Changes in biophysical properties of the skin following radiotherapy for breast cancer.

PubMed

Hu, Stephen Chu-Sung; Hou, Ming-Feng; Luo, Kuei-Hau; Chuang, Hung-Yi; Wei, Shu-Yi; Chen, Gwo-Shing; Chiang, Wenchang; Huang, Chih-Jen

2014-12-01

Acute radiation dermatitis is a common adverse effect in patients undergoing radiotherapy for breast cancer. However, the effects of radiotherapy on biophysical properties of the skin have rarely been investigated. In this prospective cohort study, we seek to determine the effects of radiotherapy for breast cancer on skin biophysical parameters. We measured various skin biophysical parameters (skin hydration, pH, sebum level, pigmentation, and blood flow) in 144 breast cancer patients by non-invasive techniques before and after radiotherapy. The measurements were simultaneously performed on the irradiated breast and the corresponding contralateral unirradiated breast for comparison. Following radiotherapy, the irradiated breast showed a significant decrease in skin hydration, increase in skin pH, increase in pigmentation, and increase in cutaneous blood flow. The contralateral unirradiated breast showed a slight increase in pigmentation but no significant changes in any of the other biophysical parameters after radiotherapy. No significant associations were found between patient characteristics (diabetes mellitus, hypertension, type of surgery, chemotherapy, hormone therapy) and changes in skin biophysical parameters following radiotherapy. In conclusion, radiation therapy for breast cancer induces measurable and significant changes in biophysical properties of the skin including hydration, pH, pigmentation, and blood flow. These findings give us a greater understanding of the effects of ionizing radiation on skin physiology, and provide non-invasive and objective methods to assess radiation dermatitis. © 2014 Japanese Dermatological Association.

Hybrid System for Ex Vivo Hemorheological and Hemodynamic Analysis: A Feasibility Study

PubMed Central

Yeom, Eunseop; Jun Kang, Yang; Joon Lee, Sang

2015-01-01

Precise measurement of biophysical properties is important to understand the relation between these properties and the outbreak of cardiovascular diseases (CVDs). However, a systematic measurement for these biophysical parameters under in vivo conditions is nearly impossible because of complex vessel shape and limited practicality. In vitro measurements can provide more biophysical information, but in vitro exposure changes hemorheological properties. In this study, a hybrid system composed of an ultrasound system and microfluidic device is proposed for monitoring hemorheological and hemodynamic properties under more reasonable experimental conditions. Biophysical properties including RBC aggregation, viscosity, velocity, and pressure of blood flows are simultaneously measured under various conditions to demonstrate the feasibility and performance of this measurement system. The proposed technique is applied to a rat extracorporeal loop which connects the aorta and jugular vein directly. As a result, the proposed system is found to measure biophysical parameters reasonably without blood collection from the rat and provided more detailed information. This hybrid system, combining ultrasound imaging and microfluidic techniques to ex vivo animal models, would be useful for monitoring the variations of biophysical properties induced by chemical agents. It can be used to understand the relation between biophysical parameters and CVDs. PMID:26090816

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 comparisons show significant improved results over non-a priori based retrievals.

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 (LST) product were found useful for empirical estimations of GPP in needleleaf forests, but were not useful for the other land cover types, whereas the land surface water index (LSWI) was more sensitive to noise from snowmelt, ground water table levels, and wet soils than to the canopy moisture levels. Also the MODIS EVI was better correlated with LST than was NDVI. Finally, the cross-site comparisons of GPP and multi-products from MODIS showed that the relationships between EVI and GPP were the strongest while LST and GPP was the weakest. EVI may thus be useful in scaling across landscapes, including heterogeneous ones, for regional estimations of GPP, especially if BRDF effects have been taken into account (such as with the NBAR product). Thus, the relationships of EVI-GPP over space and time would potentially provide much useful information for studies of the global carbon cycle.

Carbon-Water-Energy Relations for Selected River Basins

NASA Technical Reports Server (NTRS)

Choudhury, B. J.

1998-01-01

A biophysical process-based model was run using satellite, assimilated and ancillary data for four years (1987-1990) to calculate components of total evaporation (transpiration, interception, soil and snow evaporation), net radiation, absorbed photosynthetically active radiation and net primary productivity over the global land surface. Satellite observations provided fractional vegetation cover, solar and photosynthetically active radiation incident of the surface, surface albedo, fractional cloud cover, air temperature and vapor pressure. The friction velocity and surface air pressure are obtained from a four dimensional data assimilation results, while precipitation is either only surface observations or a blended product of surface and satellite observations. All surface and satellite data are monthly mean values; precipitation has been disaggregated into daily values. All biophysical parameters of the model are prescribed according to published records. From these global land surface calculations results for river basins are derived using digital templates of basin boundaries. Comparisons with field observations (micrometeorologic, catchment water balance, biomass production) and atmospheric water budget analysis for monthly evaporation from six river basins have been done to assess errors in the calculations. Comparisons are also made with previous estimates of zonal variations of evaporation and net primary productivity. Efficiencies of transpiration, total evaporation and radiation use, and evaporative fraction for selected river basins will be presented.

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 developed is very effective in predicting the dominant features of the scattering signatures required by the identification process and will be effective for informing further improvements in the instrumentation.

Characterizing Olive Grove Canopies by Means of Ground-Based Hemispherical Photography and Spaceborne RADAR Data

PubMed Central

Molina, Iñigo; Morillo, Carmen; García-Meléndez, Eduardo; Guadalupe, Rafael; Roman, Maria Isabel

2011-01-01

One of the main strengths of active microwave remote sensing, in relation to frequency, is its capacity to penetrate vegetation canopies and reach the ground surface, so that information can be drawn about the vegetation and hydrological properties of the soil surface. All this information is gathered in the so called backscattering coefficient (σ0). The subject of this research have been olive groves canopies, where which types of canopy biophysical variables can be derived by a specific optical sensor and then integrated into microwave scattering models has been investigated. This has been undertaken by means of hemispherical photographs and gap fraction procedures. Then, variables such as effective and true Leaf Area Indices have been estimated. Then, in order to characterize this kind of vegetation canopy, two models based on Radiative Transfer theory have been applied and analyzed. First, a generalized two layer geometry model made up of homogeneous layers of soil and vegetation has been considered. Then, a modified version of the Xu and Steven Water Cloud Model has been assessed integrating the canopy biophysical variables derived by the suggested optical procedure. The backscattering coefficients at various polarized channels have been acquired from RADARSAT 2 (C-band), with 38.5° incidence angle at the scene center. For the soil simulation, the best results have been reached using a Dubois scattering model and the VV polarized channel (r2 = 0.88). In turn, when effective LAI (LAIeff) has been taken into account, the parameters of the scattering canopy model are better estimated (r2 = 0.89). Additionally, an inversion procedure of the vegetation microwave model with the adjusted parameters has been undertaken, where the biophysical values of the canopy retrieved by this methodology fit properly with field measured values. PMID:22164028

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 rainfall amounts and green vegetation changes than were near-infrared changes. The information in the NDVI related to green leaf density changes primarily was from the visible reflectance. The contribution of the near-infrared reflectance to explaining green vegetation is largely reduced when there is a bright substrate.

Reconstruction of Cell Surface Densities of Ion Pumps, Exchangers, and Channels from mRNA Expression, Conductance Kinetics, Whole-Cell Calcium, and Current-Clamp Voltage Recordings, with an Application to Human Uterine Smooth Muscle Cells

PubMed Central

Atia, Jolene; McCloskey, Conor; Shmygol, Anatoly S.; Rand, David A.; van den Berg, Hugo A.; Blanks, Andrew M.

2016-01-01

Uterine smooth muscle cells remain quiescent throughout most of gestation, only generating spontaneous action potentials immediately prior to, and during, labor. This study presents a method that combines transcriptomics with biophysical recordings to characterise the conductance repertoire of these cells, the ‘conductance repertoire’ being the total complement of ion channels and transporters expressed by an electrically active cell. Transcriptomic analysis provides a set of potential electrogenic entities, of which the conductance repertoire is a subset. Each entity within the conductance repertoire was modeled independently and its gating parameter values were fixed using the available biophysical data. The only remaining free parameters were the surface densities for each entity. We characterise the space of combinations of surface densities (density vectors) consistent with experimentally observed membrane potential and calcium waveforms. This yields insights on the functional redundancy of the system as well as its behavioral versatility. Our approach couples high-throughput transcriptomic data with physiological behaviors in health and disease, and provides a formal method to link genotype to phenotype in excitable systems. We accurately predict current densities and chart functional redundancy. For example, we find that to evoke the observed voltage waveform, the BK channel is functionally redundant whereas hERG is essential. Furthermore, our analysis suggests that activation of calcium-activated chloride conductances by intracellular calcium release is the key factor underlying spontaneous depolarisations. PMID:27105427

A Fuzzy Cognitive Model of aeolian instability across the South Texas Sandsheet

NASA Astrophysics Data System (ADS)

Houser, C.; Bishop, M. P.; Barrineau, C. P.

2014-12-01

Characterization of aeolian systems is complicated by rapidly changing surface-process regimes, spatio-temporal scale dependencies, and subjective interpretation of imagery and spatial data. This paper describes the development and application of analytical reasoning to quantify instability of an aeolian environment using scale-dependent information coupled with conceptual knowledge of process and feedback mechanisms. Specifically, a simple Fuzzy Cognitive Model (FCM) for aeolian landscape instability was developed that represents conceptual knowledge of key biophysical processes and feedbacks. Model inputs include satellite-derived surface biophysical and geomorphometric parameters. FCMs are a knowledge-based Artificial Intelligence (AI) technique that merges fuzzy logic and neural computing in which knowledge or concepts are structured as a web of relationships that is similar to both human reasoning and the human decision-making process. Given simple process-form relationships, the analytical reasoning model is able to map the influence of land management practices and the geomorphology of the inherited surface on aeolian instability within the South Texas Sandsheet. Results suggest that FCMs can be used to formalize process-form relationships and information integration analogous to human cognition with future iterations accounting for the spatial interactions and temporal lags across the sand sheets.

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 compared to 15.8/28.5 for ISODATA. Three hyperspectral flights over the Kevin Dome area, covering 1843 ha, acquired 06/21/2014, 06/24/2015 and 06/26/2016 are examined with different methods of anomaly detection. Detection of anomalies within a single data set is examined to determine, on a local scale, areas that are significantly different from the surrounding area. Additionally, the detection and identification of persistent anomalies and non-persistent anomalies was investigated across multiple data sets.

Derivation of global vegetation biophysical parameters from EUMETSAT Polar System

NASA Astrophysics Data System (ADS)

García-Haro, Francisco Javier; Campos-Taberner, Manuel; Muñoz-Marí, Jordi; Laparra, Valero; Camacho, Fernando; Sánchez-Zapero, Jorge; Camps-Valls, Gustau

2018-05-01

This paper presents the algorithm developed in LSA-SAF (Satellite Application Facility for Land Surface Analysis) for the derivation of global vegetation parameters from the AVHRR (Advanced Very High Resolution Radiometer) sensor on board MetOp (Meteorological-Operational) satellites forming the EUMETSAT (European Organization for the Exploitation of Meteorological Satellites) Polar System (EPS). The suite of LSA-SAF EPS vegetation products includes the leaf area index (LAI), the fractional vegetation cover (FVC), and the fraction of absorbed photosynthetically active radiation (FAPAR). LAI, FAPAR, and FVC characterize the structure and the functioning of vegetation and are key parameters for a wide range of land-biosphere applications. The algorithm is based on a hybrid approach that blends the generalization capabilities offered by physical radiative transfer models with the accuracy and computational efficiency of machine learning methods. One major feature is the implementation of multi-output retrieval methods able to jointly and more consistently estimate all the biophysical parameters at the same time. We propose a multi-output Gaussian process regression (GPRmulti), which outperforms other considered methods over PROSAIL (coupling of PROSPECT and SAIL (Scattering by Arbitrary Inclined Leaves) radiative transfer models) EPS simulations. The global EPS products include uncertainty estimates taking into account the uncertainty captured by the retrieval method and input errors propagation. A sensitivity analysis is performed to assess several sources of uncertainties in retrievals and maximize the positive impact of modeling the noise in training simulations. The paper discusses initial validation studies and provides details about the characteristics and overall quality of the products, which can be of interest to assist the successful use of the data by a broad user's community. The consistent generation and distribution of the EPS vegetation products will constitute a valuable tool for monitoring of earth surface dynamic processes.

The hydrological cycle at European Fluxnet sites: modeling seasonal water and energy budgets at local scale.

NASA Astrophysics Data System (ADS)

Stockli, R.; Vidale, P. L.

2003-04-01

The importance of correctly including land surface processes in climate models has been increasingly recognized in the past years. Even on seasonal to interannual time scales land surface - atmosphere feedbacks can play a substantial role in determining the state of the near-surface climate. The availability of soil moisture for both runoff and evapotranspiration is dependent on biophysical processes occuring in plants and in the soil acting on a wide time-scale from minutes to years. Fluxnet site measurements in various climatic zones are used to drive three generations of LSM's (land surface models) in order to assess the level of complexity needed to represent vegetation processes at the local scale. The three models were the Bucket model (Manabe 1969), BATS 1E (Dickinson 1984) and SiB 2 (Sellers et al. 1996). Evapotranspiration and runoff processes simulated by these models range from simple one-layer soils and no-vegetation parameterizations to complex multilayer soils, including realistic photosynthesis-stomatal conductance models. The latter is driven by satellite remote sensing land surface parameters inheriting the spatiotemporal evolution of vegetation phenology. In addition a simulation with SiB 2 not only including vertical water fluxes but also lateral soil moisture transfers by downslope flow is conducted for a pre-alpine catchment in Switzerland. Preliminary results are presented and show that - depending on the climatic environment and on the season - a realistic representation of evapotranspiration processes including seasonally and interannually-varying state of vegetation is significantly improving the representation of observed latent and sensible heat fluxes on the local scale. Moreover, the interannual evolution of soil moisture availability and runoff is strongly dependent on the chosen model complexity. Biophysical land surface parameters from satellite allow to represent the seasonal changes in vegetation activity, which has great impact on the yearly budget of transpiration fluxes. For some sites, however, the hydrological cycle is simulated reasonably well even with simple land surface representations.

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.

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

NASA Astrophysics Data System (ADS)

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

2013-02-01

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

Plasma membrane--cortical cytoskeleton interactions: a cell biology approach with biophysical considerations.

PubMed

Kapus, András; Janmey, Paul

2013-07-01

From a biophysical standpoint, the interface between the cell membrane and the cytoskeleton is an intriguing site where a "two-dimensional fluid" interacts with an exceedingly complex three-dimensional protein meshwork. The membrane is a key regulator of the cytoskeleton, which not only provides docking sites for cytoskeletal elements through transmembrane proteins, lipid binding-based, and electrostatic interactions, but also serves as the source of the signaling events and molecules that control cytoskeletal organization and remolding. Conversely, the cytoskeleton is a key determinant of the biophysical and biochemical properties of the membrane, including its shape, tension, movement, composition, as well as the mobility, partitioning, and recycling of its constituents. From a cell biological standpoint, the membrane-cytoskeleton interplay underlies--as a central executor and/or regulator--a multitude of complex processes including chemical and mechanical signal transduction, motility/migration, endo-/exo-/phagocytosis, and other forms of membrane traffic, cell-cell, and cell-matrix adhesion. The aim of this article is to provide an overview of the tight structural and functional coupling between the membrane and the cytoskeleton. As biophysical approaches, both theoretical and experimental, proved to be instrumental for our understanding of the membrane/cytoskeleton interplay, this review will "oscillate" between the cell biological phenomena and the corresponding biophysical principles and considerations. After describing the types of connections between the membrane and the cytoskeleton, we will focus on a few key physical parameters and processes (force generation, curvature, tension, and surface charge) and will discuss how these contribute to a variety of fundamental cell biological functions. © 2013 American Physiological Society.

Spatio-temporal footprints of urbanisation in Surat, the Diamond City of India (1990-2009).

PubMed

Sharma, Richa; Ghosh, Aniruddha; Joshi, Pawan Kumar

2013-04-01

Urbanisation is a ubiquitous phenomenon with greater prominence in developing nations. Urban expansion involves land conversions from vegetated moisture-rich to impervious moisture-deficient land surfaces. The urban land transformations alter biophysical parameters in a mode that promotes development of heat islands and degrades environmental health. This study elaborates relationships among various environmental variables using remote sensing dataset to study spatio-temporal footprint of urbanisation in Surat city. Landsat Thematic Mapper satellite data were used in conjugation with geo-spatial techniques to study urbanisation and correlation among various satellite-derived biophysical parameters, [Normalised Difference Vegetation Index, Normalised Difference Built-up Index, Normalised Difference Water Index, Normalised Difference Bareness Index, Modified NDWI and land surface temperature (LST)]. Land use land cover was prepared using hierarchical decision tree classification with an accuracy of 90.4 % (kappa = 0.88) for 1990 and 85 % (kappa = 0.81) for 2009. It was found that the city has expanded over 42.75 km(2) within a decade, and these changes resulted in elevated surface temperatures. For example, transformation from vegetation to built-up has resulted in 5.5 ± 2.6 °C increase in land surface temperature, vegetation to fallow 6.7 ± 3 °C, fallow to built-up is 3.5 ± 2.9 °C and built-up to dense built-up is 5.3 ± 2.8 °C. Directional profiling for LST was done to study spatial patterns of LST in and around Surat city. Emergence of two new LST peaks for 2009 was observed in N-S and NE-SW profiles.

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 local climate, water cycle, ecosystems, their productivity and biodiversity, and thus important to consider in the formulation of adaptation policy. However before considering the inclusion of biophysical climate effects of LCC under the UNFCCC, science has to provide robust tools and methods for estimation of both country and global level effects.

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.

Essential climatic variables estimation with satellite imagery

NASA Astrophysics Data System (ADS)

Kolotii, A.; Kussul, N.; Shelestov, A.; Lavreniuk, M. S.

2016-12-01

According to Sendai Framework for Disaster Risk Reduction 2015 - 2030 Leaf Area Index (LAI) is considered as one of essential climatic variables. This variable represents the amount of leaf material in ecosystems and controls the links between biosphere and atmosphere through various processes and enables monitoring and quantitative assessment of vegetation state. LAI has added value for such important global resources monitoring tasks as drought mapping and crop yield forecasting with use of data from different sources [1-2]. Remote sensing data from space can be used to estimate such biophysical parameter at regional and national scale. High temporal satellite imagery is usually required to capture main parameters of crop growth [3]. Sentinel-2 mission launched in 2015 be ESA is a source of high spatial and temporal resolution satellite imagery for mapping biophysical parameters. Products created with use of automated Sen2-Agri system deployed during Sen2-Agri country level demonstration project for Ukraine will be compared with our independent results of biophysical parameters mapping. References Shelestov, A., Kolotii, A., Camacho, F., Skakun, S., Kussul, O., Lavreniuk, M., & Kostetsky, O. (2015, July). Mapping of biophysical parameters based on high resolution EO imagery for JECAM test site in Ukraine. In 2015 IEEE International Geoscience and Remote Sensing Symposium (IGARSS), 1733-1736 Kolotii, A., Kussul, N., Shelestov, A., Skakun, S., Yailymov, B., Basarab, R., ... & Ostapenko, V. (2015). Comparison of biophysical and satellite predictors for wheat yield forecasting in Ukraine. The International Archives of Photogrammetry, Remote Sensing and Spatial Information Sciences, 40(7), 39-44. Kussul, N., Lemoine, G., Gallego, F. J., Skakun, S. V., Lavreniuk, M., & Shelestov, A. Y. Parcel-Based Crop Classification in Ukraine Using Landsat-8 Data and Sentinel-1A Data. IEEE Journal of Selected Topics in Applied Earth Observations and Remote Sensing , 9 (6), 2500-2508.

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

Surface electrostatics of lipid bilayers by EPR of a pH-sensitive spin-labeled lipid.

PubMed

Voinov, Maxim A; Rivera-Rivera, Izarys; Smirnov, Alex I

2013-01-08

Many biophysical processes such as insertion of proteins into membranes and membrane fusion are governed by bilayer electrostatic potential. At the time of this writing, the arsenal of biophysical methods for such measurements is limited to a few techniques. Here we describe a, to our knowledge, new spin-probe electron paramagnetic resonance (EPR) approach for assessing the electrostatic surface potential of lipid bilayers that is based on a recently synthesized EPR probe (IMTSL-PTE) containing a reversibly ionizable nitroxide tag attached to the lipids' polar headgroup. EPR spectra of the probe directly report on its ionization state and, therefore, on electrostatic potential through changes in nitroxide magnetic parameters and the degree of rotational averaging. Further, the lipid nature of the probe provides its full integration into lipid bilayers. Tethering the nitroxide moiety directly to the lipid polar headgroup defines the location of the measured potential with respect to the lipid bilayer interface. Electrostatic surface potentials measured by EPR of IMTSL-PTE show a remarkable (within ±2%) agreement with the Gouy-Chapman theory for anionic DMPG bilayers in fluid (48°C) phase at low electrolyte concentration (50 mM) and in gel (17°C) phase at 150-mM electrolyte concentration. This agreement begins to diminish for DMPG vesicles in gel phase (17°C) upon varying electrolyte concentration and fluid phase bilayers formed from DMPG/DMPC and POPG/POPC mixtures. Possible reasons for such deviations, as well as the proper choice of an electrostatically neutral reference interface, have been discussed. Described EPR method is expected to be fully applicable to more-complex models of cellular membranes. Copyright © 2013 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Ionizable Nitroxides for Studying Local Electrostatic Properties of Lipid Bilayers and Protein Systems by EPR

PubMed Central

Voinov, Maxim A.; Smirnov, Alex I.

2016-01-01

Electrostatic interactions are known to play one of the major roles in the myriad of biochemical and biophysical processes. In this Chapter we describe biophysical methods to probe local electrostatic potentials of proteins and lipid bilayer systems that is based on an observation of reversible protonation of nitroxides by EPR. Two types of the electrostatic probes are discussed. The first one includes methanethiosulfonate derivatives of protonatable nitroxides that could be used for highly specific covalent modification of the cysteine’s sulfhydryl groups. Such spin labels are very similar in magnetic parameters and chemical properties to conventional MTSL making them suitable for studying local electrostatic properties of protein-lipid interfaces. The second type of EPR probes is designed as spin-labeled phospholipids having a protonatable nitroxide tethered to the polar head group. The probes of both types report on their ionization state through changes in magnetic parameters and a degree of rotational averaging, thus, allowing one to determine the electrostatic contribution to the interfacial pKa of the nitroxide, and, therefore, determining the local electrostatic potential. Due to their small molecular volume these probes cause a minimal perturbation to the protein or lipid system while covalent attachment secure the position of the reporter nitroxides. Experimental procedures to characterize and calibrate these probes by EPR and also the methods to analyze the EPR spectra by least-squares simulations are also outlined. The ionizable nitroxide labels and the nitroxide-labeled phospholipids described so far cover an exceptionally wide pH range from ca. 2.5 to 7.0 pH units making them suitable to study a broad range of biophysical phenomena especially at the negatively charged lipid bilayer surfaces. The rationale for selecting proper electrostatically neutral interface for calibrating such probes and example of studying surface potential of lipid bilayer is also described. PMID:26477252

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

NASA Astrophysics Data System (ADS)

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

2013-10-01

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

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

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.

The influence of larval migration and dispersal depth on potential larval trajectories of a deep-sea bivalve

NASA Astrophysics Data System (ADS)

McVeigh, Doreen M.; Eggleston, David B.; Todd, Austin C.; Young, Craig M.; He, Ruoying

2017-09-01

Many fundamental questions in marine ecology require an understanding of larval dispersal and connectivity, yet direct observations of larval trajectories are difficult or impossible to obtain. Although biophysical models provide an alternative approach, in the deep sea, essential biological parameters for these models have seldom been measured empirically. In this study, we used a biophysical model to explore the role of behaviorally mediated migration from two methane seep sites in the Gulf of Mexico on potential larval dispersal patterns and population connectivity of the deep-sea mussel ;Bathymodiolus; childressi, a species for which some biological information is available. Three possible larval dispersal strategies were evaluated for larvae with a Planktonic Larval Duration (PLD) of 395 days: (1) demersal drift, (2) dispersal near the surface early in larval life followed by an extended demersal period before settlement, and (3) dispersal near the surface until just before settlement. Upward swimming speeds varied in the model based on the best data available. Average dispersal distances for simulated larvae varied between 16 km and 1488 km. Dispersal in the upper water column resulted in the greatest dispersal distance (1173 km ± 2.00), followed by mixed dispersal depth (921 km ± 2.00). Larvae originating in the Gulf of Mexico can potentially seed most known seep metapopulations on the Atlantic continental margin, whereas larvae drifting demersally cannot (237 km ± 1.43). Depth of dispersal is therefore shown to be a critical parameter for models of deep-sea connectivity.

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.

A Simplified Biosphere Model for Global Climate Studies.

NASA Astrophysics Data System (ADS)

Xue, Y.; Sellers, P. J.; Kinter, J. L.; Shukla, J.

1991-03-01

The Simple Biosphere Model (SiB) as described in Sellers et al. is a bio-physically based model of land surface-atmosphere interaction. For some general circulation model (GCM) climate studies, further simplifications are desirable to have greater computation efficiency, and more important, to consolidate the parametric representation. Three major reductions in the complexity of SiB have been achieved in the present study.The diurnal variation of surface albedo is computed in SiB by means of a comprehensive yet complex calculation. Since the diurnal cycle is quite regular for each vegetation type, this calculation can be simplified considerably. The effect of root zone soil moisture on stomatal resistance is substantial, but the computation in SiB is complicated and expensive. We have developed approximations, which simulate the effects of reduced soil moisture more simply, keeping the essence of the biophysical concepts used in SiB.The surface stress and the fluxes of heat and moisture between the top of the vegetation canopy and an atmospheric reference level have been parameterized in an off-line version of SiB based upon the studies by Businger et al. and Paulson. We have developed a linear relationship between Richardson number and aero-dynamic resistance. Finally, the second vegetation layer of the original model does not appear explicitly after simplification. Compared to the model of Sellers et al., we have reduced the number of input parameters from 44 to 21. A comparison of results using the reduced parameter biosphere with those from the original formulation in a GCM and a zero-dimensional model shows the simplified version to reproduce the original results quite closely. After simplification, the computational requirement of SiB was reduced by about 55%.

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.

Ionizable Nitroxides for Studying Local Electrostatic Properties of Lipid Bilayers and Protein Systems by EPR.

PubMed

Voinov, Maxim A; Smirnov, Alex I

2015-01-01

Electrostatic interactions are known to play a major role in the myriad of biochemical and biophysical processes. Here, we describe biophysical methods to probe local electrostatic potentials of proteins and lipid bilayer systems that are based on an observation of reversible protonation of nitroxides by electron paramagnetic resonance (EPR). Two types of probes are described: (1) methanethiosulfonate derivatives of protonatable nitroxides for highly specific covalent modification of the cysteine's sulfhydryl groups and (2) spin-labeled phospholipids with a protonatable nitroxide tethered to the polar head group. The probes of both types report on their ionization state through changes in magnetic parameters and degree of rotational averaging, thus, allowing the electrostatic contribution to the interfacial pKa of the nitroxide, and, therefore, the local electrostatic potential to be determined. Due to their small molecular volume, these probes cause a minimal perturbation to the protein or lipid system. Covalent attachment secures the position of the reporter nitroxides. Experimental procedures to characterize and calibrate these probes by EPR, and also the methods to analyze the EPR spectra by simulations are outlined. The ionizable nitroxide labels and the nitroxide-labeled phospholipids described so far cover an exceptionally wide range of ca. 2.5-7.0 pH units, making them suitable to study a broad range of biophysical phenomena, especially at the negatively charged lipid bilayer surfaces. The rationale for selecting proper electrostatically neutral interface for probe calibration, and examples of lipid bilayer surface potential studies, are also described. © 2015 Elsevier Inc. All rights reserved.

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.

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.

Measuring grassland structure for recovery of grassland species at risk

NASA Astrophysics Data System (ADS)

Guo, Xulin; Gao, Wei; Wilmshurst, John

2005-09-01

An action plan for recovering species at risk (SAR) depends on an understanding of the plant community distribution, vegetation structure, quality of the food source and the impact of environmental factors such as climate change at large scale and disturbance at small scale, as these are fundamental factors for SAR habitat. Therefore, it is essential to advance our knowledge of understanding the SAR habitat distribution, habitat quality and dynamics, as well as developing an effective tool for measuring and monitoring SAR habitat changes. Using the advantages of non-destructive, low cost, and high efficient land surface vegetation biophysical parameter characterization, remote sensing is a potential tool for helping SAR recovery action. The main objective of this paper is to assess the most suitable techniques for using hyperspectral remote sensing to quantify grassland biophysical characteristics. The challenge of applying remote sensing in semi-arid and arid regions exists simply due to the lower biomass vegetation and high soil exposure. In conservation grasslands, this problem is enhanced because of the presence of senescent vegetation. Results from this study demonstrated that hyperspectral remote sensing could be the solution for semi-arid grassland remote sensing applications. Narrow band raw data and derived spectral vegetation indices showed stronger relationships with biophysical variables compared to the simulated broad band vegetation indices.

PRince: a web server for structural and physicochemical analysis of protein-RNA interface.

PubMed

Barik, Amita; Mishra, Abhishek; Bahadur, Ranjit Prasad

2012-07-01

We have developed a web server, PRince, which analyzes the structural features and physicochemical properties of the protein-RNA interface. Users need to submit a PDB file containing the atomic coordinates of both the protein and the RNA molecules in complex form (in '.pdb' format). They should also mention the chain identifiers of interacting protein and RNA molecules. The size of the protein-RNA interface is estimated by measuring the solvent accessible surface area buried in contact. For a given protein-RNA complex, PRince calculates structural, physicochemical and hydration properties of the interacting surfaces. All these parameters generated by the server are presented in a tabular format. The interacting surfaces can also be visualized with software plug-in like Jmol. In addition, the output files containing the list of the atomic coordinates of the interacting protein, RNA and interface water molecules can be downloaded. The parameters generated by PRince are novel, and users can correlate them with the experimentally determined biophysical and biochemical parameters for better understanding the specificity of the protein-RNA recognition process. This server will be continuously upgraded to include more parameters. PRince is publicly accessible and free for use. Available at http://www.facweb.iitkgp.ernet.in/~rbahadur/prince/home.html.

BIOPHYSICAL PARAMETERS DURING RADIOFREQUENCY CATHETER ABLATION OF SCAR-MEDIATED VENTRICULAR TACHYCARDIA: EPICARDIAL AND ENDOCARDIAL APPLICATIONS VIA MANUAL AND MAGNETIC NAVIGATION

PubMed Central

Bourke, Tara; Buch, Eric; Mathuria, Nilesh; Michowitz, Yoav; Yu, Ricky; Mandapati, Ravi; Shivkumar, Kalyanam; Tung, Roderick

2014-01-01

Background There is a paucity of data on biophysical parameters during radiofrequency ablation of scar-mediated ventricular tachycardia (VT). Methods and Results Data was collected from consecutive patients undergoing VT ablation with open-irrigation. Complete data was available for 372 lesions in 21 patients. The frequency of biophysical parameter changes were: >10Ω reduction (80%), bipolar EGM reduction (69%), while loss of capture was uncommon (32%). Unipolar injury current was seen in 72% of radiofrequency applications. Both EGM reduction and impedance drop were seen in 57% and a change in all 3 parameters was seen in only 20% of lesions. Late potentials were eliminated in 33%, reduced/modified in 56%, and remained after ablation in 11%. Epicardial lesions exhibited an impedance drop (90% vs 76%, p=0.002) and loss of capture (46% vs 27%, p<0.001) more frequently than endocardial lesions. Lesions delivered manually exhibited a >10Ω impedance drop (83% vs 71%, p=0.02) and an EGM reduction (71% vs 40%, p< 0.001) more frequently than lesions applied using magnetic navigation, although loss of capture, elimination of LPs, and a change in all 3 parameters were similarly observed. Conclusions VT ablation is inefficient as the majority of radiofrequency lesions do not achieve more than one targeted biophysical parameter. Only one-third of RF applications targeted at LPs result in complete elimination. Epicardial ablation within scar may be more effective than endocardial lesions and lesions applied manually may be more effective than lesions applied using magnetic navigation. New technologies directed at identifying and optimizing ablation effectiveness in scar are clinically warranted. PMID:24946895

Biophysical parameters during radiofrequency catheter ablation of scar-mediated ventricular tachycardia: epicardial and endocardial applications via manual and magnetic navigation.

PubMed

Bourke, Tara; Buch, Eric; Mathuria, Nilesh; Michowitz, Yoav; Yu, Ricky; Mandapati, Ravi; Shivkumar, Kalyanam; Tung, Roderick

2014-11-01

There is a paucity of data on biophysical parameters during radiofrequency ablation of scar-mediated ventricular tachycardia (VT). Data were collected from consecutive patients undergoing VT ablation with open-irrigation. Complete data were available for 372 lesions in 21 patients. The frequency of biophysical parameter changes were: >10Ω reduction (80%), bipolar EGM reduction (69%), while loss of capture was uncommon (32%). Unipolar injury current was seen in 72% of radiofrequency applications. Both EGM reduction and impedance drop were seen in 57% and a change in all 3 parameters was seen in only 20% of lesions. Late potentials were eliminated in 33%, reduced/modified in 56%, and remained after ablation in 11%. Epicardial lesions exhibited an impedance drop (90% vs. 76%, P = 0.002) and loss of capture (46% vs. 27%, P < 0.001) more frequently than endocardial lesions. Lesions delivered manually exhibited a >10Ω impedance drop (83% vs. 71%, P = 0.02) and an EGM reduction (71% vs. 40%, P < 0.001) more frequently than lesions applied using magnetic navigation, although loss of capture, elimination of LPs, and a change in all 3 parameters were similarly observed. VT ablation is inefficient as the majority of radiofrequency lesions do not achieve more than one targeted biophysical parameter. Only one-third of RF applications targeted at LPs result in complete elimination. Epicardial ablation within scar may be more effective than endocardial lesions, and lesions applied manually may be more effective than lesions applied using magnetic navigation. New technologies directed at identifying and optimizing ablation effectiveness in scar are clinically warranted. © 2014 Wiley Periodicals, Inc.

Characterization of atopic skin and the effect of a hyperforin-rich cream by laser scanning microscopy.

PubMed

Meinke, Martina C; Richter, Heike; Kleemann, Anke; Lademann, Juergen; Tscherch, Kathrin; Rohn, Sascha; Schempp, Christoph M

2015-05-01

Atopic dermatitis (AD) is a multifactorial inflammatory skin disease that affects both children and adults in an increasing manner. The treatment of AD often reduces subjective skin parameters, such as itching, dryness, and tension, but the inflammation cannot be cured. Laser scanning microscopy was used to investigate the skin surface, epidermal, and dermal characteristics of dry and atopic skin before and after treatment with an ointment rich in hyperforin, which is known for its anti-inflammatory effects. The results were compared to subjective parameters and transepidermal water loss, stratum corneum moisture, and stratum corneum lipids. Using biophysical methods, in particular laser scanning microscopy, it was found that atopic skin has distinct features compared to healthy skin. Treatment with a hyperforin-rich ointment resulted in an improvement of the stratum corneum moisture, skin surface dryness, skin lipids, and the subjective skin parameters, indicating that the barrier is stabilized and improved by the ointment. But in contrast to the improved skin surface, the inflammation in the deeper epidermis/dermis often continues to exist. This could be clearly shown by the reflectance confocal microscopy (RCM) measurements. Therefore, RCM measurements could be used to investigate the progress in treatment of atopic dermatitis.

Characterization of atopic skin and the effect of a hyperforin-rich cream by laser scanning microscopy

NASA Astrophysics Data System (ADS)

Meinke, Martina C.; Richter, Heike; Kleemann, Anke; Lademann, Juergen; Tscherch, Kathrin; Rohn, Sascha; Schempp, Christoph M.

2015-05-01

Atopic dermatitis (AD) is a multifactorial inflammatory skin disease that affects both children and adults in an increasing manner. The treatment of AD often reduces subjective skin parameters, such as itching, dryness, and tension, but the inflammation cannot be cured. Laser scanning microscopy was used to investigate the skin surface, epidermal, and dermal characteristics of dry and atopic skin before and after treatment with an ointment rich in hyperforin, which is known for its anti-inflammatory effects. The results were compared to subjective parameters and transepidermal water loss, stratum corneum moisture, and stratum corneum lipids. Using biophysical methods, in particular laser scanning microscopy, it was found that atopic skin has distinct features compared to healthy skin. Treatment with a hyperforin-rich ointment resulted in an improvement of the stratum corneum moisture, skin surface dryness, skin lipids, and the subjective skin parameters, indicating that the barrier is stabilized and improved by the ointment. But in contrast to the improved skin surface, the inflammation in the deeper epidermis/dermis often continues to exist. This could be clearly shown by the reflectance confocal microscopy (RCM) measurements. Therefore, RCM measurements could be used to investigate the progress in treatment of atopic dermatitis.

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.

Unmanned Aerial System (UAS)-based phenotyping of soybean using multi-sensor data fusion and extreme learning machine

NASA Astrophysics Data System (ADS)

Maimaitijiang, Maitiniyazi; Ghulam, Abduwasit; Sidike, Paheding; Hartling, Sean; Maimaitiyiming, Matthew; Peterson, Kyle; Shavers, Ethan; Fishman, Jack; Peterson, Jim; Kadam, Suhas; Burken, Joel; Fritschi, Felix

2017-12-01

Estimating crop biophysical and biochemical parameters with high accuracy at low-cost is imperative for high-throughput phenotyping in precision agriculture. Although fusion of data from multiple sensors is a common application in remote sensing, less is known on the contribution of low-cost RGB, multispectral and thermal sensors to rapid crop phenotyping. This is due to the fact that (1) simultaneous collection of multi-sensor data using satellites are rare and (2) multi-sensor data collected during a single flight have not been accessible until recent developments in Unmanned Aerial Systems (UASs) and UAS-friendly sensors that allow efficient information fusion. The objective of this study was to evaluate the power of high spatial resolution RGB, multispectral and thermal data fusion to estimate soybean (Glycine max) biochemical parameters including chlorophyll content and nitrogen concentration, and biophysical parameters including Leaf Area Index (LAI), above ground fresh and dry biomass. Multiple low-cost sensors integrated on UASs were used to collect RGB, multispectral, and thermal images throughout the growing season at a site established near Columbia, Missouri, USA. From these images, vegetation indices were extracted, a Crop Surface Model (CSM) was advanced, and a model to extract the vegetation fraction was developed. Then, spectral indices/features were combined to model and predict crop biophysical and biochemical parameters using Partial Least Squares Regression (PLSR), Support Vector Regression (SVR), and Extreme Learning Machine based Regression (ELR) techniques. Results showed that: (1) For biochemical variable estimation, multispectral and thermal data fusion provided the best estimate for nitrogen concentration and chlorophyll (Chl) a content (RMSE of 9.9% and 17.1%, respectively) and RGB color information based indices and multispectral data fusion exhibited the largest RMSE 22.6%; the highest accuracy for Chl a + b content estimation was obtained by fusion of information from all three sensors with an RMSE of 11.6%. (2) Among the plant biophysical variables, LAI was best predicted by RGB and thermal data fusion while multispectral and thermal data fusion was found to be best for biomass estimation. (3) For estimation of the above mentioned plant traits of soybean from multi-sensor data fusion, ELR yields promising results compared to PLSR and SVR in this study. This research indicates that fusion of low-cost multiple sensor data within a machine learning framework can provide relatively accurate estimation of plant traits and provide valuable insight for high spatial precision in agriculture and plant stress assessment.

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

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.

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 parameters in a wheat producer region in southern Brazil

NASA Astrophysics Data System (ADS)

Leivas, Janice F.; de C. Teixeira, Antonio Heriberto; Andrade, Ricardo G.; de C. Victoria, Daniel; Bolfe, Edson L.; Cruz, Caroline R.

2014-10-01

Wheat (Triticum aestivum) is the second most produced cereal in the world, and has major importance in the global agricultural economy. Brazil is a large producer of wheat, especially the Rio Grande do Sul state, located in the south of the country. The purpose of this study was to analyze the estimation of biophysical parameters - evapotranspiration (ET), biomass (BIO) and water productivity (WP) - from satellite images of the municipalities with large areas planted with wheat in Rio Grande do Sul (RS). The evapotranspiration rate was obtained using the SAFER Model (Simple Algorithm for Retrieving Evapotranspiration) on MODIS (Moderate Resolution Imaging Spectroradiometer) images taken in the agricultural year 2012. In order to obtain biomass and water productivity rates we applied the Monteith model and the ratio between BIO and ET. In the beginning of the cycle (the planting period) we observed low values for ET, BIO and WP. During the development period, we observed an increase in the values of the parameters and decline at the end of the cycle, for the period of the wheat harvest. The SAFER model proved effective for estimating the biophysical parameters evapotranspiration, biomass production and water productivity in areas planted with wheat in Brazilian Southern. The methodology can be used for monitoring the crops' water conditions and biomass using satellite images, assisting in estimates of productivity and crop yield. The results may assist the understanding of biophysical properties of important agro-ecosystems, like wheat crop, and are important to improve the rational use of water resources.

Comparative effects of a fixed Polypodium leucotomos/Pomegranate combination versus Polypodium leucotomos alone on skin biophysical parameters.

PubMed

Emanuele, Enzo; Bertona, Marco; Biagi, Marco

2017-02-01

Polypodium leucotomos extract is a commonly used systemic photoprotective agent. In an exploratory fashion, the current study aimed to compare the effects of oral supplementation with a fixed Polypodium leucotomos/pomegranate combination (PPmix®) versus Polypodium leucotomos alone (Fernblock®) on skin biophysical parameters of Caucasian adults. Forty healthy adult volunteers (20 males and 20 females; mean age: 37.2±5.5 years) were randomized in a 1:1 fashion to a fixed Polypodium leucotomos/pomegranate combination (480 mg/day; n=20) or Polypodium leucotomos alone (480 mg/day; n=20) for 3 months. Six skin biophysical parameters (skin sebum content, hydration, transepidermal water loss [TEWL], erythema index, melanin index, and elasticity) were measured at baseline and after 3 months by personnel blinded to participant allocation. At the end of the study, hydration and elasticity were significantly improved and TEWL was reduced in both groups, without significant intergroup differences. The erythema index was decreased by both treatments, although the fixed Polypodium leucotomos/pomegranate combination was significantly more effective. Finally, melanin index and skin sebum content were reduced by the fixed Polypodium leucotomos/pomegranate combination, whereas Polypodium leucotomos alone did not affect them. Our results suggest that a fixed Polypodium leucotomos/pomegranate combination provides a greater improvement of skin biophysical parameters compared to Polypodium leucotomos alone in adult Caucasians. Our findings may have implications for optimizing systemic skin photoprotection and beautification strategies.

The Correlation of Arterial Stiffness with Biophysical Parameters and Blood Biochemistry.

PubMed

Khiyami, Anamil M; Dore, Fiona J; Mammadova, Aytan; Amdur, Richard L; Sen, Sabyasachi

2017-05-01

Type 2 diabetes presents with numerous macrovascular and microvascular impairments, which in turn lead to various co-morbidities. Vascular co-morbidities can be seen when examining arterial stiffness (AS), which is a predictor for endothelial health and cardiovascular disease risk. Pulse wave analysis (PWA) and pulse wave velocity (PWV) are two tests that are commonly used to measure AS. Currently, disease states and progression are tracked via blood biochemistry. These gold standards in monitoring diabetes are expensive and need optimization. To investigate which biophysical and biochemical parameters correlated best with AS, which may reduce the number of biochemical tests and biophysical parameter measurements needed to track disease progression. Data from 42 subjects with type 2 diabetes mellitus for ≤10 years, aged 40-70 years, were analyzed at a single time point. We investigated various blood biochemistry, body composition, and AS parameters. A combination of fat mass and fat-free mass was most associated with PWA over any other parameters. Leptin and high-sensitivity C-reactive protein seem to be the next two parameters that correlate with augmentation index. No other parameters had strong correlations to either PWA or PWV values. Body composition methods seemed to be better predictors of type 2 diabetes mellitus patient's vascular disease progression. Our study indicates that body composition measurements may help replace expensive tests. This may have public health and health surveillance implications in countries facing financial challenges.

Brownian Motion and the Temperament of Living Cells

NASA Astrophysics Data System (ADS)

Tsekov, Roumen; Lensen, Marga C.

2013-07-01

The migration of living cells usually obeys the laws of Brownian motion. While the latter is due to the thermal motion of the surrounding matter, the locomotion of cells is generally associated with their vitality. We study what drives cell migration and how to model memory effects in the Brownian motion of cells. The concept of temperament is introduced as an effective biophysical parameter driving the motion of living biological entities in analogy with the physical parameter of temperature, which dictates the movement of lifeless physical objects. The locomemory of cells is also studied via the generalized Langevin equation. We explore the possibility of describing cell locomemory via the Brownian self-similarity concept. An heuristic expression for the diffusion coefficient of cells on structured surfaces is derived.

An Overview of the First International Satellite Land Surface Climatology Project (ISLSCP) Field Experiment (FIFE)

NASA Astrophysics Data System (ADS)

Sellers, P. J.; Hall, F. G.; Asrar, G.; Strebel, D. E.; Murphy, R. E.

1992-11-01

In the summer of 1983 a group of scientists working in the fields of meteorology, biology, and remote sensing met to discuss methods for modeling and observing land-surface—atmosphere interactions on regional and global scales. They concluded, first, that the existing climate models contained poor representations of the processes controlling the exchanges of energy, water, heat, and carbon between the land surface and the atmosphere and, second, that satellite remote sensing had been underutilized as a means of specifying global fields of the governing biophysical parameters. Accordingly, a multiscale, multidisciplinary experiment, FIFE, was initiated to address these two issues. The objectives of FIFE were specified as follows: (1) Upscale integration of models: The experiment was designed to test the soil-plant-atmosphere models developed by biometeorologists for small-scale applications (millimeters to meters) and to develop methods to apply them at the larger scales (kilometers) appropriate to atmospheric models and satellite remote sensing. (2) Application of satellite remote sensing: Even if the first goal were achieved to yield a "perfect" model of vegetation-atmosphere exchanges, it would have very limited applications without a global observing system for initialization and validation. As a result, the experiment was tasked with exploring methods for using satellite data to quantify important biophysical states and rates for model input. The experiment was centered on a 15 × 15 km grassland site near Manhattan, Kansas. This area became the focus for an extended monitoring program of satellite, meteorological, biophysical, and hydrological data acquisition from early 1987 through October 1989 and a series of 12- to 20-day intensive field campaigns (IFCs), four in 1987 and one in 1989. During the IFCs the fluxes of heat, moisture, carbon dioxide, and radiation were measured with surface and airborne equipment in coordination with measurements of surface and atmospheric parameters and satellite overpasses. The resulting data are held in a single integrated data base and continue to be analyzed by the participating scientists and others. The first two sections of this paper recount the history and scientific background leading up to FIFE; the third and fourth sections review the experiment design, the scientific teams and equipment involved, and the actual execution of the experiment; the fifth section provides an overview of the contents of this special issue; the sixth section summarizes the management and resources of the project; and the last section lists the acknowledgments.

Monitoring the resilience of rivers as social-ecological systems: a paradigm shift for river assessment in the 21st Century

EPA Science Inventory

First, we briefly describe the development of the major, biophysically-focused river assessment and monitoring approaches over the last 50 years. We then assess the utility of biophysical parameters for assessing rivers as social-ecological systems. We then develop a framework de...

Radiation budget changes with dry forest clearing in temperate Argentina.

PubMed

Houspanossian, Javier; Nosetto, Marcelo; Jobbágy, Esteban G

2013-04-01

Land cover changes may affect climate and the energy balance of the Earth through their influence on the greenhouse gas composition of the atmosphere (biogeochemical effects) but also through shifts in the physical properties of the land surface (biophysical effects). We explored how the radiation budget changes following the replacement of temperate dry forests by crops in central semiarid Argentina and quantified the biophysical radiative forcing of this transformation. For this purpose, we computed the albedo and surface temperature for a 7-year period (2003-2009) from MODIS imagery at 70 paired sites occupied by native forests and crops and calculated the radiation budget at the tropopause and surface levels using a columnar radiation model parameterized with satellite data. Mean annual black-sky albedo and diurnal surface temperature were 50% and 2.5 °C higher in croplands than in dry forests. These contrasts increased the outgoing shortwave energy flux at the top of the atmosphere in croplands by a quarter (58.4 vs. 45.9 W m(-2) ) which, together with a slight increase in the outgoing longwave flux, yielded a net cooling of -14 W m(-2) . This biophysical cooling effect would be equivalent to a reduction in atmospheric CO2 of 22 Mg C ha(-1) , which involves approximately a quarter to a half of the typical carbon emissions that accompany deforestation in these ecosystems. We showed that the replacement of dry forests by crops in central Argentina has strong biophysical effects on the energy budget which could counterbalance the biogeochemical effects of deforestation. Underestimating or ignoring these biophysical consequences of land-use changes on climate will certainly curtail the effectiveness of many warming mitigation actions, particularly in semiarid regions where high radiation load and smaller active carbon pools would increase the relative importance of biophysical forcing. © 2012 Blackwell Publishing Ltd.

Protein-ligand interactions investigated by thermal shift assays (TSA) and dual polarization interferometry (DPI).

PubMed

Grøftehauge, Morten K; Hajizadeh, Nelly R; Swann, Marcus J; Pohl, Ehmke

2015-01-01

Over the last decades, a wide range of biophysical techniques investigating protein-ligand interactions have become indispensable tools to complement high-resolution crystal structure determinations. Current approaches in solution range from high-throughput-capable methods such as thermal shift assays (TSA) to highly accurate techniques including microscale thermophoresis (MST) and isothermal titration calorimetry (ITC) that can provide a full thermodynamic description of binding events. Surface-based methods such as surface plasmon resonance (SPR) and dual polarization interferometry (DPI) allow real-time measurements and can provide kinetic parameters as well as binding constants. DPI provides additional spatial information about the binding event. Here, an account is presented of new developments and recent applications of TSA and DPI connected to crystallography.

Protein–ligand interactions investigated by thermal shift assays (TSA) and dual polarization interferometry (DPI)

PubMed Central

Grøftehauge, Morten K.; Hajizadeh, Nelly R.; Swann, Marcus J.; Pohl, Ehmke

2015-01-01

Over the last decades, a wide range of biophysical techniques investigating protein–ligand interactions have become indispensable tools to complement high-resolution crystal structure determinations. Current approaches in solution range from high-throughput-capable methods such as thermal shift assays (TSA) to highly accurate techniques including microscale thermophoresis (MST) and isothermal titration calorimetry (ITC) that can provide a full thermodynamic description of binding events. Surface-based methods such as surface plasmon resonance (SPR) and dual polarization interferometry (DPI) allow real-time measurements and can provide kinetic parameters as well as binding constants. DPI provides additional spatial information about the binding event. Here, an account is presented of new developments and recent applications of TSA and DPI connected to crystallography. PMID:25615858

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

The overarching goal of this study was to establish optimal hyperspectral vegetation indices (HVIs) and hyperspectral narrowbands (HNBs) that best characterize, classify, model, and map the world's main agricultural crops. The primary objectives were: (1) crop biophysical modeling through HNBs and HVIs, (2) accuracy assessment of crop type discrimination using Wilks' Lambda through a discriminant model, and (3) meta-analysis to select optimal HNBs and HVIs for applications related to agriculture. The study was conducted using two Earth Observing One (EO-1) Hyperion scenes and other surface hyperspectral data for the eight leading worldwide crops (wheat, corn, rice, barley, soybeans, pulses, cotton, and alfalfa) that occupy approx. 70% of all cropland areas globally. This study integrated data collected from multiple study areas in various agroecosystems of Africa, the Middle East, Central Asia, and India. Data were collected for the eight crop types in six distinct growth stages. These included (a) field spectroradiometer measurements (350-2500 nm) sampled at 1-nm discrete bandwidths, and (b) field biophysical variables (e.g., biomass, leaf area index) acquired to correspond with spectroradiometer measurements. The eight crops were described and classified using approx. 20 HNBs. The accuracy of classifying these 8 crops using HNBs was around 95%, which was approx. 25% better than the multi-spectral results possible from Landsat-7's Enhanced Thematic Mapper+ or EO-1's Advanced Land Imager. Further, based on this research and meta-analysis involving over 100 papers, the study established 33 optimal HNBs and an equal number of specific two-band normalized difference HVIs to best model and study specific biophysical and biochemical quantities of major agricultural crops of the world. Redundant bands identified in this study will help overcome the Hughes Phenomenon (or "the curse of high dimensionality") in hyperspectral data for a particular application (e.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.

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.

Molecular mechanism of direct proflavine-DNA intercalation: evidence for drug-induced minimum base-stacking penalty pathway.

PubMed

Sasikala, Wilbee D; Mukherjee, Arnab

2012-10-11

DNA intercalation, a biophysical process of enormous clinical significance, has surprisingly eluded molecular understanding for several decades. With appropriate configurational restraint (to prevent dissociation) in all-atom metadynamics simulations, we capture the free energy surface of direct intercalation from minor groove-bound state for the first time using an anticancer agent proflavine. Mechanism along the minimum free energy path reveals that intercalation happens through a minimum base stacking penalty pathway where nonstacking parameters (Twist→Slide/Shift) change first, followed by base stacking parameters (Buckle/Roll→Rise). This mechanism defies the natural fluctuation hypothesis and provides molecular evidence for the drug-induced cavity formation hypothesis. The thermodynamic origin of the barrier is found to be a combination of entropy and desolvation energy.

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.

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.

Variation of Biophysical Parameters of the Skin with Age, Gender, and Body Region

PubMed Central

Firooz, Alireza; Sadr, Bardia; Babakoohi, Shahab; Sarraf-Yazdy, Maryam; Fanian, Ferial; Kazerouni-Timsar, Ali; Nassiri-Kashani, Mansour; Naghizadeh, Mohammad Mehdi; Dowlati, Yahya

2012-01-01

Background. Understanding the physiological, chemical, and biophysical characteristics of the skin helps us to arrange a proper approach to the management of skin diseases. Objective. The aim of this study was to measure 6 biophysical characteristics of normal skin (sebum content, hydration, transepidermal water loss (TEWL), erythema index, melanin index, and elasticity) in a normal population and assess the effect of sex, age, and body location on them. Methods. Fifty healthy volunteers in 5 age groups (5 males and females in each) were enrolled in this study. A multifunctional skin physiology monitor (Courage & Khazaka electronic GmbH, Germany) was used to measure skin sebum content, hydration, TEWL, erythema index, melanin index, and elasticity in 8 different locations of the body. Results. There were significant differences between the hydration, melanin index, and elasticity of different age groups. Regarding the locations, forehead had the highest melanin index, where as palm had the lowest value. The mean values of erythema index and melanin index and TEWL were significantly higher in males and anatomic location was a significant independent factor for all of 6 measured parameters. Conclusion. Several biophysical properties of the skin vary among different gender, age groups, and body locations. PMID:22536139

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.

Monitoring of biophysical parameters of cashew plants in Cambodia using ALOS/PALSAR data.

PubMed

Avtar, Ram; Takeuchi, Wataru; Sawada, Haruo

2013-02-01

An accurate estimation of a plant's age is required for the prediction of yield and management practices. This study demonstrates the relationship between backscattering properties (σ°) of Phased Array type L-band Synthetic Aperture Radar (PALSAR) dual polarimetric data with cashew plants' biophysical parameters (height, age, crown diameter, diameter at breast height, basal area, tree density, and biomass) in Cambodia. PALSAR σ° has shown a positive correlation with the biophysical parameters of cashew plants. The value of σ° increases with the age of cashew plants. At a young stage, the cashew plants show a higher rate of an increase in σ° compared to that at the mature stage. The σ° horizontal polarization transmitted and vertical received (HV) shows higher sensitivity to the plant's growth than σ° horizontal polarization transmitted and received (HH). High backscattering and low variations were observed at mature stage (8-12 years) of cashew plantation. Saturation in backscattering has shown from the age of about 13 years. The validation results indicate strong coefficient of determination (R(2) = 0.86 and 0.88) for PALSAR-predicted age and biomass of cashew plants with root mean square error = 1.8 years and 16.3 t/ha for age and biomass, respectively. The correlations of σ° (HH) with biophysical parameters observed in the dry season were better than those of the rainy season because soil moisture interferes with backscattering in the rainy season. Biomass accumulation rate of cashew plants has been predicted that would be useful for selection of plants species to enhance carbon sequestration. This study provides an insight to use PALSAR for the monitoring of growth stages of plants at the regional level.

Improving Access to MODIS Biophysical Science Products for NACP Investigators

NASA Technical Reports Server (NTRS)

Wolfe, Robert E.; Gao, Feng; Morisette, Jeffrey T.; Ederer, Gregory A.; Pedelty, Jeffrey A.

2007-01-01

MODIS 4 NACP is a NASA-funded project supporting the North American Carbon Program (NACP). The purpose of this Advancing Collaborative Connections for Earth-Sun System Science (ACCESS) project is to provide researchers with Moderate Resolution Imaging Spectroradiometer (MODIS) biophysical data products that are custom tailored for use in NACP model studies. Standard MODIS biophysical products provide used to improve our understanding on the climate and ecosystem changes. However, direct uses of the MODIS biophysical parameters are constrained by retrieval quality and cloud contamination. Another challenge that NACP users face is acquiring MODIS data in formats and at spatial-temporal resolutions consistent with other data sets they use. We have been working closely with key NACP users to tailor the MODIS products to fit their needs. First, we provide new temporally smoothed and spatially continuous MODIS biophysical data sets. Second, we are distributing MODIS data at suitable spatial-temporal resolutions and in formats consistent with other data integration into model studies.

