WorldWideScience

Sample records for important biophysical processes

  1. Biophysical processes in the Indian Ocean

    Digital Repository Service at National Institute of Oceanography (India)

    Mc; Murtugudde, R.; Vialard, J.; Vinayachandran, P.N.; Wiggert, J.D.; Hood, R.R.; Shankar, D.; Shetye, S.R.

    Ocean Biogeochemical Processes and Ecological Variability Geophysical Monograph Series 185 Copyright 200� by the American Geophysical Union. 10.102�/2008GM000768 Biophysical Processes in the Indian Ocean J. P. McCreary, 1 R. Murtugudde, 2 J. Vialard, 3...) also plots the upper-layer thickness, h 1 , from the model of McCreary et al. [1��3] (hereinafter referred to as MKM); h 1 simulates the structure of the top of the actual thermocline reasonably well, except that it is somewhat too thin from 5...

  2. Biophysics conference 1978

    International Nuclear Information System (INIS)

    1978-01-01

    The main subject on the biophysics meeting was the biophysics of membranes with practical subjects from photosynthesis and the transfer processes on membranes. In radiation biophysics, problems of radiation sensitisation, immunological problems after radiation exposure, the oxygen effect and inhibitory processes in RNS synthesis after radiation exposure were discussed with a view to tumour therapy. (AJ) [de

  3. Biophysics An Introduction

    CERN Document Server

    Glaser, Roland

    2012-01-01

    Biophysics is the science of physical principles underlying all processes of life, including the dynamics and kinetics of biological systems. This fully revised 2nd English edition is an introductory text that spans all steps of biological organization, from the molecular, to the organism level, as well as influences of environmental factors. In response to the enormous progress recently made, especially in theoretical and molecular biophysics, the author has updated the text, integrating new results and developments concerning protein folding and dynamics, molecular aspects of membrane assembly and transport, noise-enhanced processes, and photo-biophysics. The advances made in theoretical biology in the last decade call for a fully new conception of the corresponding sections. Thus, the book provides the background needed for fundamental training in biophysics and, in addition, offers a great deal of advanced biophysical knowledge.

  4. Biophysics of protein evolution and evolutionary protein biophysics

    Science.gov (United States)

    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

  5. Role of Membrane Biophysics in Alzheimer's - related cell pathways

    Directory of Open Access Journals (Sweden)

    Donghui eZhu

    2015-05-01

    Full Text Available Cellular membrane alterations are commonly observed in many diseases, including Alzheimer’s disease (AD. Membrane biophysical properties, such as membrane molecular order, membrane fluidity, organization of lipid rafts, and adhesion between membrane and cytoskeleton, play an important role in various cellular activities and functions. While membrane biophysics impacts a broad range of cellular pathways, this review addresses the role of membrane biophysics in amyloid-β peptide aggregation, Aβ-induced oxidative pathways, amyloid precursor protein processing, and cerebral endothelial functions in AD. Understanding the mechanism(s underlying the effects of cell membrane properties on cellular processes should shed light on the development of new preventive and therapeutic strategies for this devastating disease.

  6. Methods in Modern Biophysics

    CERN Document Server

    Nölting, Bengt

    2010-01-01

    Incorporating recent dramatic advances, this textbook presents a fresh and timely introduction to modern biophysical methods. An array of new, faster and higher-power biophysical methods now enables scientists to examine the mysteries of life at a molecular level. This innovative text surveys and explains the ten key biophysical methods, including those related to biophysical nanotechnology, scanning probe microscopy, X-ray crystallography, ion mobility spectrometry, mass spectrometry, proteomics, and protein folding and structure. Incorporating much information previously unavailable in tutorial form, Nölting employs worked examples and about 270 illustrations to fully detail the techniques and their underlying mechanisms. Methods in Modern Biophysics is written for advanced undergraduate and graduate students, postdocs, researchers, lecturers, and professors in biophysics, biochemistry and related fields. Special features in the 3rd edition: Introduces rapid partial protein ladder sequencing - an important...

  7. Biophysics of Human Hair Structural, Nanomechanical, and Nanotribological Studies

    CERN Document Server

    Bhushan, Bharat

    2010-01-01

    This book presents the biophysics of hair. It deals with the structure of hair, its mechanical properties, the nanomechanical characterization, tensile deformation, tribological characterization, the thickness distribution and binding interactions on hair surface. Another important topic of the book is the health of hair, human hair and skin, hair care, cleaning and conditioning treatments and damaging processes. It is the first book on the biophysical properties of hair.

  8. Fundamental Concepts in Biophysics Volume 1

    CERN Document Server

    Jue, Thomas

    2009-01-01

    HANDBOOK OF MODERN BIOPHYSICS Series Editor Thomas Jue, PhD Handbook of Modern Biophysics brings current biophysics topics into focus, so that biology, medical, engineering, mathematics, and physical-science students or researchers can learn fundamental concepts and the application of new techniques in addressing biomedical challenges. Chapters explicate the conceptual framework of the physics formalism and illustrate the biomedical applications. With the addition of problem sets, guides to further study, and references, the interested reader can continue to explore independently the ideas presented. Volume I: Fundamental Concepts in Biophysics Editor Thomas Jue, PhD In Fundamental Concepts in Biophysics, prominent professors have established a foundation for the study of biophysics related to the following topics: Mathematical Methods in Biophysics Quantum Mechanics Basic to Biophysical Methods Computational Modeling of Receptor–Ligand Binding and Cellular Signaling Processes Fluorescence Spectroscopy Elec...

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

    Science.gov (United States)

    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

  10. Handbook of Single-Molecule Biophysics

    CERN Document Server

    Hinterdorfer, Peter

    2009-01-01

    The last decade has seen the development of a number of novel biophysical methods that allow the manipulation and study of individual biomolecules. The ability to monitor biological processes at this fundamental level of sensitivity has given rise to an improved understanding of the underlying molecular mechanisms. Through the removal of ensemble averaging, distributions and fluctuations of molecular properties can be characterized, transient intermediates identified, and catalytic mechanisms elucidated. By applying forces on biomolecules while monitoring their activity, important information can be obtained on how proteins couple function to structure. The Handbook of Single-Molecule Biophysics provides an introduction to these techniques and presents an extensive discussion of the new biological insights obtained from them. Coverage includes: Experimental techniques to monitor and manipulate individual biomolecules The use of single-molecule techniques in super-resolution and functional imaging Single-molec...

  11. Mathematical biophysics

    CERN Document Server

    Rubin, Andrew

    2014-01-01

    This book presents concise descriptions and analysis of the classical and modern models used in mathematical biophysics. The authors ask the question "what new information can be provided by the models that cannot be obtained directly from experimental data?" Actively developing fields such as regulatory mechanisms in cells and subcellular systems and electron transport and energy transport in membranes are addressed together with more classical topics such as metabolic processes, nerve conduction and heart activity, chemical kinetics, population dynamics, and photosynthesis. The main approach is to describe biological processes using different mathematical approaches necessary to reveal characteristic features and properties of simulated systems. With the emergence of powerful mathematics software packages such as MAPLE, Mathematica, Mathcad, and MatLab, these methodologies are now accessible to a wide audience. Provides succinct but authoritative coverage of a broad array of biophysical topics and models Wr...

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

    Science.gov (United States)

    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.

  13. Biophysical aspects of photodynamic therapy.

    Science.gov (United States)

    Juzeniene, Asta; Nielsen, Kristian Pagh; Moan, Johan

    2006-01-01

    Over the last three decades photodynamic therapy (PDT) has been developed to a useful clinical tool, a viable alternative in the treatment of cancer and other diseases. Several disciplines have contributed to this development: chemistry in the development of new photosensitizing agents, biology in the elucidation of cellular processes involved in PDT, pharmacology and physiology in identifying the mechanisms of distribution of photosensitizers in an organism, and, last but not least, physics in the development of better light sources, dosimetric concepts and construction of imaging devices, optical sensors and spectroscopic methods for determining sensitizer concentrations in different tissues. Physics and biophysics have also helped to focus on the role of pH for sensitizer accumulation, dose rate effects, oxygen depletion, temperature, and optical penetration of light of different wavelengths into various types of tissue. These are all important parameters for optimally effective PDT. The present review will give a brief, physically based, overview of PDT and then discuss some of the main biophysical aspects of this therapeutic modality.

  14. Theoretical Molecular Biophysics

    CERN Document Server

    Scherer, Philipp

    2010-01-01

    "Theoretical Molecular Biophysics" is an advanced study book for students, shortly before or after completing undergraduate studies, in physics, chemistry or biology. It provides the tools for an understanding of elementary processes in biology, such as photosynthesis on a molecular level. A basic knowledge in mechanics, electrostatics, quantum theory and statistical physics is desirable. The reader will be exposed to basic concepts in modern biophysics such as entropic forces, phase separation, potentials of mean force, proton and electron transfer, heterogeneous reactions coherent and incoherent energy transfer as well as molecular motors. Basic concepts such as phase transitions of biopolymers, electrostatics, protonation equilibria, ion transport, radiationless transitions as well as energy- and electron transfer are discussed within the frame of simple models.

  15. A quantitative overview of biophysical forces impinging on neural function

    International Nuclear Information System (INIS)

    Mueller, Jerel K; Tyler, William J

    2014-01-01

    The fundamentals of neuronal membrane excitability are globally described using the Hodgkin-Huxley (HH) model. The HH model, however, does not account for a number of biophysical phenomena associated with action potentials or propagating nerve impulses. Physical mechanisms underlying these processes, such as reversible heat transfer and axonal swelling, have been compartmentalized and separately investigated to reveal neuronal activity is not solely influenced by electrical or biochemical factors. Instead, mechanical forces and thermodynamics also govern neuronal excitability and signaling. To advance our understanding of neuronal function and dysfunction, compartmentalized analyses of electrical, chemical, and mechanical processes need to be revaluated and integrated into more comprehensive theories. The present perspective is intended to provide a broad overview of biophysical forces that can influence neural function, but which have been traditionally underappreciated in neuroscience. Further, several examples where mechanical forces have been shown to exert their actions on nervous system development, signaling, and plasticity are highlighted to underscore their importance in sculpting neural function. By considering the collective actions of biophysical forces influencing neuronal activity, our working models can be expanded and new paradigms can be applied to the investigation and characterization of brain function and dysfunction. (topical review)

  16. The biophysical link between climate, water, and vegetation in bioenergy agro-ecosystems

    International Nuclear Information System (INIS)

    Bagley, Justin E.; Davis, Sarah C.; Georgescu, Matei; Hussain, Mir Zaman; Miller, Jesse; Nesbitt, Stephen W.; VanLoocke, Andy; Bernacchi, Carl J.

    2014-01-01

    Land use change for bioenergy feedstocks is likely to intensify as energy demand rises simultaneously with increased pressure to minimize greenhouse gas emissions. Initial assessments of the impact of adopting bioenergy crops as a significant energy source have largely focused on the potential for bioenergy agroecosystems to provide global-scale climate regulating ecosystem services via biogeochemical processes. Such as those processes associated with carbon uptake, conversion, and storage that have the potential to reduce global greenhouse gas emissions (GHG). However, the expansion of bioenergy crops can also lead to direct biophysical impacts on climate through water regulating services. Perturbations of processes influencing terrestrial energy fluxes can result in impacts on climate and water across a spectrum of spatial and temporal scales. Here, we review the current state of knowledge about biophysical feedbacks between vegetation, water, and climate that would be affected by bioenergy-related land use change. The physical mechanisms involved in biophysical feedbacks are detailed, and interactions at leaf, field, regional, and global spatial scales are described. Locally, impacts on climate of biophysical changes associated with land use change for bioenergy crops can meet or exceed the biogeochemical changes in climate associated with rising GHG's, but these impacts have received far less attention. Realization of the importance of ecosystems in providing services that extend beyond biogeochemical GHG regulation and harvestable yields has led to significant debate regarding the viability of various feedstocks in many locations. The lack of data, and in some cases gaps in knowledge associated with biophysical and biochemical influences on land–atmosphere interactions, can lead to premature policy decisions. - Highlights: • The physical basis for biophysical impacts of expanding bioenergy agroecosystems on climate and water is described. • We

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

    Science.gov (United States)

    Xiao, Yun; Ahadian, Samad; Radisic, Milica

    2017-02-01

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

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

    Science.gov (United States)

    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

  19. Modelling benthic biophysical drivers of ecosystem structure and biogeochemical response

    Science.gov (United States)

    Stephens, Nicholas; Bruggeman, Jorn; Lessin, Gennadi; Allen, Icarus

    2016-04-01

    The fate of carbon deposited at the sea floor is ultimately decided by biophysical drivers that control the efficiency of remineralisation and timescale of carbon burial in sediments. Specifically, these drivers include bioturbation through ingestion and movement, burrow-flushing and sediment reworking, which enhance vertical particulate transport and solute diffusion. Unfortunately, these processes are rarely satisfactorily resolved in models. To address this, a benthic model that explicitly describes the vertical position of biology (e.g., habitats) and biogeochemical processes is presented that includes biological functionality and biogeochemical response capturing changes in ecosystem structure, benthic-pelagic fluxes and biodiversity on inter-annual timescales. This is demonstrated by the model's ability to reproduce temporal variability in benthic infauna, vertical pore water nutrients and pelagic-benthic solute fluxes compared to in-situ data. A key advance is the replacement of bulk parameterisation of bioturbation by explicit description of the bio-physical processes responsible. This permits direct comparison with observations and determination of key parameters in experiments. Crucially, the model resolves the two-way interaction between sediment biogeochemistry and ecology, allowing exploration of the benthic response to changing environmental conditions, the importance of infaunal functional traits in shaping benthic ecological structure and the feedback the resulting bio-physical processes exert on pore water nutrient profiles. The model is actively being used to understand shelf sea carbon cycling, the response of the benthos to climatic change, food provision and other societal benefits.

