a SVR model is learned to precisely predict the time-along evolutions of the physical parameters of signals. Second, such predicted time-along evolutions are employed as feedback to control the QKD system for achieving the optimal performance and practical security. Finally, our proposed approach is exemplified by using the intensity evolution of laser light and a local oscillator pulse in the Gaussian modulated coherent state QKD system. Our experimental results have demonstrated three significant benefits of our SVR-based approach: (1) it can allow the QKD system to achieve optimal performance and practical security, (2) it does not require any additional resources and any real-time monitoring module to support automatic prediction of the time-along evolutions of the physical parameters of signals, and (3) it is applicable to any measurable physical parameter of signals in the practical QKD system.

Going beyond the biophysical when mapping national forests

Treesearch

Geoff Koch; Lee Cerveny

2018-01-01

Resource managers have long mapped biophysical forest data. Often lacking, however, is relevant social science data for understanding the variety of human needs a given landscape fulfills.For nearly a decade, Lee Cerveny has been exploring how to provide this data on public lands around the Pacific Northwest. Cerveny is a research...

A fully synthetic human Fab antibody library based on fixed VH/VL framework pairings with favorable biophysical properties

PubMed Central

Tiller, Thomas; Schuster, Ingrid; Deppe, Dorothée; Siegers, Katja; Strohner, Ralf; Herrmann, Tanja; Berenguer, Marion; Poujol, Dominique; Stehle, Jennifer; Stark, Yvonne; Heßling, Martin; Daubert, Daniela; Felderer, Karin; Kaden, Stefan; Kölln, Johanna; Enzelberger, Markus; Urlinger, Stefanie

2013-01-01

This report describes the design, generation and testing of Ylanthia, a fully synthetic human Fab antibody library with 1.3E+11 clones. Ylanthia comprises 36 fixed immunoglobulin (Ig) variable heavy (VH)/variable light (VL) chain pairs, which cover a broad range of canonical complementarity-determining region (CDR) structures. The variable Ig heavy and Ig light (VH/VL) chain pairs were selected for biophysical characteristics favorable to manufacturing and development. The selection process included multiple parameters, e.g., assessment of protein expression yield, thermal stability and aggregation propensity in fragment antigen binding (Fab) and IgG1 formats, and relative Fab display rate on phage. The framework regions are fixed and the diversified CDRs were designed based on a systematic analysis of a large set of rearranged human antibody sequences. Care was taken to minimize the occurrence of potential posttranslational modification sites within the CDRs. Phage selection was performed against various antigens and unique antibodies with excellent biophysical properties were isolated. Our results confirm that quality can be built into an antibody library by prudent selection of unmodified, fully human VH/VL pairs as scaffolds. PMID:23571156

An ethnographic study: Becoming a physics expert in a biophysics research group

NASA Astrophysics Data System (ADS)

Rodriguez, Idaykis

Expertise in physics has been traditionally studied in cognitive science, where physics expertise is understood through the difference between novice and expert problem solving skills. The cognitive perspective of physics experts only create a partial model of physics expertise and does not take into account the development of physics experts in the natural context of research. This dissertation takes a social and cultural perspective of learning through apprenticeship to model the development of physics expertise of physics graduate students in a research group. I use a qualitative methodological approach of an ethnographic case study to observe and video record the common practices of graduate students in their biophysics weekly research group meetings. I recorded notes on observations and conduct interviews with all participants of the biophysics research group for a period of eight months. I apply the theoretical framework of Communities of Practice to distinguish the cultural norms of the group that cultivate physics expert practices. Results indicate that physics expertise is specific to a topic or subfield and it is established through effectively publishing research in the larger biophysics research community. The participant biophysics research group follows a learning trajectory for its students to contribute to research and learn to communicate their research in the larger biophysics community. In this learning trajectory students develop expert member competencies to learn to communicate their research and to learn the standards and trends of research in the larger research community. Findings from this dissertation expand the model of physics expertise beyond the cognitive realm and add the social and cultural nature of physics expertise development. This research also addresses ways to increase physics graduate student success towards their PhD. and decrease the 48% attrition rate of physics graduate students. Cultivating effective research

Representing biophysical landscape interactions in soil models by bridging disciplines and scales.

NASA Astrophysics Data System (ADS)

van der Ploeg, M. J.; Carranza, C.; Teixeira da Silva, R.; te Brake, B.; Baartman, J.; Robinson, D.

2017-12-01

The combination of climate change, population growth and soil threats including carbon loss, biodiversity decline and erosion, increasingly confront the global community (Schwilch et al., 2016). One major challenge in studying processes involved in soil threats, landscape resilience, ecosystem stability, sustainable land management and resulting economic consequences, is that it is an interdisciplinary field (Pelletier et al., 2012). Less stringent scientific disciplinary boundaries are therefore important (Liu et al., 2007), because as a result of disciplinary focus, ambiguity may arise on the understanding of landscape interactions. This is especially true in the interaction between a landscape's physical and biological processes (van der Ploeg et al. 2012). Biophysical landscape interactions are those biotic and abiotic processes in a landscape that have an influence on the developments within and evolution of a landscape. An important aspect in biophysical landscape interactions is the differences in scale related to the various processes that play a role in these systems. Moreover, the interplay between the physical landscape and the occurring vegetation, which often co-evolve, and the resulting heterogeneity and emerging patterns are the reason why it is so challenging to establish a theoretical basis to describe biophysical processes in landscapes (e.g. te Brake et al. 2013, Robinson et al. 2016). Another complicating factor is the response of vegetation to changing environmental conditions, including a possible, and often unknown, time-lag (e.g. Metzger et al., 2009). An integrative description for modelling biophysical interactions has been a long standing goal in soil science (Vereecken et al., 2016). We need the development of soil models that are more focused on networks, connectivity and feedbacks incorporating the most important aspects of our detailed mechanistic modelling (Paola & Leeder, 2011). Additionally, remote sensing measurement techniques

A no-key-exchange secure image sharing scheme based on Shamir's three-pass cryptography protocol and the multiple-parameter fractional Fourier transform.

PubMed

Lang, Jun

2012-01-30

In this paper, we propose a novel secure image sharing scheme based on Shamir's three-pass protocol and the multiple-parameter fractional Fourier transform (MPFRFT), which can safely exchange information with no advance distribution of either secret keys or public keys between users. The image is encrypted directly by the MPFRFT spectrum without the use of phase keys, and information can be shared by transmitting the encrypted image (or message) three times between users. Numerical simulation results are given to verify the performance of the proposed algorithm.

Remote sensing of the Canadian Arctic: Modelling biophysical variables

NASA Astrophysics Data System (ADS)

Liu, Nanfeng

It is anticipated that Arctic vegetation will respond in a variety of ways to altered temperature and precipitation patterns expected with climate change, including changes in phenology, productivity, biomass, cover and net ecosystem exchange. Remote sensing provides data and data processing methodologies for monitoring and assessing Arctic vegetation over large areas. The goal of this research was to explore the potential of hyperspectral and high spatial resolution multispectral remote sensing data for modelling two important Arctic biophysical variables: Percent Vegetation Cover (PVC) and the fraction of Absorbed Photosynthetically Active Radiation (fAPAR). A series of field experiments were conducted to collect PVC and fAPAR at three Canadian Arctic sites: (1) Sabine Peninsula, Melville Island, NU; (2) Cape Bounty Arctic Watershed Observatory (CBAWO), Melville Island, NU; and (3) Apex River Watershed (ARW), Baffin Island, NU. Linear relationships between biophysical variables and Vegetation Indices (VIs) were examined at different spatial scales using field spectra (for the Sabine Peninsula site) and high spatial resolution satellite data (for the CBAWO and ARW sites). At the Sabine Peninsula site, hyperspectral VIs exhibited a better performance for modelling PVC than multispectral VIs due to their capacity for sampling fine spectral features. The optimal hyperspectral bands were located at important spectral features observed in Arctic vegetation spectra, including leaf pigment absorption in the red wavelengths and at the red-edge, leaf water absorption in the near infrared, and leaf cellulose and lignin absorption in the shortwave infrared. At the CBAWO and ARW sites, field PVC and fAPAR exhibited strong correlations (R2 > 0.70) with the NDVI (Normalized Difference Vegetation Index) derived from high-resolution WorldView-2 data. Similarly, high spatial resolution satellite-derived fAPAR was correlated to MODIS fAPAR (R2 = 0.68), with a systematic

Increasing the Effectiveness of Vaginal Microbicides: A Biophysical Framework to Rethink Behavioral Acceptability

PubMed Central

Verguet, Stéphane; Young Holt, Bethany; Szeri, Andrew J.

2010-01-01

Background Microbicide candidates delivered via gel vehicles are intended to coat the vaginal epithelium after application. The coating process depends on intrinsic biophysical properties of the gel texture, which restricts the potential choices for an effective product: the gel first must be physically synthesizable, then acceptable to the user, and finally applied in a manner promoting timely adequate coating, so that the user adherence is optimized. We present a conceptual framework anchoring microbicide behavioral acceptability within the fulfillment of the product biophysical requirements. Methods We conducted a semi-qualitative/quantitative study targeting women aged 18–55 in Northern California to assess user preferences for microbicide gel attributes. Attributes included: (i) the wait time between application and intercourse, (ii) the gel texture and (iii) the trade-off between wait time and gel texture. Wait times were assessed using a mathematical model determining coating rates depending upon the gel's physical attributes. Results 71 women participated. Results suggest that women would independently prefer a gel spreading rapidly, in 2 to 15 minutes (P<0.0001), as well as one that is thick or slippery (P<0.02). Clearly, thick gels do not spread rapidly; hence the motivation to study the trade-off. When asked the same question ‘constrained’ by the biophysical reality, women indicated no significant preference for a particular gel thickness (and therefore waiting time) (P>0.10) for use with a steady partner, a preference for a watery gel spreading rapidly rather than one having intermediate properties for use with a casual partner (P = 0.024). Conclusions Biophysical constraints alter women's preferences regarding acceptable microbicide attributes. Product developers should offer a range of formulations in order to address all preferences. We designed a conceptual framework to rethink behavioral acceptability in terms of biophysical requirements

Biophysical constraints on leaf expansion in a tall conifer.

Treesearch

Fredrick C. Meinzer; Barbara J. Bond; Jennifer A. Karanian

2008-01-01

The physiological mechanisms responsible for reduced extension growth as trees increase in height remain elusive. We evaluated biophysical constraints on leaf expansion in old-growth Douglas-fir (Psuedotsuga menziesii (Mirb.) Franco) trees. Needle elongation rates, plastic and elastic extensibility, bulk leaf water, (L...

Integrating socio-economic and biophysical data to enhance watershed management and planning

NASA Astrophysics Data System (ADS)

Pirani, Farshad Jalili; Mousavi, Seyed Alireza

2016-09-01

Sustainability has always been considered as one of the main aspects of watershed management plans. In many developing countries, watershed management practices and planning are usually performed by integrating biophysical layers, and other existing layers which cannot be identified as geographic layers are ignored. We introduce an approach to consider some socioeconomic parameters which are important for watershed management decisions. Ganj basin in Chaharmahal-Bakhtiari Province was selected as the case study area, which includes three traditional sanctums: Ganj, Shiremard and Gerdabe Olya. Socioeconomic data including net agricultural income, net ranching income, population and household number, literacy rate, unemployment rate, population growth rate and active population were mapped within traditional sanctums and then were integrated into other biophysical layers. After overlaying and processing these data to determine management units, different quantitative and qualitative approaches were adopted to achieve a practical framework for watershed management planning and relevant plans for homogeneous units were afterwards proposed. Comparing the results with current plans, the area of allocated lands to different proposed operations considering both qualitative and quantitative approaches were the same in many cases and there was a meaningful difference with current plans; e.g., 3820 ha of lands are currently managed under an enclosure plan, while qualitative and quantitative approaches in this study suggest 1388 and 1428 ha to be allocated to this operation type, respectively. Findings show that despite the ambiguities and complexities, different techniques could be adopted to incorporate socioeconomic conditions in watershed management plans. This introductory approach will help to enhance watershed management decisions with more attention to societal background and economic conditions, which will presumably motivate local communities to participate in

Structural, biological and biophysical properties of glycated and glycoxidized phosphatidylethanolamines

PubMed Central

Annibal, Andrea; Riemer, Thomas; Jovanovic, Olga; Westphal, Dennis; Griesser, Eva; Pohl, Elena E.; Schiller, Jürgen; Hoffmann, Ralf; Fedorova, Maria

2018-01-01

Glycation and glycoxidation of proteins and peptides have been intensively studied and are considered as reliable diagnostic biomarkers of hyperglycemia and early stages of type II diabetes. However, glucose can also react with primary amino groups present in other cellular components, such as aminophospholipids (aminoPLs). Although it is proposed that glycated aminoPLs can induce many cellular responses and contribute to the development and progression of diabetes, the routes of their formation and their biological roles are only partially revealed. The same is true for the influence of glucose-derived modifications on the biophysical properties of PLs. Here we studied structural, signaling, and biophysical properties of glycated and glycoxidized phosphatidylethanolamines (PEs). By combining high resolution mass spectrometry and nuclear magnetic resonance spectroscopy it was possible to deduce the structures of several intermediates indicating an oxidative cleavage of the Amadori product yielding glycoxidized PEs including advanced glycation end products, such as carboxyethyl- and carboxymethyl-ethanolamines. The pro-oxidative role of glycated PEs was demonstrated and further associated with several cellular responses including activation of NFκB signaling pathways. Label free proteomics indicated significant alterations in proteins regulating cellular metabolisms. Finally, the biophysical properties of PL membranes changed significantly upon PE glycation, such as melting temperature (Tm), membrane surface charge, and ion transport across the phospholipid bilayer. PMID:27012418

Environmental Learning Experiences: Bio-Physical, Senior High School.

ERIC Educational Resources Information Center

Junglas, Mary R.; And Others

This environmental education curriculum guide was developed for teacher use at the senior high school level. Although the guide deals with the bio-physical aspects of the environment, it is designed to encourage an integration of the disciplines into an inter-disciplinary approach. The volume consists of a set of ideas, activities, and opinions…

Biophysical characterization of the outer membrane polysaccharide export protein and the polysaccharide co-polymerase protein from Xanthomonas campestris.

PubMed

Bianco, M I; Jacobs, M; Salinas, S R; Salvay, A G; Ielmini, M V; Ielpi, L

2014-09-01

This study investigated the structural and biophysical characteristics of GumB and GumC, two Xanthomonas campestris membrane proteins that are involved in xanthan biosynthesis. Xanthan is an exopolysaccharide that is thought to be a virulence factor that contributes to bacterial in planta growth. It also is one of the most important industrial biopolymers. The first steps of xanthan biosynthesis are well understood, but the polymerization and export mechanisms remain unclear. For this reason, the key proteins must be characterized to better understand these processes. Here we characterized, by biochemical and biophysical techniques, GumB, the outer membrane polysaccharide export protein, and GumC, the polysaccharide co-polymerase protein of the xanthan biosynthesis system. Our results suggested that recombinant GumB is a tetrameric protein in solution. On the other hand, we observed that both native and recombinant GumC present oligomeric conformation consistent with dimers and higher-order oligomers. The transmembrane segments of GumC are required for GumC expression and/or stability. These initial results provide a starting point for additional studies that will clarify the roles of GumB and GumC in the xanthan polymerization and export processes and further elucidate their functions and mechanisms of action. Copyright © 2014 Elsevier Inc. All rights reserved.

The Biophysics and Cell Biology of Lipid Droplets

PubMed Central

Thiam, A. Rachid; Farese, Robert V.; Walther, Tobias C.

2015-01-01

Lipid droplets (LDs) are intracellular organelles that are found in most cells, where they have fundamental and dynamic roles in metabolism. Recent investigations showed the importance of basic biophysical principles of emulsions for LD biology. At their essence, LDs are the dispersed phase of an oil-in-water emulsion in the aqueous cytosol of cells. They function prominently in storing oil-based reserves of metabolic energy and components of membrane lipids. Because of their unique architecture, with an interface between the dispersed oil phase and the aqueous cytosol, LDs require specialized mechanisms for their formation, growth, and shrinkage. Such mechanisms enable cells to use emulsified oil in a controlled manner (e.g., when demands for metabolic energy or membrane synthesis increase). Regulation of the composition of the phospholipid surfactants at the LD surface is crucial for LD growth and catabolism and also modifies protein targeting to LD surfaces. Here, we review new insights into the cell biology of LDs, with an emphasis on concepts of emulsion science and biophysics that apply to this organelle. PMID:24220094

Introductory Biophysics Course: Presentation of Physics in a Biological Context

ERIC Educational Resources Information Center

Henderson, B. J.; Henderson, M. A.

1976-01-01

An introductory biophysics course for science students who have previously taken two quarters of noncalculus physics is described. Material covered emphasizes the physical principles of sound, light, electricity, energy, and information. (Author/CP)

Watershed-Scale Heterogeneity of the Biophysical Controls on Soil Respiration

NASA Astrophysics Data System (ADS)

Riveros, D. A.; Pacific, V. J.; McGlynn, B. L.; Welsch, D. L.; Epstein, H. E.; Muth, D. J.; Marshall, L.; Wraith, J.

2006-12-01

Large gaps exist in our understanding of the variability of soil respiration response to changing hydrologic conditions across spatial and temporal scales. Determining the linkages between the hydrologic cycle and the biophysical controls of soil respiration from the local point, to the plot, to the watershed scale is critical to understanding the dynamics of net ecosystem CO2 exchange (NEE). To study the biophysical controls of soil respiration, we measured soil CO2 concentration, soil CO2 flux, dissolved CO2 in stream water, soil moisture, soil temperature, groundwater dynamics, and precipitation at 20-minute intervals throughout the growing season at 4 sites and at weekly intervals at 62 sites covering the range of topographic position, slope, aspect, land cover, and upslope accumulated area conditions in a 555-ha subalpine watershed in central Montana. Our goal was to quantify watershed-scale heterogeneity in soil CO2 concentrations and surface efflux and gain understanding of the biophysical controls on soil respiration. We seek to improve our ability to evaluate and predict soil respiration responses to a dynamic hydrologic cycle across multiple temporal and spatial scales. We found that time lags between biophysical controls and soil respiration can occur from hourly to daily scales. The sensitivity of soil respiration to changes in environmental conditions is controlled by the antecedent soil moisture and by topographic position. At the watershed scale, significant differences in soil respiration exist between upland (dry) and lowland (wet) sites. However, differences in the magnitude and timing of soil respiration also exist within upland settings due to heterogeneity in soil temperature, soil moisture, and soil organic matter. Finally, we used a process-based model to simulate respiration at different times of the year across spatial locations. Our simulations highlight the importance of autotrophic and heterotrophic respiration (production) over

Early integration of the individual student in academic activities: a novel classroom concept for graduate education in molecular biophysics and structural biology

PubMed Central

2014-01-01

Background A key challenge in interdisciplinary research is choosing the best approach from a large number of techniques derived from different disciplines and their interfaces. Results To address this challenge in the area of Biophysics and Structural Biology, we have designed a graduate level course to teach students insightful use of experimental biophysical approaches in relationship to addressing biological questions related to biomolecular interactions and dynamics. A weekly seminar and data and literature club are used to compliment the training in class. The course contains wet-laboratory experimental demonstration and real-data analysis as well as lectures, grant proposal preparation and assessment, and student presentation components. Active student participation is mandatory in all aspects of the class. Students prepare materials for the class receiving individual and iterative feedback from course directors and local experts generating high quality classroom presentations. Conclusions The ultimate goal of the course is to teach students the skills needed to weigh different experimental approaches against each other in addressing a specific biological question by thinking and executing academic tasks like faculty. PMID:25132964

Early integration of the individual student in academic activities: a novel classroom concept for graduate education in molecular biophysics and structural biology.

PubMed

Leuba, Sanford H; Carney, Sean M; Dahlburg, Elizabeth M; Eells, Rebecca J; Ghodke, Harshad; Yanamala, Naveena; Schauer, Grant; Klein-Seetharaman, Judith

2014-01-01

A key challenge in interdisciplinary research is choosing the best approach from a large number of techniques derived from different disciplines and their interfaces. To address this challenge in the area of Biophysics and Structural Biology, we have designed a graduate level course to teach students insightful use of experimental biophysical approaches in relationship to addressing biological questions related to biomolecular interactions and dynamics. A weekly seminar and data and literature club are used to compliment the training in class. The course contains wet-laboratory experimental demonstration and real-data analysis as well as lectures, grant proposal preparation and assessment, and student presentation components. Active student participation is mandatory in all aspects of the class. Students prepare materials for the class receiving individual and iterative feedback from course directors and local experts generating high quality classroom presentations. The ultimate goal of the course is to teach students the skills needed to weigh different experimental approaches against each other in addressing a specific biological question by thinking and executing academic tasks like faculty.

Ecophysiology of nickel phytoaccumulation: a simplified biophysical approach.

PubMed

Coinchelin, David; Bartoli, François; Robin, Christophe; Echevarria, Guillaume

2012-10-01

Solute active transport or exclusion by plants can be identified by the values of the Transpiration Stream Concentration Factor (TSCF=xylem:solution solute concentration ratio). The aim of this study was to estimate this parameter for Ni uptake by the Ni-hyperaccumulator Leptoplax emarginata or the Ni-excluder Triticum aestivum cultivar 'Fidel'. The Intact Plant TSCF for nickel (IPTSCF(Ni)) was calculated as the ratio between the nickel mass accumulation in the leaves and the nickel concentration in solution per volume of water transpired. Predominantly, Ni active transport occurred for L. emarginata, with IPTSCF(Ni) values of 4.7-7.2 and convective component proportions of the root Ni uptake flow of only 15-20% for a range of Ni concentrations in solutions of 2-16 µmol Ni l(-1), regardless of the growth period and the time of Ni uptake. Hyperaccumulator roots were permeable to both water and nickel (mean reflection coefficient for Ni, σ(Ni), of 0.06), which was mainly attributed to an absence of exodermis. Results provide a new view of the mechanisms of Ni hyperaccumulation. By contrast, the wheat excluder was characterized by an extremely low mean IPTSCF(Ni) value of 0.006, characterizing a predominantly Ni sequestration in roots. From a methodological viewpoint, the 'microscopic' TSCF(Ni), measured directly on excised plants was 2.4 times larger than its recommended 'macroscopic' IPTSCF(Ni) counterpart. Overall, IPTSCF and σ determined on intact transpiring plants appeared to be very useful biophysical parameters in the study of the mechanisms involved in metal uptake and accumulation by plants, and in their modelling.

A biotic video game smart phone kit for formal and informal biophysics education

NASA Astrophysics Data System (ADS)

Kim, Honesty; Lee, Seung Ah; Riedel-Kruse, Ingmar

2015-03-01

Novel ways for formal and informal biophysics education are important. We present a low-cost biotic game design kit that incorporates microbial organisms into an interactive gaming experience: A 3D-printable microscope containing four LEDs controlled by a joystick enable human players to provide directional light stimuli to the motile single-celled organism Euglena gracilis. These cellular behaviors are displayed on the integrated smart phone. Real time cell-tracking couples these cells into interactive biotic video game play, i.e., the human player steers Euglena to play soccer with virtual balls and goals. The player's learning curve in mastering this fun game is intrinsically coupled to develop a deeper knowledge about Euglena's cell morphology and the biophysics of its phototactic behavior. This kit is dual educational - via construction and via play - and it provides an engaging theme for a formal biophysics devices class as well as to be presented in informal outreach activities; its low cost and open soft- and hardware should enable wide adoption.

Modeling disordered protein interactions from biophysical principles

PubMed Central

Christoffer, Charles; Terashi, Genki

2017-01-01

Disordered protein-protein interactions (PPIs), those involving a folded protein and an intrinsically disordered protein (IDP), are prevalent in the cell, including important signaling and regulatory pathways. IDPs do not adopt a single dominant structure in isolation but often become ordered upon binding. To aid understanding of the molecular mechanisms of disordered PPIs, it is crucial to obtain the tertiary structure of the PPIs. However, experimental methods have difficulty in solving disordered PPIs and existing protein-protein and protein-peptide docking methods are not able to model them. Here we present a novel computational method, IDP-LZerD, which models the conformation of a disordered PPI by considering the biophysical binding mechanism of an IDP to a structured protein, whereby a local segment of the IDP initiates the interaction and subsequently the remaining IDP regions explore and coalesce around the initial binding site. On a dataset of 22 disordered PPIs with IDPs up to 69 amino acids, successful predictions were made for 21 bound and 18 unbound receptors. The successful modeling provides additional support for biophysical principles. Moreover, the new technique significantly expands the capability of protein structure modeling and provides crucial insights into the molecular mechanisms of disordered PPIs. PMID:28394890

A Review on the Role of Vibrational Spectroscopy as An Analytical Method to Measure Starch Biochemical and Biophysical Properties in Cereals and Starchy Foods

PubMed Central

Cozzolino, D.; Degner, S.; Eglinton, J.

2014-01-01

Starch is the major component of cereal grains and starchy foods, and changes in its biophysical and biochemical properties (e.g., amylose, amylopectin, pasting, gelatinization, viscosity) will have a direct effect on its end use properties (e.g., bread, malt, polymers). The use of rapid and non-destructive methods to study and monitor starch properties, such as gelatinization, retrogradation, water absorption in cereals and starchy foods, is of great interest in order to improve and assess their quality. In recent years, near infrared reflectance (NIR) and mid infrared (MIR) spectroscopy have been explored to predict several quality parameters, such as those generated by instrumental methods commonly used in routine analysis like the rapid visco analyser (RVA) or viscometers. In this review, applications of both NIR and MIR spectroscopy to measure and monitor starch biochemical (amylose, amylopectin, starch) and biophysical properties (e.g., pasting properties) will be presented and discussed. PMID:28234340

Clinical Biophysics; A New Concept in Undergraduate Medical Education.

ERIC Educational Resources Information Center

Anbar, Michael

1981-01-01

The abilities to understand medical technology, to evaluate new devices and procedures, and to assess their effectiveness, reliability, costs, and risks in comparison with existing methods are discussed. A course in clinical biophysics offered at the State University of New York at Buffalo is described. (Author/MLW)

A note on the roles of quantum and mechanical models in social biophysics.

PubMed

Takahashi, Taiki; Kim, Song-Ju; Naruse, Makoto

2017-11-01

Recent advances in the applications of quantum models into various disciplines such as cognitive science, social sciences, economics, and biology witnessed enormous achievements and possible future progress. In this paper, we propose one of the most promising directions in the applications of quantum models: the combination of quantum and mechanical models in social biophysics. The possible resulting discipline may be called as experimental quantum social biophysics and could foster our understandings of the relationships between the society and individuals. Copyright © 2017 Elsevier Ltd. All rights reserved.

Biophysical processes supporting the diversity of microbial life in soil

PubMed Central

Tecon, Robin

2017-01-01

Abstract Soil, the living terrestrial skin of the Earth, plays a central role in supporting life and is home to an unimaginable diversity of microorganisms. This review explores key drivers for microbial life in soils under different climates and land-use practices at scales ranging from soil pores to landscapes. We delineate special features of soil as a microbial habitat (focusing on bacteria) and the consequences for microbial communities. This review covers recent modeling advances that link soil physical processes with microbial life (termed biophysical processes). Readers are introduced to concepts governing water organization in soil pores and associated transport properties and microbial dispersion ranges often determined by the spatial organization of a highly dynamic soil aqueous phase. The narrow hydrological windows of wetting and aqueous phase connectedness are crucial for resource distribution and longer range transport of microorganisms. Feedbacks between microbial activity and their immediate environment are responsible for emergence and stabilization of soil structure—the scaffolding for soil ecological functioning. We synthesize insights from historical and contemporary studies to provide an outlook for the challenges and opportunities for developing a quantitative ecological framework to delineate and predict the microbial component of soil functioning. PMID:28961933

Hierarchy and Interactions in Environmental Interfaces Regarded as Biophysical Complex Systems

NASA Astrophysics Data System (ADS)

Mihailovic, Dragutin T.; Balaz, Igor

The field of environmental sciences is abundant with various interfaces and is the right place for the application of new fundamental approaches leading towards a better understanding of environmental phenomena. For example, following the definition of environmental interface by Mihailovic and Balaž [23], such interface can be placed between: human or animal bodies and surrounding air, aquatic species and water and air around them, and natural or artificially built surfaces (vegetation, ice, snow, barren soil, water, urban communities) and the atmosphere. Complex environmental interface systems are open and hierarchically organised, interactions between their constituent parts are nonlinear, and the interaction with the surrounding environment is noisy. These systems are therefore very sensitive to initial conditions, deterministic external perturbations and random fluctuations always present in nature. The study of noisy non-equilibrium processes is fundamental for modelling the dynamics of environmental interface systems and for understanding the mechanisms of spatio-temporal pattern formation in contemporary environmental sciences, particularly in environmental fluid mechanics. In modelling complex biophysical systems one of the main tasks is to successfully create an operative interface with the external environment. It should provide a robust and prompt translation of the vast diversity of external physical and/or chemical changes into a set of signals, which are "understandable" for an organism. Although the establishment of organisation in any system is of crucial importance for its functioning, it should not be forgotten that in biophysical systems we deal with real-life problems where a number of other conditions should be reached in order to put the system to work. One of them is the proper supply of the system by the energy. Therefore, we will investigate an aspect of dynamics of energy flow based on the energy balance equation. The energy as well as

A Biophysical Model for the Staircase Geometry of Stereocilia

PubMed Central

Orly, Gilad; Manor, Uri; Gov, Nir S.

2015-01-01

Cochlear hair cell bundles, made up of 10s to 100s of individual stereocilia, are essential for hearing, and even relatively minor structural changes, due to mutations or injuries, can result in total deafness. Consistent with its specialized role, the staircase geometry (SCG) of hair cell bundles presents one of the most striking, intricate, and precise organizations of actin-based cellular shapes. Composed of rows of actin-filled stereocilia with increasing lengths, the hair cell’s staircase-shaped bundle is formed from a progenitor field of smaller, thinner, and uniformly spaced microvilli with relatively invariant lengths. While recent genetic studies have provided a significant increase in information on the multitude of stereocilia protein components, there is currently no model that integrates the basic physical forces and biochemical processes necessary to explain the emergence of the SCG. We propose such a model derived from the biophysical and biochemical characteristics of actin-based protrusions. We demonstrate that polarization of the cell’s apical surface, due to the lateral polarization of the entire epithelial layer, plays a key role in promoting SCG formation. Furthermore, our model explains many distinct features of the manifestations of SCG in different species and in the presence of various deafness-associated mutations. PMID:26207893

Effect of varying two key parameters in simulating evacuation for a dormitory in China

NASA Astrophysics Data System (ADS)

Lei, Wenjun; Li, Angui; Gao, Ran

2013-01-01

Student dormitories are both living and resting areas for students in their spare time. There are many small rooms in the dormitories. And the students are distributed densely in the dormitories. High occupant density is the main characteristic of student dormitories. Once there is an accident, such as fire or earthquake, the losses will be cruel. Computer evacuation models developed overseas are commonly applied in working out safety management schemes. The average minimum widths of corridor and exit are the two key parameters affecting the evacuation for the dormitory. The effect of varying these two parameters will be studied in this paper by taking a dormitory in our university as an example. Evacuation performance is predicted with the software FDS + Evac. The default values in the software are used and adjusted through a field survey. The effect of varying either of the two parameters is discussed. It is found that the simulated results agree well with the experimental results. From our study it seems that the evacuation time is not in proportion to the evacuation distance. And we also named a phenomenon of “the closer is not the faster”. For the building researched in this article, a corridor width of 3 m is the most appropriate. And the suitable exit width of the dormitory for evacuation is about 2.5 to 3 m. The number of people has great influence on the walking speed of people. The purpose of this study is to optimize the building, and to make the building in favor of personnel evacuation. Then the damage could be minimized.

Linking biophysical models and public preferences for ecosystem service assessments: a case study for the Southern Rocky Mountains

USGS Publications Warehouse

Bagstad, Kenneth J.; Reed, James; Semmens, Darius J.; Sherrouse, Ben C.; Troy, Austin

2016-01-01

Through extensive research, ecosystem services have been mapped using both survey-based and biophysical approaches, but comparative mapping of public values and those quantified using models has been lacking. In this paper, we mapped hot and cold spots for perceived and modeled ecosystem services by synthesizing results from a social-values mapping study of residents living near the Pike–San Isabel National Forest (PSI), located in the Southern Rocky Mountains, with corresponding biophysically modeled ecosystem services. Social-value maps for the PSI were developed using the Social Values for Ecosystem Services tool, providing statistically modeled continuous value surfaces for 12 value types, including aesthetic, biodiversity, and life-sustaining values. Biophysically modeled maps of carbon sequestration and storage, scenic viewsheds, sediment regulation, and water yield were generated using the Artificial Intelligence for Ecosystem Services tool. Hotspots for both perceived and modeled services were disproportionately located within the PSI’s wilderness areas. Additionally, we used regression analysis to evaluate spatial relationships between perceived biodiversity and cultural ecosystem services and corresponding biophysical model outputs. Our goal was to determine whether publicly valued locations for aesthetic, biodiversity, and life-sustaining values relate meaningfully to results from corresponding biophysical ecosystem service models. We found weak relationships between perceived and biophysically modeled services, indicating that public perception of ecosystem service provisioning regions is limited. We believe that biophysical and social approaches to ecosystem service mapping can serve as methodological complements that can advance ecosystem services-based resource management, benefitting resource managers by showing potential locations of synergy or conflict between areas supplying ecosystem services and those valued by the public.

3-D simulations of M9 earthquakes on the Cascadia Megathrust: Key parameters and uncertainty

USGS Publications Warehouse

Wirth, Erin; Frankel, Arthur; Vidale, John; Marafi, Nasser A.; Stephenson, William J.

2017-01-01

Geologic and historical records indicate that the Cascadia subduction zone is capable of generating large, megathrust earthquakes up to magnitude 9. The last great Cascadia earthquake occurred in 1700, and thus there is no direct measure on the intensity of ground shaking or specific rupture parameters from seismic recordings. We use 3-D numerical simulations to generate broadband (0-10 Hz) synthetic seismograms for 50 M9 rupture scenarios on the Cascadia megathrust. Slip consists of multiple high-stress drop subevents (~M8) with short rise times on the deeper portion of the fault, superimposed on a background slip distribution with longer rise times. We find a >4x variation in the intensity of ground shaking depending upon several key parameters, including the down-dip limit of rupture, the slip distribution and location of strong-motion-generating subevents, and the hypocenter location. We find that extending the down-dip limit of rupture to the top of the non-volcanic tremor zone results in a ~2-3x increase in peak ground acceleration for the inland city of Seattle, Washington, compared to a completely offshore rupture. However, our simulations show that allowing the rupture to extend to the up-dip limit of tremor (i.e., the deepest rupture extent in the National Seismic Hazard Maps), even when tapering the slip to zero at the down-dip edge, results in multiple areas of coseismic coastal uplift. This is inconsistent with coastal geologic evidence (e.g., buried soils, submerged forests), which suggests predominantly coastal subsidence for the 1700 earthquake and previous events. Defining the down-dip limit of rupture as the 1 cm/yr locking contour (i.e., mostly offshore) results in primarily coseismic subsidence at coastal sites. We also find that the presence of deep subevents can produce along-strike variations in subsidence and ground shaking along the coast. Our results demonstrate the wide range of possible ground motions from an M9 megathrust earthquake in

Historical contingency and its biophysical basis in glucocorticoid receptor evolution.

PubMed

Harms, Michael J; Thornton, Joseph W

2014-08-14

Understanding how chance historical events shape evolutionary processes is a central goal of evolutionary biology. Direct insights into the extent and causes of evolutionary contingency have been limited to experimental systems, because it is difficult to know what happened in the deep past and to characterize other paths that evolution could have followed. Here we combine ancestral protein reconstruction, directed evolution and biophysical analysis to explore alternative 'might-have-been' trajectories during the ancient evolution of a novel protein function. We previously found that the evolution of cortisol specificity in the ancestral glucocorticoid receptor (GR) was contingent on permissive substitutions, which had no apparent effect on receptor function but were necessary for GR to tolerate the large-effect mutations that caused the shift in specificity. Here we show that alternative mutations that could have permitted the historical function-switching substitutions are extremely rare in the ensemble of genotypes accessible to the ancestral GR. In a library of thousands of variants of the ancestral protein, we recovered historical permissive substitutions but no alternative permissive genotypes. Using biophysical analysis, we found that permissive mutations must satisfy at least three physical requirements--they must stabilize specific local elements of the protein structure, maintain the correct energetic balance between functional conformations, and be compatible with the ancestral and derived structures--thus revealing why permissive mutations are rare. These findings demonstrate that GR evolution depended strongly on improbable, non-deterministic events, and this contingency arose from intrinsic biophysical properties of the protein.

Biophysical climate impacts of recent changes in global forest cover.

PubMed

Alkama, Ramdane; Cescatti, Alessandro

2016-02-05

Changes in forest cover affect the local climate by modulating the land-atmosphere fluxes of energy and water. The magnitude of this biophysical effect is still debated in the scientific community and currently ignored in climate treaties. Here we present an observation-driven assessment of the climate impacts of recent forest losses and gains, based on Earth observations of global forest cover and land surface temperatures. Our results show that forest losses amplify the diurnal temperature variation and increase the mean and maximum air temperature, with the largest signal in arid zones, followed by temperate, tropical, and boreal zones. In the decade 2003-2012, variations of forest cover generated a mean biophysical warming on land corresponding to about 18% of the global biogeochemical signal due to CO2 emission from land-use change. Copyright © 2016, American Association for the Advancement of Science.