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 albedo feedback dominates simulated warming in spring in all three scenarios, while in summer, evapotranspiration feedback, governing the partitioning of the return energy flux from the surface to the atmosphere into latent and sensible heat, exerts evaporative cooling effects, the magnitude of which depends on the severity of climate change, in turn driven by the underlying GHG emissions pathway, resulting in shift in the sign of net biophysical at higher levels of warming. Spatially, western Siberia is identified as the most susceptible location, experiencing the potential to reverse biophysical feedbacks in all seasons. We further analyze how the pattern of vegetation shifts triggers different signs of net effects of biophysical feedbacks.

Satellites reveal contrasting responses of regional climate to the widespread greening of Earth.

PubMed

Forzieri, Giovanni; Alkama, Ramdane; Miralles, Diego G; Cescatti, Alessandro

2017-06-16

Changes in vegetation cover associated with the observed greening may affect several biophysical processes, whose net effects on climate are unclear. We analyzed remotely sensed dynamics in leaf area index (LAI) and energy fluxes in order to explore the associated variation in local climate. We show that the increasing trend in LAI contributed to the warming of boreal zones through a reduction of surface albedo and to an evaporation-driven cooling in arid regions. The interplay between LAI and surface biophysics is amplified up to five times under extreme warm-dry and cold-wet years. Altogether, these signals reveal that the recent dynamics in global vegetation have had relevant biophysical impacts on the local climates and should be considered in the design of local mitigation and adaptation plans. Copyright © 2017, American Association for the Advancement of Science.

To what extent does urbanisation affect fragmented grassland functioning?

PubMed

van der Walt, L; Cilliers, S S; Kellner, K; Du Toit, M J; Tongway, D

2015-03-15

Urbanisation creates altered environments characterised by increased human habitation, impermeable surfaces, artificial structures, landscape fragmentation, habitat loss, resulting in different resource loss pathways. The vulnerable Rand Highveld Grassland vegetation unit in the Tlokwe Municipal area, South Africa, has been extensively affected and transformed by urbanisation, agriculture, and mining. Grassland fragments in urban areas are often considered to be less species rich and less functional than in the more untransformed or "natural" exurban environments, and are therefore seldom a priority for conservation. Furthermore, urban grassland fragments are often being more intensely managed than exurban areas, such as consistent mowing in open urban areas. Four urbanisation measures acting as indicators for patterns and processes associated with urban areas were calculated for matrix areas surrounding each selected grassland fragment to quantify the position of each grassland remnant along an urbanisation gradient. The grassland fragments were objectively classified into two classes of urbanisation, namely "exurban" and "urban" based on the urbanisation measure values. Grazing was recorded in some exurban grasslands and mowing in some urban grassland fragments. Unmanaged grassland fragments were present in both urban and exurban areas. Fine-scale biophysical landscape function was determined by executing the Landscape Function Analysis (LFA) method. LFA assesses fine-scale landscape patchiness (entailing resource conserving potential and erosion resistance) and 11 soil surface indicators to produce three main LFA parameters (stability, infiltration, and nutrient cycling), which indicates how well a system is functioning in terms of fine-scale biophysical soil processes and characteristics. The aim of this study was to determine the effects of urbanisation and associated management practices on fine-scale biophysical landscape function of urban and exurban grassland fragments, as well as to determine the potential for the use of LFA in decision-making involving the conservation of grassland fragments. The results indicated that the occurrence, size and characteristics of vegetated patches, and especially the presence of litter abundances, were the main factors determining differences in the LFA indices. Furthermore, mowing resulted in the overall fine-scale biophysical indices being higher for some of the urban grassland fragments. This implied that it is not necessarily the influence of urbanisation entailing high or low resource conserving patchiness and patch quality, but rather the management practices associated with urban and exurban areas. Therefore, from a conservation point of view, the grassland fragments in the City of Potchefstroom are just as conservable (on a biophysical function level involving soil processes) than the more "natural" exurban grassland fragments. Copyright © 2014 Elsevier Ltd. All rights reserved.

Spatially Complete Surface Albedo Data Sets: Value-Added Products Derived from Terra MODIS Land Products

NASA Technical Reports Server (NTRS)

Moody, Eric G.; King, Michael D.; Platnick, Steven; Schaaf, Crystal B.; Gao, Feng

2004-01-01

Spectral land surface albedo is an important parameter for describing the radiative properties of the Earth. Accordingly it reflects the consequences of natural and human interactions, such as anthropogenic, meteorological, and phenological effects, on global and local climatological trends. Consequently, albedos are integral parts in a variety of research areas, such as general circulation models (GCMs), energy balance studies, modeling of land use and land use change, and biophysical, oceanographic, and meteorological studies. Recent observations of diffuse bihemispherical (white-sky) and direct beam directional hemispherical (black-sky ) land surface albedo included in the MOD43B3 product from MODIS instruments aboard NASA's Terra and Aqua satellite platforms have provided researchers with unprecedented spatial, spectral, and temporal characteristics. Cloud and seasonal snow cover, however, curtail retrievals to approximately half the global land surfaces on an annual equal-angle basis, precluding MOD43B3 albedo products from direct inclusion in some research projects and production environments.

Regression approach to non-invasive determination of bilirubin in neonatal blood

NASA Astrophysics Data System (ADS)

Lysenko, S. A.; Kugeiko, M. M.

2012-07-01

A statistical ensemble of structural and biophysical parameters of neonatal skin was modeled based on experimental data. Diffuse scattering coefficients of the skin in the visible and infrared regions were calculated by applying a Monte-Carlo method to each realization of the ensemble. The potential accuracy of recovering the bilirubin concentration in dermis (which correlates closely with that in blood) was estimated from spatially resolved spectrometric measurements of diffuse scattering. The possibility to determine noninvasively the bilirubin concentration was shown by measurements of diffuse scattering at λ = 460, 500, and 660 nm at three source-detector separations under conditions of total variability of the skin biophysical parameters.

A New Paradigm for Habitability in Planetary Systems: the Extremophilic Zone

NASA Astrophysics Data System (ADS)

Janot-Pacheco, E., Bernardes, L., Lage, C. A. S.

2014-03-01

More than a thousand exoplanets have been discovered so far. Planetary surface temperature may strongly depends on its albedo and geodynamic conditions. We have fed exoplanets from the Encyclopedia database with a comprehensive model of Earth's atmosphere and plate tectonics. As CO2 is the main agent responsible for the greenhouse effect, its partial pressure has been taken as a free parameter to estimate the surface temperature of some known planets. We also investigated the possible presence of "exomoons" belonging to giant planets in the Habitable Zone capable of harbour dynamic stability, to retain an atmosphere and to keep geodynamic activity for long time spans. Biological data on earthly micro-organisms classified as "extremophiles" indicate that such kind of microbial species could dwell on the surface of many exoplanets and exomoons. We thus propose an extension of the mainly astronomically defined "Habitable Zone" concept into the more astrobiologically one, the "Extremophililic Zone", that takes into account other parameters allowing survival of more robust life forms. This contribution comes from an ongoing project developed by a French-Brazilian colaboration in Astrophysics and Biophysics to search for living fingerprints in astrobiologically promising exoplanets.

Heavy Cigarette Smokers in a Chinese Population Display a Compromised Permeability Barrier

PubMed Central

Xin, Shujun; Ye, Li; Lv, Chengzhi; Elias, Peter M.

2016-01-01

Cigarette smoking is associated with various cutaneous disorders with defective permeability. Yet, whether cigarette smoking influences epidermal permeability barrier function is largely unknown. Here, we measured skin biophysical properties, including permeability barrier homeostasis, stratum corneum (SC) integrity, SC hydration, skin surface pH, and skin melanin/erythema index, in cigarette smokers. A total of 99 male volunteers were enrolled in this study. Smokers were categorized as light-to-moderate (<20 cigarettes/day) or heavy smokers (≥20 cigarettes/day). An MPA5 was used to measure SC hydration and skin melanin/erythema index on the dorsal hand, forehead, and cheek. Basal transepidermal water loss (TEWL) and barrier recovery rates were assessed on the forearm. A Skin-pH-Meter pH900 was used to measure skin surface pH. Our results showed that heavy cigarette smokers exhibited delayed barrier recovery after acute abrogation (1.02% ± 13.06 versus 16.48% ± 6.07), and barrier recovery rates correlated negatively with the number of daily cigarettes consumption (p = 0.0087). Changes in biophysical parameters in cigarette smokers varied with body sites. In conclusion, heavy cigarette smokers display compromised permeability barrier homeostasis, which could contribute, in part, to the increased prevalence of certain cutaneous disorders characterized by defective permeability. Thus, improving epidermal permeability barrier should be considered for heavy cigarette smokers. PMID:27437403

Applications of the EOS SAR to monitoring global change

NASA Technical Reports Server (NTRS)

Schier, Marguerite; Way, Jobea; Holt, Benjamin

1991-01-01

The SAR employed by NASA's Earth Observing System (EOS) is a multifrequency multipolarization radar which can conduct global monitoring of geophysical and biophysical parameters. The present discussion of the EOS SAR's role in global monitoring emphasizes geophysical product variables applicable to global hydrologic, biogeochemical, and energy cycle models. EOS SAR products encompass biomass, wetland areas, and phenologic and environmental states, in the field of ecosystem dynamics; soil moisture, snow moisture and extent, and glacier and ice sheet extent and velocity, in hydrologic cycle studies; surface-wave fields and sea ice properties, in ocean/atmosphere circulation; and the topography, erosion, and land forms of the solid earth.

An isoline separating relatively warm from relatively cool wintertime forest surface temperatures for the southeastern United States

NASA Astrophysics Data System (ADS)

Wickham, J.; Wade, T. G.; Riitters, K. H.

2014-09-01

Forest-oriented climate mitigation policies promote forestation as a means to increase uptake of atmospheric carbon to counteract global warming. Some have pointed out that a carbon-centric forest policy may be overstated because it discounts biophysical aspects of the influence of forests on climate. In extra-tropical regions, many climate models have shown that forests tend to be warmer than grasslands and croplands because forest albedos tend to be lower than non-forest albedos. A lower forest albedo results in higher absorption of solar radiation and increased sensible warming that is not offset by the cooling effects of carbon uptake in extra-tropical regions. However, comparison of forest warming potential in the context of climate models is based on a coarse classification system of tropical, temperate, and boreal. There is considerable variation in climate within the broad latitudinal zonation of tropical, temperate, and boreal, and the relationship between biophysical (albedo) and biogeochemical (carbon uptake) mechanisms may not be constant within these broad zones. We compared wintertime forest and non-forest surface temperatures for the southeastern United States and found that forest surface temperatures shifted from being warmer than non-forest surface temperatures north of approximately 36°N to cooler south of 36°N. Our results suggest that the biophysical aspects of forests' influence on climate reinforce the biogeochemical aspects of forests' influence on climate south of 36°N. South of 36°N, both biophysical and biogeochemical properties of forests appear to support forestation as a climate mitigation policy. We also provide some quantitative evidence that evergreen forests tend to have cooler wintertime surface temperatures than deciduous forests that may be attributable to greater evapotranspiration rates.

Potential and limits for rapid genetic adaptation to warming in a Great Barrier Reef coral.

PubMed

Matz, Mikhail V; Treml, Eric A; Aglyamova, Galina V; Bay, Line K

2018-04-01

Can genetic adaptation in reef-building corals keep pace with the current rate of sea surface warming? Here we combine population genomics, biophysical modeling, and evolutionary simulations to predict future adaptation of the common coral Acropora millepora on the Great Barrier Reef (GBR). Genomics-derived migration rates were high (0.1-1% of immigrants per generation across half the latitudinal range of the GBR) and closely matched the biophysical model of larval dispersal. Both genetic and biophysical models indicated the prevalence of southward migration along the GBR that would facilitate the spread of heat-tolerant alleles to higher latitudes as the climate warms. We developed an individual-based metapopulation model of polygenic adaptation and parameterized it with population sizes and migration rates derived from the genomic analysis. We find that high migration rates do not disrupt local thermal adaptation, and that the resulting standing genetic variation should be sufficient to fuel rapid region-wide adaptation of A. millepora populations to gradual warming over the next 20-50 coral generations (100-250 years). Further adaptation based on novel mutations might also be possible, but this depends on the currently unknown genetic parameters underlying coral thermal tolerance and the rate of warming realized. Despite this capacity for adaptation, our model predicts that coral populations would become increasingly sensitive to random thermal fluctuations such as ENSO cycles or heat waves, which corresponds well with the recent increase in frequency of catastrophic coral bleaching events.

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.

Comparison of surface energy budgets and feedbacks to microclimate among different land use types in an agro-pastoral ecotone of northern China.

PubMed

Zhao, Wei; Hu, Zhongmin; Li, Shenggong; Guo, Qun; Liu, Zhengjia; Zhang, Leiming

2017-12-01

The biophysical effect of land use conversion plays a significant role in regulating climate change. Owing to albedo and evapotranspiration (ET) change, the effect of energy budget difference on land surface temperature (LST) is important but unclear among contrasting land use types, especially in temperate semi-arid regions. Based on moderate-resolution imaging spectroradiometer (MODIS) data, we compared the differences in albedo, ET, and LST between cropland and grassland (CR-GR), and between planted forest and grassland (PF-GR) in the Horqin Sandy Land of Inner Mongolia, an agro-pastoral ecotone of northern China. Our main objective was to explore the magnitude and direction of albedo and ET change during the growing season and, subsequently, to estimate the biophysical effects on LST as a result of land use and land cover change. Our results indicate no significant difference in mean monthly albedo for CR-GR and PF-GR. Cropland lost more water through ET and significantly decreased daytime LST compared with grassland from July to September, but no significant differences in ET and LST were observed for PF-GR in any month. The biophysical climate effects were more pronounced for CR-GR compared with PF-GR. The response of LST to the changes in energy budget confirmed that ET was the critical driving factor relative to albedo. Compared with grassland, cropland and planted forest tended to cool the land surface by 5.15°C and 1.51°C during the growing season, respectively, because of the biophysical effects. Our findings suggest the significance of local-scale biophysical effect on climate variation after land use conversion in semi-arid regions. Copyright © 2017 Elsevier B.V. All rights reserved.

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.

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 and the current multi-spectral and multi-angular satellite data (MODIS, MISR), a robust retrieval system to estimate woody vegetation structural/biophysical parameters is proposed.

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.

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.

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.

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.

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.

Hydrological Relevant Parameters from Remote Sensing - Spatial Modelling Input and Validation Basis

NASA Astrophysics Data System (ADS)

Hochschild, V.

2012-12-01

This keynote paper will demonstrate how multisensoral remote sensing data is used as spatial input for mesoscale hydrological modeling as well as for sophisticated validation purposes. The tasks of Water Resources Management are subject as well as the role of remote sensing in regional catchment modeling. Parameters derived from remote sensing discussed in this presentation will be land cover, topographical information from digital elevation models, biophysical vegetation parameters, surface soil moisture, evapotranspiration estimations, lake level measurements, determination of snow covered area, lake ice cycles, soil erosion type, mass wasting monitoring, sealed area, flash flood estimation. The actual possibilities of recent satellite and airborne systems are discussed, as well as the data integration into GIS and hydrological modeling, scaling issues and quality assessment will be mentioned. The presentation will provide an overview of own research examples from Germany, Tibet and Africa (Ethiopia, South Africa) as well as other international research activities. Finally the paper gives an outlook on upcoming sensors and concludes the possibilities of remote sensing in hydrology.

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

Acoustic sensors as a biophysical tool for probing cell attachment and cell/surface interactions.

PubMed

Saitakis, Michael; Gizeli, Electra

2012-02-01

Acoustic biosensors offer the possibility to analyse cell attachment and spreading. This is due to the offered speed of detection, the real-time non-invasive approach and their high sensitivity not only to mass coupling, but also to viscoelastic changes occurring close to the sensor surface. Quartz crystal microbalance (QCM) and surface acoustic wave (Love-wave) systems have been used to monitor the adhesion of animal cells to various surfaces and record the behaviour of cell layers under various conditions. The sensors detect cells mostly via their sensitivity in viscoelasticity and mechanical properties. Particularly, the QCM sensor detects cytoskeletal rearrangements caused by specific drugs affecting either actin microfilaments or microtubules. The Love-wave sensor directly measures cell/substrate bonds via acoustic damping and provides 2D kinetic and affinity parameters. Other studies have applied the QCM sensor as a diagnostic tool for leukaemia and, potentially, for chemotherapeutic agents. Acoustic sensors have also been used in the evaluation of the cytocompatibility of artificial surfaces and, in general, they have the potential to become powerful tools for even more diverse cellular analysis.

Spatially Complete Global Surface Albedos Derived from Terra/MODIS Data

NASA Technical Reports Server (NTRS)

King, Michael D.; Moody, Eric G.; Platnick, Steven; Schaaf, Crystal B.

2005-01-01

Spectral land surface albedo is an important parameter for describing the radiative properties of the Earth. Accordingly it reflects the consequences of natural and human interactions, such as anthropogenic, meteorological, and phenological effects, on global and local climatological trends. Consequently, albedos are integral parts in a variety of research areas, such as general circulation models (GCMs), energy balance studies, modeling of land use and land use change, and biophysical, oceanographic, and meteorological studies. Recent production of land surface anisotropy, diffuse bihemispherical (white-sky) albedo and direct beam directional hemispherical (black-sky) albedo from observations acquired by the MODIS instruments aboard NASA's Terra and &la satellite platforms have provided researchers with unprecedented spatial, spectral, and temporal information on the land surface's radiative characteristics. Cloud cover, which curtails retrievals, and the presence of ephemeral and seasonal snow limit the snow-free data to approximately half the global land surfaces on an annual equal-angle basis. This precludes the MOD43B3 albedo products from being used in some remote sensing and ground-based applications, &mate models, and global change research projects.

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.

Vegetation and soils field research data base: Experiment summaries

NASA Technical Reports Server (NTRS)

Biehl, L. L.; Daughtry, C. S. T.; Bauer, M. E.

1984-01-01

Understanding of the relationships between the optical, spectral characteristics and important biological-physical parameters of earth-surface features can best be obtained by carefully controlled studies over fields and plots where complete data describing the condition of targets are attainable and where frequent, timely spectral measurement can be obtained. Development of a vegetation and soils field research data base was initiated in 1972 at Purdue University's Laboratory for Applications of Remote Sensing and expanded in the fall of 1974 by NASA as part of LACIE. Since then, over 250,000 truck-mounted and helicopter-borne spectrometer/multiband radiometer observations have been obtained of more than 50 soil series and 20 species of crops, grasses, and trees. These data are supplemented by an extensive set of biophysical and meteorological data acquired during each mission. The field research data form one of the most complete and best-documented data sets acquired for agricultural remote sensing research. Thus, they are well-suited to serve as a data base for research to: (1) quantiatively determine the relationships of spectral and biophysical characteristics of vegetation, (2) define future sensor systems, and (3) develop advanced data analysis techniques.

Autocrine signal transmission with extracellular ligand degradation

NASA Astrophysics Data System (ADS)

Muratov, C B; Posta, F; Shvartsman, S Y

2009-03-01

Traveling waves of cell signaling in epithelial layers orchestrate a number of important processes in developing and adult tissues. These waves can be mediated by positive feedback autocrine loops, a mode of cell signaling where binding of a diffusible extracellular ligand to a cell surface receptor can lead to further ligand release. We formulate and analyze a biophysical model that accounts for ligand-induced ligand release, extracellular ligand diffusion and ligand-receptor interaction. We focus on the case when the main mode for ligand degradation is extracellular and analyze the problem with the sharp threshold positive feedback nonlinearity. We derive expressions that link the speed of propagation and other characteristics of traveling waves to the parameters of the biophysical processes, such as diffusion rates, receptor expression level, etc. Analyzing the derived expressions we found that traveling waves in such systems can exhibit a number of unusual properties, e.g. non-monotonic dependence of the speed of propagation on ligand diffusivity. Our results for the fully developed traveling fronts can be used to analyze wave initiation from localized perturbations, a scenario that frequently arises in the in vitro models of epithelial wound healing, and guide future modeling studies of cell communication in epithelial layers.

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 motility was obtained with freezing rates between 50 degrees C/min and 80 degrees C/min for rat and at 20 degrees C/min with a sharp drop at 50 degrees C/min for mouse. In summary, DSC experiments on mouse and rat sperm yielded a difference in membrane permeability parameters in the two sperm types that, when implemented in a biophysical model of water transport, reasonably predict different optimal cooling rate outcomes for each sperm after cryopreservation.

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

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.

A method to investigate the diffusion properties of nuclear calcium.

PubMed

Queisser, Gillian; Wittum, Gabriel

2011-10-01

Modeling biophysical processes in general requires knowledge about underlying biological parameters. The quality of simulation results is strongly influenced by the accuracy of these parameters, hence the identification of parameter values that the model includes is a major part of simulating biophysical processes. In many cases, secondary data can be gathered by experimental setups, which are exploitable by mathematical inverse modeling techniques. Here we describe a method for parameter identification of diffusion properties of calcium in the nuclei of rat hippocampal neurons. The method is based on a Gauss-Newton method for solving a least-squares minimization problem and was formulated in such a way that it is ideally implementable in the simulation platform uG. Making use of independently published space- and time-dependent calcium imaging data, generated from laser-assisted calcium uncaging experiments, here we could identify the diffusion properties of nuclear calcium and were able to validate a previously published model that describes nuclear calcium dynamics as a diffusion process.

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.

Evaluation of the biophysical limitations on photosynthesis of four varietals of Brassica rapa

NASA Astrophysics Data System (ADS)

Pleban, J. R.; Mackay, D. S.; Aston, T.; Ewers, B.; Weinig, C.

2014-12-01

Evaluating performance of agricultural varietals can support the identification of genotypes that will increase yield and can inform management practices. The biophysical limitations of photosynthesis are amongst the key factors that necessitate evaluation. This study evaluated how four biophysical limitations on photosynthesis, stomatal response to vapor pressure deficit, maximum carboxylation rate by Rubisco (Ac), rate of photosynthetic electron transport (Aj) and triose phosphate use (At) vary between four Brassica rapa genotypes. Leaf gas exchange data was used in an ecophysiological process model to conduct this evaluation. The Terrestrial Regional Ecosystem Exchange Simulator (TREES) integrates the carbon uptake and utilization rate limiting factors for plant growth. A Bayesian framework integrated in TREES here used net A as the target to estimate the four limiting factors for each genotype. As a first step the Bayesian framework was used for outlier detection, with data points outside the 95% confidence interval of model estimation eliminated. Next parameter estimation facilitated the evaluation of how the limiting factors on A different between genotypes. Parameters evaluated included maximum carboxylation rate (Vcmax), quantum yield (ϕJ), the ratio between Vc-max and electron transport rate (J), and trios phosphate utilization (TPU). Finally, as trios phosphate utilization has been shown to not play major role in the limiting A in many plants, the inclusion of At in models was evaluated using deviance information criteria (DIC). The outlier detection resulted in a narrowing in the estimated parameter distributions allowing for greater differentiation of genotypes. Results show genotypes vary in the how limitations shape assimilation. The range in Vc-max , a key parameter in Ac, was 203.2 - 223.9 umol m-2 s-1 while the range in ϕJ, a key parameter in AJ, was 0.463 - 0.497 umol m-2 s-1. The added complexity of the TPU limitation did not improve model performance in the genotypes assessed based on DIC. By identifying how varietals differ in their biophysical limitations on photosynthesis genotype selection can be informed for agricultural goals. Further work aims at applying this approach to a fifth limiting factor on photosynthesis, mesophyll conductance.

The effect of dimethylsulfoxide on the water transport response of rat hepatocytes during freezing.

PubMed

Smith, D J; Schulte, M; Bischof, J C

1998-10-01

Successful improvement of cryopreservation protocols for cells in suspension requires knowledge of how such cells respond to the biophysical stresses of freezing (intracellular ice formation, water transport) while in the presence of a cryoprotective agent (CPA). This work investigates the biophysical water transport response in a clinically important cell type--isolated hepatocytes--during freezing in the presence of dimethylsulfoxide (DMSO). Sprague-Dawley rat liver hepatocytes were frozen in Williams E media supplemented with 0, 1, and 2 M DMSO, at rates of 5, 10, and 50 degrees C/min. The water transport was measured by cell volumetric changes as assessed by cryomicroscopy and image analysis. Assuming that water is the only species transported under these conditions, a water transport model of the form dV/dT = f(Lpg([CPA]), ELp([CPA]), T(t)) was curve-fit to the experimental data to obtain the biophysical parameters of water transport--the reference hydraulic permeability (Lpg) and activation energy of water transport (ELp)--for each DMSO concentration. These parameters were estimated two ways: (1) by curve-fitting the model to the average volume of the pooled cell data, and (2) by curve-fitting individual cell volume data and averaging the resulting parameters. The experimental data showed that less dehydration occurs during freezing at a given rate in the presence of DMSO at temperatures between 0 and -10 degrees C. However, dehydration was able to continue at lower temperatures (< -10 degrees C) in the presence of DMSO. The values of Lpg and ELp obtained using the individual cell volume data both decreased from their non-CPA values--4.33 x 10(-13) m3/N-s (2.69 microns/min-atm) and 317 kJ/mol (75.9 kcal/mol), respectively--to 0.873 x 10(-13) m3/N-s (0.542 micron/min-atm) and 137 kJ/mol (32.8 kcal/mol), respectively, in 1 M DMSO and 0.715 x 10(-13) m3/N-s (0.444 micron/min-atm) and 107 kJ/mol (25.7 kcal/mol), respectively, in 2 M DMSO. The trends in the pooled volume values for Lpg and ELp were very similar, but the overall fit was considered worse than for the individual volume parameters. A unique way of presenting the curve-fitting results supports a clear trend of reduction of both biophysical parameters in the presence of DMSO, and no clear trend in cooling rate dependence of the biophysical parameters. In addition, these results suggest that close proximity of the experimental cell volume data to the equilibrium volume curve may significantly reduce the efficiency of the curve-fitting process.

Progress in Integrative Biomaterial Systems to Approach Three-Dimensional Cell Mechanotransduction

PubMed Central

Zhang, Ying; Liao, Kin; Li, Chuan; Lai, Alvin C.K.; Foo, Ji-Jinn

2017-01-01

Mechanotransduction between cells and the extracellular matrix regulates major cellular functions in physiological and pathological situations. The effect of mechanical cues on biochemical signaling triggered by cell–matrix and cell–cell interactions on model biomimetic surfaces has been extensively investigated by a combination of fabrication, biophysical, and biological methods. To simulate the in vivo physiological microenvironment in vitro, three dimensional (3D) microstructures with tailored bio-functionality have been fabricated on substrates of various materials. However, less attention has been paid to the design of 3D biomaterial systems with geometric variances, such as the possession of precise micro-features and/or bio-sensing elements for probing the mechanical responses of cells to the external microenvironment. Such precisely engineered 3D model experimental platforms pave the way for studying the mechanotransduction of multicellular aggregates under controlled geometric and mechanical parameters. Concurrently with the progress in 3D biomaterial fabrication, cell traction force microscopy (CTFM) developed in the field of cell biophysics has emerged as a highly sensitive technique for probing the mechanical stresses exerted by cells onto the opposing deformable surface. In the current work, we first review the recent advances in the fabrication of 3D micropatterned biomaterials which enable the seamless integration with experimental cell mechanics in a controlled 3D microenvironment. Then, we discuss the role of collective cell–cell interactions in the mechanotransduction of engineered tissue equivalents determined by such integrative biomaterial systems under simulated physiological conditions. PMID:28952551

Extended ecosystem signatures with application to Eos synergism requirements

NASA Technical Reports Server (NTRS)

Ulaby, Fawwaz T.; Dobson, M. Craig; Sarabandi, Kamal

1993-01-01

The primary objective is to define the advantages of synergistically combining optical and microwave remote sensing measurements for the determination of biophysical properties important in ecosystem modeling. This objective was approached in a stepwise fashion starting with ground-based observations of controlled agricultural and orchard canopies and progressing to airborne observations of more natural forest ecosystems. This observational program is complemented by a parallel effort to model the visible reflectance and microwave scattering properties of composite vegetation canopies. The goals of the modeling studies are to verify our basic understanding of the sensor-scene interaction physics and to provide the basis for development of inverse models optimized for retrieval of key biophysical properties. These retrieval algorithms can then be used to simulate the expected performance of various aspects of Eos including the need for simultaneous SAR and HIRIS observations or justification for other (non-synchronous) relative timing constraints and the frequency, polarization, and angle of incidence requirements for accurate biophysical parameter extractions. This program completed a very successful series of truck-mounted experiments, made remarkable progress in development and validation of optical reflectance and microwave scattering models for vegetation, extended the scattering models to accommodate discontinuous and periodic canopies, developed inversion approaches for surface and canopy properties, and disseminated these results widely through symposia and journal publications. In addition, the third generation of the computer code for the microwave scattering models was provided to a number of other US, Canadian, Australian, and European investigators who are currently presenting and publishing results using the MIMICS research code.

Online determination of biophysical parameters of mucous membranes of a human body

NASA Astrophysics Data System (ADS)

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

2013-07-01

We have developed a method for online determination of biophysical parameters of mucous membranes (MMs) of a human body (transport scattering coefficient, scattering anisotropy factor, haemoglobin concentration, degrees of blood oxygenation, average diameter of capillaries with blood) from measurements of spectral and spatial characteristics of diffuse reflection. The method is based on regression relationships between linearly independent components of the measured light signals and the unknown parameters of MMs, obtained by simulation of the radiation transfer in the MM under conditions of its general variability. We have proposed and justified the calibration-free fibre-optic method for determining the concentration of haemoglobin in MMs by measuring the light signals diffusely reflected by the tissue in four spectral regions at two different distances from the illumination spot. We have selected the optimal wavelengths of optical probing for the implementation of the method.

Anionic lipids and the maintenance of membrane electrostatics in eukaryotes.

PubMed

Platre, Matthieu Pierre; Jaillais, Yvon

2017-02-01

A wide range of signaling processes occurs at the cell surface through the reversible association of proteins from the cytosol to the plasma membrane. Some low abundant lipids are enriched at the membrane of specific compartments and thereby contribute to the identity of cell organelles by acting as biochemical landmarks. Lipids also influence membrane biophysical properties, which emerge as an important feature in specifying cellular territories. Such parameters are crucial for signal transduction and include lipid packing, membrane curvature and electrostatics. In particular, membrane electrostatics specifies the identity of the plasma membrane inner leaflet. Membrane surface charges are carried by anionic phospholipids, however the exact nature of the lipid(s) that powers the plasma membrane electrostatic field varies among eukaryotes and has been hotly debated during the last decade. Herein, we discuss the role of anionic lipids in setting up plasma membrane electrostatics and we compare similarities and differences that were found in different eukaryotic cells.

BOREAS Level-2 MAS Surface Reflectance and Temperature Images in BSQ Format

NASA Technical Reports Server (NTRS)

Hall, Forrest G. (Editor); Newcomer, Jeffrey (Editor); Lobitz, Brad; Spanner, Michael; Strub, Richard; Lobitz, Brad

2000-01-01

The BOReal Ecosystem-Atmosphere Study (BOREAS) Staff Science Aircraft Data Acquisition Program focused on providing the research teams with the remotely sensed aircraft data products they needed to compare and spatially extend point results. The MODIS Airborne Simulator (MAS) images, along with other remotely sensed data, were collected to provide spatially extensive information over the primary study areas. This information includes biophysical parameter maps such as surface reflectance and temperature. Collection of the MAS images occurred over the study areas during the 1994 field campaigns. The level-2 MAS data cover the dates of 21-Jul-1994, 24-Jul-1994, 04-Aug-1994, and 08-Aug-1994. The data are not geographically/geometrically corrected; however, files of relative X and Y coordinates for each image pixel were derived by using the C130 navigation data in a MAS scan model. The data are provided in binary image format files.

Assessment of alterations in the electrical impedance of muscle after experimental nerve injury via finite-element analysis.

PubMed

Wang, Lucy L; Ahad, Mohammad; McEwan, Alistair; Li, Jia; Jafarpoor, Mina; Rutkove, Seward B

2011-06-01

The surface measurement of electrical impedance of muscle, incorporated as the technique of electrical impedance myography (EIM), provides a noninvasive approach for evaluating neuromuscular diseases, including amyotrophic lateral sclerosis. However, the relationship between alterations in surface impedance and the electrical properties of muscle remains uncertain. In order to investigate this further, a group of healthy adult rats, a group of rats two weeks postsciatic crush, and a group of animals six months postcrush underwent EIM of the gastrocnemius-soleus complex. The animals were then killed and the conductivity and permittivity of the extracted muscle measured. Finite-element models based on MRI data were then constructed for each group. The characteristic EIM parameter, 50 kHz phase (±standard error), obtained with surface impedance measurements was 17.3° ± 0.3° for normal animals, 13.8° ± 0.7° for acutely injured animals, and 16.1° ± 0.5° for chronically injured animals. The models predicted parallel changes with phase values of 24.3°, 18.8°, and 21.2° for the normal, acute, and chronic groups, respectively. Other multifrequency impedance parameters showed similar alterations. These results confirm that surface impedance measurements taken in conjunction with anatomical data and finite-element models may offer a noninvasive approach for assessing biophysical alterations in muscle in neuromuscular disease states.

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.

Toward Linking Aboveground Vegetation Properties and Soil Microbial Communities Using Remote Sensing

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

Hamada, Yuki; Gilbert, Jack A.; Larsen, Peter E.

2014-04-01

Despite their vital role in terrestrial ecosystem function, the distributions and dynamics of soil microbial communities (SMCs) are poorly understood. Vegetation and soil properties are the primary factors that influence SMCs. This paper discusses the potential effectiveness of remote sensing science and technologies for mapping SMC biogeography by characterizing surface biophysical properties (e.g., plant traits and community composition) strongly correlated with SMCs. Using remotely sensed biophysical properties to predict SMC distributions is extremely challenging because of the intricate interactions between biotic and abiotic factors and between above- and belowground ecosystems. However, the integration of biophysical and soil remote sensing withmore » geospatial information about the e nvironment holds great promise for mapping SMC biogeography. Additional research needs invol ve microbial taxonomic definition, soil environmental complexity, and scaling strategies. The collaborative effort of experts from diverse disciplines is essential to linking terrestrial surface biosphere observations with subsurface microbial community distributions using remote sensing.« less

Toward Linking Aboveground Vegetation Properties and Soil Microbial Communities Using Remote Sensing

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

Hamada, Yuki; Gilbert, Jack A.; Larsen, Peter E.

2014-04-01

Despite their vital role in terrestrial ecosystem function, the distributions and dynamics of soil microbial communities (SMCs) are poorly understood. Vegetation and soil properties are the primary factors that influence SMCs. This paper discusses the potential effectiveness of remote sensing science and technologies for mapping SMC biogeography by characterizing surface biophysical properties (e.g., plant traits and community composition) strongly correlated with SMCs. Using remotely sensed biophysical properties to predict SMC distributions is extremely challenging because of the intricate interactions between biotic and abiotic factors and between above- and below-ground ecosystems. However, the integration of biophysical and soil remote sensing withmore » geospatial information about the environment holds great promise for mapping SMC biogeography. Additional research needs involve microbial taxonomic definition, soil environmental complexity, and scaling strategies. The collaborative effort of experts from diverse disciplines is essential to linking terrestrial surface biosphere observations with subsurface microbial community distributions using remote sensing.« less

Surface Electrostatics of Lipid Bilayers by EPR of a pH-Sensitive Spin-Labeled Lipid

PubMed Central

Voinov, Maxim A.; Rivera-Rivera, Izarys; Smirnov, Alex I.

2013-01-01

Many biophysical processes such as insertion of proteins into membranes and membrane fusion are governed by bilayer electrostatic potential. At the time of this writing, the arsenal of biophysical methods for such measurements is limited to a few techniques. Here we describe a, to our knowledge, new spin-probe electron paramagnetic resonance (EPR) approach for assessing the electrostatic surface potential of lipid bilayers that is based on a recently synthesized EPR probe (IMTSL-PTE) containing a reversibly ionizable nitroxide tag attached to the lipids’ polar headgroup. EPR spectra of the probe directly report on its ionization state and, therefore, on electrostatic potential through changes in nitroxide magnetic parameters and the degree of rotational averaging. Further, the lipid nature of the probe provides its full integration into lipid bilayers. Tethering the nitroxide moiety directly to the lipid polar headgroup defines the location of the measured potential with respect to the lipid bilayer interface. Electrostatic surface potentials measured by EPR of IMTSL-PTE show a remarkable (within ±2%) agreement with the Gouy-Chapman theory for anionic DMPG bilayers in fluid (48°C) phase at low electrolyte concentration (50 mM) and in gel (17°C) phase at 150-mM electrolyte concentration. This agreement begins to diminish for DMPG vesicles in gel phase (17°C) upon varying electrolyte concentration and fluid phase bilayers formed from DMPG/DMPC and POPG/POPC mixtures. Possible reasons for such deviations, as well as the proper choice of an electrostatically neutral reference interface, have been discussed. Described EPR method is expected to be fully applicable to more-complex models of cellular membranes. PMID:23332063

Climate changes impact the surface albedo of a forest ecosystem based on MODIS satellite data

NASA Astrophysics Data System (ADS)

Zoran, M. A.; Nemuc, A. V.

2007-10-01

Surface albedo is one of the most important biophysical parameter responsible for energy balance control and the surface temperature and boundary-layer structure of the atmosphere. Forest land surface albedo is also highly variable temporally showing both diurnal as well as seasonal variations. In forest systems, albedo controls the microclimate conditions which affects ecosystem physical, physiological, and biogeochemical processes such as energy balance, evapotranspiration, photosynthesis. Due to anthropogenic and natural factors, land cover and land use changes result is the land surfaces albedo change. The main aim of this paper is to investigate the albedo patterns due to the impact of atmospheric pollution and climate variations of a forest ecosystem Branesti-Cernica, placed to the North-East of Bucharest city, Romania based on satellite Landsat ETM+, IKONOS and MODIS data and climate station observations. Our study focuses on 3 years of data (2003-2005), each of which had a different climatic regime. As the physical climate system is very sensitive to surface albedo, forest ecosystems could significantly feedback to the projected climate change modeling scenarios through albedo changes. The results of this research have a number of applications in weather forecasting, climate change, and forest ecosystem studies.

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.

Landscape Variation in Tree Species Richness in Northern Iran Forests

PubMed Central

Bourque, Charles P.-A.; Bayat, Mahmoud

2015-01-01

Mapping landscape variation in tree species richness (SR) is essential to the long term management and conservation of forest ecosystems. The current study examines the prospect of mapping field assessments of SR in a high-elevation, deciduous forest in northern Iran as a function of 16 biophysical variables representative of the area’s unique physiography, including topography and coastal placement, biophysical environment, and forests. Basic to this study is the development of moderate-resolution biophysical surfaces and associated plot-estimates for 202 permanent sampling plots. The biophysical variables include: (i) three topographic variables generated directly from the area’s digital terrain model; (ii) four ecophysiologically-relevant variables derived from process models or from first principles; and (iii) seven variables of Landsat-8-acquired surface reflectance and two, of surface radiance. With symbolic regression, it was shown that only four of the 16 variables were needed to explain 85% of observed plot-level variation in SR (i.e., wind velocity, surface reflectance of blue light, and topographic wetness indices representative of soil water content), yielding mean-absolute and root-mean-squared error of 0.50 and 0.78, respectively. Overall, localised calculations of wind velocity and surface reflectance of blue light explained about 63% of observed variation in SR, with wind velocity accounting for 51% of that variation. The remaining 22% was explained by linear combinations of soil-water-related topographic indices and associated thresholds. In general, SR and diversity tended to be greatest for plots dominated by Carpinus betulus (involving ≥ 33% of all trees in a plot), than by Fagus orientalis (median difference of one species). This study provides a significant step towards describing landscape variation in SR as a function of modelled and satellite-based information and symbolic regression. Methods in this study are sufficiently general to be applicable to the characterisation of SR in other forested regions of the world, providing plot-scale data are available for model generation. PMID:25849029

Landscape variation in tree species richness in northern Iran forests.

PubMed

Bourque, Charles P-A; Bayat, Mahmoud

2015-01-01

Mapping landscape variation in tree species richness (SR) is essential to the long term management and conservation of forest ecosystems. The current study examines the prospect of mapping field assessments of SR in a high-elevation, deciduous forest in northern Iran as a function of 16 biophysical variables representative of the area's unique physiography, including topography and coastal placement, biophysical environment, and forests. Basic to this study is the development of moderate-resolution biophysical surfaces and associated plot-estimates for 202 permanent sampling plots. The biophysical variables include: (i) three topographic variables generated directly from the area's digital terrain model; (ii) four ecophysiologically-relevant variables derived from process models or from first principles; and (iii) seven variables of Landsat-8-acquired surface reflectance and two, of surface radiance. With symbolic regression, it was shown that only four of the 16 variables were needed to explain 85% of observed plot-level variation in SR (i.e., wind velocity, surface reflectance of blue light, and topographic wetness indices representative of soil water content), yielding mean-absolute and root-mean-squared error of 0.50 and 0.78, respectively. Overall, localised calculations of wind velocity and surface reflectance of blue light explained about 63% of observed variation in SR, with wind velocity accounting for 51% of that variation. The remaining 22% was explained by linear combinations of soil-water-related topographic indices and associated thresholds. In general, SR and diversity tended to be greatest for plots dominated by Carpinus betulus (involving ≥ 33% of all trees in a plot), than by Fagus orientalis (median difference of one species). This study provides a significant step towards describing landscape variation in SR as a function of modelled and satellite-based information and symbolic regression. Methods in this study are sufficiently general to be applicable to the characterisation of SR in other forested regions of the world, providing plot-scale data are available for model generation.

Polarimetric SAR Interferometry based modeling for tree height and aboveground biomass retrieval in a tropical deciduous forest

NASA Astrophysics Data System (ADS)

Kumar, Shashi; Khati, Unmesh G.; Chandola, Shreya; Agrawal, Shefali; Kushwaha, Satya P. S.

2017-08-01

The regulation of the carbon cycle is a critical ecosystem service provided by forests globally. It is, therefore, necessary to have robust techniques for speedy assessment of forest biophysical parameters at the landscape level. It is arduous and time taking to monitor the status of vast forest landscapes using traditional field methods. Remote sensing and GIS techniques are efficient tools that can monitor the health of forests regularly. Biomass estimation is a key parameter in the assessment of forest health. Polarimetric SAR (PolSAR) remote sensing has already shown its potential for forest biophysical parameter retrieval. The current research work focuses on the retrieval of forest biophysical parameters of tropical deciduous forest, using fully polarimetric spaceborne C-band data with Polarimetric SAR Interferometry (PolInSAR) techniques. PolSAR based Interferometric Water Cloud Model (IWCM) has been used to estimate aboveground biomass (AGB). Input parameters to the IWCM have been extracted from the decomposition modeling of SAR data as well as PolInSAR coherence estimation. The technique of forest tree height retrieval utilized PolInSAR coherence based modeling approach. Two techniques - Coherence Amplitude Inversion (CAI) and Three Stage Inversion (TSI) - for forest height estimation are discussed, compared and validated. These techniques allow estimation of forest stand height and true ground topography. The accuracy of the forest height estimated is assessed using ground-based measurements. PolInSAR based forest height models showed enervation in the identification of forest vegetation and as a result height values were obtained in river channels and plain areas. Overestimation in forest height was also noticed at several patches of the forest. To overcome this problem, coherence and backscatter based threshold technique is introduced for forest area identification and accurate height estimation in non-forested regions. IWCM based modeling for forest AGB retrieval showed R2 value of 0.5, RMSE of 62.73 (t ha-1) and a percent accuracy of 51%. TSI based PolInSAR inversion modeling showed the most accurate result for forest height estimation. The correlation between the field measured forest height and the estimated tree height using TSI technique is 62% with an average accuracy of 91.56% and RMSE of 2.28 m. The study suggested that PolInSAR coherence based modeling approach has significant potential for retrieval of forest biophysical parameters.

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.

Identifying potential recommendation domains for conservation agriculture in Ethiopia, Kenya, and Malawi.

PubMed

Tesfaye, Kindie; Jaleta, Moti; Jena, Pradyot; Mutenje, Munyaradzi

2015-02-01

Conservation agriculture (CA) is being promoted as an option for reducing soil degradation, conserving water, enhancing crop productivity, and maintaining yield stability. However, CA is a knowledge- and technology-intensive practice, and may not be feasible or may not perform better than conventional agriculture under all conditions and farming systems. Using high resolution (≈1 km(2)) biophysical and socioeconomic geospatial data, this study identified potential recommendation domains (RDs) for CA in Ethiopia, Kenya, and Malawi. The biophysical variables used were soil texture, surface slope, and rainfall while the socioeconomic variables were market access and human and livestock population densities. Based on feasibility and comparative performance of CA over conventional agriculture, the biophysical and socioeconomic factors were first used to classify cultivated areas into three biophysical and three socioeconomic potential domains, respectively. Combinations of biophysical and socioeconomic domains were then used to develop potential RDs for CA based on adoption potential within the cultivated areas. About 39, 12, and 5% of the cultivated areas showed high biophysical and socioeconomic potential while 50, 39, and 21% of the cultivated areas showed high biophysical and medium socioeconomic potential for CA in Malawi, Kenya, and Ethiopia, respectively. The results indicate considerable acreages of land with high CA adoption potential in the mixed crop-livestock systems of the studied countries. However, there are large differences among countries depending on biophysical and socio-economic conditions. The information generated in this study could be used for targeting CA and prioritizing CA-related agricultural research and investment priorities in the three countries.

Identifying Potential Recommendation Domains for Conservation Agriculture in Ethiopia, Kenya, and Malawi

NASA Astrophysics Data System (ADS)

Tesfaye, Kindie; Jaleta, Moti; Jena, Pradyot; Mutenje, Munyaradzi

2015-02-01

Conservation agriculture (CA) is being promoted as an option for reducing soil degradation, conserving water, enhancing crop productivity, and maintaining yield stability. However, CA is a knowledge- and technology-intensive practice, and may not be feasible or may not perform better than conventional agriculture under all conditions and farming systems. Using high resolution (≈1 km2) biophysical and socioeconomic geospatial data, this study identified potential recommendation domains (RDs) for CA in Ethiopia, Kenya, and Malawi. The biophysical variables used were soil texture, surface slope, and rainfall while the socioeconomic variables were market access and human and livestock population densities. Based on feasibility and comparative performance of CA over conventional agriculture, the biophysical and socioeconomic factors were first used to classify cultivated areas into three biophysical and three socioeconomic potential domains, respectively. Combinations of biophysical and socioeconomic domains were then used to develop potential RDs for CA based on adoption potential within the cultivated areas. About 39, 12, and 5 % of the cultivated areas showed high biophysical and socioeconomic potential while 50, 39, and 21 % of the cultivated areas showed high biophysical and medium socioeconomic potential for CA in Malawi, Kenya, and Ethiopia, respectively. The results indicate considerable acreages of land with high CA adoption potential in the mixed crop-livestock systems of the studied countries. However, there are large differences among countries depending on biophysical and socio-economic conditions. The information generated in this study could be used for targeting CA and prioritizing CA-related agricultural research and investment priorities in the three countries.

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

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

Safety Assessment of Tretinoin Loaded Nano Emulsion and Nanostructured Lipid Carriers: A Non-invasive Trial on Human Volunteers.

PubMed

Nasrollahi, Saman Ahmad; Hassanzade, Hurnaz; Moradi, Azadeh; Sabouri, Mahsa; Samadi, Aniseh; Kashani, Mansour Nassiri; Firooz, Alireza

2017-01-01

Topical application of tretinoin (TRE) is followed by a high incidence of side effects. One method to overcome the problem is loading TRE into lipid nanoparticles. The potential safety of the nanoparticle materials has been always considered as a major concern. In this in vivo study, changes in human skin biophysical parameters including hydration, TEWL, erythema, and pH have been used to determine the safety of tretinoin loaded nano emulsion (NE) and nanostructured lipid carriers (NLC). TRE loaded NE and NLC were prepared using a high pressure homogenizer. Skin biophysical parameters were measured on the volar forearms of twenty healthy volunteers, before and after applying TRE-NE and TRE-NLC lotions. All the measurements were done using respective probes of MPA 580Cutometer®. We obtained particles of nanometric size (<130 nm) with narrow distribution and optimal physical stability. None of the formulations made any statistically significant change in any of the measured skin properties. P-values were 0.646, 0.139, 0.386, 0.169 after applying TRE-NE and 0.508, 0.051, 0.139, 0.333 after applying TRE-NLC, respectively. Both formulations are reasonably safe to apply on human skin and topical application of TRE-NE and TRE-NLC had almost similar effects on skin biophysical parameters. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

An overview of surface radiance and biology studies in FIFE

NASA Astrophysics Data System (ADS)

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

1992-11-01

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

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. Our results reveal the occurrence of a significant hysteresis between λET and gC during the dry season for the pasture sites, which is attributed to relatively low soil water availability as compared to the rainforests, likely due to differences in rooting depth between the two systems. Evaporation was significantly influenced by gA for all the PFTs and across all wetness conditions. Our analytical framework logically captures the responses of gC and gA to changes in atmospheric radiation, DA, and surface radiometric temperature, and thus appears to be promising for the improvement of existing land-surface-atmosphere exchange parameterizations across a range of spatial scales.

Spatially Complete Global Spectral Surface Albedos: Value-Added Datasets Derived from Terra MODIS Land Products

NASA Technical Reports Server (NTRS)

Moody, Eric G.; King, Michael D.; Platnick, Steven; Schaaf, Crystal B.; Gao, Feng

2004-01-01

Land surface albedo is an important parameter in describing the radiative properties of the earth s surface as it represents the amount of incoming solar radiation that is reflected from the surface. The amount and type of vegetation of the surface dramatically alters the amount of radiation that is reflected; for example, croplands that contain leafy vegetation will reflect radiation very differently than blacktop associated with urban areas. In addition, since vegetation goes through a growth, or phenological, cycle, the amount of radiation that is reflected changes over the course of a year. As a result, albedo is both temporally and spatially dependant upon global location as there is a distribution of vegetated surface types and growing conditions. Land surface albedo is critical for a wide variety of earth system research projects including but not restricted to remote sensing of atmospheric aerosol and cloud properties from space, ground-based analysis of aerosol optical properties from surface-based sun/sky radiometers, biophysically-based land surface modeling of the exchange of energy, water, momentum, and carbon for various land use categories, and surface energy balance studies. These projects require proper representation of the surface albedo s spatial, spectral, and temporal variations, however, these representations are often lacking in datasets prior to the latest generation of land surface albedo products.

The zipper mechanism in phagocytosis: energetic requirements and variability in phagocytic cup shape

PubMed Central

2010-01-01

Background Phagocytosis is the fundamental cellular process by which eukaryotic cells bind and engulf particles by their cell membrane. Particle engulfment involves particle recognition by cell-surface receptors, signaling and remodeling of the actin cytoskeleton to guide the membrane around the particle in a zipper-like fashion. Despite the signaling complexity, phagocytosis also depends strongly on biophysical parameters, such as particle shape, and the need for actin-driven force generation remains poorly understood. Results Here, we propose a novel, three-dimensional and stochastic biophysical model of phagocytosis, and study the engulfment of particles of various sizes and shapes, including spiral and rod-shaped particles reminiscent of bacteria. Highly curved shapes are not taken up, in line with recent experimental results. Furthermore, we surprisingly find that even without actin-driven force generation, engulfment proceeds in a large regime of parameter values, albeit more slowly and with highly variable phagocytic cups. We experimentally confirm these predictions using fibroblasts, transfected with immunoreceptor FcγRIIa for engulfment of immunoglobulin G-opsonized particles. Specifically, we compare the wild-type receptor with a mutant receptor, unable to signal to the actin cytoskeleton. Based on the reconstruction of phagocytic cups from imaging data, we indeed show that cells are able to engulf small particles even without support from biological actin-driven processes. Conclusions This suggests that biochemical pathways render the evolutionary ancient process of phagocytic highly robust, allowing cells to engulf even very large particles. The particle-shape dependence of phagocytosis makes a systematic investigation of host-pathogen interactions and an efficient design of a vehicle for drug delivery possible. PMID:21059234

GOSAILT: A hybrid of GOMS and SAILT with topography consideration

NASA Astrophysics Data System (ADS)

Wu, S.; Wen, J.

2017-12-01

Heterogeneous terrain significantly complicated the energy, mass and momentum exchange between the atmosphere and terrestrial ecosystem. Understanding of topographic effect on the forest reflectance is critical for biophysical parameters retrieval over rugged area. In this paper, a new hybrid bidirectional reflectance distribution function (BRDF) model of geometric optical mutual shadowing and scattering-from-arbitrarily-inclined-leaves model coupled topography (GOSAILT) for sloping forest was proposed. The effects of slope, aspect, gravity field of tree crown, multiple scattering scheme, and diffuse skylight are considered. The area proportions of scene components estimated by the GOSAILT model were compared with the geometric optical model for sloping terrains (GOST) model. The 3-D discrete anisotropic radiative transfer (DART) simulations were used to evaluate the performance of GOSAILT. The results indicate that the canopy reflectance is distorted by the slopes with a maximum variation of 78.3% in the red band and 17.3% in the NIR band on a steep 60 º slope. Compared with the DART simulations, the proposed GOSAILT model can capture anisotropic reflectance well with a determine coefficient (R2) of 0.9720 and 0.6701, root-mean-square error (RMSE) of 0.0024 and 0.0393, mean absolute percentage error of 2.4% and 4.61% for the red and near-infrared (NIR) band. The comparison results indicate the GOSAIL model can accurately reproducing the angular feature of discrete canopy over rugged terrain conditions. The GOSAILT model is promising for the land surface biophysical parameters retrieval (e.g. albedo, leaf area index) over the heterogeneous terrain.

Correlating yeast cell stress physiology to changes in the cell surface morphology: atomic force microscopic studies.

PubMed

Canetta, Elisabetta; Walker, Graeme M; Adya, Ashok K

2006-07-06

Atomic Force Microscopy (AFM) has emerged as a powerful biophysical tool in biotechnology and medicine to investigate the morphological, physical, and mechanical properties of yeasts and other biological systems. However, properties such as, yeasts' response to environmental stresses, metabolic activities of pathogenic yeasts, cell-cell/cell-substrate adhesion, and cell-flocculation have rarely been investigated so far by using biophysical tools. Our recent results obtained by AFM on one strain each of Saccharomyces cerevisiae and Schizosaccharomyces pombe show a clear correlation between the physiology of environmentally stressed yeasts and the changes in their surface morphology. The future directions of the AFM related techniques in relation to yeasts are also discussed.

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 between microenvironments are reflected in diffusion MRI measurements. We focus on the use of biophysical models for extracting tissue-specific parameters from data obtained with single PGSE sequences on clinical MRI scanners, but results obtained with animal MRI scanners are also considered. While modelling of white matter is the central theme, experiments on model systems that highlight important aspects of the biophysical models are also reviewed.

Characterizing Facial Skin Ageing in Humans: Disentangling Extrinsic from Intrinsic Biological Phenomena

PubMed Central

Trojahn, Carina; Dobos, Gabor; Lichterfeld, Andrea; Blume-Peytavi, Ulrike; Kottner, Jan

2015-01-01

Facial skin ageing is caused by intrinsic and extrinsic mechanisms. Intrinsic ageing is highly related to chronological age. Age related skin changes can be measured using clinical and biophysical methods. The aim of this study was to evaluate whether and how clinical characteristics and biophysical parameters are associated with each other with and without adjustment for chronological age. Twenty-four female subjects of three age groups were enrolled. Clinical assessments (global facial skin ageing, wrinkling, and sagging), and biophysical measurements (roughness, colour, skin elasticity, and barrier function) were conducted at both upper cheeks. Pearson's correlations and linear regression models adjusted for age were calculated. Most of the measured parameters were correlated with chronological age (e.g., association with wrinkle score, r = 0.901) and with each other (e.g., residual skin deformation and wrinkle score, r = 0.606). After statistical adjustment for age, only few associations remained (e.g., mean roughness (R z) and luminance (L *),  β = −0.507, R 2 = 0.377). Chronological age as surrogate marker for intrinsic ageing has the most important influence on most facial skin ageing signs. Changes in skin elasticity, wrinkling, sagging, and yellowness seem to be caused by additional extrinsic ageing. PMID:25767806

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.

Analytical model of diffuse reflectance spectrum of skin tissue

NASA Astrophysics Data System (ADS)

Lisenko, S. A.; Kugeiko, M. M.; Firago, V. A.; Sobchuk, A. N.

2014-01-01

We have derived simple analytical expressions that enable highly accurate calculation of diffusely reflected light signals of skin in the spectral range from 450 to 800 nm at a distance from the region of delivery of exciting radiation. The expressions, taking into account the dependence of the detected signals on the refractive index, transport scattering coefficient, absorption coefficient and anisotropy factor of the medium, have been obtained in the approximation of a two-layer medium model (epidermis and dermis) for the same parameters of light scattering but different absorption coefficients of layers. Numerical experiments on the retrieval of the skin biophysical parameters from the diffuse reflectance spectra simulated by the Monte Carlo method show that commercially available fibre-optic spectrophotometers with a fixed distance between the radiation source and detector can reliably determine the concentration of bilirubin, oxy- and deoxyhaemoglobin in the dermis tissues and the tissue structure parameter characterising the size of its effective scatterers. We present the examples of quantitative analysis of the experimental data, confirming the correctness of estimates of biophysical parameters of skin using the obtained analytical expressions.

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

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

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

[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.

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.

Contributions of Microtubule Dynamic Instability and Rotational Diffusion to Kinetochore Capture.