  20. Integrated Molecular and Cellular Biophysics

    CERN Document Server

    Raicu, Valerica

    2008-01-01

    This book integrates concepts and methods from physics, biology, biochemistry and physical chemistry into a standalone, unitary text of biophysics that aims to provide a quantitative description of structures and processes occurring in living matter. The book introduces graduate physics students and physicists interested in biophysics research to 'classical' as well as emerging areas of biophysics. The advanced undergraduate physics students and the life scientists are also invited to join in, by building on their knowledge of basic physics. Essential notions of biochemistry and biology are introduced, as necessary, throughout the book, while the reader's familiarity with basic knowledge of physics is assumed. Topics covered include interactions between biological molecules, physical chemistry of phospholipids association into bilayer membranes, DNA and protein structure and folding, passive and active electrical properties of the cell membrane, classical as well as fractal aspects of reaction kinetics and di...

  1. Biophysics

    CERN Document Server

    Glaser, Roland

    1999-01-01

    The message of this book is that biophysics is the science of physical principles underlying the "phenomenon life" on all levels of organization. Rather than teaching "physics for biologists" or "physical methods applied to biology", it regards its subject as a defined discipline with its own network of ideas and approaches. The book starts by explaining molecular structures of biological systems, various kinds of atomic, molecular and ionic interactions, movements, energy transfer, self organization of supramolecular structures and dynamic properties of biological membranes. It then goes on to introduce the biological organism as a non-equilibrium system, before treating thermodynamic concepts of osmotic and electrolyte equilibria as well as currents and potential profiles. It continues with topics of environmental biophysics and such medical aspects as the influence of electromagnetic fields or radiation on living systems and the biophysics of hearing and noice protection. The book concludes with a discussi...

  2. Methods in Modern Biophysics

    CERN Document Server

    Nölting, Bengt

    2006-01-01

    Incorporating recent dramatic advances, this textbook presents a fresh and timely introduction to modern biophysical methods. An array of new, faster and higher-power biophysical methods now enables scientists to examine the mysteries of life at a molecular level. This innovative text surveys and explains the ten key biophysical methods, including those related to biophysical nanotechnology, scanning probe microscopy, X-ray crystallography, ion mobility spectrometry, mass spectrometry, proteomics, and protein folding and structure. Incorporating much information previously unavailable in tutorial form, Nölting employs worked examples and 267 illustrations to fully detail the techniques and their underlying mechanisms. Methods in Modern Biophysics is written for advanced undergraduate and graduate students, postdocs, researchers, lecturers and professors in biophysics, biochemistry and related fields. Special features in the 2nd edition: • Illustrates the high-resolution methods for ultrashort-living protei...

  3. Biophysical models of larval dispersal in the Benguela Current ...

    African Journals Online (AJOL)

    We synthesise and update results from the suite of biophysical, larval-dispersal models developed in the Benguela Current ecosystem. Biophysical models of larval dispersal use outputs of physical hydrodynamic models as inputs to individual-based models in which biological processes acting during the larval life are ...

  4. The biophysics of neuronal growth

    International Nuclear Information System (INIS)

    Franze, Kristian; Guck, Jochen

    2010-01-01

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

  5. Smoothing of, and parameter estimation from, noisy biophysical recordings.

    Directory of Open Access Journals (Sweden)

    Quentin J M Huys

    2009-05-01

    Full Text Available Biophysically detailed models of single cells are difficult to fit to real data. Recent advances in imaging techniques allow simultaneous access to various intracellular variables, and these data can be used to significantly facilitate the modelling task. These data, however, are noisy, and current approaches to building biophysically detailed models are not designed to deal with this. We extend previous techniques to take the noisy nature of the measurements into account. Sequential Monte Carlo ("particle filtering" methods, in combination with a detailed biophysical description of a cell, are used for principled, model-based smoothing of noisy recording data. We also provide an alternative formulation of smoothing where the neural nonlinearities are estimated in a non-parametric manner. Biophysically important parameters of detailed models (such as channel densities, intercompartmental conductances, input resistances, and observation noise are inferred automatically from noisy data via expectation-maximization. Overall, we find that model-based smoothing is a powerful, robust technique for smoothing of noisy biophysical data and for inference of biophysical parameters in the face of recording noise.

  6. Global energy modeling - A biophysical approach

    Energy Technology Data Exchange (ETDEWEB)

    Dale, Michael

    2010-09-15

    This paper contrasts the standard economic approach to energy modelling with energy models using a biophysical approach. Neither of these approaches includes changing energy-returns-on-investment (EROI) due to declining resource quality or the capital intensive nature of renewable energy sources. Both of these factors will become increasingly important in the future. An extension to the biophysical approach is outlined which encompasses a dynamic EROI function that explicitly incorporates technological learning. The model is used to explore several scenarios of long-term future energy supply especially concerning the global transition to renewable energy sources in the quest for a sustainable energy system.

  7. 2. biophysical work meeting

    International Nuclear Information System (INIS)

    1992-11-01

    The report comprises 18 papers held at the 2nd Biophysical Work Meeting, 11 - 13 September 1991 in Schlema, Germany. The history of biophysics in Germany particularly of radiation biophysics and radon research, measurements of the radiation effects of radon and the derivation of limits, radon balneotherapy and consequences of uranium ore mining are dealt with. (orig.) [de

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

    OpenAIRE

    Xiao, Yun; Ahadian, Samad; Radisic, Milica

    2017-01-01

    Progress in biomaterial science and engineering and increasing knowledge in cell biology have enabled us to develop functional biomaterials providing appropriate biochemical and biophysical cues for tissue regeneration applications. Tissue regeneration is particularly important to treat chronic wounds of people with diabetes. Understanding and controlling the cellular microenvironment of the wound tissue are important to improve the wound healing process. In this study, we review different bi...

  9. Structural and biophysical characteristics of human skin in maintaining proper epidermal barrier function

    Directory of Open Access Journals (Sweden)

    Magdalena Boer

    2016-02-01

    Full Text Available The complex structure of human skin and its physicochemical properties turn it into an efficient outermost defence line against exogenous factors, and help maintain homeostasis of the human body. This role is played by the epidermal barrier with its major part – stratum corneum. The condition of the epidermal barrier depends on individual and environmental factors. The most important biophysical parameters characterizing the status of this barrier are the skin pH, epidermal hydration, transepidermal water loss and sebum excretion. The knowledge of biophysical skin processes may be useful for the implementation of prophylactic actions whose aim is to restore the barrier function.

  10. Biophysics of molecular gastronomy.

    Science.gov (United States)

    Brenner, Michael P; Sörensen, Pia M

    2015-03-26

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

  11. New horizons in Biophysics

    Science.gov (United States)

    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

  12. Encyclopedia of biophysics

    CERN Document Server

    2013-01-01

    The Encyclopedia of Biophysics is envisioned both as an easily accessible source of information and as an introductory guide to the scientific literature. It includes entries describing both Techniques and Systems.  In the Techniques entries, each of the wide range of methods which fall under the heading of Biophysics are explained in detail, together with the value and the limitations of the information each provides. Techniques covered range from diffraction (X-ray, electron and neutron) through a wide range of spectroscopic methods (X-ray, optical, EPR, NMR) to imaging (from electron microscopy to live cell imaging and MRI), as well as computational and simulation approaches. In the Systems entries, biophysical approaches to specific biological systems or problems – from protein and nucleic acid structure to membranes, ion channels and receptors – are described. These sections, which place emphasis on the integration of the different techniques, therefore provide an inroad into Biophysics from a biolo...

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

    Science.gov (United States)

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

    2016-12-01

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

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

    Science.gov (United States)

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

    2018-06-01

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

  15. Large-scale biophysical evaluation of protein PEGylation effects

    DEFF Research Database (Denmark)

    Vernet, Erik; Popa, Gina; Pozdnyakova, Irina

    2016-01-01

    PEGylation is the most widely used method to chemically modify protein biopharmaceuticals, but surprisingly limited public data is available on the biophysical effects of protein PEGylation. Here we report the first large-scale study, with site-specific mono-PEGylation of 15 different proteins...... of PEGylation on the thermal stability of a protein based on data generated by circular dichroism (CD), differential scanning calorimetry (DSC), or differential scanning fluorimetry (DSF). In addition, DSF was validated as a fast and inexpensive screening method for thermal unfolding studies of PEGylated...... proteins. Multivariate data analysis revealed clear trends in biophysical properties upon PEGylation for a subset of proteins, although no universal trends were found. Taken together, these findings are important in the consideration of biophysical methods and evaluation of second...

  16. Biophysical Regulation of Vascular Differentiation and Assembly

    CERN Document Server

    Gerecht, Sharon

    2011-01-01

    The ability to grow stem cells in the laboratory and to guide their maturation to functional cells allows us to study the underlying mechanisms that govern vasculature differentiation and assembly in health and disease. Accumulating evidence suggests that early stages of vascular growth are exquisitely tuned by biophysical cues from the microenvironment, yet the scientific understanding of such cellular environments is still in its infancy. Comprehending these processes sufficiently to manipulate them would pave the way to controlling blood vessel growth in therapeutic applications. This book assembles the works and views of experts from various disciplines to provide a unique perspective on how different aspects of its microenvironment regulate the differentiation and assembly of the vasculature. In particular, it describes recent efforts to exploit modern engineering techniques to study and manipulate various biophysical cues. Biophysical Regulation of Vascular Differentiation and Assembly provides an inter...

  17. Delineating Biophysical Environments of the Sunda Banda Seascape, Indonesia

    Directory of Open Access Journals (Sweden)

    Mingshu Wang

    2015-01-01

    Full Text Available 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.

  18. Preface: Special Topic on Single-Molecule Biophysics.

    Science.gov (United States)

    Makarov, Dmitrii E; Schuler, Benjamin

    2018-03-28

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

  19. A dataset mapping the potential biophysical effects of vegetation cover change

    Science.gov (United States)

    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.

  20. Advanced Techniques in Biophysics

    CERN Document Server

    Arrondo, José Luis R

    2006-01-01

    Technical advancements are basic elements in our life. In biophysical studies, new applications and improvements in well-established techniques are being implemented every day. This book deals with advancements produced not only from a technical point of view, but also from new approaches that are being taken in the study of biophysical samples, such as nanotechniques or single-cell measurements. This book constitutes a privileged observatory for reviewing novel applications of biophysical techniques that can help the reader enter an area where the technology is progressing quickly and where a comprehensive explanation is not always to be found.

  1. Biophysics of Hair Cell Sensory Systems

    NARCIS (Netherlands)

    Duifhuis, Hendrikus; Horst, Johannes; van Dijk, Pim; van Netten, Sietse

    1993-01-01

    The last decade revealed to auditory researchers that hair cells can not only detect and process mechanical energy, but are also able to produce it. Thanks to the active hair cell, ears can produce otoacoustic emissions. This book gives the newest insights into the biophysics and physiology of

  2. Remote sensing of the Canadian Arctic: Modelling biophysical variables

    Science.gov (United States)

    Liu, Nanfeng

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

  3. Synergistic linkage between remote sensing and biophysical models for estimating plant ecophysiological and ecosystem processes

    International Nuclear Information System (INIS)

    Inoue, Y.; Olioso, A.

    2004-01-01

    Abstract Information on the ecological and physiological status of crops is essential for growth diagnostics and yield prediction. Within-field or between-field spatial information is required, especially with the recent trend toward precision agriculture, which seeks the efficient use of agrochemicals, water, and energy. The study of carbon and nitrogen cycles as well as environmental management on local and regional scales requires assessment of the spatial variability of biophysical and ecophysiological variables, scaling up of which is also needed for scientific and decision-making purposes. Remote sensing has great potential for these applications because it enables wide-area non-destructive, and real-time acquisition of information about ecophysiological conditions of vegetation. With recent advances in sensor technology, a variety of electromagnetic signatures, such as hyperspectral reflectance, thermal-infrared temperature, and microwave backscattering coefficients, can be acquired for both plants and ecosystems using ground-based, airborne, and satellite platforms. Their spatial and temporal resolutions have both recently been improved. This article reviews the state of the art in the remote sensing of plant ecophysiological data, with special emphasis on the synergy between remote sensing signatures and biophysical and ecophysiological process models. Several case studies for the optical, thermal, and microwave domains have demonstrated the potential of this synergistic linkage. Remote sensing and process modeling methods complement each other when combined synergistically. Further research on this approach is needed f or a wide range of ecophysiological and ecosystem studies, as well as for practical crop management

  4. Theoretical molecular biophysics

    CERN Document Server

    Scherer, Philipp O J

    2017-01-01

    This book gives an introduction to molecular biophysics. It starts from material properties at equilibrium related to polymers, dielectrics and membranes. Electronic spectra are developed for the understanding of elementary dynamic processes in photosynthesis including proton transfer and dynamics of molecular motors. Since the molecular structures of functional groups of bio-systems were resolved, it has become feasible to develop a theory based on the quantum theory and statistical physics with emphasis on the specifics of the high complexity of bio-systems. This introduction to molecular aspects of the field focuses on solvable models. Elementary biological processes provide as special challenge the presence of partial disorder in the structure which does not destroy the basic reproducibility of the processes. Apparently the elementary molecular processes are organized in a way to optimize the efficiency. Learning from nature by means exploring the relation between structure and function may even help to b...

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

    Science.gov (United States)

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

    2017-12-01

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

  6. X-Ray structure and biophysical properties of rabbit fibroblast growth factor 1

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Jihun; Blaber, Sachiko I.; Irsigler, Andre; Aspinwall, Eric; Blaber, Michael; (FSU)

    2010-01-14

    The rabbit is an important and de facto animal model in the study of ischemic disease and angiogenic therapy. Additionally, fibroblast growth factor 1 (FGF-1) is emerging as one of the most important growth factors for novel pro-angiogenic and pro-arteriogenic therapy. However, despite its significance, the fundamental biophysical properties of rabbit FGF-1, including its X-ray structure, have never been reported. Here, the cloning, crystallization, X-ray structure and determination of the biophysical properties of rabbit FGF-1 are described. The X-ray structure shows that the amino-acid differences between human and rabbit FGF-1 are solvent-exposed and therefore potentially immunogenic, while the biophysical studies identify differences in thermostability and receptor-binding affinity that distinguish rabbit FGF-1 from human FGF-1.