Combining biophysical methods for the analysis of protein complex stoichiometry and affinity in SEDPHAT

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

Zhao, Huaying, E-mail: zhaoh3@mail.nih.gov; Schuck, Peter, E-mail: zhaoh3@mail.nih.gov

2015-01-01

Global multi-method analysis for protein interactions (GMMA) can increase the precision and complexity of binding studies for the determination of the stoichiometry, affinity and cooperativity of multi-site interactions. The principles and recent developments of biophysical solution methods implemented for GMMA in the software SEDPHAT are reviewed, their complementarity in GMMA is described and a new GMMA simulation tool set in SEDPHAT is presented. Reversible macromolecular interactions are ubiquitous in signal transduction pathways, often forming dynamic multi-protein complexes with three or more components. Multivalent binding and cooperativity in these complexes are often key motifs of their biological mechanisms. Traditional solution biophysicalmore » techniques for characterizing the binding and cooperativity are very limited in the number of states that can be resolved. A global multi-method analysis (GMMA) approach has recently been introduced that can leverage the strengths and the different observables of different techniques to improve the accuracy of the resulting binding parameters and to facilitate the study of multi-component systems and multi-site interactions. Here, GMMA is described in the software SEDPHAT for the analysis of data from isothermal titration calorimetry, surface plasmon resonance or other biosensing, analytical ultracentrifugation, fluorescence anisotropy and various other spectroscopic and thermodynamic techniques. The basic principles of these techniques are reviewed and recent advances in view of their particular strengths in the context of GMMA are described. Furthermore, a new feature in SEDPHAT is introduced for the simulation of multi-method data. In combination with specific statistical tools for GMMA in SEDPHAT, simulations can be a valuable step in the experimental design.« less

Biophysics of BK Channel Gating.

PubMed

Pantazis, A; Olcese, R

2016-01-01

BK channels are universal regulators of cell excitability, given their exceptional unitary conductance selective for K(+), joint activation mechanism by membrane depolarization and intracellular [Ca(2+)] elevation, and broad expression pattern. In this chapter, we discuss the structural basis and operational principles of their activation, or gating, by membrane potential and calcium. We also discuss how the two activation mechanisms interact to culminate in channel opening. As members of the voltage-gated potassium channel superfamily, BK channels are discussed in the context of archetypal family members, in terms of similarities that help us understand their function, but also seminal structural and biophysical differences that confer unique functional properties. © 2016 Elsevier Inc. All rights reserved.

At-line monitoring of key parameters of nisin fermentation by near infrared spectroscopy, chemometric modeling and model improvement.

PubMed

Guo, Wei-Liang; Du, Yi-Ping; Zhou, Yong-Can; Yang, Shuang; Lu, Jia-Hui; Zhao, Hong-Yu; Wang, Yao; Teng, Li-Rong

2012-03-01

An analytical procedure has been developed for at-line (fast off-line) monitoring of 4 key parameters including nisin titer (NT), the concentration of reducing sugars, cell concentration and pH during a nisin fermentation process. This procedure is based on near infrared (NIR) spectroscopy and Partial Least Squares (PLS). Samples without any preprocessing were collected at intervals of 1 h during fifteen batch of fermentations. These fermentation processes were implemented in 3 different 5 l fermentors at various conditions. NIR spectra of the samples were collected in 10 min. And then, PLS was used for modeling the relationship between NIR spectra and the key parameters which were determined by reference methods. Monte Carlo Partial Least Squares (MCPLS) was applied to identify the outliers and select the most efficacious methods for preprocessing spectra, wavelengths and the suitable number of latent variables (n (LV)). Then, the optimum models for determining NT, concentration of reducing sugars, cell concentration and pH were established. The correlation coefficients of calibration set (R (c)) were 0.8255, 0.9000, 0.9883 and 0.9581, respectively. These results demonstrated that this method can be successfully applied to at-line monitor of NT, concentration of reducing sugars, cell concentration and pH during nisin fermentation processes.

Biophysical synaptic dynamics in an analog VLSI network of Hodgkin-Huxley neurons.

PubMed

Yu, Theodore; Cauwenberghs, Gert

2009-01-01

We study synaptic dynamics in a biophysical network of four coupled spiking neurons implemented in an analog VLSI silicon microchip. The four neurons implement a generalized Hodgkin-Huxley model with individually configurable rate-based kinetics of opening and closing of Na+ and K+ ion channels. The twelve synapses implement a rate-based first-order kinetic model of neurotransmitter and receptor dynamics, accounting for NMDA and non-NMDA type chemical synapses. The implemented models on the chip are fully configurable by 384 parameters accounting for conductances, reversal potentials, and pre/post-synaptic voltage-dependence of the channel kinetics. We describe the models and present experimental results from the chip characterizing single neuron dynamics, single synapse dynamics, and multi-neuron network dynamics showing phase-locking behavior as a function of synaptic coupling strength. The 3mm x 3mm microchip consumes 1.29 mW power making it promising for applications including neuromorphic modeling and neural prostheses.

Winnowing and Flocculation in Bio-physical Cohesive Substrate: A Flume Experimental and Estuarine Study

NASA Astrophysics Data System (ADS)

Ye, L.; Parsons, D. R.; Manning, A. J.

2016-12-01

Cohesive sediment, or mud, is ubiquitously found in most aqueous environments, such as coasts and estuaries. The study of cohesive sediment behaviors requires the synchronous description of mutual interactions of grains (e.g., winnowing and flocculation), their physical properties (e.g., grain size) and also the ambient water. Herein, a series of flume experiments (14 runs) with different substrate mixtures of sand-clay-EPS (Extracellular Polymeric Substrates: secreted by aquatic microorganisms) are combined with an estuarine field survey (Dee estuary, NW England) to investigate the behavior of suspensions over bio-physical cohesive substrates. The experimental results indicate that winnowing and flocculation occur pervasively in bio-physical cohesive flow systems. Importantly however, the evolution of the bed and bedform dynamics and hence turbulence production can be lower when cohesivity is high. The estuarine survey also revealed that the bio-physical cohesion provided by both the clay and microorganism fractions in the bed, that pervasively exists in many natural estuarine systems, plays a significant role in controlling the interactions between bed substrate and sediment suspension and deposition, including controlling processes such as sediment winnowing, flocculation and re-deposition. Full understanding of these processes are essential in advancing sediment transport modelling and prediction studies across natural estuarine systems and the work will report on an improved conceptual model for sediment sorting deposition in bio-physical cohesive substrates.

Biophysical Characterization of Supported Lipid Bilayers Using Parallel Dual-Wavelength Surface Plasmon Resonance and Quartz Crystal Microbalance Measurements.

PubMed

Parkkila, Petteri; Elderdfi, Mohamed; Bunker, Alex; Viitala, Tapani

2018-06-25

Supported lipid bilayers (SLBs) have been used extensively as an effective model of biological membranes, in the context of in vitro biophysics research, and the membranes of liposomes, in the context of the development of nanoscale drug delivery devices. Despite numerous surface-sensitive techniques having been applied to their study, the comprehensive optical characterization of SLBs using surface plasmon resonance (SPR) has not been conducted. In this study, Fresnel multilayer analysis is utilized to effectively calculate layer parameters (thickness and refractive indices) with the aid of dual-wavelength and dispersion coefficient analysis, in which the linear change in the refractive index as a function of wavelength is assumed. Using complementary information from impedance-based quartz crystal microbalance experiments, biophysical properties, for example, area-per-lipid-molecule and the quantity of lipid-associated water molecules, are calculated for different lipid types and mixtures, one of which is representative of a raft-forming lipid mixture. It is proposed that the hydration layer beneath the bilayer is, in fact, an integral part of the measured optical signal. Also, the traditional Jung model analysis and the ratio of SPR responses are investigated in terms of assessing the structure of the lipid layer that is formed.

An information-based approach to change-point analysis with applications to biophysics and cell biology.

PubMed

Wiggins, Paul A

2015-07-21

This article describes the application of a change-point algorithm to the analysis of stochastic signals in biological systems whose underlying state dynamics consist of transitions between discrete states. Applications of this analysis include molecular-motor stepping, fluorophore bleaching, electrophysiology, particle and cell tracking, detection of copy number variation by sequencing, tethered-particle motion, etc. We present a unified approach to the analysis of processes whose noise can be modeled by Gaussian, Wiener, or Ornstein-Uhlenbeck processes. To fit the model, we exploit explicit, closed-form algebraic expressions for maximum-likelihood estimators of model parameters and estimated information loss of the generalized noise model, which can be computed extremely efficiently. We implement change-point detection using the frequentist information criterion (which, to our knowledge, is a new information criterion). The frequentist information criterion specifies a single, information-based statistical test that is free from ad hoc parameters and requires no prior probability distribution. We demonstrate this information-based approach in the analysis of simulated and experimental tethered-particle-motion data. Copyright © 2015 Biophysical Society. Published by Elsevier Inc. All rights reserved.

A collaborative environment for developing and validating predictive tools for protein biophysical characteristics

NASA Astrophysics Data System (ADS)

Johnston, Michael A.; Farrell, Damien; Nielsen, Jens Erik

2012-04-01

The exchange of information between experimentalists and theoreticians is crucial to improving the predictive ability of theoretical methods and hence our understanding of the related biology. However many barriers exist which prevent the flow of information between the two disciplines. Enabling effective collaboration requires that experimentalists can easily apply computational tools to their data, share their data with theoreticians, and that both the experimental data and computational results are accessible to the wider community. We present a prototype collaborative environment for developing and validating predictive tools for protein biophysical characteristics. The environment is built on two central components; a new python-based integration module which allows theoreticians to provide and manage remote access to their programs; and PEATDB, a program for storing and sharing experimental data from protein biophysical characterisation studies. We demonstrate our approach by integrating PEATSA, a web-based service for predicting changes in protein biophysical characteristics, into PEATDB. Furthermore, we illustrate how the resulting environment aids method development using the Potapov dataset of experimentally measured ΔΔGfold values, previously employed to validate and train protein stability prediction algorithms.

Anti-pulmonary fibrotic activity of salvianolic acid B was screened by a novel method based on the cyto-biophysical properties

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

Liu, Miao; Zheng, Mingjing; Xu, Hanying

Various methods have been used to evaluate anti-fibrotic activity of drugs. However, most of them are complicated, labor-intensive and lack of efficiency. This study was intended to develop a rapid method for anti-fibrotic drugs screening based on biophysical properties. A549 cells in vitro were stimulated with transforming growth factor-β1 (TGF-β1), and fibrogenesis was confirmed by conventional immunological assays. Meanwhile, the alterations of cyto-biophysical properties including morphology, roughness and stiffness were measured utilizing atomic force microscopy (AFM). It was found that fibrogenesis was accompanied with changes of cellular biophysical properties. TGF-β1-stimulated A549 cells became remarkably longer, rougher and stiffer than the control.more » Then, the effect of N-acetyl-L-cysteine (NAC) as a positive drug on ameliorating fibrogenesis in TGF-β1-stimulated A549 cells was verified respectively by immunological and biophysical markers. The result of Principal Component Analysis showed that stiffness was a leading index among all biophysical markers during fibrogenesis. Salvianolic acid B (SalB), a natural anti-oxidant, was detected by AFM to protect TGF-β1-stimulated A549 cells against stiffening. Then, SalB treatment was provided in preventive mode on a rat model of bleomycin (BLM) -induced pulmonary fibrosis. The results showed that SalB treatment significantly ameliorated BLM-induced histological alterations, blocked collagen accumulations and reduced α-SMA expression in lung tissues. All these results revealed the anti-pulmonary fibrotic activity of SalB. Detection of cyto-biophysical properties were therefore recommended as a rapid method for anti-pulmonary fibrotic drugs screening. - Highlights: • Fibrogenesis was accompanied with the changes of cyto-biophysical properties. • Cyto-biophysical properties could be markers for anti-fibrotic drugs screening. • Stiffness is a leading index among all biophysical markers. • Sal

Mass spectrometry for the biophysical characterization of therapeutic monoclonal antibodies.

PubMed

Zhang, Hao; Cui, Weidong; Gross, Michael L

2014-01-21

Monoclonal antibodies (mAbs) are powerful therapeutics, and their characterization has drawn considerable attention and urgency. Unlike small-molecule drugs (150-600 Da) that have rigid structures, mAbs (∼150 kDa) are engineered proteins that undergo complicated folding and can exist in a number of low-energy structures, posing a challenge for traditional methods in structural biology. Mass spectrometry (MS)-based biophysical characterization approaches can provide structural information, bringing high sensitivity, fast turnaround, and small sample consumption. This review outlines various MS-based strategies for protein biophysical characterization and then reviews how these strategies provide structural information of mAbs at the protein level (intact or top-down approaches), peptide, and residue level (bottom-up approaches), affording information on higher order structure, aggregation, and the nature of antibody complexes. Copyright © 2013 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Short-Term Memory and Its Biophysical Model

NASA Astrophysics Data System (ADS)

Wang, Wei; Zhang, Kai; Tang, Xiao-wei

1996-12-01

The capacity of short-term memory has been studied using an integrate-and-fire neuronal network model. It is found that the storage of events depend on the manner of the correlation between the events, and the capacity is dominated by the value of after-depolarization potential. There is a monotonic increasing relationship between the value of after-depolarization potential and the memory numbers. The biophysics relevance of the network model is discussed and different kinds of the information processes are studied too.

From global change to a butterfly flapping: biophysics and behaviour affect tropical climate change impacts.

PubMed

Bonebrake, Timothy C; Boggs, Carol L; Stamberger, Jeannie A; Deutsch, Curtis A; Ehrlich, Paul R

2014-10-22

Difficulty in characterizing the relationship between climatic variability and climate change vulnerability arises when we consider the multiple scales at which this variation occurs, be it temporal (from minute to annual) or spatial (from centimetres to kilometres). We studied populations of a single widely distributed butterfly species, Chlosyne lacinia, to examine the physiological, morphological, thermoregulatory and biophysical underpinnings of adaptation to tropical and temperate climates. Microclimatic and morphological data along with a biophysical model documented the importance of solar radiation in predicting butterfly body temperature. We also integrated the biophysics with a physiologically based insect fitness model to quantify the influence of solar radiation, morphology and behaviour on warming impact projections. While warming is projected to have some detrimental impacts on tropical ectotherms, fitness impacts in this study are not as negative as models that assume body and air temperature equivalence would suggest. We additionally show that behavioural thermoregulation can diminish direct warming impacts, though indirect thermoregulatory consequences could further complicate predictions. With these results, at multiple spatial and temporal scales, we show the importance of biophysics and behaviour for studying biodiversity consequences of global climate change, and stress that tropical climate change impacts are likely to be context-dependent. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

From global change to a butterfly flapping: biophysics and behaviour affect tropical climate change impacts

PubMed Central

Bonebrake, Timothy C.; Boggs, Carol L.; Stamberger, Jeannie A.; Deutsch, Curtis A.; Ehrlich, Paul R.

2014-01-01

Difficulty in characterizing the relationship between climatic variability and climate change vulnerability arises when we consider the multiple scales at which this variation occurs, be it temporal (from minute to annual) or spatial (from centimetres to kilometres). We studied populations of a single widely distributed butterfly species, Chlosyne lacinia, to examine the physiological, morphological, thermoregulatory and biophysical underpinnings of adaptation to tropical and temperate climates. Microclimatic and morphological data along with a biophysical model documented the importance of solar radiation in predicting butterfly body temperature. We also integrated the biophysics with a physiologically based insect fitness model to quantify the influence of solar radiation, morphology and behaviour on warming impact projections. While warming is projected to have some detrimental impacts on tropical ectotherms, fitness impacts in this study are not as negative as models that assume body and air temperature equivalence would suggest. We additionally show that behavioural thermoregulation can diminish direct warming impacts, though indirect thermoregulatory consequences could further complicate predictions. With these results, at multiple spatial and temporal scales, we show the importance of biophysics and behaviour for studying biodiversity consequences of global climate change, and stress that tropical climate change impacts are likely to be context-dependent. PMID:25165769

Bio-physical vs. Economic Uncertainty in the Analysis of Climate Change Impacts on World Agriculture

NASA Astrophysics Data System (ADS)

Hertel, T. W.; Lobell, D. B.

2010-12-01

Accumulating evidence suggests that agricultural production could be greatly affected by climate change, but there remains little quantitative understanding of how these agricultural impacts would affect economic livelihoods in poor countries. The recent paper by Hertel, Burke and Lobell (GEC, 2010) considers three scenarios of agricultural impacts of climate change, corresponding to the fifth, fiftieth, and ninety fifth percentiles of projected yield distributions for the world’s crops in 2030. They evaluate the resulting changes in global commodity prices, national economic welfare, and the incidence of poverty in a set of 15 developing countries. Although the small price changes under the medium scenario are consistent with previous findings, their low productivity scenario reveals the potential for much larger food price changes than reported in recent studies which have hitherto focused on the most likely outcomes. The poverty impacts of price changes under the extremely adverse scenario are quite heterogeneous and very significant in some population strata. They conclude that it is critical to look beyond central case climate shocks and beyond a simple focus on yields and highly aggregated poverty impacts. In this paper, we conduct a more formal, systematic sensitivity analysis (SSA) with respect to uncertainty in the biophysical impacts of climate change on agriculture, by explicitly specifying joint distributions for global yield changes - this time focusing on 2050. This permits us to place confidence intervals on the resulting price impacts and poverty results which reflect the uncertainty inherited from the biophysical side of the analysis. We contrast this with the economic uncertainty inherited from the global general equilibrium model (GTAP), by undertaking SSA with respect to the behavioral parameters in that model. This permits us to assess which type of uncertainty is more important for regional price and poverty outcomes. Finally, we undertake a

Key Parameters Evaluation for Hip Prosthesis with Finite Element Analysis

NASA Astrophysics Data System (ADS)

Guo, Hongqiang; Li, Dichen; Lian, Qin; Li, Xiang; Jin, Zhongmin

2007-09-01

Stem length and cross section are two key parameters that influence the stability and longevity of metallic hip prosthesis in the total hip arthroplasty (THA). In order to assess their influence to the stress and fatigue behavior of hip prosthesis, a series model of hip prosthesis with round-shaped or drum-shaped cross section, and with different stem lengths were created. These models were analyzed under both static and dynamic loading conditions with finite element analysis, and dynamic loading represents normal walking was used in the dynamic analysis. The stress on the metallic stem, cement, and adjacent bone were got, micromotion on the cement-metal interface were got too. Safety factors for fatigue life of the hip prothesis were calculated based on data obtained from dynamic analysis. Static analysis shows that drum-shaped cross section can decrease the displacement of the stem, that stress on drum-shaped stem focus on the corner of the femoral neck and the distal part of hip prosthesis, whereas the stress on the round-shaped stem distributes evenly over most part of the stem, and maximum stress on stem prosthesis fluctuates with stem length bottoming out at stem length range from 80 mm to 110 mm, that drum-shaped stems with drum height 8 mm generate more stress at the distal part of stem than drum-shaped stems with drum height 10 mm and round stems do. Dynamic and fatigue analysis shows that drum-shaped stem with drum height 10 mm and stem length 90 mm has the greatest safety factor therefore long fatigue life.

Enhancing the biophysical properties of mRFP1 through incorporation of fluoroproline

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

Deepankumar, Kanagavel; Nadarajan, Saravanan Prabhu; Ayyadurai, Niraikulam

2013-11-01

Graphical abstract: Enhancing the biophysical properties of mRFP1 through incorporation of (2S, 4R)-4-fluoroproline at proline residues after mutating non-permissive site Pro63 into Ala. -- Highlights: •We incorporate (4S)-FP into mRFP1 led to insoluble protein. •Whereas, incorporation of (4R)-FP resulted in soluble but lost its fluorescence. •mRFP1-P63A mutant accommodate (4R)-FP and gave soluble protein with fluorescence. •Moreover mRFP1-P63A[(4R)-FP] showed enhanced biophysical properties of protein. -- Abstract: Here we enhanced the stability and biophysical properties of mRFP1 through a combination of canonical and non-canonical amino acid mutagenesis. The global replacement of proline residue with (2S, 4R)-4-fluoroproline [(4R)-FP] into mRFP1 led to solublemore » protein but lost its fluorescence, whereas (2S, 4S)-4-fluoroproline [(4S)-FP] incorporation resulted in insoluble protein. The bioinformatics analysis revealed that (4R)-FP incorporation at Pro63 caused fluorescence loss due to the steric hindrance of fluorine atom of (4R)-FP with the chromophore. Therefore, Pro63 residue was mutated with the smallest amino acid Ala to maintain non coplanar conformation of the chromophore and helps to retain its fluorescence with (4R)-FP incorporation. The incorporation of (4R)-FP into mRFP1-P63A showed about 2–3-fold enhancement in thermal and chemical stability. The rate of maturation is also greatly accelerated over the presence of (4R)-FP into mRFP1-P63A. Our study showed that a successful enhancement in the biophysical property of mRFP1-P63A[(4R)-FP] using non-canonical amino acid mutagenesis after mutating non-permissive site Pro63 into Ala.« less

Biophysical characterization of V3-lipopeptide liposomes influencing HIV-1 infectivity

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

Rizos, Apostolos K.; Baritaki, Stavroula; Department of Virology, Medical School, University of Crete, Heraklion, Crete

2007-04-20

The V3-loop of the HIV-1 gp120 alters host cell immune function and modulates infectivity. We investigated biophysical parameters of liposome constructs with embedded lipopeptides from the principle neutralizing domain of the V3-loop and their influence on viral infectivity. Dynamic light scattering measurements showed liposome supramolecular structures with hydrodynamic radius of the order of 900 and 1300 nm for plain and V3-lipopeptide liposomes. Electron paramagnetic resonance measurements showed almost identical local microenvironment. The difference in liposome hydrodynamic radius was attributed to the fluctuating ionic environment of the V3-lipopeptide liposomes. In vitro HIV-1 infectivity assays showed that plain liposomes reduced virus productionmore » in all cell cultures, probably due to the hydrophobic nature of the aggregates. Liposomes carrying V3-lipopeptides with different cationic potentials restored and even enhanced infectivity (p < 0.05). These results highlight the need for elucidation of the involvement of lipid bilayers as dynamic components in supramolecular structures and in HIV-1 fusion mechanisms.« less

Biophysically Inspired Rational Design of Structured Chimeric Substrates for DNAzyme Cascade Engineering

PubMed Central

Lakin, Matthew R.; Brown, Carl W.; Horwitz, Eli K.; Fanning, M. Leigh; West, Hannah E.; Stefanovic, Darko; Graves, Steven W.

2014-01-01

The development of large-scale molecular computational networks is a promising approach to implementing logical decision making at the nanoscale, analogous to cellular signaling and regulatory cascades. DNA strands with catalytic activity (DNAzymes) are one means of systematically constructing molecular computation networks with inherent signal amplification. Linking multiple DNAzymes into a computational circuit requires the design of substrate molecules that allow a signal to be passed from one DNAzyme to another through programmed biochemical interactions. In this paper, we chronicle an iterative design process guided by biophysical and kinetic constraints on the desired reaction pathways and use the resulting substrate design to implement heterogeneous DNAzyme signaling cascades. A key aspect of our design process is the use of secondary structure in the substrate molecule to sequester a downstream effector sequence prior to cleavage by an upstream DNAzyme. Our goal was to develop a concrete substrate molecule design to achieve efficient signal propagation with maximal activation and minimal leakage. We have previously employed the resulting design to develop high-performance DNAzyme-based signaling systems with applications in pathogen detection and autonomous theranostics. PMID:25347066

Chiropractic biophysics technique: a linear algebra approach to posture in chiropractic.

PubMed

Harrison, D D; Janik, T J; Harrison, G R; Troyanovich, S; Harrison, D E; Harrison, S O

1996-10-01

This paper discusses linear algebra as applied to human posture in chiropractic, specifically chiropractic biophysics technique (CBP). Rotations, reflections and translations are geometric functions studied in vector spaces in linear algebra. These mathematical functions are termed rigid body transformations and are applied to segmental spinal movement in the literature. Review of the literature indicates that these linear algebra concepts have been used to describe vertebral motion. However, these rigid body movers are presented here as applying to the global postural movements of the head, thoracic cage and pelvis. The unique inverse functions of rotations, reflections and translations provide a theoretical basis for making postural corrections in neutral static resting posture. Chiropractic biophysics technique (CBP) uses these concepts in examination procedures, manual spinal manipulation, instrument assisted spinal manipulation, postural exercises, extension traction and clinical outcome measures.

Letting the cat out of the bag: a personal journey in Biophysics.

PubMed

Bustamante, Carlos J

2014-10-08

When the author arrived in Berkeley, in the mid 1970s, to study Biophysics he soon felt as if he was engaging himself in a somewhat marginal activity. Biology was then entering another of its cyclical periods of annotation that was to culminate with the human genome project. Two decades later, however, at the end of this process, it had become clear that two main tasks were acquiring a central importance in biological research: a renewed push for a quantitative, precise description of biological systems at the molecular level, and efforts towards an integrated understanding of the operation, control, and coordination of cellular processes. Today, these have become two of the most fertile research areas in Biophysics.

Biophysics of protein-DNA interactions and chromosome organization

PubMed Central

Marko, John F.

2014-01-01

The function of DNA in cells depends on its interactions with protein molecules, which recognize and act on base sequence patterns along the double helix. These notes aim to introduce basic polymer physics of DNA molecules, biophysics of protein-DNA interactions and their study in single-DNA experiments, and some aspects of large-scale chromosome structure. Mechanisms for control of chromosome topology will also be discussed. PMID:25419039

Radiation-induced total-deletion mutations in the human hprt gene: a biophysical model based on random walk interphase chromatin geometry

NASA Technical Reports Server (NTRS)

Wu, H.; Sachs, R. K.; Yang, T. C.

1998-01-01

PURPOSE: To develop a biophysical model that explains the sizes of radiation-induced hprt deletions. METHODS: Key assumptions: (1) Deletions are produced by two DSB that are closer than an interaction distance at the time of DSB induction; (2) Interphase chromatin is modelled by a biphasic random walk distribution; and (3) Misrejoining of DSB from two separate tracks dominates at low-LET and misrejoining of DSB from a single track dominates at high-LET. RESULTS: The size spectra for radiation-induced total deletions of the hprt gene are calculated. Comparing with the results of Yamada and coworkers for gamma-irradiated human fibroblasts the study finds that an interaction distance of 0.75 microm will fit both the absolute frequency and the size spectrum of the total deletions. It is also shown that high-LET radiations produce, relatively, more total deletions of sizes below 0.5 Mb. The model predicts an essential gene to be located between 2 and 3 Mb from the hprt locus towards the centromere. Using the same assumptions and parameters as for evaluating mutation frequencies, a frequency of intra-arm chromosome deletions is calculated that is in agreement with experimental data. CONCLUSIONS: Radiation-induced total-deletion mutations of the human hprt gene and intrachange chromosome aberrations share a common mechanism for their induction.

An Integrated Biogeochemical and Biophysical Analysis of Bioenergy Crops

NASA Astrophysics Data System (ADS)

Liang, M.; Song, Y.; Barman, R.; Jain, A. K.

2010-12-01

Bioenergy crops are becoming increasingly important with growing concerns about the energy demand and climate change and the need to replace fossil fuels with carbon-neutral renewable sources of energy. The transition to a biofuel-based energy supply raises many questions such as: how and where to grow energy crops, what will be the impacts of growing large scale biofuel crops on climate system, the hydrological cycle and soil biogeochemistry. We are developing and applying an integrated system modeling framework to investigate the biophysical, physiological, and biogeochemical systems governing important processes that regulate crop growth such as water, energy and nutrient cycles. The framework has a two-big-leaf canopy scheme for photosynthesis, stomatal conductance, leaf temperature and energy fluxes. The soil/snow hydrology consists of 10 layers for soil and up to 5 layers for snow. The biogeochemistry component explicitly accounts for coupled carbon and nitrogen dynamics. The feedstocks currently considered include corn stover, Miscanthus and switchgrass. The parameters used for simulation of each crop have been calibrated using field experimental data from the US. The use of this modeling capability will be demonstrated through its applications to study the environmental effects (through changes in albedo and evapotranspiration) of biofuel production as well as the effective management practice in the United States.

Perspectives and Plans for Graduate Studies. 16. Biophysics 1974.

ERIC Educational Resources Information Center

Ontario Council on Graduate Studies, Toronto. Advisory Committee on Academic Planning.

In March, 1973, after a review of the Ontario universities' three-year plans, a provisional embargo was placed on doctoral work in biophysics. A full-scale assessment with outside consultants was not necessary in the case of a provisional embargo. Instead, the method used to remove the embargo was self-study by the discipline group leading to a…

Southwest Ecological Restoration Institutes (SWERI) Biophysical Monitoring Workshop Report

Treesearch

Joseph Seidenberg; Judy Springer; Tessa Nicolet; Mike Battaglia; Christina Vothja

2009-01-01

On October 15-16, 2009, the Southwest Ecological Restoration Institutes (SWERI) hosted a workshop in which the participants would 1) build a common understanding of the types of monitoring that are occurring in forested ecosystems of the Southwest; 2) analyze and agree on an efficient, yet robust set of biophysical variables that can be used by land mangers and...

Key parameters and practices controlling pesticide degradation efficiency of biobed substrates.

PubMed

Karanasios, Evangelos; Karpouzas, Dimitrios G; Tsiropoulos, Nikolaos G

2012-01-01

We studied the contribution of each of the components of a compost-based biomixture (BX), commonly used in Europe, on pesticide degradation. The impact of other key parameters including pesticide dose, temperature and repeated applications on the degradation of eight pesticides, applied as a mixture, in a BX and a peat-based biomixture (OBX) was compared and contrasted to their degradation in soil. Incubation studies showed that straw was essential in maintaining a high pesticide degradation capacity of the biomixture, whereas compost, when mixed with soil, retarded pesticide degradation. The highest rates of degradation were shown in the biomixture composed of soil/compost/straw suggesting that all three components are essential for maximum biobed performance. Increasing doses prolonged the persistence of most pesticides with biomixtures showing a higher tolerance to high pesticide dose levels compared to soil. Increasing the incubation temperature from 15 °C to 25 °C resulted in lower t(1/2) values, with biomixtures performing better than soil at the lower temperature. Repeated applications led to a decrease in the degradation rates of most pesticides in all the substrates, with the exception of iprodione and metalaxyl. Overall, our results stress the ability of biomixtures to perform better than soil under unfavorable conditions and extreme pesticide dose levels. Copyright © Taylor & Francis Group, LLC

Assessing the performance of community-available global MHD models using key system parameters and empirical relationships

NASA Astrophysics Data System (ADS)

Gordeev, E.; Sergeev, V.; Honkonen, I.; Kuznetsova, M.; Rastätter, L.; Palmroth, M.; Janhunen, P.; Tóth, G.; Lyon, J.; Wiltberger, M.

2015-12-01

Global magnetohydrodynamic (MHD) modeling is a powerful tool in space weather research and predictions. There are several advanced and still developing global MHD (GMHD) models that are publicly available via Community Coordinated Modeling Center's (CCMC) Run on Request system, which allows the users to simulate the magnetospheric response to different solar wind conditions including extraordinary events, like geomagnetic storms. Systematic validation of GMHD models against observations still continues to be a challenge, as well as comparative benchmarking of different models against each other. In this paper we describe and test a new approach in which (i) a set of critical large-scale system parameters is explored/tested, which are produced by (ii) specially designed set of computer runs to simulate realistic statistical distributions of critical solar wind parameters and are compared to (iii) observation-based empirical relationships for these parameters. Being tested in approximately similar conditions (similar inputs, comparable grid resolution, etc.), the four models publicly available at the CCMC predict rather well the absolute values and variations of those key parameters (magnetospheric size, magnetic field, and pressure) which are directly related to the large-scale magnetospheric equilibrium in the outer magnetosphere, for which the MHD is supposed to be a valid approach. At the same time, the models have systematic differences in other parameters, being especially different in predicting the global convection rate, total field-aligned current, and magnetic flux loading into the magnetotail after the north-south interplanetary magnetic field turning. According to validation results, none of the models emerges as an absolute leader. The new approach suggested for the evaluation of the models performance against reality may be used by model users while planning their investigations, as well as by model developers and those interesting to quantitatively

Marco Todeschini - Space Dynamics and Psycho-Biophysics

NASA Astrophysics Data System (ADS)

Teodorani, M.

2006-03-01

This book is dedicated to the theoretical and experimental research carried out in the 20-th century, by Italian engineer and technical physicist Marco Todeschini. It describes the subjects of "space dynamics" and "psycho-biophysics" - two related physical sciences - whose foundations lay in the existence of the ether and of the vortexes that all bodies with mass produce in it. An entirely new cosmology is derived in which all the bodies in the universe - elementary particles, astronomical bodies, and the human being - are strictly related together.

Biophysical mechanisms complementing "classical" cell biology.

PubMed

Funk, Richard H W

2018-01-01

This overview addresses phenomena in cell- and molecular biology which are puzzling by their fast and highly coordinated way of organization. Generally, it appears that informative processes probably involved are more on the biophysical than on the classical biochemical side. The coordination problem is explained within the first part of the review by the topic of endogenous electrical phenomena. These are found e.g. in fast tissue organization and reorganization processes like development, wound healing and regeneration. Here, coupling into classical biochemical signaling and reactions can be shown by modern microscopy, electronics and bioinformatics. Further, one can follow the triggered reactions seamlessly via molecular biology till into genetics. Direct observation of intracellular electric processes is very difficult because of e.g. shielding through the cell membrane and damping by other structures. Therefore, we have to rely on photonic and photon - phonon coupling phenomena like molecular vibrations, which are addressed within the second part. Molecules normally possess different charge moieties and thus small electromagnetic (EMF) patterns arise during molecular vibration. These patterns can now be measured best within the optical part of the spectrum - much less in the lower terahertz till kHz and lower Hz part (third part of this review). Finally, EMFs facilitate quantum informative processes in coherent domains of molecular, charge and electron spin motion. This helps to coordinate such manifold and intertwined processes going on within cells, tissues and organs (part 4). Because the phenomena described in part 3 and 4 of the review still await really hard proofs we need concerted efforts and a combination of biophysics, molecular biology and informatics to unravel the described mysteries in "physics of life".

Social and Biophysical Predictors of Public Perceptions of Extreme Fires

NASA Astrophysics Data System (ADS)

Hall, T. E.; Kooistra, C. M.; Paveglio, T.; Gress, S.; Smith, A. M.

2013-12-01

To date, what constitutes an 'extreme' fire has been approached separately by biophysical and social scientists. Research on the biophysical characteristics of fires has identified potential dimensions of extremity, including fire size and vegetation mortality. On the social side, factors such as the degree of immediate impact to one's life and property or the extent of social disruption in the community contribute to a perception of extremity. However, some biophysical characteristics may also contribute to perceptions of extremity, including number of simultaneous ignitions, rapidity of fire spread, atypical fire behavior, and intensity of smoke. Perceptions of these impacts can vary within and across communities, but no studies to date have investigated such perceptions in a comprehensive way. In this study, we address the question, to what extent is the magnitude of impact of fires on WUI residents' well-being explained by measurable biophysical characteristics of the fire and subjective evaluations of the personal and community-level impacts of the fire? We bring together diverse strands of psychological theory, including landscape perception, mental models, risk perception, and community studies. The majority of social science research on fires has been in the form of qualitative case studies, and our study is methodologically unique by using a nested design (hierarchical modeling) to enable generalizable conclusions across a wide range of fires and human communities. We identified fires that burned in 2011 or 2012 in the northern Rocky Mountain region that were at least 1,000 acres and that intersected (within 15 km) urban clusters or identified Census places. For fires where an adequately large number of households was located in proximity to the fire, we drew random samples of approximately 150 individuals for each fire. We used a hybrid internet (Qualtrics) and mail survey, following the Dillman method, to measure individual perceptions. We developed two

Past and present biophysical redundancy of countries as a buffer to changes in food supply

NASA Astrophysics Data System (ADS)

Fader, Marianela; Rulli, Maria Cristina; Carr, Joel; Dell'Angelo, Jampel; D'Odorico, Paolo; Gephart, Jessica A.; Kummu, Matti; Magliocca, Nicholas; Porkka, Miina; Prell, Christina; Puma, Michael J.; Ratajczak, Zak; Seekell, David A.; Suweis, Samir; Tavoni, Alessandro

2016-05-01

Spatially diverse trends in population growth, climate change, industrialization, urbanization and economic development are expected to change future food supply and demand. These changes may affect the suitability of land for food production, implying elevated risks especially for resource-constrained, food-importing countries. We present the evolution of biophysical redundancy for agricultural production at country level, from 1992 to 2012. Biophysical redundancy, defined as unused biotic and abiotic environmental resources, is represented by the potential food production of ‘spare land’, available water resources (i.e., not already used for human activities), as well as production increases through yield gap closure on cultivated areas and potential agricultural areas. In 2012, the biophysical redundancy of 75 (48) countries, mainly in North Africa, Western Europe, the Middle East and Asia, was insufficient to produce the caloric nutritional needs for at least 50% (25%) of their population during a year. Biophysical redundancy has decreased in the last two decades in 102 out of 155 countries, 11 of these went from high to limited redundancy, and nine of these from limited to very low redundancy. Although the variability of the drivers of change across different countries is high, improvements in yield and population growth have a clear impact on the decreases of redundancy towards the very low redundancy category. We took a more detailed look at countries classified as ‘Low Income Economies (LIEs)’ since they are particularly vulnerable to domestic or external food supply changes, due to their limited capacity to offset for food supply decreases with higher purchasing power on the international market. Currently, nine LIEs have limited or very low biophysical redundancy. Many of these showed a decrease in redundancy over the last two decades, which is not always linked with improvements in per capita food availability.

Past and Present Biophysical Redundancy of Countries as a Buffer to Changes in Food Supply

NASA Technical Reports Server (NTRS)

Fader, Marianela; Rulli, Maria Cristina; Carr, Joel; Dell' Angelo, Jampel; D' Odorico, Paolo; Gephart, Jessica A.; Kummu, Matti; Magliocca, Nicholas; Porkka, Miina; Prell, Christina;

Biophysical and Functional Characterization of Rhesus Macaque IgG Subclasses

PubMed Central

Boesch, Austin W.; Osei-Owusu, Nana Yaw; Crowley, Andrew R.; Chu, Thach H.; Chan, Ying N.; Weiner, Joshua A.; Bharadwaj, Pranay; Hards, Rufus; Adamo, Mark E.; Gerber, Scott A.; Cocklin, Sarah L.; Schmitz, Joern E.; Miles, Adam R.; Eckman, Joshua W.; Belli, Aaron J.; Reimann, Keith A.; Ackerman, Margaret E.