PubMed

Blackwell, Robert; Sweezy-Schindler, Oliver; Edelmaier, Christopher; Gergely, Zachary R; Flynn, Patrick J; Montes, Salvador; Crapo, Ammon; Doostan, Alireza; McIntosh, J Richard; Glaser, Matthew A; Betterton, Meredith D

2017-02-07

Microtubule dynamic instability allows search and capture of kinetochores during spindle formation, an important process for accurate chromosome segregation during cell division. Recent work has found that microtubule rotational diffusion about minus-end attachment points contributes to kinetochore capture in fission yeast, but the relative contributions of dynamic instability and rotational diffusion are not well understood. We have developed a biophysical model of kinetochore capture in small fission-yeast nuclei using hybrid Brownian dynamics/kinetic Monte Carlo simulation techniques. With this model, we have studied the importance of dynamic instability and microtubule rotational diffusion for kinetochore capture, both to the lateral surface of a microtubule and at or near its end. Over a range of biologically relevant parameters, microtubule rotational diffusion decreased capture time, but made a relatively small contribution compared to dynamic instability. At most, rotational diffusion reduced capture time by 25%. Our results suggest that while microtubule rotational diffusion can speed up kinetochore capture, it is unlikely to be the dominant physical mechanism for typical conditions in fission yeast. In addition, we found that when microtubules undergo dynamic instability, lateral captures predominate even in the absence of rotational diffusion. Counterintuitively, adding rotational diffusion to a dynamic microtubule increases the probability of end-on capture. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Size and dielectric properties of skeletal stem cells change critically after enrichment and expansion from human bone marrow: consequences for microfluidic cell sorting.

PubMed

Xavier, Miguel; de Andrés, María C; Spencer, Daniel; Oreffo, Richard O C; Morgan, Hywel

2017-08-01

The capacity of bone and cartilage to regenerate can be attributed to skeletal stem cells (SSCs) that reside within the bone marrow (BM). Given SSCs are rare and lack specific surface markers, antibody-based sorting has failed to deliver the cell purity required for clinical translation. Microfluidics offers new methods of isolating cells based on biophysical features including, but not limited to, size, electrical properties and stiffness. Here we report the characterization of the dielectric properties of unexpanded SSCs using single-cell microfluidic impedance cytometry (MIC). Unexpanded SSCs had a mean size of 9.0 µm; larger than the majority of BM cells. During expansion, often used to purify and increase the number of SSCs, cell size and membrane capacitance increased significantly, highlighting the importance of characterizing unaltered SSCs. In addition, MIC was used to track the osteogenic differentiation of SSCs and showed an increased membrane capacitance with differentiation. The electrical properties of primary SSCs were indistinct from other BM cells precluding its use as an isolation method. However, the current studies indicate that cell size in combination with another biophysical parameter, such as stiffness, could be used to design label-free devices for sorting SSCs with significant clinical impact. © 2017 The Authors.

Size and dielectric properties of skeletal stem cells change critically after enrichment and expansion from human bone marrow: consequences for microfluidic cell sorting

PubMed Central

2017-01-01

The capacity of bone and cartilage to regenerate can be attributed to skeletal stem cells (SSCs) that reside within the bone marrow (BM). Given SSCs are rare and lack specific surface markers, antibody-based sorting has failed to deliver the cell purity required for clinical translation. Microfluidics offers new methods of isolating cells based on biophysical features including, but not limited to, size, electrical properties and stiffness. Here we report the characterization of the dielectric properties of unexpanded SSCs using single-cell microfluidic impedance cytometry (MIC). Unexpanded SSCs had a mean size of 9.0 µm; larger than the majority of BM cells. During expansion, often used to purify and increase the number of SSCs, cell size and membrane capacitance increased significantly, highlighting the importance of characterizing unaltered SSCs. In addition, MIC was used to track the osteogenic differentiation of SSCs and showed an increased membrane capacitance with differentiation. The electrical properties of primary SSCs were indistinct from other BM cells precluding its use as an isolation method. However, the current studies indicate that cell size in combination with another biophysical parameter, such as stiffness, could be used to design label-free devices for sorting SSCs with significant clinical impact. PMID:28835540

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.

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

Exploration of scaling effects on coarse resolution land surface phenology

USDA-ARS?s Scientific Manuscript database

A great number of land surface phenoloy (LSP) data have been produced from various coarse resolution satellite datasets and detection algorithms across regional and global scales. Unlike field- measured phenological events which are quantitatively defined with clear biophysical meaning, current LSP ...

The scaling of urban surface water abundance and impairment with city size

NASA Astrophysics Data System (ADS)

Steele, M. K.

2018-03-01

Urbanization alters surface water compared to nonurban landscapes, yet little is known regarding how basic aquatic ecosystem characteristics, such as the abundance and impairment of surface water, differ with population size or regional context. This study examined the abundance, scaling, and impairment of surface water by quantifying the stream length, water body area, and impaired stream length for 3520 cities in the United States with populations from 2500 to 18 million. Stream length, water body area, and impaired stream length were quantified using the National Hydrography Dataset and the EPA's 303(d) list. These metrics were scaled with population and city area using single and piecewise power-law models and related to biophysical factors (precipitation, topography) and land cover. Results show that abundance of stream length and water body area in cities actually increases with city area; however, the per person abundance decreases with population size. Relative to population, impaired stream length did not increase until city populations were > 25,000 people, then scaled linearly with population. Some variation in abundance and impairment was explained by biophysical context and land cover. Development intensity correlated with stream density and impairment; however, those relationships depended on the orientation of the land covers. When high intensity development occupied the local elevation highs (+ 15 m) and undeveloped land the elevation lows, the percentage of impaired streams was less than the opposite land cover orientation (- 15 m) or very flat land. These results show that surface water abundance and impairment across contiguous US cities are influenced by city size and by biophysical setting interacting with land cover intensity.

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.

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

Observed increase in local cooling effect of deforestation at higher latitudes.

PubMed

Lee, Xuhui; Goulden, Michael L; Hollinger, David Y; Barr, Alan; Black, T Andrew; Bohrer, Gil; Bracho, Rosvel; Drake, Bert; Goldstein, Allen; Gu, Lianhong; Katul, Gabriel; Kolb, Thomas; Law, Beverly E; Margolis, Hank; Meyers, Tilden; Monson, Russell; Munger, William; Oren, Ram; Paw U, Kyaw Tha; Richardson, Andrew D; Schmid, Hans Peter; Staebler, Ralf; Wofsy, Steven; Zhao, Lei

2011-11-16

Deforestation in mid- to high latitudes is hypothesized to have the potential to cool the Earth's surface by altering biophysical processes. In climate models of continental-scale land clearing, the cooling is triggered by increases in surface albedo and is reinforced by a land albedo-sea ice feedback. This feedback is crucial in the model predictions; without it other biophysical processes may overwhelm the albedo effect to generate warming instead. Ongoing land-use activities, such as land management for climate mitigation, are occurring at local scales (hectares) presumably too small to generate the feedback, and it is not known whether the intrinsic biophysical mechanism on its own can change the surface temperature in a consistent manner. Nor has the effect of deforestation on climate been demonstrated over large areas from direct observations. Here we show that surface air temperature is lower in open land than in nearby forested land. The effect is 0.85 ± 0.44 K (mean ± one standard deviation) northwards of 45° N and 0.21 ± 0.53 K southwards. Below 35° N there is weak evidence that deforestation leads to warming. Results are based on comparisons of temperature at forested eddy covariance towers in the USA and Canada and, as a proxy for small areas of cleared land, nearby surface weather stations. Night-time temperature changes unrelated to changes in surface albedo are an important contributor to the overall cooling effect. The observed latitudinal dependence is consistent with theoretical expectation of changes in energy loss from convection and radiation across latitudes in both the daytime and night-time phase of the diurnal cycle, the latter of which remains uncertain in climate models. © 2011 Macmillan Publishers Limited. All rights reserved

Adaptation of a canopy reflectance model for sub-aqueous vegetation: Definition and sensitivity analysis

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

Plummer, S.E.; Malthus, T.J.; Clark, C.D.

1997-06-01

Seagrass meadows are a key component of shallow coastal environments acting as a food resource, nursery and contributing to water oxygenation. Given the importance of these meadows and their susceptibility to anthropogenic disturbance, it is vital that the extent and growth of seagrass is monitored. Remote sensing techniques offer the potential to determine biophysical characteristics of seagrass. This paper presents observations on the development and testing of an invertible model of seagrass canopy reflectance. The model is an adaptation of a land surface reflectance model to incorporate the effects of attenuation and scattering of incoming radiative flux in water. Sensitivitymore » analysis reveals that the subsurface reflectance is strongly dependent on the water depth, vegetation amount, the parameter which we wish to determine, and turbidity respectively. By contrast the chlorophyll concentration of water and gelbstoff are relatively unimportant. Water depth and turbidity need to be known or accommodated in any inversion as free parameters.« less

The Instrumentation of a Microfluidic Analyzer Enabling the Characterization of the Specific Membrane Capacitance, Cytoplasm Conductivity, and Instantaneous Young's Modulus of Single Cells.

PubMed

Wang, Ke; Zhao, Yang; Chen, Deyong; Huang, Chengjun; Fan, Beiyuan; Long, Rong; Hsieh, Chia-Hsun; Wang, Junbo; Wu, Min-Hsien; Chen, Jian

2017-06-19

This paper presents the instrumentation of a microfluidic analyzer enabling the characterization of single-cell biophysical properties, which includes seven key components: a microfluidic module, a pressure module, an imaging module, an impedance module, two LabVIEW platforms for instrument operation and raw data processing, respectively, and a Python code for data translation. Under the control of the LabVIEW platform for instrument operation, the pressure module flushes single cells into the microfluidic module with raw biophysical parameters sampled by the imaging and impedance modules and processed by the LabVIEW platform for raw data processing, which were further translated into intrinsic cellular biophysical parameters using the code developed in Python. Based on this system, specific membrane capacitance, cytoplasm conductivity, and instantaneous Young's modulus of three cell types were quantified as 2.76 ± 0.57 μF/cm², 1.00 ± 0.14 S/m, and 3.79 ± 1.11 kPa for A549 cells ( n cell = 202); 1.88 ± 0.31 μF/cm², 1.05 ± 0.16 S/m, and 3.74 ± 0.75 kPa for 95D cells ( n cell = 257); 2.11 ± 0.38 μF/cm², 0.87 ± 0.11 S/m, and 5.39 ± 0.89 kPa for H460 cells ( n cell = 246). As a semi-automatic instrument with a throughput of roughly 1 cell per second, this prototype instrument can be potentially used for the characterization of cellular biophysical properties.

The Instrumentation of a Microfluidic Analyzer Enabling the Characterization of the Specific Membrane Capacitance, Cytoplasm Conductivity, and Instantaneous Young’s Modulus of Single Cells

PubMed Central

Wang, Ke; Zhao, Yang; Chen, Deyong; Huang, Chengjun; Fan, Beiyuan; Long, Rong; Hsieh, Chia-Hsun; Wang, Junbo; Wu, Min-Hsien; Chen, Jian

2017-01-01

This paper presents the instrumentation of a microfluidic analyzer enabling the characterization of single-cell biophysical properties, which includes seven key components: a microfluidic module, a pressure module, an imaging module, an impedance module, two LabVIEW platforms for instrument operation and raw data processing, respectively, and a Python code for data translation. Under the control of the LabVIEW platform for instrument operation, the pressure module flushes single cells into the microfluidic module with raw biophysical parameters sampled by the imaging and impedance modules and processed by the LabVIEW platform for raw data processing, which were further translated into intrinsic cellular biophysical parameters using the code developed in Python. Based on this system, specific membrane capacitance, cytoplasm conductivity, and instantaneous Young’s modulus of three cell types were quantified as 2.76 ± 0.57 μF/cm2, 1.00 ± 0.14 S/m, and 3.79 ± 1.11 kPa for A549 cells (ncell = 202); 1.88 ± 0.31 μF/cm2, 1.05 ± 0.16 S/m, and 3.74 ± 0.75 kPa for 95D cells (ncell = 257); 2.11 ± 0.38 μF/cm2, 0.87 ± 0.11 S/m, and 5.39 ± 0.89 kPa for H460 cells (ncell = 246). As a semi-automatic instrument with a throughput of roughly 1 cell per second, this prototype instrument can be potentially used for the characterization of cellular biophysical properties. PMID:28629175

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.

Remote estimation of a managed pine forest evapotranspiration with geospatial technology

Treesearch

S. Panda; D.M. Amatya; G Sun; A. Bowman

2016-01-01

Remote sensing has increasingly been used to estimate evapotranspiration (ET) and its supporting parameters in a rapid, accurate, and cost-effective manner. The goal of this study was to develop remote sensing-based models for estimating ET and the biophysical parameters canopy conductance (gc), upper-canopy temperature, and soil moisture for a mature loblolly pine...

A revised surface resistance parameterisation for estimating latent heat flux from remotely sensed data

NASA Astrophysics Data System (ADS)

Song, Yi; Wang, Jiemin; Yang, Kun; Ma, Mingguo; Li, Xin; Zhang, Zhihui; Wang, Xufeng

2012-07-01

Estimating evapotranspiration (ET) is required for many environmental studies. Remote sensing provides the ability to spatially map latent heat flux. Many studies have developed approaches to derive spatially distributed surface energy fluxes from various satellite sensors with the help of field observations. In this study, remote-sensing-based λE mapping was conducted using a Landsat Thematic Mapper (TM) image and an Enhanced Thematic Mapper Plus (ETM+) image. The remotely sensed data and field observations employed in this study were obtained from Watershed Allied Telemetry Experimental Research (WATER). A biophysics-based surface resistance model was revised to account for water stress and temperature constraints. The precision of the results was validated using 'ground truth' data obtained by eddy covariance (EC) system. Scale effects play an important role, especially for parameter optimisation and validation of the latent heat flux (λE). After considering the footprint of EC, the λE derived from the remote sensing data was comparable to the EC measured value during the satellite's passage. The results showed that the revised surface resistance parameterisation scheme was useful for estimating the latent heat flux over cropland in arid regions.

On the complexity of Engh and Huber refinement restraints: the angle τ as example

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

Touw, Wouter G.; Vriend, Gert, E-mail: vriend@cmbi.ru.nl

2010-12-01

The angle τ (backbone N—C{sup α}—C) is the most contested Engh and Huber refinement target parameter. It is shown that this parameter is ‘correct’ as a PDB-wide average, but can be improved by taking into account residue types, secondary structures and many other aspects of our knowledge of the biophysical relations between residue type and protein structure. The Engh and Huber parameters for bond lengths and bond angles have been used uncontested in macromolecular structure refinement from 1991 until very recently, despite critical discussion of their ubiquitous validity by many authors. An extensive analysis of the backbone angle τ (N—C{supmore » α}—C) illustrates that the Engh and Huber parameters can indeed be improved and a recent study [Tronrud et al. (2010 ▶), Acta Cryst. D66, 834–842] confirms these ideas. However, the present study of τ shows that improving the Engh and Huber parameters will be considerably more complex than simply making the parameters a function of the backbone ϕ, ψ angles. Many other aspects, such as the cooperativity of hydrogen bonds, the bending of secondary-structure elements and a series of biophysical aspects of the 20 amino-acid types, will also need to be taken into account. Different sets of Engh and Huber parameters will be needed for conceptually different refinement programs.« less

Anionic lipids and the maintenance of membrane electrostatics in eukaryotes

PubMed Central

Platre, Matthieu Pierre

2017-01-01

ABSTRACT A wide range of signaling processes occurs at the cell surface through the reversible association of proteins from the cytosol to the plasma membrane. Some low abundant lipids are enriched at the membrane of specific compartments and thereby contribute to the identity of cell organelles by acting as biochemical landmarks. Lipids also influence membrane biophysical properties, which emerge as an important feature in specifying cellular territories. Such parameters are crucial for signal transduction and include lipid packing, membrane curvature and electrostatics. In particular, membrane electrostatics specifies the identity of the plasma membrane inner leaflet. Membrane surface charges are carried by anionic phospholipids, however the exact nature of the lipid(s) that powers the plasma membrane electrostatic field varies among eukaryotes and has been hotly debated during the last decade. Herein, we discuss the role of anionic lipids in setting up plasma membrane electrostatics and we compare similarities and differences that were found in different eukaryotic cells. PMID:28102755

Gold nanoparticles: sonocatalytic synthesis using ethanolic extract of Andrographis paniculata and functionalization with polycaprolactone-gelatin composites

NASA Astrophysics Data System (ADS)

Babu, Punuri Jayasekhar; Saranya, Sibyala; Sharma, Pragya; Tamuli, Ranjan; Bora, Utpal

2012-09-01

Gold nanoparticles (AuNPs) were synthesized by sonication using ethanolic leaf extract of Andrographis paniculata. We investigated the optimum parameters for AuNP synthesis and functionalization with polycaprolactone-gelatin (PCL-GL) composites. The AuNPs were characterized with various biophysical techniques such as TEM, XRD, FT-IR and EDX spectroscopy. TEM images showed that nanoparticles were spherical in shape with a size range from 5 to 75 nm. EDX analysis revealed the presence of molecular oxygen and carbon on the surface of AuNPs. The synthesized AuNPs were tested for their effect on HeLa (human cervical cancer) and MCF-7 (human breast cancer) cell lines and found to be nontoxic and biocompatible, which are potential carriers for hydrophobic drugs.

Functional identification of spike-processing neural circuits.

PubMed

Lazar, Aurel A; Slutskiy, Yevgeniy B

2014-02-01

We introduce a novel approach for a complete functional identification of biophysical spike-processing neural circuits. The circuits considered accept multidimensional spike trains as their input and comprise a multitude of temporal receptive fields and conductance-based models of action potential generation. Each temporal receptive field describes the spatiotemporal contribution of all synapses between any two neurons and incorporates the (passive) processing carried out by the dendritic tree. The aggregate dendritic current produced by a multitude of temporal receptive fields is encoded into a sequence of action potentials by a spike generator modeled as a nonlinear dynamical system. Our approach builds on the observation that during any experiment, an entire neural circuit, including its receptive fields and biophysical spike generators, is projected onto the space of stimuli used to identify the circuit. Employing the reproducing kernel Hilbert space (RKHS) of trigonometric polynomials to describe input stimuli, we quantitatively describe the relationship between underlying circuit parameters and their projections. We also derive experimental conditions under which these projections converge to the true parameters. In doing so, we achieve the mathematical tractability needed to characterize the biophysical spike generator and identify the multitude of receptive fields. The algorithms obviate the need to repeat experiments in order to compute the neurons' rate of response, rendering our methodology of interest to both experimental and theoretical neuroscientists.

Biophysical characterization and management effects on semiarid rangeland observed from Landsat ETM+ data

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

Fang, Hongliang; Liang, Shunlin; McClaran, Mitchell P.

2005-01-20

Semi-arid rangelands are very sensitive to global climatic change; studies of their biophysical attributes are crucial to understanding the dynamics of rangeland ecosystems under human disturbance. In the Santa Rita Experimental Range (SRER), Arizona, the vegetation has changed considerably and there have been many management activities applied. This study calculates seven surface variables: the enhanced vegetation index (EVI), the normalized difference vegetation index (NDVI), surface albedos (total shortwave, visible and near-infrared), leaf area index (LAI) and the fraction of photosynthetically active radiation absorbed by green vegetation (FPAR) from the Enhanced Thematic Mapper (ETM+) data. Comparison with the MODIS (Moderate Resolutionmore » Imaging Spectroradiometer) vegetation index and albedo products indicate they agree well with our estimates from ETM+ while their LAI and FPAR are larger than ETM+. Human disturbance has significantly changed the cover types and biophysical conditions. Statistical tests indicate that surface albedos increased and FPAR decreased at all sites. The recovery will require more than 67 years, and is about 50% complete within 40 years at the higher elevation. Grass cover, vegetation indices, albedos and LAI recovered from cutting faster at the higher elevation. Woody plants, vegetation indices and LAI have recovered to their original characteristics after 65 years at the lower elevation. More studies are needed to examine the spectral characteristics of different ground components.« less

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.

A comparison of surface biophysical properties and remotely sensed variables from FIFE

NASA Technical Reports Server (NTRS)

Sellers, Piers; Heiser, Mark; Walthall, C. W.; Huemmrich, F.; Strebel, D. E.; Hall, F. G.

1990-01-01

A method for calculating surface energy balances is investigated which incorporates the vegetation index and/or other indicators of surface conductance at visible and near-IR channels. Data from the Konza Prairie are employed to confirm the hypothesized relationship between maximum canopy conductance and the observed simple-ratio vegetation index. The relationship is established, but more data regarding soil-surface contributions are required to estimate the total surface conductance to evapotranspiration.

Biophysical characteristics of Adelges tsugae feeding sites on six hemlock (Tsuga) species and a hybrid: implications for resistance

USDA-ARS?s Scientific Manuscript database

Characteristics of the plant surface significantly affect host-plant selection by phytophagous insects. Surface morphology of six hemlock species (Tsuga spp.) and a hybrid was investigated using low-temperature scanning electron microscopy. Observations focused on trichome presence and placement a...

Generating 30-m land surface albedo by integrating landsat and MODIS data for understanding the disturbance evolution

USDA-ARS?s Scientific Manuscript database

Land cover changes affect climate through both biogeochemical (carbon-cycle) impacts and biogeophysical processes such as changes in surface albedo, temperature, evapotranspiration, atmospheric water vapor, and cloud cover. Recent studies have examined both the greenhouse gas and biophysical consequ...

Canopy reflectance modelling of semiarid vegetation

NASA Technical Reports Server (NTRS)

Franklin, Janet

1994-01-01

Three different types of remote sensing algorithms for estimating vegetation amount and other land surface biophysical parameters were tested for semiarid environments. These included statistical linear models, the Li-Strahler geometric-optical canopy model, and linear spectral mixture analysis. The two study areas were the National Science Foundation's Jornada Long Term Ecological Research site near Las Cruces, NM, in the northern Chihuahuan desert, and the HAPEX-Sahel site near Niamey, Niger, in West Africa, comprising semiarid rangeland and subtropical crop land. The statistical approach (simple and multiple regression) resulted in high correlations between SPOT satellite spectral reflectance and shrub and grass cover, although these correlations varied with the spatial scale of aggregation of the measurements. The Li-Strahler model produced estimated of shrub size and density for both study sites with large standard errors. In the Jornada, the estimates were accurate enough to be useful for characterizing structural differences among three shrub strata. In Niger, the range of shrub cover and size in short-fallow shrublands is so low that the necessity of spatially distributed estimation of shrub size and density is questionable. Spectral mixture analysis of multiscale, multitemporal, multispectral radiometer data and imagery for Niger showed a positive relationship between fractions of spectral endmembers and surface parameters of interest including soil cover, vegetation cover, and leaf area index.

Shape Transformation of the Nuclear Envelope during Closed Mitosis.

PubMed

Zhu, Qian; Zheng, Fan; Liu, Allen P; Qian, Jin; Fu, Chuanhai; Lin, Yuan

2016-11-15

The nuclear envelope (NE) in lower eukaryotes such as Schizosaccharomyces pombe undergoes large morphology changes during closed mitosis. However, which physical parameters are important in governing the shape evolution of the NE, and how defects in the dividing chromosomes/microtubules are reflected in those parameters, are fundamental questions that remain unresolved. In this study, we show that improper separation of chromosomes in genetically deficient cells leads to membrane tethering or asymmetric division in contrast to the formation of two equal-sized daughter nuclei in wild-type cells. We hypothesize that the poleward force is transmitted to the nuclear membrane through its physical contact with the separated sister chromatids at the two spindle poles. A theoretical model is developed to predict the morphology evolution of the NE where key factors such as the work done by the poleward force and bending and surface energies stored in the membrane have been taken into account. Interestingly, the predicted phase diagram, summarizing the dependence of nuclear shape on the size of the load transmission regions, and the pole-to-pole distance versus surface area relationship all quantitatively agree well with our experimental observations, suggesting that this model captures the essential physics involved in closed mitosis. Copyright © 2016 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Benchmarking sensitivity of biophysical processes to leaf area changes in land surface models

NASA Astrophysics Data System (ADS)

Forzieri, Giovanni; Duveiller, Gregory; Georgievski, Goran; Li, Wei; Robestson, Eddy; Kautz, Markus; Lawrence, Peter; Ciais, Philippe; Pongratz, Julia; Sitch, Stephen; Wiltshire, Andy; Arneth, Almut; Cescatti, Alessandro

2017-04-01

Land surface models (LSM) are widely applied as supporting tools for policy-relevant assessment of climate change and its impact on terrestrial ecosystems, yet knowledge of their performance skills in representing the sensitivity of biophysical processes to changes in vegetation density is still limited. This is particularly relevant in light of the substantial impacts on regional climate associated with the changes in leaf area index (LAI) following the observed global greening. Benchmarking LSMs on the sensitivity of the simulated processes to vegetation density is essential to reduce their uncertainty and improve the representation of these effects. Here we present a novel benchmark system to assess model capacity in reproducing land surface-atmosphere energy exchanges modulated by vegetation density. Through a collaborative effort of different modeling groups, a consistent set of land surface energy fluxes and LAI dynamics has been generated from multiple LSMs, including JSBACH, JULES, ORCHIDEE, CLM4.5 and LPJ-GUESS. Relationships of interannual variations of modeled surface fluxes to LAI changes have been analyzed at global scale across different climatological gradients and compared with satellite-based products. A set of scoring metrics has been used to assess the overall model performances and a detailed analysis in the climate space has been provided to diagnose possible model errors associated to background conditions. Results have enabled us to identify model-specific strengths and deficiencies. An overall best performing model does not emerge from the analyses. However, the comparison with other models that work better under certain metrics and conditions indicates that improvements are expected to be potentially achievable. A general amplification of the biophysical processes mediated by vegetation is found across the different land surface schemes. Grasslands are characterized by an underestimated year-to-year variability of LAI in cold climates, ultimately affecting the amount of absorbed radiation. In addition patterns of simulated turbulent fluxes appear opposite to observations. Such systematic errors shed light on the current partial understanding of some of the mechanisms controlling the surface energy balance. In contrast forests appear reasonably well represented with respect to the interactions between LAI and turbulent fluxes across most climatological gradients, while for net radiation this is only true for warm climates. These proven strengths increase the confidence on how certain processes are simulated in LSMs. The model capacity to mimic the vegetation-biophysics interplay has been tested over the real scenario of greening that occurred in the last 30 years. We found that the modeled trends in surface heat fluxes associated with the long-term changes in leaf area could vary largely from those observed, with different discrepancies across models and climate zones. Our findings help to identify knowledge gaps and improve model representation of the sensitivity of biophysical processes to changes in leaf area density. In particular, comparing models and observations over a wide range of climate and vegetation conditions, as analyzed here, allowed capturing non-linearity of system responses that may emerge more frequently in future climate scenarios.

Influence of Extracellular Matrix Proteins and Substratum Topography on Corneal Epithelial Cell Alignment and Migration

PubMed Central

Raghunathan, VijayKrishna; McKee, Clayton; Cheung, Wai; Naik, Rachel; Nealey, Paul F.; Russell, Paul

2013-01-01

The basement membrane (BM) of the corneal epithelium presents biophysical cues in the form of topography and compliance that can impact the phenotype and behaviors of cells and their nuclei through modulation of cytoskeletal dynamics. In addition, it is also well known that the intrinsic biochemical attributes of BMs can modulate cell behaviors. In this study, the influence of the combination of exogenous coating of extracellular matrix proteins (ECM) (fibronectin-collagen [FNC]) with substratum topography was investigated on cytoskeletal architecture as well as alignment and migration of immortalized corneal epithelial cells. In the absence of FNC coating, a significantly greater percentage of cells aligned parallel with the long axis of the underlying anisotropically ordered topographic features; however, their ability to migrate was impaired. Additionally, changes in the surface area, elongation, and orientation of cytoskeletal elements were differentially influenced by the presence or absence of FNC. These results suggest that the effects of topographic cues on cells are modulated by the presence of surface-associated ECM proteins. These findings have relevance to experiments using cell cultureware with biomimetic biophysical attributes as well as the integration of biophysical cues in tissue-engineering strategies and the development of improved prosthetics. PMID:23488816

City landscape changes effects on land surface temperature in Bucharest metropolitan area

NASA Astrophysics Data System (ADS)

Savastru, Dan M.; Zoran, Maria A.; Savastru, Roxana S.; Dida, Adrian I.

2017-10-01

This study investigated the influences of city land cover changes and extreme climate events on land surface temperature in relationship with several biophysical variables in Bucharest metropolitan area of Romania through satellite and in-situ monitoring data. Remote sensing data from IKONOS, Landsat TM/ETM+ and time series MODIS Terra/Aqua and NOAA AVHRR sensors have been used to assess urban land cover- temperature interactions over 2000 - 2016 period. Time series Thermal InfraRed (TIR) satellite remote sensing data in synergy with meteorological data (air temperatureAT, precipitations, wind, solar radiation, etc.) were applied mainly for analyzing land surface temperature (LST) pattern and its relationship with surface landscape characteristics, assessing urban heat island (UHI), and relating urban land cover temperatures (LST). The land surface temperature, a key parameter for urban thermal characteristics analysis, was also analyzed in relation with the Normalized Difference Vegetation Index (NDVI) at city level. Results show that in the metropolitan area ratio of impervious surface in Bucharest increased significantly during investigated period, the intensity of urban heat island and heat wave events being most significant. The correlation analyses revealed that, at the pixel-scale, LST and AT possessed a strong positive correlation with percent impervious surfaces and negative correlation with vegetation abundances at metropolitan scale respectively. The NDVI was significantly correlated with precipitation. The spatial average air temperatures in urban test areas rise with the expansion of the urban size.

Spatial variability and landscape controls of near-surface permafrost within the Alaskan Yukon River Basin

USGS Publications Warehouse

Pastick, Neal J.; Jorgenson, M. Torre; Wylie, Bruce K.; Rose, Joshua R.; Rigge, Matthew; Walvoord, Michelle Ann

2014-01-01

The distribution of permafrost is important to understand because of permafrost's influence on high-latitude ecosystem structure and functions. Moreover, near-surface (defined here as within 1 m of the Earth's surface) permafrost is particularly susceptible to a warming climate and is generally poorly mapped at regional scales. Subsequently, our objectives were to (1) develop the first-known binary and probabilistic maps of near-surface permafrost distributions at a 30 m resolution in the Alaskan Yukon River Basin by employing decision tree models, field measurements, and remotely sensed and mapped biophysical data; (2) evaluate the relative contribution of 39 biophysical variables used in the models; and (3) assess the landscape-scale factors controlling spatial variations in permafrost extent. Areas estimated to be present and absent of near-surface permafrost occupy approximately 46% and 45% of the Alaskan Yukon River Basin, respectively; masked areas (e.g., water and developed) account for the remaining 9% of the landscape. Strong predictors of near-surface permafrost include climatic indices, land cover, topography, and Landsat 7 Enhanced Thematic Mapper Plus spectral information. Our quantitative modeling approach enabled us to generate regional near-surface permafrost maps and provide essential information for resource managers and modelers to better understand near-surface permafrost distribution and how it relates to environmental factors and conditions.

Modeling Coniferous Canopy Structure over Extensive Areas for Ray Tracing Simulations: Scaling from the Leaf to the Stand Level

NASA Astrophysics Data System (ADS)

van Aardt, J. A.; van Leeuwen, M.; Kelbe, D.; Kampe, T.; Krause, K.

2015-12-01

Remote sensing is widely accepted as a useful technology for characterizing the Earth surface in an objective, reproducible, and economically feasible manner. To date, the calibration and validation of remote sensing data sets and biophysical parameter estimates remain challenging due to the requirements to sample large areas for ground-truth data collection, and restrictions to sample these data within narrow temporal windows centered around flight campaigns or satellite overpasses. The computer graphics community have taken significant steps to ameliorate some of these challenges by providing an ability to generate synthetic images based on geometrically and optically realistic representations of complex targets and imaging instruments. These synthetic data can be used for conceptual and diagnostic tests of instrumentation prior to sensor deployment or to examine linkages between biophysical characteristics of the Earth surface and at-sensor radiance. In the last two decades, the use of image generation techniques for remote sensing of the vegetated environment has evolved from the simulation of simple homogeneous, hypothetical vegetation canopies, to advanced scenes and renderings with a high degree of photo-realism. Reported virtual scenes comprise up to 100M surface facets; however, due to the tighter coupling between hardware and software development, the full potential of image generation techniques for forestry applications yet remains to be fully explored. In this presentation, we examine the potential computer graphics techniques have for the analysis of forest structure-function relationships and demonstrate techniques that provide for the modeling of extremely high-faceted virtual forest canopies, comprising billions of scene elements. We demonstrate the use of ray tracing simulations for the analysis of gap size distributions and characterization of foliage clumping within spatial footprints that allow for a tight matching between characteristics derived from these virtual scenes and typical pixel resolutions of remote sensing imagery.

Elucidating Inherent Uncertainties in Data Assimilation for Predictions Incorporating Non-stationary Processes - Focus on Predictive Phenology

NASA Astrophysics Data System (ADS)

Lowman, L.; Barros, A. P.

2017-12-01

Data assimilation (DA) is the widely accepted procedure for estimating parameters within predictive models because of the adaptability and uncertainty quantification offered by Bayesian methods. DA applications in phenology modeling offer critical insights into how extreme weather or changes in climate impact the vegetation life cycle. Changes in leaf onset and senescence, root phenology, and intermittent leaf shedding imply large changes in the surface radiative, water, and carbon budgets at multiple scales. Models of leaf phenology require concurrent atmospheric and soil conditions to determine how biophysical plant properties respond to changes in temperature, light and water demand. Presently, climatological records for fraction of photosynthetically active radiation (FPAR) and leaf area index (LAI), the modelled states indicative of plant phenology, are not available. Further, DA models are typically trained on short periods of record (e.g. less than 10 years). Using limited records with a DA framework imposes non-stationarity on estimated parameters and the resulting predicted model states. This talk discusses how uncertainty introduced by the inherent non-stationarity of the modeled processes propagates through a land-surface hydrology model coupled to a predictive phenology model. How water demand is accounted for in the upscaling of DA model inputs and analysis period serves as a key source of uncertainty in the FPAR and LAI predictions. Parameters estimated from different DA effectively calibrate a plant water-use strategy within the land-surface hydrology model. For example, when extreme droughts are included in the DA period, the plants are trained to uptake water, transpire, and assimilate carbon under favorable conditions and quickly shut down at the onset of water stress.

Biophysical properties and computational modeling of calcium spikes in serotonergic neurons of the dorsal raphe nucleus.

PubMed

Tuckwell, Henry C

2013-06-01

Serotonergic neurons of the dorsal raphe nuclei, with their extensive innervation of nearly the whole brain have important modulatory effects on many cognitive and physiological processes. They play important roles in clinical depression and other psychiatric disorders. In order to quantify the effects of serotonergic transmission on target cells it is desirable to construct computational models and to this end these it is necessary to have details of the biophysical and spike properties of the serotonergic neurons. Here several basic properties are reviewed with data from several studies since the 1960s to the present. The quantities included are input resistance, resting membrane potential, membrane time constant, firing rate, spike duration, spike and afterhyperpolarization (AHP) amplitude, spike threshold, cell capacitance, soma and somadendritic areas. The action potentials of these cells are normally triggered by a combination of sodium and calcium currents which may result in autonomous pacemaker activity. We here analyse the mechanisms of high-threshold calcium spikes which have been demonstrated in these cells the presence of TTX (tetrodotoxin). The parameters for calcium dynamics required to give calcium spikes are quite different from those for regular spiking which suggests the involvement of restricted parts of the soma-dendritic surface as has been found, for example, in hippocampal neurons. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

[Biochemical and biophysical investigation of liposome action in artificially induced ARDS in rabbit lungs].

PubMed

Petkova, D; Steneva, I; Iordanova, A; Khristova, E; Lalchev, Z

2007-01-01

The aim of this study is to evaluate the application of phospholipid liposomes in HCl--induced RDS in rabbits. Acute respiratory distress syndrome was induced by administration of 0.2 N HCl via intratracheal instillation for 45 min. After induced ARDS animals under artificial lung ventilation were retreated with liposomes for 60 min. Arterial blood gas analysis was performed at 30, 45 and 60 min after liposome application. Untreated animals were ventilated for the same time. Rabbits were killed with thiopental and bronhoalveolar lavage fluid biochemical and biophysical parameters were investigated. HCl- lung injury caused decrease of arterial oxygen pressure/ fraction of inspired oxygen ratio more than 50% compared to the control. We obtained high respiratory acidosis as well. The instillation of liposomes led to reversion of gas exchange at 60 min. after application almost to the control value. In order to characterize the rabbit lung tissue changes after HCl-treatment histological and ultra thin slices were obtained. Electron microscopic preparations demonstrate disappearance of surface active film in treated animals. Application of liposomes led to visualization of osmophilic material forming lamellae in lamellar bodies. On the basis of the results obtained we may assume that it is likely that the liposomes assessed in this study might be used for in vivo improvement of oxygenation in acid aspiration induced ARDS.

Biophysical response of young pomegranate trees to surface and sub-surface drip irrigation and deficit irrigation

USDA-ARS?s Scientific Manuscript database

Due to recurring agricultural water shortages, many farmers are looking for crops that have both some degree of drought resistance and a higher economic value. Pomegranate has been identified as a crop with potential drought tolerance, and high economic values. To manage limited water effectively, i...

Bidirectional Reflectance Modeling of Non-homogeneous Plant Canopies

NASA Technical Reports Server (NTRS)

Norman, J. M. (Principal Investigator)

1985-01-01

The objective of this research is to develop a 3-dimensional radiative transfer model for predicting the bidirectional reflectance distribution function (BRDF) for heterogeneous vegetation canopies. The model (named BIGAR) considers the angular distribution of leaves, leaf area index, the location and size of individual subcanopies such as widely spaced rows or trees, spectral and directional properties of leaves, multiple scattering, solar position and sky condition, and characteristics of the soil. The model relates canopy biophysical attributes to down-looking radiation measurements for nadir and off-nadir viewing angles. Therefore, inversion of this model, which is difficult but practical should provide surface biophysical pattern; a fundamental goal of remote sensing. Such a model also will help to evaluate atmospheric limitations to satellite remote sensing by providing a good surface boundary condition for many different kinds of canopies. Furthermore, this model can relate estimates of nadir reflectance, which is approximated by most satellites, to hemispherical reflectance, which is necessary in the energy budget of vegetated surfaces.

Biophysical Impacts of Tropical Land Transformation from Forest to Oil Palm and Rubber Plantations in Indonesia

NASA Astrophysics Data System (ADS)

Knohl, Alexander; Meijide, Ana; Fan, Yuanchao; Gunawan, Dodo; Hölscher, Dirk; June, Tania; Niu, Furong; Panferov, Oleg; Ringeler, Andre; Röll, Alexander; Sabajo, Clifton; Tiralla, Nina

2016-04-01

Indonesia currently experiences rapid and large-scale land-use changes resulting in forest loss and the expansion of cash crop plantations such as oil palm and rubber. Such land transformations are associated with changes in surface properties that affect biophysical processes influencing the atmosphere. Yet, the overall effect of such land transformations on the atmosphere at local and regional scale remains unclear. In our study, we combine measurements of microclimate, transpiration via sap-flux, surface energy fluxes via eddy covariance, surface temperature via remote sensing, land surface (CLM) and regional climate modeling (WRF) for Jambi Province in Indonesia. Our microclimatic measurements showed that air temperature within the canopy was on average 0.7-0.8°C higher in monoculture plantations (oil palm and rubber) compared to forest. Remote sensing analysis using MODIS and Landsat revealed a higher canopy surface temperature for oil palm plantations (+1.5°C) compared to forest, but only little differences for rubber plantations. Transpiration (T) and evapotranspiration (ET) as well as the contribution of T to ET of oil palm showed a strong age-dependent increase. The sensible to latent heat flux ratio decreased with age. Overall, rubber plantations showed the lowest transpirations rates (320 mm year-1), oil palm intermediate rates (414 mm year-1), and forest the highest rates (558 mm year-1) indicating substantial differences in water use. Despite the differences in water use and the higher within-canopy and surface temperatures of the plantations compared to the forest, there was only a minor effect of land transformation on the atmosphere at the regional scale (<0.2 °C), irrespectively of the large spatial extend of the transformation. In conclusion, our study shows a strong local scale biophysical impact affecting the conditions at the stand level, which is however mitigated in the atmosphere at the regional level.

Biophysical Impacts of Tropical Land Transformation from Forest to Oil Palm and Rubber Plantations in Indonesia

NASA Astrophysics Data System (ADS)

Knohl, A.; Meijide, A.; Fan, Y.; Hölscher, D.; June, T.; Niu, F.; Panferov, O.; Ringeler, A.; Röll, A.; Sabajo, C.; Tiralla, N.

2015-12-01

Indonesia currently experiences rapid and large-scale land-use changes resulting in forest loss and the expansion of cash crop plantations such as oil palm and rubber. Such land transformations are associated with changes in surface properties that affect biophysical processes influencing the atmosphere. Yet, the overall effect of such land transformations on the atmosphere at local and regional scale remains unclear. In our study, we combine measurements of microclimate, transpiration via sap-flux, surface energy fluxes via eddy covariance, surface temperature via remote sensing, land surface (CLM) and regional climate modeling (WRF) for Jambi Province in Indonesia. Our microclimatic measurements showed that air temperature within the canopy was on average 0.7-0.8°C higher in monoculture plantations (oil palm and rubber) compared to forest. Remote sensing analysis using MODIS and Landsat revealed a higher canopy surface temperature for oil palm plantations (+1.5°C) compared to forest, but only little differences for rubber plantations. Transpiration (T) and evapotranspiration (ET) as well as the contribution of T to ET of oil palm showed a strong age-dependent increase. The sensible to latent heat flux ratio decreased with age. Overall, rubber plantations showed the lowest transpirations rates (320 mm year-1), oil palm intermediate rates (414 mm year-1), and forest the highest rates (558 mm year-1) indicating substantial differences in water use. Despite the differences in water use and the higher within-canopy and surface temperatures of the plantations compared to the forest, there was only a minor effect of land transformation on the atmosphere at the regional scale (<0.2 °C), irrespectively of the large spatial extend of the transformation. In conclusion, our study shows a strong local scale biophysical impact affecting the conditions at the stand level, which is however mitigated in the atmosphere at the regional level.

Impacts of large scale afforestation on regional climate: a case study in the Kubuqi Desert, Inner Mongolia based on WRF model

NASA Astrophysics Data System (ADS)

Wang, L.; Lin, G.; Feng, D.; Chen, S.; Schultz, N. M.; Fu, C.; Wei, Z.; Yin, C.; Wang, W.; Lee, X.

2017-12-01

To better design climate mitigation strategies, it is important to understand the response of regional climatic indicators and related biophysical forcings to large scale afforestation projects. The response of surface temperature (Ts) caused by afforestation activities in the Kubuqi Desert, Inner Mongolia, China is simulated by the weather research and forecasting (WRF) model and the temperature changes (ΔTs) are decomposed into contributions from changes in surface albedo, surface roughness, Bowen ratio and ground heat flux using the intrinsic biophysical mechanism (IBPM). The 30-m resolution land cover maps of the Kubuqi Desert corresponding to 2000 and 2010 conditions are analyzed and the major land use changes are found to be an increase in the area of grassland (6%) and shrubland (15%), but a decrease in the area of bare land (21%) owed to the aerial seeding afforestation activities organized by Elion Resources Group, Co. and local government agencies. Our WRF simulations show that during winter, the increased cover of vegetation mainly has a warming effect (0.38 K) in the daytime due to the changes in albedo (0.24 K) and Bowen ratio (0.15 K). In the nighttime, the vegetation has a slight warming effect (0.2 K) mainly caused by energy redistribution associated with roughness change (0.2 K) as a result of vegetation turbulence, which brought heat from aloft to the surface. Although both roughness change (-0.35 K) and Bowen ratio change (-0.35 K) have cooling effects during summer days, the warming effect caused by radiative forcing (0.93 K) dominates the ΔTs. During summer nights, the change in surface temperature is not significant. Our findings demonstrate that the large-scale afforestation project in the Kubuqi Desert during a decade alters the regional surface temperature and the analysis of biophysical forcings changes using WRF simulation provides useful information for developing climate change mitigation strategies in semi-arid and arid regions.

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.

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.

Interactions of surfactants with lipid membranes.

PubMed

Heerklotz, Heiko

2008-01-01

Surfactants are surface-active, amphiphilic compounds that are water-soluble in the micro- to millimolar range, and self-assemble to form micelles or other aggregates above a critical concentration. This definition comprises synthetic detergents as well as amphiphilic peptides and lipopeptides, bile salts and many other compounds. This paper reviews the biophysics of the interactions of surfactants with membranes of insoluble, naturally occurring lipids. It discusses structural, thermodynamic and kinetic aspects of membrane-water partitioning, changes in membrane properties induced by surfactants, membrane solubilisation to micelles and other phases formed by lipid-surfactant systems. Each section defines and derives key parameters, mentions experimental methods for their measurement and compiles and discusses published data. Additionally, a brief overview is given of surfactant-like effects in biological systems, technical applications of surfactants that involve membrane interactions, and surfactant-based protocols to study biological membranes.

Detecting chlorophyll, Secchi disk depth and surface temperature in a sub-alpine lake using Landsat imagery.

PubMed

Giardino, C; Pepe, M; Brivio, P A; Ghezzi, P; Zilioli, E

2001-03-14

Some bio-physical parameters, such as chlorophyll a concentration, Secchi disk depth and water surface temperature were mapped in the sub-alpine Lake Iseo (Italy) using Landsat Thematic Mapper (TM) data acquired on the 7 March 1997. In order to adequately investigate the water-leaving radiance, TM data were atmospherically corrected using a partially image-based method, and the atmospheric transmittance was measured in synchrony with the satellite passage. An empirical approach of relating atmospherically corrected TM spectral reflectance values to in situ measurements, collected during the satellite data acquisition, was used. The models developed were used to map the chlorophyll concentration and Secchi disk depth throughout the lake. Both models gave high determination coefficients (R2 = 0.99 for chlorophyll and R2 = 0.85 for the Secchi disk) and the spatial distribution of chlorophyll concentration and Secchi disk depth was mapped with contour intervals of 1 mg/m3 and 1 m, respectively. A scene-independent procedure was used to derive the surface temperature of the lake from the TM data with a root mean square error of 0.3 degrees C.

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

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.

Scaling up of Carbon Exchange Dynamics from AmeriFlux Sites to a Super-Region in the Eastern United States

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

Hans Peter Schmid; Craig Wayson

The primary objective of this project was to evaluate carbon exchange dynamics across a region of North America between the Great Plains and the East Coast. This region contains about 40 active carbon cycle research (AmeriFlux) sites in a variety of climatic and landuse settings, from upland forest to urban development. The core research involved a scaling strategy that uses measured fluxes of CO{sub 2}, energy, water, and other biophysical and biometric parameters to train and calibrate surface-vegetation-atmosphere models, in conjunction with satellite (MODIS) derived drivers. To achieve matching of measured and modeled fluxes, the ecosystem parameters of the modelsmore » will be adjusted to the dynamically variable flux-tower footprints following Schmid (1997). High-resolution vegetation index variations around the flux sites have been derived from Landsat data for this purpose. The calibrated models are being used in conjunction with MODIS data, atmospheric re-analysis data, and digital land-cover databases to derive ecosystem exchange fluxes over the study domain.« less

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.

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.

Does surface roughness dominate biophysical forcing of land use and land cover change in the eastern United States?

NASA Astrophysics Data System (ADS)

Burakowski, E. A.; Tawfik, A. B.; Ouimette, A.; Lepine, L. C.; Ollinger, S. V.; Bonan, G. B.; Zarzycki, C. M.; Novick, K. A.

2016-12-01

Changes in land use, land cover, or both promote changes in surface temperature that can amplify or dampen long-term trends driven by natural and anthropogenic climate change by modifying the surface energy budget, primarily through differences in albedo, evapotranspiration, and aerodynamic roughness. Recent advances in variable resolution global models provide the tools necessary to investigate local and global impacts of land use and land cover change by embedding a high-resolution grid over areas of interest in a seamless and computationally efficient manner. Here, we used two eddy covariance tower clusters in the Eastern US (University of New Hampshire UNH and Duke Forest) to validate simulation of surface energy fluxes and properties by the uncoupled Community Land Model (PTCLM4.5) and coupled land-atmosphere Variable-Resolution Community Earth System Model (VR-CESM1.3). Surface energy fluxes and properties are generally well captured by the models for grassland sites, however forested sites tend to underestimate latent heat and overestimate sensible heat flux. Surface roughness emerged as the dominant biophysical forcing factor affecting surface temperature in the eastern United States, generally leading to warmer nighttime temperatures and cooler daytime temperatures. However, the sign and magnitude of the roughness effect on surface temperature was highly sensitive to the calculation of aerodynamic resistance to heat transfer.

The seasonal variation in skin hydration, sebum, scaliness, brightness and elasticity in Korean females.

PubMed

Nam, G W; Baek, J H; Koh, J S; Hwang, J-K

2015-02-01

Age, gender, regional, and ethnic differences influence skin conditions. The purpose of this study was to observe the effects of environments, especially the air temperature, relative humidity, air pressure, duration of sunshine, and precipitation on skin, and the seasonal variation in skin hydration, sebum, scales, brightness, and elasticity in Korean females. The study included 89 Korean subjects, aged 29.7 ± 6.2 years. The five skin biophysical parameters (skin hydration, sebum, scales, brightness, and elasticity) were measured at six sites: forehead, under the eye, frontal cheek, crow's foot, lateral cheek, and inner forearm. Skin hydration was measured using the Corneometer® CM 825. Skin sebum was measured with Sebumeter® SM 815. Skin scaliness was measured with Visioscan® VC 98. Skin brightness (L* value) was measured by using Spectrophotometer. A suction chamber device, Cutometer® MPA 580, was used to measure the skin elasticity. The measurements were performed every month for 13 months, from April 2007 to April 2008. There were significantly seasonal variations in environmental factors. The air temperature was the lowest in January (-1.7°C), and the highest in August (26.5°C). The relative humidity was the lowest in February (46%), and the highest in July and August (75%). There was a negative correlation between skin scaliness and three environmental factors such as air temperature, relative humidity, and highest precipitation. There was a positive correlation between skin scaliness and two environmental factors such as air pressure and duration of sunshine. Elasticity was correlated with air temperature positively and with air pressure negatively. The correlations shown between the skin biophysical parameters and environmental factors demonstrate that the skin biophysical parameters are affected by environmental factors. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

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.

Albedo and its Relationship to Land Cover and the Urban Heat Island in the Boston Metropolitan Region

NASA Astrophysics Data System (ADS)

Trlica, A.; Hutyra, L.; Wang, J.; Schaaf, C.; Erb, A.

2016-12-01

The urban built environment creates key changes in the biophysical character of the landscape, including the creation of Urban Heat Islands (UHIs) with increased near-surface temperatures in and around cities. Alteration in surface albedo is believed to partially drive UHIs through greater absorption of solar energy, but few empirical studies have specifically quantified albedo across a heterogeneous urban landscape, or investigated linkages between albedo, the UHI, and other surface socio-biophysical characteristics at a high enough spatial resolution to discern urban-scale features. This study used data derived from observations by Landsat and other remote sensing platforms to measure albedo across a varied urban landscape centered on Boston, Massachusetts, and examined the relationship between albedo, several key indicators of urban surface character (canopy cover, impervious fraction, and population density) and land surface temperature at resolutions of both 30 and 500 m. Albedo tended to be lower in areas with highest urbanization intensity indicators compared to rural undeveloped areas, and areas with lower albedo tended also to have higher median daytime summer surface temperatures. A k-means classification utilizing all the data available for each pixel revealed several distinct patterns of urban land cover corresponding mainly to the density of population and constructed surfaces and their impact on tree canopy cover. Mean 30-m summer surface temperatures ranged from 40.0 °C (SD = 2.6) in urban core areas to 26.2 °C (SD = 1.1) in nearby forest, but we only observed correspondingly large albedo decreases in the highest density urban core, with mean albedo of 0.116 (SD = 0.015) compared with 0.155 (SD = 0.015) in forest. Observations show that lower albedo in the Boston metropolitan region may be an important component of the local UHI in the most densely built-up urban core regions, while the UHI temperature effect in less densely settled peripheral regions is more likely to be driven primarily by reduced evapotranspiration due to diminished tree canopy and greater impervious surface coverage. These results empirically characterize surface albedo across a suite of land cover categories and biophysical characteristics and reveal how albedo relates to surface temperatures in this urbanized region.

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.

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

Correlative live and super-resolution imaging reveals the dynamic structure of replication domains.

PubMed

Xiang, Wanqing; Roberti, M Julia; Hériché, Jean-Karim; Huet, Sébastien; Alexander, Stephanie; Ellenberg, Jan

2018-06-04

Chromosome organization in higher eukaryotes controls gene expression, DNA replication, and DNA repair. Genome mapping has revealed the functional units of chromatin at the submegabase scale as self-interacting regions called topologically associating domains (TADs) and showed they correspond to replication domains (RDs). A quantitative structural and dynamic description of RD behavior in the nucleus is, however, missing because visualization of dynamic subdiffraction-sized RDs remains challenging. Using fluorescence labeling of RDs combined with correlative live and super-resolution microscopy in situ, we determined biophysical parameters to characterize the internal organization, spacing, and mechanical coupling of RDs. We found that RDs are typically 150 nm in size and contain four co-replicating regions spaced 60 nm apart. Spatially neighboring RDs are spaced 300 nm apart and connected by highly flexible linker regions that couple their motion only <550 nm. Our pipeline allows a robust quantitative characterization of chromosome structure in situ and provides important biophysical parameters to understand general principles of chromatin organization. © 2018 Xiang et al.

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.

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.

Biophysics of selectin-ligand interactions in inflammation and cancer

NASA Astrophysics Data System (ADS)

Siu-Lun Cheung, Luthur; Raman, Phrabha S.; Balzer, Eric M.; Wirtz, Denis; Konstantopoulos, Konstantinos

2011-02-01

Selectins (l-, e- and p-selectin) are calcium-dependent transmembrane glycoproteins that are expressed on the surface of circulating leukocytes, activated platelets, and inflamed endothelial cells. Selectins bind predominantly to sialofucosylated glycoproteins and glycolipids (e-selectin only) present on the surface of apposing cells, and mediate transient adhesive interactions pertinent to inflammation and cancer metastasis. The rapid turnover of selectin-ligand bonds, due to their fast on- and off-rates along with their remarkably high tensile strengths, enables them to mediate cell tethering and rolling in shear flow. This paper presents the current body of knowledge regarding the role of selectins in inflammation and cancer metastasis, and discusses experimental methodologies and mathematical models used to resolve the biophysics of selectin-mediated cell adhesion. Understanding the biochemistry and biomechanics of selectin-ligand interactions pertinent to inflammatory disorders and cancer metastasis may provide insights for developing promising therapies and/or diagnostic tools to combat these disorders.

Sub-nanometer Resolution Imaging with Amplitude-modulation Atomic Force Microscopy in Liquid

PubMed Central

Farokh Payam, Amir; Piantanida, Luca; Cafolla, Clodomiro; Voïtchovsky, Kislon

2016-01-01

Atomic force microscopy (AFM) has become a well-established technique for nanoscale imaging of samples in air and in liquid. Recent studies have shown that when operated in amplitude-modulation (tapping) mode, atomic or molecular-level resolution images can be achieved over a wide range of soft and hard samples in liquid. In these situations, small oscillation amplitudes (SAM-AFM) enhance the resolution by exploiting the solvated liquid at the surface of the sample. Although the technique has been successfully applied across fields as diverse as materials science, biology and biophysics and surface chemistry, obtaining high-resolution images in liquid can still remain challenging for novice users. This is partly due to the large number of variables to control and optimize such as the choice of cantilever, the sample preparation, and the correct manipulation of the imaging parameters. Here, we present a protocol for achieving high-resolution images of hard and soft samples in fluid using SAM-AFM on a commercial instrument. Our goal is to provide a step-by-step practical guide to achieving high-resolution images, including the cleaning and preparation of the apparatus and the sample, the choice of cantilever and optimization of the imaging parameters. For each step, we explain the scientific rationale behind our choices to facilitate the adaptation of the methodology to every user's specific system. PMID:28060262

Alteration of biophysical activity of pulmonary surfactant by aluminosilicate nanoparticles.

PubMed

Kondej, Dorota; Sosnowski, Tomasz R

2013-02-01

The influence of five different types of aluminosilicate nanoparticles (NPs) on the dynamic surface activity of model pulmonary surfactant (PS) (Survanta) was studied experimentally using oscillating bubble tensiometry. Bentonite, halloysite and montmorillonite (MM) NPs, which are used as fillers of polymer composites, were characterized regarding the size distribution, morphology and surface area. Particle doses applied in the studies were estimated based on the inhalation rate and duration, taking into account the expected aerosol concentration and deposition efficiency after penetration of NPs into the alveolar region. The results indicate that aluminosilicate NPs at concentrations in the pulmonary liquid above 0.1 mg cm(-3) are capable of promoting alterations of the original dynamic biophysical activity of the PS. This effect is indicated by deviation of the minimum surface tension, stability index and the size of surface tension hysteresis. Such response is dependent on the type of NPs present in the system and is stronger when particle concentration increases. It is suggested that interactions between NPs and the PS must be related to the surfactant adsorption on the suspended particles, while in the case of surface-modified clay NPs the additional washout of surface-active components may be expected. It is speculated that observed changes in surface properties of the surfactant may be associated with undesired health effects following extensive inhalation of aluminosilicate NPs in the workplace.

What is the role of historical anthropogenically-induced land-cover change on the surface climate of West Africa? Results from the LUCID intercomparison project

NASA Astrophysics Data System (ADS)

Souleymane, S.