  7. Biotic games and cloud experimentation as novel media for biophysics education

    Science.gov (United States)

    Riedel-Kruse, Ingmar; Blikstein, Paulo

    2014-03-01

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

  8. Biophysical pathology in cancer transformation

    Czech Academy of Sciences Publication Activity Database

    Pokorný, Jiří; Pokorný, Jan

    S1, Nov (2013), s. 1-9 ISSN 2324-9110 R&D Projects: GA ČR(CZ) GAP102/11/0649 Institutional support: RVO:68378271 ; RVO:67985882 Keywords : cancer biophysics * Warburg effect * reverse Warburg effect * biological electrodynamics * coherent states Subject RIV: BO - Biophysics

  9. Hierarchy and Interactions in Environmental Interfaces Regarded as Biophysical Complex Systems

    Science.gov (United States)

    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

  10. [Biophysical methods in assessment of the skin microcirculation system].

    Science.gov (United States)

    Dynnik, O B; Mostovoĭ, S E; Berezovskiĭ, V A

    2008-01-01

    In this work has been analyzed the potential of biophysics methods in estimations of the microcirculatory system. Capillaroresistometry, Computer capillaroscopy and Laser Doppler Flowmetry can to detect of the endothelial dysfunction in the patients with chronic hepatic diseases. This instrumentals biophysics methods may be used in clinical investigations for screening early pathological conditions with dysfunction of the microcirculatory system. The methods Laser Doppler Flowmetry is important for investigations the patients with others diseases and for dynamical monitoring by quality of the treatment. The purpose of these methods an objective estimation of disorders in the microcirculatory system.

  11. MODELLING BIOPHYSICAL PARAMETERS OF MAIZE USING LANDSAT 8 TIME SERIES

    Directory of Open Access Journals (Sweden)

    T. Dahms

    2016-06-01

    Full Text Available Open and free access to multi-frequent high-resolution data (e.g. Sentinel – 2 will fortify agricultural applications based on satellite data. The temporal and spatial resolution of these remote sensing datasets directly affects the applicability of remote sensing methods, for instance a robust retrieving of biophysical parameters over the entire growing season with very high geometric resolution. In this study we use machine learning methods to predict biophysical parameters, namely the fraction of absorbed photosynthetic radiation (FPAR, the leaf area index (LAI and the chlorophyll content, from high resolution remote sensing. 30 Landsat 8 OLI scenes were available in our study region in Mecklenburg-Western Pomerania, Germany. In-situ data were weekly to bi-weekly collected on 18 maize plots throughout the summer season 2015. The study aims at an optimized prediction of biophysical parameters and the identification of the best explaining spectral bands and vegetation indices. For this purpose, we used the entire in-situ dataset from 24.03.2015 to 15.10.2015. Random forest and conditional inference forests were used because of their explicit strong exploratory and predictive character. Variable importance measures allowed for analysing the relation between the biophysical parameters with respect to the spectral response, and the performance of the two approaches over the plant stock evolvement. Classical random forest regression outreached the performance of conditional inference forests, in particular when modelling the biophysical parameters over the entire growing period. For example, modelling biophysical parameters of maize for the entire vegetation period using random forests yielded: FPAR: R² = 0.85; RMSE = 0.11; LAI: R² = 0.64; RMSE = 0.9 and chlorophyll content (SPAD: R² = 0.80; RMSE=4.9. Our results demonstrate the great potential in using machine-learning methods for the interpretation of long-term multi-frequent remote sensing

  12. Modelling Biophysical Parameters of Maize Using Landsat 8 Time Series

    Science.gov (United States)

    Dahms, Thorsten; Seissiger, Sylvia; Conrad, Christopher; Borg, Erik

    2016-06-01

    Open and free access to multi-frequent high-resolution data (e.g. Sentinel - 2) will fortify agricultural applications based on satellite data. The temporal and spatial resolution of these remote sensing datasets directly affects the applicability of remote sensing methods, for instance a robust retrieving of biophysical parameters over the entire growing season with very high geometric resolution. In this study we use machine learning methods to predict biophysical parameters, namely the fraction of absorbed photosynthetic radiation (FPAR), the leaf area index (LAI) and the chlorophyll content, from high resolution remote sensing. 30 Landsat 8 OLI scenes were available in our study region in Mecklenburg-Western Pomerania, Germany. In-situ data were weekly to bi-weekly collected on 18 maize plots throughout the summer season 2015. The study aims at an optimized prediction of biophysical parameters and the identification of the best explaining spectral bands and vegetation indices. For this purpose, we used the entire in-situ dataset from 24.03.2015 to 15.10.2015. Random forest and conditional inference forests were used because of their explicit strong exploratory and predictive character. Variable importance measures allowed for analysing the relation between the biophysical parameters with respect to the spectral response, and the performance of the two approaches over the plant stock evolvement. Classical random forest regression outreached the performance of conditional inference forests, in particular when modelling the biophysical parameters over the entire growing period. For example, modelling biophysical parameters of maize for the entire vegetation period using random forests yielded: FPAR: R² = 0.85; RMSE = 0.11; LAI: R² = 0.64; RMSE = 0.9 and chlorophyll content (SPAD): R² = 0.80; RMSE=4.9. Our results demonstrate the great potential in using machine-learning methods for the interpretation of long-term multi-frequent remote sensing datasets to model

  13. Ultrasound assessment of the fetal biophysical profile: What does an radiologist need to know?

    International Nuclear Information System (INIS)

    Guimaraes Filho, Helio Antonio; Araujo Junior, Edward; Marcondes Machado Nardozza, Luciano; Linhares Dias da Costa, Lavoisier; Fernandes Moron, Antonio; Mattar, Rosiane

    2008-01-01

    Proposed by Frank Manning about 26 years ago, fetal biophysical profile has been incorporated to the propaedeutics of non-invasive fetal well being assessment in high-risk gestations. Despite the existence of other methods for assessing fetal vitality, as Doppler flowmetry, the biophysical profile continues to be important in estimating the risk of hypoxia and perinatal morbimortality for those fetuses. In the present article, the authors review the regulatory mechanisms of fetal biophysical activities, as well as physiological and pathological factors that interfere with them. The main objective of the study is to discuss the present and important aspects of the method, and the practical applications and interpretation of its findings, in order to help radiologists improve their knowledge in this specific area of fetal ultrasonography

  14. Enhancing Irreversible Electroporation by Manipulating Cellular Biophysics with a Molecular Adjuvant.

    Science.gov (United States)

    Ivey, Jill W; Latouche, Eduardo L; Richards, Megan L; Lesser, Glenn J; Debinski, Waldemar; Davalos, Rafael V; Verbridge, Scott S

    2017-07-25

    Pulsed electric fields applied to cells have been used as an invaluable research tool to enhance delivery of genes or other intracellular cargo, as well as for tumor treatment via electrochemotherapy or tissue ablation. These processes involve the buildup of charge across the cell membrane, with subsequent alteration of transmembrane potential that is a function of cell biophysics and geometry. For traditional electroporation parameters, larger cells experience a greater degree of membrane potential alteration. However, we have recently demonstrated that the nuclear/cytoplasm ratio (NCR), rather than cell size, is a key predictor of response for cells treated with high-frequency irreversible electroporation (IRE). In this study, we leverage a targeted molecular therapy, ephrinA1, known to markedly collapse the cytoplasm of cells expressing the EphA2 receptor, to investigate how biophysical cellular changes resulting from NCR manipulation affect the response to IRE at varying frequencies. We present evidence that the increase in the NCR mitigates the cell death response to conventional electroporation pulsed-electric fields (∼100 μs), consistent with the previously noted size dependence. However, this same molecular treatment enhanced the cell death response to high-frequency electric fields (∼1 μs). This finding demonstrates the importance of considering cellular biophysics and frequency-dependent effects in developing electroporation protocols, and our approach provides, to our knowledge, a novel and direct experimental methodology to quantify the relationship between cell morphology, pulse frequency, and electroporation response. Finally, this novel, to our knowledge, combinatorial approach may provide a paradigm to enhance in vivo tumor ablation through a molecular manipulation of cellular morphology before IRE application. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  15. Biophysical applications of satellite remote sensing

    CERN Document Server

    Hanes, Jonathan

    2014-01-01

    Including an introduction and historical overview of the field, this comprehensive synthesis of the major biophysical applications of satellite remote sensing includes in-depth discussion of satellite-sourced biophysical metrics such as leaf area index.

  16. Historical and Critical Review on Biophysical Economics

    Science.gov (United States)

    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.

  17. A mathematical approach to protein biophysics

    CERN Document Server

    Scott, L Ridgway

    2017-01-01

    This book explores quantitative aspects of protein biophysics and attempts to delineate certain rules of molecular behavior that make atomic scale objects behave in a digital way.  This book will help readers to understand how certain biological systems involving proteins function as digital information systems despite the fact that underlying processes are analog in nature. The in-depth explanation of proteins from a quantitative point of view and the variety of level of exercises (including physical experiments) at the end of each chapter will appeal to graduate and senior undergraduate students in mathematics, computer science, mechanical engineering, and physics, wanting to learn about the biophysics of proteins.  L. Ridgway Scott has been Professor of Computer Science and of Mathematics at the University of Chicago since 1998, and the Louis Block Professor since 2001.  He obtained a B.S. degree (Magna Cum Laude) from Tulane University in 1969 and a PhD degree in Mathematics from the Massachusetts Ins...

  18. Coupling Biophysical and Socioeconomic Models for Coral Reef Systems in Quintana Roo, Mexican Caribbean

    Directory of Open Access Journals (Sweden)

    Jessica Melbourne-Thomas

    2011-09-01

    Full Text Available Transdisciplinary approaches that consider both socioeconomic and biophysical processes are central to understanding and managing rapid change in coral reef systems worldwide. To date, there have been limited attempts to couple the two sets of processes in dynamic models for coral reefs, and these attempts are confined to reef systems in developed countries. We present an approach to coupling existing biophysical and socioeconomic models for coral reef systems in the Mexican state of Quintana Roo. The biophysical model is multiscale, using dynamic equations to capture local-scale ecological processes on individual reefs, with reefs connected at regional scales by the ocean transport of larval propagules. The agent-based socioeconomic model simulates changes in tourism, fisheries, and urbanization in the Quintana Roo region. Despite differences in the formulation and currencies of the two models, we were able to successfully modify and integrate them to synchronize and define information flows and feedbacks between them. A preliminary evaluation of the coupled model system indicates that the model gives reasonable predictions for fisheries and ecological variables and can be used to examine scenarios for future social-ecological change in Quintana Roo. We provide recommendations for where efforts might usefully be focused in future attempts to integrate models of biophysical and socioeconomic processes, based on the limitations of our coupled system.

  19. Biophysical functionality in polysaccharides: from Lego-blocks to nano-particles.

    Science.gov (United States)

    Cesàro, Attilio; Bellich, Barbara; Borgogna, Massimiliano

    2012-04-01

    The objective of the paper is to show the very important biophysical concepts that have been developed with polysaccharides. In particular, an attempt will be made to relate "a posteriori" the fundamental aspects, both experimental and theoretical, with some industrial applications of polysaccharide-based materials. The overview of chain conformational aspects includes relationships between topological features and local dynamics, exemplified for some naturally occurring carbohydrate polymers. Thus, by using simulation techniques and computational studies, the physicochemical properties of aqueous solutions of polysaccharides are interpreted. The relevance of conformational disorder-order transitions, chain aggregation, and phase separation to the underlying role of the ionic contribution to these processes is discussed. We stress the importance of combining information from analysis of experimental data with that from statistical-thermodynamic models for understanding the conformation, size, and functional stability of industrially important polysaccharides. The peculiar properties of polysaccharides in industrial applications are summarized for the particularly important example of nanoparticles production, a field of growing relevance and scientific interest.

  20. Biophysical Evaluation of Food Decontamination Effects on Tissue and Bacteria

    DEFF Research Database (Denmark)

    Andersen, Ann Zahle; Duelund, Lars; Brewer, Jonathan

    2011-01-01

    Traditionally, the effects and efficiency of food surface decontamination processes, such as chlorine washing, radiation, or heating, have been evaluated by sensoric analysis and colony-forming unit (CFU) counts of surface swabs or carcass rinses. These methods suffice when determining probable...... consumer responses or meeting legislative contamination limits. However, in the often very costly, optimization process of a new method, more quantitative and unbiased results are invaluable. In this study, we employed a biophysical approach for the investigation of qualitative and quantitative changes...... that there are no contradictions between data obtained by either approach. However, the biophysical methods draw a much more nuanced picture of the effects and efficiency of the investigated decontamination method, revealing, e.g., an exponential dose/response relationship between SonoSteam® treatment time and changes in collagen...

  1. Research Institute for Medical Biophysics

    International Nuclear Information System (INIS)

    Wynchank, S.

    1989-01-01

    The effects of ionising and non-ionising radiation on rodent tumours and normal tissue were studied in terms of cellular repair and the relevant biochemical and biophysical changes following radiation. Rodent tumours investigated in vivo were the CaNT adenocarcinoma and a chemically induced transplantable rhabdomyosarcoma. Radiations used were 100KVp of X-Rays, neutron beams, various magnetic fields, and microwave radiation of 2450MHz. The biochemical parameters measured were, inter alia, levels of adenosine-5'-triphoshate (ATP) and the specific activity of hexokinase (HK). Metabolic changes in ATP levels and the activity of HK were observed in tumour and normal tissues following ionising and non-ionising radiation in normoxia and hypoxia. The observation that the effect of radiation and chemotherapeutic treatment of some tumours may be size dependent can possibly now be explained by the variation of ATP content with tumour size. The enhanced tumour HK specific activity implies increased metabolism, possibly a consequence of cellular requirements to maintain homeostasis during repair processes. Other research projects of the Research Institute for Medical Biophysics involved, inter alia, gastroesophageal scintigraphies to evaluate the results of new forms of therapy. 1 ill

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

    Science.gov (United States)

    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.