2016-01-01

Antibodies raised in Indian rhesus macaques [Macaca mulatta (MM)] in many preclinical vaccine studies are often evaluated in vitro for titer, antigen-recognition breadth, neutralization potency, and/or effector function, and in vivo for potential associations with protection. However, despite reliance on this key animal model in translation of promising candidate vaccines for evaluation in first in man studies, little is known about the properties of MM immunoglobulin G (IgG) subclasses and how they may compare to human IgG subclasses. Here, we evaluate the binding of MM IgG1, IgG2, IgG3, and IgG4 to human Fc gamma receptors (FcγR) and their ability to elicit the effector functions of human FcγR-bearing cells, and unlike in humans, find a notable absence of subclasses with dramatically silent Fc regions. Biophysical, in vitro, and in vivo characterization revealed MM IgG1 exhibited the greatest effector function activity followed by IgG2 and then IgG3/4. These findings in rhesus are in contrast with the canonical understanding that IgG1 and IgG3 dominate effector function in humans, indicating that subclass-switching profiles observed in rhesus studies may not strictly recapitulate those observed in human vaccine studies. PMID:28018355

BIOPHYSICAL PROPERTIES OF NUCLEIC ACIDS AT SURFACES RELEVANT TO MICROARRAY PERFORMANCE.

PubMed

Rao, Archana N; Grainger, David W

2014-04-01

Both clinical and analytical metrics produced by microarray-based assay technology have recognized problems in reproducibility, reliability and analytical sensitivity. These issues are often attributed to poor understanding and control of nucleic acid behaviors and properties at solid-liquid interfaces. Nucleic acid hybridization, central to DNA and RNA microarray formats, depends on the properties and behaviors of single strand (ss) nucleic acids (e.g., probe oligomeric DNA) bound to surfaces. ssDNA's persistence length, radius of gyration, electrostatics, conformations on different surfaces and under various assay conditions, its chain flexibility and curvature, charging effects in ionic solutions, and fluorescent labeling all influence its physical chemistry and hybridization under assay conditions. Nucleic acid (e.g., both RNA and DNA) target interactions with immobilized ssDNA strands are highly impacted by these biophysical states. Furthermore, the kinetics, thermodynamics, and enthalpic and entropic contributions to DNA hybridization reflect global probe/target structures and interaction dynamics. Here we review several biophysical issues relevant to oligomeric nucleic acid molecular behaviors at surfaces and their influences on duplex formation that influence microarray assay performance. Correlation of biophysical aspects of single and double-stranded nucleic acids with their complexes in bulk solution is common. Such analysis at surfaces is not commonly reported, despite its importance to microarray assays. We seek to provide further insight into nucleic acid-surface challenges facing microarray diagnostic formats that have hindered their clinical adoption and compromise their research quality and value as genomics tools.

BIOPHYSICAL PROPERTIES OF NUCLEIC ACIDS AT SURFACES RELEVANT TO MICROARRAY PERFORMANCE

PubMed Central

Rao, Archana N.; Grainger, David W.

2014-01-01

Both clinical and analytical metrics produced by microarray-based assay technology have recognized problems in reproducibility, reliability and analytical sensitivity. These issues are often attributed to poor understanding and control of nucleic acid behaviors and properties at solid-liquid interfaces. Nucleic acid hybridization, central to DNA and RNA microarray formats, depends on the properties and behaviors of single strand (ss) nucleic acids (e.g., probe oligomeric DNA) bound to surfaces. ssDNA’s persistence length, radius of gyration, electrostatics, conformations on different surfaces and under various assay conditions, its chain flexibility and curvature, charging effects in ionic solutions, and fluorescent labeling all influence its physical chemistry and hybridization under assay conditions. Nucleic acid (e.g., both RNA and DNA) target interactions with immobilized ssDNA strands are highly impacted by these biophysical states. Furthermore, the kinetics, thermodynamics, and enthalpic and entropic contributions to DNA hybridization reflect global probe/target structures and interaction dynamics. Here we review several biophysical issues relevant to oligomeric nucleic acid molecular behaviors at surfaces and their influences on duplex formation that influence microarray assay performance. Correlation of biophysical aspects of single and double-stranded nucleic acids with their complexes in bulk solution is common. Such analysis at surfaces is not commonly reported, despite its importance to microarray assays. We seek to provide further insight into nucleic acid-surface challenges facing microarray diagnostic formats that have hindered their clinical adoption and compromise their research quality and value as genomics tools. PMID:24765522

Biophysical Approach to Mechanisms of Cancer Prevention and Treatment with Green Tea Catechins.

PubMed

Suganuma, Masami; Takahashi, Atsushi; Watanabe, Tatsuro; Iida, Keisuke; Matsuzaki, Takahisa; Yoshikawa, Hiroshi Y; Fujiki, Hirota

2016-11-18

Green tea catechin and green tea extract are now recognized as non-toxic cancer preventives for humans. We first review our brief historical development of green tea cancer prevention. Based on exciting evidence that green tea catechin, (-)-epigallocatechin gallate (EGCG) in drinking water inhibited lung metastasis of B16 melanoma cells, we and other researchers have studied the inhibitory mechanisms of metastasis with green tea catechins using biomechanical tools, atomic force microscopy (AFM) and microfluidic optical stretcher. Specifically, determination of biophysical properties of cancer cells, low cell stiffness, and high deformability in relation to migration, along with biophysical effects, were studied by treatment with green tea catechins. The study with AFM revealed that low average values of Young's moduli, indicating low cell stiffness, are closely associated with strong potential of cell migration and metastasis for various cancer cells. It is important to note that treatments with EGCG and green tea extract elevated the average values of Young's moduli resulting in increased stiffness (large elasticity) of melanomas and various cancer cells. We discuss here the biophysical basis of multifunctions of green tea catechins and green tea extract leading to beneficial effects for cancer prevention and treatment.

[Advances of studies on the biophysical and biochemical properties of meridians].

PubMed

Liu, Fang; Huang, Guang-yin

2007-08-01

The essence of meridian-collateral system is one of the momentous theoretical topics of the life science. In recent years, many authors have been trying to elucidate various kinds of meridian phenomenon from different points of view including physics, chemistry, biology, traditional Chinese medicine, modern science and so on. The physical detection results intuitively indicated biophysics specificities of meridians, including electricity, heat, sound, light, magnesium, the migration of the injected isotope along the running route of meridians and so on. Results of the studies on chemical materials (ion, PO2, neurotransmitters) within the tissues along the meridian and those of cell junction communications showed that some chemical substances have a close relation with the meridian activities. This review summarizes recent research results on meridian and acupoints from biophysics and biochemistry in order to have a comprehensive understanding in this field.

Barophysiology and Biophysics

NASA Technical Reports Server (NTRS)

Powell, Michael R.

1999-01-01

Decompression is an important aspect of extravehicular activity (EVA). Errors can result in decompression sickness (DCS) if the protective measures are too liberal, while valuable on-orbit time is dissipated in prophylactic methodologies that are excessively conservative. Nucleation is an important consideration in many natural events, and its control is very important in many industrial procedures. The amount of Extravehicular Activity (EVA) that will be required during the construction of the International Space Station exceeds all of the other activity combined. The requirements in astronaut time and consumables (breathing oxygen and air) will be considerable. In an attempt to mitigate these requirements, Project ARGO was investigated in 1990 to investigate the effects of gravitational forces on the musculoskeletal system. This work has led to the present plans for the reduction of prebreathe duration. Over the past decade, research has been directed towards an understanding of the biophysical basis of the formation and growth of the decompression gas phase with the goal of improving the efficiency of the EVA process. In the past, we have direct work towards a more complete understanding of gas bubble formation and growth and exercise-enhanced washout during oxygen prebreathe.

Photobiology of Symbiodinium revisited: bio-physical and bio-optical signatures

NASA Astrophysics Data System (ADS)

Hennige, S. J.; Suggett, D. J.; Warner, M. E.; McDougall, K. E.; Smith, D. J.

2009-03-01

Light is often the most abundant resource within the nutrient-poor waters surrounding coral reefs. Consequently, zooxanthellae ( Symbiodinium spp.) must continually photoacclimate to optimise productivity and ensure coral success. In situ coral photobiology is becoming dominated by routine assessments using state-of-the-art non-invasive bio-optical or chlorophyll a fluorescence (bio-physical) techniques. Multiple genetic types of Symbiodinium are now known to exist; however, little focus has been given as to how these types differ in terms of characteristics that are observable using these techniques. Therefore, this investigation aimed to revisit and expand upon a pivotal study by Iglesias-Prieto and Trench (1994) by comparing the photoacclimation characteristics of different Symbiodinium types based on their bio-physical (chlorophyll a fluorescence, reaction centre counts) and bio-optical (optical absorption, pigment concentrations) ‘signatures’. Signatures described here are unique to Symbiodinium type and describe phenotypic responses to set conditions, and hence are not suitable to describe taxonomic structure of in hospite Symbiodinium communities. In this study, eight Symbiodinium types from clades and sub-clades (A-B, F) were grown under two PFDs (Photon Flux Density) and examined. The photoacclimation response by Symbiodinium was highly variable between algal types for all bio-physical and for many bio-optical measurements; however, a general preference to modifying reaction centre content over effective antennae-absorption was observed. Certain bio-optically derived patterns, such as light absorption, were independent of algal type and, when considered per photosystem, were matched by reaction centre stoichiometry. Only by better understanding genotypic and phenotypic variability between Symbiodinium types can future studies account for the relative taxonomic and physiological contribution by Symbiodinium to coral acclimation.

Biophysical EPR Studies Applied to Membrane Proteins

PubMed Central

Sahu, Indra D; Lorigan, Gary A

2015-01-01

Membrane proteins are very important in controlling bioenergetics, functional activity, and initializing signal pathways in a wide variety of complicated biological systems. They also represent approximately 50% of the potential drug targets. EPR spectroscopy is a very popular and powerful biophysical tool that is used to study the structural and dynamic properties of membrane proteins. In this article, a basic overview of the most commonly used EPR techniques and examples of recent applications to answer pertinent structural and dynamic related questions on membrane protein systems will be presented. PMID:26855825

Single-molecule techniques in biophysics: a review of the progress in methods and applications.

PubMed

Miller, Helen; Zhou, Zhaokun; Shepherd, Jack; Wollman, Adam J M; Leake, Mark C

2018-02-01

Single-molecule biophysics has transformed our understanding of biology, but also of the physics of life. More exotic than simple soft matter, biomatter lives far from thermal equilibrium, covering multiple lengths from the nanoscale of single molecules to up to several orders of magnitude higher in cells, tissues and organisms. Biomolecules are often characterized by underlying instability: multiple metastable free energy states exist, separated by levels of just a few multiples of the thermal energy scale k B T, where k B is the Boltzmann constant and T absolute temperature, implying complex inter-conversion kinetics in the relatively hot, wet environment of active biological matter. A key benefit of single-molecule biophysics techniques is their ability to probe heterogeneity of free energy states across a molecular population, too challenging in general for conventional ensemble average approaches. Parallel developments in experimental and computational techniques have catalysed the birth of multiplexed, correlative techniques to tackle previously intractable biological questions. Experimentally, progress has been driven by improvements in sensitivity and speed of detectors, and the stability and efficiency of light sources, probes and microfluidics. We discuss the motivation and requirements for these recent experiments, including the underpinning mathematics. These methods are broadly divided into tools which detect molecules and those which manipulate them. For the former we discuss the progress of super-resolution microscopy, transformative for addressing many longstanding questions in the life sciences, and for the latter we include progress in 'force spectroscopy' techniques that mechanically perturb molecules. We also consider in silico progress of single-molecule computational physics, and how simulation and experimentation may be drawn together to give a more complete understanding. Increasingly, combinatorial techniques are now used, including

Single-molecule techniques in biophysics: a review of the progress in methods and applications

NASA Astrophysics Data System (ADS)

Miller, Helen; Zhou, Zhaokun; Shepherd, Jack; Wollman, Adam J. M.; Leake, Mark C.

2018-02-01

Single-molecule biophysics has transformed our understanding of biology, but also of the physics of life. More exotic than simple soft matter, biomatter lives far from thermal equilibrium, covering multiple lengths from the nanoscale of single molecules to up to several orders of magnitude higher in cells, tissues and organisms. Biomolecules are often characterized by underlying instability: multiple metastable free energy states exist, separated by levels of just a few multiples of the thermal energy scale k B T, where k B is the Boltzmann constant and T absolute temperature, implying complex inter-conversion kinetics in the relatively hot, wet environment of active biological matter. A key benefit of single-molecule biophysics techniques is their ability to probe heterogeneity of free energy states across a molecular population, too challenging in general for conventional ensemble average approaches. Parallel developments in experimental and computational techniques have catalysed the birth of multiplexed, correlative techniques to tackle previously intractable biological questions. Experimentally, progress has been driven by improvements in sensitivity and speed of detectors, and the stability and efficiency of light sources, probes and microfluidics. We discuss the motivation and requirements for these recent experiments, including the underpinning mathematics. These methods are broadly divided into tools which detect molecules and those which manipulate them. For the former we discuss the progress of super-resolution microscopy, transformative for addressing many longstanding questions in the life sciences, and for the latter we include progress in ‘force spectroscopy’ techniques that mechanically perturb molecules. We also consider in silico progress of single-molecule computational physics, and how simulation and experimentation may be drawn together to give a more complete understanding. Increasingly, combinatorial techniques are now used, including

Exact solutions of a two parameter flux model and cryobiological applications.

PubMed

Benson, James D; Chicone, Carmen C; Critser, John K

2005-06-01

Solute-solvent transmembrane flux models are used throughout biological sciences with applications in plant biology, cryobiology (transplantation and transfusion medicine), as well as circulatory and kidney physiology. Using a standard two parameter differential equation model of solute and solvent transmembrane flux described by Jacobs [The simultaneous measurement of cell permeability to water and to dissolved substances, J. Cell. Comp. Physiol. 2 (1932) 427-444], we determine the functions that describe the intracellular water volume and moles of intracellular solute for every time t and every set of initial conditions. Here, we provide several novel biophysical applications of this theory to important biological problems. These include using this result to calculate the value of cell volume excursion maxima and minima along with the time at which they occur, a novel result that is of significant relevance to the addition and removal of permeating solutes during cryopreservation. We also present a methodology that produces extremely accurate sum of squares estimates when fitting data for cellular permeability parameter values. Finally, we show that this theory allows a significant increase in both accuracy and speed of finite element methods for multicellular volume simulations, which has critical clinical biophysical applications in cryosurgical approaches to cancer treatment.

Biophysical and biological contributions of polyamine-coated carbon nanotubes and bidimensional buckypapers in the delivery of miRNAs to human cells.

PubMed

Celluzzi, Antonella; Paolini, Alessandro; D'Oria, Valentina; Risoluti, Roberta; Materazzi, Stefano; Pezzullo, Marco; Casciardi, Stefano; Sennato, Simona; Bordi, Federico; Masotti, Andrea

2018-01-01

Recent findings in nanomedicine have revealed that carbon nanotubes (CNTs) can be used as potential drug carriers, therapeutic agents and diagnostics tools. Moreover, due to their ability to cross cellular membranes, their nanosize dimension, high surface area and relatively good biocompatibility, CNTs have also been employed as a novel gene delivery vector system. In our previous work, we functionalized CNTs with two polyamine polymers, polyethyleneimine (PEI) and polyamidoamine dendrimer (PAMAM). These compounds have low cytotoxicity, ability to conjugate microRNAs (such as miR-503) and, at the same time, transfect efficiently endothelial cells. The parameters contributing to the good efficiency of transfection that we observed were not investigated in detail. In fact, the diameter and length of CNTs are important parameters to be taken into account when evaluating the effects on drug delivery efficiency. In order to investigate the biophysical and biological contributions of polymer-coated CNTs in delivery of miRNAs to human cells, we decided to investigate three different preparations, characterized by different dimensions and aspect ratios. In particular, we took into account very small CNTs, a suspension of CNTs starting from the commercial product and a 2D material based on CNTs (ie, buckypapers [BPs]) to examine the transfection efficiency of a rigid scaffold. In conclusion, we extensively investigated the biophysical and biological contributions of polyamine-coated CNTs and bidimensional BPs in the delivery of miRNAs to human cells, in order to optimize the transfection efficiency of these compounds to be employed as efficient drug delivery vectors in biomedical applications.

Developing a Physics Expert Identity in a Biophysics Research Group

ERIC Educational Resources Information Center

Rodriguez, Idaykis; Goertzen, Renee Michelle; Brewe, Eric; Kramer, Laird H.

2015-01-01

We investigate the development of expert identities through the use of the sociocultural perspective of learning as participating in a community of practice. An ethnographic case study of biophysics graduate students focuses on the experiences the students have in their research group meetings. The analysis illustrates how the communities of…

A historical forest management conundrum: do social and biophysical mix?

Treesearch

Heidi Bigler-Cole

2005-01-01

Forest managers face an array of prickly, seemingly intractable environmental problems. They have traditionally turned to the biophysical sciences to help gauge potential management effects, weigh alternatives, and set priorities. Over the past several decades, forest managers have watched management plans disintegrate in the face of grassroots-level protests, quarrels...

BIOPHYSICAL EVALUATION OF INDIVIDUAL COMPONENT LEVELS AND SELECTED CONFIGURATIONS OF THE UNITED STATES MARINE CORPS COLD-WEATHER CLOTHING ENSEMBLE

DTIC Science & Technology

2018-01-02

TECHNICAL REPORT NO. T18-01 DATE January 2018 BIOPHYSICAL EVALUATION OF INDIVIDUAL COMPONENT...USARIEM TECHNICAL REPORT T18-01 BIOPHYSICAL EVALUATION OF INDIVIDUAL COMPONENT LEVELS AND...OF TABLES Table Page Table 1. Clothing and individual equipment descriptions ................................................. 3 Table 2. Surface

Key management of the double random-phase-encoding method using public-key encryption

NASA Astrophysics Data System (ADS)

Saini, Nirmala; Sinha, Aloka

2010-03-01

Public-key encryption has been used to encode the key of the encryption process. In the proposed technique, an input image has been encrypted by using the double random-phase-encoding method using extended fractional Fourier transform. The key of the encryption process have been encoded by using the Rivest-Shamir-Adelman (RSA) public-key encryption algorithm. The encoded key has then been transmitted to the receiver side along with the encrypted image. In the decryption process, first the encoded key has been decrypted using the secret key and then the encrypted image has been decrypted by using the retrieved key parameters. The proposed technique has advantage over double random-phase-encoding method because the problem associated with the transmission of the key has been eliminated by using public-key encryption. Computer simulation has been carried out to validate the proposed technique.

Soil functional types: surveying the biophysical dimensions of soil security

NASA Astrophysics Data System (ADS)

Cécillon, Lauric; Barré, Pierre

2015-04-01

Soil is a natural capital that can deliver key ecosystem services (ES) to humans through the realization of a series of soil processes controlling ecosystem functioning. Soil is also a diverse and endangered natural resource. A huge pedodiversity has been described at all scales, which is strongly altered by global change. The multidimensional concept soil security, encompassing biophysical, economic, social, policy and legal frameworks of soils has recently been proposed, recognizing the role of soils in global environmental sustainability challenges. The biophysical dimensions of soil security focus on the functionality of a given soil that can be viewed as the combination of its capability and its condition [1]. Indeed, all soils are not equal in term of functionality. They show different processes, provide different ES to humans and respond specifically to global change. Knowledge of soil functionality in space and time is thus a crucial step towards the achievement soil security. All soil classification systems incorporate some functional information, but soil taxonomy alone cannot fully describe the functioning, limitations, resistance and resilience of soils. Droogers and Bouma [2] introduced functional variants (phenoforms) for each soil type (genoform) so as to fit more closely to soil functionality. However, different genoforms can have the same functionality. As stated by McBratney and colleagues [1], there is a great need of an agreed methodology for defining the reference state of soil functionality. Here, we propose soil functional types (SFT) as a relevant classification system for the biophysical dimensions of soil security. Following the definition of plant functional types widely used in ecology, we define a soil functional type as "a set of soil taxons or phenoforms sharing similar processes (e.g. soil respiration), similar effects on ecosystem functioning (e.g. primary productivity) and similar responses to global change (land-use, management or

Predictive biophysical modeling and understanding of the dynamics of mRNA translation and its evolution

PubMed Central

Zur, Hadas; Tuller, Tamir

2016-01-01

mRNA translation is the fundamental process of decoding the information encoded in mRNA molecules by the ribosome for the synthesis of proteins. The centrality of this process in various biomedical disciplines such as cell biology, evolution and biotechnology, encouraged the development of dozens of mathematical and computational models of translation in recent years. These models aimed at capturing various biophysical aspects of the process. The objective of this review is to survey these models, focusing on those based and/or validated on real large-scale genomic data. We consider aspects such as the complexity of the models, the biophysical aspects they regard and the predictions they may provide. Furthermore, we survey the central systems biology discoveries reported on their basis. This review demonstrates the fundamental advantages of employing computational biophysical translation models in general, and discusses the relative advantages of the different approaches and the challenges in the field. PMID:27591251

The value of mechanistic biophysical information for systems-level understanding of complex biological processes such as cytokinesis.

PubMed

Pollard, Thomas D

2014-12-02

This review illustrates the value of quantitative information including concentrations, kinetic constants and equilibrium constants in modeling and simulating complex biological processes. Although much has been learned about some biological systems without these parameter values, they greatly strengthen mechanistic accounts of dynamical systems. The analysis of muscle contraction is a classic example of the value of combining an inventory of the molecules, atomic structures of the molecules, kinetic constants for the reactions, reconstitutions with purified proteins and theoretical modeling to account for the contraction of whole muscles. A similar strategy is now being used to understand the mechanism of cytokinesis using fission yeast as a favorable model system. Copyright © 2014 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Experiences Gained Creating a Biophysics Major at a Predominately Undergraduate Institution

NASA Astrophysics Data System (ADS)

Link, Justin; Herbert, Steven

2014-03-01

Xavier University, a liberal arts predominately undergraduate institution (PUI) located in Cincinnati, OH, implemented a Biophysics major in the Department of Physics in spring 2012. The program is built upon foundational physics courses and is unique due to the possible selection of upper-division courses that students elect to take towards their undergraduate degree. A capstone course is offered to bring all prior knowledge in the fundamental sciences together to approach complex problems in biology. Due to the flexibility of the program, it serves students well who are interested in pursuing advanced degrees in Biophysics or Biomedical Engineering. It also offers students interested in the health professions an alternate path towards medical school which can be advantageous in the application process. This session will express some of the advantages and challenges to creating such a program at a liberal arts PUI and discuss the capstone course within the major.

Biophysical basis for the geometry of conical stromatolites.

PubMed

Petroff, Alexander P; Sim, Min Sub; Maslov, Andrey; Krupenin, Mikhail; Rothman, Daniel H; Bosak, Tanja

2010-06-01

Stromatolites may be Earth's oldest macroscopic fossils; however, it remains controversial what, if any, biological processes are recorded in their morphology. Although the biological interpretation of many stromatolite morphologies is confounded by the influence of sedimentation, conical stromatolites form in the absence of sedimentation and are, therefore, considered to be the most robust records of biophysical processes. A qualitative similarity between conical stromatolites and some modern microbial mats suggests a photosynthetic origin for ancient stromatolites. To better understand and interpret ancient fossils, we seek a quantitative relationship between the geometry of conical stromatolites and the biophysical processes that control their growth. We note that all modern conical stromatolites and many that formed in the last 2.8 billion years display a characteristic centimeter-scale spacing between neighboring structures. To understand this prominent-but hitherto uninterpreted-organization, we consider the role of diffusion in mediating competition between stromatolites. Having confirmed this model through laboratory experiments and field observation, we find that organization of a field of stromatolites is set by a diffusive time scale over which individual structures compete for nutrients, thus linking form to physiology. The centimeter-scale spacing between modern and ancient stromatolites corresponds to a rhythmically fluctuating metabolism with a period of approximately 20 hr. The correspondence between the observed spacing and the day length provides quantitative support for the photosynthetic origin of conical stromatolites throughout geologic time.

Key parameters of the sediment surface morphodynamics in an estuary - An assessment of model solutions

NASA Astrophysics Data System (ADS)

Sampath, D. M. R.; Boski, T.

2018-05-01

Large-scale geomorphological evolution of an estuarine system was simulated by means of a hybrid estuarine sedimentation model (HESM) applied to the Guadiana Estuary, in Southwest Iberia. The model simulates the decadal-scale morphodynamics of the system under environmental forcing, using a set of analytical solutions to simplified equations of tidal wave propagation in shallow waters, constrained by empirical knowledge of estuarine sedimentary dynamics and topography. The key controlling parameters of the model are bed friction (f), current velocity power of the erosion rate function (N), and sea-level rise rate. An assessment of sensitivity of the simulated sediment surface elevation (SSE) change to these controlling parameters was performed. The model predicted the spatial differentiation of accretion and erosion, the latter especially marked in the mudflats within mean sea level and low tide level and accretion was mainly in a subtidal channel. The average SSE change mutually depended on both the friction coefficient and power of the current velocity. Analysis of the average annual SSE change suggests that the state of intertidal and subtidal compartments of the estuarine system vary differently according to the dominant processes (erosion and accretion). As the Guadiana estuarine system shows dominant erosional behaviour in the context of sea-level rise and sediment supply reduction after the closure of the Alqueva Dam, the most plausible sets of parameter values for the Guadiana Estuary are N = 1.8 and f = 0.8f0, or N = 2 and f = f0, where f0 is the empirically estimated value. For these sets of parameter values, the relative errors in SSE change did not exceed ±20% in 73% of simulation cells in the studied area. Such a limit of accuracy can be acceptable for an idealized modelling of coastal evolution in response to uncertain sea-level rise scenarios in the context of reduced sediment supply due to flow regulation. Therefore, the idealized but cost

Interpreting landscape change: measured biophysical change and surrounding social context

Treesearch

Mimi M. Wagner; Paul H. Gobster

2007-01-01

Although research assessing both biophysical landscape conditions and social perceptions provide critical data on change, these methods are seldom integrated. In this study, we examined landscape change in the Central Iowa region by pairing quantitative data on changes to natural areas, streams, and housing density over the past 60 years with a qualitative social...

Talk to the Hand: U.S. Army Biophysical Testing.

PubMed

Santee, William R; Potter, Adam W; Friedl, Karl E

2017-07-01

Many people are unaware of the science underlying the biophysical properties of Soldier clothing and personal protective equipment, yet there is a well-refined biomedical methodology initiated by Army physiologists in World War II. This involves a methodical progression of systematic material testing technologies, computer modeling, and human testing that enables more efficient development and rapid evaluation of new concepts for Soldier health and performance. Sophisticated manikins that sweat and move are a central part of this testing continuum. This report briefly summarizes the evolution and use of one specialized form of the manikin technologies, the thermal hand model, and its use in research on Soldier hand-wear items that sustain dexterity and protect the hand in extreme environments. Thermal manikin testing methodologies were developed to provide an efficient and consistent analytical tool for the rapid evaluation of new clothing concepts. These methods have been upgraded since the original World War II and Korean War eras to include articulation and sweating capabilities, as characterized and illustrated in this article. The earlier "retired" versions of thermal hand models have now been transferred to the National Museum of Health and Science. The biophysical values from manikin testing are critical inputs to the U.S. Army Research Institute of Environmental Medicine mathematical models that provide predictions of soldier comfort, duration of exposure before loss of manual dexterity, and time to significant risk of freezing (skin temperature <-1°C) and nonfreezing cold injuries (skin temperature <5°C). The greater thickness of better insulated handwear reduces dexterity and also increases surface area which makes added insulation increasingly less effective in retaining heat. Measurements of both thermal resistance (insulation) and evaporative resistance (permeability) collectively characterize the biophysical properties and enable mathematical

Bio-Physics Manifesto -- for the Future of Physics and Biology

NASA Astrophysics Data System (ADS)

Oono, Y.

2008-04-01

The Newtonian revolution taught us how to dissect phenomena into contingencies (e.g., initial conditions) and fundamental laws (e.g., equations of motion). Since then, `fundamental physics' has been pursuing purer and leaner fundamental laws. Consequently, to explain real phenomena a lot of auxiliary conditions become required. Isn't it now the time to start studying `auxiliary conditions' seriously? The study of biological systems has a possibility of shedding light on this neglected side of phenomena in physics, because we organisms were constructed by our parents who supplied indispensable auxiliary conditions; we never self-organize. Thus, studying the systems lacking self-organizing capability (such as complex systems) may indicate new directions to physics and biology (biophysics). There have been attempts to construct a `general theoretical framework' of biology, but most of them never seriously looked at the actual biological world. Every serious natural science must start with establishing a phenomenological framework. Therefore, this must be the main part of bio-physics. However, this article is addressed mainly to theoretical physicists and discusses only certain theoretical aspects (with real illustrative examples).

High-resolution biophysical analysis of the dynamics of nucleosome formation

PubMed Central

Hatakeyama, Akiko; Hartmann, Brigitte; Travers, Andrew; Nogues, Claude; Buckle, Malcolm

2016-01-01

We describe a biophysical approach that enables changes in the structure of DNA to be followed during nucleosome formation in in vitro reconstitution with either the canonical “Widom” sequence or a judiciously mutated sequence. The rapid non-perturbing photochemical analysis presented here provides ‘snapshots’ of the DNA configuration at any given moment in time during nucleosome formation under a very broad range of reaction conditions. Changes in DNA photochemical reactivity upon protein binding are interpreted as being mainly induced by alterations in individual base pair roll angles. The results strengthen the importance of the role of an initial (H3/H4)2 histone tetramer-DNA interaction and highlight the modulation of this early event by the DNA sequence. (H3/H4)2 binding precedes and dictates subsequent H2A/H2B-DNA interactions, which are less affected by the DNA sequence, leading to the final octameric nucleosome. Overall, our results provide a novel, exciting way to investigate those biophysical properties of DNA that constitute a crucial component in nucleosome formation and stabilization. PMID:27263658

Estimation of Key Parameters of the Coupled Energy and Water Model by Assimilating Land Surface Data

NASA Astrophysics Data System (ADS)

Abdolghafoorian, A.; Farhadi, L.

2017-12-01

Accurate estimation of land surface heat and moisture fluxes, as well as root zone soil moisture, is crucial in various hydrological, meteorological, and agricultural applications. Field measurements of these fluxes are costly and cannot be readily scaled to large areas relevant to weather and climate studies. Therefore, there is a need for techniques to make quantitative estimates of heat and moisture fluxes using land surface state observations that are widely available from remote sensing across a range of scale. In this work, we applies the variational data assimilation approach to estimate land surface fluxes and soil moisture profile from the implicit information contained Land Surface Temperature (LST) and Soil Moisture (SM) (hereafter the VDA model). The VDA model is focused on the estimation of three key parameters: 1- neutral bulk heat transfer coefficient (CHN), 2- evaporative fraction from soil and canopy (EF), and 3- saturated hydraulic conductivity (Ksat). CHN and EF regulate the partitioning of available energy between sensible and latent heat fluxes. Ksat is one of the main parameters used in determining infiltration, runoff, groundwater recharge, and in simulating hydrological processes. In this study, a system of coupled parsimonious energy and water model will constrain the estimation of three unknown parameters in the VDA model. The profile of SM (LST) at multiple depths is estimated using moisture diffusion (heat diffusion) equation. In this study, the uncertainties of retrieved unknown parameters and fluxes are estimated from the inverse of Hesian matrix of cost function which is computed using the Lagrangian methodology. Analysis of uncertainty provides valuable information about the accuracy of estimated parameters and their correlation and guide the formulation of a well-posed estimation problem. The results of proposed algorithm are validated with a series of experiments using a synthetic data set generated by the simultaneous heat and

Unbounded and revocable hierarchical identity-based encryption with adaptive security, decryption key exposure resistant, and short public parameters

PubMed Central

Wang, Baosheng; Tao, Jing

2018-01-01

Revocation functionality and hierarchy key delegation are two necessary and crucial requirements to identity-based cryptosystems. Revocable hierarchical identity-based encryption (RHIBE) has attracted a lot of attention in recent years, many RHIBE schemes have been proposed but shown to be either insecure or bounded where they have to fix the maximum hierarchical depth of RHIBE at setup. In this paper, we propose a new unbounded RHIBE scheme with decryption key exposure resilience and with short public system parameters, and prove our RHIBE scheme to be adaptively secure. Our system model is scalable inherently to accommodate more levels of user adaptively with no adding workload or restarting the system. By carefully designing the hybrid games, we overcome the subtle obstacle in applying the dual system encryption methodology for the unbounded and revocable HIBE. To the best of our knowledge, this is the first construction of adaptively secure unbounded RHIBE scheme. PMID:29649326

Micromachined piconewton force sensor for biophysics investigations

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

Koch, Steven J.; Thayer, Gayle E.; Corwin, Alex D.

2006-10-23

We describe a micromachined force sensor that is able to measure forces as small as 1 pN in both air and water. First, we measured the force field produced by an electromagnet on individual 2.8 {mu}m magnetic beads glued to the sensor. By repeating with 11 different beads, we measured a 9% standard deviation in saturation magnetization. We next demonstrated that the sensor was fully functional when immersed in physiological buffer. These results show that the force sensors can be useful for magnetic force calibration and also for measurement of biophysical forces on chip.

Development of an Agent-Based Model (ABM) to Simulate the Immune System and Integration of a Regression Method to Estimate the Key ABM Parameters by Fitting the Experimental Data

PubMed Central

Tong, Xuming; Chen, Jinghang; Miao, Hongyu; Li, Tingting; Zhang, Le

2015-01-01

Agent-based models (ABM) and differential equations (DE) are two commonly used methods for immune system simulation. However, it is difficult for ABM to estimate key parameters of the model by incorporating experimental data, whereas the differential equation model is incapable of describing the complicated immune system in detail. To overcome these problems, we developed an integrated ABM regression model (IABMR). It can combine the advantages of ABM and DE by employing ABM to mimic the multi-scale immune system with various phenotypes and types of cells as well as using the input and output of ABM to build up the Loess regression for key parameter estimation. Next, we employed the greedy algorithm to estimate the key parameters of the ABM with respect to the same experimental data set and used ABM to describe a 3D immune system similar to previous studies that employed the DE model. These results indicate that IABMR not only has the potential to simulate the immune system at various scales, phenotypes and cell types, but can also accurately infer the key parameters like DE model. Therefore, this study innovatively developed a complex system development mechanism that could simulate the complicated immune system in detail like ABM and validate the reliability and efficiency of model like DE by fitting the experimental data. PMID:26535589

Finite-key analysis for measurement-device-independent quantum key distribution.

PubMed

Curty, Marcos; Xu, Feihu; Cui, Wei; Lim, Charles Ci Wen; Tamaki, Kiyoshi; Lo, Hoi-Kwong

2014-04-29

Quantum key distribution promises unconditionally secure communications. However, as practical devices tend to deviate from their specifications, the security of some practical systems is no longer valid. In particular, an adversary can exploit imperfect detectors to learn a large part of the secret key, even though the security proof claims otherwise. Recently, a practical approach--measurement-device-independent quantum key distribution--has been proposed to solve this problem. However, so far its security has only been fully proven under the assumption that the legitimate users of the system have unlimited resources. Here we fill this gap and provide a rigorous security proof against general attacks in the finite-key regime. This is obtained by applying large deviation theory, specifically the Chernoff bound, to perform parameter estimation. For the first time we demonstrate the feasibility of long-distance implementations of measurement-device-independent quantum key distribution within a reasonable time frame of signal transmission.

Selection of Hyperspectral Narrowbands (HNBs) and Composition of Hyperspectral Twoband Vegetation Indices (HVIs) for Biophysical Characterization and Discrimination of Crop Types Using Field Reflectance and Hyperion-EO-1 Data

NASA Technical Reports Server (NTRS)

Thenkabail, Prasad S.; Mariotto, Isabella; Gumma, Murali Krishna; Middleton, Elizabeth M.; Landis, David R.; Huemmrich, K. Fred

2013-01-01

.g., biophysical characterization of crops). The findings of this study will make a significant contribution to future hyperspectral missions such as NASA's HyspIRI. Index Terms-Hyperion, field reflectance, imaging spectroscopy, HyspIRI, biophysical parameters, hyperspectral vegetation indices, hyperspectral narrowbands, broadbands.

Characterization of oily mature skin by biophysical and skin imaging techniques.

PubMed

de Melo, M O; Maia Campos, P M B G

2018-02-13

The skin is a complex biological system and may suffer change according to the environmental factors, as higher temperatures can increase sebum excretion, presenting oiliness and acne. These alterations can persist during the aging and provoke more changes in aged skin. In this study we evaluated the mature oily skin characteristics using biophysical and skin imaging techniques. Sixty healthy female subjects, aged between 39 and 55 years old were recruited and separated into 2 groups according to their skin type: normal/dry and oily skin. The skin was evaluated in terms of stratum corneum water content, transepidermal water loss (TEWL) sebum content, dermis thickness and echogenicity, skin microrelief, and pores content. The mature oily skin presented no significant differences when compared to the normal/dry skin on the stratum corneum water content and TEWL parameters. The sebum content was significantly higher on the oily skin group. The microrelief analysis showed an increase of skin roughness values in the oily skin and increase of scaliness in the normal/dry skin. The oily skin showed lower dermis echogenicity mainly in the frontal region and higher dermis thickness when compared to normal/dry skin. The mature oily skin showed different characteristics from normal/dry skin in terms of sebum content, microrelief parameters, and dermis thickness. This way, the characterization of mature oily skin in an objective way is very important to development of dermocosmetic products for more effective treatments focused specially on this type of skin. © 2018 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

The Biophysics Microgravity Initiative

NASA Technical Reports Server (NTRS)

Gorti, S.

2016-01-01

Biophysical microgravity research on the International Space Station using biological materials has been ongoing for several decades. The well-documented substantive effects of long duration microgravity include the facilitation of the assembly of biological macromolecules into large structures, e.g., formation of large protein crystals under micro-gravity. NASA is invested not only in understanding the possible physical mechanisms of crystal growth, but also promoting two flight investigations to determine the influence of µ-gravity on protein crystal quality. In addition to crystal growth, flight investigations to determine the effects of shear on nucleation and subsequent formation of complex structures (e.g., crystals, fibrils, etc.) are also supported. It is now considered that long duration microgravity research aboard the ISS could also make possible the formation of large complex biological and biomimetic materials. Investigations of various materials undergoing complex structure formation in microgravity will not only strengthen NASA science programs, but may also provide invaluable insight towards the construction of large complex tissues, organs, or biomimetic materials on Earth.