2015-12-01

West Africa has been highlighted as a hot spot of land surface-atmosphere interactions. This study analyses the outputs of the project Land-Use and Climate, IDentification of Robust Impacts (LUCID) over West Africa. LUCID used seven atmosphere-land models with a common experimental design to explore the impacts of Land Use induced Land Cover Change (LULCC) that are robust and consistent across the climate models. Focusing the analysis on Sahel and Guinea, this study shows that, even though the seven climate models use the same atmospheric and land cover forcing, there are significant differences of West African Monsoon variability across the climate models. The magnitude of that variability differs significantly from model to model resulting two major "features": (1) atmosphere dynamics models; (2) how the land-surface functioning is parameterized in the Land surface Model, in particular regarding the evapotranspiration partitioning within the different land-cover types, as well as the role of leaf area index (LAI) in the flux calculations and how strongly the surface is coupled to the atmosphere. The major role that the models'sensitivity to land-cover perturbations plays in the resulting climate impacts of LULCC has been analysed in this study. The climate models show, however, significant differences in the magnitude and the seasonal partitioning of the temperature change. The LULCC induced cooling is directed by decreases in net shortwave radiation that reduced the available energy (QA) (related to changes in land-cover properties other than albedo, such as LAI and surface roughness), which decreases during most part of the year. The biophysical impacts of LULCC were compared to the impact of elevated greenhouse gases resulting changes in sea surface temperatures and sea ice extent (CO2SST). The results show that the surface cooling (related a decrease in QA) induced by the biophysical effects of LULCC are insignificant compared to surface warming (related an increase in QA), which is induced by the regional significance effect of CO2SST due to a small LULCC imposed. In contrast, the decrease of surface water balance resulting from LULCC effect is a similar sign to those resulting from CO2SST but the signal resulting of the biophysical effects of LULCC is stronger than the regional CO2SST impact.

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 parameters dynamics. Spectral vegetation indices sensitive to chlorophyll content (such as Meris Terrestrial ChIorophyll Index, Vogelmann Indices) showed a good linear correlation with fAPAR, daily Gross Primary Production and chlorophyll content (R2> 0.8 for all the three variables). The SWIR-based Vegetation Indices (e.g. Normalised Difference Infrared Index, Moisture Stress Index) confirmed their ability to estimate Canopy Water Content. Most of the analyzed indices showed to be linearly related with Green Herbage Ratio (explaining more than 80% of variance). The Near Infrared Difference Index (Vescovo et al., 2012) confirmed his potential in predicting canopy structural parameters such as Plant Area Index and biomass (R2> 0.90).

Incorporating Prognostic Marine Nitrogen Fixers and Related Bio-Physical Feedbacks in an Earth System Model

NASA Astrophysics Data System (ADS)

Paulsen, H.; Ilyina, T.; Six, K. D.

2016-02-01

Marine nitrogen fixers play a fundamental role in the oceanic nitrogen and carbon cycles by providing a major source of `new' nitrogen to the euphotic zone that supports biological carbon export and sequestration. Furthermore, nitrogen fixers may regionally have a direct impact on ocean physics and hence the climate system as they form extensive surface mats which can increase light absorption and surface albedo and reduce the momentum input by wind. Resulting alterations in temperature and stratification may feed back on nitrogen fixers' growth itself.We incorporate nitrogen fixers as a prognostic 3D tracer in the ocean biogeochemical component (HAMOCC) of the Max Planck Institute Earth system model and assess for the first time the impact of related bio-physical feedbacks on biogeochemistry and the climate system.The model successfully reproduces recent estimates of global nitrogen fixation rates, as well as the observed distribution of nitrogen fixers, covering large parts of the tropical and subtropical oceans. First results indicate that including bio-physical feedbacks has considerable effects on the upper ocean physics in this region. Light absorption by nitrogen fixers leads locally to surface heating, subsurface cooling, and mixed layer depth shoaling in the subtropical gyres. As a result, equatorial upwelling is increased, leading to surface cooling at the equator. This signal is damped by the effect of the reduced wind stress due to the presence of cyanobacteria mats, which causes a reduction in the wind-driven circulation, and hence a reduction in equatorial upwelling. The increase in surface albedo due to nitrogen fixers has only inconsiderable effects. The response of nitrogen fixers' growth to the alterations in temperature and stratification varies regionally. Simulations with the fully coupled Earth system model are in progress to assess the implications of the biologically induced changes in upper ocean physics for the global climate system.

Imaging the effect of hemoglobin on properties of RBCs using common-path digital holographic microscope

NASA Astrophysics Data System (ADS)

Joglekar, M.; Shah, H.; Trivedi, V.; Mahajan, S.; Chhaniwal, V.; Leitgeb, R.; Javidi, B.; Anand, A.

2017-07-01

Adequate supply of oxygen to the body is the most essential requirement. In vertebrate species this function is performed by Hemoglobin contained in red blood cells. The mass concentration of the Hb determines the oxygen carrying capacity of the blood. Thus it becomes necessary to determine its concentration in the blood, which helps in monitoring the health of a person. If the amount of Hb crosses certain range, then it is considered critical. As the Hb constitutes upto 96% of red blood cells dry content, it would be interesting to examine various physical and mechanical parameters of RBCs which depends upon its concentration. Various diseases bring about significant variation in the amount of hemoglobin which may alter certain parameters of the RBC such as surface area, volume, membrane fluctuation etc. The study of the variations of these parameters may be helpful in determining Hb content which will reflect the state of health of a human body leading to disease diagnosis. Any increase or decrease in the amount of Hb will change the density and hence the optical thickness of the RBCs, which affects the cell membrane and thereby changing its mechanical and physical properties. Here we describe the use of lateral shearing digital holographic microscope for quantifying the cell parameters for studying the change in biophysical properties of cells due to variation in hemoglobin concentration.

Emergent relation between surface vapor conductance and relative humidity profiles yields evaporation rates from weather data

NASA Astrophysics Data System (ADS)

Salvucci, Guido D.; Gentine, Pierre

2013-04-01

The ability to predict terrestrial evapotranspiration (E) is limited by the complexity of rate-limiting pathways as water moves through the soil, vegetation (roots, xylem, stomata), canopy air space, and the atmospheric boundary layer. The impossibility of specifying the numerous parameters required to model this process in full spatial detail has necessitated spatially upscaled models that depend on effective parameters such as the surface vapor conductance (Csurf). Csurf accounts for the biophysical and hydrological effects on diffusion through the soil and vegetation substrate. This approach, however, requires either site-specific calibration of Csurf to measured E, or further parameterization based on metrics such as leaf area, senescence state, stomatal conductance, soil texture, soil moisture, and water table depth. Here, we show that this key, rate-limiting, parameter can be estimated from an emergent relationship between the diurnal cycle of the relative humidity profile and E. The relation is that the vertical variance of the relative humidity profile is less than would occur for increased or decreased evaporation rates, suggesting that land-atmosphere feedback processes minimize this variance. It is found to hold over a wide range of climate conditions (arid-humid) and limiting factors (soil moisture, leaf area, energy). With this relation, estimates of E and Csurf can be obtained globally from widely available meteorological measurements, many of which have been archived since the early 1900s. In conjunction with precipitation and stream flow, long-term E estimates provide insights and empirical constraints on projected accelerations of the hydrologic cycle.

Emergent relation between surface vapor conductance and relative humidity profiles yields evaporation rates from weather data.

PubMed

Salvucci, Guido D; Gentine, Pierre

2013-04-16

The ability to predict terrestrial evapotranspiration (E) is limited by the complexity of rate-limiting pathways as water moves through the soil, vegetation (roots, xylem, stomata), canopy air space, and the atmospheric boundary layer. The impossibility of specifying the numerous parameters required to model this process in full spatial detail has necessitated spatially upscaled models that depend on effective parameters such as the surface vapor conductance (C(surf)). C(surf) accounts for the biophysical and hydrological effects on diffusion through the soil and vegetation substrate. This approach, however, requires either site-specific calibration of C(surf) to measured E, or further parameterization based on metrics such as leaf area, senescence state, stomatal conductance, soil texture, soil moisture, and water table depth. Here, we show that this key, rate-limiting, parameter can be estimated from an emergent relationship between the diurnal cycle of the relative humidity profile and E. The relation is that the vertical variance of the relative humidity profile is less than would occur for increased or decreased evaporation rates, suggesting that land-atmosphere feedback processes minimize this variance. It is found to hold over a wide range of climate conditions (arid-humid) and limiting factors (soil moisture, leaf area, energy). With this relation, estimates of E and C(surf) can be obtained globally from widely available meteorological measurements, many of which have been archived since the early 1900s. In conjunction with precipitation and stream flow, long-term E estimates provide insights and empirical constraints on projected accelerations of the hydrologic cycle.

Melting of the Dipalmitoylphosphatidylcholine Monolayer.

PubMed

Xu, Lu; Bosiljevac, Gordon; Yu, Kyle; Zuo, Yi Y

2018-04-17

Langmuir monolayer self-assembled at the air-water interface represents an excellent model for studying phase transition and lipid polymorphism in two dimensions. Compared with numerous studies of phospholipid phase transitions induced by isothermal compression, there are very scarce reports on two-dimensional phase transitions induced by isobaric heating. This is mainly due to technical difficulties of continuously regulating temperature variations while maintaining a constant surface pressure in a classical Langmuir-type film balance. Here, with technological advances in constrained drop surfactometry and closed-loop axisymmetric drop shape analysis, we studied the isobaric heating process of the dipalmitoylphosphatidylcholine (DPPC) monolayer. It is found that temperature and surface pressure are two equally important intensive properties that jointly determine the phase behavior of the phospholipid monolayer. We have determined a critical point of the DPPC monolayer at a temperature of 44 °C and a surface pressure of 57 mN/m. Beyond this critical point, no phase transition can exist in the DPPC monolayer, either by isothermal compression or by isobaric heating. The melting process of the DPPC monolayer studied here provides novel insights into the understanding of a wide range of physicochemical and biophysical phenomena, such as surface thermodynamics, critical phenomena, and biophysical study of pulmonary surfactants.

Nonenzymatic Reactions above Phospholipid Surfaces of Biological Membranes: Reactivity of Phospholipids and Their Oxidation Derivatives

PubMed Central

Solís-Calero, Christian; Ortega-Castro, Joaquín; Frau, Juan; Muñoz, Francisco

2015-01-01

Phospholipids play multiple and essential roles in cells, as components of biological membranes. Although phospholipid bilayers provide the supporting matrix and surface for many enzymatic reactions, their inherent reactivity and possible catalytic role have not been highlighted. As other biomolecules, phospholipids are frequent targets of nonenzymatic modifications by reactive substances including oxidants and glycating agents which conduct to the formation of advanced lipoxidation end products (ALEs) and advanced glycation end products (AGEs). There are some theoretical studies about the mechanisms of reactions related to these processes on phosphatidylethanolamine surfaces, which hypothesize that cell membrane phospholipids surface environment could enhance some reactions through a catalyst effect. On the other hand, the phospholipid bilayers are susceptible to oxidative damage by oxidant agents as reactive oxygen species (ROS). Molecular dynamics simulations performed on phospholipid bilayers models, which include modified phospholipids by these reactions and subsequent reactions that conduct to formation of ALEs and AGEs, have revealed changes in the molecular interactions and biophysical properties of these bilayers as consequence of these reactions. Then, more studies are desirable which could correlate the biophysics of modified phospholipids with metabolism in processes such as aging and diseases such as diabetes, atherosclerosis, and Alzheimer's disease. PMID:25977746

A comparison of different radiative transfer model inversion methods for canopy water content retrieval

NASA Astrophysics Data System (ADS)

Boren, E. J.; Boschetti, L.; Johnson, D.

2016-12-01

With near-future droughts predicted to become both more frequent and more intense (Allen et al. 2015, Diffenbaugh et al. 2015), the estimation of satellite-derived vegetation water content would benefit a wide range of environmental applications including agricultural, vegetation, and fire risk monitoring. No vegetation water content thematic product is currently available (Yebra et al. 2013), but the successful launch of the Landsat 8 OLI and Sentinel 2A satellites, and the forthcoming Sentinel 2B, provide the opportunity for monitoring biophysical variables at a scale (10-30m) and temporal resolution (5 days) needed by most applications. Radiative transfer models (RTM) use a set of biophysical parameters to produce an estimated spectral response and - when used in inverse mode - provide a way to use satellite spectral data to estimate vegetation biophysical parameters, including water content (Zarco-Tejada et al. 2003). Using the coupled leaf and canopy level model PROSAIL5, and Landsat 8 OLI and Sentinel 2A MSI optical satellite data, the present research compares the results of three model inversion techniques: iterative optimization (OPT), look-up table (LUT), and artificial neural network (ANN) training. Ancillary biophysical data, needed for constraining the inversion process, were collected from various crop species grown in a controlled setting and under different water stress conditions. The measurements included fresh weight, dry weight, leaf area, and spectral leaf transmittance and reflectance in the 350-2500 nm range. Plot-level data, collected coincidently with satellite overpasses during three summer field campaigns in northern Idaho (2014 to 2016), are used to evaluate the results of the model inversion. Field measurements included fresh weight, dry weight, leaf area index, plant height, and top of canopy reflectance in the 350-2500 nm range. The results of the model inversion intercomparison exercised are used to characterize the uncertainties of vegetation water content estimation from Landsat 8 OLI and Sentinel 2A data.

Climate mitigation from vegetation biophysical feedbacks during the past three decades

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

Zeng, Zhenzhong; Piao, Shilong; Li, Laurent Z. X.

The surface air temperature response to vegetation changes has been studied for the extreme case of land-cover change; yet, it has never been quantified for the slow but persistent increase in leaf area index (LAI) observed over the past 30 years (Earth greening). We isolate the fingerprint of increasing LAI on surface air temperature using a coupled land–atmosphere global climate model prescribed with satellite LAI observations. Furthermore, we found that the global greening has slowed down the rise in global land-surface air temperature by 0.09 ± 0.02 °C since 1982. This net cooling effect is the sum of cooling frommore » increased evapotranspiration (70%), changed atmospheric circulation (44%), decreased shortwave transmissivity (21%), and warming from increased longwave air emissivity (-29%) and decreased albedo (-6%). The global cooling originated from the regions where LAI has increased, including boreal Eurasia, Europe, India, northwest Amazonia, and the Sahel. Increasing LAI did not, but, significantly change surface air temperature in eastern North America and East Asia, where the effects of large-scale atmospheric circulation changes mask local vegetation feedbacks. Overall, the sum of biophysical feedbacks related to the greening of the Earth mitigated 12% of global land-surface warming for the past 30 years.« less

[Fluctuations in biophysical measurements as a result of variations in solar activity].

PubMed

Peterson, T F

1995-01-01

A theory is proposed to explain variations in the net electrical charge of biological substances at the Earth's surface. These are shown to occur in association with changes in the solar wind and geomagnetic field. It is suggested that a liquid dielectric's net volume charge will imitate pH effects, influence chemical reaction rates, and alter ion transfer mechanisms in biophysical systems. An experiment is described which measures dielectric volume charge, or non-neutrality, to allow correlation of this property with daily, 28-day, and 11-year fluctuation patterns in geophysical and satellite data associated with solar activity and the interplanetary magnetic field.

A new space-time information expression and analysis approach based on 3S technology: a case study of China's coastland

NASA Astrophysics Data System (ADS)

Cao, Bao; Luo, Hong; Gao, Zhenji

2009-10-01

Space-time Information Expression and Analysis (SIEA) uses vivid graphic images of thinking to deal with information units according to series distribution rules with a variety of arranging, which combined with the use of information technology, powerful data-processing capabilities to carry out analysis and integration of information units. In this paper, a new SIEA approach was proposed and its model was constructed. And basic units, methodologies and steps of SIEA were discussed. Taking China's coastland as an example, the new SIEA approach were applied for the parameters of air humidity, rainfall and surface temperature from the year 1981 to 2000. The case study shows that the parameters change within month alternation, but little change within year alternation. From the view of spatial distribution, it was significantly different for the parameters in north and south of China's coastland. The new SIEA approach proposed in this paper not only has the intuitive, image characteristics, but also can solved the problem that it is difficult to express the biophysical parameters of space-time distribution using traditional charts and tables. It can reveal the complexity of the phenomenon behind the movement of things and laws of nature. And it can quantitatively analyze the phenomenon and nature law of the parameters, which inherited the advantages of graphics of traditional ways of thinking. SIEA provides a new space-time analysis and expression approach, using comprehensive 3S technologies, for the research of Earth System Science.

Tackling both the player and the ball: lessons from crystallographic studies on the N-utilization substance B (NusB) from Mycobacterium tuberculosis

NASA Astrophysics Data System (ADS)

Haire, L. F.; Gopal, B.

2001-11-01

The N-utilization substance B (NusB) from Mycobacterium tuberculosis is an important element in a complex assembly of other proteins and ribonucleic acid effecting transcription antitermination in this organism. The cloning and overexpression of the protein in E. coli, followed by the purification, crystallization, and use of selenomethionine samples to obtain phase information by anomalous dispersion techniques, allows us to investigate the fine interplay of sample engineering and modification of crystallization parameters leading to successful structure determination. Knowledge of the crystal structure and the surface properties of the protein allows an analysis of the packing of the NusB dimers in the crystal lattice. This exercise, albeit post facto, helps to demonstrate how biophysical and functional information could help 'rationalize' the course of obtaining protein crystals suitable for structural studies.

Effect of Molecular Structure of Cationic Surfactants on Biophysical Interactions of the Surfactant-modified Nanoparticles with a Model Membrane and Cellular Uptake

PubMed Central

Peetla, Chiranjeevi; Labhasetwar, Vinod

2009-01-01

The aim of this study was to test the hypothesis that the molecular structure of cationic surfactants at the nanoparticle (NP)-interface influences the biophysical interactions of NPs with a model membrane and cellular uptake of NPs. Polystyrene NPs (surfactant free, 130 nm) were modified with cationic surfactants. These surfactants were of either dichained (didodecyldimethylammonium bromide [DMAB]) or single chained (cetyltrimethylammonium bromide [CTAB] and dodecyltrimethylammonium bromide [DTAB]) forms, the latter two with different hydrophobic chain lengths. Biophysical interactions of these surfactant-modified NPs with an endothelial cell model membrane (EMM) were studied using a Langmuir film balance. Changes in surface pressure (SP) of EMM as a function of time following interaction with NPs and in the compression isotherm (π - A) of the lipid mixture of EMM in the presence of NPs were analyzed. Langmuir-Schaeffer (LS) films, which are EMMs that have been transferred onto a suitable substrate, were imaged by atomic force microscopy (AFM), and the images were analyzed to determine the mechanisms of the NP-EMM interaction. DMAB-modified NPs showed a greater increase in SP and a shift towards higher mean molecular area (mmA) than CTAB- and DTAB-modified NPs, indicating stronger interactions of DMAB-modified NPs with the EMM. However, analysis of the AFM phase and height images of the LS films revealed that both DMAB- and CTAB-modified NPs interacted with the EMM but via different mechanisms: DMAB-modified NPs penetrated the EMM, thus explaining the increase in SP, whereas CTAB-modified NPs anchored onto the EMM's condensed lipid domains, and hence did not cause any significant change in SP. Human umbilical vein endothelial cells showed greater uptake of DMAB- and CTAB-modified NPs than of DTAB-modified or unmodified NPs. We conclude that (i) the dichained and single-chained cationic surfactants on NPs have different mechanisms of interaction with the model membrane and (ii) NPs that demonstrate greater biophysical interactions with the membrane also show greater cellular uptake. Biophysical interactions of NPs with a model membrane thus could be effectively used for developing nanocarriers with optimized surface properties for drug delivery and imaging applications. PMID:19161268

Myxococcus xanthus Gliding Motors Are Elastically Coupled to the Substrate as Predicted by the Focal Adhesion Model of Gliding Motility

PubMed Central

Balagam, Rajesh; Litwin, Douglas B.; Czerwinski, Fabian; Sun, Mingzhai; Kaplan, Heidi B.; Shaevitz, Joshua W.; Igoshin, Oleg A.

2014-01-01

Myxococcus xanthus is a model organism for studying bacterial social behaviors due to its ability to form complex multi-cellular structures. Knowledge of M. xanthus surface gliding motility and the mechanisms that coordinated it are critically important to our understanding of collective cell behaviors. Although the mechanism of gliding motility is still under investigation, recent experiments suggest that there are two possible mechanisms underlying force production for cell motility: the focal adhesion mechanism and the helical rotor mechanism, which differ in the biophysics of the cell–substrate interactions. Whereas the focal adhesion model predicts an elastic coupling, the helical rotor model predicts a viscous coupling. Using a combination of computational modeling, imaging, and force microscopy, we find evidence for elastic coupling in support of the focal adhesion model. Using a biophysical model of the M. xanthus cell, we investigated how the mechanical interactions between cells are affected by interactions with the substrate. Comparison of modeling results with experimental data for cell-cell collision events pointed to a strong, elastic attachment between the cell and substrate. These results are robust to variations in the mechanical and geometrical parameters of the model. We then directly measured the motor-substrate coupling by monitoring the motion of optically trapped beads and find that motor velocity decreases exponentially with opposing load. At high loads, motor velocity approaches zero velocity asymptotically and motors remain bound to beads indicating a strong, elastic attachment. PMID:24810164

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.

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

Seasonality and Management Affect Land Surface Temperature Differences Between Loblolly Pine and Switchgrass Ecosystems in Central Virginia

NASA Astrophysics Data System (ADS)

Ahlswede, B.; Thomas, R. Q.; O'Halloran, T. L.; Rady, J.; LeMoine, J.

2017-12-01

Changes in land-use and land management can have biogeochemical and biophysical effects on local and global climate. While managed ecosystems provide known food and fiber benefits, their influence on climate is less well quantified. In the southeastern United States, there are numerous types of intensely managed ecosystems but pine plantations and switchgrass fields represent two biogeochemical and biophysical extremes; a tall, low albedo forest with trees harvested after multiple decades vs. a short, higher albedo C4 grass field that is harvested annually. Despite the wide spread use of these ecosystems for timber and bioenergy, a quantitative, empirical evaluation of the net influence of these ecosystems on climate is lacking because it requires measuring both the greenhouse gas and energy balance of the ecosystems while controlling for the background weather and soil environment. To address this need, we established a pair of eddy flux towers in these ecosystems that are co-located (1.5 km apart) in Central Virginia and measured the radiative energy, non-radiative energy and carbon fluxes, along with associated biometeorology variables; the paired site has run since April 2016. During the first 1.5 years (two growing seasons), we found strong seasonality in the difference in surface temperature between the two ecosystems. In the growing seasons, both sites had similar surface temperature despite higher net radiation in pine. Following harvest of the switchgrass in September, the switchgrass temperatures increased relative to pine. In the winter, the pine ecosystem was warmer. We evaluate the drivers of these intra-annual dynamics and compare the climate influence of these biophysical differences to the differences in carbon fluxes between the sites using a suite of established climate regulation services metrics. Overall, our results show tradeoffs exist between the biogeochemical and biophysical climate services in managed ecosystems in the southeastern United States and highlight the importance of seasonality when quantifying how land-use and land-cover change influence climate. These data, when combined with earth system models, will help inform our understanding of how land-use and land change decisions in the southeastern United States will influence local, regional, and global climate.

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.

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

Seasonal evolution of soil and plant parameters on the agricultural Gebesee test site: a database for the set-up and validation of EO-LDAS and satellite-aided retrieval models

NASA Astrophysics Data System (ADS)

Truckenbrodt, Sina C.; Schmullius, Christiane C.

2018-03-01

Ground reference data are a prerequisite for the calibration, update, and validation of retrieval models facilitating the monitoring of land parameters based on Earth Observation data. Here, we describe the acquisition of a comprehensive ground reference database which was created to test and validate the recently developed Earth Observation Land Data Assimilation System (EO-LDAS) and products derived from remote sensing observations in the visible and infrared range. In situ data were collected for seven crop types (winter barley, winter wheat, spring wheat, durum, winter rape, potato, and sugar beet) cultivated on the agricultural Gebesee test site, central Germany, in 2013 and 2014. The database contains information on hyperspectral surface reflectance factors, the evolution of biophysical and biochemical plant parameters, phenology, surface conditions, atmospheric states, and a set of ground control points. Ground reference data were gathered at an approximately weekly resolution and on different spatial scales to investigate variations within and between acreages. In situ data collected less than 1 day apart from satellite acquisitions (RapidEye, SPOT 5, Landsat-7 and -8) with a cloud coverage ≤ 25 % are available for 10 and 15 days in 2013 and 2014, respectively. The measurements show that the investigated growing seasons were characterized by distinct meteorological conditions causing interannual variations in the parameter evolution. Here, the experimental design of the field campaigns, and methods employed in the determination of all parameters, are described in detail. Insights into the database are provided and potential fields of application are discussed. The data will contribute to a further development of crop monitoring methods based on remote sensing techniques. The database is freely available at PANGAEA (https://doi.org/10.1594/PANGAEA.874251).

Evaluation of GIS Technology in Assessing and Modeling Land Management Practices

NASA Technical Reports Server (NTRS)

Archer, F.; Coleman, T. L.; Manu, A.; Tadesse, W.; Liu, G.

1997-01-01

There is an increasing concern of land owners to protect and maintain healthy and sustainable agroecosystems through the implementation of best management practices (BMP). The objectives of this study were: (1) To develop and evaluate the use of a Geographic Information System (GIS) technology for enhancing field-scale management practices; (2) evaluate the use of 2-dimensional displays of the landscape and (3) define spatial classes of variables from interpretation of geostatistical parameters. Soil samples were collected to a depth of 2 m at 15 cm increments. Existing data from topographic, land use, and soil survey maps of the Winfred Thomas Agricultural Research Station were converted to digital format. Additional soils data which included texture, pH, and organic matter were also generated. The digitized parameters were used to create a multilayered field-scale GIS. Two dimensional (2-D) displays of the parameters were generated using the ARC/INFO software. The spatial distribution of the parameters evaluated in both fields were similar which could be attributed to the similarity in vegetation and surface elevation. The ratio of the nugget to total semivariance, expressed as a percentage, was used to assess the degree of spatial variability. The results indicated that most of the parameters were moderate spatially dependent Biophysical constraint maps were generated from the database layers, and used in multiple combination to visualize results of the BMP. Understanding the spatial relationships of physical and chemical parameters that exists within a field should enable land managers to more effectively implement BMP to ensure a safe and sustainable environment.

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 flown in summer and spring; 4) create new products, called Relative Uncertainty Surfaces (RUS), from lidar waveform-derived metrics and determine their utility; and 5) develop and test five nonparametric regression model algorithms (MARS -- Multivariate Adaptive Regression, CART -- Classification and Regression Trees, TreeNet, Random Forests, and GPSM -- Generalized Path Seeker) with 13 predictor variables derived from both discrete and full waveform lidar sources in order to develop a method of improving lidar DEM quality. Results of this study indicate strong correlations for Spartina alterniflora (r > 0.9) between vertical biomass (VB), the distribution of vegetation biomass by height, and vertical obscuration (VO), the measure of the vertical distribution of the ratio of vegetation to airspace. It was determined that simple, feature-based lidar waveform metrics, such as waveform width, can provide new information to estimate salt marsh vegetation biophysical parameters such as vegetation height. The results also clearly illustrate the importance of seasonality, species, and lidar interpolation and filtering methods on elevation uncertainty in salt marshes. Relative uncertainty surfaces generated from lidar waveform features were determined useful in qualitative/visual assessment of lidar elevation uncertainty and correlate well with vegetation height and presence of Spartina alterniflora. Finally, DEMs generated using full-waveform predictor models produced corrections (compared to ground based RTK GNSS elevations) with R2 values of up to 0.98 and slopes within 4% of a perfect 1:1 correlation. The findings from this research have strong potential to advance tidal marsh mapping, research and management initiatives.

Observed increase in local cooling effect of deforestation at higher latitudes

Treesearch

Xuhui Lee; Michael L. Goulden; David Y. Hollinger; Alan Barr; T. Andrew Black; Gil Bohrer; Rosvel Bracho; Bert Drake; Allen Goldstein; Lianhong Gu; Gabriel Katul; Thomas Kolb; Beverly E. Law; Hank Margolis; Tilden Meyers; Russell Monson; William Munger; Ram Oren; Kyaw Tha Paw U; Andrew D. Richardson; Hans Peter Schmid; Ralf Staebler; Steven Wofsy; Lei Zhao

2011-01-01

Deforestation in mid- to high latitudes is hypothesized to have the potential to cool the Earth's surface by altering biophysical processes. In climate models of continental-scale land clearing, the cooling is triggered by increases in surface albedo and is reinforced by a land albedo–sea ice feedback. This feedback is crucial in the model predictions; without it...

Vegetation species composition and canopy architecture information expressed in leaf water absorption measured in the 1000 nm and 2200 spectral region by an imaging spectrometer

NASA Technical Reports Server (NTRS)

Green, Robert O.; Roberts, Dar A.

1995-01-01

Plant species composition and plant architectural attributes are critical parameters required for the measuring, monitoring, and modeling of terrestrial ecosystems. Remote sensing is commonly cited as an important tool for deriving vegetation properties at an appropriate scale for ecosystem studies, ranging from local to regional and even synoptic scales. Classical approaches rely on vegetation indices such as the normalized difference vegetation index (NDVI) to estimate biophysical parameters such as leaf area index or intercepted photosynthetically active radiation (IPAR). Another approach is to apply a variety of classification schemes to map vegetation and thus extrapolate fine-scale information about specific sites to larger areas of similar composition. Imaging spectrometry provides additional information that is not obtainable through broad-band sensors and that may provide improved inputs both to direct biophysical estimates as well as classification schemes. Some of this capability has been demonstrated through improved discrimination of vegetation, estimates of canopy biochemistry, and liquid water estimates from vegetation. We investigate further the potential of leaf water absorption estimated from Airborne Visible/Infrared Imaging Spectrometer (AVIRIS) data as a means for discriminating vegetation types and deriving canopy architectural information. We expand our analysis to incorporate liquid water estimates from two spectral regions, the 1000-nm region and the 2200-nm region. The study was conducted in the vicinity of Jasper Ridge, California, which is located on the San Francisco peninsula to the west of the Stanford University campus. AVIRIS data were acquired over Jasper Ridge, CA, on June 2, 1992, at 19:31 UTC. Spectra from three sites in this image were analyzed. These data are from an area of healthy grass, oak woodland, and redwood forest, respectively. For these analyses, the AVIRIS-measured upwelling radiance spectra for the entire Jasper Ridge scene were transformed to apparent surface reflectance using a radiative transfer code-based inversion algorithm.

Semi-empirical modelling for forest above ground biomass estimation using hybrid and fully PolSAR data

NASA Astrophysics Data System (ADS)

Tomar, Kiledar S.; Kumar, Shashi; Tolpekin, Valentyn A.; Joshi, Sushil K.

2016-05-01

Forests act as sink of carbon and as a result maintains carbon cycle in atmosphere. Deforestation leads to imbalance in global carbon cycle and changes in climate. Hence estimation of forest biophysical parameter like biomass becomes a necessity. PolSAR has the ability to discriminate the share of scattering element like surface, double bounce and volume scattering in a single SAR resolution cell. Studies have shown that volume scattering is a significant parameter for forest biophysical characterization which mainly occurred from vegetation due to randomly oriented structures. This random orientation of forest structure causes shift in orientation angle of polarization ellipse which ultimately disturbs the radar signature and shows overestimation of volume scattering and underestimation of double bounce scattering after decomposition of fully PolSAR data. Hybrid polarimetry has the advantage of zero POA shift due to rotational symmetry followed by the circular transmission of electromagnetic waves. The prime objective of this study was to extract the potential of Hybrid PolSAR and fully PolSAR data for AGB estimation using Extended Water Cloud model. Validation was performed using field biomass. The study site chosen was Barkot Forest, Uttarakhand, India. To obtain the decomposition components, m-alpha and Yamaguchi decomposition modelling for Hybrid and fully PolSAR data were implied respectively. The RGB composite image for both the decomposition techniques has generated. The contribution of all scattering from each plot for m-alpha and Yamaguchi decomposition modelling were extracted. The R2 value for modelled AGB and field biomass from Hybrid PolSAR and fully PolSAR data were found 0.5127 and 0.4625 respectively. The RMSE for Hybrid and fully PolSAR between modelled AGB and field biomass were 63.156 (t ha-1) and 73.424 (t ha-1) respectively. On the basis of RMSE and R2 value, this study suggests Hybrid PolSAR decomposition modelling to retrieve scattering element for AGB estimation from forest.

Positron beam studies of solids and surfaces: A summary

NASA Astrophysics Data System (ADS)

Coleman, P. G.

2006-02-01

A personal overview is given of the advances in positron beam studies of solids and surfaces presented at the 10th International Workshop on Positron Beams, held in Doha, Qatar, in March 2005. Solids studied include semiconductors, metals, alloys and insulators, as well as biophysical systems. Surface studies focussed on positron annihilation-induced Auger electron spectroscopy (PAES), but interesting applications of positron-surface interactions in fields as diverse as semiconductor technology and studies of the interstellar medium serve to illustrate once again the breadth of scientific endeavour covered by slow positron beam investigations.

Vegetation Coverage and Impervious Surface Area Estimated Based on the Estarfm Model and Remote Sensing Monitoring

NASA Astrophysics Data System (ADS)

Hu, Rongming; Wang, Shu; Guo, Jiao; Guo, Liankun

2018-04-01

Impervious surface area and vegetation coverage are important biophysical indicators of urban surface features which can be derived from medium-resolution images. However, remote sensing data obtained by a single sensor are easily affected by many factors such as weather conditions, and the spatial and temporal resolution can not meet the needs for soil erosion estimation. Therefore, the integrated multi-source remote sensing data are needed to carry out high spatio-temporal resolution vegetation coverage estimation. Two spatial and temporal vegetation coverage data and impervious data were obtained from MODIS and Landsat 8 remote sensing images. Based on the Enhanced Spatial and Temporal Adaptive Reflectance Fusion Model (ESTARFM), the vegetation coverage data of two scales were fused and the data of vegetation coverage fusion (ESTARFM FVC) and impervious layer with high spatiotemporal resolution (30 m, 8 day) were obtained. On this basis, the spatial variability of the seepage-free surface and the vegetation cover landscape in the study area was measured by means of statistics and spatial autocorrelation analysis. The results showed that: 1) ESTARFM FVC and impermeable surface have higher accuracy and can characterize the characteristics of the biophysical components covered by the earth's surface; 2) The average impervious surface proportion and the spatial configuration of each area are different, which are affected by natural conditions and urbanization. In the urban area of Xi'an, which has typical characteristics of spontaneous urbanization, landscapes are fragmented and have less spatial dependence.

QUARTERLY PROGRESS REPORT NO. 83,

DTIC Science & Technology

Topics included are: microwave spectroscopy; radio astronomy; solid-state microwave electronics; optical and infrared spectroscopy; physical electronics and surface physics; physical acoustics; plasma physics; gaseous electronics; plasmas and controlled nuclear fusion ; energy conversion research; statistical communication theory; linguistics; cognitive information processing; communications biophysics; neurophysiology; computation research.

Sensitivity of June Near-Surface Temperatures and Precipitation in the Eastern United States to Historical Land Cover Changes Since European Settlement

NASA Technical Reports Server (NTRS)

Strack, John E.; Pielke, Roger A.; Steyaert, Louis T.; Knox, Robert G.

2008-01-01

Land cover changes alter the near surface weather and climate. Changes in land surface properties such as albedo, roughness length, stomatal resistance, and leaf area index alter the surface energy balance, leading to differences in near surface temperatures. This study utilized a newly developed land cover data set for the eastern United States to examine the influence of historical land cover change on June temperatures and precipitation. The new data set contains representations of the land cover and associated biophysical parameters for 1650, 1850, 1920, and 1992, capturing the clearing of the forest and the expansion of agriculture over the eastern United States from 1650 to the early twentieth century and the subsequent forest regrowth. The data set also includes the inferred distribution of potentially water-saturated soils at each time slice for use in the sensitivity tests. The Regional Atmospheric Modeling System, equipped with the Land Ecosystem-Atmosphere Feedback (LEAF-2) land surface parameterization, was used to simulate the weather of June 1996 using the 1992, 1920, 1850, and 1650 land cover representations. The results suggest that changes in surface roughness and stomatal resistance have caused present-day maximum and minimum temperatures in the eastern United States to warm by about 0.3 C and 0.4 C, respectively, when compared to values in 1650. In contrast, the maximum temperatures have remained about the same, while the minimums have cooled by about 0.1 C when compared to 1920. Little change in precipitation was found.

Sensitivity of June near‐surface temperatures and precipitation in the eastern United States to historical land cover changes since European settlement

USGS Publications Warehouse

Strack, John E.; Pielke, Roger A.; Steyaert, Louis T.; Knox, Robert G.

2008-01-01

Land cover changes alter the near surface weather and climate. Changes in land surface properties such as albedo, roughness length, stomatal resistance, and leaf area index alter the surface energy balance, leading to differences in near surface temperatures. This study utilized a newly developed land cover data set for the eastern United States to examine the influence of historical land cover change on June temperatures and precipitation. The new data set contains representations of the land cover and associated biophysical parameters for 1650, 1850, 1920, and 1992, capturing the clearing of the forest and the expansion of agriculture over the eastern United States from 1650 to the early twentieth century and the subsequent forest regrowth. The data set also includes the inferred distribution of potentially water‐saturated soils at each time slice for use in the sensitivity tests. The Regional Atmospheric Modeling System, equipped with the Land Ecosystem‐Atmosphere Feedback (LEAF‐2) land surface parameterization, was used to simulate the weather of June 1996 using the 1992, 1920, 1850, and 1650 land cover representations. The results suggest that changes in surface roughness and stomatal resistance have caused present‐day maximum and minimum temperatures in the eastern United States to warm by about 0.3°C and 0.4°C, respectively, when compared to values in 1650. In contrast, the maximum temperatures have remained about the same, while the minimums have cooled by about 0.1°C when compared to 1920. Little change in precipitation was found.

Global satellite data highlights the diurnal asymmetry of the surface temperature response to deforestation

NASA Astrophysics Data System (ADS)

Schultz, Natalie M.; Lawrence, Peter J.; Lee, Xuhui

2017-04-01

Uncertainties remain about the spatial pattern and magnitude of the biophysical effects of deforestation. In particular, a diurnal asymmetry in the magnitude and sign of the surface temperature response to deforestation (ΔTS) has been observed, but the biophysical processes that contribute to day and nighttime ΔTS are not fully understood. In this study, we use a space-for-time approach with satellite and reanalysis data to investigate the biophysical processes that control the day and nighttime ΔTS. Additionally, we incorporate flux-tower data to examine two hypotheses for nighttime forest warming relative to open lands: (1) that forests generate turbulence in the stable nocturnal boundary layer, which brings heat aloft down to the surface, and (2) that forests store more heat during the day and release it at night. Our results confirm a diurnal asymmetry in ΔTS. Over most regions of the world, deforestation results in daytime warming and nighttime cooling. The strongest daytime warming is in the tropics, where the average ΔTS is 4.4 ± 0.07 K. The strongest nighttime cooling is observed in the boreal zone, where open lands are cooler than forests by an average of 1.4 ± 0.04 K. Daytime patterns of ΔTS are explained by differences in the latent heat flux (ΔLE) and absorbed solar radiation (ΔKa). We find that nighttime ΔTS is related to the strength of the nocturnal temperature inversion, with stronger temperature inversions at high latitudes and weak inversions in the tropics. Forest turbulence at night combined with stored heat release drives nighttime ΔTS patterns.

Multi-year coupled biogeochemical and biophysical impacts of restoring drained agricultural peatlands to wetlands across the Sacramento-San Joaquin Delta, California, USA.

NASA Astrophysics Data System (ADS)

Hemes, K. S.; Eichelmann, E.; Chamberlain, S.; Knox, S. H.; Oikawa, P.; Sturtevant, C.; Verfaillie, J. G.; Baldocchi, D. D.

2017-12-01

Globally, delta ecosystems are critical for human livelihoods, but are at increasingly greater risk of degradation. The Sacramento-San Joaquin River Delta (`Delta') has been subsiding dramatically, losing close to 100 Tg of carbon since the mid 19th century due in large part to agriculture-induced oxidation of the peat soils through drainage and cultivation. Efforts to re-wet the peat soils through wetland restoration are attractive as climate mitigation activities. While flooded wetland systems have the potential to sequester significant amounts of carbon as photosynthesis outpaces aerobic respiration, the highly-reduced conditions can result in significant methane emissions. This study will utilize three years (2014-2016) of continuous, gap-filled, CO2 and CH4 flux data from a mesonetwork of seven eddy covariance towers in the Delta to compute GHG budgets for the restored wetlands and agricultural baseline sites measured. Along with biogeochemical impacts of wetland restoration, biophysical impacts such as changes in reflectance, energy partitioning, and surface roughness, can have significant local to regional impacts on air temperature and heat fluxes. We hypothesize that despite flooded wetlands reducing albedo, wetland land cover will cool the near-surface air temperature due to increased net radiation being preferentially partitioned into latent heat flux and rougher canopy conditions allowing for more turbulent mixing with the atmosphere. This study will investigate the seasonal and diurnal patterns of turbulent energy fluxes and the surface properties that drive them. With nascent policy mechanisms set to compensate landowners and farmers for low emission land use practices beyond reforestation, it is essential that policy mechanisms take into consideration how the biophysical impacts of land use change could drive local to regional-scale climatic perturbations, enhancing or attenuating the biogeochemical impacts.

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.

Modeling of the Light Speckle Field Structure Inside a Multilayer Human Skin Tissue

NASA Astrophysics Data System (ADS)

Barun, V. V.; Dik, S. K.; Ivanov, A. P.; Abramovich, N. D.

2013-11-01

We present an analytic method and the results of investigating the characteristics of the interference pattern formed by multiply scattered light in a multilayer biological tissue of the type of human skin at the wavelengths of the visible and neat IR spectral regions under laser irradiation. Calculations were performed with the use of the known solutions of the equations of radiation transfer in the biotissue and the relation between the theory of propagation of light in a scattering medium and the coherence theory. The radial structure of the light field in the depth of the human skin formed by coherent and incoherent radiation depending on its biophysical parameters has been investigated. The characteristic sizes of speckles in each layer of the skin have been estimated. The biophysical factors connected with the volume concentration of blood in the dermis and the degree of its oxygenation influencing the contrast of the speckle pattern in the dermis have been discussed. The possibility of formulating and solving inverse problems of biomedical optics on the restoration of blood parameters from measurements of speckle characteristics has been shown.

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.

Energy balance model applied to pasture experimental areas in São Paulo State, Brazil

NASA Astrophysics Data System (ADS)

Bayma-Silva, Gustavo; de Castro Teixeira, Antonio Heriberto; de Castro Victoria, Daniel; Furlan Nogueira, Sandra; Freitas Leivas, Janice; Coaguila, Daniel N.; Rodrigues Herling, Valdo

2016-10-01

The Simple Algorithm for Evapotranspiration Retrieving (SAFER) was used to estimate biophysical parameters and the energy balance components in two different pasture experimental areas, in the São Paulo state, Brazil. The experimental pastures consist in six rotational (RGS) and three continuous grazing systems (CGS) paddocks. Landsat-8 images from 2013 and 2015 dry and rainy seasons were used, as these presented similar hydrological cycle, with 1,600 mm and 1,613 mm of annual precipitation, resulting in 19 cloud-free images. Bands 1 to 7 and thermal bands 10 and 11 were used with weather data from a station located near the experimental area. NDVI, biomass, evapotranspiration and latent heat flux (λE) temporal values statistically differ CGS from RGS areas. Grazing systems influences the energy partition and these results indicate that RGS benefits biomass production, evapotranspiration and the microclimate, due higher LE values. SAFER is a feasible tool to estimate biophysical parameters and energy balance components in pasture and has potential to discriminate continuous and rotation grazing systems in a temporal analysis.

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 facilitate non-interfering observation of biophysical interactions on a landscape scale. A joint effort to connect Earth's (sub)surface processes by a combination of innovative big data-assimilation, measurement and modelling techniques will enable the scientific community to accurately address vital issues.

Mechanics of Fluid-Filled Interstitial Gaps. II. Gap Characteristics in Xenopus Embryonic Ectoderm.

PubMed

Barua, Debanjan; Parent, Serge E; Winklbauer, Rudolf

2017-08-22

The ectoderm of the Xenopus embryo is permeated by a network of channels that appear in histological sections as interstitial gaps. We characterized this interstitial space by measuring gap sizes, angles formed between adjacent cells, and curvatures of cell surfaces at gaps. From these parameters, and from surface-tension values measured previously, we estimated the values of critical mechanical variables that determine gap sizes and shapes in the ectoderm, using a general model of interstitial gap mechanics. We concluded that gaps of 1-4 μm side length can be formed by the insertion of extracellular matrix fluid at three-cell junctions such that cell adhesion is locally disrupted and a tension difference between cell-cell contacts and the free cell surface at gaps of 0.003 mJ/m 2 is generated. Furthermore, a cell hydrostatic pressure of 16.8 ± 1.7 Pa and an interstitial pressure of 3.9 ± 3.6 Pa, relative to the central blastocoel cavity of the embryo, was found to be consistent with the observed gap size and shape distribution. Reduction of cell adhesion by the knockdown of C-cadherin increased gap volume while leaving intracellular and interstitial pressures essentially unchanged. In both normal and adhesion-reduced ectoderm, cortical tension of the free cell surfaces at gaps does not return to the high values characteristic of the free surface of the whole tissue. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

[Biophysical models in investigations of exogenous surfactant activities on the surface tension and their theurapeutic effectiveness].

PubMed

Todorov, R; Iordanova, A; Georgiev, G A; Petkova, Kh; Stoimenova, E; Georgieva, R; Khristova, E; Vasiliev, Kh; Lalchev, Z

2007-01-01

Surfactant therapy leads to significant clinical improvement in infants at risk for, or having, respiratory distress syndrome (RDS). The development of exogenous surfactant (ES) as a therapy for neonatal respiratory disorders was a significant advance in neonatal intensive care that has led to a decrease in neonatal mortality. Two broad categories of surfactants are available for exogenous therapy: surfactants derived from animal sources or 'natural' surfactants; and synthetic surfactants. The physical properties of natural and synthetic surfactants have been studied using techniques such as the Wilhelmy surface balance and the bilayer black film (BBF) method. Here we report some data from a comparative study of ES (Exosurf, Survanta, Curosurf and Alveofact) and clinical samples of tracheal aspirate (TA) of newborns with RDS treated with Curosurf. Measured interfacial physico-chemical parameters prove "better" properties in vitro of the surfactant proteins (SP-B and SP-C) containing preparations Curosurf and Alveofact. Their properties are similar, Alveofact showing a higher surface tension lowering capacity under dynamic conditions. A compendious comparison of results for dynamic surface properties of monolayers of TA from newborns treated with Curosurf with data for newborns treated with Exosurf is presented. Both ES yield the desired lowering of the surface tension during cyclic film compression, being larger after treatment with Curosurf. Observations concerning the properties of BFF of ES (dependence on surfactant concentration, adsorption time, film drainage time and BFF formation time) are also reported and discussed.

Verification of satellite radar remote sensing based estimates of boreal and subalpine growing seasons using an ecosystem process model and surface biophysical measurement network information

NASA Technical Reports Server (NTRS)

McDonald, K. C.; Kimball, J. S.; Zimmerman, R.

2002-01-01

We employ daily surface Radar backscatter data from the SeaWinds Ku-band Scatterometer onboard Quikscat to estimate landscape freeze-thaw state and associated length of the seasonal non-frozen period as a surrogate for determining the annual growing season across boreal and subalpine regions of North America for 2000 and 2001.

Biophysical properties of the human finger for touch comprehension: influences of ageing and gender

PubMed Central

Djaghloul, M.; Thieulin, C.; Vargiolu, R.; Pailler-Mattei, C. ; Zahouani, H.

2017-01-01

The human finger plays an extremely important role in tactile perception, but little is known about how age and gender affect its biophysical properties and their role in tactile perception. We combined studies on contact characteristics, mechanical properties and surface topography to understand age and gender effects on the human finger. The values obtained regarding contact characteristics (i.e. adhesive force) were significantly higher for women than for men. As for mechanical properties (i.e. Young's modulus E), a significant and positive correlation with age was observed and found to be higher for women. A positive correlation was observed between age and the arithmetic mean of surface roughness for men. However, an inverse age effect was highlighted for women. The age and gender effects obtained have never been reported previously in the literature. These results open new perspectives for understanding the weakening of tactile perception across ages and how it differs between men and women. PMID:28878982

Cytotoxic Helix-Rich Oligomer Formation by Melittin and Pancreatic Polypeptide

PubMed Central

Singh, Pradeep K.; Ghosh, Dhiman; Tewari, Debanjan; Mohite, Ganesh M.; Carvalho, Edmund; Jha, Narendra Nath; Jacob, Reeba S.; Sahay, Shruti; Banerjee, Rinti; Bera, Amal K.; Maji, Samir K.

2015-01-01

Conversion of amyloid fibrils by many peptides/proteins involves cytotoxic helix-rich oligomers. However, their toxicity and biophysical studies remain largely unknown due to their highly dynamic nature. To address this, we chose two helical peptides (melittin, Mel and pancreatic polypeptide, PP) and studied their aggregation and toxicity. Mel converted its random coil structure to oligomeric helical structure upon binding to heparin; however, PP remained as helix after oligomerization. Interestingly, similar to Parkinson’s associated α-synuclein (AS) oligomers, Mel and PP also showed tinctorial properties, higher hydrophobic surface exposure, cellular toxicity and membrane pore formation after oligomerization in the presence of heparin. We suggest that helix-rich oligomers with exposed hydrophobic surface are highly cytotoxic to cells irrespective of their disease association. Moreover as Mel and PP (in the presence of heparin) instantly self-assemble into stable helix-rich amyloidogenic oligomers; they could be represented as models for understanding the biophysical and cytotoxic properties of helix-rich intermediates in detail. PMID:25803428

In vitro assays of molecular motors--impact of motor-surface interactions.

PubMed

Mansson, Alf; Balaz, Martina; Albet-Torres, Nuria; Rosengren, K Johan

2008-05-01

In many types of biophysical studies of both single molecules and ensembles of molecular motors the motors are adsorbed to artificial surfaces. Some of the most important assay systems of this type (in vitro motility assays and related single molecule techniques) will be briefly described together with an account of breakthroughs in the understanding of actomyosin function that have resulted from their use. A poorly characterized, but potentially important, entity in these studies is the mechanism of motor adsorption to surfaces and the effects of motor surface interactions on experimental results. A better understanding of these phenomena is also important for the development of commercially viable nanotechnological applications powered by molecular motors. Here, we will consider several aspects of motor surface interactions with a particular focus on heavy meromyosin (HMM) from skeletal muscle. These aspects will be related to heavy meromyosin structure and relevant parts of the vast literature on protein-surface interactions for non-motor proteins. An overview of methods for studying motor-surface interactions will also be given. The information is used as a basis for further development of a model for HMM-surface interactions and is discussed in relation to experiments where nanopatterning has been employed for in vitro reconstruction of actomyosin order. The challenges and potentials of this approach in biophysical studies, compared to the use of self-assembly of biological components into supramolecular protein aggregates (e.g. myosin filaments) will be considered. Finally, this review will consider the implications for further developments of motor-powered lab-on-a-chip devices.

Rhodopsin-lipid interactions studied by NMR.

PubMed

Soubias, Olivier; Gawrisch, Klaus

2013-01-01

The biophysical properties of the lipid matrix are known to influence function of integral membrane proteins. We report on a sample preparation method for reconstitution of membrane proteins which uses porous anodic aluminum oxide (AAO) filters with 200-nm-wide pores of high density. The substrate permits formation of tubular, single membranes that line the inner surface of pores. One square centimeter of filter with a thickness of 60μm yields on the order of 500cm(2) of solid-supported single bilayer surface, sufficient for NMR studies. The tubular bilayers are free of detergent, fully hydrated, and accessible for ligands from one side of the membrane. The use of AAO filters greatly improves reproducibility of the reconstitution process such that the influence of protein on lipid order parameters can be studied with high resolution. As an example, results for the G protein-coupled receptor of class A, bovine rhodopsin, are shown. By (2)H NMR order parameter measurements, it is detected that rhodopsin insertion elastically deforms membranes near the protein. Furthermore, by (1)H saturation-transfer NMR under conditions of magic angle spinning, we demonstrate detection of preferences in interactions of rhodopsin with particular lipid species. It is assumed that function of integral membrane proteins depends on both protein-induced elastic deformations of the lipid matrix and preferences for interaction of the protein with particular lipid species in the first layer of lipids surrounding the protein. Copyright © 2013 Elsevier Inc. All rights reserved.

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.

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.

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.

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.

Bio-physical changes in the coastal ocean triggered by typhoon: A case of Typhoon Meari in summer 2011

NASA Astrophysics Data System (ADS)

Wu, Xiao; Wang, Houjie; Bi, Naishuang; Song, Zhenjie; Zang, Zhengchen; Kineke, Gail C.

2016-12-01

Based on the combination of synchronous satellite and in-situ observations, we here, for the first time, provide the compelling evidence of bio-physical response of coastal environment in the Bohai Sea (China) to the passage of Typhoon Meari over the northern Yellow Sea on June 26, 2011. Strong sustained winds induced a tongue-like intrusion of cool water from the northern Yellow Sea into the Bohai Sea, resulting in significant surface cooling and an anomalous increase in sea surface height along the coast of the western Bohai Sea. This, in return, produced downwelling and transport of the warm and nutrient-rich coastal water from the western coast to the central Bohai Sea, as driven by the barotropic pressure gradient force. In-situ observational data confirmed the cooling of both surface and bottom layers with salinity increase; however, the measured temperature increase by 2-3 °C, concomitant salinity decrease by 0.3 PSU and two-fold increase in chlorophyll-a in the middle layers suggested an influence from coastal downwelling. Ekman transport and typhoon-enhanced mixing redistributed the nutrients and thus resulted in higher chlorophyll-a concentrations in the upper layers.

Mechanics of Fluid-Filled Interstitial Gaps. I. Modeling Gaps in a Compact Tissue.

PubMed

Parent, Serge E; Barua, Debanjan; Winklbauer, Rudolf

2017-08-22

Fluid-filled interstitial gaps are a common feature of compact tissues held together by cell-cell adhesion. Although such gaps can in principle be the result of weak, incomplete cell attachment, adhesion is usually too strong for this to occur. Using a mechanical model of tissue cohesion, we show that, instead, a combination of local prevention of cell adhesion at three-cell junctions by fluidlike extracellular material and a reduction of cortical tension at the gap surface are sufficient to generate stable gaps. The size and shape of these interstitial gaps depends on the mechanical tensions between cells and at gap surfaces, and on the difference between intracellular and interstitial pressures that is related to the volume of the interstitial fluid. As a consequence of the dependence on tension/tension ratios, the presence of gaps does not depend on the absolute strength of cell adhesion, and similar gaps are predicted to occur in tissues of widely differing cohesion. Tissue mechanical parameters can also vary within and between cells of a given tissue, generating asymmetrical gaps. Within limits, these can be approximated by symmetrical gaps. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

A PI4P-driven electrostatic field controls cell membrane identity and signaling in plants

PubMed Central

Simon, Mathilde Laetitia Audrey; Platre, Matthieu Pierre; Marquès-Bueno, Maria Mar; Armengot, Laia; Stanislas, Thomas; Bayle, Vincent; Caillaud, Marie-Cécile; Jaillais, Yvon

2016-01-01

Many signaling proteins permanently or transiently localize to specific organelles for function. It is well established that certain lipids act as biochemical landmarks to specify compartment identity. However, they also influence membrane biophysical properties, which emerge as important features in specifying cellular territories. Such parameters include the membrane inner surface potential, which varies according to the lipid composition of each organelle. Here, we found that the plant plasma membrane (PM) and the cell plate of dividing cells have a unique electrostatic signature controlled by phosphatidylinositol-4-phosphate (PI4P). Our results further reveal that, contrarily to other eukaryotes, PI4P massively accumulates at the PM, establishing it as a critical hallmark of this membrane in plants. Membrane surface charges control the PM localization and function of the polar auxin transport regulator PINOID, as well as proteins from the BRI1 KINASE INHIBITOR1 (BKI1)/MEMBRANE ASSOCIATED KINASE REGULATORs (MAKRs) family, which are involved in brassinosteroid and receptor-like kinase signaling. We anticipate that this PI4P-driven physical membrane property will control the localization and function of many proteins involved in development, reproduction, immunity and nutrition. PMID:27322096

A PtdIns(4)P-driven electrostatic field controls cell membrane identity and signalling in plants.

PubMed

Simon, Mathilde Laetitia Audrey; Platre, Matthieu Pierre; Marquès-Bueno, Maria Mar; Armengot, Laia; Stanislas, Thomas; Bayle, Vincent; Caillaud, Marie-Cécile; Jaillais, Yvon

2016-06-20

Many signalling proteins permanently or transiently localize to specific organelles. It is well established that certain lipids act as biochemical landmarks to specify compartment identity. However, they also influence membrane biophysical properties, which emerge as important features in specifying cellular territories. Such parameters include the membrane inner surface potential, which varies according to the lipid composition of each organelle. Here, we found that the plant plasma membrane (PM) and the cell plate of dividing cells have a unique electrostatic signature controlled by phosphatidylinositol-4-phosphate (PtdIns(4)P). Our results further reveal that, contrarily to other eukaryotes, PtdIns(4)P massively accumulates at the PM, establishing it as a critical hallmark of this membrane in plants. Membrane surface charges control the PM localization and function of the polar auxin transport regulator PINOID as well as proteins from the BRI1 KINASE INHIBITOR1 (BKI1)/MEMBRANE ASSOCIATED KINASE REGULATOR (MAKR) family, which are involved in brassinosteroid and receptor-like kinase signalling. We anticipate that this PtdIns(4)P-driven physical membrane property will control the localization and function of many proteins involved in development, reproduction, immunity and nutrition.