  3. Biophysical mechanisms complementing "classical" cell biology.

    Science.gov (United States)

    Funk, Richard H W

    2018-01-01

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

  4. Biophysical behavior of Scomberoides commersonianus skin collagen.

    Science.gov (United States)

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

    2002-06-01

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

  5. Biophysics an introduction

    CERN Document Server

    Cotteril, Rodney

    2002-01-01

    Biophysics: An Introduction, is a concise balanced introduction to this subject. Written in an accessible and readable style, the book takes a fresh, modern approach with the author successfully combining key concepts and theory with relevant applications and examples drawn from the field as a whole. Beginning with a brief introduction to the origins of biophysics, the book takes the reader through successive levels of complexity, from atoms to molecules, structures, systems and ultimately to the behaviour of organisms. The book also includes extensive coverage of biopolymers, biomembranes, biological energy, and nervous systems. The text not only explores basic ideas, but also discusses recent developments, such as protein folding, DNA/RNA conformations, molecular motors, optical tweezers and the biological origins of consciousness and intelligence.

  6. Biophysical models of radiobiological effects

    International Nuclear Information System (INIS)

    Obaturov, G.M.

    1987-01-01

    Radiobiological effect models at different organization levels, developed by the author, are presented. Classification and analysis of concepts and biophysical models at molecular, genetic and cellular levels, developed by Soviet and foreign authors in comparison to inherent models, are conducted from the viewpoint of system approach to radiobiological processes and of modelling principles. Models are compared with each other, limits of their applicability and drawbacks are determined. Evaluation of the model truthfulness is conducted according to a number of criteria, ways of further investigations and experimental examination of some models are proposed

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

    Science.gov (United States)

    Zur, Hadas; Tuller, Tamir

    2016-01-01

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

  8. Biophysics of DNA

    CERN Document Server

    Vologodskii, Alexander

    2015-01-01

    Surveying the last sixty years of research, this book describes the physical properties of DNA in the context of its biological functioning. It is designed to enable both students and researchers of molecular biology, biochemistry and physics to better understand the biophysics of DNA, addressing key questions and facilitating further research. The chapters integrate theoretical and experimental approaches, emphasising throughout the importance of a quantitative knowledge of physical properties in building and analysing models of DNA functioning. For example, the book shows how the relationship between DNA mechanical properties and the sequence specificity of DNA-protein binding can be analyzed quantitatively by using our current knowledge of the physical and structural properties of DNA. Theoretical models and experimental methods in the field are critically considered to enable the reader to engage effectively with the current scientific literature on the physical properties of DNA.

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

    Science.gov (United States)

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

    2015-04-15

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

  10. Structure and biophysics

    CERN Document Server

    Puglisi, Joseph D

    2007-01-01

    This volume is a collection of articles from the proceedings of the ISSBMR 7th Course: Structure and Biophysics - New Technologies for Current Challenges in Biology and Beyond. This NATO Advanced Institute (ASI) was held in Erice at the Ettore Majorana Foundation and Centre for Scientific Culture on 22 June through 3 July 2005. The ASI brought together a diverse group of experts in the fields of Structural Biology, Biophysics and Physics. Prominent lecturers, from seven different countries, and students from around the world participated in the NATO ASI organized by Professors Joseph Puglisi (Stanford University, USA) and Alexander Arseniev (Moscow, RU). Advances in nuclear magnetic resonance spectroscopy (NMR) and x-ray crystallography have allowed the three-dimensional structures of many biological macromolecules and their complexes, including the ribosome and RNA polymerase to be solved. Fundamental principles of NMR spectroscopy and dynamics, x-ray crystallography, computation and experimental dynamics we...

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

    Science.gov (United States)

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

    2017-12-01

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

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

    Science.gov (United States)

    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.

  13. Biophysical Aspects of Alzheimer's Disease: Implications for Pharmaceutical Sciences : Theme: Drug Discovery, Development and Delivery in Alzheimer's Disease Guest Editor: Davide Brambilla.

    Science.gov (United States)

    Arosio, Paolo

    2017-12-01

    An increasing amount of findings suggests that the aggregation of soluble peptides and proteins into amyloid fibrils is a relevant upstream process in the complex cascade of events leading to the pathology of Alzheimer's disease and several other neurodegenerative disorders. Nevertheless, several aspects of the correlation between the aggregation process and the onset and development of the pathology remain largely elusive. In this context, biophysical and biochemical studies in test tubes have proven extremely powerful in providing quantitative information about the structure and the reactivity of amyloids at the molecular level. In this review we use selected recent examples to illustrate the importance of such biophysical research to complement phenomenological studies based on cellular and molecular biology, and we discuss the implications for pharmaceutical applications associated with Alzheimer's disease and other neurodegenerative disorders in both academic and industrial contexts.

  14. Biophysical basis for the geometry of conical stromatolites.

    Science.gov (United States)

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

    2010-06-01

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

  15. Synchrotron radiation applications in biophysics and medicine

    International Nuclear Information System (INIS)

    Burattini, E.

    1985-01-01

    The peculiar properties of synchrotron radiation are briefly summarized. A short review on the possible applications of synchrotron radiation in two important fields like Biophysics and Medicine is presented. Details are given on experiments both in progress and carried out in many synchrotron radiation facilities, all over the world, using different techniques like X-ray absorption and fluorescence spectroscopy, X-ray fluorescence microanalysis, X-ray microscopy and digital subtraction angiography. Some news about the photon-activation therapy are briefly reported too

  16. Effects of LiDAR point density, sampling size and height threshold on estimation accuracy of crop biophysical parameters.

    Science.gov (United States)

    Luo, Shezhou; Chen, Jing M; Wang, Cheng; Xi, Xiaohuan; Zeng, Hongcheng; Peng, Dailiang; Li, Dong

    2016-05-30

    Vegetation leaf area index (LAI), height, and aboveground biomass are key biophysical parameters. Corn is an important and globally distributed crop, and reliable estimations of these parameters are essential for corn yield forecasting, health monitoring and ecosystem modeling. Light Detection and Ranging (LiDAR) is considered an effective technology for estimating vegetation biophysical parameters. However, the estimation accuracies of these parameters are affected by multiple factors. In this study, we first estimated corn LAI, height and biomass (R2 = 0.80, 0.874 and 0.838, respectively) using the original LiDAR data (7.32 points/m2), and the results showed that LiDAR data could accurately estimate these biophysical parameters. Second, comprehensive research was conducted on the effects of LiDAR point density, sampling size and height threshold on the estimation accuracy of LAI, height and biomass. Our findings indicated that LiDAR point density had an important effect on the estimation accuracy for vegetation biophysical parameters, however, high point density did not always produce highly accurate estimates, and reduced point density could deliver reasonable estimation results. Furthermore, the results showed that sampling size and height threshold were additional key factors that affect the estimation accuracy of biophysical parameters. Therefore, the optimal sampling size and the height threshold should be determined to improve the estimation accuracy of biophysical parameters. Our results also implied that a higher LiDAR point density, larger sampling size and height threshold were required to obtain accurate corn LAI estimation when compared with height and biomass estimations. In general, our results provide valuable guidance for LiDAR data acquisition and estimation of vegetation biophysical parameters using LiDAR data.

  17. Biophysical dosimetry using electron paramagnetic resonance in human tooth

    International Nuclear Information System (INIS)

    Khan, R.F.H.; Boreham, D.R.; Rink, W.J.

    2002-01-01

    Accidental dosimetry utilizing radiation induced paramagnetic species in biophysical tissues like teeth is a technique; that can measure the amount of radiation exposure to an individual. The major problem in implementing this technique at low doses is the presence of native organic signal, and various other artifacts produced as a result of sample processing. After a series of experimental trials, we developed an optimum set of rules, which uses high temperature ultrasonic treatment of enamel in KOH, multiple sample rotation during in-cavity measurement of natural and calibrated added irradiations, and dose construction using a backward extrapolation method. By using this we report the successful dose reconstruction in a few of our laboratory samples in 100 mGy range (76.29 ± 30.14) mGy with reasonably low uncertainty. Keywords: biophysical dosimetry, human tooth enamel, low dose measurements, accidental dosimetry (author)

  18. Radiation dosimetry and radiation biophysics

    International Nuclear Information System (INIS)

    Anon.

    1981-01-01

    Radiation dosimetry and radiation biophysics are two closely integrated programs whose joint purpose is to explore the connections between the primary physical events produced by radiation and their biological consequences in cellular systems. The radiation dosimetry program includes the theoretical description of primary events and their connection with the observable biological effects. This program also is concerned with the design and measurement of physical parameters used in theory or to support biological experiments. The radiation biophysics program tests and uses the theoretical developments for experimental design, and provides information for further theoretical development through experiments on cellular systems

  19. Radiation dosimetry and radiation biophysics

    International Nuclear Information System (INIS)

    Anon.

    1979-01-01

    Radiation dosimetry and radiation biophysics are two closely integrated programs whose joint purpose is to explore the connections between the primary physical events produced by radiation and their biological consequences in cellular systems. The radiation dosimetry program includes the theoretical description of primary events and their connection with the observable biological effects. This program also is concerned with design and measurement of those physical parameters used in the theory or to support biological experiments. The radiation biophysics program tests and makes use of the theoretical developments for experimental design. Also, this program provides information for further theoretical development through experiments on cellular systems

  20. Integrating understanding of biophysical processes governing larval fish dispersal with basin-scale management decisions: lessons from the Missouri River, USA

    Science.gov (United States)

    Erwin, S. O.; Jacobson, R. B.; Fischenich, C. J.; Bulliner, E. A., IV; McDonald, R.; DeLonay, A. J.; Braaten, P.; Elliott, C. M.; Chojnacki, K.

    2017-12-01

    Management of the Missouri River—the longest river in the USA, with a drainage basin covering one sixth of the conterminous USA—is increasingly driven by the need to understand biophysical processes governing the dispersal of 8-mm long larval pallid sturgeon. In both the upper and lower basin, survival of larval sturgeon is thought to be a bottleneck limiting populations, but because of different physical processes at play, different modeling frameworks and resolutions are required to link management actions with population-level responses. In the upper basin, a series of impoundments reduce the length of river for the drifting larval sturgeon to complete their development. Downstream from the mainstem dams, recruitment is most likely diminished by channelization and reduced floodplain connectivity that limit the benthic habitat available for larval sturgeon to settle and initiate feeding. We present a synthesis of complementary field studies, laboratory observations, and numerical simulations that evaluate the physical processes related to larval dispersal of sturgeon in the Missouri River basin. In the upper basin, we use one-dimensional advection-dispersion models, calibrated with field experiments conducted in 2016-2017 using surrogate particles and tracers, to evaluate reservoir management alternatives. Results of field experimentation and numerical modeling show that proposed management alternatives in the upper basin may be limited by insufficient lengths of flowing river for drifting larvae to fully develop into their juvenile lifestage. In the intensively engineered lower basin, we employ higher resolution measurements and models to evaluate potential for channel reconfiguration and flow alteration to promote successful interception of drifting larvae into supportive benthic habitats for the initiation of feeding and transition to the juvenile life stage. We illustrate how refined understanding of small-scale biophysical process has been incorporated

  1. Short-Term Memory and Its Biophysical Model

    Science.gov (United States)

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

    1996-12-01

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

  2. Biophysics of DNA-Protein Interactions From Single Molecules to Biological Systems

    CERN Document Server

    Williams, Mark C

    2011-01-01

    This book presents a concise overview of current research on the biophysics of DNA-protein interactions. A wide range of new and classical methods are presented by authors investigating physical mechanisms by which proteins interact with DNA. For example, several chapters address the mechanisms by which proteins search for and recognize specific binding sites on DNA, a process critical for cellular function. Single molecule methods such as force spectroscopy as well as fluorescence imaging and tracking are described in these chapters as well as other parts of the book that address the dynamics of protein-DNA interactions. Other important topics include the mechanisms by which proteins engage DNA sequences and/or alter DNA structure. These simple but important model interactions are then placed in the broader biological context with discussion of larger protein-DNA complexes . Topics include replication forks, recombination complexes, DNA repair interactions, and ultimately, methods to understand the chromatin...

  3. Developing A Transdisciplinary Process and Community Partnerships to Anticipate Climate Change at the Local Level: The Role of Biophysical and Sociocultural Calendars

    Science.gov (United States)

    Kassam, K. A.; Samimi, C.; Trabucco, A.

    2017-12-01

    Difference is essential to solving the most complex problems faced by humanity. Anthropogenic climate change is one such "wicked problem" that demands cognitive diversity. Biophysical and social scientists must collaborate with scholars from the humanities to address practical issues of concern to local communities, which are at the forefront of impacts of climatic variation. As such, communities of inquirers (e.g. biophysical and social sciences, humanities) must work in tandem with communities of practice (e.g. farmers, fishers, gatherers, herders, hunters). This leads to co-generated knowledge where an adaptation strategy to climatic variation is locally grounded in the biophysical and sociocultural context of the communities where the impacts of climatic variation are most felt. We will present an innovative and `real time' example participatory and transdisciplinary research from an international project where we are developing integrated biophysical and sociocultural calendars, in short, ecological calendars, which are ecologically and culturally grounded in the local context to develop anticipatory capacity to anthropogenic climate change.

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

    Science.gov (United States)

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

    2004-01-01

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

  5. Biophysical regulation of stem cell differentiation.

    Science.gov (United States)

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

    2013-06-01

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

  6. Satellite mapping of surface biophysical parameters at the biome scale over the North American grasslands: A case study

    Science.gov (United States)

    Wylie, B.K.; Meyer, D.J.; Tieszen, L.L.; Mannel, S.