Key Physiological Parameters Dictate Triggering of Activity-Dependent Bulk Endocytosis in Hippocampal Synapses

PubMed Central

Wenzel, Eva M.; Morton, Andrew; Ebert, Katrin; Welzel, Oliver; Kornhuber, Johannes; Cousin, Michael A.; Groemer, Teja W.

2012-01-01

To maintain neurotransmission in central neurons, several mechanisms are employed to retrieve synaptically exocytosed membrane. The two major modes of synaptic vesicle (SV) retrieval are clathrin-mediated endocytosis and activity-dependent bulk endocytosis (ADBE). ADBE is the dominant SV retrieval mode during intense stimulation, however the precise physiological conditions that trigger this mode are not resolved. To determine these parameters we manipulated rat hippocampal neurons using a wide spectrum of stimuli by varying both the pattern and duration of stimulation. Using live-cell fluorescence imaging and electron microscopy approaches, we established that stimulation frequency, rather than the stimulation load, was critical in the triggering of ADBE. Thus two hundred action potentials, when delivered at high frequency, were sufficient to induce near maximal bulk formation. Furthermore we observed a strong correlation between SV pool size and ability to perform ADBE. We also identified that inhibitory nerve terminals were more likely to utilize ADBE and had a larger SV recycling pool. Thus ADBE in hippocampal synaptic terminals is tightly coupled to stimulation frequency and is more likely to occur in terminals with large SV pools. These results implicate ADBE as a key modulator of both hippocampal neurotransmission and plasticity. PMID:22675521

Elucidating the molecular mechanisms underlying cellular response to biophysical cues using synthetic biology approaches

PubMed Central

Denning, Denise; Roos, Wouter H.

2016-01-01

ABSTRACT The use of synthetic surfaces and materials to influence and study cell behavior has vastly progressed our understanding of the underlying molecular mechanisms involved in cellular response to physicochemical and biophysical cues. Reconstituting cytoskeletal proteins and interfacing them with a defined microenvironment has also garnered deep insight into the engineering mechanisms existing within the cell. This review presents recent experimental findings on the influence of several parameters of the extracellular environment on cell behavior and fate, such as substrate topography, stiffness, chemistry and charge. In addition, the use of synthetic environments to measure physical properties of the reconstituted cytoskeleton and their interaction with intracellular proteins such as molecular motors is discussed, which is relevant for understanding cell migration, division and structural integrity, as well as intracellular transport. Insight is provided regarding the next steps to be taken in this interdisciplinary field, in order to achieve the global aim of artificially directing cellular response. PMID:27266767

Modelling the influence of land-use changes on biophysical and biochemical interactions at regional and global scales.

PubMed

Devaraju, N; Bala, G; Nemani, R

2015-09-01

Land-use changes since the start of the industrial era account for nearly one-third of the cumulative anthropogenic CO2 emissions. In addition to the greenhouse effect of CO2 emissions, changes in land use also affect climate via changes in surface physical properties such as albedo, evapotranspiration and roughness length. Recent modelling studies suggest that these biophysical components may be comparable with biochemical effects. In regard to climate change, the effects of these two distinct processes may counterbalance one another both regionally and, possibly, globally. In this article, through hypothetical large-scale deforestation simulations using a global climate model, we contrast the implications of afforestation on ameliorating or enhancing anthropogenic contributions from previously converted (agricultural) land surfaces. Based on our review of past studies on this subject, we conclude that the sum of both biophysical and biochemical effects should be assessed when large-scale afforestation is used for countering global warming, and the net effect on global mean temperature change depends on the location of deforestation/afforestation. Further, although biochemical effects trigger global climate change, biophysical effects often cause strong local and regional climate change. The implication of the biophysical effects for adaptation and mitigation of climate change in agriculture and agroforestry sectors is discussed. © 2014 John Wiley & Sons Ltd.

Spatial Variations in CO2 Mixing Ratios Over a Heterogenous Landscape - Linking Airborne Measurements With Remote Sensing Derived Biophysical Parameters

NASA Astrophysics Data System (ADS)

Choi, Y.; Vadrevu, K. P.; Vay, S. A.; Woo, J.

2006-12-01

North American terrestrial ecosystems are major sources and sinks of carbon. Precise measurement of atmospheric CO2 concentrations plays an important role in the development and testing of carbon cycle models quantifying the influence of terrestrial CO2 exchange on the North American carbon budget. During the summer 2004 Intercontinental Chemical Transport Experiment North America (INTEX-NA) campaign, regional scale in-situ measurements of atmospheric CO2 were made from the NASA DC-8 affording the opportunity to explore how land surface heterogeneity relates to the airborne observations utilizing remote-sensing data products and GIS-based methods. These 1 Hz data reveal the seasonal biospheric uptake of CO2 over portions of the U.S. continent, especially east of 90°W below 2 km, compared to higher mixing ratios over water as well as within the upper troposphere where well-mixed, aged air masses were sampled. In this study, we use several remote sensing derived biophysical parameters from the LANDSAT, NOAA AVHRR, and MODIS sensors to specify spatiotemporal patterns of land use cover and vegetation characteristics for linking the airborne measurements of CO2 data with terrestrial sources of carbon. Also, CO2 flux footprint outputs from a 3-D Lagrangian atmospheric model have been integrated with satellite remote sensing data to infer CO2 variations across heterogeneous landscapes. In examining the landscape mosaic utilizing these available tools, preliminary results suggest that the lowest CO2 mixing ratios observed during INTEX-NA were over agricultural fields in Illinois dominated by corn then secondarily soybean crops. Low CO2 concentrations are attributable to sampling during the peak growing season over such C4 plants as corn having a higher photosynthetic rate via the C4-dicarboxylic acid pathway of carbon fixation compared to C3 plants such as soybeans. In addition to LANDSAT derived land cover data, results from comparisons of the airborne CO2 observations

The logic of comparative life history studies for estimating key parameters, with a focus on natural mortality rate

USGS Publications Warehouse

Hoenig, John M; Then, Amy Y.-H.; Babcock, Elizabeth A.; Hall, Norman G.; Hewitt, David A.; Hesp, Sybrand A.

2016-01-01

There are a number of key parameters in population dynamics that are difficult to estimate, such as natural mortality rate, intrinsic rate of population growth, and stock-recruitment relationships. Often, these parameters of a stock are, or can be, estimated indirectly on the basis of comparative life history studies. That is, the relationship between a difficult to estimate parameter and life history correlates is examined over a wide variety of species in order to develop predictive equations. The form of these equations may be derived from life history theory or simply be suggested by exploratory data analysis. Similarly, population characteristics such as potential yield can be estimated by making use of a relationship between the population parameter and bio-chemico–physical characteristics of the ecosystem. Surprisingly, little work has been done to evaluate how well these indirect estimators work and, in fact, there is little guidance on how to conduct comparative life history studies and how to evaluate them. We consider five issues arising in such studies: (i) the parameters of interest may be ill-defined idealizations of the real world, (ii) true values of the parameters are not known for any species, (iii) selecting data based on the quality of the estimates can introduce a host of problems, (iv) the estimates that are available for comparison constitute a non-random sample of species from an ill-defined population of species of interest, and (v) the hierarchical nature of the data (e.g. stocks within species within genera within families, etc., with multiple observations at each level) warrants consideration. We discuss how these issues can be handled and how they shape the kinds of questions that can be asked of a database of life history studies.

Riparian influences on the biophysical characteristics of seston in headwater streams.

Treesearch

Scott R. Elliott; Robert J. Naiman; Peter A. Bisson

2004-01-01

Suspended particles (seston) in streams are an important source of nutrition for many invertebrates, forming a strong trophic link between plant and animal production. In forested regions the management of riparian corridors may alter alloehthonous and autochthonous contributions to streams, ultimately changing the biophysical characteristics of seston. This article...

Using biophysical models to manage nitrogen pollution from agricultural sources: Utopic or realistic approach for non-scientist users? Case study of a drinking water catchment area in Lorraine, France.

PubMed

Bernard, Pierre-Yves; Benoît, Marc; Roger-Estrade, Jean; Plantureux, Sylvain

2016-12-01

The objectives of this comparison of two biophysical models of nitrogen losses were to evaluate first whether results were similar and second whether both were equally practical for use by non-scientist users. Results were obtained with the crop model STICS and the environmental model AGRIFLUX based on nitrogen loss simulations across a small groundwater catchment area (<1 km(2)) located in the Lorraine region in France. Both models simulate the influences of leaching and cropping systems on nitrogen losses in a relevant manner. The authors conclude that limiting the simulations to areas where soils with a greater risk of leaching cover a significant spatial extent would likely yield acceptable results because those soils have more predictable leaching of nitrogen. In addition, the choice of an environmental model such as AGRIFLUX which requires fewer parameters and input variables seems more user-friendly for agro-environmental assessment. The authors then discuss additional challenges for non-scientists such as lack of parameter optimization, which is essential to accurately assessing nitrogen fluxes and indirectly not to limit the diversity of uses of simulated results. Despite current restrictions, with some improvement, biophysical models could become useful environmental assessment tools for non-scientists. Copyright © 2016 Elsevier Ltd. All rights reserved.

6th International Conference on Biophysics & Synchrotron Radiation. Final report

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

Moffat, Keith

1999-08-03

The 6th International Conference on Biophysics and Synchrotron Rdiation was held at the Advanced Photon Source, Argonne National Laboratory, from August 4-8, 1998, with pre-conference activities on August 3. Over 300 attendees and 65 presenters participated in the conference that was collaboratively hosted by the University of Chicago, Center for Advanced Radiation Sources and the Advanced Photon Source.

Age of oil palm plantations causes a strong change in surface biophysical variables

NASA Astrophysics Data System (ADS)

Sabajo, Clifton; le Maire, Guerric; Knohl, Alexander

2016-04-01

Over the last decades, Indonesia has experienced dramatic land transformations with an expansion of oil palm plantations at the expense of tropical forests. As vegetation is a modifier of the climate near the ground these large-scale land transformations are expected to have major impacts on the surface biophysical variables i.e. surface temperature, albedo, and vegetation indices, e.g. the NDVI. Remote sensing data are needed to assess such changes at regional scale. We used 2 Landsat images from Jambi Province in Sumatra/Indonesia covering a chronosequence of oil palm plantations to study the 20 - 25 years life cycle of oil palm plantations and its relation with biophysical variables. Our results show large differences between the surface temperature of young oil palm plantations and forest (up to 9.5 ± 1.5 °C) indicating that the surface temperature is raised substantially after the establishment of oil palm plantations following the removal of forests. During the oil palm plantation lifecycle the surface temperature differences gradually decreases and approaches zero around an oil palm plantation age of 10 years. Similarly, NDVI increases and the albedo decreases approaching typical values of forests. Our results show that in order to assess the full climate effects of oil palm expansion biophysical processes play an important role and the full life cycle of oil palm plantations need to be considered.

Biophysical aspects of human thermoregulation during heat stress.

PubMed

Cramer, Matthew N; Jay, Ollie

2016-04-01

Humans maintain a relatively constant core temperature through the dynamic balance between endogenous heat production and heat dissipation to the surrounding environment. In response to metabolic or environmental disturbances to heat balance, the autonomic nervous system initiates cutaneous vasodilation and eccrine sweating to facilitate higher rates of dry (primarily convection and radiation) and evaporative transfer from the body surface; however, absolute heat losses are ultimately governed by the properties of the skin and the environment. Over the duration of a heat exposure, the cumulative imbalance between heat production and heat dissipation leads to body heat storage, but the consequent change in core temperature, which has implications for health and safety in occupational and athletic settings particularly among certain clinical populations, involves a complex interaction between changes in body heat content and the body's morphological characteristics (mass, surface area, and tissue composition) that collectively determine the body's thermal inertia. The aim of this review is to highlight the biophysical aspects of human core temperature regulation by outlining the principles of human energy exchange and examining the influence of body morphology during exercise and environmental heat stress. An understanding of the biophysical factors influencing core temperature will enable researchers and practitioners to better identify and treat individuals/populations most vulnerable to heat illness and injury during exercise and extreme heat events. Further, appropriate guidelines may be developed to optimize health, safety, and work performance during heat stress. Copyright © 2016 Elsevier B.V. All rights reserved.

Finite-key analysis for quantum key distribution with weak coherent pulses based on Bernoulli sampling

NASA Astrophysics Data System (ADS)

Kawakami, Shun; Sasaki, Toshihiko; Koashi, Masato

2017-07-01

An essential step in quantum key distribution is the estimation of parameters related to the leaked amount of information, which is usually done by sampling of the communication data. When the data size is finite, the final key rate depends on how the estimation process handles statistical fluctuations. Many of the present security analyses are based on the method with simple random sampling, where hypergeometric distribution or its known bounds are used for the estimation. Here we propose a concise method based on Bernoulli sampling, which is related to binomial distribution. Our method is suitable for the Bennett-Brassard 1984 (BB84) protocol with weak coherent pulses [C. H. Bennett and G. Brassard, Proceedings of the IEEE Conference on Computers, Systems and Signal Processing (IEEE, New York, 1984), Vol. 175], reducing the number of estimated parameters to achieve a higher key generation rate compared to the method with simple random sampling. We also apply the method to prove the security of the differential-quadrature-phase-shift (DQPS) protocol in the finite-key regime. The result indicates that the advantage of the DQPS protocol over the phase-encoding BB84 protocol in terms of the key rate, which was previously confirmed in the asymptotic regime, persists in the finite-key regime.

6th international conference on biophysics and synchrotron radiation. Program/Abstracts

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

Pittroff, Connie; Strasser, Susan Barr

1999-08-03

This STI product consists of the Program/Abstracts book that was prepared for the participants in the Sixth International Conference on Biophysics and Synchrotron Radiation that was held August 4-8, 1998, at the Advanced Photon Source, Argonne National Laboratory. This book contains the full conference program and abstracts of the scientific presentations.

Testing the Simple Biosphere model (SiB) using point micrometeorological and biophysical data

NASA Technical Reports Server (NTRS)

Sellers, P. J.; Dorman, J. L.

1987-01-01

The suitability of the Simple Biosphere (SiB) model of Sellers et al. (1986) for calculation of the surface fluxes for use within general circulation models is assessed. The structure of the SiB model is described, and its performance is evaluated in terms of its ability to realistically and accurately simulate biophysical processes over a number of test sites, including Ruthe (Germany), South Carolina (U.S.), and Central Wales (UK), for which point biophysical and micrometeorological data were available. The model produced simulations of the energy balances of barley, wheat, maize, and Norway Spruce sites over periods ranging from 1 to 40 days. Generally, it was found that the model reproduced time series of latent, sensible, and ground-heat fluxes and surface radiative temperature comparable with the available data.

A synthesized biophysical and social vulnerability assessment for Taiwan

NASA Astrophysics Data System (ADS)

Lee, Yung-Jaan

2017-11-01

Taiwan, located in the Western Pacific, is a country that is one of the most vulnerable to disasters that are associated with the changing climate; it is located within the Ring of Fire, which is the most geologically active region in the world. The environmental and geological conditions in Taiwan are sensitive and vulnerable to such disasters. Owing to increasing urbanization in Taiwan, floods and climate-related disasters have taken an increasing toll on human lives. As global warming accelerates the rising of sea levels and increasing of the frequency of extreme weather events, disasters will continue to affect socioeconomic development and human conditions. Under such circumstances, researchers and policymakers alike must recognize the importance of providing useful knowledge concerning vulnerability, disaster recovery and resilience. Strategies for reducing vulnerability and climate-related disaster risks and for increasing resilience involve preparedness, mitigation and adaptation. In the last two decades, extreme climate events have caused severe flash floods, debris flows, landslides, and other disasters and have had negative effects of many sectors, including agriculture, infrastructure and health. Since climate change is expected to have a continued impact on socio-economic development, this work develops a vulnerability assessment framework that integrates both biophysical and social vulnerability and supports synthesized vulnerability analyses to identify vulnerable areas in Taiwan. Owing to its geographical, geological and climatic features, Taiwan is susceptible to earthquakes, typhoons, droughts and various induced disasters. Therefore, Taiwan has the urgent task of establishing a framework for assessing vulnerability as a planning and policy tool that can be used to identify not only the regions that require special attention but also hotspots in which efforts should be made to reduce vulnerability and the risk of climate-related disaster. To

Biophysical and X-ray crystallographic analysis of Mps1 kinase inhibitor complexes.

PubMed

Chu, Matthew L H; Lang, Zhaolei; Chavas, Leonard M G; Neres, João; Fedorova, Olga S; Tabernero, Lydia; Cherry, Mike; Williams, David H; Douglas, Kenneth T; Eyers, Patrick A

2010-03-02

The dual-specificity protein kinase monopolar spindle 1 (Mps1) is a central component of the mitotic spindle assembly checkpoint (SAC), a sensing mechanism that prevents anaphase until all chromosomes are bioriented on the metaphase plate. Partial depletion of Mps1 protein levels sensitizes transformed, but not untransformed, human cells to therapeutic doses of the anticancer agent Taxol, making it an attractive novel therapeutic cancer target. We have previously determined the X-ray structure of the catalytic domain of human Mps1 in complex with the anthrapyrazolone kinase inhibitor SP600125. In order to validate distinct inhibitors that target this enzyme and improve our understanding of nucleotide binding site architecture, we now report a biophysical and structural evaluation of the Mps1 catalytic domain in the presence of ATP and the aspecific model kinase inhibitor staurosporine. Collective in silico, enzymatic, and fluorescent screens also identified several new lead quinazoline Mps1 inhibitors, including a low-affinity compound termed Compound 4 (Cpd 4), whose interaction with the Mps1 kinase domain was further characterized by X-ray crystallography. A novel biophysical analysis demonstrated that the intrinsic fluorescence of SP600125 changed markedly upon Mps1 binding, allowing spectrophotometric displacement analysis and determination of dissociation constants for ATP-competitive Mps1 inhibitors. By illuminating the structure of the Mps1 ATP-binding site our results provide novel biophysical insights into Mps1-ligand interactions that will be useful for the development of specific Mps1 inhibitors, including those employing a therapeutically validated quinazoline template.

Determining Biophysical Controls on Forest Structure using Hyperspatial Satellite Imagery and Ecological Gradient Modeling

NASA Astrophysics Data System (ADS)

Dobrowski, S. Z.; Greenberg, J. A.; Schladow, G.

2006-12-01

There is evidence from the Sierra Nevada that sub-alpine and alpine environments are currently experiencing landscape-mediated changes in growth and recruitment due to recent climate change. Understanding the biophysical controls of forest structure, growth, and recruitment in these environments is critical for interpreting and predicting the direction and magnitude of biotic responses to climate shift. We examined the abiotic controls of forest biomass within a 305 km2 region of the Carson Range on the eastern shore of Lake Tahoe, CA USA using estimates of forest structure and biophysical drivers developed continuously over the landscape. The study area ranged from 1900 m to 3400 m a.s.l. and encompassed montane, sub-alpine, and alpine environments. From hyperspatial optical imagery (IKONOS), we derived per-tree positions and crown sizes using a template matching approach applied to a pre-classified image of sunlit and shadowed vegetation pixels. From this remote sensing derived stem map, we calculated plot-level estimates of stem density, tree cover and average crown size. Additionally, we developed high resolution (30 m) estimates of climate variables within the study area using meteorological station data, topographic data, and a combination of empirical and mechanistic modeling approaches. From these climate surfaces, digital elevation data, and soil survey data, we derived estimates of direct and indirect biophysical drivers including heat loading, reference evapotranspiration, water deficit, solar radiation, topographic convergence, soil depth, and soil water holding capacity. Using these data sets, we conducted a regression tree analysis with stem density, tree cover, and average tree size as response and biophysical drivers as predictors. Trees were fit using half of the dataset randomly sampled (168,000 samples) and pruned using cost-complexity pruning based on 10-fold cross- validation. Predictions from pruned trees were then assessed against the hold

Improved key-rate bounds for practical decoy-state quantum-key-distribution systems

NASA Astrophysics Data System (ADS)

Zhang, Zhen; Zhao, Qi; Razavi, Mohsen; Ma, Xiongfeng

2017-01-01

The decoy-state scheme is the most widely implemented quantum-key-distribution protocol in practice. In order to account for the finite-size key effects on the achievable secret key generation rate, a rigorous statistical fluctuation analysis is required. Originally, a heuristic Gaussian-approximation technique was used for this purpose, which, despite its analytical convenience, was not sufficiently rigorous. The fluctuation analysis has recently been made rigorous by using the Chernoff bound. There is a considerable gap, however, between the key-rate bounds obtained from these techniques and that obtained from the Gaussian assumption. Here we develop a tighter bound for the decoy-state method, which yields a smaller failure probability. This improvement results in a higher key rate and increases the maximum distance over which secure key exchange is possible. By optimizing the system parameters, our simulation results show that our method almost closes the gap between the two previously proposed techniques and achieves a performance similar to that of conventional Gaussian approximations.

Landscape context and the biophysical response of rivers to dam removal in the United States

PubMed Central

Magilligan, Francis J.; Torgersen, Christian E.; Major, Jon J.; Anderson, Chauncey W.; Connolly, Patrick J.; Wieferich, Daniel; Shafroth, Patrick B.; Evans, James E.; Infante, Dana; Craig, Laura S.

2017-01-01

Dams have been a fundamental part of the U.S. national agenda over the past two hundred years. Recently, however, dam removal has emerged as a strategy for addressing aging, obsolete infrastructure and more than 1,100 dams have been removed since the 1970s. However, only 130 of these removals had any ecological or geomorphic assessments, and fewer than half of those included before- and after-removal (BAR) studies. In addition, this growing, but limited collection of dam-removal studies is limited to distinct landscape settings. We conducted a meta-analysis to compare the landscape context of existing and removed dams and assessed the biophysical responses to dam removal for 63 BAR studies. The highest concentration of removed dams was in the Northeast and Upper Midwest, and most have been removed from 3rd and 4th order streams, in low-elevation (< 500 m) and low-slope (< 5%) watersheds that have small to moderate upstream watershed areas (10–1000 km2) with a low risk of habitat degradation. Many of the BAR-studied removals also have these characteristics, suggesting that our understanding of responses to dam removals is based on a limited range of landscape settings, which limits predictive capacity in other environmental settings. Biophysical responses to dam removal varied by landscape cluster, indicating that landscape features are likely to affect biophysical responses to dam removal. However, biophysical data were not equally distributed across variables or clusters, making it difficult to determine which landscape features have the strongest effect on dam-removal response. To address the inconsistencies across dam-removal studies, we provide suggestions for prioritizing and standardizing data collection associated with dam removal activities. PMID:28692693

Landscape context and the biophysical response of rivers to dam removal in the United States

USGS Publications Warehouse

Foley, Melissa M.; Magilligan, Francis J.; Torgersen, Christian E.; Major, Jon J.; Anderson, Chauncey; Connolly, Patrick J.; Wieferich, Daniel; Shafroth, Patrick B.; Evans, James E.; Infante, Dana M.; Craig, Laura

2017-01-01

Dams have been a fundamental part of the U.S. national agenda over the past two hundred years. Recently, however, dam removal has emerged as a strategy for addressing aging, obsolete infrastructure and more than 1,100 dams have been removed since the 1970s. However, only 130 of these removals had any ecological or geomorphic assessments, and fewer than half of those included before- and after-removal (BAR) studies. In addition, this growing, but limited collection of dam-removal studies is limited to distinct landscape settings. We conducted a meta-analysis to compare the landscape context of existing and removed dams and assessed the biophysical responses to dam removal for 63 BAR studies. The highest concentration of removed dams was in the Northeast and Upper Midwest, and most have been removed from 3rd and 4th order streams, in low-elevation (< 500 m) and low-slope (< 5%) watersheds that have small to moderate upstream watershed areas (10–1000 km2) with a low risk of habitat degradation. Many of the BAR-studied removals also have these characteristics, suggesting that our understanding of responses to dam removals is based on a limited range of landscape settings, which limits predictive capacity in other environmental settings. Biophysical responses to dam removal varied by landscape cluster, indicating that landscape features are likely to affect biophysical responses to dam removal. However, biophysical data were not equally distributed across variables or clusters, making it difficult to determine which landscape features have the strongest effect on dam-removal response. To address the inconsistencies across dam-removal studies, we provide suggestions for prioritizing and standardizing data collection associated with dam removal activities.

Biophysics: Breaking the Nanometer Barrier

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

Block, Steven

2006-03-20

A new field of scientific exploration – single molecule biophysics – is currently reshaping and redefining our understanding of the mechanochemistry of life. The development of laser-based optical traps, or ‘optical tweezers,’ has allowed for physiological assessments of such precision that bio-molecules can now be measured and studied one at a time. In this colloquium, Professor Block will present findings based on his group’s construction of optical trapping instrumentation that has broken the nanometer barrier, allowing researchers to study single-molecule displacements on the Angstrom level. Focusing on RNA polymerase, the motor enzyme responsible for transcribing the genetic code contained inmore » DNA, Block’s group has been able to measure, in real time, the motion of a single molecule of RNA polymerase as it moves from base to base along the DNA template. A remarkable opportunity to gain insight into one of the most fundamental biological processes of life, this colloquium can not be missed!« less

Quantify the Biophysical and Socioeconomic Drivers of Changes in Forest and Agricultural Land in South and Southeast Asia

NASA Astrophysics Data System (ADS)

Xu, X.; Jain, A. K.; Calvin, K. V.

2017-12-01

Due to the rapid socioeconomic development and biophysical factors, South and Southeast Asia (SSEA) has become a hotspot region of land use and land cover changes (LULCCs) in past few decades. Uncovering the drivers of LULCC is crucial for improving the understanding of LULCC processes. Due to the differences from spatiotemporal scales, methods and data sources in previous studies, the quantitative relationships between the LULCC activities and biophysical and socioeconomic drivers at the regional scale of SSEA have not been established. Here we present a comprehensive estimation of the biophysical and socioeconomic drivers of the major LULCC activities in SSEA: changes in forest and agricultural land. We used the Climate Change Initiative land cover data developed by European Space Agency to reveal the dynamics of forest and agricultural land from 1992 to 2015. Then we synthesized 200 publications about LULCC drivers at different spatial scales in SSEA to identify the major drivers of these LULCC activities. Corresponding representative variables of the major drivers were collected. The geographically weighted regression was employed to assess the spatiotemporally heterogeneous drivers of LULCC. Moreover, we validated our results with some national level case studies in SSEA. The results showed that both biophysical conditions such as terrain, soil, and climate, and socioeconomic factors such as migration, poverty, and economy played important roles in driving the changes of forest and agricultural land. The major drivers varied in different locations and periods. Our study integrated the bottom-up knowledge from local scale case studies with the top-down estimation of LULCC drivers, therefore generated more accurate and credible results. The identified biophysical and socioeconomic components could be used to improve the LULCC modelling and projection.

A biophysical approach to daunorubicin interaction with model membranes: relevance for the drug's biological activity.

PubMed

Alves, Ana Catarina; Ribeiro, Daniela; Horta, Miguel; Lima, José L F C; Nunes, Cláudia; Reis, Salette

2017-08-01

Daunorubicin is extensively used in chemotherapy for diverse types of cancer. Over the years, evidence has suggested that the mechanisms by which daunorubicin causes cytotoxic effects are also associated with interactions at the membrane level. The aim of the present work was to study the interplay between daunorubicin and mimetic membrane models composed of different ratios of 1,2-dimyristoyl- sn -glycero- 3 -phosphocholine (DMPC), sphingomyelin (SM) and cholesterol (Chol). Several biophysical parameters were assessed using liposomes as mimetic model membranes. Thereby, the ability of daunorubicin to partition into lipid bilayers, its apparent location within the membrane and its effect on membrane fluidity were investigated. The results showed that daunorubicin has higher affinity for lipid bilayers composed of DMPC, followed by DMPC : SM, DMPC : Chol and lastly by DMPC : SM : Chol. The addition of SM or Chol into DMPC membranes not only increases the complexity of the model membrane but also decreases its fluidity, which, in turn, reduces the amount of anticancer drug that can partition into these mimetic models. Fluorescence quenching studies suggest a broad distribution of the drug across the bilayer thickness, with a preferential location in the phospholipid tails. The gathered data support that daunorubicin permeates all types of membranes to different degrees, interacts with phospholipids through electrostatic and hydrophobic bonds and causes alterations in the biophysical properties of the bilayers, namely in membrane fluidity. In fact, a decrease in membrane fluidity can be observed in the acyl region of the phospholipids. Ultimately, such outcomes can be correlated with daunorubicin's biological action, where membrane structure and lipid composition have an important role. In fact, the results indicate that the intercalation of daunorubicin between the phospholipids can also take place in rigid domains, such as rafts that are known to be involved in

Indoor Fast Neutron Generator for Biophysical and Electronic Applications

NASA Astrophysics Data System (ADS)

Cannuli, A.; Caccamo, M. T.; Marchese, N.; Tomarchio, E. A.; Pace, C.; Magazù, S.

2018-05-01

This study focuses the attention on an indoor fast neutron generator for biophysical and electronic applications. More specifically, the findings obtained by several simulations with the MCNP Monte Carlo code, necessary for the realization of a shield for indoor measurements, are presented. Furthermore, an evaluation of the neutron spectrum modification caused by the shielding is reported. Fast neutron generators are a valid and interesting available source of neutrons, increasingly employed in a wide range of research fields, such as science and engineering. The employed portable pulsed neutron source is a MP320 Thermo Scientific neutron generator, able to generate 2.5 MeV neutrons with a neutron yield of 2.0 x 106 n/s, a pulse rate of 250 Hz to 20 KHz and a duty factor varying from 5% to 100%. The neutron generator, based on Deuterium-Deuterium nuclear fusion reactions, is employed in conjunction with a solid-state photon detector, made of n-type high-purity germanium (PINS-GMX by ORTEC) and it is mainly addressed to biophysical and electronic studies. The present study showed a proposal for the realization of a shield necessary for indoor applications for MP320 neutron generator, with a particular analysis of the transport of neutrons simulated with Monte Carlo code and described the two main lines of research in which the source will be used.

Biophysical landscape interactions: Bridging disciplines and scale with connectivity

NASA Astrophysics Data System (ADS)

van der Ploeg, Martine; Baartman, Jantiene; Robinson, David

2017-04-01

concepts of biophysical landscape interactions are needed to evaluate soil water availability in relation to the stability of natural vegetation, especially in the perspective of soil threats, population growth, climate change, and global water scarcity. An integrated concept can only be established by bridging the gap between several disciplines, but needs to be appealing to those disciplines at the same time. As evidence suggests interdisciplinary work is more challenging to get funded [6]. The key aspect of the connectivity concept is that it can create pathways for feedbacks which are so often missing in soil and water models. Connectivity could thus play an important role in bridging disciplines and scales. [1] Schwilch G, Bernet L. Fleskens L, Giannakis E, Leventon J, Marañón T, Mills J, Short C, Stolte J, van Delden H, Verzandvoort S. 2016. Operationalizing ecosystem services for the mitigation of soil threats: A proposed framework. Ecological Indicators 67: 586-597,doi:10.1016/j.ecolind.2016.03.016 [2] Pelletier JD, DeLong SB, Orem CA, Becerra P, Compton K, Gressett K, Lyons-Baral J, McGuire LA, Molaro JL, Spinler JCCF. 2012. How do vegetation bands form in dry lands? Insights from numerical modeling and field studies in southern Nevada, USA. Journal of Geophysical Research: Earth Surface 117: F04026,doi:10.1029/2012JF002465 [3] Liu J, Dietz T, Carpenter SR, Alberti M, Folke C, Moran E, ..., Ostrom E. 2007. Complexity of coupled human and natural systems. Science 317.5844: 1513-1516,doi:10.1126/science.1144004 [4] Cook BJ, Hauer FR. 2007. Effects of hydrologic connectivity on water chemistry, soils, and vegetation structure and function in an intermontane depressional wetland landscape. Wetlands 27.3: 719-738,doi:10.1672/0277-5212(2007)27 [5] Roth K. 2008. Scaling of water flow through porous media and soils. European journal of soil science, 59(1), 125-130, doi: 10.1111/j.1365-2389.2007.00986.x [6] Bromham, L, Dinnage R, Hua X. 2016. Interdisciplinary research

Strengths and Limitations of Operational Use of 1 Km EO Biophysical Products for Regional Prediction of Grain Yelds in Europe (wheat, barley and maize)

NASA Astrophysics Data System (ADS)

Meroni, M.; LEO, O.; Lopez-Lozano, R.; Baruth, B.; Duveiller, G.; Garcia-Condado, S.; Hooker, J.; Seguini, L.

2014-12-01

The site-specific relationship between EO indicators and actual crop yields has been explored in many different studies, describing semi-empirical regression models between spatially aggregated biophysical parameters or vegetation indices and observed yields (from field measurements or official statistics). However, when considering larger extensions -from countries to continents- agro-climatic conditions and crop management may differ substantially among regions, and these differences may greatly influence the relationship between biophysical indicators and the observed yields, which may be also driven by limiting factors other than green biomass formation. The present study aims to better assess the contribution of EO indicators within an operational crop yield forecasting system in Europe and neighbouring countries, by evaluating how these above mentioned geographic differences influence the relationship between biophysical indicators and crop yield. We therefore explore, as a first step, the correspondence between fAPAR time-series (1999-2013) and the inter-annual yield variability of wheat, barley and grain maize, at sub-national level across Europe (270-450 Administrative Units, depending on crop). In a second step, we map the agro-climatic contexts in which EO indicators better explain the observed yield inter-annual variability, identify the influence of some meteorological events on the fAPAR -yield relationship and provide some recommendations for further investigation. The results indicate that in water-limited environments (e.g. Mediterranean and Black Sea areas), fAPAR is highly correlated with yields whereas in northern Europe, crop yield appears much less limited by leaf area expansion along the season, and the relationship between yield and EO products becomes more difficult to interpret.

Biophysical mechanism of spike threshold dependence on the rate of rise of the membrane potential by sodium channel inactivation or subthreshold axonal potassium current

PubMed Central

Wester, Jason C.

2013-01-01

Spike threshold filters incoming inputs and thus gates activity flow through neuronal networks. Threshold is variable, and in many types of neurons there is a relationship between the threshold voltage and the rate of rise of the membrane potential (dVm/dt) leading to the spike. In primary sensory cortex this relationship enhances the sensitivity of neurons to a particular stimulus feature. While Na+ channel inactivation may contribute to this relationship, recent evidence indicates that K+ currents located in the spike initiation zone are crucial. Here we used a simple Hodgkin-Huxley biophysical model to systematically investigate the role of K+ and Na+ current parameters (activation voltages and kinetics) in regulating spike threshold as a function of dVm/dt. Threshold was determined empirically and not estimated from the shape of the Vm prior to a spike. This allowed us to investigate intrinsic currents and values of gating variables at the precise voltage threshold. We found that Na+ inactivation is sufficient to produce the relationship provided it occurs at hyperpolarized voltages combined with slow kinetics. Alternatively, hyperpolarization of the K+ current activation voltage, even in the absence of Na+ inactivation, is also sufficient to produce the relationship. This hyperpolarized shift of K+ activation allows an outward current prior to spike initiation to antagonize the Na+ inward current such that it becomes self-sustaining at a more depolarized voltage. Our simulations demonstrate parameter constraints on Na+ inactivation and the biophysical mechanism by which an outward current regulates spike threshold as a function of dVm/dt. PMID:23344915

Assessment of the biophysical impacts of utility-scale photovoltaics through observations and modelling

NASA Astrophysics Data System (ADS)

Broadbent, A. M.; Georgescu, M.; Krayenhoff, E. S.; Sailor, D.

2017-12-01

Utility-scale solar power plants are a rapidly growing component of the solar energy sector. Utility-scale photovoltaic (PV) solar power generation in the United States has increased by 867% since 2012 (EIA, 2016). This expansion is likely to continue as the cost PV technologies decrease. While most agree that solar power can decrease greenhouse gas emissions, the biophysical effects of PV systems on surface energy balance (SEB), and implications for surface climate, are not well understood. To our knowledge, there has never been a detailed observational study of SEB at a utility-scale solar array. This study presents data from an eddy covariance observational tower, temporarily placed above a utility-scale PV array in Southern Arizona. Comparison of PV SEB with a reference (unmodified) site, shows that solar panels can alter the SEB and near surface climate. SEB observations are used to develop and validate a new and more complete SEB PV model. In addition, the PV model is compared to simpler PV modelling methods. The simpler PV models produce differing results to our newly developed model and cannot capture the more complex processes that influence PV SEB. Finally, hypothetical scenarios of PV expansion across the continental United States (CONUS) were developed using various spatial mapping criteria. CONUS simulations of PV expansion reveal regional variability in biophysical effects of PV expansion. The study presents the first rigorous and validated simulations of the biophysical effects of utility-scale PV arrays.

Quantifying Vegetation Biophysical Variables from Imaging Spectroscopy Data: A Review on Retrieval Methods

NASA Astrophysics Data System (ADS)

Verrelst, Jochem; Malenovský, Zbyněk; Van der Tol, Christiaan; Camps-Valls, Gustau; Gastellu-Etchegorry, Jean-Philippe; Lewis, Philip; North, Peter; Moreno, Jose

2018-06-01

An unprecedented spectroscopic data stream will soon become available with forthcoming Earth-observing satellite missions equipped with imaging spectroradiometers. This data stream will open up a vast array of opportunities to quantify a diversity of biochemical and structural vegetation properties. The processing requirements for such large data streams require reliable retrieval techniques enabling the spatiotemporally explicit quantification of biophysical variables. With the aim of preparing for this new era of Earth observation, this review summarizes the state-of-the-art retrieval methods that have been applied in experimental imaging spectroscopy studies inferring all kinds of vegetation biophysical variables. Identified retrieval methods are categorized into: (1) parametric regression, including vegetation indices, shape indices and spectral transformations; (2) nonparametric regression, including linear and nonlinear machine learning regression algorithms; (3) physically based, including inversion of radiative transfer models (RTMs) using numerical optimization and look-up table approaches; and (4) hybrid regression methods, which combine RTM simulations with machine learning regression methods. For each of these categories, an overview of widely applied methods with application to mapping vegetation properties is given. In view of processing imaging spectroscopy data, a critical aspect involves the challenge of dealing with spectral multicollinearity. The ability to provide robust estimates, retrieval uncertainties and acceptable retrieval processing speed are other important aspects in view of operational processing. Recommendations towards new-generation spectroscopy-based processing chains for operational production of biophysical variables are given.