Incorporating Plant Phenology Dynamics in a Biophysical Canopy Model

NASA Technical Reports Server (NTRS)

Barata, Raquel A.; Drewry, Darren

2012-01-01

The Multi-Layer Canopy Model (MLCan) is a vegetation model created to capture plant responses to environmental change. Themodel vertically resolves carbon uptake, water vapor and energy exchange at each canopy level by coupling photosynthesis, stomatal conductance and leaf energy balance. The model is forced by incoming shortwave and longwave radiation, as well as near-surface meteorological conditions. The original formulation of MLCan utilized canopy structural traits derived from observations. This project aims to incorporate a plant phenology scheme within MLCan allowing these structural traits to vary dynamically. In the plant phenology scheme implemented here, plant growth is dependent on environmental conditions such as air temperature and soil moisture. The scheme includes functionality that models plant germination, growth, and senescence. These growth stages dictate the variation in six different vegetative carbon pools: storage, leaves, stem, coarse roots, fine roots, and reproductive. The magnitudes of these carbon pools determine land surface parameters such as leaf area index, canopy height, rooting depth and root water uptake capacity. Coupling this phenology scheme with MLCan allows for a more flexible representation of the structure and function of vegetation as it responds to changing environmental conditions.

Land observation from geosynchronous earth orbit (LOGEO): Mission concept and preliminary engineering analysis

NASA Astrophysics Data System (ADS)

Román-Colón, Miguel O.; Strahler, Alan H.

2007-06-01

We propose an Earth-observation mission Land Observation from Geosynchronous Earth Orbit (LOGEO) to place two spin-scan-stabilized 500-m resolution 9-band VNIR-SWIR imagers in a near-geosynchronous inclined orbit, allowing 15 min observations with a full range of daily sun angles and 30∘ variations in view angle. LOGEO drifts westward at about 4∘ per day, providing geostationary-style coverage for all points on the globe eight times per year. This unique imaging geometry allows accurate retrievals of daily changes in surface bidirectional reflectance, which in turn enhances direct retrieval of biophysical properties, as well as long term and consistent land surface parameters for modeling studies that seek to understand the Earth system and its interactions. For studies of climate and environmental dynamics, LOGEO provides accurate observations of atmospheric aerosols, clouds, as well as other atmospheric constituents across a diverse number of spatial and temporal scales. This collection of land, atmospheric, and climate data products are directly applicable to seven of the nine GEOSS societal benefits areas, providing great opportunities for international collaboration. We also present an overview of LOGEO's systems architecture, as well as top-level design-trade studies and orbital scenarios.

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

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.

A hybrid HDRF model of GOMS and SAIL: GOSAIL

NASA Astrophysics Data System (ADS)

Dou, B.; Wu, S.; Wen, J.

2016-12-01

Understanding the surface reflectance anisotropy is the key facet in interpreting the features of land surface from remotely sensed information, which describes the property of land surface to reflect the solar radiation directionally. Most reflectance anisotropy models assumed the nature surface was illuminated only by the direct solar radiation, while the diffuse skylight becomes dominant especially for the over cast sky conditions and high rugged terrain. Correcting the effect of diffuse skylight on the reflectance anisotropy to obtain the intrinsic directional reflectance of land surface is highly desirable for remote sensing applications. This paper developed a hybrid HDRF model of GOMS and SAIL called GOSAIL model for discrete canopies. The accurate area proportions of four scene components are calculated by the GOMS model and the spectral signatures of scene components are provided by the SAIL model. Both the single scattering contribution and the multiple scattering contributions within and between the canopy and background under the clear and diffuse illumination conditions are considered in the GOSAIL model. The HDRF simulated by the 3-D Discrete Anisotropic Radiative Transfer (DART) model and the HDRF measurements over the 100m×100m mature pine stand at the Järvselja, Estonia are used for validating and evaluating the performance of proposed GOSAIL model. The comparison results indicate the GOSAIL model can accurately reproducing the angular feature of discrete canopy for both the clear and overcast atmospheric conditions. The GOSAIL model is promising for the land surface biophysical parameters retrieval (e.g. albedo, leaf area index) over the heterogeneous terrain.

Fragment screening by SPR and advanced application to GPCRs.

PubMed

Shepherd, Claire A; Hopkins, Andrew L; Navratilova, Iva

2014-01-01

Surface plasmon resonance (SPR) is one of the primary biophysical methods for the screening of low molecular weight 'fragment' libraries, due to its low protein consumption and 'label-free' methodology. SPR biosensor interaction analysis is employed to both screen and confirm the binding of compounds in fragment screening experiments, as it provides accurate information on the affinity and kinetics of molecular interactions. The most advanced application of the use of SPR for fragment screening is against membrane protein drug targets, such G-protein coupled receptors (GPCRs). Biophysical GPCR assays using SPR have been validated with pharmacological measurements approximate to cell-based methods, yet provide the advantage of biophysical methods in their ability to measure the weak affinities of low molecular weight fragments. A number of SPR fragment screens against GPCRs have now been disclosed in the literature. SPR fragment screening is proving versatile to screen both thermostabilised GPCRs and solubilised wild type receptors. In this chapter, we discuss the state-of-the-art in GPCR fragment screening by SPR and the technical considerations in performing such experiments. Copyright © 2014 The Authors. Published by Elsevier Ltd.. All rights reserved.

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

How well do we characterize the biophysical effects of vegetation cover change? Benchmarking land surface models against satellite observations.

NASA Astrophysics Data System (ADS)

Duveiller, Gregory; Forzieri, Giovanni; Robertson, Eddy; Georgievski, Goran; Li, Wei; Lawrence, Peter; Ciais, Philippe; Pongratz, Julia; Sitch, Stephen; Wiltshire, Andy; Arneth, Almut; Cescatti, Alessandro

2017-04-01

Changes in vegetation cover can affect the climate by altering the carbon, water and energy cycles. The main tools to characterize such land-climate interactions for both the past and future are land surface models (LSMs) that can be embedded in larger Earth System models (ESMs). While such models have long been used to characterize the biogeochemical effects of vegetation cover change, their capacity to model biophysical effects accurately across the globe remains unclear due to the complexity of the phenomena. The result of competing biophysical processes on the surface energy balance varies spatially and seasonally, and can lead to warming or cooling depending on the specific vegetation change and on the background climate (e.g. presence of snow or soil moisture). Here we present a global scale benchmarking exercise of four of the most commonly used LSMs (JULES, ORCHIDEE, JSBACH and CLM) against a dedicated dataset of satellite observations. To facilitate the understanding of the causes that lead to discrepancies between simulated and observed data, we focus on pure transitions amongst major plant functional types (PFTs): from different tree types (evergreen broadleaf trees, deciduous broadleaf trees and needleleaf trees) to either grasslands or crops. From the modelling perspective, this entails generating a separate simulation for each PFT in which all 1° by 1° grid cells are uniformly covered with that PFT, and then analysing the differences amongst them in terms of resulting biophysical variables (e.g net radiation, latent and sensible heat). From the satellite perspective, the effect of pure transitions is obtained by unmixing the signal of different 0.05° spatial resolution MODIS products (albedo, latent heat, upwelling longwave radiation) over a local moving window using PFT maps derived from the ESA Climate Change Initiative land cover map. After aggregating to a common spatial support, the observation and model-driven datasets are confronted and analysed across different climate zones. Results indicate that models tend to catch better radiative than non-radiative energy fluxes. However, for various vegetation transitions, models do not agree amongst themselves on the magnitude nor the sign of the change. In particular, predicting the impact of land cover change on the partitioning of the available energy between latent and sensible heat proves to be a challenging task for vegetation models. We expect that this benchmarking exercise will shed a light on where to prioritize the efforts in model development as well as inform where consensus between model and observations is already met. Improving the robustness and consistency of land-model is essential to develop and inform land-based mitigation and adaptation policies that account for both biogeochemical and biophysical vegetation impacts on climate.

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.…

XXIst century magnetotherapy.

PubMed

Markov, M

2015-09-01

This paper discusses the state of the art therapeutic application of magnetic and electromagnetic fields (EMF) in treatment of various medical problems - from pain relief to musculoskeletal trauma, to vascular and endocrine disorders. The paper describes problems related to physical parameters of used fields, biophysical dosimetry, clinical protocols, and safety of the device operators. Clinical benefits and mechanisms of action are also discussed.

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

Surface hydration amplifies single-well protein atom diffusion propagating into the macromolecular core

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

Hong, Liang; Cheng, Xiaolin; Glass, Dennis C.

2012-06-05

The effect of surface hydration water on internal protein motion is of fundamental interest in molecular biophysics. Here, by decomposing the picosecond to nanosecond atomic motion in molecular dynamics simulations of lysozyme at different hydration levels into three components localized single-well diffusion, methyl group rotation, and nonmethyl jumps we show that the effect of surface hydration is mainly to increase the volume of the localized single-well diffusion. As a result, these diffusive motions are coupled in such a way that the hydration effect propagates from the protein surface into the dry core.

The mark of vegetation change on Earth's surface energy balance: data-driven diagnostics and model validation

NASA Astrophysics Data System (ADS)

Cescatti, A.; Duveiller, G.; Hooker, J.

2017-12-01

Changing vegetation cover not only affects the atmospheric concentration of greenhouse gases but also alters the radiative and non-radiative properties of the surface. The result of competing biophysical processes on Earth's surface energy balance varies spatially and seasonally, and can lead to warming or cooling depending on the specific vegetation change and on the background climate. To date these effects are not accounted for in land-based climate policies because of the complexity of the phenomena, contrasting model predictions and the lack of global data-driven assessments. To overcome the limitations of available observation-based diagnostics and of the on-going model inter-comparison, here we present a new benchmarking dataset derived from satellite remote sensing. This global dataset provides the potential changes induced by multiple vegetation transitions on the single terms of the surface energy balance. We used this dataset for two major goals: 1) Quantify the impact of actual vegetation changes that occurred during the decade 2000-2010, showing the overwhelming role of tropical deforestation in warming the surface by reducing evapotranspiration despite the concurrent brightening of the Earth. 2) Benchmark a series of ESMs against data-driven metrics of the land cover change impacts on the various terms of the surface energy budget and on the surface temperature. We anticipate that the dataset could be also used to evaluate 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.

"Illustrating the Machinery of Life": Viruses

ERIC Educational Resources Information Center

Goodsell, David S.

2012-01-01

Data from electron microscopy, X-ray crystallography, and biophysical analysis are used to create illustrations of viruses in their cellular context. This report describes the scientific data and artistic methods used to create three illustrations: a depiction of the poliovirus lifecycle, budding of influenza virus from a cell surface, and a…

Natural regeneration of eastern hemlock: a review

Treesearch

Daniel L. Goerlich; Ralph D. Nyland

2000-01-01

Successful regeneration of eastern hemlock involves a complex biophysical process that commonly spans many years. Critical factors include a reliable source of seed, a suitable seedbed, a partially shaded environment, and several years of favorable moisture. Surface scarification appears critical as a means of site preparation. Even then, young hemlocks grow slowly,...

Distilling allometric and environmental information from time series of conduit size: the standardization issue and its relationship to tree hydraulic architecture.

PubMed

Carrer, Marco; von Arx, Georg; Castagneri, Daniele; Petit, Giai

2015-01-01

Trees are among the best natural archives of past environmental information. Xylem anatomy preserves information related to tree allometry and ecophysiological performance, which is not available from the more customary ring-width or wood-density proxy parameters. Recent technological advances make tree-ring anatomy very attractive because time frames of many centuries can now be covered. This calls for the proper treatment of time series of xylem anatomical attributes. In this article, we synthesize current knowledge on the biophysical and physiological mechanisms influencing the short- to long-term variation in the most widely used wood-anatomical feature, namely conduit size. We also clarify the strong mechanistic link between conduit-lumen size, tree hydraulic architecture and height growth. Among the key consequences of these biophysical constraints is the pervasive, increasing trend of conduit size during ontogeny. Such knowledge is required to process time series of anatomical parameters correctly in order to obtain the information of interest. An appropriate standardization procedure is fundamental when analysing long tree-ring-related chronologies. When dealing with wood-anatomical parameters, this is even more critical. Only an interdisciplinary approach involving ecophysiology, wood anatomy and dendrochronology will help to distill the valuable information about tree height growth and past environmental variability correctly. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

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.

Properties of human brain sodium channel α-subunits expressed in HEK293 cells and their modulation by carbamazepine, phenytoin and lamotrigine

PubMed Central

Qiao, Xin; Sun, Guangchun; Clare, Jeffrey J; Werkman, Taco R; Wadman, Wytse J

2014-01-01

Background and purpose Voltage-activated Na+ channels contain one distinct α-subunit. In the brain NaV1.1, NaV1.2, NaV1.3 and NaV1.6 are the four most abundantly expressed α-subunits. The antiepileptic drugs (AEDs) carbamazepine, phenytoin and lamotrigine have voltage-gated Na+ channels as their primary therapeutic targets. This study provides a systematic comparison of the biophysical properties of these four α-subunits and characterizes their interaction with carbamazepine, phenytoin and lamotrigine. Experimental approach Na+ currents were recorded in voltage-clamp mode in HEK293 cells stably expressing one of the four α-subunits. Key results NaV1.2 and NaV1.3 subunits have a relatively slow recovery from inactivation, compared with the other subunits and NaV1.1 subunits generate the largest window current. Lamotrigine evokes a larger maximal shift of the steady-state inactivation relationship than carbamazepine or phenytoin. Carbamazepine shows the highest binding rate to the α-subunits. Lamotrigine binding to NaV1.1 subunits is faster than to the other α-subunits. Lamotrigine unbinding from the α-subunits is slower than that of carbamazepine and phenytoin. Conclusions and implications The four Na+ channel α-subunits show subtle differences in their biophysical properties, which, in combination with their (sub)cellular expression patterns in the brain, could contribute to differences in neuronal excitability. We also observed differences in the parameters that characterize AED binding to the Na+ channel subunits. Particularly, lamotrigine binding to the four α-subunits suggests a subunit-specific response. Such differences will have consequences for the clinical efficacy of AEDs. Knowledge of the biophysical and binding parameters could be employed to optimize therapeutic strategies and drug development. PMID:24283699

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

Analyzing Single-Molecule Time Series via Nonparametric Bayesian Inference

PubMed Central

Hines, Keegan E.; Bankston, John R.; Aldrich, Richard W.

2015-01-01

The ability to measure the properties of proteins at the single-molecule level offers an unparalleled glimpse into biological systems at the molecular scale. The interpretation of single-molecule time series has often been rooted in statistical mechanics and the theory of Markov processes. While existing analysis methods have been useful, they are not without significant limitations including problems of model selection and parameter nonidentifiability. To address these challenges, we introduce the use of nonparametric Bayesian inference for the analysis of single-molecule time series. These methods provide a flexible way to extract structure from data instead of assuming models beforehand. We demonstrate these methods with applications to several diverse settings in single-molecule biophysics. This approach provides a well-constrained and rigorously grounded method for determining the number of biophysical states underlying single-molecule data. PMID:25650922

Quantifying the biophysical characteristics of Plasmodium-falciparum-parasitized red blood cells in microcirculation

PubMed Central

Fedosov, D. A.; Caswell, B.; Suresh, S.; Karniadakis, G. E.

2011-01-01

The pathogenicity of Plasmodium falciparum (Pf) malaria results from the stiffening of red blood cells (RBCs) and its ability to adhere to endothelial cells (cytoadherence). The dynamics of Pf-parasitized RBCs is studied by three-dimensional mesoscopic simulations of flow in cylindrical capillaries in order to predict the flow resistance enhancement at different parasitemia levels. In addition, the adhesive dynamics of Pf-RBCs is explored for various parameters revealing several types of cell dynamics such as firm adhesion, very slow slipping along the wall, and intermittent flipping. The parasite inside the RBC is modeled explicitly in order to capture phenomena such as “hindered tumbling” motion of the RBC and the sudden transition from firm RBC cytoadherence to flipping on the endothelial surface. These predictions are in quantitative agreement with recent experimental observations, and thus the three-dimensional modeling method presented here provides new capabilities for guiding and interpreting future in vitro and in vivo studies of malaria. PMID:21173269

In vitro bio-functionality of gallium nitride sensors for radiation biophysics.

PubMed

Hofstetter, Markus; Howgate, John; Schmid, Martin; Schoell, Sebastian; Sachsenhauser, Matthias; Adigüzel, Denis; Stutzmann, Martin; Sharp, Ian D; Thalhammer, Stefan

2012-07-27

There is an increasing interest in the integration of hybrid bio-semiconductor systems for the non-invasive evaluation of physiological parameters. High quality gallium nitride and its alloys show promising characteristics to monitor cellular parameters. Nevertheless, such applications not only request appropriate sensing capabilities but also the biocompatibility and especially the biofunctionality of materials. Here we show extensive biocompatibility studies of gallium nitride and, for the first time, a biofunctionality assay using ionizing radiation. Analytical sensor devices are used in medical settings, as well as for cell- and tissue engineering. Within these fields, semiconductor devices have increasingly been applied for online biosensing on a cellular and tissue level. Integration of advanced materials such as gallium nitride into these systems has the potential to increase the range of applicability for a multitude of test devices and greatly enhance sensitivity and functionality. However, for such applications it is necessary to optimize cell-surface interactions and to verify the biocompatibility of the semiconductor. In this work, we present studies of mouse fibroblast cell activity grown on gallium nitride surfaces after applying external noxa. Cell-semiconductor hybrids were irradiated with X-rays at air kerma doses up to 250 mGy and the DNA repair dynamics, cell proliferation, and cell growth dynamics of adherent cells were compared to control samples. The impact of ionizing radiation on DNA, along with the associated cellular repair mechanisms, is well characterized and serves as a reference tool for evaluation of substrate effects. The results indicate that gallium nitride does not require specific surface treatments to ensure biocompatibility and suggest that cell signaling is not affected by micro-environmental alterations arising from gallium nitride-cell interactions. The observation that gallium nitride provides no bio-functional influence on the cellular environment confirms that this material is well suited for future biosensing applications without the need for additional chemical surface modification. Copyright © 2012 Elsevier Inc. All rights reserved.

The Virtual Brain: Modeling Biological Correlates of Recovery after Chronic Stroke

PubMed Central

Falcon, Maria Inez; Riley, Jeffrey D.; Jirsa, Viktor; McIntosh, Anthony R.; Shereen, Ahmed D.; Chen, E. Elinor; Solodkin, Ana

2015-01-01

There currently remains considerable variability in stroke survivor recovery. To address this, developing individualized treatment has become an important goal in stroke treatment. As a first step, it is necessary to determine brain dynamics associated with stroke and recovery. While recent methods have made strides in this direction, we still lack physiological biomarkers. The Virtual Brain (TVB) is a novel application for modeling brain dynamics that simulates an individual’s brain activity by integrating their own neuroimaging data with local biophysical models. Here, we give a detailed description of the TVB modeling process and explore model parameters associated with stroke. In order to establish a parallel between this new type of modeling and those currently in use, in this work we establish an association between a specific TVB parameter (long-range coupling) that increases after stroke with metrics derived from graph analysis. We used TVB to simulate the individual BOLD signals for 20 patients with stroke and 10 healthy controls. We performed graph analysis on their structural connectivity matrices calculating degree centrality, betweenness centrality, and global efficiency. Linear regression analysis demonstrated that long-range coupling is negatively correlated with global efficiency (P = 0.038), but is not correlated with degree centrality or betweenness centrality. Our results suggest that the larger influence of local dynamics seen through the long-range coupling parameter is closely associated with a decreased efficiency of the system. We thus propose that the increase in the long-range parameter in TVB (indicating a bias toward local over global dynamics) is deleterious because it reduces communication as suggested by the decrease in efficiency. The new model platform TVB hence provides a novel perspective to understanding biophysical parameters responsible for global brain dynamics after stroke, allowing the design of focused therapeutic interventions. PMID:26579071

Evaluation and attribution of vegetation contribution to seasonal climate predictability

NASA Astrophysics Data System (ADS)

Catalano, Franco; Alessandri, Andrea; De Felice, Matteo

2015-04-01

The land surface model of EC-Earth has been modified to include dependence of vegetation densities on the Leaf Area Index (LAI), based on the Lambert-Beer formulation. Effective vegetation fractional coverage can now vary at seasonal and interannual time-scales and therefore affect biophysical parameters such as the surface roughness, albedo and soil field capacity. The modified model is used to perform a real predictability seasonal hindcast experiment. LAI is prescribed using a recent observational dataset based on the third generation GIMMS and MODIS satellite data. Hindcast setup is: 7 months forecast length, 2 start dates (1st May and 1st November), 10 members, 28 years (1982-2009). The effect of the realistic LAI prescribed from observation is evaluated with respect to a control experiment where LAI does not vary. Hindcast results demonstrate that a realistic representation of vegetation significantly improves the forecasts of temperature and precipitation. The sensitivity is particularly large for temperature during boreal winter over central North America and Central Asia. This may be attributed in particular to the effect of the high vegetation component on the snow cover. Summer forecasts are improved in particular for precipitation over Europe, Sahel, North America, West Russia and Nordeste. Correlation improvements depends on the links between targets (temperature and precipitation) and drivers (surface heat fluxes, albedo, soil moisture, evapotranspiration, moisture divergence) which varies from region to region.

A Simplified Land Model (SLM) for use in cloud-resolving models: Formulation and evaluation

NASA Astrophysics Data System (ADS)

Lee, Jungmin M.; Khairoutdinov, Marat

2015-09-01

A Simplified Land Model (SLM) that uses a minimalist set of parameters with a single-layer vegetation and multilevel soil structure has been developed distinguishing canopy and undercanopy energy budgets. The primary motivation has been to design a land model for use in the System for Atmospheric Modeling (SAM) cloud-resolving model to study land-atmosphere interactions with a sufficient level of realism. SLM uses simplified expressions for the transport of heat, moisture, momentum, and radiation in soil-vegetation system. The SLM performance has been evaluated over several land surface types using summertime tower observations of micrometeorological and biophysical data from three AmeriFlux sites, which include grassland, cropland, and deciduous-broadleaf forest. In general, the SLM captures the observed diurnal cycle of surface energy budget and soil temperature reasonably well, although reproducing the evolution of soil moisture, especially after rain events, has been challenging. The SLM coupled to SAM has been applied to the case of summertime shallow cumulus convection over land based on the Atmospheric Radiation Measurements (ARM) Southern Great Plain (SGP) observations. The simulated surface latent and sensible heat fluxes as well as the evolution of thermodynamic profiles in convective boundary layer agree well with the estimates based on the observations. Sensitivity of atmospheric boundary layer development to the soil moisture and different land cover types has been also examined.

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...

Fundamental remote sensing science research program. Part 1: Scene radiation and atmospheric effects characterization project

NASA Technical Reports Server (NTRS)

Murphy, R. E.; Deering, D. W.

1984-01-01

Brief articles summarizing the status of research in the scene radiation and atmospheric effect characterization (SRAEC) project are presented. Research conducted within the SRAEC program is focused on the development of empirical characterizations and mathematical process models which relate the electromagnetic energy reflected or emitted from a scene to the biophysical parameters of interest.

BOREAS Level-0 NS001 TMS Imagery: Digital Counts in BIL Format

NASA Technical Reports Server (NTRS)

Hall, Forrest G. (Editor); Newcomer, Jeffrey A.; Dominguez, Roseanne

2000-01-01

For BOREAS, the NS001 TMS imagery, along with the other remotely sensed images, was collected in order to provide spatially extensive information over the primary study areas. This information includes detailed land cover and biophysical parameter maps such as fPAR and LAI. Data collections occurred over the study areas during the 1994 field campaigns.

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.

Improved estimation of anomalous diffusion exponents in single-particle tracking experiments

NASA Astrophysics Data System (ADS)

Kepten, Eldad; Bronshtein, Irena; Garini, Yuval

2013-05-01

The mean square displacement is a central tool in the analysis of single-particle tracking experiments, shedding light on various biophysical phenomena. Frequently, parameters are extracted by performing time averages on single-particle trajectories followed by ensemble averaging. This procedure, however, suffers from two systematic errors when applied to particles that perform anomalous diffusion. The first is significant at short-time lags and is induced by measurement errors. The second arises from the natural heterogeneity in biophysical systems. We show how to estimate and correct these two errors and improve the estimation of the anomalous parameters for the whole particle distribution. As a consequence, we manage to characterize ensembles of heterogeneous particles even for rather short and noisy measurements where regular time-averaged mean square displacement analysis fails. We apply this method to both simulations and in vivo measurements of telomere diffusion in 3T3 mouse embryonic fibroblast cells. The motion of telomeres is found to be subdiffusive with an average exponent constant in time. Individual telomere exponents are normally distributed around the average exponent. The proposed methodology has the potential to improve experimental accuracy while maintaining lower experimental costs and complexity.

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 the construction of biophysical neuron models. PMID:22396632

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 the protective environment of Earth, the biophysical properties underlying these changes must be studied, characterized and understood. This lecture reviews the current state of NASA biophysics research accomplishments and identifies future trends and challenges for biophysics research on the International Space Station and beyond.

The beginning of Space Life Science in China exploration rockets for biological experiment during 1960's

NASA Astrophysics Data System (ADS)

Jiang, Peidong; Zhang, Jingxue

The first step of space biological experiment in China was a set of five exploration rockets launched during 1964 to 1966, by Shanghai Institute of Machine and Electricity, and Institute of Biophysics of The Chinese Academy of Sciences. Three T-7AS1rockets for rats, mice and other samples in a biological cabin were launched and recovered safely in July of 1964 and June of 1965. Two T-7AS2rockets for dog, rats, mice and other samples in a biological cabin were launched and recovered safely in July of 1966. Institute of Biophysics in charged of the general design of biological experiments, telemetry of physiological parameters, and selection and training of experiment animals. The samples on-board were: rats, mice, dogs, and test tubes with fruit fly, enzyme, bacteria, E. Coli., lysozyme, bacteriaphage, RNAase, DNAase, crystals of enzyme, etc. Physiological, biochemical, bacte-riological, immunological, genetic, histochemical studies had been conducted, in cellular and sub cellular level. The postures of rat and dog were monitored during flight and under weight-lessness. Physiological parameters of ECG, blood pressure, respiration rate, body temperature were recorded. A dog named"Xiao Bao"was flight in 1966 with video monitor, life support system and conditioned reflex equipment. It flighted for more than 20 minutes and about 70km high. After 40 years, the experimental data recorded of its four physiological parameters during the flight process was reviewed. The change of 4 parameters during various phase of total flight process were compared, analyzed and discussed.

Ground and surface temperature variability for remote sensing of soil moisture in a heterogeneous landscape

USDA-ARS?s Scientific Manuscript database

At the Little River Watershed (LRW) heterogeneous landscape near Tifton Georgia US an in situ network of stations operated by the US Department of Agriculture-Agriculture Research Service (USDA-ARS-SEWRL) was established in 2003 for the long term study of climatic and soil biophysical processes. To ...

Simulating crop phenology in the Community Land Model and its impact on energy and carbon fluxes

USDA-ARS?s Scientific Manuscript database

A reasonable representation of crop phenology and biophysical processes in land surface models is necessary to accurately simulate energy, water and carbon budgets at the field, regional, and global scales. However, the evaluation of crop models that can be coupled to earth system models is relative...

Evolutionary and biophysical relationships among the papillomavirus E2 proteins.

PubMed

Blakaj, Dukagjin M; Fernandez-Fuentes, Narcis; Chen, Zigui; Hegde, Rashmi; Fiser, Andras; Burk, Robert D; Brenowitz, Michael

2009-01-01

Infection by human papillomavirus (HPV) may result in clinical conditions ranging from benign warts to invasive cancer. The HPV E2 protein represses oncoprotein transcription and is required for viral replication. HPV E2 binds to palindromic DNA sequences of highly conserved four base pair sequences flanking an identical length variable 'spacer'. E2 proteins directly contact the conserved but not the spacer DNA. Variation in naturally occurring spacer sequences results in differential protein affinity that is dependent on their sensitivity to the spacer DNA's unique conformational and/or dynamic properties. This article explores the biophysical character of this core viral protein with the goal of identifying characteristics that associated with risk of virally caused malignancy. The amino acid sequence, 3d structure and electrostatic features of the E2 protein DNA binding domain are highly conserved; specific interactions with DNA binding sites have also been conserved. In contrast, the E2 protein's transactivation domain does not have extensive surfaces of highly conserved residues. Rather, regions of high conservation are localized to small surface patches. Implications to cancer biology are discussed.

Multiscale Characterization of Bacterial Swarming Illuminates Principles Governing Directed Surface Motility

NASA Astrophysics Data System (ADS)

Strickland, Ben; Hoeger, Kentaro; Ursell, Tristan

In many systems, individual characteristics interact, leading to the spontaneous emergence of order and complexity. In biological settings like microbes, such collective behaviors can imbue a variety of benefits to constituent individuals, including increased spatial range, improved access to nutrients, and enhanced resistance to antibiotic threats. To untangle the biophysical underpinnings of collective motility, we use passive tracers and a curated genetic library of Bacillus subtilis, including motile, non-motile, biofilm-deficient, and non-chemotactic mutants. We characterize and connect individual behavior on the microscopic scale to macroscopic colony morphology and motility of dendritic swarming. We analyze the persistence and dynamics of coordinated movement on length scales up to 4 orders of magnitude larger than that of individual cells, revealing rapid and directed responses of microbial groups to external stimuli, such as avoidance dynamics across chemical gradients. Our observations uncover the biophysical interplay between individual motility, surface wetness, phenotypic diversity, and external physical forces that robustly precipitate coordinated group behavior in microbes, and suggest general principles that govern the transition from individual to group behavior.

[Spatio-temporal analysis of the biophysical and ecological conditions of Triatoma dimidiata (Hemiptera: Reduviidae: Triatominae) in the northeast region of Colombia].

PubMed

Badel-Mogollón, Jaime; Rodríguez-Figueroa, Laura; Parra-Henao, Gabriel

2017-03-29

Due to the lack of information regarding biophysical and spatio-temporal conditions (hydrometheorologic and vegetal coverage density) in areas with Triatoma dimidiata in the Colombian departments of Santander and Boyacá, there is a need to elucidate the association patterns of these variables to determine the distribution and control of this species. To make a spatio-temporal analysis of biophysical variables related to the distribution of T. dimidiate observed in the northeast region of Colombia. We used the Intergovernmental Panel on Climate Change Special Report on Emissions Scenarios (IPCC SRES) data bases registering vector presence and hydrometheorologic data. We studied the variables of environmental temperature, relative humidity, rainfall and vegetal coverage density at regional and local levels, and we conducted spatial geostatistic, descriptive statistical and Fourier temporal series analyses. Temperatures two meters above the ground and on covered surface ranged from 14,5°C to 18,8°C in the areas with the higher density of T. dimidiata. The environmental temperature fluctuated between 30 and 32°C. Vegetal coverage density and rainfall showed patterns of annual and biannual peaks. Relative humidity values fluctuated from 66,8 to 85,1%. Surface temperature and soil coverage were the variables that better explained the life cycle of T. dimidiata in the area. High relative humidity promoted the seek of shelters and an increase of the geographic distribution in the annual and biannual peaks of regional rainfall. The ecologic and anthropic conditions suggest that T. dimidiata is a highly resilient species.

Distribution of near-surface permafrost in Alaska: estimates of present and future conditions

USGS Publications Warehouse

Pastick, Neal J.; Jorgenson, M. Torre; Wylie, Bruce K.; Nield, Shawn J.; Johnson, Kristofer D.; Finley, Andrew O.

2015-01-01

High-latitude regions are experiencing rapid and extensive changes in ecosystem composition and function as the result of increases in average air temperature. Increasing air temperatures have led to widespread thawing and degradation of permafrost, which in turn has affected ecosystems, socioeconomics, and the carbon cycle of high latitudes. Here we overcome complex interactions among surface and subsurface conditions to map nearsurface permafrost through decision and regression tree approaches that statistically and spatially extend field observations using remotely sensed imagery, climatic data, and thematic maps of a wide range of surface and subsurface biophysical characteristics. The data fusion approach generated medium-resolution (30-m pixels) maps of near-surface (within 1 m) permafrost, active-layer thickness, and associated uncertainty estimates throughout mainland Alaska. Our calibrated models (overall test accuracy of ~85%) were used to quantify changes in permafrost distribution under varying future climate scenarios assuming no other changes in biophysical factors. Models indicate that near-surface permafrost underlies 38% of mainland Alaska and that near-surface permafrost will disappear on 16 to 24% of the landscape by the end of the 21st Century. Simulations suggest that near-surface permafrost degradation is more probable in central regions of Alaska than more northerly regions. Taken together, these results have obvious implications for potential remobilization of frozen soil carbon pools under warmer temperatures. Additionally, warmer and drier conditions may increase fire activity and severity, which may exacerbate rates of permafrost thaw and carbon remobilization relative to climate alone. The mapping of permafrost distribution across Alaska is important for land-use planning, environmental assessments, and a wide-array of geophysical studies.

Rheological effects of micropolar slime on the gliding motility of bacteria with slip boundary condition

NASA Astrophysics Data System (ADS)

Asghar, Z.; Ali, N.; Anwar Bég, O.; Javed, T.

2018-06-01

Gliding bacteria are virtually everywhere. These organisms are phylogenetically diverse with their hundreds of types, different shapes and several modes of motility. One possible mode of gliding motility in the rod shaped bacteria is that they propel themselves by producing undulating waves in their body. Few bacteria glides near the solid surface over the slime without any aid of flagella so the classical Navier-Stokes equations are incapable of explaining the slime rheology at the microscopic level. Micropolar fluid dynamics however provides a solid framework for mimicking bacterial physical phenomena at both micro and nano-scales, and therefore we use the micropolar fluid to characterize the rheology of a thin layer of slime and its dominant microrotation effects. It is also assumed that there is a certain degree of slip between slime and bacterial undulating surface and also between slime and solid substrate. The flow equations are formulated under long wavelength and low Reynolds number assumptions. Exact expressions for stream function and pressure gradient are obtained. The speed of the gliding bacteria is numerically calculated by using a modified Newton-Raphson method. Slip effects and effects of non-Newtonian slime parameters on bacterial speed and power are also quantified. In addition, when the glider is fixed, the effects of slip and rheological properties of micropolar slime parameters on the velocity, micro-rotation (angular velocity) of spherical slime particles, pressure rise per wavelength, pumping and trapping phenomena are also shown graphically and discussed in detail. The study is relevant to emerging biofuel cell technologies and also bacterial biophysics.

Manipulating nanoparticle transport within blood flow through external forces: an exemplar of mechanics in nanomedicine

PubMed Central

Ye, Huilin; Shen, Zhiqiang; Wei, Mei; Li, Ying

2018-01-01

A large number of nanoparticles (NPs) have been raised for diverse biomedical applications and some of them have shown great potential in treatment and imaging of diseases. Design of NPs is essential for delivery efficacy due to a number of biophysical barriers, which prevents the circulation of NPs in vascular flow and their accumulation at tumour sites. The physiochemical properties of NPs, so-called ‘4S’ parameters, such as size, shape, stiffness and surface functionalization, play crucial roles in their life journey to be delivered to tumour sites. NPs can be modified in various ways to extend their blood circulation time and avoid their clearance by phagocytosis, and efficiently diffuse into tumour cells. However, it is difficult to overcome these barriers simultaneously by a simple combination of ‘4S’ parameters for NPs. At this moment, external triggerings are necessary to guide the movement of NPs, which include light, ultrasound, magnetic field, electrical field and chemical interaction. The delivery system can be constructed to be sensitive to these external stimuli which can reduce the non-specific toxicity and improve the efficacy of the drug-delivery system. From a mechanics point of view, we discuss how different forces play their roles in the margination of NPs in blood flow and tumour microvasculature. PMID:29662344

Manipulating nanoparticle transport within blood flow through external forces: an exemplar of mechanics in nanomedicine

NASA Astrophysics Data System (ADS)

Ye, Huilin; Shen, Zhiqiang; Yu, Le; Wei, Mei; Li, Ying

2018-03-01

A large number of nanoparticles (NPs) have been raised for diverse biomedical applications and some of them have shown great potential in treatment and imaging of diseases. Design of NPs is essential for delivery efficacy due to a number of biophysical barriers, which prevents the circulation of NPs in vascular flow and their accumulation at tumour sites. The physiochemical properties of NPs, so-called `4S' parameters, such as size, shape, stiffness and surface functionalization, play crucial roles in their life journey to be delivered to tumour sites. NPs can be modified in various ways to extend their blood circulation time and avoid their clearance by phagocytosis, and efficiently diffuse into tumour cells. However, it is difficult to overcome these barriers simultaneously by a simple combination of `4S' parameters for NPs. At this moment, external triggerings are necessary to guide the movement of NPs, which include light, ultrasound, magnetic field, electrical field and chemical interaction. The delivery system can be constructed to be sensitive to these external stimuli which can reduce the non-specific toxicity and improve the efficacy of the drug-delivery system. From a mechanics point of view, we discuss how different forces play their roles in the margination of NPs in blood flow and tumour microvasculature.

Synergy between optical and microwave remote sensing to derive soil and vegetation parameters from MAC Europe 1991 Experiment

NASA Technical Reports Server (NTRS)

Taconet, O.; Benallegue, M.; Vidal, A.; Vidal-Madjar, D.; Prevot, L.; Normand, M.

1993-01-01

The ability of remote sensing for monitoring vegetation density and soil moisture for agricultural applications is extensively studied. In optical bands, vegetation indices (NDVI, WDVI) in visible and near infrared reflectances are related to biophysical quantities as the leaf area index, the biomass. In active microwave bands, the quantitative assessment of crop parameters and soil moisture over agricultural areas by radar multiconfiguration algorithms remains prospective. Furthermore the main results are mostly validated on small test sites, but have still to be demonstrated in an operational way at a regional scale. In this study, a large data set of radar backscattering has been achieved at a regional scale on a French pilot watershed, the Orgeval, along two growing seasons in 1988 and 1989 (mainly wheat and corn). The radar backscattering was provided by the airborne scatterometer ERASME, designed at CRPE, (C and X bands and HH and VV polarizations). Empirical relationships to estimate water crop and soil moisture over wheat in CHH band under actual field conditions and at a watershed scale are investigated. Therefore, the algorithms developed in CHH band are applied for mapping the surface conditions over wheat fields using the AIRSAR and TMS images collected during the MAC EUROPE 1991 experiment. The synergy between optical and microwave bands is analyzed.

Structural and biophysical analysis of interactions between cod and human uracil-DNA N-glycosylase (UNG) and UNG inhibitor (Ugi)

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

Assefa, Netsanet Gizaw; Niiranen, Laila; University of Turku, FIN-20014 Turku

2014-08-01

A structural and biophysical study of the interactions between cod and human uracil-DNA N-glycosylase (UNG) and their inhibitor Ugi is presented. The stronger interaction between cod UNG and Ugi can be explained by a greater positive electrostatic surface potential. Uracil-DNA N-glycosylase from Atlantic cod (cUNG) shows cold-adapted features such as high catalytic efficiency, a low temperature optimum for activity and reduced thermal stability compared with its mesophilic homologue human UNG (hUNG). In order to understand the role of the enzyme–substrate interaction related to the cold-adapted properties, the structure of cUNG in complex with a bacteriophage encoded natural UNG inhibitor (Ugi)more » has been determined. The interaction has also been analyzed by isothermal titration calorimetry (ITC). The crystal structure of cUNG–Ugi was determined to a resolution of 1.9 Å with eight complexes in the asymmetric unit related through noncrystallographic symmetry. A comparison of the cUNG–Ugi complex with previously determined structures of UNG–Ugi shows that they are very similar, and confirmed the nucleotide-mimicking properties of Ugi. Biophysically, the interaction between cUNG and Ugi is very strong and shows a binding constant (K{sub b}) which is one order of magnitude larger than that for hUNG–Ugi. The binding of both cUNG and hUNG to Ugi was shown to be favoured by both enthalpic and entropic forces; however, the binding of cUNG to Ugi is mainly dominated by enthalpy, while the entropic term is dominant for hUNG. The observed differences in the binding properties may be explained by an overall greater positive electrostatic surface potential in the protein–Ugi interface of cUNG and the slightly more hydrophobic surface of hUNG.« less

Spatially Complete Global Surface Albedos Derived from Terra/MODIS Data

NASA Technical Reports Server (NTRS)

King, Michael D.; Moody, Eric G.; Schaaf, Crystal B.; Platnick, Steven

2006-01-01

Spectral land surface albedo is an important parameter for describing the radiative properties of the Earth. Accordingly it reflects the consequences of natural and human interactions, such as anthropogenic, meteorological, and phenological effects, on global and local climatological trends. Consequently, albedos are integral parts in a variety of research areas, such as general circulation models (GCMs), energy balance studies, modeling of land use and land use change, and biophysical, oceanographic, and meteorological studies. , Over five years of land surface anisotropy, diffuse bihemispherical (white-sky) albedo and direct beam directional hemispherical (black-sky) albedo from observations acquired by the MODIS instruments aboard NASA s Terra and Aqua satellite platforms have provided researchers with unprecedented spatial, spectral, and temporal information on the land surface s radiative characteristics. However, roughly 30% of the global land surface, on an annual equal-angle basis, is obscured due to persistent and transient cloud cover, while another 207% is obscured due to ephemeral and seasonal snow effects. This precludes the MOD43B3 albedo products from being directly used in some remote sensing and ground-based applications, climate models, and global change research projects. To provide researchers with the requisite spatially complete global snow-free land surface albedo dataset, an ecosystem-dependent temporal interpolation technique was developed to fill missing or lower quality data and snow covered values from the official MOD43B3 dataset with geophysically realistic values. The method imposes pixel-level and local regional ecosystem-dependent phenological behavior onto retrieved pixel temporal data in such a way as to maintain pixel-level spatial and spectral detail and integrity. The phenological curves are derived from statistics based on the MODIS MOD12Q1 IGBP land cover classification product geolocated with the MOD43B3 data.

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 effectiveness for a proton SOBP used to treat eye melanoma in Catania, Italy. The survival of AG01522 cells at different depths was reproduced, and the survival of V79 cells was predicted. For both cell lines, the simulations also predicted yields of chromosome aberrations, some of which can be regarded as indicators of the risk to normal tissues.

The molecular determinants of CD8 co-receptor function.

PubMed

Cole, David K; Laugel, Bruno; Clement, Mathew; Price, David A; Wooldridge, Linda; Sewell, Andrew K

2012-10-01

CD8(+) T cells respond to signals mediated through a specific interaction between the T-cell receptor (TCR) and a composite antigen in the form of an epitopic peptide bound between the polymorphic α1 and α2 helices of an MHC class I (MHCI) molecule. The CD8 glycoprotein 'co-receives' antigen by binding to an invariant region of the MHCI molecule and can enhance ligand recognition by up to 1 million-fold. In recent years, a number of structural and biophysical investigations have shed light on the role of the CD8 co-receptor during T-cell antigen recognition. Here, we provide a collated resource for these data, and discuss how the structural and biophysical parameters governing CD8 co-receptor function further our understanding of T-cell cross-reactivity and the productive engagement of low-affinity antigenic ligands. © 2012 The Authors. Immunology © 2012 Blackwell Publishing Ltd.

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.

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.

A remote sensing based vegetation classification logic for global land cover analysis

USGS Publications Warehouse

Running, Steven W.; Loveland, Thomas R.; Pierce, Lars L.; Nemani, R.R.; Hunt, E. Raymond

1995-01-01

This article proposes a simple new logic for classifying global vegetation. The critical features of this classification are that 1) it is based on simple, observable, unambiguous characteristics of vegetation structure that are important to ecosystem biogeochemistry and can be measured in the field for validation, 2) the structural characteristics are remotely sensible so that repeatable and efficient global reclassifications of existing vegetation will be possible, and 3) the defined vegetation classes directly translate into the biophysical parameters of interest by global climate and biogeochemical models. A first test of this logic for the continental United States is presented based on an existing 1 km AVHRR normalized difference vegetation index database. Procedures for solving critical remote sensing problems needed to implement the classification are discussed. Also, some inferences from this classification to advanced vegetation biophysical variables such as specific leaf area and photosynthetic capacity useful to global biogeochemical modeling are suggested.

In vivo evaluation of some biophysical parameters of the facial skin of Indian women. Part I: variability with age and geographical locations.

PubMed

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

2018-02-01

India is a large country (a subcontinent) of about 3.3 million km 2 that covers large ranges in latitude and longitude. The last Indian census counted about 1.21 billion of inhabitants of many origins, creating a vast human diversity and skin types, the variability of which having been previously established. The present study aimed at deepening this knowledge through a set of biophysical measurements to describe, along the skin ageing process, the specificities of various Indian subjects living in different geographical locations. A total of 1204 women, aged 18-84 years, of all socio-economic status, were recruited in four Indian cities (Mumbai, Kolkata, Chennai and Delhi). Measurements of face skin colour properties, elastic properties, sebum production, skin pores and microrelief roughness were performed. With regard skin colour, this study indicates, with age, a darkening of very low amplitude that leads to an increased skin colour heterogeneity. In all subjects, at all ages, the ocular region (dark circles) presents a much darker pigmentation than the cheeks, creating a contrast that appears constant at all ages. In addition to an increased skin colour heterogeneity, a progressive alteration of the skin surface relief, increased sizes of skin pores, a loss of skin elasticity and a drop in sebum production, post-menopause, are observed. This study confirms, in Indian women, some skin ageing measurements found on women from other ethnic groups (i.e. sebum, firmness, wrinkles and pores size) and also identifies some Indian specificities: a high and constant contrast between the ocular region and the cheek colour, associated to a very slow darkening effect along the lifespan. © 2017 Society of Cosmetic Scientists and the Société Française de Cosmétologie.

The reliability of non-invasive biophysical outcome measures for evaluating normal and hyperkeratotic foot skin.

PubMed

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

2015-01-01

Hyperkeratosis of foot skin is a common skin problem affecting people of different ages. The clinical presentation of this condition can range from dry flaky skin, which can lead to fissures, to hard callused skin which is often painful and debilitating. The purpose of this study was to test the reliability of certain non-invasive skin measurement devices on foot skin in normal and hyperkeratotic states, with a view to confirming their use as quantitative outcome measures in future clinical trials. Twelve healthy adult participants with a range of foot skin conditions (xerotic skin, heel fissures and plantar calluses) were recruited to the study. Measurements of normal and hyperkeratotic skin sites were taken using the following devices: Corneometer® CM 825, Cutometer® 580 MPA, Reviscometer® RVM 600, Visioline® VL 650 Quantiride® and Visioscan® VC 98, by two investigators on two consecutive days. The intra and inter rater reliability and standard error of measurement for each device was calculated. The data revealed the majority of the devices to be reliable measurement tools for normal and hyperkeratotic foot skin (ICC values > 0.6). The surface evaluation parameters for skin: SEsc and SEsm have greater reliability compared to the SEr measure. The Cutometer® is sensitive to soft tissue movement within the probe, therefore measurement of plantar soft tissue areas should be approached with caution. Reviscometer® measures on callused skin demonstrated an unusually high degree of error. These results confirm the intra and inter rater reliability of the Corneometer®, Cutometer®, Visioline® and Visioscan® in quantifying specific foot skin biophysical properties.

Urban Growth Detection Using Filtered Landsat Dense Time Trajectory in an Arid City

NASA Astrophysics Data System (ADS)

Ye, Z.; Schneider, A.

2014-12-01

Among all remote sensing environment monitoring techniques, time series analysis of biophysical index is drawing increasing attention. Although many of them studied forest disturbance and land cover change detection, few focused on urban growth mapping at medium spatial resolution. As Landsat archive becomes open accessible, methods using Landsat time-series imagery to detect urban growth is possible. It is found that a time trajectory from a newly developed urban area shows a dramatic drop of vegetation index. This enable the utilization of time trajectory analysis to distinguish impervious surface and crop land that has a different temporal biophysical pattern. Also, the time of change can be estimated, yet many challenges remain. Landsat data has lower temporal resolution, which may be worse when cloud-contaminated pixels and SLC-off effect exist. It is difficult to tease apart intra-annual, inter-annual, and land cover difference in a time series. Here, several methods of time trajectory analysis are utilized and compared to find a computationally efficient and accurate way on urban growth detection. A case study city, Ankara, Turkey is chosen for its arid climate and various landscape distributions. For preliminary research, Landsat TM and ETM+ scenes from 1998 to 2002 are chosen. NDVI, EVI, and SAVI are selected as research biophysical indices. The procedure starts with a seasonality filtering. Only areas with seasonality need to be filtered so as to decompose seasonality and extract overall trend. Harmonic transform, wavelet transform, and a pre-defined bell shape filter are used to estimate the overall trend in the time trajectory for each pixel. The point with significant drop in the trajectory is tagged as change point. After an urban change is detected, forward and backward checking is undertaken to make sure it is really new urban expansion other than short time crop fallow or forest disturbance. The method proposed here can capture most of the urban growth during research time period, although the accuracy of time point determination is a bit lower than this. Results from several biophysical indices and filtering methods are similar. Some fallows and bare lands in arid area are easily confused with urban impervious surface.

Terrestrial Ecosystems of the Conterminous United States

USGS Publications Warehouse

Sayre, Roger G.; Comer, Patrick; Cress, Jill; Warner, Harumi

2010-01-01

The U.S. Geological Survey (USGS), with support from NatureServe, has modeled the potential distribution of 419 terrestrial ecosystems for the conterminous United States using a comprehensive biophysical stratification approach that identifies distinct biophysical environments and associates them with known vegetation distributions (Sayre and others, 2009). This standardized ecosystem mapping effort used an ecosystems classification developed by NatureServe (Comer and others, 2003). The ecosystem mapping methodology was developed for South America (Sayre and others, 2008) and is now being implemented globally (Sayre and others, 2007). The biophysical stratification approach is based on mapping the major structural components of ecosystems (land surface forms, topographic moisture potential, surficial lithology, isobioclimates and biogeographic regions) and then spatially combining them to produce a set of unique biophysical environments. These physically distinct areas are considered as the fundamental structural units ('building blocks') of ecosystems, and are subsequently aggregated and labeled using the NatureServe classification. The structural footprints were developed from the geospatial union of several base layers including biogeographic regions, isobioclimates (Cress and others, 2009a), land surface forms (Cress and others, 2009b), topographic moisture potential (Cress and others, 2009c), and surficial lithology (Cress and others, in press). Among the 49,168 unique structural footprint classes that resulted from the union, 13,482 classes met a minimum pixel count threshold (20,000 pixels) and were aggregated into 419 NatureServe ecosystems using a semiautomated labeling process based on rule-set formulations for attribution of each ecosystem. The resulting ecosystems are those that are expected to occur based on the combination of the bioclimate, biogeography, and geomorphology. Where land use by humans has not altered land cover, natural vegetation assemblages are expected to occur, and these are described in the ecosystems classification. The map does not show the distribution of urban and agricultural areas - these will be masked out in subsequent analyses to depict the current land cover in addition to the potential distribution of natural ecosystems. This map depicts the smoothed and generalized image of the terrestrial ecosystems dataset. Additional information about this map and any data developed for the ecosystems modeling of the conterminous United States is available online at: http://rmgsc.cr.usgs.gov/ecosystems/.

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 diffusivity and soil physical properties (transport). Our work begins to address the disconnect between point, footprint, watershed scale estimates of ecosystem respiration and the role of a dynamic hydrologic cycle.

Remote sensing-based predictors improve distribution models of rare, early successional and boradleaf tree species in Utah

Treesearch

N. E. Zimmermann; T. C. Edwards; G. G. Moisen; T. S. Frescino; J. A. Blackard

2007-01-01

Compared to bioclimatic variables, remote sensing predictors are rarely used for predictive species modelling. When used, the predictors represent typically habitat classifications or filters rather than gradual spectral, surface or biophysical properties. Consequently, the full potential of remotely sensed predictors for modelling the spatial distribution of species...

Boltzmann Energy-based Image Analysis Demonstrates that Extracellular Domain Size Differences Explain Protein Segregation at Immune Synapses

PubMed Central

Burroughs, Nigel J.; Köhler, Karsten; Miloserdov, Vladimir; Dustin, Michael L.; van der Merwe, P. Anton; Davis, Daniel M.

2011-01-01

Immune synapses formed by T and NK cells both show segregation of the integrin ICAM1 from other proteins such as CD2 (T cell) or KIR (NK cell). However, the mechanism by which these proteins segregate remains unclear; one key hypothesis is a redistribution based on protein size. Simulations of this mechanism qualitatively reproduce observed segregation patterns, but only in certain parameter regimes. Verifying that these parameter constraints in fact hold has not been possible to date, this requiring a quantitative coupling of theory to experimental data. Here, we address this challenge, developing a new methodology for analysing and quantifying image data and its integration with biophysical models. Specifically we fit a binding kinetics model to 2 colour fluorescence data for cytoskeleton independent synapses (2 and 3D) and test whether the observed inverse correlation between fluorophores conforms to size dependent exclusion, and further, whether patterned states are predicted when model parameters are estimated on individual synapses. All synapses analysed satisfy these conditions demonstrating that the mechanisms of protein redistribution have identifiable signatures in their spatial patterns. We conclude that energy processes implicit in protein size based segregation can drive the patternation observed in individual synapses, at least for the specific examples tested, such that no additional processes need to be invoked. This implies that biophysical processes within the membrane interface have a crucial impact on cell∶cell communication and cell signalling, governing protein interactions and protein aggregation. PMID:21829338

Investigation of Polarization Phase Difference Related to Forest Fields Characterizations

NASA Astrophysics Data System (ADS)

Majidi, M.; Maghsoudi, Y.

2013-09-01

The information content of Synthetic Aperture Radar (SAR) data significantly included in the radiometric polarization channels, hence polarimetric SAR data should be analyzed in relation with target structure. The importance of the phase difference between two co-polarized scattered signals due to the possible association between the biophysical parameters and the measured Polarization Phase Difference (PPD) statistics of the backscattered signal recorded components has been recognized in geophysical remote sensing. This paper examines two Radarsat-2 images statistics of the phase difference to describe the feasibility of relationship with the physical properties of scattering targets and tries to understand relevance of PPD statistics with various types of forest fields. As well as variation of incidence angle due to affecting on PPD statistics is investigated. The experimental forest pieces that are used in this research are characterized white pine (Pinus strobus L.), red pine (Pinus resinosa Ait.), jack pine (Pinus banksiana Lamb.), white spruce (Picea glauca (Moench Voss), black spruce (Picea mariana (Mill) B.S.P.), poplar (Populus L.), red oak (Quercus rubra L.) , aspen and ground vegetation. The experimental results show that despite of biophysical parameters have a wide diversity, PPD statistics are almost the same. Forest fields distributions as distributed targets have close to zero means regardless of the incidence angle. Also, The PPD distribution are function of both target and sensor parameters, but for more appropriate examination related to PPD statistics the observations should made in the leaf-off season or in bands with lower frequencies.

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.

Do the energy fluxes and surface conductance of boreal coniferous forests in Europe scale with leaf area?

PubMed

Launiainen, Samuli; Katul, Gabriel G; Kolari, Pasi; Lindroth, Anders; Lohila, Annalea; Aurela, Mika; Varlagin, Andrej; Grelle, Achim; Vesala, Timo

2016-12-01

Earth observing systems are now routinely used to infer leaf area index (LAI) given its significance in spatial aggregation of land surface fluxes. Whether LAI is an appropriate scaling parameter for daytime growing season energy budget, surface conductance (G s ), water- and light-use efficiency and surface-atmosphere coupling of European boreal coniferous forests was explored using eddy-covariance (EC) energy and CO 2 fluxes. The observed scaling relations were then explained using a biophysical multilayer soil-vegetation-atmosphere transfer model as well as by a bulk G s representation. The LAI variations significantly alter radiation regime, within-canopy microclimate, sink/source distributions of CO 2 , H 2 O and heat, and forest floor fluxes. The contribution of forest floor to ecosystem-scale energy exchange is shown to decrease asymptotically with increased LAI, as expected. Compared with other energy budget components, dry-canopy evapotranspiration (ET) was reasonably 'conservative' over the studied LAI range 0.5-7.0 m 2 m -2 . Both ET and G s experienced a minimum in the LAI range 1-2 m 2 m -2 caused by opposing nonproportional response of stomatally controlled transpiration and 'free' forest floor evaporation to changes in canopy density. The young forests had strongest coupling with the atmosphere while stomatal control of energy partitioning was strongest in relatively sparse (LAI ~2 m 2 m -2 ) pine stands growing on mineral soils. The data analysis and model results suggest that LAI may be an effective scaling parameter for net radiation and its partitioning but only in sparse stands (LAI <3 m 2 m -2 ). This finding emphasizes the significance of stand-replacing disturbances on the controls of surface energy exchange. In denser forests, any LAI dependency varies with physiological traits such as light-saturated water-use efficiency. The results suggest that incorporating species traits and site conditions are necessary when LAI is used in upscaling energy exchanges of boreal coniferous forests. © 2016 John Wiley & Sons Ltd.

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.

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.

Identifiability, reducibility, and adaptability in allosteric macromolecules.

PubMed

Bohner, Gergő; Venkataraman, Gaurav

2017-05-01

The ability of macromolecules to transduce stimulus information at one site into conformational changes at a distant site, termed "allostery," is vital for cellular signaling. Here, we propose a link between the sensitivity of allosteric macromolecules to their underlying biophysical parameters, the interrelationships between these parameters, and macromolecular adaptability. We demonstrate that the parameters of a canonical model of the mSlo large-conductance Ca 2+ -activated K + (BK) ion channel are non-identifiable with respect to the equilibrium open probability-voltage relationship, a common functional assay. We construct a reduced model with emergent parameters that are identifiable and expressed as combinations of the original mechanistic parameters. These emergent parameters indicate which coordinated changes in mechanistic parameters can leave assay output unchanged. We predict that these coordinated changes are used by allosteric macromolecules to adapt, and we demonstrate how this prediction can be tested experimentally. We show that these predicted parameter compensations are used in the first reported allosteric phenomena: the Bohr effect, by which hemoglobin adapts to varying pH. © 2017 Bohner and Venkataraman.