    2002-01-01

    Quantification of biophysical parameters is needed by terrestrial process modeling and other applications. A study testing the role of multispectral data for monitoring biophysical parameters was conducted over a network of grassland field sites in the Great Plains of North America. Grassland biophysical parameters [leaf area index (LAI), fraction of absorbed photosynthetically active radiation (fPAR), and biomass] and their relationships with ground radiometer normalized difference vegetation index (NDVI) were established in this study (r2=.66–.85) from data collected across the central and northern Great Plains in 1995. These spectral/biophysical relationships were compared to 1996 field data from the Tallgrass Prairie Preserve in northeastern Oklahoma and showed no consistent biases, with most regression estimates falling within the respective 95% confidence intervals. Biophysical parameters were estimated for 21 “ground pixels” (grids) at the Tallgrass Prairie Preserve in 1996, representing three grazing/burning treatments. Each grid was 30×30 m in size and was systematically sampled with ground radiometer readings. The radiometric measurements were then converted to biophysical parameters and spatially interpolated using geostatistical kriging. Grid-based biophysical parameters were monitored through the growing season and regressed against Landsat Thematic Mapper (TM) NDVI (r2=.92–.94). These regression equations were used to estimate biophysical parameters for grassland TM pixels over the Tallgrass Prairie Preserve in 1996. This method maintained consistent regression development and prediction scales and attempted to minimize scaling problems associated with mixed land cover pixels. A method for scaling Landsat biophysical parameters to coarser resolution satellite data sets (1 km2) was also investigated.

  7. The relationship between fetal biophysical profile and cord blood PH

    Directory of Open Access Journals (Sweden)

    Valadan M

    2009-02-01

    Full Text Available "nBackground: The Biophysical Profile (BPP is a noninvasive test that predicts the presence or absence of fetal asphyxia and, ultimately, the risk of fetal death in the antenatal period. Intervention on the basis of an abnormal biophysical profile result has been reported to yield a significant reduction in prenatal mortality, and an association exists between biophysical profile scoring and a decreased cerebral palsy rate in a given population. The BPP evaluates five characteristics: fetal movement, tone, breathing, heart reactivity, and amniotic fluid (AF volume estimation. The purpose of study was to determine whether there are different degree of acidosis at which the biophysical activity (acute marker are affected. "nMethods: In a prospective study of 140 patients undergoing cesarean section before onset of labor, the fetal biophysical profile was performed 24h before the time of cesarean and was matched with cord arterial PH that was obtained from a cord segment (10-20cm that was double clamped after delivery of newborn. (using cord arterial PH less than 7.20 for the diagnosis of acidosis. "nResults: The fetal biophysical profile was found to have a significant relationship with umbilical blood PH. The sensitivity, specificity, positive predictive value, negative predictive value of fetal biophysical profile score were: 88.9%, 88.6%, 50%, 98.1%. "nConclusion: The first manifestations of fetal acidosis are nonreactive nonstress testing and fetal breathing loss; in advanced acidemia fetal movements and fetal tone are compromised. A protocol of antepartum fetal evaluation is suggested based upon the individual biophysical components rather than the score alone.

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

    Science.gov (United States)

    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.

  9. Nanoscale biophysics of the cell

    CERN Document Server

    Ashrafuzzaman, Mohammad

    2018-01-01

    Macroscopic cellular structures and functions are generally investigated using biological and biochemical approaches. But these methods are no longer adequate when one needs to penetrate deep into the small-scale structures and understand their functions. The cell is found to hold various physical structures, molecular machines, and processes that require physical and mathematical approaches to understand and indeed manipulate them. Disorders in general cellular compartments, perturbations in single molecular structures, drug distribution therein, and target specific drug-binding, etc. are mostly physical phenomena. This book will show how biophysics has revolutionized our way of addressing the science and technology of nanoscale structures of cells, and also describes the potential for manipulating the events that occur in them.

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

    Science.gov (United States)

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

    2015-03-01

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

  11. Biophysical Evaluation of SonoSteam®:

    DEFF Research Database (Denmark)

    Andersen, Ann Zahle; Duelund, Lars; Brewer, Jonathan R.

    and safety evaluations. Our results show that there are no contradictions between data obtained by either approach. However, the biophysical methods draw a much more nuanced picture of the effects and efficiency of the investigated decontamination method, revealing e.g. an exponential dose/response...... relationship between SonoSteam treatment time and changes in collagen I, and a depth dependency in bacterial reduction, which points toward CFU counts overestimating total bacterial reduction. In conclusion the biophysical methods provide a less biased, reproducible and highly detailed system description...

  12. Biophysical Cancer Transformation Pathway

    Czech Academy of Sciences Publication Activity Database

    Pokorný, Jiří

    2009-01-01

    Roč. 28, č. 2 (2009), s. 105-123 ISSN 1536-8378 Institutional research plan: CEZ:AV0Z20670512 Keywords : Biophysics * Cancer * Electromagnetic fields Subject RIV: JA - Electronics ; Optoelectronics, Electrical Engineering Impact factor: 0.729, year: 2009

  13. Biophysical EPR Studies Applied to Membrane Proteins

    Science.gov (United States)

    Sahu, Indra D; Lorigan, Gary A

    2015-01-01

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

  14. Use of an integrated biophysical process for the treatment of halo- and nitro- organic wastes

    Directory of Open Access Journals (Sweden)

    Liron Shoshani

    2017-07-01

    Full Text Available This study assessed the use of an integrated biophysical process incorporating the addition of powdered activated carbon (PAC to a dual-sludge biological process, in order to improve the removal of problematic contaminants from complex herbicides production wastewater. The main focus was on the removal of nitrogen compounds, total organic carbon (TOC, and halogenated organics (AOX. The dual-sludge pilot setup comprised a conventional activated sludge (CAS system followed by a membrane bioreactor (MBR system. The dilution ratio of raw wastewater was gradually decreased (with groundwater from 0.8 to 0 (no dilution, and PAC was added in the last phase of the study to maintain an equilibrium concentration of 2000 mg/L. PAC addition stimulated a high and steady removal (98% of the ammoniacal nitrogen, conforming to the sea discharge limit of 5 mg/L. However, the effluent concentrations of total nitrogen, TOC, and AOX were still above the stringent discharge limits of 20, 100 and 0.5 mg/L respectively. Furthermore, it was shown that synergistic effect of various toxic organic compounds, rather than mineral salinity, was the major cause for the acute inhibitions of nitrification and AOX removal. The study showed that the proposed process can function as an efficient treatment system for the complex wastewater typically produced in the herbicide industry, however, it is recommended that complementary physico-chemical treatment steps be added to the treatment process.

  15. Biophysical and sociocultural factors underlying spatial trade-offs of ecosystem services in semiarid watersheds

    Directory of Open Access Journals (Sweden)

    Marina García-Llorente

    2015-09-01

    Full Text Available Biophysical and social systems are linked to form social-ecological systems whose sustainability depends on their capacity to absorb uncertainty and cope with disturbances. In this study, we explored the key biophysical and socio-cultural factors underlying ecosystem service supply in two semiarid watersheds of southern Spain. These included variables associated with the role that freshwater flows and biodiversity play in securing the system's capacity to sustain essential ecosystem services and their relationship with social demand for services, local water governance, and land-use intensification. Our results reveal the importance of considering the invisible dimensions of water and biodiversity, i.e. green freshwater flows and trait-based indicators, because of their relevance to the supply of ecosystem services. Furthermore, they uncover the importance of traditional irrigation canals, a local water governance system, in maintaining the ecosystems' capacity to supply services. The study also highlights the complex trade-offs that occur because of the spatial mismatch between ecosystem service supply (upstream and ecosystem service demand (downstream in watersheds. Finally, we found that land-use intensification generally resulted in losses of the biophysical factors that underpin the supply of some ecosystem services, increases in social demand for less diversified services, and the abandonment of local governance practices. Attempts to manage social-ecological systems toward sustainability at the local scale should identify the key biophysical and socio-cultural factors that are essential for maintaining ecosystem services and should recognize existing interrelationships between them. Land-use management should also take into account ecosystem service trade-offs and the consequences resulting from land-use intensification.

  16. The physical basis of biochemistry the foundations of molecular biophysics

    CERN Document Server

    Bergethon, Peter R

    1998-01-01

    The objective of this book is to provide a unifying approach to the study of biophysical chemistry for the advanced undergraduate who has had a year of physics, organic chem­ istry, calculus, and biology. This book began as a revised edition of Biophysical Chemistry: Molecules to Membranes, which Elizabeth Simons and I coauthored. That short volume was written in an attempt to provide a concise text for a one-semester course in biophysical chemistry at the graduate level. The experience of teaching biophysical chemistry to bi­ ologically oriented students over the last decade has made it clear that the subject requires a more fundamental text that unifies the many threads of modem science: physics, chem­ istry, biology, mathematics, and statistics. This book represents that effort. This volume is not a treatment of modem biophysical chemistry with its rich history and many contro­ versies, although a book on that topic is also needed. The Physical Basis of Biochemistry is an introduction to the philosophy...

  17. Biophysics of radiation action

    International Nuclear Information System (INIS)

    Dertinger, H.

    1984-01-01

    Understanding the cellular response to ionizing radiation is not only necessary to meet the requirements of radioprotection, but also for medical application of radiation in cancer treatment. In terms of radiobiology, cancer therapy means the selective inactivation of malignant cells without affecting the normal healthy tissue. However, for several physical and biological reasons, this ideal situation is normally not attained. The elaboration of biophysical parameters that could be used to improve the selective sterilization of tumor cells has become one of the main activities of cellular radiobiology during the last two decades. Progress in this field has been facilitated by the development of tissue culture techniques allowing to grow and analyze cells in a synthetic nutrient medium. This chapter describes the physical and biological factors which determine cellular radiosensitivity and which are important to know for better understanding the cellular radiation action, in particular with reference to cancer treatment

  18. Biophysics and systems biology.

    Science.gov (United States)

    Noble, Denis

    2010-03-13

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

  19. Radiation biophysics in space

    International Nuclear Information System (INIS)

    Buecker, H.; Horneck, G.

    1983-01-01

    In a demonstration experiment bacterium sporules have been exposed to the space vacuum and to the solar radiation field at 254 nm, with the following results: 1) a short vacuum exposition of 1.3 h does not affect the vitality of the sporules, 2) the survival rate of humid sporules after UV-irradiation is consistent with terrestrial control samples, 3) after a simultaneous exposition to vacuum and solar UV-radiation the effect on the sporules is enhanced by a factor of ten as compared to the situation without vaccum exposition. Additional studies in biophysical simulation systems revealed, that the enhanced UV sensitivity is caused by the dehydration of the sporules. By this process the structure of the essential macromolecules in cell, such as DNA and proteins, is modified such that new photo-products can be formed. For these products the cells have no effective repair systems. (AJ) [de

  20. Low temperature experiments in radiation biophysics

    International Nuclear Information System (INIS)

    Moan, J.

    1977-01-01

    The reasons for performing experiments in radiation biophysics at low temperatures, whereby electron spectra may be studied, are explained. The phenomenon of phosphorescence spectra observed in frozen aqueous solutions of tryptophan and adenosine is also described. Free radicals play an important part in biological radiation effects and may be studied by ESR spectroscopy. An ESR spectrum of T 1 bacteriophages irradiated dry at 130K is illustrated and discussed. Hydrogen atoms, which give lines on the spectrum, are believed to be those radiation products causing most biological damage in a dry system. Low temperature experiments are of great help in explaining the significance of direct and indirect effects. This is illustrated for the case of trypsin. (JIW)

  1. Structural biophysics

    International Nuclear Information System (INIS)

    Anon.

    1979-01-01

    Summaries of research projects conducted during 1978 and 1979 are presented. The structural biophysics group explores the high-resolution structure of biological macromolecules and cell organelles. Specific subject areas include: the basic characteristics of photosynthesis in plants; the chemical composition of individual fly ash particles at the site of their damaging action in tissues; direct analysis of frozen-hydrated biological samples by scanning electron microscopy; yeast genetics; the optical activity of DNA aggregates; measurement and characterization of lipoproteins; function of lipoproteins; and the effect of radiation and pollutants on mammalian cells

  2. From autopoiesis to neurophenomenology: Francisco Varela's exploration of the biophysics of being

    Directory of Open Access Journals (Sweden)

    DAVID RUDRAUF

    2003-01-01

    Full Text Available This paper reviews in detail Francisco Varela's work on subjectivity and consciousness in the biological sciences. His original approach to this "hard problem" presents a subjectivity that is radically intertwined with its biological and physical roots. It must be understood within the framework of his theory of a concrete, embodied dynamics, grounded in his general theory of autonomous systems. Through concepts and paradigms such as biological autonomy, embodiment and neurophenomenology, the article explores the multiple levels of circular causality assumed by Varela to play a fundamental role in the emergence of human experience. The concept of biological autonomy provides the necessary and sufficient conditions for characterizing biological life and identity as an emergent and circular self-producing process. Embodiment provides a systemic and dynamical framework for understanding how a cognitive -a mind- can arise in an organism in the midst of its operational cycles of internal regulation and ongoing sensorimotor coupling. Global subjective properties can emerge at different levels from the interactions of components and can reciprocally constrain local processes through an ongoing, recursive morphodynamics. Neurophenomenology is a supplementary step in the study of consciousness. Through a rigorous method, it advocates the careful examination of experience with first-person methodologies. It attempts to create heuristic mutual constraints between biophysical data and data produced by accounts of subjective experience. The aim is to explicitly ground the active and disciplined insight the subject has about his/her experience in a biophysical emergent process. Finally, we discuss Varela's essential contribution to our understanding of the generation of consciousness in the framework of what we call his "biophysics of being."