Biophysical Stimulation for Engineering Functional Skeletal Muscle.

PubMed

Somers, Sarah M; Spector, Alexander A; DiGirolamo, Douglas J; Grayson, Warren L

2017-08-01

Tissue engineering is a promising therapeutic strategy to regenerate skeletal muscle. However, ex vivo cultivation methods typically result in a low differentiation efficiency of stem cells as well as grafts that resemble the native tissues morphologically, but lack contractile function. The application of biomimetic tensile strain provides a potent stimulus for enhancing myogenic differentiation and engineering functional skeletal muscle grafts. We reviewed integrin-dependent mechanisms that potentially link mechanotransduction pathways to the upregulation of myogenic genes. Yet, gaps in our understanding make it challenging to use these pathways to theoretically determine optimal ex vivo strain regimens. A multitude of strain protocols have been applied to in vitro cultures for the cultivation of myogenic progenitors (adipose- and bone marrow-derived stem cells and satellite cells) and transformed murine myoblasts, C2C12s. Strain regimens are characterized by orientation, amplitude, and time-dependent factors (effective frequency, duration, and the rest period between successive strain cycles). Analysis of published data has identified possible minimum/maximum values for these parameters and suggests that uniaxial strains may be more potent than biaxial strains, possibly because they more closely mimic physiologic strain profiles. The application of these biophysical stimuli for engineering 3D skeletal muscle grafts is nontrivial and typically requires custom-designed bioreactors used in combination with biomaterial scaffolds. Consideration of the physical properties of these scaffolds is critical for effective transmission of the applied strains to encapsulated cells. Taken together, these studies demonstrate that biomimetic tensile strain generally results in improved myogenic outcomes in myogenic progenitors and differentiated myoblasts. However, for 3D systems, the optimization of the strain regimen may require the entire system including cells, biomaterials

‘The physics of life,’ an undergraduate general education biophysics course

NASA Astrophysics Data System (ADS)

Parthasarathy, Raghuveer

2015-05-01

Improving the scientific literacy of non-scientists is an important aim, both because of the ever-increasing impact of science on our lives and because understanding science enriches our experience of the natural world. One route to improving scientific literacy is via general education undergraduate courses—i.e. courses for students not majoring in the sciences or engineering. Because it encompasses a variety of important scientific concepts, demonstrates connections between basic science and real-world applications and illustrates the creative ways in which scientific insights develop, biophysics is a useful subject with which to promote scientific literacy. I describe here a course on biophysics for non-science-major undergraduates recently developed at the University of Oregon (Eugene, OR, USA), noting its design, which spans both macroscopic and microscopic topics, and the specific content of a few of its modules. I also describe evidence-based pedagogical approaches adopted in teaching the course and aspects of course enrollment and evaluation.

Contributions of computational chemistry and biophysical techniques to fragment-based drug discovery.

PubMed

Gozalbes, Rafael; Carbajo, Rodrigo J; Pineda-Lucena, Antonio

2010-01-01

In the last decade, fragment-based drug discovery (FBDD) has evolved from a novel approach in the search of new hits to a valuable alternative to the high-throughput screening (HTS) campaigns of many pharmaceutical companies. The increasing relevance of FBDD in the drug discovery universe has been concomitant with an implementation of the biophysical techniques used for the detection of weak inhibitors, e.g. NMR, X-ray crystallography or surface plasmon resonance (SPR). At the same time, computational approaches have also been progressively incorporated into the FBDD process and nowadays several computational tools are available. These stretch from the filtering of huge chemical databases in order to build fragment-focused libraries comprising compounds with adequate physicochemical properties, to more evolved models based on different in silico methods such as docking, pharmacophore modelling, QSAR and virtual screening. In this paper we will review the parallel evolution and complementarities of biophysical techniques and computational methods, providing some representative examples of drug discovery success stories by using FBDD.

Biophysical isolation and identification of circulating tumor cells.

PubMed

Che, James; Yu, Victor; Garon, Edward B; Goldman, Jonathan W; Di Carlo, Dino

2017-04-11

Isolation and enumeration of circulating tumor cells (CTCs) from blood is important for determining patient prognosis and monitoring treatment. Methods based on affinity to cell surface markers have been applied to both purify (via immunoseparation) and identify (via immunofluorescence) CTCs. However, variability of cell biomarker expression associated with tumor heterogeneity and evolution and cross-reactivity of antibody probes have long complicated CTC enrichment and immunostaining. Here, we report a truly label-free high-throughput microfluidic approach to isolate, enumerate, and characterize the biophysical properties of CTCs using an integrated microfluidic device. Vortex-mediated deformability cytometry (VDC) consists of an initial vortex region which enriches large CTCs, followed by release into a downstream hydrodynamic stretching region which deforms the cells. Visualization and quantification of cell deformation with a high-speed camera revealed populations of large (>15 μm diameter) and deformable (aspect ratio >1.2) CTCs from 16 stage IV lung cancer samples, that are clearly distinguished by increased deformability compared to contaminating blood cells and rare large cells isolated from healthy patients. The VDC technology demonstrated a comparable positive detection rate of putative CTCs above healthy baseline (93.8%) with respect to standard immunofluorescence (71.4%). Automation allows full enumeration of CTCs from a 10 mL vial of blood within <1 h after sample acquisition, compared with 4+ hours with standard approaches. Moreover, cells are released into any collection vessel for further downstream analysis. VDC shows potential for accurate CTC enumeration without labels and confirms the unique highly deformable biophysical properties of large CTCs circulating in blood.

Microwave Tissue Ablation: Biophysics, Technology and Applications

PubMed Central

2010-01-01

Microwave ablation is an emerging treatment option for many cancers, cardiac arrhythmias and other medical conditions. During treatment, microwaves are applied directly to tissues to produce rapid temperature elevations sufficient to produce immediate coagulative necrosis. The engineering design criteria for each application differ, with individual consideration for factors such as desired ablation zone size, treatment duration, and procedural invasiveness. Recent technological developments in applicator cooling, power control and system optimization for specific applications promise to increase the utilization of microwave ablation in the future. This article will review the basic biophysics of microwave tissue heating, provide an overview of the design and operation of current equipment, and outline areas for future research for microwave ablation. PMID:21175404

Biophysical Technologies for Management of Wound Bioburden

PubMed Central

Korzendorfer, Holly; Hettrick, Heather

2014-01-01

Significance: Chronic wounds commonly have high levels of bioburden and antibiotic-resistant pathogens. This review article focuses on findings from current literature related to four biophysical technologies (ultrasound, electrical stimulation, phototherapy, and negative pressure wound therapy) believed to be beneficial for managing wound bioburden and support healing. Recent Advances and Critical Issues: Recent advances for each modality are provided as a basic synopsis of the technology followed by brief overviews of the most recent literature addressing its effectiveness for managing wound bioburden, and critical issues for each modality are provided as conclusions. Future Directions: This review highlights the need for further clinically relevant studies examining bacterial levels in addition to healing progression for each technology. PMID:25493207

Key Parameters for the Use of AbobotulinumtoxinA in Aesthetics: Onset and Duration

PubMed Central

Ablon, Glynis; Pickett, Andy

2017-01-01

Abstract Time to onset of response and duration of response are key measures of botulinum toxin efficacy that have a considerable influence on patient satisfaction with aesthetic treatment. However, there is no overall accepted definition of efficacy for aesthetic uses of botulinumtoxinA (BoNT-A). Mechanical methods of assessment do not lend themselves to clinical practice and clinicians rely instead on assessment scales such as the Frontalis Activity Measurement Standard, Frontalis Rating Scale, Wrinkle Severity Scale, and Subject Global Assessment Scale, but not all of these have been fully validated. Onset of activity is typically seen within 5 days of injection, but has also been recorded within 12 hours with abobotulinumtoxinA. Duration of effect is more variable, and is influenced by parameters such as muscle mass (including the effects of age and sex) and type of product used. Even when larger muscles are treated with higher doses of BoNT-A, the duration of effect is still shorter than that for smaller muscles. Muscle injection technique, including dilution of the toxin, the volume of solution injected, and the positioning of the injections, can also have an important influence on onset and duration of activity. Comparison of the efficacy of different forms of BoNT-A must be made with the full understanding that the dosing units are not equivalent. Range of equivalence studies for abobotulinumtoxinA (Azzalure; Ipsen Limited, Slough UK/Galderma, Lausanne CH/Dysport, Ipsen Biopharm Limited, Wrexham UK/Galderma LP, Fort Worth, TX) and onabotulinumtoxinA (Botox; Allergan, Parsippany, NJ) have been conducted, and results indicate that the number of units of abobotulinumtoxinA needs to be approximately twice as high as that of onabotulinumtoxinA to achieve the same effect. An appreciation of the potential influence of all of the parameters that influence onset and duration of activity of BoNT-A, along with a thorough understanding of the anatomy of the face and

Importance of biophysical effects on climate warming mitigation potential of biofuel crops over the conterminous United States

DOE PAGES

Zhu, Peng; Zhuang, Qianlai; Eva, Joo; ...

2016-06-21

Current quantification of climate warming mitigation potential (CWMP) of biomass-derived energy has focused primarily on its biogeochemical effects. This study used site-level observations of carbon, water, and energy fluxes of biofuel crops to parameterize and evaluate the community land model (CLM) and estimate CO 2 fluxes, surface energy balance, soil carbon dynamics of corn (Zea mays), switchgrass (Panicum virgatum), and miscanthus (Miscanthus × giganteus) ecosystems across the conterminous United States considering different agricultural management practices and land-use scenarios. Here, we find that neglecting biophysical effects underestimates the CWMP of transitioning from croplands and marginal lands to energy crops. Biogeochemical effectsmore » alone result in changes in carbon storage of -1.9, 49.1, and 69.3 g C m -2 y -1 compared to 20.5, 78.5, and 96.2 g C m -2 y -1 when considering both biophysical and biogeochemical effects for corn, switchgrass, and miscanthus, respectively. The biophysical contribution to CWMP is dominated by changes in latent heat fluxes. Using the model to optimize growth conditions through fertilization and irrigation increases the CWMP further to 79.6, 98.3, and 118.8 g C m -2 y -1, respectively, representing the upper threshold for CWMP. Results also show that the CWMP over marginal lands is lower than that over croplands. Our study highlights that neglecting the biophysical effects of altered surface energy and water balance underestimates the CWMP of transitioning to bioenergy crops at regional scales.« less

Final report for Conference Support Grant "From Computational Biophysics to Systems Biology - CBSB12"

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

Hansmann, Ulrich H.E.

2012-07-02

This report summarizes the outcome of the international workshop From Computational Biophysics to Systems Biology (CBSB12) which was held June 3-5, 2012, at the University of Tennessee Conference Center in Knoxville, TN, and supported by DOE through the Conference Support Grant 120174. The purpose of CBSB12 was to provide a forum for the interaction between a data-mining interested systems biology community and a simulation and first-principle oriented computational biophysics/biochemistry community. CBSB12 was the sixth in a series of workshops of the same name organized in recent years, and the second that has been held in the USA. As in previousmore » years, it gave researchers from physics, biology, and computer science an opportunity to acquaint each other with current trends in computational biophysics and systems biology, to explore venues of cooperation, and to establish together a detailed understanding of cells at a molecular level. The conference grant of $10,000 was used to cover registration fees and provide travel fellowships to selected students and postdoctoral scientists. By educating graduate students and providing a forum for young scientists to perform research into the working of cells at a molecular level, the workshop adds to DOE's mission of paving the way to exploit the abilities of living systems to capture, store and utilize energy.« less

Time-resolved methods in biophysics. 9. Laser temperature-jump methods for investigating biomolecular dynamics.

PubMed

Kubelka, Jan

2009-04-01

Many important biochemical processes occur on the time-scales of nanoseconds and microseconds. The introduction of the laser temperature-jump (T-jump) to biophysics more than a decade ago opened these previously inaccessible time regimes up to direct experimental observation. Since then, laser T-jump methodology has evolved into one of the most versatile and generally applicable methods for studying fast biomolecular kinetics. This perspective is a review of the principles and applications of the laser T-jump technique in biophysics. A brief overview of the T-jump relaxation kinetics and the historical development of laser T-jump methodology is presented. The physical principles and practical experimental considerations that are important for the design of the laser T-jump experiments are summarized. These include the Raman conversion for generating heating pulses, considerations of size, duration and uniformity of the temperature jump, as well as potential adverse effects due to photo-acoustic waves, cavitation and thermal lensing, and their elimination. The laser T-jump apparatus developed at the NIH Laboratory of Chemical Physics is described in detail along with a brief survey of other laser T-jump designs in use today. Finally, applications of the laser T-jump in biophysics are reviewed, with an emphasis on the broad range of problems where the laser T-jump methodology has provided important new results and insights into the dynamics of the biomolecular processes.

Developing a physics expert identity in a biophysics research group

NASA Astrophysics Data System (ADS)

Rodriguez, Idaykis; Goertzen, Renee Michelle; Brewe, Eric; Kramer, Laird H.

2015-06-01

We investigate the development of expert identities through the use of the sociocultural perspective of learning as participating in a community of practice. An ethnographic case study of biophysics graduate students focuses on the experiences the students have in their research group meetings. The analysis illustrates how the communities of practice-based identity constructs of competencies characterize student expert membership. A microanalysis of speech, sound, tones, and gestures in video data characterize students' social competencies in the physics community of practice. Results provide evidence that students at different stages of their individual projects have opportunities to develop social competencies such as mutual engagement, negotiability of the repertoire, and accountability to the enterprises as they interact with group members. The biophysics research group purposefully designed a learning trajectory including conducting research and writing it for publication in the larger community of practice as a pathway to expertise. The students of the research group learn to become socially competent as specific experts of their project topic and methodology, ensuring acceptance, agency, and membership in their community of practice. This work expands research on physics expertise beyond the cognitive realm and has implications for how to design graduate learning experiences to promote expert identity development.

Biophysical Fitness Landscapes for Transcription Factor Binding Sites

PubMed Central

Haldane, Allan; Manhart, Michael; Morozov, Alexandre V.

2014-01-01

Phenotypic states and evolutionary trajectories available to cell populations are ultimately dictated by complex interactions among DNA, RNA, proteins, and other molecular species. Here we study how evolution of gene regulation in a single-cell eukaryote S. cerevisiae is affected by interactions between transcription factors (TFs) and their cognate DNA sites. Our study is informed by a comprehensive collection of genomic binding sites and high-throughput in vitro measurements of TF-DNA binding interactions. Using an evolutionary model for monomorphic populations evolving on a fitness landscape, we infer fitness as a function of TF-DNA binding to show that the shape of the inferred fitness functions is in broad agreement with a simple functional form inspired by a thermodynamic model of two-state TF-DNA binding. However, the effective parameters of the model are not always consistent with physical values, indicating selection pressures beyond the biophysical constraints imposed by TF-DNA interactions. We find little statistical support for the fitness landscape in which each position in the binding site evolves independently, indicating that epistasis is common in the evolution of gene regulation. Finally, by correlating TF-DNA binding energies with biological properties of the sites or the genes they regulate, we are able to rule out several scenarios of site-specific selection, under which binding sites of the same TF would experience different selection pressures depending on their position in the genome. These findings support the existence of universal fitness landscapes which shape evolution of all sites for a given TF, and whose properties are determined in part by the physics of protein-DNA interactions. PMID:25010228

Single Neuron Optimization as a Basis for Accurate Biophysical Modeling: The Case of Cerebellar Granule Cells.

PubMed

Masoli, Stefano; Rizza, Martina F; Sgritta, Martina; Van Geit, Werner; Schürmann, Felix; D'Angelo, Egidio

2017-01-01

In realistic neuronal modeling, once the ionic channel complement has been defined, the maximum ionic conductance (G i-max ) values need to be tuned in order to match the firing pattern revealed by electrophysiological recordings. Recently, selection/mutation genetic algorithms have been proposed to efficiently and automatically tune these parameters. Nonetheless, since similar firing patterns can be achieved through different combinations of G i-max values, it is not clear how well these algorithms approximate the corresponding properties of real cells. Here we have evaluated the issue by exploiting a unique opportunity offered by the cerebellar granule cell (GrC), which is electrotonically compact and has therefore allowed the direct experimental measurement of ionic currents. Previous models were constructed using empirical tuning of G i-max values to match the original data set. Here, by using repetitive discharge patterns as a template, the optimization procedure yielded models that closely approximated the experimental G i-max values. These models, in addition to repetitive firing, captured additional features, including inward rectification, near-threshold oscillations, and resonance, which were not used as features. Thus, parameter optimization using genetic algorithms provided an efficient modeling strategy for reconstructing the biophysical properties of neurons and for the subsequent reconstruction of large-scale neuronal network models.

Developing A Transdisciplinary Process and Community Partnerships to Anticipate Climate Change at the Local Level: The Role of Biophysical and Sociocultural Calendars

NASA Astrophysics Data System (ADS)

Kassam, K. A.; Samimi, C.; Trabucco, A.

2017-12-01

Difference is essential to solving the most complex problems faced by humanity. Anthropogenic climate change is one such "wicked problem" that demands cognitive diversity. Biophysical and social scientists must collaborate with scholars from the humanities to address practical issues of concern to local communities, which are at the forefront of impacts of climatic variation. As such, communities of inquirers (e.g. biophysical and social sciences, humanities) must work in tandem with communities of practice (e.g. farmers, fishers, gatherers, herders, hunters). This leads to co-generated knowledge where an adaptation strategy to climatic variation is locally grounded in the biophysical and sociocultural context of the communities where the impacts of climatic variation are most felt. We will present an innovative and `real time' example participatory and transdisciplinary research from an international project where we are developing integrated biophysical and sociocultural calendars, in short, ecological calendars, which are ecologically and culturally grounded in the local context to develop anticipatory capacity to anthropogenic climate change.

Mechanisms of Soil Aggregation: a biophysical modeling framework

NASA Astrophysics Data System (ADS)

Ghezzehei, T. A.; Or, D.

2016-12-01

Soil aggregation is one of the main crosscutting concepts in all sub-disciplines and applications of soil science from agriculture to climate regulation. The concept generally refers to adhesion of primary soil particles into distinct units that remain stable when subjected to disruptive forces. It is one of the most sensitive soil qualities that readily respond to disturbances such as cultivation, fire, drought, flooding, and changes in vegetation. These changes are commonly quantified and incorporated in soil models indirectly as alterations in carbon content and type, bulk density, aeration, permeability, as well as water retention characteristics. Soil aggregation that is primarily controlled by organic matter generally exhibits hierarchical organization of soil constituents into stable units that range in size from a few microns to centimeters. However, this conceptual model of soil aggregation as the key unifying mechanism remains poorly quantified and is rarely included in predictive soil models. Here we provide a biophysical framework for quantitative and predictive modeling of soil aggregation and its attendant soil characteristics. The framework treats aggregates as hotspots of biological, chemical and physical processes centered around roots and root residue. We keep track of the life cycle of an individual aggregate from it genesis in the rhizosphere, fueled by rhizodeposition and mediated by vigorous microbial activity, until its disappearance when the root-derived resources are depleted. The framework synthesizes current understanding of microbial life in porous media; water holding and soil binding capacity of biopolymers; and environmental controls on soil organic matter dynamics. The framework paves a way for integration of processes that are presently modeled as disparate or poorly coupled processes, including storage and protection of carbon, microbial activity, greenhouse gas fluxes, movement and storage of water, resistance of soils against

Lead-acid batteries in micro-hybrid applications. Part I. Selected key parameters

NASA Astrophysics Data System (ADS)

Schaeck, S.; Stoermer, A. O.; Kaiser, F.; Koehler, L.; Albers, J.; Kabza, H.

Micro-hybrid electric vehicles were launched by BMW in March 2007. These are equipped with brake energy regeneration (BER) and the automatic start and stop function (ASSF) of the internal combustion engine. These functions are based on common 14 V series components and lead-acid (LA) batteries. The novelty is given by the intelligent onboard energy management, which upgrades the conventional electric system to the micro-hybrid power system (MHPS). In part I of this publication the key factors for the operation of LA batteries in the MHPS are discussed. Especially for BER one is high dynamic charge acceptance (DCA) for effective boost charging. Vehicle rest time is identified as a particular negative parameter for DCA. It can be refreshed by regular fully charging at elevated charge voltage. Thus, the batteries have to be outstandingly robust against overcharge and water loss. This can be accomplished for valve-regulated lead-acid (VRLA) batteries at least if they are mounted in the trunk. ASSF goes along with frequent high-rate loads for warm cranking. The internal resistance determines the drop of the power net voltage during cranking and is preferably low for reasons of power net stability even after years of operation. Investigations have to be done with aged 90 Ah VRLA-absorbent glass mat (AGM) batteries. Battery operation at partial state-of-charge gives a higher risk of deep discharging (overdischarging). Subsequent re-charging then is likely to lead to the formation of micro-short circuits in the absorbent glass mat separator.

Simulation-based Extraction of Key Material Parameters from Atomic Force Microscopy

NASA Astrophysics Data System (ADS)

Alsafi, Huseen; Peninngton, Gray

Models for the atomic force microscopy (AFM) tip and sample interaction contain numerous material parameters that are often poorly known. This is especially true when dealing with novel material systems or when imaging samples that are exposed to complicated interactions with the local environment. In this work we use Monte Carlo methods to extract sample material parameters from the experimental AFM analysis of a test sample. The parameterized theoretical model that we use is based on the Virtual Environment for Dynamic AFM (VEDA) [1]. The extracted material parameters are then compared with the accepted values for our test sample. Using this procedure, we suggest a method that can be used to successfully determine unknown material properties in novel and complicated material systems. We acknowledge Fisher Endowment Grant support from the Jess and Mildred Fisher College of Science and Mathematics,Towson University.

Biophysical and biochemical constraints imposed by salt stress: learning from halophytes

PubMed Central

Duarte, Bernardo; Sleimi, Noomene; Caçador, Isabel

2014-01-01

Soil salinization is one of the most important factors impacting plant productivity. About 3.6 billion of the world’s 5.2 billion ha of agricultural dry land, have already suffered erosion, degradation, and salinization. Halophytes are typically considered as plants able to complete their life cycle in environments where the salt concentration is above 200 mM NaCl. Salinity adjustment is a complex phenomenon but essential mechanism to overcome salt stress, with both biophysical and biochemical implications. At this level, halophytes evolved in several directions, adopting different strategies. Otherwise, the lack of adaptation to a salt environment would negatively affect their electron transduction pathways and the entire energetic metabolism, the foundation of every plant photosynthesis and biomass production. The maintenance of ionic homeostasis is in the basis of all cellular counteractive measures, in particular in terms of redox potential and energy transduction. In the present work the biophysical mechanisms underlying energy capture and transduction in halophytes are discussed alongside with their relation with biochemical counteractive mechanisms, integrating data from photosynthetic light harvesting complexes, electron transport chains to the quinone pools, carbon fixation, and energy dissipation metabolism. PMID:25566311

Partition of some key regulating services in terrestrial ecosystems: Meta-analysis and review.

PubMed

Viglizzo, E F; Jobbágy, E G; Ricard, M F; Paruelo, J M

2016-08-15

Our knowledge about the functional foundations of ecosystem service (ES) provision is still limited and more research is needed to elucidate key functional mechanisms. Using a simplified eco-hydrological scheme, in this work we analyzed how land-use decisions modify the partition of some essential regulatory ES by altering basic relationships between biomass stocks and water flows. A comprehensive meta-analysis and review was conducted based on global, regional and local data from peer-reviewed publications. We analyzed five datasets comprising 1348 studies and 3948 records on precipitation (PPT), aboveground biomass (AGB), AGB change, evapotranspiration (ET), water yield (WY), WY change, runoff (R) and infiltration (I). The conceptual framework was focused on ES that are associated with the ecological functions (e.g., intermediate ES) of ET, WY, R and I. ES included soil protection, carbon sequestration, local climate regulation, water-flow regulation and water recharge. To address the problem of data normality, the analysis included both parametric and non-parametric regression analysis. Results demonstrate that PPT is a first-order biophysical factor that controls ES release at the broader scales. At decreasing scales, ES are partitioned as result of PPT interactions with other biophysical and anthropogenic factors. At intermediate scales, land-use change interacts with PPT modifying ES partition as it the case of afforestation in dry regions, where ET and climate regulation may be enhanced at the expense of R and water-flow regulation. At smaller scales, site-specific conditions such as topography interact with PPT and AGB displaying different ES partition formats. The probable implications of future land-use and climate change on some key ES production and partition are discussed. Copyright © 2016 Elsevier B.V. All rights reserved.

Biophysical and structural considerations for protein sequence evolution

PubMed Central

2011-01-01

Background Protein sequence evolution is constrained by the biophysics of folding and function, causing interdependence between interacting sites in the sequence. However, current site-independent models of sequence evolutions do not take this into account. Recent attempts to integrate the influence of structure and biophysics into phylogenetic models via statistical/informational approaches have not resulted in expected improvements in model performance. This suggests that further innovations are needed for progress in this field. Results Here we develop a coarse-grained physics-based model of protein folding and binding function, and compare it to a popular informational model. We find that both models violate the assumption of the native sequence being close to a thermodynamic optimum, causing directional selection away from the native state. Sampling and simulation show that the physics-based model is more specific for fold-defining interactions that vary less among residue type. The informational model diffuses further in sequence space with fewer barriers and tends to provide less support for an invariant sites model, although amino acid substitutions are generally conservative. Both approaches produce sequences with natural features like dN/dS < 1 and gamma-distributed rates across sites. Conclusions Simple coarse-grained models of protein folding can describe some natural features of evolving proteins but are currently not accurate enough to use in evolutionary inference. This is partly due to improper packing of the hydrophobic core. We suggest possible improvements on the representation of structure, folding energy, and binding function, as regards both native and non-native conformations, and describe a large number of possible applications for such a model. PMID:22171550

Association, intrinsic shape, and molecular recognition: Elucidating DNA biophysics through coarse-grained simulation

NASA Astrophysics Data System (ADS)

Freeman, Gordon Samuel

DNA is of central importance in biology as it is responsible for carrying, copying, and translating the genetic code into the building blocks that comprise life. In order to accomplish these tasks, the DNA molecule must be versatile and robust. Indeed, the underlying molecular interactions that allow DNA to execute these tasks are complex and their origins are only beginning to be understood. While experiments are able to elucidate many key biophysical phenomena, there remain many unanswered questions. Molecular simulation is able to shed light on phenomena at the molecular scale and provide information that is missing from experimental views of DNA behavior. In this dissertation I use state-of-the-art coarse-grained DNA models to address two key problems. In the first, metadynamics calculations are employed to uncover the free energy surface of two complimentary DNA strands. This free energy surface takes on the appearance of a hybridization funnel and reveals candidates for intermediate states in the hybridization of short DNA oligomers. Such short oligomers are important building blocks for DNA-driven self-assembly and the mechanism of hybridization in this regime is not well understood. The second problem is that of nucleosome formation. Nucleosomes are the fundamental subunit of genome compaction in the nucleus of a cell. As such, nucleosomes are a key epigenetic factor and affect gene expression and the ability of DNA-binding proteins to locate and bind to the appropriate position in the genome. However, the factors that drive nucleosome positioning are not well understood. While DNA sequence is known to affect nucleosome formation, the mechanism by which it does so has not been established and a number of hypotheses explaining this sequence-dependence exist in the literature. I demonstrate that DNA shape dominates this process with contributions arising from both intrinsic DNA curvature as well as DNA-protein interactions driven by sequence

Pharmacokinetics Application in Biophysics Experiments

NASA Astrophysics Data System (ADS)

Millet, Philippe; Lemoigne, Yves

Among the available computerised tomography devices, the Positron Emission Tomography (PET) has the advantage to be sensitive to pico-molar concentrations of radiotracers inside living matter. Devices adapted to small animal imaging are now commercially available and allow us to study the function rather than the structure of living tissues by in vivo analysis. PET methodology, from the physics of electron-positron annihilation to the biophysics involved in tracers, is treated by other authors in this book. The basics of coincidence detection, image reconstruction, spatial resolution and sensitivity are discussed in the paper by R. Ott. The use of compartment analysis combined with pharmacokinetics is described here to illustrate an application to neuroimaging and to show how parametric imaging can bring insight on the in vivo bio-distribution of a radioactive tracer with small animal PET scanners. After reporting on the use of an intracerebral β+ radiosensitive probe (βP), we describe a small animal PET experiment used to measure the density of 5HT 1 a receptors in rat brain.

Early T-cell activation biophysics

PubMed Central

Henry, Nelly; Hivroz, Claire

2009-01-01

The T-cell is one of the main players in the mammalian immune response. It ensures antigen recognition at the surface of antigen-presenting cells in a complex and highly sensitive and specific process, in which the encounter of the T-cell receptor with the agonist peptide associated with the major histocompatibility complex triggers T-cell activation. While signaling pathways have been elucidated in increasing detail, the mechanism of TCR triggering remains highly controversial despite active research published in the past 10 years. In this paper, we present a short overview of pending questions on critical initial events associated with T-cell triggering. In particular, we examine biophysical approaches already in use, as well as future directions. We suggest that the most recent advances in fluorescence super-resolution imaging, coupled with the new classes of genetic fluorescent probes, will play an important role in elucidation of the T-cell triggering mechanism. Beyond this aspect, we predict that exploration of mechanical cues in the triggering process will provide new clues leading to clarification of the entire mechanism. PMID:20514131

Rhizosphere biophysics and root water uptake

NASA Astrophysics Data System (ADS)

Carminati, Andrea; Zarebanadkouki, Mohsen; Ahmed, Mutez A.; Passioura, John

2016-04-01

The flow of water into the roots and the (putative) presence of a large resistance at the root-soil interface have attracted the attention of plant and soil scientists for decades. Such resistance has been attributed to a partial contact between roots and soil, large gradients in soil matric potential around the roots, or accumulation of solutes at the root surface creating a negative osmotic potential. Our hypothesis is that roots are capable of altering the biophysical properties of the soil around the roots, the rhizosphere, facilitating root water uptake in dry soils. In particular, we expect that root hairs and mucilage optimally connect the roots to the soil maintaining the hydraulic continuity across the rhizosphere. Using a pressure chamber apparatus we measured the relation between transpiration rate and the water potential difference between soil and leaf xylem during drying cycles in barley mutants with and without root hairs. The samples were grown in well structured soils. At low soil moistures and high transpiration rates, large drops in water potential developed around the roots. These drops in water potential recovered very slowly, even after transpiration was severely decreased. The drops in water potential were much bigger in barley mutants without root hairs. These mutants failed to sustain high transpiration rates in dry conditions. To explain the nature of such drops in water potential across the rhizosphere we performed high resolution neutron tomography of the rhizosphere of the barleys with and without root hairs growing in the same soil described above. The tomograms suggested that the hydraulic contact between the soil structures was the highest resistance for the water flow in dry conditions. The tomograms also indicate that root hairs and mucilage improved the hydraulic contact between roots and soil structures. At high transpiration rates and low water contents, roots extracted water from the rhizosphere, while the bulk soil, due its

Mathematical and computational modelling of skin biophysics: a review

PubMed Central

2017-01-01

The objective of this paper is to provide a review on some aspects of the mathematical and computational modelling of skin biophysics, with special focus on constitutive theories based on nonlinear continuum mechanics from elasticity, through anelasticity, including growth, to thermoelasticity. Microstructural and phenomenological approaches combining imaging techniques are also discussed. Finally, recent research applications on skin wrinkles will be presented to highlight the potential of physics-based modelling of skin in tackling global challenges such as ageing of the population and the associated skin degradation, diseases and traumas. PMID:28804267

Mathematical and computational modelling of skin biophysics: a review

NASA Astrophysics Data System (ADS)

Limbert, Georges

2017-07-01

The objective of this paper is to provide a review on some aspects of the mathematical and computational modelling of skin biophysics, with special focus on constitutive theories based on nonlinear continuum mechanics from elasticity, through anelasticity, including growth, to thermoelasticity. Microstructural and phenomenological approaches combining imaging techniques are also discussed. Finally, recent research applications on skin wrinkles will be presented to highlight the potential of physics-based modelling of skin in tackling global challenges such as ageing of the population and the associated skin degradation, diseases and traumas.

An improved strategy for regression of biophysical variables and Landsat ETM+ data.

Treesearch

Warren B. Cohen; Thomas K. Maiersperger; Stith T. Gower; David P. Turner

2003-01-01

Empirical models are important tools for relating field-measured biophysical variables to remote sensing data. Regression analysis has been a popular empirical method of linking these two types of data to provide continuous estimates for variables such as biomass, percent woody canopy cover, and leaf area index (LAI). Traditional methods of regression are not...

Time to Stop Telling Biophysics Students that Light Is Primarily a Wave.

PubMed

Nelson, Philip C

2018-02-27

Standard pedagogy introduces optics as though it were a consequence of Maxwell's equations and only grudgingly admits, usually in a rushed aside, that light has a particulate character that can somehow be reconciled with the wave picture. Recent revolutionary advances in optical imaging, however, make this approach more and more unhelpful: How are we to describe two-photon imaging, FRET, localization microscopy, and a host of related techniques to students who think of light primarily as a wave? I was surprised to find that everything I wanted my biophysics students to know about light, including image formation, x-ray diffraction, and even Bessel beams, could be expressed as well (or better) from the quantum viewpoint pioneered by Richard Feynman. Even my undergraduate students grasp this viewpoint as well as (or better than) the traditional one, and by mid-semester they are already well positioned to integrate the latest advances into their understanding. Moreover, I have found that this approach clarifies my own understanding of new techniques. Copyright © 2018 Biophysical Society. Published by Elsevier Inc. All rights reserved.

A generic implementation of replica exchange with solute tempering (REST2) algorithm in NAMD for complex biophysical simulations

NASA Astrophysics Data System (ADS)

Jo, Sunhwan; Jiang, Wei

2015-12-01

Replica Exchange with Solute Tempering (REST2) is a powerful sampling enhancement algorithm of molecular dynamics (MD) in that it needs significantly smaller number of replicas but achieves higher sampling efficiency relative to standard temperature exchange algorithm. In this paper, we extend the applicability of REST2 for quantitative biophysical simulations through a robust and generic implementation in greatly scalable MD software NAMD. The rescaling procedure of force field parameters controlling REST2 "hot region" is implemented into NAMD at the source code level. A user can conveniently select hot region through VMD and write the selection information into a PDB file. The rescaling keyword/parameter is written in NAMD Tcl script interface that enables an on-the-fly simulation parameter change. Our implementation of REST2 is within communication-enabled Tcl script built on top of Charm++, thus communication overhead of an exchange attempt is vanishingly small. Such a generic implementation facilitates seamless cooperation between REST2 and other modules of NAMD to provide enhanced sampling for complex biomolecular simulations. Three challenging applications including native REST2 simulation for peptide folding-unfolding transition, free energy perturbation/REST2 for absolute binding affinity of protein-ligand complex and umbrella sampling/REST2 Hamiltonian exchange for free energy landscape calculation were carried out on IBM Blue Gene/Q supercomputer to demonstrate efficacy of REST2 based on the present implementation.

Biophysical and electrochemical properties of Self-assembled noncovalent SWNT/DNA hybrid and electroactive nanostructure

NASA Astrophysics Data System (ADS)

Mirzapoor, Aboulfazl; Ranjbar, Bijan

2017-09-01

DNA self-assembled hybrid nanostructures are widely used in recent research in nanobiotechnology. Combination of DNA with carbon based nanoparticles such as single-walled carbon nanotube (SWNT), multi-walled carbon nanotube (MWNT) and carbon quantum dot were applied in important biological applications. Many examples of biosensors, nanowires and nanoelectronic devices, nanomachine and drug delivery systems are fabricated by these hybrid nanostructures. In this study, a new hybrid nanostructure has been fabricated by noncovalent interactions between single or double stranded DNA and SWNT nanoparticles and biophysical properties of these structures were studied comparatively. Biophysical properties of hybrid nanostructures studied by circular dichroism, UV-vis and fluorescence spectroscopy techniques. Also, electrochemical properties studied by cyclic voltammetry, linear sweep voltammetry, square wave voltammetry, choronoamperometry and impedance spectroscopy (EIS). Results revealed that the biophysical and electrochemical properties of SWNT/DNA hybrid nanostructures were different compare to ss-DNA, ds-DNA and SWNT singly. Circular dichroism results showed that ss-DNA wrapped around the nanotubes through π-π stacking interactions. The results indicated that after adding SWNT to ss-DNA and ds-DNA intensity of CD and UV-vis spectrum peaks were decreased. Electrochemical experiments indicated that the modification of single-walled carbon nanotubes by ss-DNA improves the electron transfer rate of hybrid nanostructures. It was demonstrated SWNT/DNA hybrid nanostructures should be a good electroactive nanostructure that can be used for electrochemical detection or sensing.

Introducing "biophysical redundancy": the global status and past evolution of unused water, land and productivity resources for food production

NASA Astrophysics Data System (ADS)

Fader, Marianela

2017-04-01

Countries have different resilience to sudden and long-term changes in food demand and supply. An important part of this resilience is the degree of biophysical redundancy, defined as the potential food production of 'spare land', available water resources (i.e., not already used for human activities), as well as production increases through yield gap closure on cultivated areas and potential agricultural areas. The presentation will show the results of a recently published paper1 on the evolution of biophysical redundancy for agricultural production at country level, from 1992 to 2012. Results indicate that in 2012, the biophysical redundancy of 75 (48) countries, mainly in North Africa, Western Europe, the Middle East and Asia, was insufficient to produce the caloric nutritional needs for at least 50% (25%) of their population during a year. Biophysical redundancy has decreased in the last two decades in 102 out of 155 countries, 11 of these went from high to limited redundancy, and nine of these from limited to very low redundancy. Although the variability of the drivers of change across different countries is high, improvements in yield and population growth have a clear impact on the decreases of redundancy towards the very low redundancy category. We took a more detailed look at countries classified as 'Low Income Economies (LIEs)' since they are particularly vulnerable to domestic or external food supply changes, due to their limited capacity to offset for food supply decreases with higher purchasing power on the international market. Currently, nine LIEs have limited or very low biophysical redundancy. Many of these showed a decrease in redundancy over the last two decades, which is not always linked with improvements in per capita food availability.