Identifiability, reducibility, and adaptability in allosteric macromolecules

PubMed Central

Bohner, Gergő

2017-01-01

The ability of macromolecules to transduce stimulus information at one site into conformational changes at a distant site, termed “allostery,” is vital for cellular signaling. Here, we propose a link between the sensitivity of allosteric macromolecules to their underlying biophysical parameters, the interrelationships between these parameters, and macromolecular adaptability. We demonstrate that the parameters of a canonical model of the mSlo large-conductance Ca2+-activated K+ (BK) ion channel are non-identifiable with respect to the equilibrium open probability-voltage relationship, a common functional assay. We construct a reduced model with emergent parameters that are identifiable and expressed as combinations of the original mechanistic parameters. These emergent parameters indicate which coordinated changes in mechanistic parameters can leave assay output unchanged. We predict that these coordinated changes are used by allosteric macromolecules to adapt, and we demonstrate how this prediction can be tested experimentally. We show that these predicted parameter compensations are used in the first reported allosteric phenomena: the Bohr effect, by which hemoglobin adapts to varying pH. PMID:28416647

Relevance of biophysical interactions of nanoparticles with a model membrane in predicting cellular uptake: study with TAT peptide-conjugated nanoparticles

PubMed Central

Peetla, Chiranjeevi; Rao, Kavitha S.; Labhasetwar, Vinod

2009-01-01

The aim of the study was to test the hypothesis that the biophysical interactions of the trans-activating transcriptor (TAT) peptide-conjugated nanoparticles (NPs) with a model cell membrane could predict the cellular uptake of the encapsulated therapeutic agent. To test the above hypothesis, the biophysical interactions of ritonavir-loaded poly (L-lactide) nanoparticles (RNPs), either conjugated to a TAT peptide (TAT-RNPs) or scrambled TAT peptide (sc-TAT-RNPs), were studied with an endothelial cell model membrane (EMM) using a Langmuir film balance, and the corresponding human vascular endothelial cells (HUVECs) were used to study the uptake of the encapsulated therapeutic. Biophysical interactions were determined from the changes in surface pressure (SP) of the EMM as a function of time following interaction with NPs, and the compression isotherm (π–A) of the EMM lipid mixture in the presence of NPs. In addition, the EMMs were transferred onto a silicon substrate following interactions with NPs using the Langmuir–Schaeffer (LS) technique. The transferred LS films were imaged by atomic force microscopy (AFM) to determine the changes in lipid morphology and to characterize the NP–membrane interactions. TAT-RNPs showed an increase in SP of the EMM, which was dependent upon the amount of the peptide bound to NPs and the concentration of NPs, whereas sc-TAT-RNPs and RNPs did not show any significant change in SP. The isotherm experiment showed a shift towards higher mean molecular area (mmA) in the presence of TAT-RNPs, indicating their interactions with the lipids of the EMM, whereas sc-TAT-RNPs and RNPs did not show any significant change. The AFM images showed condensation of the lipids following interaction with TAT-RNPs, indicating their penetration into the EMM, whereas RNPs did not cause any change. Surface analysis and 3-D AFM images of the EMM further confirmed penetration of TAT-RNPs into the EMM whereas RNPs were seen anchored loosely to the membrane, and were significantly less in number than TAT-RNPs. We speculate that hydrophobic tyrosine of the TAT that forms the NP–interface drives the initial interactions of TAT-RNPs with the EMM, followed by electrostatic interactions with the anionic phospholipids of the membrane. In case of sc-TAT-RNPs, hydrophilic arginine forms the NP–interface that does not interact with the EMM, despite having the similar cationic charge on these NPs as TAT-RNPs. TAT peptide alone did not show any change in SP, suggesting that the interaction occurs when the peptide is conjugated to a carrier system. HUVECs showed higher uptake of the drug with TAT-RNPs as compared to that with sc-TAT-RNPs or RNPs, suggesting that the biophysical interactions of NPs with cell membrane lipids play a role in cellular internalization of NPs. In conclusion, TAT peptide sequence and the amount of TAT conjugated to NPs significantly affect the biophysical interactions of NPs with the EMM, and these interactions correlate with the cellular delivery of the encapsulated drug. Biophysical interactions with a model membrane thus could be effectively used in developing efficient functionalized nanocarrier systems for drug delivery applications. PMID:19243206

Automated Droplet Manipulation Using Closed-Loop Axisymmetric Drop Shape Analysis.

PubMed

Yu, Kyle; Yang, Jinlong; Zuo, Yi Y

2016-05-17

Droplet manipulation plays an important role in a wide range of scientific and industrial applications, such as synthesis of thin-film materials, control of interfacial reactions, and operation of digital microfluidics. Compared to micron-sized droplets, which are commonly considered as spherical beads, millimeter-sized droplets are generally deformable by gravity, thus introducing nonlinearity into control of droplet properties. Such a nonlinear drop shape effect is especially crucial for droplet manipulation, even for small droplets, at the presence of surfactants. In this paper, we have developed a novel closed-loop axisymmetric drop shape analysis (ADSA), integrated into a constrained drop surfactometer (CDS), for manipulating millimeter-sized droplets. The closed-loop ADSA generalizes applications of the traditional drop shape analysis from a surface tension measurement methodology to a sophisticated tool for manipulating droplets in real time. We have demonstrated the feasibility and advantages of the closed-loop ADSA in three applications, including control of drop volume by automatically compensating natural evaporation, precise control of surface area variations for high-fidelity biophysical simulations of natural pulmonary surfactant, and steady control of surface pressure for in situ Langmuir-Blodgett transfer from droplets. All these applications have demonstrated the accuracy, versatility, applicability, and automation of this new ADSA-based droplet manipulation technique. Combining with CDS, the closed-loop ADSA holds great promise for advancing droplet manipulation in a variety of material and surface science applications, such as thin-film fabrication, self-assembly, and biophysical study of pulmonary surfactant.

Satellite detection of wastewater diversion plumes in Southern California

NASA Astrophysics Data System (ADS)

Gierach, Michelle M.; Holt, Benjamin; Trinh, Rebecca; Jack Pan, B.; Rains, Christine

2017-02-01

Multi-sensor satellite observations proved useful in detecting surfacing wastewater plumes during the 2006 Hyperion Treatment Plant (HTP) and 2012 Orange County Sanitation District (OCSD) wastewater diversion events in Southern California. Satellite sensors were capable of detecting biophysical signatures associated with the wastewater, compared to ambient ocean waters, enabling monitoring of environmental impacts over a greater spatial extent than in situ sampling alone. Thermal satellite sensors measured decreased sea surface temperatures (SSTs) associated with the surfacing plumes. Ocean color satellite sensors did not measure a distinguishable biological response in terms of chlorophyll-a (chl-a) concentrations during the short lived, three-day long, 2006 HTP diversion. A period of decreased chl-a concentration was observed during the three-week long 2012 OCSD diversion, likely in association with enhanced chlorination of the discharged wastewater that suppressed the phytoplankton response and/or significant uptake by heterotrophic bacteria. Synthetic aperture radar (SAR) satellite data were able to identify and track the 2006 HTP wastewater plume through changes in surface roughness related to the oily components of the treated surfacing wastewater. Overall, it was found that chl-a and SST values must have differences of at least 1 mg m-3 and 0.5 °C, respectively, in comparison with adjacent waters for wastewater plumes and their biophysical impact to be detectable from satellite. For a wastewater plume to be identifiable in SAR imagery, wind speeds must range between ∼3 and 8 m s-1. The findings of this study illustrate the benefit of utilizing multiple satellite sensors to monitor the rapidly changing environmental response to surfacing wastewater plumes, and can help inform future wastewater diversions in coastal areas.

A New Map of Standardized Terrestrial Ecosystems of the Conterminous United States

USGS Publications Warehouse

Sayre, Roger G.; Comer, Patrick; Warner, Harumi; Cress, Jill

2009-01-01

A new map of standardized, mesoscale (tens to thousands of hectares) terrestrial ecosystems for the conterminous United States was developed by using a biophysical stratification approach. The ecosystems delineated in this top-down, deductive modeling effort are described in NatureServe's classification of terrestrial ecological systems of the United States. The ecosystems were mapped as physically distinct areas and were associated with known distributions of vegetation assemblages by using a standardized methodology first developed for South America. This approach follows the geoecosystems concept of R.J. Huggett and the ecosystem geography approach of R.G. Bailey. Unique physical environments were delineated through a geospatial combination of national data layers for biogeography, bioclimate, surficial materials lithology, land surface forms, and topographic moisture potential. Combining these layers resulted in a comprehensive biophysical stratification of the conterminous United States, which produced 13,482 unique biophysical areas. These were considered as fundamental units of ecosystem structure and were aggregated into 419 potential terrestrial ecosystems. The ecosystems classification effort preceded the mapping effort and involved the independent development of diagnostic criteria, descriptions, and nomenclature for describing expert-derived ecological systems. The aggregation and labeling of the mapped ecosystem structure units into the ecological systems classification was accomplished in an iterative, expert-knowledge-based process using automated rulesets for identifying ecosystems on the basis of their biophysical and biogeographic attributes. The mapped ecosystems, at a 30-meter base resolution, represent an improvement in spatial and thematic (class) resolution over existing ecoregionalizations and are useful for a variety of applications, including ecosystem services assessments, climate change impact studies, biodiversity conservation, and resource management.

Biophysical characterization of the Lactobacillus delbrueckii subsp. bulgaricus membrane during cold and osmotic stress and its relevance for cryopreservation.

PubMed

Meneghel, Julie; Passot, Stéphanie; Dupont, Sébastien; Fonseca, Fernanda

2017-02-01

Freezing lactic acid bacteria often leads to cell death and loss of technological properties. Our objective was to provide an in-depth characterization of the biophysical properties of the Lactobacillus delbrueckii subsp. bulgaricus membrane in relation to its freeze resistance. Freezing was represented as a combination of cold and osmotic stress. This work investigated the relative incidence of increasing sucrose concentrations coupled or not with subzero temperatures without ice nucleation on the biological and biophysical responses of two strains with different membrane fatty acid compositions and freeze resistances. Following exposure of bacterial cells to the highest sucrose concentration, the sensitive strain exhibited a survival rate of less than 10 % and 5 h of acidifying activity loss. Similar biological activity losses were observed upon freeze-thawing and after osmotic treatment for each strain thus highlighting osmotic stress as the main source of cryoinjury. The direct measurement of membrane fluidity by fluorescence anisotropy was linked to membrane lipid organization characterized by FTIR spectroscopy. Both approaches made it possible to investigate the specific contributions of the membrane core and the bilayer external surface to cell degradation caused by cold and osmotic stress. Cold-induced membrane rigidification had no significant implication on bacterial freeze-thaw resistance. Interactions between extracellular sucrose and membrane phospholipid headgroups under osmotic stress were also observed. Such interactions were more evident in the sensitive strain and when increasing sucrose concentration, thus suggesting membrane permeabilization. The relevance of biophysical properties for elucidating mechanisms of cryoinjury and cryoprotection is discussed.

Satellites observed widespread greening of Earth and increase of woody biomass

NASA Astrophysics Data System (ADS)

Chen, C.; Park, T.; Myneni, R.; Xu, L.; Saatchi, S. S.; Liu, Y.; Knyazikhin, Y.

2017-12-01

Global terrestrial vegetation is an important modulator of the planetary climate system that alters Earth's hydrology, atmosphere and energy circulations through biophysical and biochemical processes. Yet the internal structural change of the vegetation is not well understood. Leaf area index (LAI), unlike radiometric parameters (e.g. NDVI), is a well-defined and ground-measurable biophysical variable, which can better represent the greenness of vegetation. We evaluate 17-year (2000-2016) satellite-derived LAI from two MODIS sensors onboard Terra and Aqua. Results show that the global annual-averaged LAI has an increasing trend at 0.036 m2m-2 per decade (2.3% per decade). The widespread greening takes up 32.5% of the vegetated area, while only 5.2% of such exhibits browning. We further investigate the biome- and regional-specific patterns of the evolution of LAI: 1) Croplands (0.062 m2m-2 per decade) and forests (0.044 m2m-2 per decade) are the paramount contributors of the greening; 2) Temperate vegetation (0.052 m2m-2 per decade) greening outperform other regions, followed by high-latitude vegetation (0.031 m2m-2 per decade), and tropical vegetation (0.025 m2m-2 per decade) at the minimum. Two independent satellite-observed datasets from multiple bandwidths (optical, thermal and microwave) provide evidence that this large-scale LAI trend is mainly owing to the spatiotemporal transition of woody biomass and the change of canopy structure. The greening (browning) at the global scale is concordant with the increase (decrease) of tree cover and vegetation optical depth (VOD), while little correlation is found for herbaceous biomass (i.e. non-tree cover). The observed greening and expansion of woody biomass will lead to a smaller land surface diurnal temperature range (DTR) due to the increase of a) the evapotranspiration, b) the water storage (higher the specific heat capacity) and c) the aerodynamic resistance (vertical mixture) of the canopy. a) and c) can augment daytime cooling, while b) and c) can boost nighttime warming. We find, consistently, the MODIS observed land surface DTR decreases over greening regions, and increases over browning regions.

A multi-sensor method for in-situ quantification of multiple biodiversity and ecosystem service indicators in wetland vegetation

NASA Astrophysics Data System (ADS)

Zlinszky, András; Prager, Katharina; Koma, Zsófia

2017-04-01

Biodiversity and ecosystem services are in the focus of biogeosciences research and conservation management worldwide. However, their quantification is notoriously difficult. Since full coverage of biodiversity and/or ecosystem services is unfeasible due to their complexity, indicators are recommended: biophysical quantities that are measureable and are expected to be closely related to biodiversity or to ecosystem processes. Nevertheless, many biodiversity and ecosystem service assessments are based on upscaling very few (if any) in-situ measurements using models driven by basic land cover data. Also, many assessments select only a single or very few indicators, which then does not enable analysis of trade-offs and interconnections. Here we propose a system of simple yet reliable field measurements, based on basic sensors, measurements, imaging and sampling technology, suitable for quantitatively representing many components of biodiversity and ecosystem services in emergent wetland vegetation. Along a transect from open water to the shore, sampling stations are laid out that include water temperature, air temperature and humidity sensors, zenith facing photographs and pole contact counts of vegetation in height intervals. Additionally, for some of these stations, small quadrats of vegetation are harvested, separated to individual species and weighed in height intervals above ground/water. Underwater surface of vegetation is estimated by counting stalks and registering average diameter. Finally, decomposition is quantified by leaving a standard amount of biomass in a plastic net bag and re-weighing it a year later. This system allows measuring alpha and beta diversity together with vertical structural diversity, leaf area (as a proxy of shading and pollution absorbtion), biomass (as a proxy of carbon sequestration), underwater surface (as a proxy of fish population sustaining), microclimate influence and soil provision. The necessary tools are temperature and humidity sensors, field scales, pruning shears, plastic net bags, measuring poles (for water depth), a digital camera and a GPS; all small and lightweight enough to be carried and operated by one person under wetland field conditions. Additionally, such measurements are suitable for remote sensing-based direct upscaling of biophysical parameters to create area-covering maps of biodiversity and ecosystem service indicators.

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 reflectance, photosynthesis, and transpiration. II - The role of biophysics in the linearity of their interdependence

NASA Technical Reports Server (NTRS)

Sellers, P. J.

1987-01-01

The ability of satellite sensor systems to estimate area-averaged canopy photosynthetic and transpirative properties is evaluated. The near linear relationship between the simple ratio (SR) and normalized difference (ND) and the surface biophysical properties of canopy photosynthetically active radiation (PAR) absorption, photosynthesis, and bulk stomatal resistance is studied. The models utilized to illustrate the processes of canopy reflectance, photosynthesis, and resistance are described. The dependence of SR, the absorbed fraction of PAR, and canopy photosynthesis and resistance on total leaf area index is analyzed. It is noted that the SR and ND vegetation indices and vegetation-dependent qualities are near-linearly related due to the proportion of leaf scattering coefficient in visible and near IR wavelength regions. The data reveal that satellite sensor systems are useful for the estimation of photosynthesis and transpirative properties.

Docosahexaenoic acid modifies the clustering and size of lipid rafts and the lateral organization and surface expression of MHC class I of EL4 cells.

PubMed

Shaikh, Saame Raza; Rockett, Benjamin Drew; Salameh, Muhammad; Carraway, Kristen

2009-09-01

An emerging molecular mechanism by which docosahexaenoic acid (DHA) exerts its effects is modification of lipid raft organization. The biophysical model, based on studies with liposomes, shows that DHA avoids lipid rafts because of steric incompatibility between DHA and cholesterol. The model predicts that DHA does not directly modify rafts; rather, it incorporates into nonrafts to modify the lateral organization and/or conformation of membrane proteins, such as the major histocompatibility complex (MHC) class I. Here, we tested predictions of the model at a cellular level by incorporating oleic acid, eicosapentaenoic acid (EPA), and DHA, compared with a bovine serum albumin (BSA) control, into the membranes of EL4 cells. Quantitative microscopy showed that DHA, but not EPA, treatment, relative to the BSA control diminished lipid raft clustering and increased their size. Approximately 30% of DHA was incorporated directly into rafts without changing the distribution of cholesterol between rafts and nonrafts. Quantification of fluorescence colocalization images showed that DHA selectively altered MHC class I lateral organization by increasing the fraction of the nonraft protein into rafts compared with BSA. Both DHA and EPA treatments increased antibody binding to MHC class I compared with BSA. Antibody titration showed that DHA and EPA did not change MHC I conformation but increased total surface levels relative to BSA. Taken together, our findings are not in agreement with the biophysical model. Therefore, we propose a model that reconciles contradictory viewpoints from biophysical and cellular studies to explain how DHA modifies lipid rafts on several length scales. Our study supports the notion that rafts are an important target of DHA's mode of action.

In vivo oxygen, temperature and pH dynamics in the female reproductive tract and their importance in human conception: a systematic review.

PubMed

Ng, Ka Ying Bonnie; Mingels, Roel; Morgan, Hywel; Macklon, Nick; Cheong, Ying

2018-01-01

Despite advances in ART, implantation and pregnancy rates per embryo transfer still remain low. IVF laboratories strive to ensure that the process of handling gametes in vitro closely mimics the in vivo environment. However, there remains a lack of knowledge regarding the in vivo regulation and dynamic variation in biophysical parameters such as oxygen concentration, pH and temperature within the reproductive tract. To undertake a systematic review of the current understanding of the physico-chemical parameters of oxygen tension (pO2), pH and temperature within the female reproductive tract, and their potential implications in clinical and pathological processes related to fertility and those pertaining to limited reproductive capacity. A comprehensive literature search was performed using electronic databases including Medline, Embase, Cochrane Library and Pubmed to identify original and review articles addressing the biophysical parameters (pO2, pH and temperature) in the female reproductive tract of any species. The search included all studies published between 1946 and November 2015. Search terms included 'oxygen', 'pH', 'hydrogen ion concentration', 'acid base' and others terms. We also used special features and truncations to identify synonyms and broaden the search. Studies were excluded if they only assessed embryo culture conditions, fetal acid-base status, oxidative stress, outcomes of pregnancy and measurements of these parameters in non-reproductive organs. Our search generated 18 685 records and 60 articles were included. pO2 within the female reproductive tract shows cyclical variation and minute-to-minute oscillations, which may be influenced by uterine contractility, hormones, the autonomic system, cardiac pulsatility, and myometrial and smooth muscle integrity. Fine balanced control of pO2 and avoidance of overwhelming oxidative stress is crucial for embryogenesis and implantation. The pH in the female reproductive tract is graduated, with lowest pH in the vagina (~pH 4.42) increasing toward the Fallopian tubes (FTs) (~pH 7.94), reflecting variation in the site-specific microbiome and acid-base buffering at the tissue/cellular level. The temperature variation in humans is cyclical by day and month. In humans, it is biphasic, increasing in the luteal phase; with the caudal region of the oviduct 1-2 degrees cooler than the cranial portion. Temperature variation is influenced by hormones, density of pelvic/uterine vascular beds and effectiveness of heat exchange locally, crucial for sperm motility and embryo development. We have identified significant deficiencies and inconsistencies in the methods used to assess these biophysical factors within the reproductive tract. We have suggested that the technological solutions including the development of methods and models for real time, in vivo recordings of biophysical parameters. The notion of 'back to nature' in assisted conception suggested 20 years ago has yet to be translated into clinical practice. While the findings from this systematic review do not provide evidence to change current in vitro protocols, it highlights our current inability to assess the in vivo reproductive tract environment in real time. Data made available through future development of sensing technology in utero may help to provide new insights into how best to optimize the in vitro embryo environment and allow for more precise and personalized fertility treatment. © The Author 2017. Published by Oxford University Press on behalf of the European Society of Human Reproduction and Embryology. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Estimating average tree crown size using spatial information from Ikonos and QuickBird images: Across-sensor and across-site comparisons

Treesearch

Conghe Song; Matthew B. Dickinson; Lihong Su; Su Zhang; Daniel Yaussey

2010-01-01

The forest canopy is the medium for energy, mass, and momentum exchanges between the forest ecosystem and the atmosphere. Tree crown size is a critical aspect of canopy structure that significantly influences these biophysical processes in the canopy. Tree crown size is also strongly related to other canopy structural parameters, such as tree height, diameter at breast...

Fitting the multitemporal curve: a fourier series approach to the missing data problem in remote sensing analysis

Treesearch

Evan Brooks; Valerie Thomas; Wynne Randolph; John Coulston

2012-01-01

With the advent of free Landsat data stretching back decades, there has been a surge of interest in utilizing remotely sensed data in multitemporal analysis for estimation of biophysical parameters. Such analysis is confounded by cloud cover and other image-specific problems, which result in missing data at various aperiodic times of the year. While there is a wealth...

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.

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.

Numerical investigation of oxygen transport by hemoglobin-based carriers through microvessels.

PubMed

Hyakutake, Toru; Kishimoto, Takumi

2017-12-01

The small size of hemoglobin-based oxygen carriers (HBOCs) may expand the realm of new treatment possibilities for various circulatory diseases. The parametric evaluation of HBOC performance for oxygen transport within tissue is essential for effectively characterizing its performance for each circulatory disease assessed. Thus, the overarching objective of this present study was to numerically investigate the reaction-diffusion phenomenon of oxygenated HBOCs and oxygen on tissues through microvessels. We considered dissociation rate coefficients, oxygen affinity, and diffusion coefficients due to Brownian motion as the biophysical parameters for estimating HBOC performance for oxygen transport. A two-dimensional computational domain, including vessel and tissue regions, was, therefore, accordingly assumed. It was observed that HBOC flows in a microvessel with a diameter of 25 μm and a length of 1 mm, and that the dissociated oxygen diffuses to the tissue region. The results indicated that oxyhemoglobin saturation and partial oxygen tension in a downstream region changed according to each biophysical parameter of HBOC. Moreover, the change in oxygen consumption rate in the tissue region had considerable influence on the oxyhemoglobin saturation level within the vessel. Comparison between simulation results and existing in vitro experimental data of actual HBOCs and RBC showed qualitatively good agreement. These results provide important information for the effective design of robust HBOCs in future.

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.

Teaching and learning the Hodgkin-Huxley model based on software developed in NEURON's programming language hoc.

PubMed

Hernández, Oscar E; Zurek, Eduardo E

2013-05-15

We present a software tool called SENB, which allows the geometric and biophysical neuronal properties in a simple computational model of a Hodgkin-Huxley (HH) axon to be changed. The aim of this work is to develop a didactic and easy-to-use computational tool in the NEURON simulation environment, which allows graphical visualization of both the passive and active conduction parameters and the geometric characteristics of a cylindrical axon with HH properties. The SENB software offers several advantages for teaching and learning electrophysiology. First, SENB offers ease and flexibility in determining the number of stimuli. Second, SENB allows immediate and simultaneous visualization, in the same window and time frame, of the evolution of the electrophysiological variables. Third, SENB calculates parameters such as time and space constants, stimuli frequency, cellular area and volume, sodium and potassium equilibrium potentials, and propagation velocity of the action potentials. Furthermore, it allows the user to see all this information immediately in the main window. Finally, with just one click SENB can save an image of the main window as evidence. The SENB software is didactic and versatile, and can be used to improve and facilitate the teaching and learning of the underlying mechanisms in the electrical activity of an axon using the biophysical properties of the squid giant axon.

Large-scale experimental technology with remote sensing in land surface hydrology and meteorology

NASA Technical Reports Server (NTRS)

Brutsaert, Wilfried; Schmugge, Thomas J.; Sellers, Piers J.; Hall, Forrest G.

1988-01-01

Two field experiments to study atmospheric and land surface processes and their interactions are summarized. The Hydrologic-Atmospheric Pilot Experiment, which tested techniques for measuring evaporation, soil moisture storage, and runoff at scales of about 100 km, was conducted over a 100 X 100 km area in France from mid-1985 to early 1987. The first International Satellite Land Surface Climatology Program field experiment was conducted in 1987 to develop and use relationships between current satellite measurements and hydrologic, climatic, and biophysical variables at the earth's surface and to validate these relationships with ground truth. This experiment also validated surface parameterization methods for simulation models that describe surface processes from the scale of vegetation leaves up to scales appropriate to satellite remote sensing.

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.

Impact of Conifer Forest Litter on Microwave Emission at L-Band

NASA Technical Reports Server (NTRS)

Kurum, Mehmet; O'Neill, Peggy E.; Lang, Roger H.; Cosh, Michael H.; Joseph, Alicia T.; Jackson, Thomas J.

2011-01-01

This study reports on the utilization of microwave modeling, together with ground truth, and L-band (1.4-GHz) brightness temperatures to investigate the passive microwave characteristics of a conifer forest floor. The microwave data were acquired over a natural Virginia Pine forest in Maryland by a ground-based microwave active/passive instrument system in 2008/2009. Ground measurements of the tree biophysical parameters and forest floor characteristics were obtained during the field campaign. The test site consisted of medium-sized evergreen conifers with an average height of 12 m and average diameters at breast height of 12.6 cm. The site is a typical pine forest site in that there is a surface layer of loose debris/needles and an organic transition layer above the mineral soil. In an effort to characterize and model the impact of the surface litter layer, an experiment was conducted on a day with wet soil conditions, which involved removal of the surface litter layer from one half of the test site while keeping the other half undisturbed. The observations showed detectable decrease in emissivity for both polarizations after the surface litter layer was removed. A first-order radiative transfer model of the forest stands including the multilayer nature of the forest floor in conjunction with the ground truth data are used to compute forest emission. The model calculations reproduced the major features of the experimental data over the entire duration, which included the effects of surface litter and ground moisture content on overall emission. Both theory and experimental results confirm that the litter layer increases the observed canopy brightness temperature and obscure the soil emission.

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.

Estimation of evapotranspiration for different land covers in a Brazilian semi-arid region: A case study of the Brígida River basin, Brazil

NASA Astrophysics Data System (ADS)

Santos, Celso Augusto Guimarães; Silva, Richarde Marques da; Silva, Alexandro Medeiros; Brasil Neto, Reginaldo Moura

2017-03-01

In this study, the Surface Energy Balance Algorithm for Land (SEBAL) was used to compute the surface albedo, vegetation indices (NDVI, SAVI and LAI), surface temperature, soil heat flux and evapotranspiration (ET) over two contrasting years (dry and wet) in the Brígida River basin, a semi-arid region of north-eastern Brazil. The actual ET was computed during satellite overpass and was integrated for 24 h on a pixel-by-pixel basis for the daily ET distribution. Due to the topographic effects, an attempt was also made to incorporate DEM information to estimate the net radiation. The land cover types identified in the watershed are cropland, bare land, dense canopy, grassland, and caatinga vegetation. In order to study the variation among the biophysical parameters and ET, two-way analysis of variance (ANOVA) was used. The ET calculated by SEBAL ranged between 2.46 and 6.87 mm/day for the dry year (1990) and 1.31 and 6.84 mm/day for the wet year (2009) for the river basin. The results showed that a reduction in vegetation cover is evident in the temporal and spatial analysis over the studied periods in the region and that these facts influence the values of the energy balance and ET. The results showed significant differences in the variables of land cover type and year at the probability level of 0.05 for all land cover types.

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 the exchange of biological, chemical and other physical quantities between interacting environmental interfaces can be represented by coupled maps. In this chapter we will address only two illustrative issues important for the modelling of interacting environmental interfaces regarded as complex systems. These are (i) use of algebra for modelling the autonomous establishment of local hierarchies in biophysical systems and (ii) numerical investigation of coupled maps representing exchange of energy, chemical and other relevant biophysical quantities between biophysical entities in their surrounding environment.

[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.

Atomic Force Microscopy Studies of Functional and Dysfunctional Pulmonary Surfactant Films. I. Micro- and Nanostructures of Functional Pulmonary Surfactant Films and the Effect of SP-A

PubMed Central

Zuo, Yi Y.; Keating, Eleonora; Zhao, Lin; Tadayyon, Seyed M.; Veldhuizen, Ruud A. W.; Petersen, Nils O.; Possmayer, Fred

2008-01-01

Monolayers of a functional pulmonary surfactant (PS) can reach very low surface tensions well below their equilibrium value. The mechanism by which PS monolayers reach such low surface tensions and maintain film stability remains unknown. As shown previously by fluorescence microscopy, phospholipid phase transition and separation seem to be important for the normal biophysical properties of PS. This work studied phospholipid phase transitions and separations in monolayers of bovine lipid extract surfactant using atomic force microscopy. Atomic force microscopy showed phospholipid phase separation on film compression and a monolayer-to-multilayer transition at surface pressure 40–50 mN/m. The tilted-condensed phase consisted of domains not only on the micrometer scale, as detected previously by fluorescence microscopy, but also on the nanometer scale, which is below the resolution limits of conventional optical methods. The nanodomains were embedded uniformly within the liquid-expanded phase. On compression, the microdomains broke up into nanodomains, thereby appearing to contribute to tilted-condensed and liquid-expanded phase remixing. Addition of surfactant protein A altered primarily the nanodomains and promoted the formation of multilayers. We conclude that the nanodomains play a predominant role in affecting the biophysical properties of PS monolayers and the monolayer-to-multilayer transition. PMID:18212010

Biophysical characterization and surface radiation balance

NASA Technical Reports Server (NTRS)

Walter-Shea, Elizabeth A.; Blad, Blaine L.; Mesarch, Mark A.; Hays, Cynthia J.; Starks, Patrick J.

1993-01-01

The Kursk 1991 Experiment (KUREX-91) was conducted as one of a suite of international studies to develop capabilities to monitor global change. The studies were designed specifically to understand the earth's land-surface vegetation and atmospheric boundary layer interaction. An intensive field campaign was conducted at a site near Kursk, Russia during the month of July in 1991 by a team of international scientists to aid in the understanding of land-surface-atmosphere interactions in an agricultural/grassland setting. We were one of several teams of scientists participating at KUREX-91 at the Streletskaya Steppe Researve near Kursk, Russia. The main goals of our research were to: (1) characterize biophysical properties of the prairie vegetation; and (2) to characterize radiation regime through measurements and from estimates derived from canopy bidirectional reflectance data. Four objectives were defined to achieve these goals: (1) determine dependence of leaf optical properties on leaf water potential of some dominant species in discrete wavebands in the visible, near-infrared, and mid-infrared (spanning 0.4-2.3 microns range); (2) characterize the effective leaf area index (LAI) and leaf angle distribution of prairie vegetation; (3) characterize the radiation regime of the prairie vegetation through measures of the radiation balance components; and (4) examine, develop, and test methods for estimating albedo, APAR, and LAI from canopy bidirectional reflectance data. Papers which were the result of the research efforts are included.

Note: Model identification and analysis of bivalent analyte surface plasmon resonance data.

PubMed

Tiwari, Purushottam Babu; Üren, Aykut; He, Jin; Darici, Yesim; Wang, Xuewen

2015-10-01

Surface plasmon resonance (SPR) is a widely used, affinity based, label-free biophysical technique to investigate biomolecular interactions. The extraction of rate constants requires accurate identification of the particular binding model. The bivalent analyte model involves coupled non-linear differential equations. No clear procedure to identify the bivalent analyte mechanism has been established. In this report, we propose a unique signature for the bivalent analyte model. This signature can be used to distinguish the bivalent analyte model from other biphasic models. The proposed method is demonstrated using experimentally measured SPR sensorgrams.

Book Review

NASA Astrophysics Data System (ADS)

Clevers, Jan G. P. W.

2018-05-01

This book provides a comprehensive and timely overview on all aspects of hyperspectral remote sensing combined with various applications. As such, it is an excellent book of reference for both students and professionals active in the field of optical remote sensing. It deals with all aspects of retrieving quantitative information on biophysical properties of the Earth's surface, the data corrections needed and the range of analysis approaches available.

2011 Dynamics at Surfaces Gordon Research Conference (August 7-12, 2011, Salve Regina University, Newport, Rhode Island)

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

Greg Sitz

2011-08-12

The 2011 Gordon Conference on Dynamics at Surfaces is the 32nd anniversary of a meeting held every two years that is attended by leading researchers in the area of experimental and theoretical dynamics at liquid and solid surfaces. The conference focuses on the dynamics of the interaction of molecules with either liquid or solid surfaces, the dynamics of the outermost layer of liquid and solid surfaces and the dynamics at the liquid-solid interface. Specific topics that are featured include state-to-state scattering dynamics, chemical reaction dynamics, non-adiabatic effects in reactive and inelastic scattering of molecules from surfaces, single molecule dynamics atmore » surfaces, surface photochemistry, ultrafast dynamics at surfaces, and dynamics at water interfaces. The conference brings together investigators from a variety of scientific disciplines including chemistry, physics, materials science, geology, biophysics, and astronomy.« less

In silico fragment-based drug design.

PubMed

Konteatis, Zenon D

2010-11-01

In silico fragment-based drug design (FBDD) is a relatively new approach inspired by the success of the biophysical fragment-based drug discovery field. Here, we review the progress made by this approach in the last decade and showcase how it complements and expands the capabilities of biophysical FBDD and structure-based drug design to generate diverse, efficient drug candidates. Advancements in several areas of research that have enabled the development of in silico FBDD and some applications in drug discovery projects are reviewed. The reader is introduced to various computational methods that are used for in silico FBDD, the fragment library composition for this technique, special applications used to identify binding sites on the surface of proteins and how to assess the druggability of these sites. In addition, the reader will gain insight into the proper application of this approach from examples of successful programs. In silico FBDD captures a much larger chemical space than high-throughput screening and biophysical FBDD increasing the probability of developing more diverse, patentable and efficient molecules that can become oral drugs. The application of in silico FBDD holds great promise for historically challenging targets such as protein-protein interactions. Future advances in force fields, scoring functions and automated methods for determining synthetic accessibility will all aid in delivering more successes with in silico FBDD.

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.

Modeling Endoplasmic Reticulum Network Maintenance in a Plant Cell.

PubMed

Lin, Congping; White, Rhiannon R; Sparkes, Imogen; Ashwin, Peter

2017-07-11

The endoplasmic reticulum (ER) in plant cells forms a highly dynamic network of complex geometry. ER network morphology and dynamics are influenced by a number of biophysical processes, including filament/tubule tension, viscous forces, Brownian diffusion, and interactions with many other organelles and cytoskeletal elements. Previous studies have indicated that ER networks can be thought of as constrained minimal-length networks acted on by a variety of forces that perturb and/or remodel the network. Here, we study two specific biophysical processes involved in remodeling. One is the dynamic relaxation process involving a combination of tubule tension and viscous forces. The other is the rapid creation of cross-connection tubules by direct or indirect interactions with cytoskeletal elements. These processes are able to remodel the ER network: the first reduces network length and complexity whereas the second increases both. Using live cell imaging of ER network dynamics in tobacco leaf epidermal cells, we examine these processes on ER network dynamics. Away from regions of cytoplasmic streaming, we suggest that the dynamic network structure is a balance between the two processes, and we build an integrative model of the two processes for network remodeling. This model produces quantitatively similar ER networks to those observed in experiments. We use the model to explore the effect of parameter variation on statistical properties of the ER network. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Relationships between gastric slow wave frequency, velocity, and extracellular amplitude studied by a joint experimental-theoretical approach.

PubMed

Wang, T H-H; Du, P; Angeli, T R; Paskaranandavadivel, N; Erickson, J C; Abell, T L; Cheng, L K; O'Grady, G

2018-01-01

Gastric slow wave dysrhythmias are accompanied by deviations in frequency, velocity, and extracellular amplitude, but the inherent association between these parameters in normal activity still requires clarification. This study quantified these associations using a joint experimental-theoretical approach. Gastric pacing was conducted in pigs with simultaneous high-resolution slow wave mapping (32-256 electrodes; 4-7.6 mm spacing). Relationships between period, velocity, and amplitude were quantified and correlated for each wavefront. Human data from two existing mapping control cohorts were analyzed to extract and correlate these same parameters. A validated biophysically based ICC model was also applied in silico to quantify velocity-period relationships during entrainment simulations and velocity-amplitude relationships from membrane potential equations. Porcine pacing studies identified positive correlations for velocity-period (0.13 mm s -1 per 1 s, r 2 =.63, P<.001) and amplitude-velocity (74 μV per 1 mm s -1 , r 2 =.21, P=.002). In humans, positive correlations were also quantified for velocity-period (corpus: 0.11 mm s -1 per 1 s, r 2 =.16, P<.001; antrum: 0.23 mm s -1 per 1 s, r 2 =.55; P<.001), and amplitude-velocity (94 μV per 1 mm s -1 , r 2 =.56; P<.001). Entrainment simulations matched the experimental velocity-period relationships and demonstrated dependence on the slow wave recovery phase. Simulated membrane potential relationships were close to these experimental results (100 μV per 1 mm s -1 ). These data quantify the relationships between slow wave frequency, velocity, and extracellular amplitude. The results from both human and porcine studies were in keeping with biophysical models, demonstrating concordance with ICC biophysics. These relationships are important in the regulation of gastric motility and will help to guide interpretations of dysrhythmias. © 2017 John Wiley & Sons Ltd.

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 combined SSA, wherein climate change-induced productivity shocks are permitted to interact with the uncertain economic parameters. This permits us to examine potential interactions between the two sources of uncertainty.

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.

Spaceborne SAR Data for Aboveground-Biomass Retrieval of Indian Tropical Forests

NASA Astrophysics Data System (ADS)

Khati, U.; Singh, G.; Musthafa, M.

2017-12-01

Forests are important and indispensable part of the terrestrial ecosystems, and have a direct impact on the global carbon cycle. Forest biophysical parameters such as forest stand height and forest above-ground biomass (AGB) are forest health indicators. Measuring the forest biomass using traditional ground survey techniques are man-power consuming and have very low spatial coverage. Satellite based remote sensing techniques provide synoptic view of the earth with continuous measurements over large, inaccessible forest regions. Satellite Synthetic Aperture Radar (SAR) data has been shown to be sensitive to these forest bio-physical parameters and have been extensively utilized over boreal and tropical forests. However, there are limited studies over Indian tropical forests due to lack of auxiliary airborne data and difficulties in manual in situ data collection. In this research work we utilize spaceborne data from TerraSAR-X/TanDEM-X and ALOS-2/PALSAR-2 and implement both Polarimetric SAR and PolInSAR techniques for retrieval of AGB of a managed tropical forest in India. The TerraSAR-X/TanDEM-X provide a single-baseline PolInSAR data robust to temporal decorrelation. This would be used to accurately estimate the forest stand height. The retrieved height would be an input parameter for modelling AGB using the L-band ALOS-2/PALSAR-2 data. The IWCM model is extensively utilized to estimate AGB from SAR observations. In this research we utilize the six component scattering power decomposition (6SD) parameters and modify the IWCM based technique for a better retrieval of forest AGB. PolInSAR data shows a high estimation accuracy with r2 of 0.8 and a RMSE of 2 m. With this accurate height provided as input to the modified model along with 6SD parameters shows promising results. The results are validated with extensive field based measurements, and are further analysed in detail.

Alternating Current Delivered into the Scala Media Alters Sound Pressure at the Eardrum

NASA Astrophysics Data System (ADS)

Hubbard, Allyn E.; Mountain, David C.

1983-11-01

Alternating current delivered into the scala media of the gerbil cochlea modulates the amplitude of a test tone measured near the eardrum. Variations in the electromechanical effect with acoustic stimulus parameters and observed physiological vulnerability suggest that cochlear hair cells are the biophysical origin of the process. Cochlear hair cells have traditionally been thought of as passive receptor cells, but they may play an active role in cochlear micromechanics.

[Biocybernetic approach to the thermometric methods of blood supply measurements of periodontal tissues].

PubMed

Pastusiak, J; Zakrzewski, J

1988-11-01

Specific biocybernetic approach to the problem of the blood supply determination of paradontium tissues by means of thermometric methods has been presented in the paper. The compartment models of the measuring procedure have been given. Dilutodynamic methology and classification has been applied. Such an approach enables to select appropriate biophysical parameters describing the state of blood supply of paradontium tissues and optimal design of transducers and measuring methods.

Marine biosurfaces research program

NASA Astrophysics Data System (ADS)

The Office of Naval Research (ONR) of the U.S. Navy is starting a basic research program to address the initial events that control colonization of surfaces by organisms in marine environments. The program “arises from the Navy's need to understand and ultimately control biofouling and biocorrosion in marine environments,” according to a Navy announcement.The program, “Biological Processes Controlling Surface Modification in the Marine Environment,” will emphasize the application of in situ techniques and modern molecular biological, biochemical, and biophysical approaches; it will also encourage the development of interdisciplinary projects. Specific areas of interest include sensing and response to environmental surface (physiology/physical chemistry), factors controlling movement to and retention at surfaces (behavior/hydrodynamics), genetic regulation of attachment (molecular genetics), and mechanisms of attachment (biochemistry/surface chemistry).

Structure and membrane interactions of the homodimeric antibiotic peptide homotarsinin

NASA Astrophysics Data System (ADS)

Verly, Rodrigo M.; Resende, Jarbas M.; Junior, Eduardo F. C.; de Magalhães, Mariana T. Q.; Guimarães, Carlos F. C. R.; Munhoz, Victor H. O.; Bemquerer, Marcelo Porto; Almeida, Fábio C. L.; Santoro, Marcelo M.; Piló-Veloso, Dorila; Bechinger, Burkhard

2017-01-01

Antimicrobial peptides (AMPs) from amphibian skin are valuable template structures to find new treatments against bacterial infections. This work describes for the first time the structure and membrane interactions of a homodimeric AMP. Homotarsinin, which was found in Phyllomedusa tarsius anurans, consists of two identical cystine-linked polypeptide chains each of 24 amino acid residues. The high-resolution structures of the monomeric and dimeric peptides were determined in aqueous buffers. The dimer exhibits a tightly packed coiled coil three-dimensional structure, keeping the hydrophobic residues screened from the aqueous environment. An overall cationic surface of the dimer assures enhanced interactions with negatively charged membranes. An extensive set of biophysical data allowed us to establish structure-function correlations with antimicrobial assays against Gram-positive and Gram-negative bacteria. Although both peptides present considerable antimicrobial activity, the dimer is significantly more effective in both antibacterial and membrane biophysical assays.

Structure and membrane interactions of the homodimeric antibiotic peptide homotarsinin

PubMed Central

Verly, Rodrigo M.; Resende, Jarbas M.; Junior, Eduardo F. C.; de Magalhães, Mariana T. Q.; Guimarães, Carlos F. C. R.; Munhoz, Victor H. O.; Bemquerer, Marcelo Porto; Almeida, Fábio C. L.; Santoro, Marcelo M.; Piló-Veloso, Dorila; Bechinger, Burkhard

2017-01-01

Antimicrobial peptides (AMPs) from amphibian skin are valuable template structures to find new treatments against bacterial infections. This work describes for the first time the structure and membrane interactions of a homodimeric AMP. Homotarsinin, which was found in Phyllomedusa tarsius anurans, consists of two identical cystine-linked polypeptide chains each of 24 amino acid residues. The high-resolution structures of the monomeric and dimeric peptides were determined in aqueous buffers. The dimer exhibits a tightly packed coiled coil three-dimensional structure, keeping the hydrophobic residues screened from the aqueous environment. An overall cationic surface of the dimer assures enhanced interactions with negatively charged membranes. An extensive set of biophysical data allowed us to establish structure-function correlations with antimicrobial assays against Gram-positive and Gram-negative bacteria. Although both peptides present considerable antimicrobial activity, the dimer is significantly more effective in both antibacterial and membrane biophysical assays. PMID:28102305

Structure and membrane interactions of the homodimeric antibiotic peptide homotarsinin.

PubMed

Verly, Rodrigo M; Resende, Jarbas M; Junior, Eduardo F C; de Magalhães, Mariana T Q; Guimarães, Carlos F C R; Munhoz, Victor H O; Bemquerer, Marcelo Porto; Almeida, Fábio C L; Santoro, Marcelo M; Piló-Veloso, Dorila; Bechinger, Burkhard

2017-01-19

Antimicrobial peptides (AMPs) from amphibian skin are valuable template structures to find new treatments against bacterial infections. This work describes for the first time the structure and membrane interactions of a homodimeric AMP. Homotarsinin, which was found in Phyllomedusa tarsius anurans, consists of two identical cystine-linked polypeptide chains each of 24 amino acid residues. The high-resolution structures of the monomeric and dimeric peptides were determined in aqueous buffers. The dimer exhibits a tightly packed coiled coil three-dimensional structure, keeping the hydrophobic residues screened from the aqueous environment. An overall cationic surface of the dimer assures enhanced interactions with negatively charged membranes. An extensive set of biophysical data allowed us to establish structure-function correlations with antimicrobial assays against Gram-positive and Gram-negative bacteria. Although both peptides present considerable antimicrobial activity, the dimer is significantly more effective in both antibacterial and membrane biophysical assays.

Synergistic Inhibition of Protein Fibrillation by Proline and Sorbitol: Biophysical Investigations

PubMed Central

Choudhary, Sinjan; Save, Shreyada N.; Kishore, Nand; Hosur, Ramakrishna V.

2016-01-01

We report here interesting synergistic effects of proline and sorbitol, two well-known chemical chaperones, in the inhibition of fibrillation of two proteins, insulin and lysozyme. A combination of many biophysical techniques has been used to understand the structural morphology and modes of interaction of the chaperones with the proteins during fibrillation. Both the chaperones establish stronger polar interactions in the elongation and saturation stages of fibrillation compared to that in the native stage. However, when presented as a mixture, we also see contribution of hydrophobic interactions. Thus, a co-operative adjustment of polar and hydrophobic interactions between the chaperones and the protein surface seems to drive the synergistic effects in the fibrillation process. In insulin, this synergy is quantitatively similar in all the stages of the fibrillation process. These observations would have significant implications for understanding protein folding concepts, in general, and for designing combination therapies against protein fibrillation, in particular. PMID:27870861

Synergistic Inhibition of Protein Fibrillation by Proline and Sorbitol: Biophysical Investigations.

PubMed

Choudhary, Sinjan; Save, Shreyada N; Kishore, Nand; Hosur, Ramakrishna V

2016-01-01

We report here interesting synergistic effects of proline and sorbitol, two well-known chemical chaperones, in the inhibition of fibrillation of two proteins, insulin and lysozyme. A combination of many biophysical techniques has been used to understand the structural morphology and modes of interaction of the chaperones with the proteins during fibrillation. Both the chaperones establish stronger polar interactions in the elongation and saturation stages of fibrillation compared to that in the native stage. However, when presented as a mixture, we also see contribution of hydrophobic interactions. Thus, a co-operative adjustment of polar and hydrophobic interactions between the chaperones and the protein surface seems to drive the synergistic effects in the fibrillation process. In insulin, this synergy is quantitatively similar in all the stages of the fibrillation process. These observations would have significant implications for understanding protein folding concepts, in general, and for designing combination therapies against protein fibrillation, in particular.

Towards in vivo focal cortical dysplasia phenotyping using quantitative MRI.

PubMed

Adler, Sophie; Lorio, Sara; Jacques, Thomas S; Benova, Barbora; Gunny, Roxana; Cross, J Helen; Baldeweg, Torsten; Carmichael, David W

2017-01-01

Focal cortical dysplasias (FCDs) are a range of malformations of cortical development each with specific histopathological features. Conventional radiological assessment of standard structural MRI is useful for the localization of lesions but is unable to accurately predict the histopathological features. Quantitative MRI offers the possibility to probe tissue biophysical properties in vivo and may bridge the gap between radiological assessment and ex-vivo histology. This review will cover histological, genetic and radiological features of FCD following the ILAE classification and will explain how quantitative voxel- and surface-based techniques can characterise these features. We will provide an overview of the quantitative MRI measures available, their link with biophysical properties and finally the potential application of quantitative MRI to the problem of FCD subtyping. Future research linking quantitative MRI to FCD histological properties should improve clinical protocols, allow better characterisation of lesions in vivo and tailored surgical planning to the individual.

Interaction of celecoxib with membranes: the role of membrane biophysics on its therapeutic and toxic effects.

PubMed

Pereira-Leite, Catarina; Nunes, Cláudia; Lima, José L F C; Reis, Salette; Lúcio, Marlene

2012-11-26

The present work provides a biophysical characterization of the interaction of celecoxib, a cyclo-oxigenase-2 selective nonsteroidal anti-inflammatory drug, with membranes using liposomes, constituted by phosphatidylcholines, as membrane model systems. In order to mimic biological conditions, the experiments were performed at physiological pH (7.4); at an acidic pH to mimic the conditions of the inflamed cells (5.0); and at different membrane physical states (gel, ripple, and fluid phase). Important information regarding the celecoxib-membrane interactions was gathered by the complementary biophysical techniques: derivative spectrophotometry was used to determine liposome/water partition coefficient of celecoxib; dynamic light scattering (DLS) measurements were performed to study the influence of celecoxib on lipid main phase transition temperature; fluorescence binding measurements were made to assess the location of celecoxib within the membrane; and small-angle and wide-angle X-ray scattering (SAXS and WAXS) were used to assess the changes in the structure and order of phosphatidylcholine bilayers caused by the presence of celecoxib. The overall results obtained indicate that celecoxib greatly interacts with membranes. Briefly, celecoxib exhibits a high liposome/water partition coefficient that is non-pH-dependent, but the location of celecoxib within the membrane is pH-dependent. In fact, celecoxib is more deeply located inside the membrane at pH 5.0, while it locates closer to the surface at pH 7.4. DLS, SAXS, and WAXS results have shown a high membrane fluidization in the presence of celecoxib, especially at pH 7.4. Overall, the current study can contribute to a biophysical characterization of the celecoxib-membrane interaction. The relevance of the gathered results will be discussed in terms of the reported celecoxib therapeutic and toxic effects.

A tool to evaluate local biophysical effects on temperature due to land cover change transitions

NASA Astrophysics Data System (ADS)

Perugini, Lucia; Caporaso, Luca; Duveiller, Gregory; Cescatti, Alessandro; Abad-Viñas, Raul; Grassi, Giacomo; Quesada, Benjamin

2017-04-01

Land Cover Changes (LCC) affect local, regional and global climate through biophysical variations of the surface energy budget mediated by albedo, evapotranspiration, and roughness. Assessment of the full climate impacts of anthropogenic LCC are incomplete without considering biophysical effects, but the high level of uncertainties in quantifying their impacts to date have made it impractical to offer clear advice on which policy makers could act. To overcome this barrier, we provide a tool to evaluate the biophysical impact of a matrix of land cover transitions, following a tiered methodological approach similar to the one provided by the IPCC to estimate the biogeochemical effects, i.e. through three levels of methodological complexity, from Tier 1 (i.e. default method and factors) to Tier 3 (i.e. specific methods and factors). In particular, the tool provides guidance for quantitative assessment of changes in temperature following a land cover transition. The tool focuses on temperature for two main reasons (i) it is the main variable of interest for policy makers at local and regional level, and (ii) temperature is able to summarize the impact of radiative and non-radiative processes following LULCC. The potential changes in annual air temperature that can be expected from various land cover transitions are derived from a dedicated dataset constructed by the JRC in the framework of the LUC4C FP7 project. The inputs for the dataset are air temperature values derived from satellite Earth Observation data (MODIS) and land cover characterization from the ESA Climate Change Initiative product reclassified into their IPCC land use category equivalent. This data, originally at 0.05 degree of spatial resolution, is aggregated and analysed at regional level to provide guidance on the expected temperature impact following specific LCC transitions.

Estimation of Some Bio-Physical Indicators for Sustainable Crop Production in the Eastern Nile Basin of Sudan Using Landsat-8 Imagery and SEBAL Model

NASA Astrophysics Data System (ADS)

Guma Biro Turk, Khalid

2016-07-01

Crop production under modern irrigation systems require unique management at field level and hence better utilization of agricultural inputs and water resources. This study aims to make use of remote sensing (RS) data and the surface energy balance algorithm for land (SEBAL) to improve the on-farm management. The study area is located in the Eastern part of the Blue Nile River about 60 km south of Khartoum, Sudan. Landsat-8 data were used to estimate a number of bio-physical indicators during the growing season of the year 2014/2015. Accordingly, in-situ weather data and SEBAL model were applied to calculate: the reference (ET0), actual (ETa) and potential (ETp) evapotranspiration, soil moisture (SM), crop factor (kc), nitrogen (N), biomass production (BP) and crop water productivity (CWP). Results revealed that ET0 showed steady variation throughout the year, varying from 5 to 7 mm/day. However, ETa and ETp showed clear temporal variation attributed to frequent cutting of the alfalfa, almost monthly. The BP of the alfalfa was observed to be high when there is no cutting activates were made before the image acquisition date. Nevertheless the CWP trends are following the biomass production ones, low when there is no biomass and high when the biomass is high. The application of SEBAL model within the study area using the Landsat-8 imagery indicates that it's possible to produce field-based bio-physical indicators, which can be useful in monitoring and managing the field during the growing season. However, a cross-calibration with the in-situ data should be considered in order to maintain the spatial variability within the field. Keywords: Bio-physical Indicators; Remote Sensing; SEBAL; Landsat-8; Eastern Nile Basin

Laser-based nanoengineering of surface topographies for biomedical applications

NASA Astrophysics Data System (ADS)

Schlie, Sabrina; Fadeeva, Elena; Koroleva, Anastasia; Ovsianikov, Aleksandr; Koch, Jürgen; Ngezahayo, Anaclet; Chichkov, Boris. N.

2011-04-01

In this study femtosecond laser systems were used for nanoengineering of special surface topographies in silicon and titanium. Besides the control of feature sizes, we demonstrated that laser structuring caused changes in material wettability due to a reduced surface contact area. These laser-engineered topographies were tested for their capability to control cellular behavior of human fibroblasts, SH-SY5Y neuroblastoma cells, and MG-63 osteoblasts. We found that fibroblasts reduced cell growth on the structures, while the other cell types proliferated at the same rate. These findings make laser-surface structuring very attractive for biomedical applications. Finally, to explain the results the correlation between topography and the biophysics of cellular adhesion, which is the key step of selective cell control, is discussed.

Computational modeling of the human auditory periphery: Auditory-nerve responses, evoked potentials and hearing loss.

PubMed

Verhulst, Sarah; Altoè, Alessandro; Vasilkov, Viacheslav

2018-03-01

Models of the human auditory periphery range from very basic functional descriptions of auditory filtering to detailed computational models of cochlear mechanics, inner-hair cell (IHC), auditory-nerve (AN) and brainstem signal processing. It is challenging to include detailed physiological descriptions of cellular components into human auditory models because single-cell data stems from invasive animal recordings while human reference data only exists in the form of population responses (e.g., otoacoustic emissions, auditory evoked potentials). To embed physiological models within a comprehensive human auditory periphery framework, it is important to capitalize on the success of basic functional models of hearing and render their descriptions more biophysical where possible. At the same time, comprehensive models should capture a variety of key auditory features, rather than fitting their parameters to a single reference dataset. In this study, we review and improve existing models of the IHC-AN complex by updating their equations and expressing their fitting parameters into biophysical quantities. The quality of the model framework for human auditory processing is evaluated using recorded auditory brainstem response (ABR) and envelope-following response (EFR) reference data from normal and hearing-impaired listeners. We present a model with 12 fitting parameters from the cochlea to the brainstem that can be rendered hearing impaired to simulate how cochlear gain loss and synaptopathy affect human population responses. The model description forms a compromise between capturing well-described single-unit IHC and AN properties and human population response features. Copyright © 2018 The Authors. Published by Elsevier B.V. All rights reserved.

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…

[Physiological basis of a possible increase in the efficacy of the photo- and magnetotherapy of the visual nerve upon partial atrophy and ischemia].

PubMed

Shlygin, V V; Tiuliaev, A P; Ioĭleva, E E; Maksimov, G V

2004-01-01

An approach to the choice of the parameters of physiotherapeutic and biophysical influence on the visual nerve was proposed. The approach is based on parallel photo- and magnetostimulation of excitable fibers in which the morphological and electrophysiological properties of fibers and some parameters of the pathological processes associated with partial artophy and ischemia are taken into account. A method for correlating the photostimulation by light flashes (intensity 65 mWt at emission wavelength 660 nm) of a portion of the retina with the choice of the parameters of magnetic influence (amplitude 73 mT, duration of the wave front of 40 ms, and frequency of pulse sequence of about 1 Hz) on the visual nerve was developed.

Evanescent field microscopy techniques for studying dynamics at the surface of living cells

NASA Astrophysics Data System (ADS)

Sund, Susan E.