  3. Soil functional types: surveying the biophysical dimensions of soil security

    Science.gov (United States)

    Cécillon, Lauric; Barré, Pierre

    2015-04-01

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

  4. Biophysical landscape interactions: Bridging disciplines and scale with connectivity

    Science.gov (United States)

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

    2017-04-01

    The combination of climate change, population growth and soil threats, such as carbon loss, biodiversity decline or erosion amongst others , increasingly confront the global community [1]. One of the major challenges in studying processes involved in soil threats, landscape resilience, ecosystem stability, sustainable land management and the economic consequences, is that it is an interdisciplinary field [2], that needs less stringent scientific disciplinary boundaries [3]. As a result of disciplinary focus, ambiguity may arise on the understanding of landscape interactions, and this is especially true in the interaction between a landscape's physical and biological processes [4]. Another important aspect in biophysical landscape interactions are the differences in scale related to the various processes that play a role in these systems. While scaling of environmental processes is possible, as long as the phenomena at hand can be described by the same set of differential equations [5], biophysical landscape interactions pose problems for scaling approaches. Landscape position and land use impact the coupled processes in soil and vegetation. Differences in micro-behavior, driven by the interplay of heterogeneous soil and vegetation dynamics, impact emergent characteristics across a landscape. A complicating factor is the response of vegetation to changing environmental conditions, including a possible and often unknown time-lag. By altering soil conditions, plants may leave an imprint in the landscape that remains even after vegetation has disappeared due to e.g. drought, wildfire or overgrazing. Plants also respond biochemically to their environment, while the models used for hydrology are often based on physical interactions. Gene-expression and genotype adaptation may further complicate our modelling efforts in for example climate change impacts. What are we missing by not having more connectivity in our thinking, and what we can solve? We think that integrated

  5. Recent progress in Biophysics

    International Nuclear Information System (INIS)

    Bemski, G.

    1980-03-01

    Recent progress in biophysics is reviewed, and three examples of the use of physical techniques and ideas in biological research are given. The first one deals with the oxygen transporting protein-hemoglobin, the second one with photosynthesis, and the third one with image formation, using nuclear magnetic resonance. (Author) [pt

  6. A biophysical process based approach for estimating net primary production using satellite and ground observations

    Science.gov (United States)

    Choudhury, Bhaskar J.

    An approach is presented for calculating interannual variation of net primary production (C) of terrestrial plant communities at regional scale using satellite and ground measurements. C has been calculated as the difference of gross photosynthesis (A g) and respiration (R), recognizing that different biophysical factors exert major control on these two processes. A g has been expressed as the product of radiation use efficiency for gross photosynthesis by an unstressed canopy and intercepted photosynthetically active radiation, which is then adjusted for stresses due to soil water shortage and temperature away from optimum. R has been calculated as the sum of growth and maintenance components (respectively, R g and R m. The R m has been determined from nitrogen content of plant tissue per unit ground area, while R g has been obtained as a fraction of the difference of A g and R m. Model parameters have not been determined by matching the calculated fluxes against observations at any location. Results are presented for cultivated and temperate deciduous forest areas over North America for five consecutive years (1986-1990) and compared with observations.

  7. Quality Saving Mechanisms of Mitochondria during Aging in a Fully Time-Dependent Computational Biophysical Model.

    Directory of Open Access Journals (Sweden)

    Daniel Mellem

    Full Text Available Mitochondria are essential for the energy production of eukaryotic cells. During aging mitochondria run through various processes which change their quality in terms of activity, health and metabolic supply. In recent years, many of these processes such as fission and fusion of mitochondria, mitophagy, mitochondrial biogenesis and energy consumption have been subject of research. Based on numerous experimental insights, it was possible to qualify mitochondrial behaviour in computational simulations. Here, we present a new biophysical model based on the approach of Figge et al. in 2012. We introduce exponential decay and growth laws for each mitochondrial process to derive its time-dependent probability during the aging of cells. All mitochondrial processes of the original model are mathematically and biophysically redefined and additional processes are implemented: Mitochondrial fission and fusion is separated into a metabolic outer-membrane part and a protein-related inner-membrane part, a quality-dependent threshold for mitophagy and mitochondrial biogenesis is introduced and processes for activity-dependent internal oxidative stress as well as mitochondrial repair mechanisms are newly included. Our findings reveal a decrease of mitochondrial quality and a fragmentation of the mitochondrial network during aging. Additionally, the model discloses a quality increasing mechanism due to the interplay of the mitophagy and biogenesis cycle and the fission and fusion cycle of mitochondria. It is revealed that decreased mitochondrial repair can be a quality saving process in aged cells. Furthermore, the model finds strategies to sustain the quality of the mitochondrial network in cells with high production rates of reactive oxygen species due to large energy demands. Hence, the model adds new insights to biophysical mechanisms of mitochondrial aging and provides novel understandings of the interdependency of mitochondrial processes.

  8. Interactive Biophysics with Microswimmers: Education, Cloud Experimentation, Programmed Swarms, and Biotic Games

    Science.gov (United States)

    Riedel-Kruse, Ingmar

    Modern biotechnology gets increasingly powerful to manipulate and measure microscopic biophysical processes. Nevertheless, no platform exists to truly interact with these processes, certainly not with the convenience that we are accustomed to from our electronic smart devices. In my talk I will provide the rational for such Interactive Biotechnology and conceptualize its core component, the BPU (biotic processing unit), which is then connected to an according user interface. The biophysical phenomena currently featured on these platforms utilize the phototactic response of motile microorganisms, e.g., Euglena gracilis, resulting in spatio-temporal dynamics from the single cell to the self-organized multi-cellular scale. I will demonstrate multiple platforms, such as scalable biology cloud experimentation labs, tangible museum exhibits, biotic video games, low-cost interactive DIY kits using smartphones, and programming languages for swarm robotics. I will discuss applications for education as well as for professional and citizen science. Hence, we turn traditionally observational microscopy into an interactive experience. I was told that presenting in the educational section does not count against the ''one author - one talk policy'' - so I submit two abstracts. In case of conflict - please contact me: ingmar@stanford.edu.

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

    Science.gov (United States)

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

    2015-09-01

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

  10. Stochastic transport processes in discrete biological systems

    CERN Document Server

    Frehland, Eckart

    1982-01-01

    These notes are in part based on a course for advanced students in the applications of stochastic processes held in 1978 at the University of Konstanz. These notes contain the results of re­ cent studies on the stochastic description of ion transport through biological membranes. In particular, they serve as an introduction to an unified theory of fluctuations in complex biological transport systems. We emphasize that the subject of this volume is not to introduce the mathematics of stochastic processes but to present a field of theoretical biophysics in which stochastic methods are important. In the last years the study of membrane noise has become an important method in biophysics. Valuable information on the ion transport mechanisms in membranes can be obtained from noise analysis. A number of different processes such as the opening and closing of ion channels have been shown to be sources of the measured current or voltage fluctuations. Bio­ logical 'transport systems can be complex. For example, the tr...

  11. Drought propagation and its relation with catchment biophysical characteristics

    Science.gov (United States)

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

    2016-12-01

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

  12. Progress and challenges of engineering a biophysical CO2-concentrating mechanism into higher plants.

    Science.gov (United States)

    Rae, Benjamin D; Long, Benedict M; Förster, Britta; Nguyen, Nghiem D; Velanis, Christos N; Atkinson, Nicky; Hee, Wei Yih; Mukherjee, Bratati; Price, G Dean; McCormick, Alistair J

    2017-06-01

    Growth and productivity in important crop plants is limited by the inefficiencies of the C3 photosynthetic pathway. Introducing CO2-concentrating mechanisms (CCMs) into C3 plants could overcome these limitations and lead to increased yields. Many unicellular microautotrophs, such as cyanobacteria and green algae, possess highly efficient biophysical CCMs that increase CO2 concentrations around the primary carboxylase enzyme, Rubisco, to enhance CO2 assimilation rates. Algal and cyanobacterial CCMs utilize distinct molecular components, but share several functional commonalities. Here we outline the recent progress and current challenges of engineering biophysical CCMs into C3 plants. We review the predicted requirements for a functional biophysical CCM based on current knowledge of cyanobacterial and algal CCMs, the molecular engineering tools and research pipelines required to translate our theoretical knowledge into practice, and the current challenges to achieving these goals. © The Author 2017. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

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

    Science.gov (United States)

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

    2016-11-18

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

  14. Irrigation Requirement Estimation Using Vegetation Indices and Inverse Biophysical Modeling

    Science.gov (United States)

    Bounoua, Lahouari; Imhoff, Marc L.; Franks, Shannon

    2010-01-01

    We explore an inverse biophysical modeling process forced by satellite and climatological data to quantify irrigation requirements in semi-arid agricultural areas. We constrain the carbon and water cycles modeled under both equilibrium, balance between vegetation and climate, and non-equilibrium, water added through irrigation. We postulate that the degree to which irrigated dry lands vary from equilibrium climate conditions is related to the amount of irrigation. The amount of water required over and above precipitation is considered as an irrigation requirement. For July, results show that spray irrigation resulted in an additional amount of water of 1.3 mm per occurrence with a frequency of 24.6 hours. In contrast, the drip irrigation required only 0.6 mm every 45.6 hours or 46% of that simulated by the spray irrigation. The modeled estimates account for 87% of the total reported irrigation water use, when soil salinity is not important and 66% in saline lands.

  15. Impacts on the biophysical economy and environment of a transition to 100% renewable electricity in Australia

    International Nuclear Information System (INIS)

    Turner, Graham M.; Elliston, Ben; Diesendorf, Mark

    2013-01-01

    We investigate the impacts on the biophysical economy, employment and environment of a transition scenario to an energy-efficient, 100% renewable electricity (RE) system by 2060, based on wind, solar and biomass technologies, and an introduction of electric vehicles. We employ a CSIRO process-based model of the physical activity of Australia’s economy and environmental resources, the Australian Stocks and Flows Framework. The RE systems are assumed to be manufactured in Australia to identify possible employment benefits. In comparison with the business-as-usual (BAU) scenario, on a national scale, the RE scenario has much lower economy-wide net emissions, remaining below contemporary levels and becoming zero in the electricity sector by 2060. Compared with BAU, the RE scenario also has significantly lower industrial water use, somewhat higher materials use, slightly lower unemployment, lower net foreign debt (relative to a GDP proxy) and, resulting from the growth in electric vehicles, reduced oil imports. The GDP per capita growth, based on the physical stocks of capital and labour, is virtually the same in both scenarios. Hence, from the viewpoint of the biophysical economy, there are no major barriers to implementing policies to facilitate the transition to a 100% renewable electricity system for Australia. - Highlights: ► Simulation of a 100% renewable electricity (RE) system in a process-based model. ► The RE scenario achieves zero GHG emissions in the electricity sector by 2060. ► Consumption of secondary materials is higher and more variable in the RE scenario. ► The RE scenario has lower water use, unemployment, foreign debt and oil imports

  16. The interface of protein structure, protein biophysics, and molecular evolution

    Science.gov (United States)

    Liberles, David A; Teichmann, Sarah A; Bahar, Ivet; Bastolla, Ugo; Bloom, Jesse; Bornberg-Bauer, Erich; Colwell, Lucy J; de Koning, A P Jason; Dokholyan, Nikolay V; Echave, Julian; Elofsson, Arne; Gerloff, Dietlind L; Goldstein, Richard A; Grahnen, Johan A; Holder, Mark T; Lakner, Clemens; Lartillot, Nicholas; Lovell, Simon C; Naylor, Gavin; Perica, Tina; Pollock, David D; Pupko, Tal; Regan, Lynne; Roger, Andrew; Rubinstein, Nimrod; Shakhnovich, Eugene; Sjölander, Kimmen; Sunyaev, Shamil; Teufel, Ashley I; Thorne, Jeffrey L; Thornton, Joseph W; Weinreich, Daniel M; Whelan, Simon

    2012-01-01

    Abstract The interface of protein structural biology, protein biophysics, molecular evolution, and molecular population genetics forms the foundations for a mechanistic understanding of many aspects of protein biochemistry. Current efforts in interdisciplinary protein modeling are in their infancy and the state-of-the art of such models is described. Beyond the relationship between amino acid substitution and static protein structure, protein function, and corresponding organismal fitness, other considerations are also discussed. More complex mutational processes such as insertion and deletion and domain rearrangements and even circular permutations should be evaluated. The role of intrinsically disordered proteins is still controversial, but may be increasingly important to consider. Protein geometry and protein dynamics as a deviation from static considerations of protein structure are also important. Protein expression level is known to be a major determinant of evolutionary rate and several considerations including selection at the mRNA level and the role of interaction specificity are discussed. Lastly, the relationship between modeling and needed high-throughput experimental data as well as experimental examination of protein evolution using ancestral sequence resurrection and in vitro biochemistry are presented, towards an aim of ultimately generating better models for biological inference and prediction. PMID:22528593

  17. Biophysical shunt theory for neuropsychopathology: Part I.

    Science.gov (United States)

    Naisberg, Y; Avnon, M; Weizman, A

    1995-11-01

    We present a new model of the origin of schizophrenia based on biophysical ionic shunts in neuronal (electrical) pathways. Microstructural and molecular evidence is presented for the way in which changes in the neuronal membrane ionic channels may facilitate membrane property rearrangement, leading to a change in the density and composition of the ion channel charge which in turn causes a change in ionic flow orientation and distribution. We suggest that, under abnormal conditions, ionic flow shunts are created which redirect the biophysical collateral neuronal (electrical) pathways, resulting in psychiatric signs and symptoms. This model is complementary to the biological basis of schizophrenia.