EDITORIAL: Focus on Heavy Ions in Biophysics and Medical Physics FOCUS ON HEAVY IONS IN BIOPHYSICS AND MEDICAL PHYSICS

NASA Astrophysics Data System (ADS)

Durante, Marco

2008-07-01

Interest in energetic heavy ions is rapidly increasing in the field of biomedicine. Heavy ions are normally excluded from radiation protection, because they are not normally experienced by humans on Earth. However, knowledge of heavy ion biophysics is necessary in two fields: charged particle cancer therapy (hadrontherapy), and radiation protection in space missions. The possibility to cure tumours using accelerated heavy charged particles was first tested in Berkeley in the sixties, but results were not satisfactory. However, about 15 years ago therapy with carbon ions was resumed first in Japan and then in Europe. Heavy ions are preferable to photons for both physical and biological characteristics: the Bragg peak and limited lateral diffusion ensure a conformal dose distribution, while the high relative biological effectiveness and low oxygen enhancement ration in the Bragg peak region make the beam very effective in treating radioresistant and hypoxic tumours. Recent results coming from the National Institute of Radiological Sciences in Chiba (see the paper by Dr Tsujii and co-workers in this issue) and GSI (Germany) provide strong clinical evidence that heavy ions are indeed an extremely effective weapon in the fight against cancer. However, more research is needed in the field, especially on optimization of the treatment planning and risk of late effects in normal tissue, including secondary cancers. On the other hand, high-energy heavy ions are present in galactic cosmic radiation and, although they are rare as compared to protons, they give a major contribution in terms of equivalent dose to the crews of manned space exploratory-class missions. Exploration of the Solar System is now the main goal of the space program, and the risk caused by exposure to galactic cosmic radiation is considered a serious hindrance toward this goal, because of the high uncertainty on late effects of energetic heavy nuclei, and the lack of effective countermeasures. Risks

Biophysical Aspects of T Lymphocyte Activation at the Immune Synapse

PubMed Central

Hivroz, Claire; Saitakis, Michael

2016-01-01

T lymphocyte activation is a pivotal step of the adaptive immune response. It requires the recognition by T-cell receptors (TCR) of peptides presented in the context of major histocompatibility complex molecules (pMHC) present at the surface of antigen-presenting cells (APCs). T lymphocyte activation also involves engagement of costimulatory receptors and adhesion molecules recognizing ligands on the APC. Integration of these different signals requires the formation of a specialized dynamic structure: the immune synapse. While the biochemical and molecular aspects of this cell–cell communication have been extensively studied, its mechanical features have only recently been addressed. Yet, the immune synapse is also the place of exchange of mechanical signals. Receptors engaged on the T lymphocyte surface are submitted to many tensile and traction forces. These forces are generated by various phenomena: membrane undulation/protrusion/retraction, cell mobility or spreading, and dynamic remodeling of the actomyosin cytoskeleton inside the T lymphocyte. Moreover, the TCR can both induce force development, following triggering, and sense and convert forces into biochemical signals, as a bona fide mechanotransducer. Other costimulatory molecules, such as LFA-1, engaged during immune synapse formation, also display these features. Moreover, T lymphocytes themselves are mechanosensitive, since substrate stiffness can modulate their response. In this review, we will summarize recent studies from a biophysical perspective to explain how mechanical cues can affect T lymphocyte activation. We will particularly discuss how forces are generated during immune synapse formation; how these forces affect various aspects of T lymphocyte biology; and what are the key features of T lymphocyte response to stiffness. PMID:26913033

Continuous variable quantum key distribution: finite-key analysis of composable security against coherent attacks.

PubMed

Furrer, F; Franz, T; Berta, M; Leverrier, A; Scholz, V B; Tomamichel, M; Werner, R F

2012-09-07

We provide a security analysis for continuous variable quantum key distribution protocols based on the transmission of two-mode squeezed vacuum states measured via homodyne detection. We employ a version of the entropic uncertainty relation for smooth entropies to give a lower bound on the number of secret bits which can be extracted from a finite number of runs of the protocol. This bound is valid under general coherent attacks, and gives rise to keys which are composably secure. For comparison, we also give a lower bound valid under the assumption of collective attacks. For both scenarios, we find positive key rates using experimental parameters reachable today.

Biophysical Properties of 9 KCNQ1 Mutations Associated with Long QT Syndrome (LQTS)

PubMed Central

Yang, Tao; Chung, Seo-Kyung; Zhang, Wei; Mullins, Jonathan G.L.; McCulley, Caroline H.; Crawford, Jackie; MacCormick, Judith; Eddy, Carey-Anne; Shelling, Andrew N.; French, John K.; Yang, Ping; Skinner, Jonathan R.; Roden, Dan M.; Rees, Mark I.

2009-01-01

Background Inherited long QT syndrome (LQTS) is characterized by prolonged QT interval on the EKG, syncope and sudden death due to ventricular arrhythmia. Causative mutations occur mostly in cardiac potassium and sodium channel subunit genes. Confidence in mutation pathogenicity is usually reached through family genotype-phenotype tracking, control population studies, molecular modelling and phylogenetic alignments, however, biophysical testing offers a higher degree of validating evidence. Methods and Results By using in-vitro electrophysiological testing of transfected mutant and wild-type LQTS constructs into Chinese Hamster Ovary cells, we investigated the biophysical properties of 9 KCNQ1 missense mutations (A46T, T265I, F269S, A302V, G316E, F339S, R360G, H455Y, and S546L) identified in a New Zealand based LQTS screening programme. We demonstrate through electrophysiology and molecular modeling that seven of the missense mutations have profound pathological dominant negative loss-of-function properties confirming their likely disease-causing nature. This supports the use of these mutations in diagnostic family screening. Two mutations (A46T, T265I) show suggestive evidence of pathogenicity within the experimental limits of biophysical testing, indicating that these variants are disease-causing via delayed or fast activation kinetics. Further investigation of the A46T family has revealed an inconsistent co-segregation of the variant with the clinical phenotype. Conclusions Electrophysiological characterisation should be used to validate LQTS pathogenicity of novel missense channelopathies. When such results are inconclusive, great care should be taken with genetic counselling and screening of such families, and alternative disease causing mechanisms should be considered. PMID:19808498

Specifications of insilicoML 1.0: a multilevel biophysical model description language.

PubMed

Asai, Yoshiyuki; Suzuki, Yasuyuki; Kido, Yoshiyuki; Oka, Hideki; Heien, Eric; Nakanishi, Masao; Urai, Takahito; Hagihara, Kenichi; Kurachi, Yoshihisa; Nomura, Taishin

2008-12-01

An extensible markup language format, insilicoML (ISML), version 0.1, describing multi-level biophysical models has been developed and available in the public domain. ISML is fully compatible with CellML 1.0, a model description standard developed by the IUPS Physiome Project, for enhancing knowledge integration and model sharing. This article illustrates the new specifications of ISML 1.0 that largely extend the capability of ISML 0.1. ISML 1.0 can describe various types of mathematical models, including ordinary/partial differential/difference equations representing the dynamics of physiological functions and the geometry of living organisms underlying the functions. ISML 1.0 describes a model using a set of functional elements (modules) each of which can specify mathematical expressions of the functions. Structural and logical relationships between any two modules are specified by edges, which allow modular, hierarchical, and/or network representations of the model. The role of edge-relationships is enriched by key words in order for use in constructing a physiological ontology. The ontology is further improved by the traceability of history of the model's development and by linking between different ISML models stored in the model's database using meta-information. ISML 1.0 is designed to operate with a model database and integrated environments for model development and simulations for knowledge integration and discovery.

Understanding moisture stress on light use efficiency across terrestrial ecosystems based on global flux and remote-sensing data

Treesearch

Yulong Zhang; Conghe Song; Ge Sun; Lawrence E. Band; Asko Noormets; Quanfa Zhang

2015-01-01

Light use efficiency (LUE) is a key biophysical parameter characterizing the ability of plants to convert absorbed light to carbohydrate. However, the environmental regulations on LUE, especially moisture stress, are poorly understood, leading to large uncertainties in primary productivity estimated by LUE models. The objective of this study is to investigate the...

Insulin amyloid fibrillation studied by terahertz spectroscopy and other biophysical methods

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

Liu, Rui; He, Mingxia; Su, Rongxin, E-mail: surx@tju.edu.cn

2010-01-01

Assembly and fibrillation of amyloid proteins are believed to play a key role in the etiology of various human diseases, including Alzheimer's, Parkinson's, Huntington's and type II diabetes. Insights into conformational changes and formation processes during amyloid fibrillation are essential for the clinical diagnosis and drug discovery. To study the changes in secondary, tertiary, quaternary structures, and the alteration in the collective vibrational mode density of states during the amyloid fibrillation, bovine insulin in 20% acetic acid was incubated at 60 {sup o}C, and its multi-level structures were followed by various biophysical techniques, including circular dichroism (CD), thioflavin T fluorescencemore » (ThT), dynamic light scattering (DLS), electron microscopy, and terahertz (THz) absorption spectroscopy. The experimental data demonstrated a transformation of {alpha}-helix into {beta}-sheet starting at 26 h. This was followed by the aggregation of insulin, as shown by ThT binding, with a transition midpoint at 41 h, and by the bulk formation of mature aggregates after about 71 h. THz is a quick and non-invasive technique, which has the advantage of allowing the study of the conformational state of biomolecules and tissues. We first applied THz spectroscopy to study the amyloid fibrillation. At the terahertz frequency range of 0.2-2.0 THz, there was an apparent increase in both the absorbance and refractive index in THz spectra. Thus, THz is expected to provide a new way of looking into amyloid fibrillation.« less

Exploring the biophysical properties of phytosterols in the plasma membrane for novel cancer prevention strategies.

PubMed

Fakih, Omar; Sanver, Didem; Kane, David; Thorne, James L

2018-05-03

Cancer is a global problem with no sign that incidences are reducing. The great costs associated with curing cancer, through developing novel treatments and applying patented therapies, is an increasing burden to developed and developing nations alike. These financial and societal problems will be alleviated by research efforts into prevention, or treatments that utilise off-patent or repurposed agents. Phytosterols are natural components of the diet found in an array of seeds, nuts and vegetables and have been added to several consumer food products for the management of cardio-vascular disease through their ability to lower LDL-cholesterol levels. In this review, we provide a connected view between the fields of structural biophysics and cellular and molecular biology to evaluate the growing evidence that phytosterols impair oncogenic pathways in a range of cancer types. The current state of understanding of how phytosterols alter the biophysical properties of plasma membrane is described, and the potential for phytosterols to be repurposed from cardio-vascular to oncology therapeutics. Through an overview of the types of biophysical and molecular biology experiments that have been performed to date, this review informs the reader of the molecular and biophysical mechanisms through which phytosterols could have anti-cancer properties via their interactions with the plasma cell membrane. We also outline emerging and under-explored areas such as computational modelling, improved biomimetic membranes and ex vivo tissue evaluation. Focus of future research in these areas should improve understanding, not just of phytosterols in cancer cell biology but also to give insights into the interaction between the plasma membrane and the genome. These fields are increasingly providing meaningful biological and clinical data but iterative experiments between molecular biology assays, biosynthetic membrane studies and computational membrane modelling improve and refine our

Biophysical mechanisms of endotoxin neutralization by cationic amphiphilic peptides.

PubMed

Kaconis, Yani; Kowalski, Ina; Howe, Jörg; Brauser, Annemarie; Richter, Walter; Razquin-Olazarán, Iosu; Iñigo-Pestaña, Melania; Garidel, Patrick; Rössle, Manfred; Martinez de Tejada, Guillermo; Gutsmann, Thomas; Brandenburg, Klaus

2011-06-08

Bacterial endotoxins (lipopolysaccharides (LPS)) are strong elicitors of the human immune system by interacting with serum and membrane proteins such as lipopolysaccharide-binding protein (LBP) and CD14 with high specificity. At LPS concentrations as low as 0.3 ng/ml, such interactions may lead to severe pathophysiological effects, including sepsis and septic shock. One approach to inhibit an uncontrolled inflammatory reaction is the use of appropriate polycationic and amphiphilic antimicrobial peptides, here called synthetic anti-LPS peptides (SALPs). We designed various SALP structures and investigated their ability to inhibit LPS-induced cytokine secretion in vitro, their protective effect in a mouse model of sepsis, and their cytotoxicity in physiological human cells. Using a variety of biophysical techniques, we investigated selected SALPs with considerable differences in their biological responses to characterize and understand the mechanism of LPS inactivation by SALPs. Our investigations show that neutralization of LPS by peptides is associated with a fluidization of the LPS acyl chains, a strong exothermic Coulomb interaction between the two compounds, and a drastic change of the LPS aggregate type from cubic into multilamellar, with an increase in the aggregate sizes, inhibiting the binding of LBP and other mammalian proteins to the endotoxin. At the same time, peptide binding to phospholipids of human origin (e.g., phosphatidylcholine) does not cause essential structural changes, such as changes in membrane fluidity and bilayer structure. The absence of cytotoxicity is explained by the high specificity of the interaction of the peptides with LPS. Copyright © 2011 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Biophysics at the Boundaries: The Next Problem Sets

NASA Astrophysics Data System (ADS)

Skolnick, Malcolm

2009-03-01

The interface between physics and biology is one of the fastest growing subfields of physics. As knowledge of such topics as cellular processes and complex ecological systems advances, researchers have found that progress in understanding these and other systems requires application of more quantitative approaches. Today, there is a growing demand for quantitative and computational skills in biological research and the commercialization of that research. The fragmented teaching of science in our universities still leaves biology outside the quantitative and mathematical culture that is the foundation of physics. This is particularly inopportune at a time when the needs for quantitative thinking about biological systems are exploding. More physicists should be encouraged to become active in research and development in the growing application fields of biophysics including molecular genetics, biomedical imaging, tissue generation and regeneration, drug development, prosthetics, neural and brain function, kinetics of nonequilibrium open biological systems, metabolic networks, biological transport processes, large-scale biochemical networks and stochastic processes in biochemical systems to name a few. In addition to moving into basic research in these areas, there is increasing opportunity for physicists in industry beginning with entrepreneurial roles in taking research results out of the laboratory and in the industries who perfect and market the inventions and developments that physicists produce. In this talk we will identify and discuss emerging opportunities for physicists in biophysical and biotechnological pursuits ranging from basic research through development of applications and commercialization of results. This will include discussion of the roles of physicists in non-traditional areas apart from academia such as patent law, financial analysis and regulatory science and the problem sets assigned in education and training that will enable future

The γ parameter of the stretched-exponential model is influenced by internal gradients: validation in phantoms.

PubMed

Palombo, Marco; Gabrielli, Andrea; De Santis, Silvia; Capuani, Silvia

2012-03-01

In this paper, we investigate the image contrast that characterizes anomalous and non-gaussian diffusion images obtained using the stretched exponential model. This model is based on the introduction of the γ stretched parameter, which quantifies deviation from the mono-exponential decay of diffusion signal as a function of the b-value. To date, the biophysical substrate underpinning the contrast observed in γ maps, in other words, the biophysical interpretation of the γ parameter (or the fractional order derivative in space, β parameter) is still not fully understood, although it has already been applied to investigate both animal models and human brain. Due to the ability of γ maps to reflect additional microstructural information which cannot be obtained using diffusion procedures based on gaussian diffusion, some authors propose this parameter as a measure of diffusion heterogeneity or water compartmentalization in biological tissues. Based on our recent work we suggest here that the coupling between internal and diffusion gradients provide pseudo-superdiffusion effects which are quantified by the stretching exponential parameter γ. This means that the image contrast of Mγ maps reflects local magnetic susceptibility differences (Δχ(m)), thus highlighting better than T(2)(∗) contrast the interface between compartments characterized by Δχ(m). Thanks to this characteristic, Mγ imaging may represent an interesting tool to develop contrast-enhanced MRI for molecular imaging. The spectroscopic and imaging experiments (performed in controlled micro-beads dispersion) that are reported here, strongly suggest internal gradients, and as a consequence Δχ(m), to be an important factor in fully understanding the source of contrast in anomalous diffusion methods that are based on a stretched exponential model analysis of diffusion data obtained at varying gradient strengths g. Copyright © 2012 Elsevier Inc. All rights reserved.

Nanoparticles for Radiation Therapy Enhancement: the Key Parameters

PubMed Central

Retif, Paul; Pinel, Sophie; Toussaint, Magali; Frochot, Céline; Chouikrat, Rima; Bastogne, Thierry; Barberi-Heyob, Muriel

2015-01-01

This review focuses on the radiosensitization strategies that use high-Z nanoparticles. It does not establish an exhaustive list of the works in this field but rather propose constructive criticisms pointing out critical factors that could improve the nano-radiation therapy. Whereas most reviews show the chemists and/or biologists points of view, the present analysis is also seen through the prism of the medical physicist. In particular, we described and evaluated the influence of X-rays energy spectra using a numerical analysis. We observed a lack of standardization in preclinical studies that could partially explain the low number of translation to clinical applications for this innovative therapeutic strategy. Pointing out the critical parameters of high-Z nanoparticles radiosensitization, this review is expected to contribute to a larger preclinical and clinical development. PMID:26155318

Nanoparticles for Radiation Therapy Enhancement: the Key Parameters.

PubMed

Retif, Paul; Pinel, Sophie; Toussaint, Magali; Frochot, Céline; Chouikrat, Rima; Bastogne, Thierry; Barberi-Heyob, Muriel

2015-01-01

This review focuses on the radiosensitization strategies that use high-Z nanoparticles. It does not establish an exhaustive list of the works in this field but rather propose constructive criticisms pointing out critical factors that could improve the nano-radiation therapy. Whereas most reviews show the chemists and/or biologists points of view, the present analysis is also seen through the prism of the medical physicist. In particular, we described and evaluated the influence of X-rays energy spectra using a numerical analysis. We observed a lack of standardization in preclinical studies that could partially explain the low number of translation to clinical applications for this innovative therapeutic strategy. Pointing out the critical parameters of high-Z nanoparticles radiosensitization, this review is expected to contribute to a larger preclinical and clinical development.

Biomechanical and biophysical environment of bone from the macroscopic to the pericellular and molecular level.

PubMed

Ren, Li; Yang, Pengfei; Wang, Zhe; Zhang, Jian; Ding, Chong; Shang, Peng

2015-10-01

Bones with complicated hierarchical configuration and microstructures constitute the load-bearing system. Mechanical loading plays an essential role in maintaining bone health and regulating bone mechanical adaptation (modeling and remodeling). The whole-bone or sub-region (macroscopic) mechanical signals, including locomotion-induced loading and external actuator-generated vibration, ultrasound, oscillatory skeletal muscle stimulation, etc., give rise to sophisticated and distinct biomechanical and biophysical environments at the pericellular (microscopic) and collagen/mineral molecular (nanoscopic) levels, which are the direct stimulations that positively influence bone adaptation. While under microgravity, the stimulations decrease or even disappear, which exerts a negative influence on bone adaptation. A full understanding of the biomechanical and biophysical environment at different levels is necessary for exploring bone biomechanical properties and mechanical adaptation. In this review, the mechanical transferring theories from the macroscopic to the microscopic and nanoscopic levels are elucidated. First, detailed information of the hierarchical structures and biochemical composition of bone, which are the foundations for mechanical signal propagation, are presented. Second, the deformation feature of load-bearing bone during locomotion is clarified as a combination of bending and torsion rather than simplex bending. The bone matrix strains at microscopic and nanoscopic levels directly induced by bone deformation are critically discussed, and the strain concentration mechanism due to the complicated microstructures is highlighted. Third, the biomechanical and biophysical environments at microscopic and nanoscopic levels positively generated during bone matrix deformation or by dynamic mechanical loadings induced by external actuators, as well as those negatively affected under microgravity, are systematically discussed, including the interstitial fluid flow

Severity of climate change dictates the direction of biophysical feedbacks of vegetation change to Arctic climate

NASA Astrophysics Data System (ADS)

Zhang, Wenxin; Jansson, Christer; Miller, Paul; Smith, Ben; Samuelsson, Patrick

2014-05-01

Vegetation-climate feedbacks induced by vegetation dynamics under climate change alter biophysical properties of the land surface that regulate energy and water exchange with the atmosphere. Simulations with Earth System Models applied at global scale suggest that the current warming in the Arctic has been amplified, with large contributions from positive feedbacks, dominated by the effect of reduced surface albedo as an increased distribution, cover and taller stature of trees and shrubs mask underlying snow, darkening the surface. However, these models generally employ simplified representation of vegetation dynamics and structure and a coarse grid resolution, overlooking local or regional scale details determined by diverse vegetation composition and landscape heterogeneity. In this study, we perform simulations using an advanced regional coupled vegetation-climate model (RCA-GUESS) applied at high resolution (0.44×0.44° ) over the Arctic Coordinated Regional Climate Downscaling Experiment (CORDEX-Arctic) domain. The climate component (RCA4) is forced with lateral boundary conditions from EC-EARTH CMIP5 simulations for three representative concentration pathways (RCP 2.6, 4.5, 8.5). Vegetation-climate response is simulated by the individual-based dynamic vegetation model (LPJ-GUESS), accounting for phenology, physiology, demography and resource competition of individual-based vegetation, and feeding variations of leaf area index and vegetative cover fraction back to the climate component, thereby adjusting surface properties and surface energy fluxes. The simulated 2m air temperature, precipitation, vegetation distribution and carbon budget for the present period has been evaluated in another paper. The purpose of this study is to elucidate the spatial and temporal characteristics of the biophysical feedbacks arising from vegetation shifts in response to different CO2 concentration pathways and their associated climate change. Our results indicate that the

AN IMPROVED STRATEGY FOR REGRESSION OF BIOPHYSICAL VARIABLES AND LANDSAT ETM+ DATA. (R828309)

EPA Science Inventory

Empirical models are important tools for relating field-measured biophysical variables to remote sensing data. Regression analysis has been a popular empirical method of linking these two types of data to provide continuous estimates for variables such as biomass, percent wood...

Parameters of Technological Growth

ERIC Educational Resources Information Center

Starr, Chauncey; Rudman, Richard

1973-01-01

Examines the factors involved in technological growth and identifies the key parameters as societal resources and societal expectations. Concludes that quality of life can only be maintained by reducing population growth, since this parameter is the product of material levels, overcrowding, food, and pollution. (JR)

Biophysical and economic limits to negative CO2 emissions

NASA Astrophysics Data System (ADS)

Smith, Pete; Davis, Steven J.; Creutzig, Felix; Fuss, Sabine; Minx, Jan; Gabrielle, Benoit; Kato, Etsushi; Jackson, Robert B.; Cowie, Annette; Kriegler, Elmar; van Vuuren, Detlef P.; Rogelj, Joeri; Ciais, Philippe; Milne, Jennifer; Canadell, Josep G.; McCollum, David; Peters, Glen; Andrew, Robbie; Krey, Volker; Shrestha, Gyami; Friedlingstein, Pierre; Gasser, Thomas; Grübler, Arnulf; Heidug, Wolfgang K.; Jonas, Matthias; Jones, Chris D.; Kraxner, Florian; Littleton, Emma; Lowe, Jason; Moreira, José Roberto; Nakicenovic, Nebojsa; Obersteiner, Michael; Patwardhan, Anand; Rogner, Mathis; Rubin, Ed; Sharifi, Ayyoob; Torvanger, Asbjørn; Yamagata, Yoshiki; Edmonds, Jae; Yongsung, Cho

2016-01-01

To have a >50% chance of limiting warming below 2 °C, most recent scenarios from integrated assessment models (IAMs) require large-scale deployment of negative emissions technologies (NETs). These are technologies that result in the net removal of greenhouse gases from the atmosphere. We quantify potential global impacts of the different NETs on various factors (such as land, greenhouse gas emissions, water, albedo, nutrients and energy) to determine the biophysical limits to, and economic costs of, their widespread application. Resource implications vary between technologies and need to be satisfactorily addressed if NETs are to have a significant role in achieving climate goals.

Biophysical Studies of Nanosecond Pulsed Electric Field Induced Cell Membrane Permeabilization

NASA Astrophysics Data System (ADS)

Wu, Yu-Hsuan

Nanosecond megavolts-per-meter pulsed electric field (nsPEF) offers a non-invasive manipulation of intracellular organelles and functions of biological cells. Accordingly, nsPEF is a potential technique for biophysical research and cancer therapy, and is of growing interest. Although, the application of nsPEF has shown electroperturbation on cell plasma membranes and intracellular membranes as well, the mechanisms underlying the electropermeabilization are still not clear. In this thesis, we systematically study nsPEFs (5 and 30 ns) induced membrane permeability change in biological cell in-vitro with different pulse parameters. In Chapter 3, we investigate the nsPEF-induced intracellular membrane permeabilization of mitochondria which play key roles in activating apoptosis in mammalian cells. The results show the evidences of nsPEF-induced membrane permeability increase in mitochondria, and suggest that nsPEF is a potential technology for cancer cell ablation without delivery of drug or gene into cells. In Chapter 2, 4 and 6, we study the properties of nsPEF-induced plasma membrane permeabilization. In the beginning, the change of plasma membrane permeability is studied by uptake of YO-PRO-1 and propidium iodide, fluorescent dyes specifically used as indicators of plasma membrane permeabilization. However, the detection is limited by the fluorescent emission efficiency and detector capability. To increase the detection sensitivity, we later develop a method based on cell volume change due to regulation of osmotic balance that causes water and small ions transport through plasma membrane. We find that even a single 10 MV/m pulse of 5 ns duration produces measureable cell swelling. The results demonstrate that cell swelling is susceptible to nsPEF and can detect membrane permeabilization more easily and precisely than fluorescent dyes. We compare the effects of different pulse parameters (pulse duration, pulse number, electric field amplitude and pulse repetition

On the biophysics and kinetics of toehold-mediated DNA strand displacement

PubMed Central

Srinivas, Niranjan; Ouldridge, Thomas E.; Šulc, Petr; Schaeffer, Joseph M.; Yurke, Bernard; Louis, Ard A.; Doye, Jonathan P. K.; Winfree, Erik

2013-01-01

Dynamic DNA nanotechnology often uses toehold-mediated strand displacement for controlling reaction kinetics. Although the dependence of strand displacement kinetics on toehold length has been experimentally characterized and phenomenologically modeled, detailed biophysical understanding has remained elusive. Here, we study strand displacement at multiple levels of detail, using an intuitive model of a random walk on a 1D energy landscape, a secondary structure kinetics model with single base-pair steps and a coarse-grained molecular model that incorporates 3D geometric and steric effects. Further, we experimentally investigate the thermodynamics of three-way branch migration. Two factors explain the dependence of strand displacement kinetics on toehold length: (i) the physical process by which a single step of branch migration occurs is significantly slower than the fraying of a single base pair and (ii) initiating branch migration incurs a thermodynamic penalty, not captured by state-of-the-art nearest neighbor models of DNA, due to the additional overhang it engenders at the junction. Our findings are consistent with previously measured or inferred rates for hybridization, fraying and branch migration, and they provide a biophysical explanation of strand displacement kinetics. Our work paves the way for accurate modeling of strand displacement cascades, which would facilitate the simulation and construction of more complex molecular systems. PMID:24019238

On the biophysics and kinetics of toehold-mediated DNA strand displacement.

PubMed

Srinivas, Niranjan; Ouldridge, Thomas E; Sulc, Petr; Schaeffer, Joseph M; Yurke, Bernard; Louis, Ard A; Doye, Jonathan P K; Winfree, Erik

2013-12-01

Dynamic DNA nanotechnology often uses toehold-mediated strand displacement for controlling reaction kinetics. Although the dependence of strand displacement kinetics on toehold length has been experimentally characterized and phenomenologically modeled, detailed biophysical understanding has remained elusive. Here, we study strand displacement at multiple levels of detail, using an intuitive model of a random walk on a 1D energy landscape, a secondary structure kinetics model with single base-pair steps and a coarse-grained molecular model that incorporates 3D geometric and steric effects. Further, we experimentally investigate the thermodynamics of three-way branch migration. Two factors explain the dependence of strand displacement kinetics on toehold length: (i) the physical process by which a single step of branch migration occurs is significantly slower than the fraying of a single base pair and (ii) initiating branch migration incurs a thermodynamic penalty, not captured by state-of-the-art nearest neighbor models of DNA, due to the additional overhang it engenders at the junction. Our findings are consistent with previously measured or inferred rates for hybridization, fraying and branch migration, and they provide a biophysical explanation of strand displacement kinetics. Our work paves the way for accurate modeling of strand displacement cascades, which would facilitate the simulation and construction of more complex molecular systems.

Towards Improving our Understanding on the Retrievals of Key Parameters Characterising Land Surface Interactions from Space: Introduction & First Results from the PREMIER-EO Project

NASA Astrophysics Data System (ADS)

Ireland, Gareth; North, Matthew R.; Petropoulos, George P.; Srivastava, Prashant K.; Hodges, Crona

2015-04-01

Acquiring accurate information on the spatio-temporal variability of soil moisture content (SM) and evapotranspiration (ET) is of key importance to extend our understanding of the Earth system's physical processes, and is also required in a wide range of multi-disciplinary research studies and applications. The utility and applicability of Earth Observation (EO) technology provides an economically feasible solution to derive continuous spatio-temporal estimates of key parameters characterising land surface interactions, including ET as well as SM. Such information is of key value to practitioners, decision makers and scientists alike. The PREMIER-EO project recently funded by High Performance Computing Wales (HPCW) is a research initiative directed towards the development of a better understanding of EO technology's present ability to derive operational estimations of surface fluxes and SM. Moreover, the project aims at addressing knowledge gaps related to the operational estimation of such parameters, and thus contribute towards current ongoing global efforts towards enhancing the accuracy of those products. In this presentation we introduce the PREMIER-EO project, providing a detailed overview of the research aims and objectives for the 1 year duration of the project's implementation. Subsequently, we make available the initial results of the work carried out herein, in particular, related to an all-inclusive and robust evaluation of the accuracy of existing operational products of ET and SM from different ecosystems globally. The research outcomes of this project, once completed, will provide an important contribution towards addressing the knowledge gaps related to the operational estimation of ET and SM. This project results will also support efforts ongoing globally towards the operational development of related products using technologically advanced EO instruments which were launched recently or planned be launched in the next 1-2 years. Key Words: PREMIER

A Self-Organizing State-Space-Model Approach for Parameter Estimation in Hodgkin-Huxley-Type Models of Single Neurons

PubMed Central

Vavoulis, Dimitrios V.; Straub, Volko A.; Aston, John A. D.; Feng, Jianfeng

2012-01-01

Traditional approaches to the problem of parameter estimation in biophysical models of neurons and neural networks usually adopt a global search algorithm (for example, an evolutionary algorithm), often in combination with a local search method (such as gradient descent) in order to minimize the value of a cost function, which measures the discrepancy between various features of the available experimental data and model output. In this study, we approach the problem of parameter estimation in conductance-based models of single neurons from a different perspective. By adopting a hidden-dynamical-systems formalism, we expressed parameter estimation as an inference problem in these systems, which can then be tackled using a range of well-established statistical inference methods. The particular method we used was Kitagawa's self-organizing state-space model, which was applied on a number of Hodgkin-Huxley-type models using simulated or actual electrophysiological data. We showed that the algorithm can be used to estimate a large number of parameters, including maximal conductances, reversal potentials, kinetics of ionic currents, measurement and intrinsic noise, based on low-dimensional experimental data and sufficiently informative priors in the form of pre-defined constraints imposed on model parameters. The algorithm remained operational even when very noisy experimental data were used. Importantly, by combining the self-organizing state-space model with an adaptive sampling algorithm akin to the Covariance Matrix Adaptation Evolution Strategy, we achieved a significant reduction in the variance of parameter estimates. The algorithm did not require the explicit formulation of a cost function and it was straightforward to apply on compartmental models and multiple data sets. Overall, the proposed methodology is particularly suitable for resolving high-dimensional inference problems based on noisy electrophysiological data and, therefore, a potentially useful tool in

A multivariate decision tree analysis of biophysical factors in tropical forest fire occurrence

Treesearch

Rey S. Ofren; Edward Harvey

2000-01-01

A multivariate decision tree model was used to quantify the relative importance of complex hierarchical relationships between biophysical variables and the occurrence of tropical forest fires. The study site is the Huai Kha Kbaeng wildlife sanctuary, a World Heritage Site in northwestern Thailand where annual fires are common and particularly destructive. Thematic...

Biophysical model for assessment of risk of acute exposures in combination with low level chronic irradiation

NASA Astrophysics Data System (ADS)

Smirnova, O. A.

A biophysical model is developed which describes the mortality dynamics in mammalian populations unexposed and exposed to radiation The model relates statistical biometric functions mortality rate life span probability density and life span probability with statistical characteristics and dynamics of a critical body system in individuals composing the population The model describing the dynamics of thrombocytopoiesis in nonirradiated and irradiated mammals is also developed this hematopoietic line being considered as the critical body system under exposures in question The mortality model constructed in the framework of the proposed approach was identified to reproduce the irradiation effects on populations of mice The most parameters of the thrombocytopoiesis model were determined from the data available in the literature on hematology and radiobiology the rest parameters were evaluated by fitting some experimental data on the dynamics of this system in acutely irradiated mice The successful verification of the thrombocytopoiesis model was fulfilled by the quantitative juxtaposition of the modeling predictions and experimental data on the dynamics of this system in mice exposed to either acute or chronic irradiation at wide ranges of doses and dose rates It is important that only experimental data on the mortality rate in nonirradiated population and the relevant statistical characteristics of the thrombocytopoiesis system in mice which are also available in the literature on radiobiology are needed for the final identification of

Laboratory Model of the Cardiovascular System for Experimental Demonstration of Pulse Wave Propagation

ERIC Educational Resources Information Center

Stojadinovic, Bojana; Nestorovic, Zorica; Djuric, Biljana; Tenne, Tamar; Zikich, Dragoslav; Žikic, Dejan

2017-01-01

The velocity by which a disturbance moves through the medium is the wave velocity. Pulse wave velocity is among the key parameters in hemodynamics. Investigation of wave propagation through the fluid-filled elastic tube has a great importance for the proper biophysical understanding of the nature of blood flow through the cardiovascular system.…

Biophysical connectivity explains population genetic structure in a highly dispersive marine species

NASA Astrophysics Data System (ADS)

Truelove, Nathan K.; Kough, Andrew S.; Behringer, Donald C.; Paris, Claire B.; Box, Stephen J.; Preziosi, Richard F.; Butler, Mark J.

2017-03-01

Connectivity, the exchange of individuals among locations, is a fundamental ecological process that explains how otherwise disparate populations interact. For most marine organisms, dispersal occurs primarily during a pelagic larval phase that connects populations. We paired population structure from comprehensive genetic sampling and biophysical larval transport modeling to describe how spiny lobster ( Panulirus argus) population differentiation is related to biological oceanography. A total of 581 lobsters were genotyped with 11 microsatellites from ten locations around the greater Caribbean. The overall F ST of 0.0016 ( P = 0.005) suggested low yet significant levels of structuring among sites. An isolation by geographic distance model did not explain spatial patterns of genetic differentiation in P. argus ( P = 0.19; Mantel r = 0.18), whereas a biophysical connectivity model provided a significant explanation of population differentiation ( P = 0.04; Mantel r = 0.47). Thus, even for a widely dispersing species, dispersal occurs over a continuum where basin-wide larval retention creates genetic structure. Our study provides a framework for future explorations of wide-scale larval dispersal and marine connectivity by integrating empirical genetic research and probabilistic modeling.

Geostatistical regularization of inverse models for the retrieval of vegetation biophysical variables

NASA Astrophysics Data System (ADS)

Atzberger, C.; Richter, K.

2009-09-01

The robust and accurate retrieval of vegetation biophysical variables using radiative transfer models (RTM) is seriously hampered by the ill-posedness of the inverse problem. With this research we further develop our previously published (object-based) inversion approach [Atzberger (2004)]. The object-based RTM inversion takes advantage of the geostatistical fact that the biophysical characteristics of nearby pixel are generally more similar than those at a larger distance. A two-step inversion based on PROSPECT+SAIL generated look-up-tables is presented that can be easily implemented and adapted to other radiative transfer models. The approach takes into account the spectral signatures of neighboring pixel and optimizes a common value of the average leaf angle (ALA) for all pixel of a given image object, such as an agricultural field. Using a large set of leaf area index (LAI) measurements (n = 58) acquired over six different crops of the Barrax test site, Spain), we demonstrate that the proposed geostatistical regularization yields in most cases more accurate and spatially consistent results compared to the traditional (pixel-based) inversion. Pros and cons of the approach are discussed and possible future extensions presented.

Interactive Biophysics with Microswimmers: Education, Cloud Experimentation, Programmed Swarms, and Biotic Games

NASA Astrophysics Data System (ADS)

Riedel-Kruse, Ingmar

Modern biotechnology gets increasingly powerful to manipulate and measure microscopic biophysical processes. Nevertheless, no platform exists to truly interact with these processes, certainly not with the convenience that we are accustomed to from our electronic smart devices. In my talk I will provide the rational for such Interactive Biotechnology and conceptualize its core component, the BPU (biotic processing unit), which is then connected to an according user interface. The biophysical phenomena currently featured on these platforms utilize the phototactic response of motile microorganisms, e.g., Euglena gracilis, resulting in spatio-temporal dynamics from the single cell to the self-organized multi-cellular scale. I will demonstrate multiple platforms, such as scalable biology cloud experimentation labs, tangible museum exhibits, biotic video games, low-cost interactive DIY kits using smartphones, and programming languages for swarm robotics. I will discuss applications for education as well as for professional and citizen science. Hence, we turn traditionally observational microscopy into an interactive experience. I was told that presenting in the educational section does not count against the ''one author - one talk policy'' - so I submit two abstracts. In case of conflict - please contact me: ingmar@stanford.edu.