This thesis presents two distinct optical microscopy techniques for applications in cell biophysics: (a)the extension to living cells of an established technique, total internal reflection/fluorescence recovery after photobleaching (TIR/FRAP) for the first time in imaging mode; and (b)the novel development of polarized total internal reflection fluorescence (p- TIRF) to study membrane orientation in living cells. Although reversible chemistry is crucial to dynamical processes in living cells, relatively little is known about the relevant chemical kinetic rates in vivo. TIR/FRAP, an established technique which can measure reversible biomolecular kinetic rates at surfaces, is extended here to measure kinetic parameters of microinjected rhodamine actin at the cytofacial surface of the plasma membrane of living cultured smooth muscle cells. For the first time, spatial imaging (with a CCD camera) is used in conjunction with TIR/FRAP. TIR/FRAP imaging allows production of spatially resolved images of kinetic data, and calculation of correlation distances, cell-wide gradients, and kinetic parameter dependence on initial fluorescence intensity. In living cells, membrane curvature occurs both in easily imaged large scale morphological features, and also in less visualizable submicroscopic regions of activity such as endocytosis, exocytosis, and cell surface ruffling. A fluorescence microscopic method, p-TIRF, is introduced here to visualize such regions. The method is based on fluorescence of the oriented membrane probe diI- C18-(3) (diI) excited by evanescent field light polarized either perpendicular or parallel to the plane of the substrate coverslip. The excitation efficiency from each polarization depends on the membrane orientation, and thus the ratio of the observed fluorescence excited by these two polarizations vividly shows regions of microscopic and submicroscopic curvature of the membrane. A theoretical background of the technique and experimental verifications are presented in samples of protein solutions, model lipid bilayers, and living cells. Sequential digital images of the polarized TIR fluorescence ratios show spatially-resolved time- course maps of membrane orientations on diI labeled macrophages from which low visibility membrane structures can be identified and quantified. The TIR images are sharpened and contrast-enhanced by deconvoluting them with an experimentally-measured point spread function.

An isoline separating relatively warm from relatively cool wintertime forest surface temperatures for the southeastern United States

Treesearch

J. Wickham; T.G. Wade; K.H. Riitters

2014-01-01

Forest-oriented climate mitigation policies promote forestation as a means to increase uptake of atmospheric carbon to counteract global warming. Some have pointed out that a carbon-centric forest policy may be overstated because it discounts biophysical aspects of the influence of forests on climate. In extra-tropical regions, many climate models have shown that...

Empirical analysis of the influence of forest extent on annual and seasonal surface temperatures for the Continental United States

Treesearch

James D. Wickham; Timothy G. Wade; Kurt H. Riitters

2013-01-01

Aim Because of the low albedo of forests and other biophysical factors, most scenario-based climate modelling studies indicate that removal of temperate forest will promote cooling, indicating that temperate forests are a source of heat relative to other classes of land cover. Our objective was to test the hypothesis that US temperate forests reduce...

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 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

In vivo measurement of age-related stiffening in the crystalline lens by Brillouin optical microscopy.

PubMed

Scarcelli, Giuliano; Kim, Pilhan; Yun, Seok Hyun

2011-09-21

The biophysical and biomechanical properties of the crystalline lens (e.g., viscoelasticity) have long been implicated in accommodation and vision problems, such as presbyopia and cataracts. However, it has been difficult to measure such parameters noninvasively. Here, we used in vivo Brillouin optical microscopy to characterize material acoustic properties at GHz frequency and measure the longitudinal elastic moduli of lenses. We obtained three-dimensional elasticity maps of the lenses in live mice, which showed biomechanical heterogeneity in the cortex and nucleus of the lens with high spatial resolution. An in vivo longitudinal study of mice over a period of 2 months revealed a marked age-related stiffening of the lens nucleus. We found remarkably good correlation (log-log linear) between the Brillouin elastic modulus and the Young's modulus measured by conventional mechanical techniques at low frequencies (~1 Hz). Our results suggest that Brillouin microscopy is potentially useful for basic and animal research and clinical ophthalmology. Copyright © 2011 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Morphogengineering roots: comparing mechanisms of morphogen gradient formation

PubMed Central

2012-01-01

Background In developmental biology, there has been a recent focus on the robustness of morphogen gradients as possible providers of positional information. It was shown that functional morphogen gradients present strong biophysical constraints and lack of robustness to noise. Here we explore how the details of the mechanism which underlies the generation of a morphogen gradient can influence those properties. Results We contrast three gradient-generating mechanisms, (i) a source-decay mechanism; and (ii) a unidirectional transport mechanism; and (iii) a so-called reflux-loop mechanism. Focusing on the dynamics of the phytohormone auxin in the root, we show that only the reflux-loop mechanism can generate a gradient that would be adequate to supply functional positional information for the Arabidopsis root, for biophysically reasonable kinetic parameters. Conclusions We argue that traits that differ in spatial and temporal time-scales can impose complex selective pressures on the mechanism of morphogen gradient formation used for the development of the particular organism. PMID:22583698

Predicting stability of alpha-helical, orthogonal-bundle proteins on surfaces

NASA Astrophysics Data System (ADS)

Wei, Shuai; Knotts, Thomas A.

2010-09-01

The interaction of proteins with surfaces is a key phenomenon in many applications, but current understanding of the biophysics involved is lacking. At present, rational design of such emerging technologies is difficult as no methods or theories exist that correctly predict how surfaces influence protein behavior. Using molecular simulation and a coarse-grain model, this study illustrates for the first time that stability of proteins on surfaces can be correlated with tertiary structural elements for alpha-helical, orthogonal-bundle proteins. Results show that several factors contribute to stability on surfaces including the nature of the loop region where the tether is placed and the ability of the protein to freely rotate on the surface. A thermodynamic analysis demonstrates that surfaces stabilize proteins entropically and that any destabilization is an enthalpic effect. Moreover, the entropic effects are concentrated on the unfolded state of the protein while the ethalpic effects are focused on the folded state.

A multi criteria analog model for assessing the vulnerability of rural catchments to road spills of hazardous substances

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

Siqueira, Hygor Evangelista; Pissarra, Teresa Cristina Tarlé; Farias do Valle Junior, Renato

Road spills of hazardous substances are common in developing countries due to increasing industrialization and traffic accidents, and represent a serious threat to soils and water in catchments. There is abundant literature on equations describing the wash-off of pollutants from roads during a storm event and there are a number of watershed models incorporating those equations in storm water quality algorithms that route runoff and pollution yields through a drainage system towards the catchment outlet. However, methods describing catchment vulnerability to contamination by road spills based solely on biophysical parameters are scarce. These methods could be particularly attractive to managersmore » because they can operate with a limited amount of easily collectable data, while still being able to provide important insights on the areas more prone to contamination within the studied watershed. The purpose of this paper was then to contribute with a new vulnerability model. To accomplish the goal, a selection of medium properties appearing in wash-off equations and routing algorithms were assembled and processed in a parametric framework based on multi criteria analysis to define the watershed vulnerability. However, parameters had to be adapted because wash-off equations and water quality models have been developed to operate primarily in the urban environment while the vulnerability model is meant to run in rural watersheds. The selected parameters were hillside slope, ground roughness (depending on land use), soil permeability (depending on soil type), distance to water courses and stream density. The vulnerability model is a spatially distributed algorithm that was prepared to run under the IDRISI Selva software, a GIS platform capable of handling spatial and alphanumeric data and execute the necessary terrain model, hydrographic and thematic analyses. For illustrative purposes, the vulnerability model was applied to the legally protected Environmental Protection Area (APA), located in the Uberaba region, state of Minas Gerais, Brazil. In this region, the risk of accidents causing chemical spills is preoccupying because large quantities of dangerous materials are transported in two important distribution highways while the APA is fundamental for the protection of water resources, the riverine ecosystems and remnants of native vegetation. In some tested scenarios, model results show 60% of vulnerable areas within the studied area. The most sensitive parameter to vulnerability is soil type. To prevent soils from contamination, specific measures were proposed involving minimization of land use conflicts that would presumably raise the soil's organic matter and in the sequel restore the soil's structural functions. Additionally, the present study proposed the preservation and reinforcement of riparian forests as one measure to protect the quality of surface water. - Highlights: • A multi criteria analog model was developed to assess rural catchment vulnerability along roads. • Model parameters were defined by analogy with urban wash-off equations and routing algorithms. • The model mixes up various biophysical and socio-economic parameters. • Model application was based on a scenario analysis. • The study is focused on the Environmental Protection Area of Uberaba River, Brazil.« less

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

Cell Surface Mechanochemistry and the Determinants of Bleb Formation, Healing, and Travel Velocity

PubMed Central

Manakova, Kathryn; Yan, Huaming; Lowengrub, John; Allard, Jun

2016-01-01

Blebs are pressure-driven cell protrusions implicated in cellular functions such as cell division, apoptosis, and cell motility, including motility of protease-inhibited cancer cells. Because of their mechanical nature, blebs inform us about general cell-surface mechanics, including membrane dynamics, pressure propagation throughout the cytoplasm, and the architecture and dynamics of the actin cortex. Mathematical models including detailed fluid dynamics have previously been used to understand bleb expansion. Here, we develop mathematical models in two and three dimensions on longer timescales that recapitulate the full bleb life cycle, including both expansion and healing by cortex reformation, in terms of experimentally accessible biophysical parameters such as myosin contractility, osmotic pressure, and turnover of actin and ezrin. The model provides conditions under which blebbing occurs, and naturally gives rise to traveling blebs. The model predicts conditions under which blebs travel or remain stationary, as well as the bleb traveling velocity, a quantity that has remained elusive in previous models. As previous studies have used blebs as reporters of membrane tension and pressure dynamics within the cell, we have used our system to investigate various pressure equilibration models and dynamic, nonuniform membrane tension to account for the shape of a traveling bleb. We also find that traveling blebs tend to expand in all directions unless otherwise constrained. One possible constraint could be provided by spatial heterogeneity in, for example, adhesion density. PMID:27074688

Surface-to-volume ratio mapping of tumor microstructure using oscillating gradient diffusion weighted imaging

PubMed Central

Reynaud, Olivier; Winters, Kerryanne Veronica; Hoang, Dung Minh; Wadghiri, Youssef Zaim; Novikov, Dmitry S; Kim, Sungheon Gene

2015-01-01

Purpose To disentangle the free diffusivity (D0) and cellular membrane restrictions, via their surface-to-volume ratio (S/V), using the frequency-dependence of the diffusion coefficient D(ω), measured in brain tumors in the short diffusion-time regime using oscillating gradients (OGSE). Methods In vivo and ex vivo OGSE experiments were performed on mice bearing the GL261 murine glioma model (n=10) to identify the relevant time/frequency (t/ω) domain where D(ω) linearly decreases with ω−1/2. Parametric maps (S/V, D0) are compared to conventional DWI metrics. The impact of frequency range and temperature (20°C vs. 37°C) on S/V and D0 is investigated ex vivo. Results The validity of the short diffusion-time regime is demonstrated in vivo and ex vivo. Ex vivo measurements confirm that the purely geometric restrictions embodied in S/V are independent from temperature and frequency range, while the temperature dependence of the free diffusivity D0 is similar to that of pure water. Conclusion Our results suggest that D(ω) in the short diffusion-time regime can be used to uncouple the purely geometric restriction effect, such as S/V, from the intrinsic medium diffusivity properties, and provides a non-empirical and objective way to interpret frequency/time-dependent diffusion changes in tumors in terms of objective biophysical tissue parameters. PMID:26207354

An Analysis of Potential Predictive Parameters of Motion Sickness Using a Computerized Biophysical Data Acquisition System.

DTIC Science & Technology

1985-12-01

Despite the problems, drug therapy was seen as the easiest and most effective treatment. Some wartime research, primarily Canadian and Australian ...sickness was further supported by the Australians when they found that small head motions greatly contributed to the onset of motion sickness (46:20). It is...particularly noteworthy that one Australian , McIntyre, laid the groundwork for modern sensory conflict theory when he stated in 1941, "In most cases

Biophysics of Cold Adaptation and Acclimatization: Microbial Decomposition.

DTIC Science & Technology

1984-03-01

plant communities. Parameters such as temperature, precipitation and relative humidity, as they are related to winds and sea ice, interact to produce the...predictable pattern, 9 the occurrence of clouds, precipitation and heavy fogs build to a maximum as the number of daily sunshine hours increases. At 12...August 2, the sun finally sets for 1 hour and 25 minutes. Climatic records kept since 1934 show low precipitation levels with a 40 year mean of 11.5 cm/yr

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 stands. These data correspond to 4.8 and 2.2 respectively from in situ Licor LAI 2200 measurements (Wilcoxon signed rank p value of 0.25, indicating there is no significant difference between LAIC and field measurements). Imagery over plots indicates about 12% canopy cover from standing dead vegetation within plots, which corresponds to about a 10% estimate of standing dead measured in the field. The next steps for analysis include calculating NDVI and CWC for plot-level vegetation, and scaling to the surrounding forested landscape. These high resolution estimates from UAS imagery will provide forest stand-to- landscape level biophysical data for forest health assessments, management, drought and disturbance monitoring and climate change modeling. Chen, J. M., and J. Cihlar. 1996. Retrieving LAI of boreal conifer forests using Landsat TM images. RSE 55:153-162. Córcoles, J., J. Ortega, D. Hernández, and M. Moreno. 2013. Use of digital photography from unmanned aerial vehicles for estimation of LAI in onion. EJoA. 45:96-104.

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

Assessment of Unmanned Aerial Vehicles Imagery for Quantitative Monitoring of Wheat Crop in Small Plots

PubMed Central

Lelong, Camille C. D.; Burger, Philippe; Jubelin, Guillaume; Roux, Bruno; Labbé, Sylvain; Baret, Frédéric

2008-01-01

This paper outlines how light Unmanned Aerial Vehicles (UAV) can be used in remote sensing for precision farming. It focuses on the combination of simple digital photographic cameras with spectral filters, designed to provide multispectral images in the visible and near-infrared domains. In 2005, these instruments were fitted to powered glider and parachute, and flown at six dates staggered over the crop season. We monitored ten varieties of wheat, grown in trial micro-plots in the South-West of France. For each date, we acquired multiple views in four spectral bands corresponding to blue, green, red, and near-infrared. We then performed accurate corrections of image vignetting, geometric distortions, and radiometric bidirectional effects. Afterwards, we derived for each experimental micro-plot several vegetation indexes relevant for vegetation analyses. Finally, we sought relationships between these indexes and field-measured biophysical parameters, both generic and date-specific. Therefore, we established a robust and stable generic relationship between, in one hand, leaf area index and NDVI and, in the other hand, nitrogen uptake and GNDVI. Due to a high amount of noise in the data, it was not possible to obtain a more accurate model for each date independently. A validation protocol showed that we could expect a precision level of 15% in the biophysical parameters estimation while using these relationships. PMID:27879893

Label-free high-throughput imaging flow cytometry

NASA Astrophysics Data System (ADS)

Mahjoubfar, A.; Chen, C.; Niazi, K. R.; Rabizadeh, S.; Jalali, B.

2014-03-01

Flow cytometry is an optical method for studying cells based on their individual physical and chemical characteristics. It is widely used in clinical diagnosis, medical research, and biotechnology for analysis of blood cells and other cells in suspension. Conventional flow cytometers aim a laser beam at a stream of cells and measure the elastic scattering of light at forward and side angles. They also perform single-point measurements of fluorescent emissions from labeled cells. However, many reagents used in cell labeling reduce cellular viability or change the behavior of the target cells through the activation of undesired cellular processes or inhibition of normal cellular activity. Therefore, labeled cells are not completely representative of their unaltered form nor are they fully reliable for downstream studies. To remove the requirement of cell labeling in flow cytometry, while still meeting the classification sensitivity and specificity goals, measurement of additional biophysical parameters is essential. Here, we introduce an interferometric imaging flow cytometer based on the world's fastest continuous-time camera. Our system simultaneously measures cellular size, scattering, and protein concentration as supplementary biophysical parameters for label-free cell classification. It exploits the wide bandwidth of ultrafast laser pulses to perform blur-free quantitative phase and intensity imaging at flow speeds as high as 10 meters per second and achieves nanometer-scale optical path length resolution for precise measurements of cellular protein concentration.

Teaching and learning the Hodgkin-Huxley model based on software developed in NEURON’s programming language hoc

PubMed Central

2013-01-01

Background We present a software tool called SENB, which allows the geometric and biophysical neuronal properties in a simple computational model of a Hodgkin-Huxley (HH) axon to be changed. The aim of this work is to develop a didactic and easy-to-use computational tool in the NEURON simulation environment, which allows graphical visualization of both the passive and active conduction parameters and the geometric characteristics of a cylindrical axon with HH properties. Results The SENB software offers several advantages for teaching and learning electrophysiology. First, SENB offers ease and flexibility in determining the number of stimuli. Second, SENB allows immediate and simultaneous visualization, in the same window and time frame, of the evolution of the electrophysiological variables. Third, SENB calculates parameters such as time and space constants, stimuli frequency, cellular area and volume, sodium and potassium equilibrium potentials, and propagation velocity of the action potentials. Furthermore, it allows the user to see all this information immediately in the main window. Finally, with just one click SENB can save an image of the main window as evidence. Conclusions The SENB software is didactic and versatile, and can be used to improve and facilitate the teaching and learning of the underlying mechanisms in the electrical activity of an axon using the biophysical properties of the squid giant axon. PMID:23675833

Hyperpolarization-Activated Current Induces Period-Doubling Cascades and Chaos in a Cold Thermoreceptor Model

PubMed Central

Xu, Kesheng; Maidana, Jean P.; Caviedes, Mauricio; Quero, Daniel; Aguirre, Pablo; Orio, Patricio

2017-01-01

In this article, we describe and analyze the chaotic behavior of a conductance-based neuronal bursting model. This is a model with a reduced number of variables, yet it retains biophysical plausibility. Inspired by the activity of cold thermoreceptors, the model contains a persistent Sodium current, a Calcium-activated Potassium current and a hyperpolarization-activated current (Ih) that drive a slow subthreshold oscillation. Driven by this oscillation, a fast subsystem (fast Sodium and Potassium currents) fires action potentials in a periodic fashion. Depending on the parameters, this model can generate a variety of firing patterns that includes bursting, regular tonic and polymodal firing. Here we show that the transitions between different firing patterns are often accompanied by a range of chaotic firing, as suggested by an irregular, non-periodic firing pattern. To confirm this, we measure the maximum Lyapunov exponent of the voltage trajectories, and the Lyapunov exponent and Lempel-Ziv's complexity of the ISI time series. The four-variable slow system (without spiking) also generates chaotic behavior, and bifurcation analysis shows that this is often originated by period doubling cascades. Either with or without spikes, chaos is no longer generated when the Ih is removed from the system. As the model is biologically plausible with biophysically meaningful parameters, we propose it as a useful tool to understand chaotic dynamics in neurons. PMID:28344550

Separation techniques: Chromatography

PubMed Central

Coskun, Ozlem

2016-01-01

Chromatography is an important biophysical technique that enables the separation, identification, and purification of the components of a mixture for qualitative and quantitative analysis. Proteins can be purified based on characteristics such as size and shape, total charge, hydrophobic groups present on the surface, and binding capacity with the stationary phase. Four separation techniques based on molecular characteristics and interaction type use mechanisms of ion exchange, surface adsorption, partition, and size exclusion. Other chromatography techniques are based on the stationary bed, including column, thin layer, and paper chromatography. Column chromatography is one of the most common methods of protein purification. PMID:28058406

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.

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

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

A new insight into the interaction of ZnO with calf thymus DNA through surface defects.

PubMed

Das, Sumita; Chatterjee, Sabyasachi; Pramanik, Srikrishna; Devi, Parukuttyamma Sujatha; Kumar, Gopinatha Suresh

2018-01-01

Experimental evidences on the binding interaction of ZnO and Calf Thymus (CT) DNA using several biophysical techniques are the centre of interest of the present study. The interaction of ZnO with CT DNA has been investigated in detail by absorption spectral study, fluorescence titration, Raman analysis, zeta potential measurement, viscometric experiment along with thermal melting study and microscopic analysis. Steady-state fluorescence study revealed the quenching (48%) of the surface defect related peak intensity of ZnO on interaction with DNA. The optimized concentration of ZnO and DNA to obtain this level of quenching has been found to be 0.049mM and 1.027μM, respectively. Additional fluorescence study with 8-hydroxy-5-quinoline (HQ) as a fluorescence probe for Zn 2+ ruled out the dissolution effect of ZnO under the experimental conditions. DNA conjugation on the surface of ZnO was also supported by Raman study. The quantitative variation in conductivity as well as electrophoretic mobility indicated significant interaction of ZnO with the DNA molecule. Circular dichroism (CD) and viscometry titrations provided clear evidence in support of the conformational retention of the DNA on interaction with ZnO. The binding interaction was found to be predominantly entropy driven in nature. The bio-physical studies presented in this paper exploring ZnO-CT DNA interaction could add a new horizon to understand the interaction between metal oxide and DNA. Copyright © 2017. Published by Elsevier B.V.

Automatic Parameterization Strategy for Cardiac Electrophysiology Simulations.

PubMed

Costa, Caroline Mendonca; Hoetzl, Elena; Rocha, Bernardo Martins; Prassl, Anton J; Plank, Gernot

2013-10-01

Driven by recent advances in medical imaging, image segmentation and numerical techniques, computer models of ventricular electrophysiology account for increasingly finer levels of anatomical and biophysical detail. However, considering the large number of model parameters involved parameterization poses a major challenge. A minimum requirement in combined experimental and modeling studies is to achieve good agreement in activation and repolarization sequences between model and experiment or patient data. In this study, we propose basic techniques which aid in determining bidomain parameters to match activation sequences. An iterative parameterization algorithm is implemented which determines appropriate bulk conductivities which yield prescribed velocities. In addition, a method is proposed for splitting the computed bulk conductivities into individual bidomain conductivities by prescribing anisotropy ratios.

Combined Screening for Early Detection of Pre-Eclampsia

PubMed Central

Park, Hee Jin; Shim, Sung Shin; Cha, Dong Hyun

2015-01-01

Although the precise pathophysiology of pre-eclampsia remains unknown, this condition continues to be a major cause of maternal and fetal mortality. Early prediction of pre-eclampsia would allow for timely initiation of preventive therapy. A combination of biophysical and biochemical markers are superior to other tests for early prediction of the development of pre-eclampsia. Apart from the use of parameters in first-trimester aneuploidy screening, cell-free fetal DNA quantification is emerging as a promising marker for prediction of pre-eclampsia. This article reviews the current research of the most important strategies for prediction of pre-eclampsia, including the use of maternal risk factors, mean maternal arterial pressure, ultrasound parameters, and biomarkers. PMID:26247944

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-out data. Preliminary results from this analysis suggest that: 1) the relative importance and dependencies of biophysical drivers on forest structure are contingent upon the position of these forests along gradients of a limiting resource, 2) stem density shows a stronger dependence on water availability than tree size and 3) that the predictive power of abiotic variables are limited with our best models accounting for only 36-40 percent of the variance in the response. These results suggest that the response of forest structure to climate change may be highly idiosyncratic and difficult to predict using abiotic drivers alone.

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 (IFF) within the lacunar-canalicular system and at the endosteum, the piezoelectricity at the deformed bone surface, and the streaming potential accompanying the IFF. Their generation mechanisms and the regulation effect on bone adaptation are presented. The IFF-induced chemotransport effect, shear stress, and fluid drag on the pericellular matrix are meaningful and noteworthy. Furthermore, we firmly believe that bone adaptation is regulated by the combination of bone biomechanical and biophysical environment, not only the commonly considered matrix strain, fluid shear stress, and hydrostatic pressure, but also the piezoelectricity and streaming potential. Especially, it is necessary to incorporate bone matrix piezoelectricity and streaming potential to explain how osteoblasts (bone formation cells) and osteoclasts (bone resorption cells) can differentiate among different types of loads. Specifically, the regulation effects and the related mechanisms of the biomechanical and biophysical environments on bone need further exploration, and the incorporation of experimental research with theoretical simulations is essential. Copyright © 2015. Published by Elsevier Ltd.

Mechanical splitting of microtubules into protofilament bundles by surface-bound kinesin-1

DOE PAGES

VanDelinder, Virginia; Adams, Peter G.; Bachand, George D.

2016-12-21

The fundamental biophysics of gliding microtubule (MT) motility by surface-tethered kinesin-1 motor proteins has been widely studied, as well as applied to capture and transport analytes in bioanalytical microdevices. In these systems, phenomena such as molecular wear and fracture into shorter MTs have been reported due the mechanical forces applied on the MT during transport. In the present work, we show that MTs can be split longitudinally into protofilament bundles (PFBs) by the work performed by surface-bound kinesin motors. We examine the properties of these PFBs using several techniques (e.g., fluorescence microscopy, SEM, AFM), and show that the PFBs continuemore » to be mobile on the surface and display very high curvature compared to MT. Further, higher surface density of kinesin motors and shorter kinesin-surface tethers promote PFB formation, whereas modifying MT with GMPCPP or higher paclitaxel concentrations did not affect PFB formation.« less

Predicting electromyographic signals under realistic conditions using a multiscale chemo-electro-mechanical finite element model.

PubMed

Mordhorst, Mylena; Heidlauf, Thomas; Röhrle, Oliver

2015-04-06

This paper presents a novel multiscale finite element-based framework for modelling electromyographic (EMG) signals. The framework combines (i) a biophysical description of the excitation-contraction coupling at the half-sarcomere level, (ii) a model of the action potential (AP) propagation along muscle fibres, (iii) a continuum-mechanical formulation of force generation and deformation of the muscle, and (iv) a model for predicting the intramuscular and surface EMG. Owing to the biophysical description of the half-sarcomere, the model inherently accounts for physiological properties of skeletal muscle. To demonstrate this, the influence of membrane fatigue on the EMG signal during sustained contractions is investigated. During a stimulation period of 500 ms at 100 Hz, the predicted EMG amplitude decreases by 40% and the AP propagation velocity decreases by 15%. Further, the model can take into account contraction-induced deformations of the muscle. This is demonstrated by simulating fixed-length contractions of an idealized geometry and a model of the human tibialis anterior muscle (TA). The model of the TA furthermore demonstrates that the proposed finite element model is capable of simulating realistic geometries, complex fibre architectures, and can include different types of heterogeneities. In addition, the TA model accounts for a distributed innervation zone, different fibre types and appeals to motor unit discharge times that are based on a biophysical description of the α motor neurons.

Predicting electromyographic signals under realistic conditions using a multiscale chemo–electro–mechanical finite element model

PubMed Central

Mordhorst, Mylena; Heidlauf, Thomas; Röhrle, Oliver

2015-01-01

This paper presents a novel multiscale finite element-based framework for modelling electromyographic (EMG) signals. The framework combines (i) a biophysical description of the excitation–contraction coupling at the half-sarcomere level, (ii) a model of the action potential (AP) propagation along muscle fibres, (iii) a continuum-mechanical formulation of force generation and deformation of the muscle, and (iv) a model for predicting the intramuscular and surface EMG. Owing to the biophysical description of the half-sarcomere, the model inherently accounts for physiological properties of skeletal muscle. To demonstrate this, the influence of membrane fatigue on the EMG signal during sustained contractions is investigated. During a stimulation period of 500 ms at 100 Hz, the predicted EMG amplitude decreases by 40% and the AP propagation velocity decreases by 15%. Further, the model can take into account contraction-induced deformations of the muscle. This is demonstrated by simulating fixed-length contractions of an idealized geometry and a model of the human tibialis anterior muscle (TA). The model of the TA furthermore demonstrates that the proposed finite element model is capable of simulating realistic geometries, complex fibre architectures, and can include different types of heterogeneities. In addition, the TA model accounts for a distributed innervation zone, different fibre types and appeals to motor unit discharge times that are based on a biophysical description of the α motor neurons. PMID:25844148

Solar dimming above temperate forests and its impact on local climate

NASA Astrophysics Data System (ADS)

Tudoroiu, M.; Genesio, L.; Gioli, B.; Schume, H.; Knohl, A.; Brümmer, C.; Miglietta, F.

2018-06-01

Vegetation has a substantial impact on the local climate. Land cover changes through afforestation or deforestation can amplify or mitigate climate warming by changes in biophysical and biogeochemical mechanisms. In the montane to subalpine area of the Eastern Alps in Europe, where forests have constantly expanded in the last four decades, data of meteorological stations show a consistent reduction in incoming global radiation for the period 2000–2015. To assess the potential role of forests in contributing to such a reduction, three site pairs in Central Europe with neighbouring forest and non-forest sites were analysed. In all the pairs, a lower amount of incoming radiation was recorded at the forest site. When biophysical mechanisms such as albedo, surface roughness and Bowen ratio changes were modelled together with changes in global radiation, the total radiative forcing accounted for a rate of change in air temperature was equal to 0.032 °C ± 0.01 °C per Wm‑2. These results suggest that local climate is influenced by land cover change through afforestation both via albedo and radiation feedbacks but also by means of indirect biophysical and species-dependent mechanisms. The data obtained for the site pairs in Central Europe are finally discussed to infer the occurrence of similar forest-driven effects in the Eastern Alps which may explain part of the solar dimming observed in high elevation weather stations.

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 with vegetation indices of NDVI and EVI derived from MODIS data were used. Higher CO2 mixing ratios anti-correlated with the vegetation indices derived from MODIS data were observed. This is attributable to the photosynthetic uptake of CO2 by plants and convective mixing of the atmosphere. Details of satellite data characteristics related with the in-situ CO2 measurements will be presented.

Fortuitous encounters between seagliders and adult female northern fur seals (Callorhinus ursinus) off the Washington (USA) coast: upper ocean variability and links to top predator behavior.

PubMed

Pelland, Noel A; Sterling, Jeremy T; Lea, Mary-Anne; Bond, Nicholas A; Ream, Rolf R; Lee, Craig M; Eriksen, Charles C

2014-01-01

Behavioral responses by top marine predators to oceanographic features such as eddies, river plumes, storms, and coastal topography suggest that biophysical interactions in these zones affect predators' prey, foraging behaviors, and potentially fitness. However, examining these pathways is challenged by the obstacles inherent in obtaining simultaneous observations of surface and subsurface environmental fields and predator behavior. In this study, migratory movements and, in some cases, diving behavior of 40 adult female northern fur seals (NFS; Callorhinus ursinus) were quantified across their range and compared to remotely-sensed environmental data in the Gulf of Alaska and California Current ecosystems, with a particular focus off the coast of Washington State (USA)--a known foraging ground for adult female NFS and where autonomous glider sampling allowed opportunistic comparison of seal behavior to subsurface biophysical measurements. The results show that in these ecosystems, adult female habitat utilization was concentrated near prominent coastal topographic, riverine, or inlet features and within 200 km of the continental shelf break. Seal dive depths, in most ecosystems, were moderated by surface light level (solar or lunar), mirroring known behaviors of diel vertically-migrating prey. However, seal dives differed in the California Current ecosystem due to a shift to more daytime diving concentrated at or below the surface mixed layer base. Seal movement models indicate behavioral responses to season, ecosystem, and surface wind speeds; individuals also responded to mesoscale eddies, jets, and the Columbia River plume. Foraging within small scale surface features is consistent with utilization of the inner coastal transition zone and habitats near coastal capes, which are known eddy and filament generation sites. These results contribute to our knowledge of NFS migratory patterns by demonstrating surface and subsurface behavioral responses to a spatially and temporally dynamic ocean environment, thus reflecting its influence on associated NFS prey species.

Fortuitous Encounters between Seagliders and Adult Female Northern Fur Seals (Callorhinus ursinus) off the Washington (USA) Coast: Upper Ocean Variability and Links to Top Predator Behavior

PubMed Central

Pelland, Noel A.; Sterling, Jeremy T.; Lea, Mary-Anne; Bond, Nicholas A.; Ream, Rolf R.; Lee, Craig M.; Eriksen, Charles C.

2014-01-01

Behavioral responses by top marine predators to oceanographic features such as eddies, river plumes, storms, and coastal topography suggest that biophysical interactions in these zones affect predators' prey, foraging behaviors, and potentially fitness. However, examining these pathways is challenged by the obstacles inherent in obtaining simultaneous observations of surface and subsurface environmental fields and predator behavior. In this study, migratory movements and, in some cases, diving behavior of 40 adult female northern fur seals (NFS; Callorhinus ursinus) were quantified across their range and compared to remotely-sensed environmental data in the Gulf of Alaska and California Current ecosystems, with a particular focus off the coast of Washington State (USA) – a known foraging ground for adult female NFS and where autonomous glider sampling allowed opportunistic comparison of seal behavior to subsurface biophysical measurements. The results show that in these ecosystems, adult female habitat utilization was concentrated near prominent coastal topographic, riverine, or inlet features and within 200 km of the continental shelf break. Seal dive depths, in most ecosystems, were moderated by surface light level (solar or lunar), mirroring known behaviors of diel vertically-migrating prey. However, seal dives differed in the California Current ecosystem due to a shift to more daytime diving concentrated at or below the surface mixed layer base. Seal movement models indicate behavioral responses to season, ecosystem, and surface wind speeds; individuals also responded to mesoscale eddies, jets, and the Columbia River plume. Foraging within small scale surface features is consistent with utilization of the inner coastal transition zone and habitats near coastal capes, which are known eddy and filament generation sites. These results contribute to our knowledge of NFS migratory patterns by demonstrating surface and subsurface behavioral responses to a spatially and temporally dynamic ocean environment, thus reflecting its influence on associated NFS prey species. PMID:25153524

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

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.

Inhibitors for Androgen Receptor Activation Surfaces

DTIC Science & Technology

2007-09-01

Inhibitor of Coregulator Binding to the Thyroid Hormone Receptor.. Molecular Endocrinology, 2007 Sep 6; [Epub ahead of print] PMID: 17823305 (related...Kiplin Guy†, Paul Webb‡, and Robert J. Fletterick* *Department of Biochemistry and Biophysics, §Department of Molecular and Cellular Pharmacology, and...are also small but significant shifts in secondary structural elements; residues 720–730 (H3) and 825–847 (H9) exhibit rmsd of 0.33 and 0.44

A Stable Human-Cell System Overexpressing Cystic Fibrosis Transmembrane Conductance Regulator Recombinant Protein at the Cell Surface

PubMed Central

Dai, Qun; Aleksandrov, Andrei A.; Bajrami, Bekim; Diego, Pamela Ann; Wu, Xing; Ray, Marjorie; Naren, Anjaparavanda P.; Riordan, John R.; Yao, Xudong; DeLucas, Lawrence J.; Urbatsch, Ina L.; Kappes, John C.

2015-01-01

Recent human clinical trials results demonstrated successful treatment for certain genetic forms of cystic fibrosis (CF). To extend treatment opportunities to those afflicted with other genetic forms of CF disease, structural and biophysical characterization of CF transmembrane conductance regulator (CFTR) is urgently needed. In this study, CFTR was modified with various tags, including a His10 purification tag, the SUMOstar (SUMO*) domain, an extracellular FLAG epitope, or an enhanced green fluorescent protein (EGFP), each alone or in various combinations. Expressed in HEK293 cells, recombinant CFTR proteins underwent complex glycosylation, compartmentalized with the plasma membrane, and exhibited regulated chloride-channel activity with only modest alterations in channel conductance and gating kinetics. Surface CFTR expression level was enhanced by the presence of SUMO* on the N-terminus. Quantitative mass-spectrometric analysis indicated approximately 10% of the total recombinant CFTR (SUMO*-CFTRFLAG-EGFP) localized to the plasma membrane. Trial purification using dodecylmaltoside for membrane protein extraction reproducibly recovered 178 ± 56 μg SUMO*-CFTRFLAG-EGFP per billion cells at 80% purity. Fluorescence size-exclusion chromatography indicated purified CFTR was monodisperse. These findings demonstrate a stable mammalian cell expression system capable of producing human CFTR of sufficient quality and quantity to augment futrure CF drug discovery efforts, including biophysical and structural studies. PMID:25577540

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.

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.

Microbial Life in Soil - Linking Biophysical Models with Observations

NASA Astrophysics Data System (ADS)

Or, Dani; Tecon, Robin; Ebrahimi, Ali; Kleyer, Hannah; Ilie, Olga; Wang, Gang

2015-04-01

Microbial life in soil occurs within fragmented aquatic habitats formed in complex pore spaces where motility is restricted to short hydration windows (e.g., following rainfall). The limited range of self-dispersion and physical confinement promote spatial association among trophically interdepended microbial species. Competition and preferences for different nutrient resources and byproducts and their diffusion require high level of spatial organization to sustain the functioning of multispecies communities. We report mechanistic modeling studies of competing multispecies microbial communities grown on hydrated surfaces and within artificial soil aggregates (represented by 3-D pore network). Results show how trophic dependencies and cell-level interactions within patchy diffusion fields promote spatial self-organization of motile microbial cells. The spontaneously forming patterns of segregated, yet coexisting species were robust to spatial heterogeneities and to temporal perturbations (hydration dynamics), and respond primarily to the type of trophic dependencies. Such spatially self-organized consortia may reflect ecological templates that optimize substrate utilization and could form the basic architecture for more permanent surface-attached microbial colonies. Hydration dynamics affect structure and spatial arrangement of aerobic and anaerobic microbial communities and their biogeochemical functions. Experiments with well-characterized artificial soil microbial assemblies grown on porous surfaces provide access to community dynamics during wetting and drying cycles detected through genetic fingerprinting. Experiments for visual observations of spatial associations of tagged bacterial species with known trophic dependencies on model porous surfaces are underway. Biophysical modeling provide a means for predicting hydration-mediated critical separation distances for activation of spatial self-organization. The study provides new modeling and observational tools that enable new mechanistic insights into how differences in substrate affinities among microbial species and soil micro-hydrological conditions may give rise to a remarkable spatial and functional order in an extremely heterogeneous soil microbial world

Microbial Life in Soil - Linking Biophysical Models with Observations

NASA Astrophysics Data System (ADS)

Or, D.; Tecon, R.; Ebrahimi, A.; Kleyer, H.; Ilie, O.; Wang, G.

2014-12-01

Microbial life in soil occurs within fragmented aquatic habitats in complex pore spaces where motility is restricted to short hydration windows (e.g., following rainfall). The limited range of self-dispersion and physical confinement promote spatial association among trophically interdepended microbial species. Competition and preferences for different nutrient resources and byproducts and their diffusion require high level of spatial organization to sustain the functioning of multispecies communities. We report mechanistic modeling studies of competing multispecies microbial communities grown on hydrated surfaces and within artificial soil aggregates (represented by 3-D pore network). Results show how trophic dependencies and cell-level interactions within patchy diffusion fields promote spatial self-organization of motile microbial cells. The spontaneously forming patterns of segregated, yet coexisting species were robust to spatial heterogeneities and to temporal perturbations (hydration dynamics), and respond primarily to the type of trophic dependencies. Such spatially self-organized consortia may reflect ecological templates that optimize substrate utilization and could form the basic architecture for more permanent surface-attached microbial colonies. Hydration dynamics affect structure and spatial arrangement of aerobic and anaerobic microbial communities and their biogeochemical functions. Experiments with well-characterized artificial soil microbial assemblies grown on porous surfaces provide access to community dynamics during wetting and drying cycles detected through genetic fingerprinting. Experiments for visual observations of spatial associations of tagged bacterial species with known trophic dependencies on model porous surfaces are underway. Biophysical modeling provide a means for predicting hydration-mediated critical separation distances for activation of spatial self-organization. The study provides new modeling and observational tools that enable new mechanistic insights into how differences in substrate affinities among microbial species and soil micro-hydrological conditions may give rise to a remarkable spatial and functional order in an extremely heterogeneous soil microbial world.

From Spiking Neuron Models to Linear-Nonlinear Models

PubMed Central

Ostojic, Srdjan; Brunel, Nicolas

2011-01-01

Neurons transform time-varying inputs into action potentials emitted stochastically at a time dependent rate. The mapping from current input to output firing rate is often represented with the help of phenomenological models such as the linear-nonlinear (LN) cascade, in which the output firing rate is estimated by applying to the input successively a linear temporal filter and a static non-linear transformation. These simplified models leave out the biophysical details of action potential generation. It is not a priori clear to which extent the input-output mapping of biophysically more realistic, spiking neuron models can be reduced to a simple linear-nonlinear cascade. Here we investigate this question for the leaky integrate-and-fire (LIF), exponential integrate-and-fire (EIF) and conductance-based Wang-Buzsáki models in presence of background synaptic activity. We exploit available analytic results for these models to determine the corresponding linear filter and static non-linearity in a parameter-free form. We show that the obtained functions are identical to the linear filter and static non-linearity determined using standard reverse correlation analysis. We then quantitatively compare the output of the corresponding linear-nonlinear cascade with numerical simulations of spiking neurons, systematically varying the parameters of input signal and background noise. We find that the LN cascade provides accurate estimates of the firing rates of spiking neurons in most of parameter space. For the EIF and Wang-Buzsáki models, we show that the LN cascade can be reduced to a firing rate model, the timescale of which we determine analytically. Finally we introduce an adaptive timescale rate model in which the timescale of the linear filter depends on the instantaneous firing rate. This model leads to highly accurate estimates of instantaneous firing rates. PMID:21283777

Design and validation of diffusion MRI models of white matter

NASA Astrophysics Data System (ADS)

Jelescu, Ileana O.; Budde, Matthew D.

2017-11-01

Diffusion MRI is arguably the method of choice for characterizing white matter microstructure in vivo. Over the typical duration of diffusion encoding, the displacement of water molecules is conveniently on a length scale similar to that of the underlying cellular structures. Moreover, water molecules in white matter are largely compartmentalized which enables biologically-inspired compartmental diffusion models to characterize and quantify the true biological microstructure. A plethora of white matter models have been proposed. However, overparameterization and mathematical fitting complications encourage the introduction of simplifying assumptions that vary between different approaches. These choices impact the quantitative estimation of model parameters with potential detriments to their biological accuracy and promised specificity. First, we review biophysical white matter models in use and recapitulate their underlying assumptions and realms of applicability. Second, we present up-to-date efforts to validate parameters estimated from biophysical models. Simulations and dedicated phantoms are useful in assessing the performance of models when the ground truth is known. However, the biggest challenge remains the validation of the “biological accuracy” of estimated parameters. Complementary techniques such as microscopy of fixed tissue specimens have facilitated direct comparisons of estimates of white matter fiber orientation and densities. However, validation of compartmental diffusivities remains challenging, and complementary MRI-based techniques such as alternative diffusion encodings, compartment-specific contrast agents and metabolites have been used to validate diffusion models. Finally, white matter injury and disease pose additional challenges to modeling, which are also discussed. This review aims to provide an overview of the current state of models and their validation and to stimulate further research in the field to solve the remaining open questions and converge towards consensus.

From spiking neuron models to linear-nonlinear models.

PubMed

Ostojic, Srdjan; Brunel, Nicolas

2011-01-20

Neurons transform time-varying inputs into action potentials emitted stochastically at a time dependent rate. The mapping from current input to output firing rate is often represented with the help of phenomenological models such as the linear-nonlinear (LN) cascade, in which the output firing rate is estimated by applying to the input successively a linear temporal filter and a static non-linear transformation. These simplified models leave out the biophysical details of action potential generation. It is not a priori clear to which extent the input-output mapping of biophysically more realistic, spiking neuron models can be reduced to a simple linear-nonlinear cascade. Here we investigate this question for the leaky integrate-and-fire (LIF), exponential integrate-and-fire (EIF) and conductance-based Wang-Buzsáki models in presence of background synaptic activity. We exploit available analytic results for these models to determine the corresponding linear filter and static non-linearity in a parameter-free form. We show that the obtained functions are identical to the linear filter and static non-linearity determined using standard reverse correlation analysis. We then quantitatively compare the output of the corresponding linear-nonlinear cascade with numerical simulations of spiking neurons, systematically varying the parameters of input signal and background noise. We find that the LN cascade provides accurate estimates of the firing rates of spiking neurons in most of parameter space. For the EIF and Wang-Buzsáki models, we show that the LN cascade can be reduced to a firing rate model, the timescale of which we determine analytically. Finally we introduce an adaptive timescale rate model in which the timescale of the linear filter depends on the instantaneous firing rate. This model leads to highly accurate estimates of instantaneous firing rates.

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.

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.

Design and validation of diffusion MRI models of white matter

PubMed Central

Jelescu, Ileana O.; Budde, Matthew D.

2018-01-01

Diffusion MRI is arguably the method of choice for characterizing white matter microstructure in vivo. Over the typical duration of diffusion encoding, the displacement of water molecules is conveniently on a length scale similar to that of the underlying cellular structures. Moreover, water molecules in white matter are largely compartmentalized which enables biologically-inspired compartmental diffusion models to characterize and quantify the true biological microstructure. A plethora of white matter models have been proposed. However, overparameterization and mathematical fitting complications encourage the introduction of simplifying assumptions that vary between different approaches. These choices impact the quantitative estimation of model parameters with potential detriments to their biological accuracy and promised specificity. First, we review biophysical white matter models in use and recapitulate their underlying assumptions and realms of applicability. Second, we present up-to-date efforts to validate parameters estimated from biophysical models. Simulations and dedicated phantoms are useful in assessing the performance of models when the ground truth is known. However, the biggest challenge remains the validation of the “biological accuracy” of estimated parameters. Complementary techniques such as microscopy of fixed tissue specimens have facilitated direct comparisons of estimates of white matter fiber orientation and densities. However, validation of compartmental diffusivities remains challenging, and complementary MRI-based techniques such as alternative diffusion encodings, compartment-specific contrast agents and metabolites have been used to validate diffusion models. Finally, white matter injury and disease pose additional challenges to modeling, which are also discussed. This review aims to provide an overview of the current state of models and their validation and to stimulate further research in the field to solve the remaining open questions and converge towards consensus. PMID:29755979

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

Interaction of silicon nanoparticles with the molecules of bovine serum albumin in aqueous solutions

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

Anenkova, K A; Sergeeva, I A; Petrova, G P

2011-05-31

Using the method of photon-correlation spectroscopy, the coefficient of translational diffusion D{sub t} and the hydrodynamic radius R of the particles in aqueous solutions of the bovine serum albumin, containing silicon nanoparticles, are determined. The character of the dependence of these parameters on the concentration of the protein indicates the absence of interaction between the studied particles in the chosen range of albumin concentrations 0.2 - 1.0 mg mL{sup -1}. (optical technologies in biophysics and medicine)

Functional stability of cerebral circulatory system

NASA Technical Reports Server (NTRS)

Moskalenko, Y. Y.

1980-01-01

The functional stability of the cerebral circulation system seems to be based on the active mechanisms and on those stemming from specific of the biophysical structure of the system under study. This latter parameter has some relevant criteria for its quantitative estimation. The data obtained suggest that the essential part of the mechanism for active responses of cerebral vessels which maintains the functional stability of this portion of the vascular system, consists of a neurogenic component involving central nervous structures localized, for instance, in the medulla oblongata.

Follow-on proposal identifying environmental features for land management decisions

NASA Technical Reports Server (NTRS)

Wright, P. M.; Ridd, M. K.

1986-01-01

Urban morphology (an examination of spatial fabric and structure), natural ecosystem (investigations emphasizing biophysical processes and patterns), and human ecosystem (emphasizing socio-economic and engineering parameters) were studied. The most critical variable, transpiration, in the ASPCON model, created by Jaynes (1978), describing the hydrology of aspen to conifer succession was studied to improve the accuracy. Transpiration is determined by a canopy transpiration model which estimates consumptive water use (CWU) for specific species and a plant activity index. Also studied was Pinyon-Juniper woodland erosion.

Digital holographic microscopy for toxicity testing and cell culture quality control

NASA Astrophysics Data System (ADS)

Kemper, Björn

2018-02-01

For the example of digital holographic microscopy (DHM), it is illustrated how label-free biophysical parameter sets can be extracted from quantitative phase images of adherent and suspended cells, and how the retrieved data can be applied for in-vitro toxicity testing and cell culture quality assessment. This includes results from the quantification of the reactions of cells to toxic substances as well as data from sophisticated monitoring of cell alterations that are related to changes of cell culture conditions.

BOREAS Level-0 ER-2 Daedalus TMS Imagery Digital Counts in BIL Format

NASA Technical Reports Server (NTRS)

Newcomer, Jeffrey A.; Dominguez, Roseanne; Hall, Forrest G. (Editor)

2000-01-01

The level-0 Daedalus Thematic Mapper Simulator (TMS) imagery, along with the other remotely sensed images, was collected to provide spatially extensive information about radiant energy over the primary BOReal Ecosystem-Atmosphere Study (BOREAS) study areas. This information includes detailed land cover and biophysical parameter maps such as fraction of Photosynthetically Active Radiation (fPAR) and Leaf Area Index (LAI). Two flights of the Daedalus TMS instrument were made onboard the ER-2 aircraft on 16-Sep-1994 and 17-Sep-1994.

Regional Scaling of Airborne Eddy Covariance Flux Observation

NASA Astrophysics Data System (ADS)

Sachs, T.; Serafimovich, A.; Metzger, S.; Kohnert, K.; Hartmann, J.

2014-12-01

The earth's surface is tightly coupled to the global climate system by the vertical exchange of energy and matter. Thus, to better understand and potentially predict changes to our climate system, it is critical to quantify the surface-atmosphere exchange of heat, water vapor, and greenhouse gases on climate-relevant spatial and temporal scales. Currently, most flux observations consist of ground-based, continuous but local measurements. These provide a good basis for temporal integration, but may not be representative of the larger regional context. This is particularly true for the Arctic, where site selection is additionally bound by logistical constraints, among others. Airborne measurements can overcome this limitation by covering distances of hundreds of kilometers over time periods of a few hours. The Airborne Measurements of Methane Fluxes (AIRMETH) campaigns are designed to quantitatively and spatially explicitly address this issue: The research aircraft POLAR 5 is used to acquire thousands of kilometers of eddy-covariance flux data. During the AIRMETH-2012 and AIRMETH-2013 campaigns we measured the turbulent exchange of energy, methane, and (in 2013) carbon dioxide over the North Slope of Alaska, USA, and the Mackenzie Delta, Canada. Here, we present the potential of environmental response functions (ERFs) for quantitatively linking flux observations to meteorological and biophysical drivers in the flux footprints. We use wavelet transforms of the original high-frequency data to improve spatial discretization of the flux observations. This also enables the quantification of continuous and biophysically relevant land cover properties in the flux footprint of each observation. A machine learning technique is then employed to extract and quantify the functional relationships between flux observations and the meteorological and biophysical drivers. The resulting ERFs are used to extrapolate fluxes over spatio-temporally explicit grids of the study area. The presentation will focus on 2012 sensible and latent heat fluxes observed over the North Slope of Alaska and the scaling performance of the ERF approach.

Influence of landslides on biophysical diversity — A perspective from British Columbia

NASA Astrophysics Data System (ADS)

Geertsema, Marten; Pojar, James J.

2007-09-01

Landslides have long been overlooked or underestimated as important natural disturbance agents. In particular the ecological role of landslides in maintaining biological diversity has been largely ignored. Here we provide a western Canadian ( British Columbian) perspective on the influences of landslides on biophysical diversity, which is related in several ways to biological diversity. We recognize several types of biophysical/ecological diversity: site diversity, soil diversity, and the derivative habitat or ecosystem (including aquatic ecosystems) diversity. There are also a variety of landslide types, depending on materials and on the rate and style of movement. We discuss the roles of different landslide types on various aspects of terrestrial diversity. Landslides are simultaneously depositional and erosional processes that influence sites by redistributing materials and changing surface expression — usually creating a complex microtopography that can include very dry ridges and hummocks, and sometimes depressions with standing water. Landslide impacts to site also influence soil and soil development. Portions of landslides with exposed parent material are set back to the initial stages of soil development and ecological succession. Landslides can also change soil density, structure, porosity, surface texture, chemistry and microclimate. By changing site and soil, landslides also influence habitat. Landslides influence habitat diversity by engendering a mosaic of seral stages (often both primary and secondary), and in overwhelmingly forested landscapes often create nodes or hotspots of non-forested habitat and biota. In some areas, like the boreal forest, there is an important interplay between landslides and fire, while on the coast of British Columbia debris and snow avalanches can be the dominant disturbance agent. Low-gradient and deep-seated landslides are often opportunistically colonized by beaver and other water and shrub-loving fauna. Sag ponds and impounded streams provide aquatic habitat — often with standing dead trees. Landslide rubble and scarps provide denning/nesting habitat, escape terrain, and cliff habitat for vertebrates.

The Tor Vergata Scattering Model Applied to L Band Backscatter During the Corn Growth Cycle

NASA Astrophysics Data System (ADS)

Joseph, A. T.; van der Velde, R.; Ferrazzoli, P.; Lang, R. H.; Gish, T.

2013-12-01

At the USDA's Optimizing Production Inputs for Economic and Environmental Enhancement (OPE3) experimental site in Beltsville (Maryland, USA) a field campaign took place throughout the 2002 corn growth cycle from May 10th (emergence of corn crops) to October 2nd (harvest). One of the microwave instruments deployed was the multi-frequency (X-, C- and L-band) quad-polarized (HH, HV, VV, VH) NASA GSFC / George Washington University (GWU) truck mounted radar. During the field campaign, this radar system provided once a week fully polarized C- and L-band (4.75 and 1.6 GHz) backscatter measurements from incidence angle of 15, 35, and 55 degrees. In support of these microwave observations, an extensive ground characterization took place, which included measurements of surface roughness, soil moisture, vegetation biomass and morphology. The field conditions during the campaign are characterized by several dry downs with a period of drought in the month of August. Peak biomass of the corn canopies was reached at July 24, 2002 with a total biomass of approximately 6.5 kg m-2. This dynamic range in both soil moisture and vegetation conditions within the data set is ideal for the validation of discrete medium vegetation scattering models. In this study, we compare the L band backscatter measurements with simulations by the Tor Vergata model (Bracaglia et al., 1995). The measured soil moisture, vegetation biomass and most reliably measured vegetation morphological parameters (e.g. number of leaves, number of stems and stem height) were used as input for the Tor Vergata model. The more uncertain model parameters (e.g. surface roughness, leaf thickness) and the stem diameter were optimized using a parameter estimation routine based on the Levenberg-Marquardt algorithm. As cost function for this optimization, the HH and VV polarized backscatter measured and simulated by the Tor Vergata model for incidence angle of 15, 35 and 55 degrees were used (6 measurements in total). The calibrated Tor Vergata model simulations are in excellent agreement with the measurements of Root Mean Squared Differences (RMSD's) of 0.8, 0.9 and 1.4 dB for incidences of 15, 35 and 55 degrees, respectively. The results from this study show that a physically based scattering model with the appropriate parameterization can accurately simulate backscatter measurements and, as such, have the potential of being used for the retrieval of biophysical variables (e.g. soil moisture and vegetation biomass). Via calibration of several parameters the Tor Vergata model is able to reproduce the L-band backscatter measured over corn very well. The resulting simulations show that: (1) At 35 degrees: the backscatter is dominated by the surface as well as the vegetation-surface scattering contribution. (2) At 55 degrees: the vegetation and vegetation-surface scattering contributions become dominant.

Evaluation of MEGAN-CLM parameter sensitivity to predictions of isoprene emissions from an Amazonian rainforest

NASA Astrophysics Data System (ADS)

Holm, J. A.; Jardine, K.; Guenther, A. B.; Chambers, J. Q.; Tribuzy, E.

2014-09-01

Tropical trees are known to be large emitters of biogenic volatile organic compounds (BVOC), accounting for up to 75% of the global isoprene budget. Once in the atmosphere, these compounds influence multiple processes associated with air quality and climate. However, uncertainty in biogenic emissions is two-fold, (1) the environmental controls over isoprene emissions from tropical forests remain highly uncertain; and (2) our ability to accurately represent these environmental controls within models is lacking. This study evaluated the biophysical parameters that drive the global Model of Emissions of Gases and Aerosols from Nature (MEGAN) embedded in a biogeochemistry land surface model, the Community Land Model (CLM), with a focus on isoprene emissions from an Amazonian forest. Upon evaluating the sensitivity of 19 parameters in CLM that currently influence isoprene emissions by using a Monte Carlo analysis, up to 61% of the uncertainty in mean isoprene emissions was caused by the uncertainty in the parameters related to leaf temperature. The eight parameters associated with photosynthetic active radiation (PAR) contributed in total to only 15% of the uncertainty in mean isoprene emissions. Leaf temperature was strongly correlated with isoprene emission activity (R2 = 0.89). However, when compared to field measurements in the Central Amazon, CLM failed to capture the upper 10-14 °C of leaf temperatures throughout the year (i.e., failed to represent ~32 to 46 °C), and the spread observed in field measurements was not representative in CLM. This is an important parameter to accurately simulate due to the non-linear response of emissions to temperature. MEGAN-CLM 4.0 overestimated isoprene emissions by 60% for a Central Amazon forest (5.7 mg m-2 h-1 vs. 3.6 mg m-2 h-1), but due to reductions in leaf area index (LAI) by 28% in MEGAN-CLM 4.5 isoprene emissions were within 7% of observed data (3.8 mg m-2 h-1). When a slight adjustment to leaf temperature was made to match observations, isoprene emissions increased 24%, up to 4.8 mg m-2 h-1. Air temperatures are very likely to increase in tropical regions as a result of human induced climate change. Reducing the uncertainty of leaf temperature in BVOC algorithms, as well as improving the accuracy of replicating leaf temperature output in land surface models is warranted in order to improve estimations of tropical BVOC emissions.

Eddy-driven stratification initiates North Atlantic spring phytoplankton blooms.

PubMed

Mahadevan, Amala; D'Asaro, Eric; Lee, Craig; Perry, Mary Jane

2012-07-06

Springtime phytoplankton blooms photosynthetically fix carbon and export it from the surface ocean at globally important rates. These blooms are triggered by increased light exposure of the phytoplankton due to both seasonal light increase and the development of a near-surface vertical density gradient (stratification) that inhibits vertical mixing of the phytoplankton. Classically and in current climate models, that stratification is ascribed to a springtime warming of the sea surface. Here, using observations from the subpolar North Atlantic and a three-dimensional biophysical model, we show that the initial stratification and resulting bloom are instead caused by eddy-driven slumping of the basin-scale north-south density gradient, resulting in a patchy bloom beginning 20 to 30 days earlier than would occur by warming.