  18. 2. biophysical work meeting. Papers; 2. Biophysikalische Arbeitstagung; Vortraege

    Energy Technology Data Exchange (ETDEWEB)

    1992-11-01

    The report comprises 18 papers held at the 2nd Biophysical Work Meeting, 11 - 13 September 1991 in Schlema, Germany. The history of biophysics in Germany particularly of radiation biophysics and radon research, measurements of the radiation effects of radon and the derivation of limits, radon balneotherapy and consequences of uranium ore mining are dealt with. (orig.) [Deutsch] Der Report enthaelt 18 Vortraege, die auf der 2. Biophysikalischen Arbeitstagung in Schlema vom 11. bis 13. September 1991 gehalten wurden. Es werden die Geschichte der Biophysik in Deutschland, speziell der Strahlenbiophysik und Radonforschung, Messungen von Radon und seinen Folgeprodukten, Epidemiologie und Strahlenbiologie zur Bestimmung der Strahlenwirkung des Radons und die Ableitung entsprechender Grenzwerte, Radon-Balneotherapie und Folgen des Uranerzbergbaus behandelt. (orig.)

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

    Science.gov (United States)

    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

  20. A multivariate decision tree analysis of biophysical factors in tropical forest fire occurrence

    Science.gov (United States)

    Rey S. Ofren; Edward Harvey

    2000-01-01

    A multivariate decision tree model was used to quantify the relative importance of complex hierarchical relationships between biophysical variables and the occurrence of tropical forest fires. The study site is the Huai Kha Kbaeng wildlife sanctuary, a World Heritage Site in northwestern Thailand where annual fires are common and particularly destructive. Thematic...

  1. Mass spectrometry in structural biology and biophysics architecture, dynamics, and interaction of biomolecules

    CERN Document Server

    Kaltashov, Igor A; Desiderio, Dominic M; Nibbering, Nico M

    2012-01-01

    The definitive guide to mass spectrometry techniques in biology and biophysics The use of mass spectrometry (MS) to study the architecture and dynamics of proteins is increasingly common within the biophysical community, and Mass Spectrometry in Structural Biology and Biophysics: Architecture, Dynamics, and Interaction of Biomolecules, Second Edition provides readers with detailed, systematic coverage of the current state of the art. Offering an unrivalled overview of modern MS-based armamentarium that can be used to solve the most challenging problems in biophysics, structural biol

  2. Biophysics at the Boundaries: The Next Problem Sets

    Science.gov (United States)

    Skolnick, Malcolm

    2009-03-01

    The interface between physics and biology is one of the fastest growing subfields of physics. As knowledge of such topics as cellular processes and complex ecological systems advances, researchers have found that progress in understanding these and other systems requires application of more quantitative approaches. Today, there is a growing demand for quantitative and computational skills in biological research and the commercialization of that research. The fragmented teaching of science in our universities still leaves biology outside the quantitative and mathematical culture that is the foundation of physics. This is particularly inopportune at a time when the needs for quantitative thinking about biological systems are exploding. More physicists should be encouraged to become active in research and development in the growing application fields of biophysics including molecular genetics, biomedical imaging, tissue generation and regeneration, drug development, prosthetics, neural and brain function, kinetics of nonequilibrium open biological systems, metabolic networks, biological transport processes, large-scale biochemical networks and stochastic processes in biochemical systems to name a few. In addition to moving into basic research in these areas, there is increasing opportunity for physicists in industry beginning with entrepreneurial roles in taking research results out of the laboratory and in the industries who perfect and market the inventions and developments that physicists produce. In this talk we will identify and discuss emerging opportunities for physicists in biophysical and biotechnological pursuits ranging from basic research through development of applications and commercialization of results. This will include discussion of the roles of physicists in non-traditional areas apart from academia such as patent law, financial analysis and regulatory science and the problem sets assigned in education and training that will enable future

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

    Science.gov (United States)

    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.

  4. Radiation biophysics

    International Nuclear Information System (INIS)

    Anon.

    1979-01-01

    Summaries of research projects conducted during 1978 and 1979 are presented. The overall thrust of the research is aimed at understanding the effects of radiation on organisms. Specific subject areas include: the effects of heavy-particle beam nuclear interactions in tissue on dosimetry; tracer studies with radioactive fragments of heavy-ion beams; the effects of heavy/ions on human kidney cells and Chinese hamster cells; the response of a rhabdomyosarcoma tumor system in rats to heavy-ion beams; the use of heavy charged particles in radiotherapy of human cancer; heavy-ion radiography; the biological effects of high magnetic fields; central nervous system neurotoxicity; and biophysical studies on cell membranes

  5. Editorial: The Sackler International Prize in Biophysical Sciences

    Science.gov (United States)

    Frydman, Lucio

    2018-02-01

    The Raymond and Beverly Sackler International Prize is awarded alternatively in the fields of Biophysics, Chemistry and Physics on a yearly basis, by Tel Aviv University. The price is intended to encourage dedication to science, originality and excellence, by rewarding outstanding scientists under 45 years of age, with a total purse of 100,000. The 2016 Raymond and Beverly Sackler Prize was awarded in the field of Magnetic Resonance last February in a festive symposium, to three excellent researchers: Professor John Morton (University College London), Professor Guido Pintacuda (Ecole Normale Supérieure de Lyon and CNRS), and Professor Charalampos Kalodimos (at the time at the University of Minnesota). John was recognized for his novel contributions to quantum information processing, by means of a range of highly elegant physical phenomena involving both NMR and EPR. Guido was recognized for his methodological advances in solid state NMR spectroscopy, including advances in proton detection under ultrafast MAS at ultrahigh magnetic field, and for his insightful applications to challenging biological systems. While Charalampos (Babis) was recognized for beautifully detailed characterizations of structure, function, and dynamics in challenging and important biological systems through solution NMR spectroscopy.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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

  8. Soil Infrastructure, Interfaces & Translocation Processes in Inner Space ("Soil-it-is": towards a road map for the constraints and crossroads of soil architecture and biophysical processes

    Directory of Open Access Journals (Sweden)

    L. W. de Jonge

    2009-08-01

    , we show the Dexter et al. (2008 threshold may also apply to hydrological and physical-chemical interface phenomena including soil-water repellency and sorption of volatile organic vapors (gas-water-solids interfaces as well as polycyclic aromatic hydrocarbons (water-solids interfaces. However, data for differently-managed soils imply that energy input, soil-moisture status, and vegetation (quality of eluded organic matter may be equally important constraints together with the complexation and degradation of organic carbon in deciding functional soil architecture and interface processes. Finally, we envision a road map to soil inner space where we search for the main controls of particle and pore network changes and structure build-up and resilience at each crossroad of biophysical parameters, where, for example, complexation between organic matter and clay, and moisture-induced changes from hydrophilic to hydrophobic surface conditions can play a role. We hypothesize that each crossroad (e.g. between organic carbon/clay ratio and matric potential may control how soil self-organization will manifest itself at a given time as affected by gradients in energy and moisture from soil use and climate. The road map may serve as inspiration for renewed and multi-disciplinary focus on functional soil architecture.

  9. Applications of synchrotron radiation in Biophysics

    International Nuclear Information System (INIS)

    Bemski, G.

    1983-01-01

    A short introduction to the generation of the synchrotron radiation is made. Following, the applications of such a radiation in biophysics with emphasis to the study of the hemoglobin molecule are presented. (L.C.) [pt

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

    Directory of Open Access Journals (Sweden)

    Masami Suganuma

    2016-11-01

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

  11. Nanoscale quantification of the biophysical characterization of combretastatin A-4-treated tumor cells using atomic force microscopy.

    Science.gov (United States)

    Li, Yanchun; Chen, Jv; Liu, Yutong; Zhang, Weige; He, Wenhui; Xu, Hanying; Liu, Lianqing; Ma, Enlong

    2017-01-01

    As an inhibitor of microtubule assembly, combretastatin A-4 (CA-4)-induced biological responses in tumor cells have been well known, but the corresponding changes in nano-biophysical properties were not investigated given the lack of an ideal tool. Using AFM technique, we investigated the alteration of nano-biophysical properties when CA-4-treated tumor cells underwent the different biological processes, including cell cycle arrest, apoptosis and autophagy. We found that CA-4-resistant cells were rougher with the presence of characteristic "ridges", indicating that the development of "ridge" structure may be a determinant of the sensitivity of cells to CA-4 compounds. CA-4 induced G2/M arrest and apoptosis in sensitive cells but triggered anti-apoptotic autophagy in resistant cells. CA-4 treatment caused an increase in stiffness in both sensitive and resistant cells. However, these cells exhibited different changes in cell surface roughness. CA-4 decreased Ra and Rq values in sensitive cells but increased these values in resistant cells. The reorganization of F-actin might contribute to the different changes of nano-biophysical properties in CA-4-sensitive and-resistant cells. Our results suggest that cellular nano-biophysical properties, such as "ridges", roughness and stiffness, could be applied as potential biomarkers for evaluating CA-4 compounds, and knowledge regarding how biological alterations cause changes in cellular nano-biophysical properties is helpful to develop a new high-resolution screening tool for anti-tumor agents.

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

    Science.gov (United States)

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

    2016-01-01

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

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

    Science.gov (United States)

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

    2016-05-01

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

  14. Biophysics of NASA radiation quality factors

    International Nuclear Information System (INIS)

    Cucinotta, Francis A.

    2015-01-01

    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. (author)

  15. Biophysical properties and functional significance of stem water storage tissues in Neotropical savanna trees.

    Science.gov (United States)

    F.G. Scholz; S.J. Bucci; G. Goldstein; F.C. Meinzer; A.C. Franco; F. Miralles-Wilhelm

    2007-01-01

    Biophysical characteristics of sapwood and outer parenchyma water storage compartments were studied in stems of eight dominant Brazilian Cerrado tree species to assess the impact of differences in tissue capacitance on whole-plant water relations. Both the sapwood and outer parenchyma tissues played an important role in regulation of internal water deficits of Cerrado...

  16. Biophysical and biochemical constraints imposed by salt stress:Learning from halophyte

    Directory of Open Access Journals (Sweden)

    Bernardo eDuarte

    2014-12-01

    Full Text Available Soil salinization is one of the most important factors impacting plant productivity. About 3.6 billion of the world’s 5.2 billion ha of agricultural dryland have already suffered erosion, degradation and salinization. Halophytes typically are considered as plants able to complete their life cycle in environments where the salt concentration is 200 mM NaCl or higher. Different strategies are known to overcome salt stress, as adaptation mechanisms from this type of plants. Salinity adjustment is a complex phenomenon characterized by both biochemical and biophysical adaptations. As photosynthesis is a prerequisite for biomass production, halophytes adapted their electronic transduction pathways and the entire energetic metabolism to overcome the salt excess. The maintenance of ionic homeostasis is in the basis of all cellular stress in particular in terms of redox potential and energy transduction. In the present work the biophysical mechanisms underlying energy capture and transduction in halophytes are discussed alongside with their relation to biochemical mechanisms, integrating data from photosystem light harvesting complexes, electronic transport chains to the quinone pools, carbon harvesting and energy dissipation metabolism.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

  19. Biophysical aspects of cancer - Electromagnetic mechanism

    Czech Academy of Sciences Publication Activity Database

    Pokorný, Jiří; Hašek, Jiří; Vaniš, Jan; Jelínek, František

    2008-01-01

    Roč. 46, č. 5 (2008), s. 310-321 ISSN 0019-5189 Institutional research plan: CEZ:AV0Z20670512; CEZ:AV0Z50200510 Keywords : Electromagnetic Fields * Biophysics * Cancer Subject RIV: JA - Electronics ; Optoelectronics, Electrical Engineering Impact factor: 0.599, year: 2008

  20. Microscale Ocean Biophysics, Aspen Center for Physics: January 11-16 2015

    Science.gov (United States)

    2017-04-19

    dissolved   organic  matter  persist  in  the  deep  ocean:  Is  the  solution   dilution ?”     8.45  –  Kwangmin  Son...AUTHORS 7. PERFORMING ORGANIZATION NAMES AND ADDRESSES 15. SUBJECT TERMS b. ABSTRACT 2. REPORT TYPE 17. LIMITATION OF ABSTRACT 15. NUMBER OF PAGES...Microscale Ocean Biophysics, Aspen Center for Physics, January 11-16, 2015 Microscopic organisms control ocean processes at global scales. However

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

    Science.gov (United States)

    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.

  2. Biophysical Chemistry of Fractal Structures and Processes in Environmental Systems

    NARCIS (Netherlands)

    Buffle, J.; Leeuwen, van H.P.

    2008-01-01

    This book aims to provide the scientific community with a novel and valuable approach based on fractal geometry concepts on the important properties and processes of diverse environmental systems. The interpretation of complex environmental systems using modern fractal approaches is compared and

  3. Coupling the biophysical and social dimensions of wildfire risk to improve wildfire mitigation planning

    Science.gov (United States)

    Alan A. Ager; Jeffrey D. Kline; A. Paige Fisher

    2015-01-01

    We describe recent advances in biophysical and social aspects of risk and their potential combined contribution to improve mitigation planning on fire-prone landscapes. The methods and tools provide an improved method for defining the spatial extent of wildfire risk to communities compared to current planning processes. They also propose an expanded role for social...