Fine-tuning key parameters of an integrated reactor system for the simultaneous removal of COD, sulfate and ammonium and elemental sulfur reclamation.

PubMed

Yuan, Ye; Chen, Chuan; Liang, Bin; Huang, Cong; Zhao, Youkang; Xu, Xijun; Tan, Wenbo; Zhou, Xu; Gao, Shuang; Sun, Dezhi; Lee, Duujong; Zhou, Jizhong; Wang, Aijie

2014-03-30

In this paper, we proposed an integrated reactor system for simultaneous removal of COD, sulfate and ammonium (integrated C-S-N removal system) and investigated the key parameters of the system for a high level of elemental sulfur (S(0)) production. The system consisted of 4 main units: sulfate reduction and organic carbon removal (SR-CR), autotrophic and heterotrophic denitrifying sulfide removal (A&H-DSR), sulfur reclamation (SR), and aerated filter for aerobic nitrification (AN). In the system, the effects of key operational parameters on production of elemental sulfur were investigated, including hydraulic retention time (HRT) of each unit, sulfide/nitrate (S(2-)-S/NO3(-)-N) ratios, reflux ratios between the A&H-DSR and AN units, and loading rates of chemical oxygen demand (COD), sulfate and ammonium. Physico-chemical characteristics of biosulfur were studied for acquiring efficient S(0) recovery. The experiments successfully explored the optimum parameters for each unit and demonstrated 98% COD, 98% sulfate and 78% nitrogen removal efficiency. The optimum HRTs for SR-CR, A&H-DSR and AN were 12h, 3h and 3h, respectively. The reflux ratio of 3 could provide adequate S(2-)-S/NO3(-)-N ratio (approximately 1:1) to the A&H-DSR unit for obtaining maximum sulfur production. In this system, the maximum production of S(0) reached 90%, but only 60% S(0) was reclaimed from effluent. The S(0) that adhered to the outer layer of granules was deposited in the bottom of the A&H-DSR unit. Finally, the microbial community structure of the corresponding unit at different operational stage were analyzed by 16S rRNA gene based high throughput Illumina MiSeq sequencing and the potential function of dominant species were discussed. Copyright © 2013 Elsevier B.V. All rights reserved.

Deciphering the Biophysical Effects of Oxidizing Sulfur-Containing Amino Acids in Interferon-beta-1a using MS and HDX-MS

NASA Astrophysics Data System (ADS)

Houde, Damian J.; Bou-Assaf, George M.; Berkowitz, Steven A.

2017-05-01

Introduction of a chemical change to one or more amino acids in a protein's polypeptide chain can result in various effects on its higher-order structure (HOS) and biophysical behavior (or properties). These effects range from no detectable change to significant structural or conformational alteration that can greatly affect the protein's biophysical properties and its resulting biological function. The ability to reliably detect the absence or presence of such changes is essential to understanding the structure-function relationship in a protein and in the successful commercial development of protein-based drugs (biopharmaceuticals). In this paper, we focus our attention on the latter by specifically elucidating the impact of oxidation on the HOS, structural dynamics, and biophysical properties of interferon beta-1a (IFNβ-1a). Oxidation is a common biochemical modification that occurs in many biopharmaceuticals, specifically in two naturally-occurring sulfur-containing amino acids, methionine and cysteine. To carry out this work, we used combinations of hydrogen peroxide and pH to differentially oxidize IFNβ-1a (to focus on only methionine oxidation versus methionine and cysteine oxidation). We then employed several analytical and biophysical techniques to acquire information about the differential impact of these two oxidation scenarios on IFNβ-1a. In particular, the use of MS-based techniques, especially HDX-MS, play a dominant role in revealing the differential effects.

Preparation and biophysical characterization of recombinant Pseudomonas aeruginosa phosphorylcholine phosphatase.

PubMed

Beassoni, Paola R; Berti, Federico Pérez de; Otero, Lisandro H; Risso, Valeria A; Ferreyra, Raul G; Lisa, Angela T; Domenech, Carlos E; Ermácora, Mario R

2010-06-01

Pseudomonas aeruginosa infections constitute a widespread health problem with high economical and social impact, and the phosphorylcholine phosphatase (PchP) of this bacterium is a potential target for antimicrobial treatment. However, drug design requires high-resolution structural information and detailed biophysical knowledge not available for PchP. An obstacle in the study of PchP is that current methods for its expression and purification are suboptimal and allowed only a preliminary kinetic characterization of the enzyme. Herein, we describe a new procedure for the efficient preparation of recombinant PchP overexpressed in Escherichia coli. The enzyme is purified from urea solubilized inclusion bodies and refolded by dialysis. The product of PchP refolding is a mixture of native PchP and a kinetically-trapped, alternatively-folded aggregate that is very slowly converted into the native state. The properly folded and fully active enzyme is isolated from the refolding mixture by size-exclusion chromatography. PchP prepared by the new procedure was subjected to chemical and biophysical characterization, and its basic optical, hydrodynamic, metal-binding, and catalytic properties are reported. The unfolding of the enzyme was also investigated, and its thermal stability was determined. The obtained information should help to compare PchP with other phosphatases and to obtain a better understanding of its catalytic mechanism. In addition, preliminary trials showed that PchP prepared by the new protocol is suitable for crystallization, opening the way for high-resolution studies of the enzyme structure.

The Conformational Stability and Biophysical Properties of the Eukaryotic Thioredoxins of Pisum Sativum Are Not Family-Conserved

PubMed Central

Aguado-Llera, David; Martínez-Gómez, Ana Isabel; Prieto, Jesús; Marenchino, Marco; Traverso, José Angel; Gómez, Javier; Chueca, Ana; Neira, José L.

2011-01-01

Thioredoxins (TRXs) are ubiquitous proteins involved in redox processes. About forty genes encode TRX or TRX-related proteins in plants, grouped in different families according to their subcellular localization. For instance, the h-type TRXs are located in cytoplasm or mitochondria, whereas f-type TRXs have a plastidial origin, although both types of proteins have an eukaryotic origin as opposed to other TRXs. Herein, we study the conformational and the biophysical features of TRXh1, TRXh2 and TRXf from Pisum sativum. The modelled structures of the three proteins show the well-known TRX fold. While sharing similar pH-denaturations features, the chemical and thermal stabilities are different, being PsTRXh1 (Pisum sativum thioredoxin h1) the most stable isoform; moreover, the three proteins follow a three-state denaturation model, during the chemical-denaturations. These differences in the thermal- and chemical-denaturations result from changes, in a broad sense, of the several ASAs (accessible surface areas) of the proteins. Thus, although a strong relationship can be found between the primary amino acid sequence and the structure among TRXs, that between the residue sequence and the conformational stability and biophysical properties is not. We discuss how these differences in the biophysical properties of TRXs determine their unique functions in pea, and we show how residues involved in the biophysical features described (pH-titrations, dimerizations and chemical-denaturations) belong to regions involved in interaction with other proteins. Our results suggest that the sequence demands of protein-protein function are relatively rigid, with different protein-binding pockets (some in common) for each of the three proteins, but the demands of structure and conformational stability per se (as long as there is a maintained core), are less so. PMID:21364950

Nexus Between Protein–Ligand Affinity Rank-Ordering, Biophysical Approaches, and Drug Discovery

PubMed Central

2013-01-01

The confluence of computational and biophysical methods to accurately rank-order the binding affinities of small molecules and determine structures of macromolecular complexes is a potentially transformative advance in the work flow of drug discovery. This viewpoint explores the impact that advanced computational methods may have on the efficacy of small molecule drug discovery and optimization, particularly with respect to emerging fragment-based methods. PMID:24900579

Soil biochar amendment as a climate change mitigation tool: Key parameters and mechanisms involved.

PubMed

Brassard, Patrick; Godbout, Stéphane; Raghavan, Vijaya

2016-10-01

Biochar, a solid porous material obtained from the carbonization of biomass under low or no oxygen conditions, has been proposed as a climate change mitigation tool because it is expected to sequester carbon (C) for centuries and to reduce greenhouse gas (GHG) emissions from soils. This review aimed to identify key biochar properties and production parameters that have an effect on these specific applications of the biochar. Moreover, mechanisms involved in interactions between biochar and soils were highlighted. Following a compilation and comparison of the characteristics of 76 biochars from 40 research studies, biochars with a lower N content, and consequently a higher C/N ratio (>30), were found to be more suitable for mitigation of N2O emissions from soils. Moreover, biochars produced at a higher pyrolysis temperature, and with O/C ratio <0.2, H/Corg ratio <0.4 and volatile matter below 80% may have high C sequestration potential. Based on these observations, biochar production and application to the field can be used as a tool to mitigate climate change. However, it is important to determine the pyrolysis conditions and feedstock needed to produce a biochar with the desired properties for a specific application. More research studies are needed to identify the exact mechanisms involved following biochar amendment to soil. Copyright © 2016 Elsevier Ltd. All rights reserved.

Melatonin reverses the enhanced oxidative damage to membrane lipids and improves skin biophysical characteristics in former-smokers - A study in postmenopausal women.

PubMed

Sagan, Dorota; Stepniak, Jan; Gesing, Adam; Lewinski, Andrzej; Karbownik-Lewinska, Malgorzata

2017-12-23

Protective antioxidative effects of melatonin have been repeatedly documented in experimental and clinical studies. One of the most spectacular exogenous prooxidative agents is cigarette smoking. The aim of the study was to evaluate the level of oxidative damage to membrane lipids (lipid peroxidation; LPO) in blood serum, and in epidermis exfoliated during microdermabrasion collected from former-smokers who were treated with melatonin. The study was performed in postmenopausal women. Ninety (90) female volunteers, aged 46-67 years, were enrolled. Two major groups, i.e. never-smokers (n=44) and former-smokers (n=46), were divided into: Control, melatonin topical skin application, Restructurer (containing antioxidants) topical skin application, and melatonin oral treatment. Microdermabrasion was performed at point '0', after 2 weeks, and after 4 weeks of treatment. The following parameters were measured: LPO in blood serum, LPO in epidermis exfoliated during microdermabrasion, and skin biophysical characteristics, such as sebum, moisture, elasticity, and pigmentation. Malondialdehyde+4-hydroxyalkenals level (LPO index) was measured spectrophotometrically. Melatonin oral treatment significantly reversed the increased serum LPO level in former-smokers already after 2 weeks of treatment. In a univariate regression model, LPO blood level constituted the only independent factor negatively associated with melatonin oral treatment. After 4 weeks of treatment, melatonin given orally increased skin sebum, moisture and elasticity levels, and melatonin applied topically increased sebum level. Exogenous melatonin reverses the enhanced oxidative damage to membrane lipids and improves skin biophysical characteristics in former-smokers.

Quantification of biophysical adaptation benefits from Climate-Smart Agriculture using a Bayesian Belief Network.

PubMed

de Nijs, Patrick J; Berry, Nicholas J; Wells, Geoff J; Reay, Dave S

2014-10-20

The need for smallholder farmers to adapt their practices to a changing climate is well recognised, particularly in Africa. The cost of adapting to climate change in Africa is estimated to be $20 to $30 billion per year, but the total amount pledged to finance adaptation falls significantly short of this requirement. The difficulty of assessing and monitoring when adaptation is achieved is one of the key barriers to the disbursement of performance-based adaptation finance. To demonstrate the potential of Bayesian Belief Networks for describing the impacts of specific activities on climate change resilience, we developed a simple model that incorporates climate projections, local environmental data, information from peer-reviewed literature and expert opinion to account for the adaptation benefits derived from Climate-Smart Agriculture activities in Malawi. This novel approach allows assessment of vulnerability to climate change under different land use activities and can be used to identify appropriate adaptation strategies and to quantify biophysical adaptation benefits from activities that are implemented. We suggest that multiple-indicator Bayesian Belief Network approaches can provide insights into adaptation planning for a wide range of applications and, if further explored, could be part of a set of important catalysts for the expansion of adaptation finance.

Quantification of biophysical adaptation benefits from Climate-Smart Agriculture using a Bayesian Belief Network

NASA Astrophysics Data System (ADS)

de Nijs, Patrick J.; Berry, Nicholas J.; Wells, Geoff J.; Reay, Dave S.

2014-10-01

The need for smallholder farmers to adapt their practices to a changing climate is well recognised, particularly in Africa. The cost of adapting to climate change in Africa is estimated to be $20 to $30 billion per year, but the total amount pledged to finance adaptation falls significantly short of this requirement. The difficulty of assessing and monitoring when adaptation is achieved is one of the key barriers to the disbursement of performance-based adaptation finance. To demonstrate the potential of Bayesian Belief Networks for describing the impacts of specific activities on climate change resilience, we developed a simple model that incorporates climate projections, local environmental data, information from peer-reviewed literature and expert opinion to account for the adaptation benefits derived from Climate-Smart Agriculture activities in Malawi. This novel approach allows assessment of vulnerability to climate change under different land use activities and can be used to identify appropriate adaptation strategies and to quantify biophysical adaptation benefits from activities that are implemented. We suggest that multiple-indicator Bayesian Belief Network approaches can provide insights into adaptation planning for a wide range of applications and, if further explored, could be part of a set of important catalysts for the expansion of adaptation finance.

Biophysics and pathology of catheter energy delivery systems.

PubMed

Nath, S; Haines, D E

1995-01-01

Catheter ablation has rapidly emerged as the treatment of choice for many symptomatic cardiac arrhythmias. The initial experience with catheter ablation used high-energy DC as the energy source. However, over the last several years radiofrequency (RF) catheter ablation has become the dominant mode of energy delivery. Currently, a major limitation of RF ablation is the small lesion size created by this technique that has reduced its success rate in ablation of larger arrhythmogenic substrates such as coronary artery disease-related ventricular tachycardia. Alternate energy sources such as microwave or ultrasound catheter ablation are being developed that have the potential for producing larger lesions than RF ablation. This review will discuss the biophysics and pathophysiology of the various energy modalities used in catheter ablation.

BIOLOGICAL AND BIOPHYSICAL PROPERTIES OF VASCULAR CONNEXIN CHANNELS

PubMed Central

Johnstone, Scott; Isakson, Brant; Locke, Darren

2010-01-01

Intercellular channels formed by connexin proteins play a pivotal role in the direct movement of ions and larger cytoplasmic solutes between vascular endothelial cells, between vascular smooth muscle cells, and between endothelial and smooth muscle cells. Multiple genetic and epigenetic factors modulate connexin expression levels and/or channel function, including cell type-independent and cell type-specific transcription factors, posttranslational modification and localized membrane targeting. Additionally, differences in protein-protein interactions, including those between connexins, significantly contribute to both vascular homeostasis and disease progression. The biophysical properties of the connexin channels identified in the vasculature, those formed by Cx37, Cx40, Cx43 and/or Cx45 proteins, are discussed in this review in the physiological and pathophysiological context of vessel function. PMID:19815177

Biophysical Properties and Motility of Human Mature Dendritic Cells Deteriorated by Vascular Endothelial Growth Factor through Cytoskeleton Remodeling

PubMed Central

Hu, Zu-Quan; Xue, Hui; Long, Jin-Hua; Wang, Yun; Jia, Yi; Qiu, Wei; Zhou, Jing; Wen, Zong-Yao; Yao, Wei-Juan; Zeng, Zhu

2016-01-01

Dendritic cells (DCs), the most potent antigen-presenting cells, play a central role in the initiation, regulation, and maintenance of the immune responses. Vascular endothelial growth factor (VEGF) is one of the important cytokines in the tumor microenvironment (TME) and can inhibit the differentiation and functional maturation of DCs. To elucidate the potential mechanisms of DC dysfunction induced by VEGF, the effects of VEGF on the biophysical characteristics and motility of human mature DCs (mDCs) were investigated. The results showed that VEGF had a negative influence on the biophysical properties, including electrophoretic mobility, osmotic fragility, viscoelasticity, and transmigration. Further cytoskeleton structure analysis by confocal microscope and gene expression profile analyses by gene microarray and real-time PCR indicated that the abnormal remodeling of F-actin cytoskeleton may be the main reason for the deterioration of biophysical properties, motility, and stimulatory capability of VEGF-treated mDCs. This is significant for understanding the biological behavior of DCs and the immune escape mechanism of tumors. Simultaneously, the therapeutic efficacies may be improved by blocking the signaling pathway of VEGF in an appropriate manner before the deployment of DC-based vaccinations against tumors. PMID:27809226

PyFolding: Open-Source Graphing, Simulation, and Analysis of the Biophysical Properties of Proteins.

PubMed

Lowe, Alan R; Perez-Riba, Albert; Itzhaki, Laura S; Main, Ewan R G

2018-02-06

For many years, curve-fitting software has been heavily utilized to fit simple models to various types of biophysical data. Although such software packages are easy to use for simple functions, they are often expensive and present substantial impediments to applying more complex models or for the analysis of large data sets. One field that is reliant on such data analysis is the thermodynamics and kinetics of protein folding. Over the past decade, increasingly sophisticated analytical models have been generated, but without simple tools to enable routine analysis. Consequently, users have needed to generate their own tools or otherwise find willing collaborators. Here we present PyFolding, a free, open-source, and extensible Python framework for graphing, analysis, and simulation of the biophysical properties of proteins. To demonstrate the utility of PyFolding, we have used it to analyze and model experimental protein folding and thermodynamic data. Examples include: 1) multiphase kinetic folding fitted to linked equations, 2) global fitting of multiple data sets, and 3) analysis of repeat protein thermodynamics with Ising model variants. Moreover, we demonstrate how PyFolding is easily extensible to novel functionality beyond applications in protein folding via the addition of new models. Example scripts to perform these and other operations are supplied with the software, and we encourage users to contribute notebooks and models to create a community resource. Finally, we show that PyFolding can be used in conjunction with Jupyter notebooks as an easy way to share methods and analysis for publication and among research teams. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Biophysical properties of dermal building-blocks affects extra cellular matrix assembly in 3D endogenous macrotissue.

PubMed

Urciuolo, F; Garziano, A; Imparato, G; Panzetta, V; Fusco, S; Casale, C; Netti, P A

2016-01-29

The fabrication of functional tissue units is one of the major challenges in tissue engineering due to their in vitro use in tissue-on-chip systems, as well as in modular tissue engineering for the construction of macrotissue analogs. In this work, we aim to engineer dermal tissue micromodules obtained by culturing human dermal fibroblasts into porous gelatine microscaffold. We proved that such stromal cells coupled with gelatine microscaffolds are able to synthesize and to assemble an endogenous extracellular matrix (ECM) resulting in tissue micromodules, which evolve their biophysical features over the time. In particular, we found a time-dependent variation of oxygen consumption kinetic parameters, of newly formed ECM stiffness and of micromodules self-aggregation properties. As consequence when used as building blocks to fabricate larger tissues, the initial tissue micromodules state strongly affects the ECM organization and maturation in the final macrotissue. Such results highlight the role of the micromodules properties in controlling the formation of three-dimensional macrotissue in vitro, defining an innovative design criterion for selecting tissue-building blocks for modular tissue engineering.

Performance of device-independent quantum key distribution

NASA Astrophysics Data System (ADS)

Cao, Zhu; Zhao, Qi; Ma, Xiongfeng

2016-07-01

Quantum key distribution provides information-theoretically-secure communication. In practice, device imperfections may jeopardise the system security. Device-independent quantum key distribution solves this problem by providing secure keys even when the quantum devices are untrusted and uncharacterized. Following a recent security proof of the device-independent quantum key distribution, we improve the key rate by tightening the parameter choice in the security proof. In practice where the system is lossy, we further improve the key rate by taking into account the loss position information. From our numerical simulation, our method can outperform existing results. Meanwhile, we outline clear experimental requirements for implementing device-independent quantum key distribution. The maximal tolerable error rate is 1.6%, the minimal required transmittance is 97.3%, and the minimal required visibility is 96.8 % .

Beyond leaf color: Comparing camera-based phenological metrics with leaf biochemical, biophysical, and spectral properties throughout the growing season of a temperate deciduous forest

NASA Astrophysics Data System (ADS)

Yang, Xi; Tang, Jianwu; Mustard, John F.

2014-03-01

Plant phenology, a sensitive indicator of climate change, influences vegetation-atmosphere interactions by changing the carbon and water cycles from local to global scales. Camera-based phenological observations of the color changes of the vegetation canopy throughout the growing season have become popular in recent years. However, the linkages between camera phenological metrics and leaf biochemical, biophysical, and spectral properties are elusive. We measured key leaf properties including chlorophyll concentration and leaf reflectance on a weekly basis from June to November 2011 in a white oak forest on the island of Martha's Vineyard, Massachusetts, USA. Concurrently, we used a digital camera to automatically acquire daily pictures of the tree canopies. We found that there was a mismatch between the camera-based phenological metric for the canopy greenness (green chromatic coordinate, gcc) and the total chlorophyll and carotenoids concentration and leaf mass per area during late spring/early summer. The seasonal peak of gcc is approximately 20 days earlier than the peak of the total chlorophyll concentration. During the fall, both canopy and leaf redness were significantly correlated with the vegetation index for anthocyanin concentration, opening a new window to quantify vegetation senescence remotely. Satellite- and camera-based vegetation indices agreed well, suggesting that camera-based observations can be used as the ground validation for satellites. Using the high-temporal resolution dataset of leaf biochemical, biophysical, and spectral properties, our results show the strengths and potential uncertainties to use canopy color as the proxy of ecosystem functioning.

Lipid phase behavior studied with a quartz crystal microbalance: A technique for biophysical studies with applications in screening

NASA Astrophysics Data System (ADS)

Peschel, Astrid; Langhoff, Arne; Uhl, Eva; Dathathreyan, Aruna; Haindl, Susanne; Johannsmann, Diethelm; Reviakine, Ilya

2016-11-01

Quartz crystal microbalance (QCM) is emerging as a versatile tool for studying lipid phase behavior. The technique is attractive for fundamental biophysical studies as well applications because of its simplicity, flexibility, and ability to work with very small amounts of material crucial for biomedical studies. Further progress hinges on the understanding of the mechanism, by which a surface-acoustic technique such as QCM, senses lipid phase changes. Here, we use a custom-built instrument with improved sensitivity to investigate phase behavior in solid-supported lipid systems of different geometries (adsorbed liposomes and bilayers). We show that we can detect a model anesthetic (ethanol) through its effect on the lipid phase behavior. Further, through the analysis of the overtone dependence of the phase transition parameters, we show that hydrodynamic effects are important in the case of adsorbed liposomes, and viscoelasticity is significant in supported bilayers, while layer thickness changes make up the strongest contribution in both systems.

Prediction of Geomagnetic Activity and Key Parameters in High-latitude Ionosphere

NASA Technical Reports Server (NTRS)

Khazanov, George V.; Lyatsky, Wladislaw; Tan, Arjun; Ridley, Aaron

2007-01-01

Prediction of geomagnetic activity and related events in the Earth's magnetosphere and ionosphere are important tasks of US Space Weather Program. Prediction reliability is dependent on the prediction method, and elements included in the prediction scheme. Two of the main elements of such prediction scheme are: an appropriate geomagnetic activity index, and an appropriate coupling function (the combination of solar wind parameters providing the best correlation between upstream solar wind data and geomagnetic activity). We have developed a new index of geomagnetic activity, the Polar Magnetic (PM) index and an improved version of solar wind coupling function. PM index is similar to the existing polar cap PC index but it shows much better correlation with upstream solar wind/IMF data and other events in the magnetosphere and ionosphere. We investigate the correlation of PM index with upstream solar wind/IMF data for 10 years (1995-2004) that include both low and high solar activity. We also have introduced a new prediction function for the predicting of cross-polar-cap voltage and Joule heating based on using both PM index and upstream solar wind/IMF data. As we show such prediction function significantly increase the reliability of prediction of these important parameters. The correlation coefficients between the actual and predicted values of these parameters are approx. 0.9 and higher.

Biophysical Determinants of Front-Crawl Swimming at Moderate and Severe Intensities.

PubMed

Ribeiro, João; Toubekis, Argyris G; Figueiredo, Pedro; de Jesus, Kelly; Toussaint, Huub M; Alves, Francisco; Vilas-Boas, João P; Fernandes, Ricardo J

2017-02-01

To conduct a biophysical analysis of the factors associated with front-crawl performance at moderate and severe swimming intensities, represented by anaerobic-threshold (vAnT) and maximal-oxygen-uptake (vV̇O 2 max) velocities. Ten high-level swimmers performed 2 intermittent incremental tests of 7 × 200 and 12 × 25 m (through a system of underwater push-off pads) to assess vAnT, and vV̇O 2 max, and power output. The 1st protocol was videotaped (3D reconstruction) for kinematic analysis to assess stroke frequency (SF), stroke length (SL), propelling efficiency (η P ), and index of coordination (IdC). V̇O 2 was measured and capillary blood samples (lactate concentrations) were collected, enabling computation of metabolic power. The 2nd protocol allowed calculating mechanical power and performance efficiency from the ratio of mechanical to metabolic power. Neither vAnT nor vV̇O 2 max was explained by SF (0.56 ± 0.06 vs 0.68 ± 0.06 Hz), SL (2.29 ± 0.21 vs 2.06 ± 0.20 m), η P (0.38 ± 0.02 vs 0.36± 0.03), IdC (-12.14 ± 5.24 vs -9.61 ± 5.49), or metabolic-power (1063.00 ± 122.90 vs 1338.18 ± 127.40 W) variability. vV̇O 2 max was explained by power to overcome drag (r = .77, P ≤ .05) and η P (r = .72, P ≤ .05), in contrast with the nonassociation between these parameters and vAnT; both velocities were well related (r = .62, P ≤ .05). The biomechanical parameters, coordination, and metabolic power seemed not to be performance discriminative at either intensity. However, the increase in power to overcome drag, for the less metabolic input, should be the focus of any intervention that aims to improve performance at severe swimming intensity. This is also true for moderate intensities, as vAnT and vV˙O2max are proportional to each other.

The effect of halogen light stimulation on duration of ultrasound parameters of biophysical profile: a randomized clinical trial.

PubMed

Hanafi, Mohammad Ghasem; Sahraeizadeh, Aliakbar

2018-02-22

The objective is to assess if fetal halogen light stimulation can reduce the time needed to obtain a normal biophysical profile (BPP). Patients scheduled for a BPP and who satisfied the inclusion criteria were prospectively randomized to halogen light stimulation and no stimulation groups. The study group was exposed to handheld halogen light for 10 s whenever fetal breathing, movement, or tone was absent through the first 5 min of BPP. The time required to achieve complete BPP score was recorded. In patients with complete BPP score who had delivery within 1 week after the test, perinatal morbidity was examined. A total of 598 patients were randomized (light = 302, no light = 296). There was no difference between the two groups in terms of gestational age, maternal age, body mass index, and indication for BPP except for preterm labor (light: 9%, no light: 4%, p = 0.03). Among the patients who had a normal BPP score (n = 507), the mean (light: 7.1 ± 6 min, no light: 12.3 ± 8 min, p < 0.0001) and median (light: 4.3, no light: 8, p = 0.004) time needed to complete the BPP score was significantly less in the light stimulation group than the no stimulation group. Perinatal outcomes were not different between groups who had delivery during the first week after BPP. Fetal halogen light stimulation can be utilized to reduce the time needed to complete a BPP. However, further studies should be conducted in order to determine the effect of this method on decreasing non-reassuring test results. The study was submitted to the Registry of Clinical Trials on 04/20/2017 (IRCT2017041633470N1). After IRCT registration on 06/07/2017, we recruited patients from 06/08/2017 till 10/15/2017.

Biophysical characteristics of HIMAC clinical irradiation system for heavy-ion radiation therapy.

PubMed

Kanai, T; Endo, M; Minohara, S; Miyahara, N; Koyama-ito, H; Tomura, H; Matsufuji, N; Futami, Y; Fukumura, A; Hiraoka, T; Furusawa, Y; Ando, K; Suzuki, M; Soga, F; Kawachi, K

1999-04-01

The irradiation system and biophysical characteristics of carbon beams are examined regarding radiation therapy. An irradiation system was developed for heavy-ion radiotherapy. Wobbler magnets and a scatterer were used for flattening the radiation field. A patient-positioning system using X ray and image intensifiers was also installed in the irradiation system. The depth-dose distributions of the carbon beams were modified to make a spread-out Bragg peak, which was designed based on the biophysical characteristics of monoenergetic beams. A dosimetry system for heavy-ion radiotherapy was established to deliver heavy-ion doses safely to the patients according to the treatment planning. A carbon beam of 80 keV/microm in the spread-out Bragg peak was found to be equivalent in biological responses to the neutron beam that is produced at cyclotron facility in National Institute Radiological Sciences (NIRS) by bombarding 30-MeV deuteron beam on beryllium target. The fractionation schedule of the NIRS neutron therapy was adapted for the first clinical trials using carbon beams. Carbon beams, 290, 350, and 400 MeV/u, were used for a clinical trial from June of 1994. Over 300 patients have already been treated by this irradiation system by the end of 1997.

The Physics of Life: A Biophysics Course for Non-science Major Undergraduates

NASA Astrophysics Data System (ADS)

Parthasarathy, Raghuveer

2014-03-01

Enhancing the scientific literacy of non-scientists is an important goal, both because of the ever-increasing impact of science and technology on people's lives, and because understanding contemporary science enables enriching insights into the workings of nature. One route to improving scientific literacy is via general education undergraduate courses - i.e. courses intended for students not majoring in the sciences or engineering - which in many cases provide these students' last formal exposure to science. I describe here a course on biophysics for non-science-major undergraduates recently developed at the University of Oregon. Biophysics, I claim, is a particularly useful vehicle for addressing scientific literacy. It involves important and general scientific concepts, demonstrates connections between basic science and tangible, familiar phenomena related to health and disease, and illustrates how scientific insights proceed not in predictable paths, but rather by applying tools and perspectives from disparate fields in creative ways. In addition, it highlights the far-reaching impact of physics research. I describe the general design of this course and the specific content of a few of its modules, as well as noting aspects of enrollment and evaluation. This work is affiliated with the University of Oregon's Science Literacy Program, supported by a grant from the Howard Hughes Medical Institute.

An ultra-sensitive biophysical risk assessment of light effect on skin cells.

PubMed

Bennet, Devasier; Viswanath, Buddolla; Kim, Sanghyo; An, Jeong Ho

2017-07-18

The aim of this study was to analyze photo-dynamic and photo-pathology changes of different color light radiations on human adult skin cells. We used a real-time biophysical and biomechanics monitoring system for light-induced cellular changes in an in vitro model to find mechanisms of the initial and continuous degenerative process. Cells were exposed to intermittent, mild and intense (1-180 min) light with On/Off cycles, using blue, green, red and white light. Cellular ultra-structural changes, damages, and ECM impair function were evaluated by up/down-regulation of biophysical, biomechanical and biochemical properties. All cells exposed to different color light radiation showed significant changes in a time-dependent manner. Particularly, cell growth, stiffness, roughness, cytoskeletal integrity and ECM proteins of the human dermal fibroblasts-adult (HDF-a) cells showed highest alteration, followed by human epidermal keratinocytes-adult (HEK-a) cells and human epidermal melanocytes-adult (HEM-a) cells. Such changes might impede the normal cellular functions. Overall, the obtained results identify a new insight that may contribute to premature aging, and causes it to look aged in younger people. Moreover, these results advance our understanding of the different color light-induced degenerative process and help the development of new therapeutic strategies.

Climate Change Effects on Agriculture: Economic Responses to Biophysical Shocks

NASA Technical Reports Server (NTRS)

Nelson, Gerald C.; Valin, Hugo; Sands, Ronald D.; Havlik, Petr; Ahammad, Helal; Deryng, Delphine; Elliott, Joshua; Fujimori, Shinichiro; Hasegawa, Tomoko; Heyhoe, Edwina

2014-01-01

Agricultural production is sensitive to weather and thus directly affected by climate change. Plausible estimates of these climate change impacts require combined use of climate, crop, and economic models. Results from previous studies vary substantially due to differences in models, scenarios, and data. This paper is part of a collective effort to systematically integrate these three types of models. We focus on the economic component of the assessment, investigating how nine global economic models of agriculture represent endogenous responses to seven standardized climate change scenarios produced by two climate and five crop models. These responses include adjustments in yields, area, consumption, and international trade. We apply biophysical shocks derived from the Intergovernmental Panel on Climate Change's representative concentration pathway with end-of-century radiative forcing of 8.5 W/m(sup 2). The mean biophysical yield effect with no incremental CO2 fertilization is a 17% reduction globally by 2050 relative to a scenario with unchanging climate. Endogenous economic responses reduce yield loss to 11%, increase area of major crops by 11%, and reduce consumption by 3%. Agricultural production, cropland area, trade, and prices show the greatest degree of variability in response to climate change, and consumption the lowest. The sources of these differences include model structure and specification; in particular, model assumptions about ease of land use conversion, intensification, and trade. This study identifies where models disagree on the relative responses to climate shocks and highlights research activities needed to improve the representation of agricultural adaptation responses to climate change.

Climate change effects on agriculture: Economic responses to biophysical shocks

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

Nelson, Gerald; Valin, Hugo; Sands, Ronald

Agricultural production is sensitive to weather and will thus be directly affected by climate change. Plausible estimates of these climate change impacts require combined use of climate, crop, and economic models. Results from previous studies vary substantially due to differences in models, scenarios, and data. This paper is part of a collective effort to systematically integrate these three types of models. We focus on the economic component of the assessment, investigating how nine global economic models of agriculture represent endogenous responses to seven standardized climate change scenarios produced by two climate and five crop models. These responses include adjustments inmore » yields, area, consumption, and international trade. We apply biophysical shocks derived from the IPCC’s Representative Concentration Pathway that result in end-of-century radiative forcing of 8.5 watts per square meter. The mean biophysical impact on crop yield with no incremental CO2 fertilization is a 17 percent reduction globally by 2050 relative to a scenario with unchanging climate. Endogenous economic responses reduce yield loss to 11 percent, increase area of major crops by 12 percent, and reduce consumption by 2 percent. Agricultural production, cropland area, trade, and prices show the greatest degree of variability in response to climate change, and consumption the lowest. The sources of these differences includes model structure and specification; in particular, model assumptions about ease of land use conversion, intensification, and trade. This study identifies where models disagree on the relative responses to climate shocks and highlights research activities needed to improve the representation of agricultural adaptation responses to climate change.« less

Climate change effects on agriculture: Economic responses to biophysical shocks

PubMed Central

Nelson, Gerald C.; Valin, Hugo; Sands, Ronald D.; Havlík, Petr; Ahammad, Helal; Deryng, Delphine; Elliott, Joshua; Fujimori, Shinichiro; Hasegawa, Tomoko; Heyhoe, Edwina; Kyle, Page; Von Lampe, Martin; Lotze-Campen, Hermann; Mason d’Croz, Daniel; van Meijl, Hans; van der Mensbrugghe, Dominique; Müller, Christoph; Popp, Alexander; Robertson, Richard; Robinson, Sherman; Schmid, Erwin; Schmitz, Christoph; Tabeau, Andrzej; Willenbockel, Dirk

2014-01-01

Agricultural production is sensitive to weather and thus directly affected by climate change. Plausible estimates of these climate change impacts require combined use of climate, crop, and economic models. Results from previous studies vary substantially due to differences in models, scenarios, and data. This paper is part of a collective effort to systematically integrate these three types of models. We focus on the economic component of the assessment, investigating how nine global economic models of agriculture represent endogenous responses to seven standardized climate change scenarios produced by two climate and five crop models. These responses include adjustments in yields, area, consumption, and international trade. We apply biophysical shocks derived from the Intergovernmental Panel on Climate Change’s representative concentration pathway with end-of-century radiative forcing of 8.5 W/m2. The mean biophysical yield effect with no incremental CO2 fertilization is a 17% reduction globally by 2050 relative to a scenario with unchanging climate. Endogenous economic responses reduce yield loss to 11%, increase area of major crops by 11%, and reduce consumption by 3%. Agricultural production, cropland area, trade, and prices show the greatest degree of variability in response to climate change, and consumption the lowest. The sources of these differences include model structure and specification; in particular, model assumptions about ease of land use conversion, intensification, and trade. This study identifies where models disagree on the relative responses to climate shocks and highlights research activities needed to improve the representation of agricultural adaptation responses to climate change. PMID:24344285

Climate change effects on agriculture: economic responses to biophysical shocks.

PubMed

Nelson, Gerald C; Valin, Hugo; Sands, Ronald D; Havlík, Petr; Ahammad, Helal; Deryng, Delphine; Elliott, Joshua; Fujimori, Shinichiro; Hasegawa, Tomoko; Heyhoe, Edwina; Kyle, Page; Von Lampe, Martin; Lotze-Campen, Hermann; Mason d'Croz, Daniel; van Meijl, Hans; van der Mensbrugghe, Dominique; Müller, Christoph; Popp, Alexander; Robertson, Richard; Robinson, Sherman; Schmid, Erwin; Schmitz, Christoph; Tabeau, Andrzej; Willenbockel, Dirk

2014-03-04

Agricultural production is sensitive to weather and thus directly affected by climate change. Plausible estimates of these climate change impacts require combined use of climate, crop, and economic models. Results from previous studies vary substantially due to differences in models, scenarios, and data. This paper is part of a collective effort to systematically integrate these three types of models. We focus on the economic component of the assessment, investigating how nine global economic models of agriculture represent endogenous responses to seven standardized climate change scenarios produced by two climate and five crop models. These responses include adjustments in yields, area, consumption, and international trade. We apply biophysical shocks derived from the Intergovernmental Panel on Climate Change's representative concentration pathway with end-of-century radiative forcing of 8.5 W/m(2). The mean biophysical yield effect with no incremental CO2 fertilization is a 17% reduction globally by 2050 relative to a scenario with unchanging climate. Endogenous economic responses reduce yield loss to 11%, increase area of major crops by 11%, and reduce consumption by 3%. Agricultural production, cropland area, trade, and prices show the greatest degree of variability in response to climate change, and consumption the lowest. The sources of these differences include model structure and specification; in particular, model assumptions about ease of land use conversion, intensification, and trade. This study identifies where models disagree on the relative responses to climate shocks and highlights research activities needed to improve the representation of agricultural adaptation responses to climate change.