Data bank of optical properties of biological tissue and blood in the visible and near infrared spectral region

NASA Astrophysics Data System (ADS)

Khairullina, Alphiya Y.; Bui, Lilia; Oleinik, Tatiana V.; Artishevsky, Nelli; Prigoun, Natalia; Sevkovsky, Jakov; Mokhort, Tatiana

1996-12-01

The data bank contains optical, ordinary biochemical and biophysical information on 120 venous blood samples of donors, healthy persons, patients with high pathology, 60 tissue samples. The optical parameters include diffuse reflection R((lambda) ) and transmission T((lambda) ) coefficients for optically thick layers, the absorption K((lambda) ) and extinction (epsilon) ((lambda) ) spectra, oxygenation degree CO2, parameter p determined by sizes and shapes of cells and their aggregates, refractive index of a disperse phase relative to surrounding media, and cooperative effects at high relative concentration. The peculiarities in absorption K((lambda) spectra are connected with different pathologies. It is shown from K((lambda) ) that the grade of pathology connected with the concentration of hemoglobin and mithohondrion together with oxygenation degree of blood and tissues, with the pathological hemoglobin's forms and its decomposition products of different levels. Parameter p is an important diagnostic parameter. We consider that it is necessary to include the oxygenation degree and erythrocyte's aggregation parameter to extend the range of common diagnostic parameters of blood by the first rota.

Integrated Water and Sanitation Risk Assessment and Modeling in the Upper Sonora River basin (Northwest, Mexico)

NASA Astrophysics Data System (ADS)

Mayer, A. S.; Robles-Morua, A.; Halvorsen, K. E.; Vivoni, E. R.; Auer, M. T.

2011-12-01

Studies that integrate human dimensions and the biophysical characteristics of watersheds are necessary to meet the challenge of sustainable water resources development. In this project, we integrated perspectives from sociology, hydrology, and environmental engineering to examine and suggest solutions for managing waterborne disease risks associated with wastewater contamination in the Sonora River basin (SRB), a semiarid rural basin in northwest Mexico. This research consisted of four sub-projects. First, we assessed the perceptions of risks associated with wastewater contamination of water resources in rural communities in the SRB through a series of semi-structured interviews Results from this study indicate that there are major differences in risk perceptions among health professionals, government officials, and lay citizens. Government officials and lay citizens tend to underestimate the severity of the problems related to water related risks. Second, a fully distributed hydrologic model was used to make streamflow predictions in the un-gauged SRB. Synthetic flows generated from the hydrologic model were used to evaluate pollutant transport processes associated with wastewater loadings to the Sonora River. The hydrologic model revealed that the high degree of spatio-temporal variability of runoff in the SRB is associated with links between runoff generation mechanisms and land-atmosphere interactions. Third, a surface water quality model was used to assess the impact of wastewater discharges and develop pathogen contamination indicators in two sites along the Sonora River. To parameterize the water quality model, pathogenic indicator loadings and removal rates were estimated, along with their uncertainty. Results from the water quality modeling show regions in the watershed that may be exceeding pathogenic standards, but also that uncertainty in model parameters requires a probabilistic approach for estimating risks. Finally, a workshop was conducted to explore the use of participatory modeling frameworks in less developed regions. Results indicate that respondents agreed strongly with the hydrologic and water quality modeling methodologies presented and considered the modeling results useful. Our results also show that participatory modeling approaches can have short term impacts as seen in the changes in water-related risk perceptions. In total, these projects revealed that water resources management solutions need to take into account variations across the human landscape (i.e. risk perceptions) and variations in the biophysical response of watersheds to natural phenomena (i.e. streamflow generation) and to anthropogenic activities (i.e. contaminant fate and transport). In addition, this work underscores the notion that sustainable water resources solutions need to contend with uncertainty in our understanding and predictions of human perceptions and biophysical systems.

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 acquired with a NIKON D70 camera. The images acquired during the field campaign are processed with the CAN-EYE software to derive LAI, FAPAR and FCOVER. The in situ biophysical values were used for producing LAI, FCOVER and FAPAR maps from optical satellite images, and provide cross-validation, and validation of global remote sensing products. The following satellite data were used: SPOT-4, RapidEye and Landsat-8. Inter-comparison of the derived products is performed. The paper presents an insight on the general methodology used within JECAM test site, the results achieved so far and challenges, and future planned activities. 1. Gallego, F.J., Kussul, N., Skakun, S., Kravchenko, O., Shelestov, A., Kussul, O. “Efficiency assessment of using satellite data for crop area estimation in Ukraine,” International Journal of Applied Earth Observation and Geoinformation, vol. 29, pp. 22-30, 2014. 2. Kogan, F., Kussul, N., Adamenko, T., Skakun, S., Kravchenko, O., Kryvobok, O., Shelestov, A., Kolotii, A., Kussul, O., Lavrenyuk, A., “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.

Thermal Transients Excite Neurons through Universal Intramembrane Mechanoelectrical Effects

NASA Astrophysics Data System (ADS)

Plaksin, Michael; Shapira, Einat; Kimmel, Eitan; Shoham, Shy

2018-01-01

Modern advances in neurotechnology rely on effectively harnessing physical tools and insights towards remote neural control, thereby creating major new scientific and therapeutic opportunities. Specifically, rapid temperature pulses were shown to increase membrane capacitance, causing capacitive currents that explain neural excitation, but the underlying biophysics is not well understood. Here, we show that an intramembrane thermal-mechanical effect wherein the phospholipid bilayer undergoes axial narrowing and lateral expansion accurately predicts a potentially universal thermal capacitance increase rate of ˜0.3 % /°C . This capacitance increase and concurrent changes in the surface charge related fields lead to predictable exciting ionic displacement currents. The new MechanoElectrical Thermal Activation theory's predictions provide an excellent agreement with multiple experimental results and indirect estimates of latent biophysical quantities. Our results further highlight the role of electro-mechanics in neural excitation; they may also help illuminate subthreshold and novel physical cellular effects, and could potentially lead to advanced new methods for neural control.

Rainfall-enhanced blooming in typhoon wakes

PubMed Central

Lin, Y.-C.; Oey, L.-Y.

2016-01-01

Strong phytoplankton blooming in tropical-cyclone (TC) wakes over the oligotrophic oceans potentially contributes to long-term changes in global biogeochemical cycles. Yet blooming has traditionally been discussed using anecdotal events and its biophysical mechanics remain poorly understood. Here we identify dominant blooming patterns using 16 years of ocean-color data in the wakes of 141 typhoons in western North Pacific. We observe right-side asymmetric blooming shortly after the storms, attributed previously to sub-mesoscale re-stratification, but thereafter a left-side asymmetry which coincides with the left-side preference in rainfall due to the large-scale wind shear. Biophysical model experiments and observations demonstrate that heavier rainfall freshens the near-surface water, leading to stronger stratification, decreased turbulence and enhanced blooming. Our results suggest that rainfall plays a previously unrecognized, critical role in TC-induced blooming, with potentially important implications for global biogeochemical cycles especially in view of the recent and projected increases in TC-intensity that harbingers stronger mixing and heavier rain under the storm. PMID:27545899

Quantitative analysis of RNA-protein interactions on a massively parallel array for mapping biophysical and evolutionary landscapes

PubMed Central

Buenrostro, Jason D.; Chircus, Lauren M.; Araya, Carlos L.; Layton, Curtis J.; Chang, Howard Y.; Snyder, Michael P.; Greenleaf, William J.

2015-01-01

RNA-protein interactions drive fundamental biological processes and are targets for molecular engineering, yet quantitative and comprehensive understanding of the sequence determinants of affinity remains limited. Here we repurpose a high-throughput sequencing instrument to quantitatively measure binding and dissociation of MS2 coat protein to >107 RNA targets generated on a flow-cell surface by in situ transcription and inter-molecular tethering of RNA to DNA. We decompose the binding energy contributions from primary and secondary RNA structure, finding that differences in affinity are often driven by sequence-specific changes in association rates. By analyzing the biophysical constraints and modeling mutational paths describing the molecular evolution of MS2 from low- to high-affinity hairpins, we quantify widespread molecular epistasis, and a long-hypothesized structure-dependent preference for G:U base pairs over C:A intermediates in evolutionary trajectories. Our results suggest that quantitative analysis of RNA on a massively parallel array (RNAMaP) relationships across molecular variants. PMID:24727714

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.

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

Rainfall-enhanced blooming in typhoon wakes.

PubMed

Lin, Y-C; Oey, L-Y

2016-08-22

Strong phytoplankton blooming in tropical-cyclone (TC) wakes over the oligotrophic oceans potentially contributes to long-term changes in global biogeochemical cycles. Yet blooming has traditionally been discussed using anecdotal events and its biophysical mechanics remain poorly understood. Here we identify dominant blooming patterns using 16 years of ocean-color data in the wakes of 141 typhoons in western North Pacific. We observe right-side asymmetric blooming shortly after the storms, attributed previously to sub-mesoscale re-stratification, but thereafter a left-side asymmetry which coincides with the left-side preference in rainfall due to the large-scale wind shear. Biophysical model experiments and observations demonstrate that heavier rainfall freshens the near-surface water, leading to stronger stratification, decreased turbulence and enhanced blooming. Our results suggest that rainfall plays a previously unrecognized, critical role in TC-induced blooming, with potentially important implications for global biogeochemical cycles especially in view of the recent and projected increases in TC-intensity that harbingers stronger mixing and heavier rain under the storm.

Rainfall-enhanced blooming in typhoon wakes

NASA Astrophysics Data System (ADS)

Lin, Y.-C.; Oey, L.-Y.

2016-08-01

Strong phytoplankton blooming in tropical-cyclone (TC) wakes over the oligotrophic oceans potentially contributes to long-term changes in global biogeochemical cycles. Yet blooming has traditionally been discussed using anecdotal events and its biophysical mechanics remain poorly understood. Here we identify dominant blooming patterns using 16 years of ocean-color data in the wakes of 141 typhoons in western North Pacific. We observe right-side asymmetric blooming shortly after the storms, attributed previously to sub-mesoscale re-stratification, but thereafter a left-side asymmetry which coincides with the left-side preference in rainfall due to the large-scale wind shear. Biophysical model experiments and observations demonstrate that heavier rainfall freshens the near-surface water, leading to stronger stratification, decreased turbulence and enhanced blooming. Our results suggest that rainfall plays a previously unrecognized, critical role in TC-induced blooming, with potentially important implications for global biogeochemical cycles especially in view of the recent and projected increases in TC-intensity that harbingers stronger mixing and heavier rain under the storm.

Rainfall-enhanced blooming in typhoon wakes

NASA Astrophysics Data System (ADS)

Lin, Y.; Oey, L. Y.

2016-12-01

Strong phytoplankton blooming in tropical-cyclone (TC) wakes over the oligotrophic oceans potentially contributes to long-term changes in global biogeochemical cycles. Yet blooming has traditionally been discussed using anecdotal events and its biophysical mechanics remain poorly understood. Here we identify dominant blooming patterns using 16 years of ocean-color data in the wakes of 141 typhoons in western North Pacific. We observe right-side asymmetric blooming shortly after the storms, attributed previously to sub-mesoscale re-stratification, but thereafter a left-side asymmetry which coincides with the left-side preference in rainfall due to the large-scale wind shear. Biophysical model experiments and observations demonstrate that heavier rainfall freshens the near-surface water, leading to stronger stratification, decreased turbulence and enhanced blooming. Our results suggest that rainfall plays a previously unrecognized, critical role in TC-induced blooming, with potentially important implications for global biogeochemical cycles especially in view of the recent and projected increases in TC-intensity that harbingers stronger mixing and heavier rain under the storm.

Application of confocal laser microscopy for monitoring mesh implants in herniology

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

Zakharov, V P; Belokonev, V I; Bratchenko, I A

2011-04-30

The state of the surface of mesh implants and their encapsulation region in herniology is investigated by laser confocal microscopy. A correlation between the probability of developing relapses and the size and density of implant microdefects is experimentally shown. The applicability limits of differential reverse scattering for monitoring the post-operation state of implant and adjacent tissues are established based on model numerical experiments. (optical technologies in biophysics and medicine)

Landscape fuel reduction, forest fire, and biophysical linkages to local habitat use and local persistence of fishers (Pekania pennanti) in Sierra Nevada mixed-conifer forests

Treesearch

R.A. Sweitzer; B.J. Furnas; R.H. Barrett; Kathryn Purcell; Craig Thompson

2016-01-01

Fire suppression and logging have contributed to major changes in California’s Sierra Nevada forests. Strategically placed landscape treatments (SPLATS) are being used to reduce density of trees, shrubs, and surface fuels to limit wildfire intensity and spread, but may negatively impact fishers (Pekania pennanti). We used camera traps to survey for...

Toxin Detection by Surface Plasmon Resonance

PubMed Central

Hodnik, Vesna; Anderluh, Gregor

2009-01-01

Significant efforts have been invested in the past years for the development of analytical methods for fast toxin detection in food and water. Immunochemical methods like ELISA, spectroscopy and chromatography are the most used in toxin detection. Different methods have been linked, e.g. liquid chromatography and mass spectrometry (LC-MS), in order to detect as low concentrations as possible. Surface plasmon resonance (SPR) is one of the new biophysical methods which enables rapid toxin detection. Moreover, this method was already included in portable sensors for on-site determinations. In this paper we describe some of the most common methods for toxin detection, with an emphasis on SPR. PMID:22573957

Systemic analysis of desertification processes taking place in the Limpopo river basin

NASA Astrophysics Data System (ADS)

Messina, Mario; Attorre, Fabio; Vitale, Marcello

2016-04-01

Desertification and land degradation are phenomena that ranks among the greatest environmental challenges of our time. Desertification is a global issue, with serious implications worldwide for biodiversity, socio-economic stability and sustainable development. Biophysical indicators of land degradation and desertification, like Net Primary Productivity (NPP) and Total Ecosystem Respiration (Reco) were provided by remote sensing technology (MODIS). The study aims to evaluate the dynamical changes of NPP and Reco in the Limpopo river basin, a Southern African region that includes, Botswana, Mozambique, South Africa and Zimbabwe, during the time period 2001-2010. In particular, the relations between NPP, Reco, environmental, physiological and land use parameters have been widely investigated through the application of a new and powerful statistical classifier, the Random Forest Analysis (RFA), and a general non-linear model, the Response Surface Regression Model (GRM). RFA highlighted that Temperature is one of the most important predictors affecting NPP and Reco in the Limpopo river basin. Conversely, other environmental parameters like, Precipitation, Evapotranspiration and Vegetation cover rarely influence NPP and Reco. Our results provide information on desertification and land degradation phenomena and a first step for identifying practices to mitigate their negative impacts. However, it must be taken into account that NPP and Reco depend by a multitude of factors (e.g. human activities, socio-economic policies) and can vary in relation to spatial and temporal scale. In order to achieve a better understanding of land degradation and desertification processes, land use and socio-economic variables should be considered.

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.

Automatic Parameterization Strategy for Cardiac Electrophysiology Simulations

PubMed Central

Costa, Caroline Mendonca; Hoetzl, Elena; Rocha, Bernardo Martins; Prassl, Anton J; Plank, Gernot

2014-01-01

Driven by recent advances in medical imaging, image segmentation and numerical techniques, computer models of ventricular electrophysiology account for increasingly finer levels of anatomical and biophysical detail. However, considering the large number of model parameters involved parameterization poses a major challenge. A minimum requirement in combined experimental and modeling studies is to achieve good agreement in activation and repolarization sequences between model and experiment or patient data. In this study, we propose basic techniques which aid in determining bidomain parameters to match activation sequences. An iterative parameterization algorithm is implemented which determines appropriate bulk conductivities which yield prescribed velocities. In addition, a method is proposed for splitting the computed bulk conductivities into individual bidomain conductivities by prescribing anisotropy ratios. PMID:24729986

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.

Characterization of new DOPC/DHPC platform for dermal applications.

PubMed

Rodríguez, Gelen; Rubio, Laia; Barba, Clara; López-Iglesias, Carmen; de la Maza, Alfons; López, Olga; Cócera, Mercedes

2013-05-01

Systems formed by mixtures of the phospholipids dioleoylphosphatidylcholine (DOPC) and dihexanoylphosphatidylcholine (DHPC) were characterized by use of differential scanning calorimetry, small angle X-ray scattering and two electron-microscopy techniques, freeze fracture electron microscopy and cryogenic transmission electron microscopy. These techniques allowed for the determination of the size, morphology, structural topology, self-assembly and thermotropic behavior of the nanostructures present in the mixtures. The interaction between the two phospholipids provides curvatures, irregularities and the increase of thickness and flexibility in the membrane. These effects led to the formation of different aggregates with a differential distribution of both phospholipids. The effect of these systems on the skin in vivo was evaluated by measurement of the biophysical skin parameters. Our results show that the DOPC/DHPC application induces a decrease in the permeability and in the hydration of the tissue. These effects in vivo are related to different microstructural changes promoted by these systems in the skin in vitro, published in a recent work. The fundamental biophysical analyses of DOPC/DHPC systems contribute to our understanding of the mechanisms that govern their interaction with the skin.

Effect of viscosity on the wave propagation: Experimental determination of compression and expansion pulse wave velocity in fluid-fill elastic tube.

PubMed

Stojadinović, Bojana; Tenne, Tamar; Zikich, Dragoslav; Rajković, Nemanja; Milošević, Nebojša; Lazović, Biljana; Žikić, Dejan

2015-11-26

The velocity by which the disturbance travels through the medium is the wave velocity. Pulse wave velocity is one of the main parameters in hemodynamics. The study of wave propagation through the fluid-fill elastic tube is of great importance for the proper biophysical understanding of the nature of blood flow through of cardiovascular system. The effect of viscosity on the pulse wave velocity is generally ignored. In this paper we present the results of experimental measurements of pulse wave velocity (PWV) of compression and expansion waves in elastic tube. The solutions with different density and viscosity were used in the experiment. Biophysical model of the circulatory flow is designed to perform measurements. Experimental results show that the PWV of the expansion waves is higher than the compression waves during the same experimental conditions. It was found that the change in viscosity causes a change of PWV for both waves. We found a relationship between PWV, fluid density and viscosity. Copyright © 2015 Elsevier Ltd. All rights reserved.

Comparing the Potential of the Sentinel-2 MSI and the Future EnMAP HSI for the Retrieval of Winter Wheat Crop Parameters in Southern Germany

NASA Astrophysics Data System (ADS)

Danner, Martin; Hank, Tobias; Mauser, Wolfram

2016-08-01

This study tests the effect of improved spectral resolution on different approaches for the estimation of crop biophysical variables of winter wheat in Southern Germany by comparing the existing Sentinel-2 MSI with the future EnMAP HSI. The experiment is based on simulated sensor data of both Sentinel-2 and EnMAP, with their individual spectral configurations and radiometric properties taken into account. An advanced multispectral setup, such as provided by Sentinel-2, proved to enable reasonable estimation of biophysical variables by applying machine learning algorithms. The augmented information content inherent in hyperspectral signatures, however, marks an advantage for the creation of novel narrow-band indices (RMSE improvement of 10.0%) and for the inversion of canopy reflectance models like PROSAIL independent from in-situ data (RMSE improvement of 18.7%). With the notable advantages of Sentinel-2 - higher revisit rates and better spectral resolution - new synergies are expected to arise, once both instruments will be operating in parallel configuration.

Tracking diurnal changes of photosynthesis and evapotranspiration using fluorescence, gas exchange and hyperspectral remote sensing measurements

NASA Astrophysics Data System (ADS)

Wang, S.; Zhang, L.; Guanter, L.; Huang, C.

2017-12-01

Photosynthesis and evapotranspiration (ET) are the two most important activities of vegetation and make a great contribution to carbon, water and energy exchanges. Remote sensing provides opportunities for monitoring these processes across time and space. This study focuses on tracking diurnal changes of photosynthesis and evapotranspiration over soybean using multiple measurement techniques. Diurnal changes of both remote sensing-based indicators, including active and passive chlorophyll fluorescence and biophysical-related parameters, including photosynthesis rate (photo) and leaf stomatal conductance (cond), were observed. Results showed that both leaf-level steady-state fluorescence (Fs) and canopy-level solar-induced chlorophyll fluorescence were linearly correlated to photosynthetically active radiation (PAR) during the daytime. A double-peak diurnal change curve was observed for leaf-level photo and cond but not for Fs or SIF. Photo and cond showed a strong nonlinear (second-order) correlation, indicating that photosynthesis, which might be remotely sensed by SIF, has the opportunity to track short-term changes of ET. Results presented in this report will be helpful for better understanding the relationship between remote-sensing-based indices and vegetation's biophysical processes.

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)

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...

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.

AVIRIS Land-Surface Mapping in Support of the Boreal Ecosystem-Atmosphere Study (BOREAS)

NASA Technical Reports Server (NTRS)

Roberts, Dar A.; Gamon, John; Keightley, Keir; Prentiss, Dylan; Reith, Ernest; Green, Robert

2001-01-01

A key scientific objective of the original Boreal Ecosystem-Atmospheric Study (BOREAS) field campaign (1993-1996) was to obtain the baseline data required for modeling and predicting fluxes of energy, mass, and trace gases in the boreal forest biome. These data sets are necessary to determine the sensitivity of the boreal forest biome to potential climatic changes and potential biophysical feedbacks on climate. A considerable volume of remotely-sensed and supporting field data were acquired by numerous researchers to meet this objective. By design, remote sensing and modeling were considered critical components for scaling efforts, extending point measurements from flux towers and field sites over larger spatial and longer temporal scales. A major focus of the BOREAS follow-on program is concerned with integrating the diverse remotely sensed and ground-based data sets to address specific questions such as carbon dynamics at local to regional scales. The Airborne Visible/Infrared Imaging Spectrometer (AVIRIS) has the potential of contributing to BOREAS through: (1) accurate retrieved apparent surface reflectance; (2) improved landcover classification; and (3) direct assessment of biochemical/biophysical information such as canopy liquid water and chlorophyll concentration through pigment fits. In this paper, we present initial products for major flux tower sites including: (1) surface reflectance of dominant cover types; (2) a land-cover classification developed using spectral mixture analysis (SMA) and Multiple Endmember Spectral Mixture Analysis (MESMA); and (3) liquid water maps. Our goal is to compare these land-cover maps to existing maps and to incorporate AVIRIS image products into models of photosynthetic flux.

Coupling biophysical processes and water rights to simulate spatially distributed water use in an intensively managed hydrologic system

NASA Astrophysics Data System (ADS)

Han, Bangshuai; Benner, Shawn G.; Bolte, John P.; Vache, Kellie B.; Flores, Alejandro N.

2017-07-01

Humans have significantly altered the redistribution of water in intensively managed hydrologic systems, shifting the spatiotemporal patterns of surface water. Evaluating water availability requires integration of hydrologic processes and associated human influences. In this study, we summarize the development and evaluation of an extensible hydrologic model that explicitly integrates water rights to spatially distribute irrigation waters in a semi-arid agricultural region in the western US, using the Envision integrated modeling platform. The model captures both human and biophysical systems, particularly the diversion of water from the Boise River, which is the main water source that supports irrigated agriculture in this region. In agricultural areas, water demand is estimated as a function of crop type and local environmental conditions. Surface water to meet crop demand is diverted from the stream reaches, constrained by the amount of water available in the stream, the water-rights-appropriated amount, and the priority dates associated with particular places of use. Results, measured by flow rates at gaged stream and canal locations within the study area, suggest that the impacts of irrigation activities on the magnitude and timing of flows through this intensively managed system are well captured. The multi-year averaged diverted water from the Boise River matches observations well, reflecting the appropriation of water according to the water rights database. Because of the spatially explicit implementation of surface water diversion, the model can help diagnose places and times where water resources are likely insufficient to meet agricultural water demands, and inform future water management decisions.

Liquid bridges at the root-soil interface

NASA Astrophysics Data System (ADS)

Carminati, Andrea; Benard, Pascal; Ahmed, Mutez; Zarebanadkouki, Mohsen

2017-04-01

The role of the root-soil interface on soil-plant water relations is unclear. Despite many experimental studies proved that the soil close to the root surface, the rhizosphere, has different properties compared to the adjacent bulk soil, the mechanisms underlying such differences are poorly understood and the implications for plant-water relations remain largely speculative. The objective of this contribution is to discuss the key elements affecting water dynamics in the rhizosphere. Special attention is dedicated to the role of mucilage exuded by roots in shaping the hydraulic properties of the rhizosphere. We identified three key properties: 1) mucilage adsorbs water decreasing its water potential; 2) mucilage decreases the surface tension of the soil solution; 3) mucilage increases the viscosity of the soil solution. These three properties determine the retention and spatial configuration of the liquid phase in porous media. The increase in viscosity and the decrease in surface tension (quantified by the Ohnesorge number) allow the persistence of long liquid filaments even at very negative water potentials. At high mucilage concentrations these filaments form a network that creates an additional matric potential and maintains the continuity of the liquid phase during drying. The biophysical interactions between mucilage and the pore space determine the physical properties of the rhizosphere. Mucilage forms a network that provides mechanical stability to soils upon drying and that maintains the continuity of the liquid phase across the soil-root interface. Such biophysical properties are functional to create an interconnected matrix that maintains the roots in contact with the soil, which is of particular importance when the soil is drying and the transpiration rate is high.

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.

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

Comparison of binding energies of SrcSH2-phosphotyrosyl peptides with structure-based prediction using surface area based empirical parameterization.

PubMed Central

Henriques, D. A.; Ladbury, J. E.; Jackson, R. M.

2000-01-01

The prediction of binding energies from the three-dimensional (3D) structure of a protein-ligand complex is an important goal of biophysics and structural biology. Here, we critically assess the use of empirical, solvent-accessible surface area-based calculations for the prediction of the binding of Src-SH2 domain with a series of tyrosyl phosphopeptides based on the high-affinity ligand from the hamster middle T antigen (hmT), where the residue in the pY+ 3 position has been changed. Two other peptides based on the C-terminal regulatory site of the Src protein and the platelet-derived growth factor receptor (PDGFR) are also investigated. Here, we take into account the effects of proton linkage on binding, and test five different surface area-based models that include different treatments for the contributions to conformational change and protein solvation. These differences relate to the treatment of conformational flexibility in the peptide ligand and the inclusion of proximal ordered solvent molecules in the surface area calculations. This allowed the calculation of a range of thermodynamic state functions (deltaCp, deltaS, deltaH, and deltaG) directly from structure. Comparison with the experimentally derived data shows little agreement for the interaction of SrcSH2 domain and the range of tyrosyl phosphopeptides. Furthermore, the adoption of the different models to treat conformational change and solvation has a dramatic effect on the calculated thermodynamic functions, making the predicted binding energies highly model dependent. While empirical, solvent-accessible surface area based calculations are becoming widely adopted to interpret thermodynamic data, this study highlights potential problems with application and interpretation of this type of approach. There is undoubtedly some agreement between predicted and experimentally determined thermodynamic parameters: however, the tolerance of this approach is not sufficient to make it ubiquitously applicable. PMID:11106171

Protonation Dynamics on Lipid Nanodiscs: Influence of the Membrane Surface Area and External Buffers.

PubMed

Xu, Lei; Öjemyr, Linda Näsvik; Bergstrand, Jan; Brzezinski, Peter; Widengren, Jerker

2016-05-10

Lipid membrane surfaces can act as proton-collecting antennae, accelerating proton uptake by membrane-bound proton transporters. We investigated this phenomenon in lipid nanodiscs (NDs) at equilibrium on a local scale, analyzing fluorescence fluctuations of individual pH-sensitive fluorophores at the membrane surface by fluorescence correlation spectroscopy (FCS). The protonation rate of the fluorophores was ∼100-fold higher when located at 9- and 12-nm diameter NDs, compared to when in solution, indicating that the proton-collecting antenna effect is maximal already for a membrane area of ∼60 nm(2). Fluorophore-labeled cytochrome c oxidase displayed a similar increase when reconstituted in 12 nm NDs, but not in 9 nm NDs, i.e., an acceleration of the protonation rate at the surface of cytochrome c oxidase is found when the lipid area surrounding the protein is larger than 80 nm(2), but not when below 30 nm(2). We also investigated the effect of external buffers on the fluorophore proton exchange rates at the ND membrane-water interfaces. With increasing buffer concentrations, the proton exchange rates were found to first decrease and then, at millimolar buffer concentrations, to increase. Monte Carlo simulations, based on a simple kinetic model of the proton exchange at the membrane-water interface, and using rate parameter values determined in our FCS experiments, could reconstruct both the observed membrane-size and the external buffer dependence. The FCS data in combination with the simulations indicate that the local proton diffusion coefficient along a membrane is ∼100 times slower than that observed over submillimeter distances by proton-pulse experiments (Ds ∼ 10(-5)cm(2)/s), and support recent theoretical studies showing that proton diffusion along membrane surfaces is time- and length-scale dependent. Copyright © 2016 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Multi-scale enhancement of climate prediction over land by increasing the model sensitivity to vegetation variability in EC-Earth

NASA Astrophysics Data System (ADS)

Alessandri, Andrea; Catalano, Franco; De Felice, Matteo; Van Den Hurk, Bart; Doblas Reyes, Francisco; Boussetta, Souhail; Balsamo, Gianpaolo; Miller, Paul

2016-04-01

The EC-Earth earth system model has been recently developed to include the dynamics of vegetation. In its original formulation, vegetation variability is simply operated by the Leaf Area Index (LAI), which affects climate basically by changing the vegetation physiological resistance to evapotranspiration. This coupling has been found to have only a weak effect on the surface climate modeled by EC-Earth. In reality, the effective sub-grid vegetation fractional coverage will vary seasonally and at interannual time-scales in response to leaf-canopy growth, phenology and senescence. Therefore it affects biophysical parameters such as the albedo, surface roughness and soil field capacity. To adequately represent this effect in EC-Earth, we included an exponential dependence of the vegetation cover on the LAI. By comparing two sets of simulations performed with and without the new variable fractional-coverage parameterization, spanning retrospective predictions at the decadal (5-years), seasonal and sub-seasonal time-scales, we show for the first time a significant multi-scale enhancement of vegetation impacts in climate simulation and prediction over land. Particularly large effects at multiple time scales are shown over boreal winter middle-to-high latitudes over Canada, West US, Eastern Europe, Russia and eastern Siberia due to the implemented time-varying shadowing effect by tree-vegetation on snow surfaces. Over Northern Hemisphere boreal forest regions the improved representation of vegetation cover tends to correct the winter warm biases, improves the climate change sensitivity, the decadal potential predictability as well as the skill of forecasts at seasonal and sub-seasonal time-scales. Significant improvements of the prediction of 2m temperature and rainfall are also shown over transitional land surface hot spots. Both the potential predictability at decadal time-scale and seasonal-forecasts skill are enhanced over Sahel, North American Great Plains, Nordeste Brazil and South East Asia, mainly related to improved performance in the surface evapotranspiration.

Multi-scale enhancement of climate prediction over land by increasing the model sensitivity to vegetation variability in EC-Earth

NASA Astrophysics Data System (ADS)

Alessandri, A.; Catalano, F.; De Felice, M.; van den Hurk, B.; Doblas-Reyes, F. J.; Boussetta, S.; Balsamo, G.; Miller, P. A.

2016-12-01

The European consortium earth system model (EC-Earth; http://www.ec-earth.org) has been recently developed to include the dynamics of vegetation. In its original formulation, vegetation variability is simply operated by the Leaf Area Index (LAI), which affects climate basically by changing the vegetation physiological resistance to evapotranspiration. This coupling has been found to have only a weak effect on the surface climate modeled by EC-Earth. In reality, the effective sub-grid vegetation fractional coverage will vary seasonally and at interannual time-scales in response to leaf-canopy growth, phenology and senescence. Therefore it affects biophysical parameters such as the albedo, surface roughness and soil field capacity. To adequately represent this effect in EC-Earth, we included an exponential dependence of the vegetation cover on the LAI. By comparing two sets of simulations performed with and without the new variable fractional-coverage parameterization, spanning from centennial (20th Century) simulations and retrospective predictions to the decadal (5-years), seasonal and weather time-scales, we show for the first time a significant multi-scale enhancement of vegetation impacts in climate simulation and prediction over land. Particularly large effects at multiple time scales are shown over boreal winter middle-to-high latitudes over Canada, West US, Eastern Europe, Russia and eastern Siberia due to the implemented time-varying shadowing effect by tree-vegetation on snow surfaces. Over Northern Hemisphere boreal forest regions the improved representation of vegetation cover tends to correct the winter warm biases, improves the climate change sensitivity, the decadal potential predictability as well as the skill of forecasts at seasonal and weather time-scales. Significant improvements of the prediction of 2m temperature and rainfall are also shown over transitional land surface hot spots. Both the potential predictability at decadal time-scale and seasonal-forecasts skill are enhanced over Sahel, North American Great Plains, Nordeste Brazil and South East Asia, mainly related to improved performance in the surface evapotranspiration.

Multi-scale enhancement of climate prediction over land by increasing the model sensitivity to vegetation variability in EC-Earth

NASA Astrophysics Data System (ADS)

Alessandri, Andrea; Catalano, Franco; De Felice, Matteo; Van Den Hurk, Bart; Doblas Reyes, Francisco; Boussetta, Souhail; Balsamo, Gianpaolo; Miller, Paul A.

2017-08-01

The EC-Earth earth system model has been recently developed to include the dynamics of vegetation. In its original formulation, vegetation variability is simply operated by the Leaf Area Index (LAI), which affects climate basically by changing the vegetation physiological resistance to evapotranspiration. This coupling has been found to have only a weak effect on the surface climate modeled by EC-Earth. In reality, the effective sub-grid vegetation fractional coverage will vary seasonally and at interannual time-scales in response to leaf-canopy growth, phenology and senescence. Therefore it affects biophysical parameters such as the albedo, surface roughness and soil field capacity. To adequately represent this effect in EC-Earth, we included an exponential dependence of the vegetation cover on the LAI. By comparing two sets of simulations performed with and without the new variable fractional-coverage parameterization, spanning from centennial (twentieth century) simulations and retrospective predictions to the decadal (5-years), seasonal and weather time-scales, we show for the first time a significant multi-scale enhancement of vegetation impacts in climate simulation and prediction over land. Particularly large effects at multiple time scales are shown over boreal winter middle-to-high latitudes over Canada, West US, Eastern Europe, Russia and eastern Siberia due to the implemented time-varying shadowing effect by tree-vegetation on snow surfaces. Over Northern Hemisphere boreal forest regions the improved representation of vegetation cover tends to correct the winter warm biases, improves the climate change sensitivity, the decadal potential predictability as well as the skill of forecasts at seasonal and weather time-scales. Significant improvements of the prediction of 2 m temperature and rainfall are also shown over transitional land surface hot spots. Both the potential predictability at decadal time-scale and seasonal-forecasts skill are enhanced over Sahel, North American Great Plains, Nordeste Brazil and South East Asia, mainly related to improved performance in the surface evapotranspiration.

Multi-scale enhancement of climate prediction over land by increasing the model sensitivity to vegetation variability in EC-Earth

NASA Astrophysics Data System (ADS)

Alessandri, Andrea; Catalano, Franco; De Felice, Matteo; Van Den Hurk, Bart; Doblas Reyes, Francisco; Boussetta, Souhail; Balsamo, Gianpaolo; Miller, Paul A.

2017-04-01

The EC-Earth earth system model has been recently developed to include the dynamics of vegetation. In its original formulation, vegetation variability is simply operated by the Leaf Area Index (LAI), which affects climate basically by changing the vegetation physiological resistance to evapotranspiration. This coupling has been found to have only a weak effect on the surface climate modeled by EC-Earth. In reality, the effective sub-grid vegetation fractional coverage will vary seasonally and at interannual time-scales in response to leaf-canopy growth, phenology and senescence. Therefore it affects biophysical parameters such as the albedo, surface roughness and soil field capacity. To adequately represent this effect in EC-Earth, we included an exponential dependence of the vegetation cover on the LAI. By comparing two sets of simulations performed with and without the new variable fractional-coverage parameterization, spanning from centennial (20th Century) simulations and retrospective predictions to the decadal (5-years), seasonal and weather time-scales, we show for the first time a significant multi-scale enhancement of vegetation impacts in climate simulation and prediction over land. Particularly large effects at multiple time scales are shown over boreal winter middle-to-high latitudes over Canada, West US, Eastern Europe, Russia and eastern Siberia due to the implemented time-varying shadowing effect by tree-vegetation on snow surfaces. Over Northern Hemisphere boreal forest regions the improved representation of vegetation cover tends to correct the winter warm biases, improves the climate change sensitivity, the decadal potential predictability as well as the skill of forecasts at seasonal and weather time-scales. Significant improvements of the prediction of 2m temperature and rainfall are also shown over transitional land surface hot spots. Both the potential predictability at decadal time-scale and seasonal-forecasts skill are enhanced over Sahel, North American Great Plains, Nordeste Brazil and South East Asia, mainly related to improved performance in the surface evapotranspiration.

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.

Piper betle-mediated green synthesis of biocompatible gold nanoparticles

NASA Astrophysics Data System (ADS)

Punuri, Jayasekhar Babu; Sharma, Pragya; Sibyala, Saranya; Tamuli, Ranjan; Bora, Utpal

2012-08-01

Here, we report the novel use of the ethonolic leaf extract of Piper betle for gold nanoparticle (AuNP) synthesis. The successful formation of AuNPs was confirmed by UV-visible spectroscopy, and different parameters such as leaf extract concentration (2%), gold salt concentration (0.5 mM), and time (18 s) were optimized. The synthesized AuNPs were characterized with different biophysical techniques such as transmission electron microscopy (TEM), Fourier transform infrared (FT-IR) spectroscopy, X-ray diffraction (XRD), and energy-dispersive X-ray spectroscopy (EDX). TEM experiments showed that nanoparticles were of various shapes and sizes ranging from 10 to 35 nm. FT-IR spectroscopy revealed that AuNPs were functionalized with biomolecules that have primary amine group -NH2, carbonyl group, -OH groups, and other stabilizing functional groups. EDX showed the presence of the elements on the surface of the AuNPs. FT-IR and EDX together confirmed the presence of biomolecules bounded on the AuNPs. Cytotoxicity of the AuNPs was tested on HeLa and MCF-7 cancer cell lines, and they were found to be nontoxic, indicating their biocompatibility. Thus, synthesized AuNPs have potential for use in various biomedical applications.

Effect of polyethylene glycol conjugation on conformational and colloidal stability of a monoclonal antibody antigen-binding fragment (Fab').

PubMed

Roque, Cristopher; Sheung, Anthony; Rahman, Nausheen; Ausar, S Fernando

2015-02-02

We have investigated the effects of site specific "hinge" polyethylene glycol conjugation (PEGylation) on thermal, pH, and colloidal stability of a monoclonal antibody antigen-binding fragment (Fab') using a variety of biophysical techniques. The results obtained by circular dichroism (CD), ultraviolet (UV) absorbance, and fluorescence spectroscopy suggested that the physical stability of the Fab' is maximized at pH 6-7 with no apparent differences due to PEGylation. Temperature-induced aggregation experiments revealed that PEGylation was able to increase the transition temperature, as well as prevent the formation of visible and subvisible aggregates. Statistical comparison of the three-index empirical phase diagram (EPD) revealed significant differences in thermal and pH stability signatures between Fab' and PEG-Fab'. Upon mechanical stress, micro-flow imaging (MFI) and measurement of the optical density at 360 nm showed that the PEG-Fab' had significantly higher resistance to surface-induced aggregation compared to the Fab'. Analysis of the interaction parameter, kD, indicated repulsive intermolecular forces for PEG-Fab' and attractive forces for Fab'. In conclusion, PEGylation appears to protect Fab' against thermal and mechanical stress-induced aggregation, likely due to a steric hindrance mechanism.

Seasonal soybean crop reflectance

NASA Technical Reports Server (NTRS)

Lemaster, E. W. (Principal Investigator); Chance, J. E.

1983-01-01

Data are presented from field measurements of 1980 including 5 acquisitions of handheld radiometer reflectance measurements, 7 complete sets of parameters for implementing the Suits mode, and other biophysical parameters to characterize the soybean canopy. LANDSAT calculations on the simulated Brazilian soybean reflectance are included along with data collected during the summer and fall on 1981 on soybean single leaf optical parameters for three irrigation treatments. Tests of the Suits vegetative canopy reflectance model for the full hemisphere of observer directions as well as the nadir direction show moderate agreement for the visible channels of the MSS and poor agreement in the near infrared channel. Temporal changes in the spectral characteristics of the single leaves were seen to occur as a function of maturity which demonstrates that the absorptance of a soybean single leaf is more a function of thetransmittancee characteristics than the seasonally consistent single leaf reflectance.

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.

Change in the Beaufort Sea ecosystem: Diverging trends in body condition and/or production in five marine vertebrate species

NASA Astrophysics Data System (ADS)

Harwood, L. A.; Smith, T. G.; George, J. C.; Sandstrom, S. J.; Walkusz, W.; Divoky, G. J.

2015-08-01

Studies of the body condition of five marine vertebrate predators in the Beaufort Sea, conducted independently during the past 2-4 decades, suggest each has been affected by biophysical changes in the marine ecosystem. We summarize a temporal trend of increasing body condition in two species (bowhead whale subadults, Arctic char), in both cases influenced by the extent and persistence of annual sea ice. Three other species (ringed seal, beluga, black guillemot chicks), consumers with a dietary preference for Arctic cod, experienced declines in condition, growth and/or production during the same time period. The proximate causes of these observed changes remain unknown, but may reflect an upward trend in secondary productivity, and a concurrent downward trend in the availability of forage fishes, such as the preferred Arctic cod. To further our understanding of these apparent ecosystem shifts, we urge the use of multiple marine vertebrate species in the design of biophysical sampling studies to identify causes of these changes. Continued long-term, standardized monitoring of vertebrate body condition should be paired with concurrent direct (stomach contents) or indirect (isotopes, fatty acids) monitoring of diet, detailed study of movements and seasonal ranges to establish and refine baselines, and identification of critical habitats of the marine vertebrates being monitored. This would be coordinated with biophysical and oceanographic sampling, at spatial and temporal scales, and geographic locations, that are relevant to the home range, critical habitats and prey of the vertebrate indicator species showing changes in condition and related parameters.

The impact of using area-averaged land surface properties —topography, vegetation condition, soil wetness—in calculations of intermediate scale (approximately 10 km 2) surface-atmosphere heat and moisture fluxes

NASA Astrophysics Data System (ADS)

Sellers, Piers J.; Heiser, Mark D.; Hall, Forrest G.; Verma, Shashi B.; Desjardins, Raymond L.; Schuepp, Peter M.; Ian MacPherson, J.

1997-03-01

It is commonly assumed that biophysically based soil-vegetation-atmosphere transfer (SVAT) models are scale-invariant with respect to the initial boundary conditions of topography, vegetation condition and soil moisture. In practice, SVAT models that have been developed and tested at the local scale (a few meters or a few tens of meters) are applied almost unmodified within general circulation models (GCMs) of the atmosphere, which have grid areas of 50-500 km 2. This study, which draws much of its substantive material from the papers of Sellers et al. (1992c, J. Geophys. Res., 97(D17): 19033-19060) and Sellers et al. (1995, J. Geophys. Res., 100(D12): 25607-25629), explores the validity of doing this. The work makes use of the FIFE-89 data set which was collected over a 2 km × 15 km grassland area in Kansas. The site was characterized by high variability in soil moisture and vegetation condition during the late growing season of 1989. The area also has moderate topography. The 2 km × 15 km 'testbed' area was divided into 68 × 501 pixels of 30 m × 30 m spatial resolution, each of which could be assigned topographic, vegetation condition and soil moisture parameters from satellite and in situ observations gathered in FIFE-89. One or more of these surface fields was area-averaged in a series of simulation runs to determine the impact of using large-area means of these initial or boundary conditions on the area-integrated (aggregated) surface fluxes. The results of the study can be summarized as follows: 1. analyses and some of the simulations indicated that the relationships describing the effects of moderate topography on the surface radiation budget are near-linear and thus largely scale-invariant. The relationships linking the simple ratio vegetation index ( SR), the canopy conductance parameter (▽ F) and the canopy transpiration flux are also near-linear and similarly scale-invariant to first order. Because of this, it appears that simple area-averaging operations can be applied to these fields with relatively little impact on the calculated surface heat flux. 2. The relationships linking surface and root-zone soil wetness to the soil surface and canopy transpiration rates are non-linear. However, simulation results and observations indicate that soil moisture variability decreases significantly as an area dries out, which partially cancels out the effects of these non-linear functions.In conclusion, it appears that simple averages of topographic slope and vegetation parameters can be used to calculate surface energy and heat fluxes over a wide range of spatial scales, from a few meters up to many kilometers at least for grassland sites and areas with moderate topography. Although the relationships between soil moisture and evapotranspiration are non-linear for intermediate soil wetnesses, the dynamics of soil drying act to progressively reduce soil moisture variability and thus the impacts of these non-linearities on the area-averaged surface fluxes. These findings indicate that we may be able to use mean values of topography, vegetation condition and soil moisture to calculate the surface-atmosphere fluxes of energy, heat and moisture at larger length scales, to within an acceptable accuracy for climate modeling work. However, further tests over areas with different vegetation types, soils and more extreme topography are required to improve our confidence in this approach.

Surface-atmosphere exchange of ammonia over peatland using QCL-based eddy-covariance measurements and inferential modeling

NASA Astrophysics Data System (ADS)

Zöll, Undine; Brümmer, Christian; Schrader, Frederik; Ammann, Christof; Ibrom, Andreas; Flechard, Christophe R.; Nelson, David D.; Zahniser, Mark; Kutsch, Werner L.

2016-09-01

Recent advances in laser spectrometry offer new opportunities to investigate ecosystem-atmosphere exchange of environmentally relevant trace gases. In this study, we demonstrate the applicability of a quantum cascade laser (QCL) absorption spectrometer to continuously measure ammonia concentrations at high time resolution and thus to quantify the net exchange between a seminatural peatland ecosystem and the atmosphere based on the eddy-covariance approach. Changing diurnal patterns of both ammonia concentration and fluxes were found during different periods of the campaign. We observed a clear tipping point in early spring with decreasing ammonia deposition velocities and increasingly bidirectional fluxes that occurred after the switch from dormant vegetation to CO2 uptake but was triggered by a significant weather change. While several biophysical parameters such as temperature, radiation, and surface wetness were identified to partially regulate ammonia exchange at the site, the seasonal concentration pattern was clearly dominated by agricultural practices in the surrounding area. Comparing the results of a compensation point model with our measurement-based flux estimates showed considerable differences in some periods of the campaign due to overestimation of non-stomatal resistances caused by low acid ratios. The total cumulative campaign exchange of ammonia after 9 weeks, however, differed only in a 6 % deviation with 911 and 857 g NH3-N ha-1 deposition being found by measurements and modeling, respectively. Extrapolating our findings to an entire year, ammonia deposition was lower than reported by Hurkuck et al. (2014) for the same site in previous years using denuder systems. This was likely due to a better representation of the emission component in the net signal of eddy-covariance fluxes as well as better adapted site-specific parameters in the model. Our study not only stresses the importance of high-quality measurements for studying and assessing land surface-atmosphere interactions but also demonstrates the potential of QCL spectrometers for continuous observation of reactive nitrogen species as important additional instruments within long-term monitoring research infrastructures such as ICOS or NEON at sites with strong nearby ammonia sources leading to relatively high mean background concentrations and fluxes.

The impact of inter-annual rainfall variability on food production in the Ganges basin

NASA Astrophysics Data System (ADS)

Siderius, Christian; Biemans, Hester; van Walsum, Paul; hellegers, Petra; van Ierland, Ekko; Kabat, Pavel

2014-05-01

Rainfall variability is expected to increase in the coming decades as the world warms. Especially in regions already water stressed, a higher rainfall variability will jeopardize food security. Recently, the impact of inter-annual rainfall variability has received increasing attention in regional to global analysis on water availability and food security. But the description of the dynamics behind it is still incomplete in most models. Contemporary land surface and hydrological models used for such analyses describe variability in production primarily as a function of yield, a process driven by biophysical parameters, thereby neglecting yearly variations in cropped area, a process driven largely by management decisions. Agricultural statistics for northern India show that the latter process could explain up to 40% of the observed inter-annual variation in food production in various states. We added a simple dynamic land use decision module to a land surface model (LPJmL) and analyzed to what extent this improved the estimation of variability in food production. Using this improved modelling framework we then assessed if and at which scale rainfall variability affects meeting the food self-sufficiency threshold. Early results for the Ganges Basin indicate that, while on basin level variability in crop production is still relatively low, several districts and states are highly affected (RSTD > 50%). Such insight can contribute to better recommendations on the most effective measures, at the most appropriate scale, to buffer variability in food production.

Spatially Complete Surface Albedo Data Sets: Value-Added Products Derived from Terra MODIS Land Products

NASA Technical Reports Server (NTRS)

Moody, E. G.; King, M. D.; Platnick, S.; Schaaf, C. B.; Gao, F.

2004-01-01

Spectral land surface albedo is an important parameter for describing the radiative properties of the Earth. Accordingly it reflects the consequences of natural and human interactions, such as anthropogenic, meteorological, and phenological effects, on global and local climatological trends. Consequently, albedos are integral parts in a variety of research areas, such as general circulation models (GCMs), energy balance studies, modeling of land use and land use change, and biophysical, oceanographic, and meteorological studies. The availability of global albedo data over a large range of spectral channels and at high spatial resolution has dramatically improved with the launch of the Moderate Resolution Imaging Spectroradiometer (MODIS) instrument aboard NASA s Earth Observing System (EOS) Terra spacecraft in December 1999. However, lack of spatial and temporal coverage due to cloud and snow effects can preclude utilization of official products in production and research studies. We report on a technique used to fill incomplete MOD43 albedo data sets with the intention of providing complete value-added maps. The technique is influenced by the phenological concept that within a certain area, a pixel s ecosystem class should exhibit similar growth cycle events over the same time period. The shape of an area s phenological temporal curve can be imposed upon existing pixel-level data to fill missing temporal points. The methodology will be reviewed by showcasing 2001 global and regional results of complete albedo and NDVl data sets.

Biophysical Variability in the Kuroshio Extension from Altimeter and SeaWiFS

DTIC Science & Technology

2010-06-01

Prediction Laboratory Department of Oceanography Naval Postgraduate School Monterey, CA 93943 Abstract— Ten years (1998- 2007 ) of Sea Level Anomaly...heights have been measured by the ERS 1/2 and TOPEX/Poseidon satellites from 1 January 1998 to 31 December 2007 at 7-day intervals. Radar altimeters...3) from January 1998 to December 2007 (10 years period). Temporal variations of sea surface elevation residuals and Chl-a along the mean KE axis

A regression approach to the mapping of bio-physical characteristics of surface sediment using in situ and airborne hyperspectral acquisitions

NASA Astrophysics Data System (ADS)

Ibrahim, Elsy; Kim, Wonkook; Crawford, Melba; Monbaliu, Jaak

2017-02-01

Remote sensing has been successfully utilized to distinguish and quantify sediment properties in the intertidal environment. Classification approaches of imagery are popular and powerful yet can lead to site- and case-specific results. Such specificity creates challenges for temporal studies. Thus, this paper investigates the use of regression models to quantify sediment properties instead of classifying them. Two regression approaches, namely multiple regression (MR) and support vector regression (SVR), are used in this study for the retrieval of bio-physical variables of intertidal surface sediment of the IJzermonding, a Belgian nature reserve. In the regression analysis, mud content, chlorophyll a concentration, organic matter content, and soil moisture are estimated using radiometric variables of two airborne sensors, namely airborne hyperspectral sensor (AHS) and airborne prism experiment (APEX) and and using field hyperspectral acquisitions by analytical spectral device (ASD). The performance of the two regression approaches is best for the estimation of moisture content. SVR attains the highest accuracy without feature reduction while MR achieves good results when feature reduction is carried out. Sediment property maps are successfully obtained using the models and hyperspectral imagery where SVR used with all bands achieves the best performance. The study also involves the extraction of weights identifying the contribution of each band of the images in the quantification of each sediment property when MR and principal component analysis are used.

Surface modification of a polyhedral oligomeric silsesquioxane poly(carbonate-urea) urethane (POSS-PCU) nanocomposite polymer as a stent coating for enhanced capture of endothelial progenitor cells

PubMed Central

Tan, Aaron; Farhatnia, Yasmin; Goh, Debbie; G, Natasha; de Mel, Achala; Lim, Jing; Teoh, Swee-Hin; Malkovskiy, Andrey V; Chawla, Reema; Rajadas, Jayakumar; Cousins, Brian G; Hamblin, Michael R; Alavijeh, Mohammad S; Seifalian, Alexander M

2013-01-01

An unmet need exists for the development of next-generation multifunctional nanocomposite materials for biomedical applications, particularly in the field of cardiovascular regenerative biology. Herein, we describe the preparation and characterization of a novel polyhedral oligomeric silsesquioxane poly(carbonate-urea) urethane (POSS-PCU) nanocomposite polymer with covalently attached anti-CD34 antibodies to enhance capture of circulating endothelial progenitor cells (EPC). This material may be used as a new coating for bare metal stents used after balloon angioplasty to improve re-endothelialization. Biophysical characterization techniques were used to assess POSS-PCU and its subsequent functionalization with anti-CD34 antibodies. Results indicated successful covalent attachment of anti-CD34 antibodies on the surface of POSS-PCU leading to an increased propensity for EPC capture, whilst maintaining in vitro biocompatibility and hemocompatibility. POSS-PCU has already been used in 3 first-in-man studies, as a bypass graft, lacrimal duct and a bioartificial trachea. We therefore postulate that its superior biocompatibility and unique biophysical properties would render it an ideal candidate for coating medical devices, with stents as a prime example. Taken together, anti-CD34 functionalized POSS-PCU could form the basis of a nano-inspired polymer platform for the next generation stent coatings. PMID:24706135

Generator localization by current source density (CSD): Implications of volume conduction and field closure at intracranial and scalp resolutions

PubMed Central

Tenke, Craig E.; Kayser, Jürgen

2012-01-01

The topographic ambiguity and reference-dependency that has plagued EEG/ERP research throughout its history are largely attributable to volume conduction, which may be concisely described by a vector form of Ohm’s Law. This biophysical relationship is common to popular algorithms that infer neuronal generators via inverse solutions. It may be further simplified as Poisson’s source equation, which identifies underlying current generators from estimates of the second spatial derivative of the field potential (Laplacian transformation). Intracranial current source density (CSD) studies have dissected the “cortical dipole” into intracortical sources and sinks, corresponding to physiologically-meaningful patterns of neuronal activity at a sublaminar resolution, much of which is locally cancelled (i.e., closed field). By virtue of the macroscopic scale of the scalp-recorded EEG, a surface Laplacian reflects the radial projections of these underlying currents, representing a unique, unambiguous measure of neuronal activity at scalp. Although the surface Laplacian requires minimal assumptions compared to complex, model-sensitive inverses, the resulting waveform topographies faithfully summarize and simplify essential constraints that must be placed on putative generators of a scalp potential topography, even if they arise from deep or partially-closed fields. CSD methods thereby provide a global empirical and biophysical context for generator localization, spanning scales from intracortical to scalp recordings. PMID:22796039

Computational and biophysical approaches to protein-protein interaction inhibition of Plasmodium falciparum AMA1/RON2 complex

NASA Astrophysics Data System (ADS)

Pihan, Emilie; Delgadillo, Roberto F.; Tonkin, Michelle L.; Pugnière, Martine; Lebrun, Maryse; Boulanger, Martin J.; Douguet, Dominique

2015-06-01

Invasion of the red blood cell by Plasmodium falciparum parasites requires formation of an electron dense circumferential ring called the Moving Junction (MJ). The MJ is anchored by a high affinity complex of two parasite proteins: Apical Membrane Antigen 1 ( PfAMA1) displayed on the surface of the parasite and Rhoptry Neck Protein 2 that is discharged from the parasite and imbedded in the membrane of the host cell. Structural studies of PfAMA1 revealed a conserved hydrophobic groove localized to the apical surface that coordinates RON2 and invasion inhibitory peptides. In the present work, we employed computational and biophysical methods to identify competitive P. falciparum AMA1-RON2 inhibitors with the goal of exploring the `druggability' of this attractive antimalarial target. A virtual screen followed by molecular docking with the PfAMA1 crystal structure was performed using an eight million compound collection that included commercial molecules, the ChEMBL malaria library and approved drugs. The consensus approach resulted in the selection of inhibitor candidates. We also developed a fluorescence anisotropy assay using a modified inhibitory peptide to experimentally validate the ability of the selected compounds to inhibit the AMA1-RON2 interaction. Among those, we identified one compound that displayed significant inhibition. This study offers interesting clues to improve the throughput and reliability of screening for new drug leads.

Structural and biophysical characterization of an epitope-specific engineered Fab fragment and complexation with membrane proteins: implications for co-crystallization.

PubMed

Johnson, Jennifer L; Entzminger, Kevin C; Hyun, Jeongmin; Kalyoncu, Sibel; Heaner, David P; Morales, Ivan A; Sheppard, Aly; Gumbart, James C; Maynard, Jennifer A; Lieberman, Raquel L

2015-04-01

Crystallization chaperones are attracting increasing interest as a route to crystal growth and structure elucidation of difficult targets such as membrane proteins. While strategies to date have typically employed protein-specific chaperones, a peptide-specific chaperone to crystallize multiple cognate peptide epitope-containing client proteins is envisioned. This would eliminate the target-specific chaperone-production step and streamline the co-crystallization process. Previously, protein engineering and directed evolution were used to generate a single-chain variable (scFv) antibody fragment with affinity for the peptide sequence EYMPME (scFv/EE). This report details the conversion of scFv/EE to an anti-EE Fab format (Fab/EE) followed by its biophysical characterization. The addition of constant chains increased the overall stability and had a negligible impact on the antigen affinity. The 2.0 Å resolution crystal structure of Fab/EE reveals contacts with larger surface areas than those of scFv/EE. Surface plasmon resonance, an enzyme-linked immunosorbent assay, and size-exclusion chromatography were used to assess Fab/EE binding to EE-tagged soluble and membrane test proteins: namely, the β-barrel outer membrane protein intimin and α-helical A2a G protein-coupled receptor (A2aR). Molecular-dynamics simulation of the intimin constructs with and without Fab/EE provides insight into the energetic complexities of the co-crystallization approach.