Crystallization, Preliminary X-ray Analysis and Biophysical Characterization of HPr Kinase/Phosphatase of Mycoplasma pneumoniae

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

Steinhauer, K.

2002-01-01

The Mycoplasma pneumoniae HPr kinase/phosphatase (HPrK/P) is a member of a large family of enzymes which are central to carbon regulation in Gram-positive bacteria. The full-length M. pneumonia HPrK/P was crystallized from solutions of polyethylene glycol 8000 and KCl or NaCl which also contained the non-hydrolysable ATP analog adenosine 5'-[{beta},{gamma}-methylene]triphosphate (AMPPCP). The crystals belong to the orthorhombic space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 117.1, b = 127.7, c = 170.7 {angstrom}. A complete X-ray intensity data set has been collected and processed to 2.50 {angstrom} resolution. The slow self-rotation function revealed the presence of amore » sixfold axis. Dynamic light-scattering (DLS) experiments indicated a molecular weight of 197 kDa for HPrK/P in the absence of AMPPCP and of 217 kDa in the presence of the ATP analog. Thus, the biophysical and crystallographic data suggest that HPrK/P is a functional hexamer that undergoes an ATP-binding-induced conformational change.« less

The Colorado Plateau II: biophysical, socioeconomic, and cultural research

USGS Publications Warehouse

Mattson, David J.; van Riper, Charles

2005-01-01

The publication of The Colorado Plateau: Cultural, Biological, and Physical Research in 2004 marked a timely summation of current research in the Four Corners states. This new volume, derived from the seventh Biennial Conference on the Colorado Plateau in 2003, complements the previous book by focusing on the integration of science into resource management issues. The 32 chapters range in content from measuring human impacts on cultural resources, through grazing and the wildland-urban interface issues, to parameters of climate change on the Plateau. The book also introduces economic perspectives by considering shifting patterns and regional disparities in the Colorado Plateau economy. A series of chapters on mountain lions explores the human-wildland interface. These chapters deal with the entire spectrum of challenges associated with managing this large mammal species in Arizona and on the Colorado Plateau, conveying a wealth of timely information of interest to wildlife managers and enthusiasts. Another provocative set of chapters on biophysical resources explores the management of forest restoration, from the micro scale all the way up to large-scale GIS analyses of ponderosa pine ecosystems on the Colorado Plateau. Given recent concerns for forest health in the wake of fires, severe drought, and bark-beetle infestation, these chapters will prove enlightening for forest service, park service, and land management professionals at both the federal and state level, as well as general readers interested in how forest management practices will ultimately affect their recreation activities. With broad coverage that touches on topics as diverse as movement patterns of rattlesnakes, calculating watersheds, and rescuing looted rockshelters, this volume stands as a compendium of cutting-edge research on the Colorado Plateau that offers a wealth of insights for many scholars.

The case for biophysics super-groups in physics departments.

PubMed

Hoogenboom, Bart W; Leake, Mark

2018-06-04

Increasing numbers of physicists engage in research activities that address biological questions from physics perspectives or strive to develop physics insights from active biological processes. The on-going development and success of such activities morph our ways of thinking about what it is to 'do biophysics' and add to our understanding of the physics of life. Many scientists in this research and teaching landscape are homed in physics departments. A challenge for a hosting department is how to group, name and structure such biophysicists to best add value to their emerging research and teaching but also to the portfolio of the whole department. Here we discuss these issues and speculate on strategies. Creative Commons Attribution license.

Frontiers in Laser Cooling, Single-Molecule Biophysics, and Energy Science: A Talk from Eric Cornell

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

Cornell, Eric

2008-08-30

Eric Cornell presents a talk at Frontiers in Laser Cooling, Single-Molecule Biophysics and Energy Science, a scientific symposium honoring Steve Chu, director of Lawrence Berkeley National Laboratory and recipient of the 1997 Nobel Prize in Physics. The symposium was held August 30, 2008 in Berkeley.

Frontiers in Laser Cooling, Single-Molecule Biophysics, and Energy Science: A Talk from Kurt Gibble

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

Gibble, Kurt

2008-08-30

Kurt Gibble presents a talk at Frontiers in Laser Cooling, Single-Molecule Biophysics and Energy Science, a scientific symposium honoring Steve Chu, director of Lawrence Berkeley National Laboratory and recipient of the 1997 Nobel Prize in Physics. The symposium was held August 30, 2008 in Berkeley.

Frontiers in Laser Cooling, Single-Molecule Biophysics, and Energy Science: A Talk from Jay Keasling

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

Keasling, Jay

2008-08-30

Jay Keasling presents a talk at Frontiers in Laser Cooling, Single-Molecule Biophysics and Energy Science, a scientific symposium honoring Steve Chu, director of Lawrence Berkeley National Laboratory and recipient of the 1997 Nobel Prize in Physics. The symposium was held August 30, 2008 in Berkeley.

Frontiers in Laser Cooling, Single-Molecule Biophysics, and Enrgy Science: A Talk by Carl Wieman

ScienceCinema

Wieman, Carl

2017-12-09

Carl Wieman presents a talk at Frontiers in Laser Cooling, Single-Molecule Biophysics and Energy Science, a scientific symposium honoring Steve Chu, director of Lawrence Berkeley National Laboratory and recipient of the 1997 Nobel Prize in Physics. The symposium was held August 30, 2008 in Berkeley.

Frontiers in Laser Cooling, Single-Molecule Biophysics, and Energy Science: A Talk from Eric Cornell

ScienceCinema

Cornell, Eric

2018-02-05

Eric Cornell presents a talk at Frontiers in Laser Cooling, Single-Molecule Biophysics and Energy Science, a scientific symposium honoring Steve Chu, director of Lawrence Berkeley National Laboratory and recipient of the 1997 Nobel Prize in Physics. The symposium was held August 30, 2008 in Berkeley.

Frontiers in Laser Cooling, Single-Molecule Biophysics, and Enrgy Science: A Talk by Carl Wieman

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

Wieman, Carl

Carl Wieman presents a talk at Frontiers in Laser Cooling, Single-Molecule Biophysics and Energy Science, a scientific symposium honoring Steve Chu, director of Lawrence Berkeley National Laboratory and recipient of the 1997 Nobel Prize in Physics. The symposium was held August 30, 2008 in Berkeley.

Frontiers in Laser Cooling, Single-Molecule Biophysics, and Energy Science: A Talk from Jay Keasling

ScienceCinema

Keasling, Jay

2018-02-14

Jay Keasling presents a talk at Frontiers in Laser Cooling, Single-Molecule Biophysics and Energy Science, a scientific symposium honoring Steve Chu, director of Lawrence Berkeley National Laboratory and recipient of the 1997 Nobel Prize in Physics. The symposium was held August 30, 2008 in Berkeley.

Frontiers in Laser Cooling, Single-Molecule Biophysics, and Energy Science: A Talk from Kurt Gibble

ScienceCinema

Gibble, Kurt

2018-02-05

Kurt Gibble presents a talk at Frontiers in Laser Cooling, Single-Molecule Biophysics and Energy Science, a scientific symposium honoring Steve Chu, director of Lawrence Berkeley National Laboratory and recipient of the 1997 Nobel Prize in Physics. The symposium was held August 30, 2008 in Berkeley.

Biophysical properties and functional significance of stem water storage tissues in Neotropical savanna trees.

Treesearch

F.G. Scholz; S.J. Bucci; G. Goldstein; F.C. Meinzer; A.C. Franco; F. Miralles-Wilhelm

2007-01-01

Biophysical characteristics of sapwood and outer parenchyma water storage compartments were studied in stems of eight dominant Brazilian Cerrado tree species to assess the impact of differences in tissue capacitance on whole-plant water relations. Both the sapwood and outer parenchyma tissues played an important role in regulation of internal water deficits of Cerrado...

Coupling the biophysical and social dimensions of wildfire risk to improve wildfire mitigation planning

Treesearch

Alan A. Ager; Jeffrey D. Kline; A. Paige Fisher

2015-01-01

We describe recent advances in biophysical and social aspects of risk and their potential combined contribution to improve mitigation planning on fire-prone landscapes. The methods and tools provide an improved method for defining the spatial extent of wildfire risk to communities compared to current planning processes. They also propose an expanded role for social...

[Parameters of cardiac muscle repolarization on the electrocardiogram when changing anatomical and electric position of the heart].

PubMed

Chaĭkovskiĭ, I A; Baum, O V; Popov, L A; Voloshin, V I; Budnik, N N; Frolov, Iu A; Kovalenko, A S

2014-01-01

While discussing the diagnostic value of the single channel electrocardiogram a set of theoretical considerations emerges inevitably, one of the most important among them is the question about dependence of the electrocardiogram parameters from the direction of electrical axis of heart. In other words, changes in what of electrocardiogram parameters are in fact liable to reflect pathological processes in myocardium, and what ones are determined by extracardiac factors, primarily by anatomic characteristics of patients. It is arguable that while analyzing electrocardiogram it is necessary to orient to such physiologically based informative indexes as ST segment displacement. Also, symmetry of the T wave shape is an important parameter which is independent of patients anatomic features. The results obtained are of interest for theoretical and applied aspects of the biophysics of the cardiac electric field.

A biophysical observation model for field potentials of networks of leaky integrate-and-fire neurons.

PubMed

Beim Graben, Peter; Rodrigues, Serafim

2012-01-01

We present a biophysical approach for the coupling of neural network activity as resulting from proper dipole currents of cortical pyramidal neurons to the electric field in extracellular fluid. Starting from a reduced three-compartment model of a single pyramidal neuron, we derive an observation model for dendritic dipole currents in extracellular space and thereby for the dendritic field potential (DFP) that contributes to the local field potential (LFP) of a neural population. This work aligns and satisfies the widespread dipole assumption that is motivated by the "open-field" configuration of the DFP around cortical pyramidal cells. Our reduced three-compartment scheme allows to derive networks of leaky integrate-and-fire (LIF) models, which facilitates comparison with existing neural network and observation models. In particular, by means of numerical simulations we compare our approach with an ad hoc model by Mazzoni et al. (2008), and conclude that our biophysically motivated approach yields substantial improvement.

[Pulmonary surfactants: in vivo structure and in vitro biophysical models for investigation and its perspectives].

PubMed

Lalchev, Z; Khristova, E; Vasiliev, Kh; Todorov, R; Ekserova, D

2007-01-01

The metabolism, composition, structure and functions of the alveolar surfactant (AS) are described. The most adequate biophysical models for investigation of AS are considered. The principals and possibilities of three mostly used models are described in details: Monolayers, Spinning drop method and Thin liquid films. Some of the studies of Bulgarian biophysical, physicochemical, biochemical and medical groups on the structure and mechanism of action of AS in vivo using samples of amniotic fluid (AF), animal pulmonary lavages (PL) and tracheal aspirates (TA) of newborns and adults are summarized. The role of specific surfactant proteins (SP-A, SP-B, SP-C and SP-D) on the properties and function of AS is demonstrated. The opportunities of the model investigations for application in laboratory pre- and postnatal diagnosis of the respiratory distress syndrome (RDS), as well as for the efficiency of RDS therapy during exogenous surfactant therapy with ALEC (UK), Survanta (USA), Exosurf (USA), Curosurf (Italy) u Alveofact (Germany) are considered.

A biophysical observation model for field potentials of networks of leaky integrate-and-fire neurons

PubMed Central

beim Graben, Peter; Rodrigues, Serafim

2013-01-01

We present a biophysical approach for the coupling of neural network activity as resulting from proper dipole currents of cortical pyramidal neurons to the electric field in extracellular fluid. Starting from a reduced three-compartment model of a single pyramidal neuron, we derive an observation model for dendritic dipole currents in extracellular space and thereby for the dendritic field potential (DFP) that contributes to the local field potential (LFP) of a neural population. This work aligns and satisfies the widespread dipole assumption that is motivated by the “open-field” configuration of the DFP around cortical pyramidal cells. Our reduced three-compartment scheme allows to derive networks of leaky integrate-and-fire (LIF) models, which facilitates comparison with existing neural network and observation models. In particular, by means of numerical simulations we compare our approach with an ad hoc model by Mazzoni et al. (2008), and conclude that our biophysically motivated approach yields substantial improvement. PMID:23316157

The Role of Parvalbumin, Sarcoplasmatic Reticulum Calcium Pump Rate, Rates of Cross-Bridge Dynamics, and Ryanodine Receptor Calcium Current on Peripheral Muscle Fatigue: A Simulation Study

PubMed Central

Neumann, Verena

2016-01-01

A biophysical model of the excitation-contraction pathway, which has previously been validated for slow-twitch and fast-twitch skeletal muscles, is employed to investigate key biophysical processes leading to peripheral muscle fatigue. Special emphasis hereby is on investigating how the model's original parameter sets can be interpolated such that realistic behaviour with respect to contraction time and fatigue progression can be obtained for a continuous distribution of the model's parameters across the muscle units, as found for the functional properties of muscles. The parameters are divided into 5 groups describing (i) the sarcoplasmatic reticulum calcium pump rate, (ii) the cross-bridge dynamics rates, (iii) the ryanodine receptor calcium current, (iv) the rates of binding of magnesium and calcium ions to parvalbumin and corresponding dissociations, and (v) the remaining processes. The simulations reveal that the first two parameter groups are sensitive to contraction time but not fatigue, the third parameter group affects both considered properties, and the fourth parameter group is only sensitive to fatigue progression. Hence, within the scope of the underlying model, further experimental studies should investigate parvalbumin dynamics and the ryanodine receptor calcium current to enhance the understanding of peripheral muscle fatigue. PMID:27980606

Performance evaluation of spectral vegetation indices using a statistical sensitivity function

USGS Publications Warehouse

Ji, Lei; Peters, Albert J.

2007-01-01

A great number of spectral vegetation indices (VIs) have been developed to estimate biophysical parameters of vegetation. Traditional techniques for evaluating the performance of VIs are regression-based statistics, such as the coefficient of determination and root mean square error. These statistics, however, are not capable of quantifying the detailed relationship between VIs and biophysical parameters because the sensitivity of a VI is usually a function of the biophysical parameter instead of a constant. To better quantify this relationship, we developed a “sensitivity function” for measuring the sensitivity of a VI to biophysical parameters. The sensitivity function is defined as the first derivative of the regression function, divided by the standard error of the dependent variable prediction. The function elucidates the change in sensitivity over the range of the biophysical parameter. The Student's t- or z-statistic can be used to test the significance of VI sensitivity. Additionally, we developed a “relative sensitivity function” that compares the sensitivities of two VIs when the biophysical parameters are unavailable.

Response of key soil parameters during compost-assisted phytostabilization in extremely acidic tailings: effect of plant species.

PubMed

Solís-Dominguez, Fernando A; White, Scott A; Hutter, Travis Borrillo; Amistadi, Mary Kay; Root, Robert A; Chorover, Jon; Maier, Raina M

2012-01-17

Phytostabilization of mine tailings acts to mitigate both eolian dispersion and water erosion events which can disseminate barren tailings over large distances. This technology uses plants to establish a vegetative cover to permanently immobilize contaminants in the rooting zone, often requiring addition of an amendment to assist plant growth. Here we report the results of a greenhouse study that evaluated the ability of six native plant species to grow in extremely acidic (pH ∼ 2.5) metalliferous (As, Pb, Zn: 2000-3000 mg kg(-1)) mine tailings from Iron King Mine Humboldt Smelter Superfund site when amended with a range of compost concentrations. Results revealed that three of the six plant species tested (buffalo grass, mesquite, and catclaw acacia) are good candidates for phytostabilization at an optimum level of 15% compost (w/w) amendment showing good growth and minimal shoot accumulation of metal(loid)s. A fourth candidate, quailbush, also met all criteria except for exceeding the domestic animal toxicity limit for shoot accumulation of zinc. A key finding of this study was that the plant species that grew most successfully on these tailings significantly influenced key tailings parameters; direct correlations between plant biomass and both increased tailings pH and neutrophilic heterotrophic bacterial counts were observed. We also observed decreased iron oxidizer counts and decreased bioavailability of metal(loid)s mainly as a result of compost amendment. Taken together, these results suggest that the phytostabilization process reduced tailings toxicity as well as the potential for metal(loid) mobilization. This study provides practical information on plant and tailings characteristics that is critically needed for successful implementation of assisted phytostabilization on acidic, metalliferous mine tailings sites.

Response of Key Soil Parameters During Compost-Assisted Phytostabilization in Extremely Acidic Tailings: Effect of Plant Species

PubMed Central

Solís-Dominguez, Fernando A.; White, Scott A.; Hutter, Travis Borrillo; Amistadi, Mary Kay; Root, Robert A.; Chorover, Jon; Maier, Raina M.

2012-01-01

Phytostabilization of mine tailings acts to mitigate both eolian dispersion and water erosion events which can disseminate barren tailings over large distances. This technology uses plants to establish a vegetative cover to permanently immobilize contaminants in the rooting zone, often requiring addition of an amendment to assist plant growth. Here we report the results of a greenhouse study that evaluated the ability of six native plant species to grow in extremely acidic (pH ~ 2.5) metalliferous (As, Pb, Zn: 2000–3000 mg kg−1) mine tailings from Iron King Mine Humboldt Smelter Superfund site when amended with a range of compost concentrations. Results revealed that three of the six plant species tested (buffalo grass, mesquite, and catclaw acacia) are good candidates for phytostabilization at an optimum level of 15% compost (w/w) amendment showing good growth and minimal shoot accumulation of metal(loid)s. A fourth candidate, quailbush, also met all criteria except for exceeding the domestic animal toxicity limit for shoot accumulation of zinc. A key finding of this study was that the plant species that grew most successfully on these tailings significantly influenced key tailings parameters; direct correlations between plant biomass and both increased tailings pH and neutrophilic heterotrophic bacterial counts were observed. We also observed decreased iron oxidizer counts and decreased bioavailability of metal(loid)s mainly as a result of compost amendment. Taken together, these results suggest that the phytostabilization process reduced tailings toxicity as well as the potential for metal(loid) mobilization. This study provides practical information on plant and tailings characteristics that is critically needed for successful implementation of assisted phytostabilization on acidic, metalliferous mine tailings sites. PMID:22191663

Lidar remote sensing of savanna biophysical attributes

NASA Astrophysics Data System (ADS)

Gwenzi, David

Although savanna ecosystems cover approximately 20 % of the terrestrial land surface and can have productivity equal to some closed forests, their role in the global carbon cycle is poorly understood. This study explored the applicability of a past spaceborne Lidar mission and the potential of future missions to estimate canopy height and carbon storage in these biomes. The research used data from two Oak savannas in California, USA: the Tejon Ranch Conservancy in Kern County and the Tonzi Ranch in Santa Clara County. In the first paper we used non-parametric regression techniques to estimate canopy height from waveform parameters derived from the Ice Cloud and land Elevation Satellite's Geoscience Laser Altimeter System (ICESat-GLAS) data. Merely adopting the methods derived for forests did not produce adequate results but the modeling was significantly improved by incorporating canopy cover information and interaction terms to address the high structural heterogeneity inherent to savannas. Paper 2 explored the relationship between canopy height and aboveground biomass. To accomplish this we developed generalized models using the classical least squares regression modeling approach to relate canopy height to above ground woody biomass and then employed Hierarchical Bayesian Analysis (HBA) to explore the implications of using generalized instead of species composition-specific models. Models that incorporated canopy cover proxies performed better than those that did not. Although the model parameters indicated interspecific variability, the distribution of the posterior densities of the differences between composition level and global level parameter values showed a high support for the use of global parameters, suggesting that these canopy height-biomass models are universally (large scale) applicable. As the spatial coverage of spaceborne lidar will remain limited for the immediate future, our objective in paper 3 was to explore the best means of extrapolating

Projected changes in diverse ecosystems from climate warming and biophysical drivers in northwest Alaska

Treesearch

Mark Torre Jorgenson; Bruce G. Marcot; David K. Swanson; Janet C. Jorgenson; Anthony R. DeGange

2015-01-01

Climate warming affects arctic and boreal ecosystems by interacting with numerous biophysical factors across heterogeneous landscapes. To assess potential effects of warming on diverse local-scale ecosystems (ecotypes) across northwest Alaska, we compiled data on historical areal changes over the last 25–50 years. Based on historical rates of change relative to time...

The Nexus Land-Use model version 1.0, an approach articulating biophysical potentials and economic dynamics to model competition for land-use

NASA Astrophysics Data System (ADS)

Souty, F.; Brunelle, T.; Dumas, P.; Dorin, B.; Ciais, P.; Crassous, R.; Müller, C.; Bondeau, A.

2012-10-01

Interactions between food demand, biomass energy and forest preservation are driving both food prices and land-use changes, regionally and globally. This study presents a new model called Nexus Land-Use version 1.0 which describes these interactions through a generic representation of agricultural intensification mechanisms within agricultural lands. The Nexus Land-Use model equations combine biophysics and economics into a single coherent framework to calculate crop yields, food prices, and resulting pasture and cropland areas within 12 regions inter-connected with each other by international trade. The representation of cropland and livestock production systems in each region relies on three components: (i) a biomass production function derived from the crop yield response function to inputs such as industrial fertilisers; (ii) a detailed representation of the livestock production system subdivided into an intensive and an extensive component, and (iii) a spatially explicit distribution of potential (maximal) crop yields prescribed from the Lund-Postdam-Jena global vegetation model for managed Land (LPJmL). The economic principles governing decisions about land-use and intensification are adapted from the Ricardian rent theory, assuming cost minimisation for farmers. In contrast to the other land-use models linking economy and biophysics, crops are aggregated as a representative product in calories and intensification for the representative crop is a non-linear function of chemical inputs. The model equations and parameter values are first described in details. Then, idealised scenarios exploring the impact of forest preservation policies or rising energy price on agricultural intensification are described, and their impacts on pasture and cropland areas are investigated.

Device-independent secret-key-rate analysis for quantum repeaters

NASA Astrophysics Data System (ADS)

Holz, Timo; Kampermann, Hermann; Bruß, Dagmar

2018-01-01

The device-independent approach to quantum key distribution (QKD) aims to establish a secret key between two or more parties with untrusted devices, potentially under full control of a quantum adversary. The performance of a QKD protocol can be quantified by the secret key rate, which can be lower bounded via the violation of an appropriate Bell inequality in a setup with untrusted devices. We study secret key rates in the device-independent scenario for different quantum repeater setups and compare them to their device-dependent analogon. The quantum repeater setups under consideration are the original protocol by Briegel et al. [Phys. Rev. Lett. 81, 5932 (1998), 10.1103/PhysRevLett.81.5932] and the hybrid quantum repeater protocol by van Loock et al. [Phys. Rev. Lett. 96, 240501 (2006), 10.1103/PhysRevLett.96.240501]. For a given repeater scheme and a given QKD protocol, the secret key rate depends on a variety of parameters, such as the gate quality or the detector efficiency. We systematically analyze the impact of these parameters and suggest optimized strategies.

An investigation of the key parameters for predicting PV soiling losses

DOE PAGES

Micheli, Leonardo; Muller, Matthew

2017-01-25

One hundred and two environmental and meteorological parameters have been investigated and compared with the performance of 20 soiling stations installed in the USA, in order to determine their ability to predict the soiling losses occurring on PV systems. The results of this investigation showed that the annual average of the daily mean particulate matter values recorded by monitoring stations deployed near the PV systems are the best soiling predictors, with coefficients of determination ( R 2) as high as 0.82. The precipitation pattern was also found to be relevant: among the different meteorological parameters, the average length of drymore » periods had the best correlation with the soiling ratio. Lastly, a preliminary investigation of two-variable regressions was attempted and resulted in an adjusted R 2 of 0.90 when a combination of PM 2.5 and a binary classification for the average length of the dry period was introduced.« less

Long-term plant responses to climate are moderated by biophysical attributes in a North American desert

USGS Publications Warehouse

Munson, Seth M.; Webb, Robert H.; Housman, David C.; Veblen, Kari E.; Nussear, Kenneth E.; Beever, Erik A.; Hartney, Kristine B.; Miriti, Maria N.; Phillips, Susan L.; Fulton, Robert E.; Tallent, Nita G.

2015-01-01

Synthesis. Our results emphasize the importance of understanding climate-vegetation relationships in the context of biophysical attributes that influence water availability and provide an important forecast of climate-change effects, including plant mortality and land degradation in dryland regions throughout the world.

Estimating crop biophysical properties from remote sensing data by inverting linked radiative transfer and ecophysiological models

USDA-ARS?s Scientific Manuscript database

Remote sensing technology can rapidly provide spatial information on crop growth status, which ideally could be used to invert radiative transfer models or ecophysiological models for estimating a variety of crop biophysical properties. However, the outcome of the model inversion procedure will be ...

Human Visual System as a Double-Slit Single Photon Interference Sensor: A Comparison between Modellistic and Biophysical Tests

PubMed Central

Pizzi, Rita; Wang, Rui; Rossetti, Danilo

2016-01-01

This paper describes a computational approach to the theoretical problems involved in the Young's single-photon double-slit experiment, focusing on a simulation of this experiment in the absence of measuring devices. Specifically, the human visual system is used in place of a photomultiplier or similar apparatus. Beginning with the assumption that the human eye perceives light in the presence of very few photons, we measure human eye performance as a sensor in a double-slit one-photon-at-a-time experimental setup. To interpret the results, we implement a simulation algorithm and compare its results with those of human subjects under identical experimental conditions. In order to evaluate the perceptive parameters exactly, which vary depending on the light conditions and on the subject’s sensitivity, we first review the existing literature on the biophysics of the human eye in the presence of a dim light source, and then use the known values of the experimental variables to set the parameters of the computational simulation. The results of the simulation and their comparison with the experiment involving human subjects are reported and discussed. It is found that, while the computer simulation indicates that the human eye has the capacity to detect the corpuscular nature of photons under these conditions, this was not observed in practice. The possible reasons for the difference between theoretical prediction and experimental results are discussed. PMID:26816029

Colloquium: Biophysical principles of undulatory self-propulsion in granular media

NASA Astrophysics Data System (ADS)

Goldman, Daniel I.

2014-07-01

Biological locomotion, movement within environments through self-deformation, encompasses a range of time and length scales in an organism. These include the electrophysiology of the nervous system, the dynamics of muscle activation, the mechanics of the skeletal system, and the interaction mechanics of such structures within natural environments like water, air, sand, and mud. Unlike the many studies of cellular and molecular scale biophysical processes, movement of entire organisms (like flies, lizards, and snakes) is less explored. Further, while movement in fluids like air and water is also well studied, little is known in detail of the mechanics that organisms use to move on and within flowable terrestrial materials such as granular media, ensembles of small particles that collectively display solid, fluid, and gaslike behaviors. This Colloquium reviews recent progress to understand principles of biomechanics and granular physics responsible for locomotion of the sandfish, a small desert-dwelling lizard that "swims" within sand using undulation of its body. Kinematic and muscle activity measurements of sand swimming using high speed x-ray imaging and electromyography are discussed. This locomotion problem poses an interesting challenge: namely, that equations that govern the interaction of the lizard with its environment do not yet exist. Therefore, complementary modeling approaches are also described: resistive force theory for granular media, multiparticle simulation modeling, and robotic physical modeling. The models reproduce biomechanical and neuromechanical aspects of sand swimming and give insight into how effective locomotion arises from the coupling of the body movement and flow of the granular medium. The argument is given that biophysical study of movement provides exciting opportunities to investigate emergent aspects of living systems that might not depend sensitively on biological details.

Can Simple Biophysical Principles Yield Complicated Biological Functions?

NASA Astrophysics Data System (ADS)

Liphardt, Jan

2011-03-01

About once a year, a new regulatory paradigm is discovered in cell biology. As of last count, eukaryotic cells have more than 40 distinct ways of regulating protein concentration and function. Regulatory possibilities include site-specific phosphorylation, epigenetics, alternative splicing, mRNA (re)localization, and modulation of nucleo-cytoplasmic transport. This raises a simple question. Do all the remarkable things cells do, require an intricately choreographed supporting cast of hundreds of molecular machines and associated signaling networks? Alternatively, are there a few simple biophysical principles that can generate apparently very complicated cellular behaviors and functions? I'll discuss two problems, spatial organization of the bacterial chemotaxis system and nucleo-cytoplasmic transport, where the latter might be true. In both cases, the ability to precisely quantify biological organization and function, at the single-molecule level, helped to find signatures of basic biological organizing principles.

Quenching of Tryptophan Fluorescence in Unfolded Cytochrome "c": A Biophysics Experiment for Physical Chemistry Students

ERIC Educational Resources Information Center

Schlamadinger, Diana E.; Kats, Dina I.; Kim, Judy E.

2010-01-01

Laboratory experiments that focus on protein folding provide excellent opportunities for undergraduate students to learn important topics in the expanding interdisciplinary field of biophysics. Here, we describe the use of Stern-Volmer plots to determine the extent of solvent accessibility of the single tryptophan residue (trp-59) in unfolded and…

Measurement of Key Pool BOiling Parameters in nanofluids for Nuclerar Applications

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

Bang, In C; Buongiorno, Jdacopo; Hu, Lin-wen

Nanofluids, colloidal dispersions of nanoparticles in a base fluid such as water, can afford very significant Critical Heat Flux (CHF) enhancement. Such engineered fluids potentially could be employed in reactors as advanced coolants in safety systems with significant safety and economic advantages. However, a satisfactory explanation of the CHF enhancement mechanism in nanofluids is lacking. To close this gap, we have identified the important boiling parameters to be measured. These are the properties (e.g., density, viscosity, thermal conductivity, specific heat, vaporization enthalpy, surface tension), hydrodynamic parameters (i.e., bubble size, bubble velocity, departure frequency, hot/dry spot dynamics) and surface conditions (i.e.,more » contact angle, nucleation site density). We have also deployed a pool boiling facility in which many such parameters can be measured. The facility is equipped with a thin indium-tin-oxide heater deposited over a sapphire substrate. An infra-red high-speed camera and an optical probe are used to measure the temperature distribution on the heater and the hydrodynamics above the heater, respectively. The first data generated with this facility already provide some clue on the CHF enhancement mechanism in nanofluids. Specifically, the progression to burnout in a pure fluid (ethanol in this case) is characterized by a smoothly-shaped and steadily-expanding hot spot. By contrast, in the ethanol-based nanofluid the hot spot pulsates and the progression to burnout lasts longer, although the nanofluid CHF is higher than the pure fluid CHF. The presence of a nanoparticle deposition layer on the heater surface seems to enhance wettability and aid hot spot dissipation, thus delaying burnout.« less

FIACH: A biophysical model for automatic retrospective noise control in fMRI.

PubMed

Tierney, Tim M; Weiss-Croft, Louise J; Centeno, Maria; Shamshiri, Elhum A; Perani, Suejen; Baldeweg, Torsten; Clark, Christopher A; Carmichael, David W

2016-01-01

Different noise sources in fMRI acquisition can lead to spurious false positives and reduced sensitivity. We have developed a biophysically-based model (named FIACH: Functional Image Artefact Correction Heuristic) which extends current retrospective noise control methods in fMRI. FIACH can be applied to both General Linear Model (GLM) and resting state functional connectivity MRI (rs-fcMRI) studies. FIACH is a two-step procedure involving the identification and correction of non-physiological large amplitude temporal signal changes and spatial regions of high temporal instability. We have demonstrated its efficacy in a sample of 42 healthy children while performing language tasks that include overt speech with known activations. We demonstrate large improvements in sensitivity when FIACH is compared with current methods of retrospective correction. FIACH reduces the confounding effects of noise and increases the study's power by explaining significant variance that is not contained within the commonly used motion parameters. The method is particularly useful in detecting activations in inferior temporal regions which have proven problematic for fMRI. We have shown greater reproducibility and robustness of fMRI responses using FIACH in the context of task induced motion. In a clinical setting this will translate to increasing the reliability and sensitivity of fMRI used for the identification of language lateralisation and eloquent cortex. FIACH can benefit studies of cognitive development in young children, patient populations and older adults. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

Lipid peroxidation in sarcoplasmic reticulum membranes: effect on functional and biophysical properties.

PubMed

Dinis, T C; Almeida, L M; Madeira, V M

1993-03-01

The fluorescent polyunsaturated parinaric acid (PnA) incorporated in sarcoplasmic reticulum membranes (SR) was used to probe the initial stages of membrane lipid peroxidation. The experimental set up of the PnA assay was investigated by means of several peroxidation initiators to ascertain peroxidation conditions. This assay in SR is particularly useful to evaluate the membrane susceptibility to peroxidation and to ascertain suitable conditions (concentration of initiators and cofactors) to challenge peroxidation in each preparation under study. On the basis of the PnA assay, Fe2+/ascorbate was selected among the different initiator systems to assess the effect of lipid peroxidation upon biochemical and biophysical parameters of SR membranes. Under mildly controlled conditions at 25 degrees C, the lipid degradative process, as detected by fatty acid analysis, decreases the Ca2+ uptake (up to about 50% of control) and reduces the Ca2+ pump efficiency (Ca2+/ATP ratio) up to about 58% of control, without inactivation the ATPase enzyme turnover. The effect of lipid peroxidation on the SR bilayer organization is dependent either on the extent of lipid peroxidation or on the depth of the bilayer as probed by fluorescence polarization of 1,6-diphenyl-1,3,5-hexatriene and by intramolecular excimerization of 1,3-di(1-pyrenyl)propane. It is concluded that the effect of mild lipid peroxidation on Ca2+ pump activity is partially exerted through the alteration of physical properties in the lipid phase or lipid-protein interfaces.

Concept design theory and model for multi-use space facilities: Analysis of key system design parameters through variance of mission requirements

NASA Astrophysics Data System (ADS)

Reynerson, Charles Martin

This research has been performed to create concept design and economic feasibility data for space business parks. A space business park is a commercially run multi-use space station facility designed for use by a wide variety of customers. Both space hardware and crew are considered as revenue producing payloads. Examples of commercial markets may include biological and materials research, processing, and production, space tourism habitats, and satellite maintenance and resupply depots. This research develops a design methodology and an analytical tool to create feasible preliminary design information for space business parks. The design tool is validated against a number of real facility designs. Appropriate model variables are adjusted to ensure that statistical approximations are valid for subsequent analyses. The tool is used to analyze the effect of various payload requirements on the size, weight and power of the facility. The approach for the analytical tool was to input potential payloads as simple requirements, such as volume, weight, power, crew size, and endurance. In creating the theory, basic principles are used and combined with parametric estimation of data when necessary. Key system parameters are identified for overall system design. Typical ranges for these key parameters are identified based on real human spaceflight systems. To connect the economics to design, a life-cycle cost model is created based upon facility mass. This rough cost model estimates potential return on investments, initial investment requirements and number of years to return on the initial investment. Example cases are analyzed for both performance and cost driven requirements for space hotels, microgravity processing facilities, and multi-use facilities. In combining both engineering and economic models, a design-to-cost methodology is created for more accurately estimating the commercial viability for multiple space business park markets.

Bone Marrow Regeneration Promoted by Biophysically Sorted Osteoprogenitors From Mesenchymal Stromal Cells

PubMed Central

Poon, Zhiyong; Lee, Wong Cheng; Guan, Guofeng; Nyan, Lin Myint; Lim, Chwee Teck; Han, Jongyoon

2015-01-01

Human tissue repair deficiencies can be supplemented through strategies to isolate, expand in vitro, and reimplant regenerative cells that supplant damaged cells or stimulate endogenous repair mechanisms. Bone marrow-derived mesenchymal stromal cells (MSCs), a subset of which is described as mesenchymal stem cells, are leading candidates for cell-mediated bone repair and wound healing, with hundreds of ongoing clinical trials worldwide. An outstanding key challenge for successful clinical translation of MSCs is the capacity to produce large quantities of cells in vitro with uniform and relevant therapeutic properties. By leveraging biophysical traits of MSC subpopulations and label-free microfluidic cell sorting, we hypothesized and experimentally verified that MSCs of large diameter within expanded MSC cultures were osteoprogenitors that exhibited significantly greater efficacy over other MSC subpopulations in bone marrow repair. Systemic administration of osteoprogenitor MSCs significantly improved survival rates (>80%) as compared with other MSC subpopulations (0%) for preclinical murine bone marrow injury models. Osteoprogenitor MSCs also exerted potent therapeutic effects as “cell factories” that secreted high levels of regenerative factors such as interleukin-6 (IL-6), interleukin-8 (IL-8), vascular endothelial growth factor A, bone morphogenetic protein 2, epidermal growth factor, fibroblast growth factor 1, and angiopoietin-1; this resulted in increased cell proliferation, vessel formation, and reduced apoptosis in bone marrow. This MSC subpopulation mediated rescue of damaged marrow tissue via restoration of the hematopoiesis-supporting stroma, as well as subsequent hematopoiesis. Together, the capabilities described herein for label-freeisolation of regenerative osteoprogenitor MSCs can markedly improve the efficacy of MSC-based therapies. PMID:25411477

Western white pine development in relation to biophysical characteristics across different spatial scales in the Coeur d'Alene River basin in northern Idaho, U.S.A

Treesearch

Theresa B. Jain; Russell T. Graham; Penelope Morgan

2002-01-01

Many studies have assessed tree development beneath canopies in forest ecosystems, but results are seldom placed within the context of broad-scale biophysical factors. Mapped landscape characteristics for three watersheds, located within the Coeur d’Alene River basin in northern Idaho, were integrated to create a spatial hierarchy reflecting biophysical factors that...

Microcomputer-Analyzed Initial Rate Kinetics of the Benzene-Enhanced Unfolding of Myoglobin: A Biophysical Chemistry Experiment.

ERIC Educational Resources Information Center

Schuh, Merlyn D.

1988-01-01

Describes a biophysical chemistry experiment that introduces students to globular protein conformation and microcomputer analysis of initial rate data for the unfolding of proteins. Presents background, materials needed and methodology. Uses a visible spectrometer for analysis. Lists educational benefits derived from the experiment. (ML)