  4. An ultra-sensitive biophysical risk assessment of light effect on skin cells.

    Science.gov (United States)

    Bennet, Devasier; Viswanath, Buddolla; Kim, Sanghyo; An, Jeong Ho

    2017-07-18

    The aim of this study was to analyze photo-dynamic and photo-pathology changes of different color light radiations on human adult skin cells. We used a real-time biophysical and biomechanics monitoring system for light-induced cellular changes in an in vitro model to find mechanisms of the initial and continuous degenerative process. Cells were exposed to intermittent, mild and intense (1-180 min) light with On/Off cycles, using blue, green, red and white light. Cellular ultra-structural changes, damages, and ECM impair function were evaluated by up/down-regulation of biophysical, biomechanical and biochemical properties. All cells exposed to different color light radiation showed significant changes in a time-dependent manner. Particularly, cell growth, stiffness, roughness, cytoskeletal integrity and ECM proteins of the human dermal fibroblasts-adult (HDF-a) cells showed highest alteration, followed by human epidermal keratinocytes-adult (HEK-a) cells and human epidermal melanocytes-adult (HEM-a) cells. Such changes might impede the normal cellular functions. Overall, the obtained results identify a new insight that may contribute to premature aging, and causes it to look aged in younger people. Moreover, these results advance our understanding of the different color light-induced degenerative process and help the development of new therapeutic strategies.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    Pirani, Farshad Jalili; Mousavi, Seyed Alireza

    2016-09-01

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

  7. Institute of Biochemistry and Biophysics. Research Report 1996-1997

    International Nuclear Information System (INIS)

    1998-01-01

    Scientific interests of the Institute of Biochemistry and Biophysics of the Polish Academy of Sciences have evolved from classical biochemistry, biophysics and physiological chemistry to up-to-date molecular biology. Research interests are focussed on replication, mutagenesis and repair of DNA; regulation of gene expression at various levels; biosynthesis and post-translational modifications of proteins; gene sequencing and functional analysis of open reading frames; structure, function and regulation of enzymes; conformation of proteins and peptides; modelling of structures and prediction of functions of proteins; mechanisms of electron transfer in polypeptides

  8. Institute of Biochemistry and Biophysics. Research Report 1996-1997

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1998-07-01

    Scientific interests of the Institute of Biochemistry and Biophysics of the Polish Academy of Sciences have evolved from classical biochemistry, biophysics and physiological chemistry to up-to-date molecular biology. Research interests are focussed on replication, mutagenesis and repair of DNA; regulation of gene expression at various levels; biosynthesis and post-translational modifications of proteins; gene sequencing and functional analysis of open reading frames; structure, function and regulation of enzymes; conformation of proteins and peptides; modelling of structures and prediction of functions of proteins; mechanisms of electron transfer in polypeptides.

  9. Biophysical Influence of Airborne Carbon Nanomaterials on Natural Pulmonary Surfactant

    OpenAIRE

    Valle, Russell P.; Wu, Tony; Zuo, Yi Y.

    2015-01-01

    Inhalation of nanoparticles (NP), including lightweight airborne carbonaceous nanomaterials (CNM), poses a direct and systemic health threat to those who handle them. Inhaled NP penetrate deep pulmonary structures in which they first interact with the pulmonary surfactant (PS) lining at the alveolar air–water interface. In spite of many research efforts, there is a gap of knowledge between in vitro biophysical study and in vivo inhalation toxicology since all existing biophysical models handl...

  10. Similar Biophysical Abnormalities in Glomeruli and Podocytes from Two Distinct Models.

    Science.gov (United States)

    Embry, Addie E; Liu, Zhenan; Henderson, Joel M; Byfield, F Jefferson; Liu, Liping; Yoon, Joonho; Wu, Zhenzhen; Cruz, Katrina; Moradi, Sara; Gillombardo, C Barton; Hussain, Rihanna Z; Doelger, Richard; Stuve, Olaf; Chang, Audrey N; Janmey, Paul A; Bruggeman, Leslie A; Miller, R Tyler

    2018-03-23

    Background FSGS is a pattern of podocyte injury that leads to loss of glomerular function. Podocytes support other podocytes and glomerular capillary structure, oppose hemodynamic forces, form the slit diaphragm, and have mechanical properties that permit these functions. However, the biophysical characteristics of glomeruli and podocytes in disease remain unclear. Methods Using microindentation, atomic force microscopy, immunofluorescence microscopy, quantitative RT-PCR, and a three-dimensional collagen gel contraction assay, we studied the biophysical and structural properties of glomeruli and podocytes in chronic (Tg26 mice [HIV protein expression]) and acute (protamine administration [cytoskeletal rearrangement]) models of podocyte injury. Results Compared with wild-type glomeruli, Tg26 glomeruli became progressively more deformable with disease progression, despite increased collagen content. Tg26 podocytes had disordered cytoskeletons, markedly abnormal focal adhesions, and weaker adhesion; they failed to respond to mechanical signals and exerted minimal traction force in three-dimensional collagen gels. Protamine treatment had similar but milder effects on glomeruli and podocytes. Conclusions Reduced structural integrity of Tg26 podocytes causes increased deformability of glomerular capillaries and limits the ability of capillaries to counter hemodynamic force, possibly leading to further podocyte injury. Loss of normal podocyte mechanical integrity could injure neighboring podocytes due to the absence of normal biophysical signals required for podocyte maintenance. The severe defects in podocyte mechanical behavior in the Tg26 model may explain why Tg26 glomeruli soften progressively, despite increased collagen deposition, and may be the basis for the rapid course of glomerular diseases associated with severe podocyte injury. In milder injury (protamine), similar processes occur but over a longer time. Copyright © 2018 by the American Society of Nephrology.

  11. Polish Academy of Sciences Institute of Biochemistry and Biophysics research report 1994-1995

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1997-12-31

    Scientific interests of Institute of Biochemistry and Biophysics Polish Academy of Sciences are focused on DNA replication and repair, gene expression, gene sequencing and molecular biophysics. The work reviews research projects of the Institute in 1994-1995.

  12. Polish Academy of Sciences Institute of Biochemistry and Biophysics research report 1994-1995

    International Nuclear Information System (INIS)

    1996-01-01

    Scientific interests of Institute of Biochemistry and Biophysics Polish Academy of Sciences are focused on DNA replication and repair, gene expression, gene sequencing and molecular biophysics. The work reviews research projects of the Institute in 1994-1995

  13. Polish Academy of Sciences Institute of Biochemistry and Biophysics research report 1994-1995

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1996-12-31

    Scientific interests of Institute of Biochemistry and Biophysics Polish Academy of Sciences are focused on DNA replication and repair, gene expression, gene sequencing and molecular biophysics. The work reviews research projects of the Institute in 1994-1995.

  14. Surface-enhanced Raman scattering: a new optical probe in molecular biophysics and biomedicine

    DEFF Research Database (Denmark)

    Kneipp, J.; Wittig, B.; Bohr, Henrik

    2010-01-01

    Sensitive and detailed molecular structural information plays an increasing role in molecular biophysics and molecular medicine. Therefore, vibrational spectroscopic techniques, such as Raman scattering, which provide high structural information content are of growing interest in biophysical and ...

  15. Biophysics of NASA radiation quality factors.

    Science.gov (United States)

    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.

  16. A Method Sustaining the Bioelectric, Biophysical, and Bioenergetic Function of Cultured Rabbit Atrial Cells

    Directory of Open Access Journals (Sweden)

    Noa Kirschner Peretz

    2017-08-01

    Full Text Available Culturing atrial cells leads to a loss in their ability to be externally paced at physiological rates and to maintain their shape. We aim to develop a culture method that sustains the shape of atrial cells along with their biophysical and bioenergetic properties in response to physiological pacing. We hypothesize that adding 2,3-Butanedione 2-monoxime (BDM, which inhibits contraction during the culture period, will preserve these biophysical and bioenergetic properties. Rabbit atrial cells were maintained in culture for 24 h in a medium enriched with a myofilament contraction inhibitor, BDM. The morphology and volume of the cells, including their ability to contract in response to 1–3 Hz electrical pacing, was maintained at the same level as fresh cells. Importantly, the cells could be successfully infected with a GFP adenovirus. Action potentials, Ca2+ transients, and local Ca2+ spark parameters were similar in the cultured and in fresh cells. Finally, these cultured cells' flavoprotein autofluorescence was maintained at a constant level in response to electrical pacing, a response similar to that of fresh cells. Thus, eliminating contraction during the culture period preserves the bioelectric, biophysical and bioenergetic properties of rabbit atrial myocytes. This method therefore has the potential to further improve our understanding of energetic and biochemical regulation in the atria.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    Boda, Sunil Kumar; Basu, Bikramjit

    2017-10-01

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

  19. Predicting Variation of DNA Shape Preferences in Protein-DNA Interaction in Cancer Cells with a New Biophysical Model.

    Science.gov (United States)

    Batmanov, Kirill; Wang, Junbai

    2017-09-18

    DNA shape readout is an important mechanism of transcription factor target site recognition, in addition to the sequence readout. Several machine learning-based models of transcription factor-DNA interactions, considering DNA shape features, have been developed in recent years. Here, we present a new biophysical model of protein-DNA interactions by integrating the DNA shape properties. It is based on the neighbor dinucleotide dependency model BayesPI2, where new parameters are restricted to a subspace spanned by the dinucleotide form of DNA shape features. This allows a biophysical interpretation of the new parameters as a position-dependent preference towards specific DNA shape features. Using the new model, we explore the variation of DNA shape preferences in several transcription factors across various cancer cell lines and cellular conditions. The results reveal that there are DNA shape variations at FOXA1 (Forkhead Box Protein A1) binding sites in steroid-treated MCF7 cells. The new biophysical model is useful for elucidating the finer details of transcription factor-DNA interaction, as well as for predicting cancer mutation effects in the future.

  20. Cellular normoxic biophysical markers of hydroxyurea treatment in sickle cell disease

    OpenAIRE

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

    2016-01-01

    There exists a critical need for developing biomarkers reflecting clinical outcomes and for evaluating the effectiveness of treatments for sickle cell disease patients. Prior attempts to find such patient-specific markers have mostly relied upon chemical biomarkers or biophysical properties at hypoxia with limited success. We introduce unique biomarkers based on characterization of cellular biophysical properties at normoxia and show that these markers correlate sensitively with treatment usi...

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

    Science.gov (United States)

    Zeng, Y

    2017-04-29

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

  2. The case for biophysics super-groups in physics departments.

    Science.gov (United States)

    Hoogenboom, Bart W; Leake, Mark

    2018-06-04

    Increasing numbers of physicists engage in research activities that address biological questions from physics perspectives or strive to develop physics insights from active biological processes. The on-going development and success of such activities morph our ways of thinking about what it is to 'do biophysics' and add to our understanding of the physics of life. Many scientists in this research and teaching landscape are homed in physics departments. A challenge for a hosting department is how to group, name and structure such biophysicists to best add value to their emerging research and teaching but also to the portfolio of the whole department. Here we discuss these issues and speculate on strategies. Creative Commons Attribution license.

  3. Sonographic biophysical profile in detection of foetal hypoxia in 100 cases of suspected high risk pregnancy

    International Nuclear Information System (INIS)

    Ullah, N.; Khan, A.R.; Usman, M.

    2010-01-01

    Background: The foetus has become increasingly accessible and visible as a patient over the last two decades. Ultrasound imaging has broadened the scope of foetal assessment. Dynamic real time B-Mode ultrasound is used to monitor cluster of biophysical variables, both dynamic and static collectively termed as biophysical profile. The purpose of this study was to determine the effect of sonographic biophysical profile score on perinatal outcome in terms of mortality and morbidity. Methods: This descriptive study was carried on 100 randomly select ed high risk pregnant patients in Radiology Department PGMI, Government Lady Reading Hospital, Peshawar from December 2007 to June 2008. Manning biophysical profile including non-stress was employed for foetal screening, using Toshiba ultrasound machine model Nemio SSA-550A and 7.5 MHZ probe. Results: Out of 100 cases 79 (79%) had a normal biophysical profile in the last scan of 10/10 and had a normal perinatal outcome with 5 minutes Apgar score >7/10. In 13 (13%) cases Apgar score at 5 minute was < 7/10 and babies were shifted to nursery. There were 2 (2%) false positive cases that showed abnormal biophysical profile scores of 6/10 but babies were born with an Apgar score of 8/10 at 5 minutes. There were 2 (2%) neonatal deaths in this study group. The sensitivity of biophysical profile was 79.1%, specificity 92.9%. Predictive value for a positive test was 98.55%; predictive value for a negative test was 41.93%. Conclusion: Biophysical profile is highly accurate and reliable test of diagnosing foetal hypoxia. (author)

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

    Science.gov (United States)

    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.

  5. Single Nucleobase Identification Using Biophysical Signatures from Nanoelectronic Quantum Tunneling.

    Science.gov (United States)

    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.

  6. Synthetic Biology: Engineering Living Systems from Biophysical Principles.

    Science.gov (United States)

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

    2017-03-28

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

  7. A synthesized biophysical and social vulnerability assessment for Taiwan

    Science.gov (United States)

    Lee, Yung-Jaan

    2017-11-01

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

  8. Biophysics and the Challenges of Emerging Threats

    CERN Document Server

    Puglisi, Joseph D

    2009-01-01

    This volume is a collection of articles from the proceedings of the International School of Structural Biology and Magnetic Resonance 8th Course: Biophysics and the Challenges of Emerging Threats. This NATO Advance Study Institute (ASI) was held in Erice at the Ettore Majorana Foundation and Centre for Scientific Culture on 19 through 30 June 2007. The ASI brought together a diverse group of experts who bridged the fields of virology and biology, biophysics, chemistry and physics. Prominent lecturers and students from around the world representant a total of 24 countries participated in the NATO ASI organized by Professors Joseph Puglisi (Stanford University, USA) and Alexander Arseniev (Moscow, RU). The central hypothesis underlying this ASI was that interdisciplinary research, merging principles of physics, chemistry and biology, can drive new discovery in detecting and fighting bioterrorism agents, lead to cleaner environments, and help propel development in NATO partner countries. The ASI merged the relat...

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

    Science.gov (United States)

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

    2016-12-01

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

  10. Maximum likelihood estimation of biophysical parameters of synaptic receptors from macroscopic currents

    Directory of Open Access Journals (Sweden)

    Andrey eStepanyuk

    2014-10-01

    Full Text Available Dendritic integration and neuronal firing patterns strongly depend on biophysical properties of synaptic ligand-gated channels. However, precise estimation of biophysical parameters of these channels in their intrinsic environment is complicated and still unresolved problem. Here we describe a novel method based on a maximum likelihood approach that allows to estimate not only the unitary current of synaptic receptor channels but also their multiple conductance levels, kinetic constants, the number of receptors bound with a neurotransmitter and the peak open probability from experimentally feasible number of postsynaptic currents. The new method also improves the accuracy of evaluation of unitary current as compared to the peak-scaled non-stationary fluctuation analysis, leading to a possibility to precisely estimate this important parameter from a few postsynaptic currents recorded in steady-state conditions. Estimation of unitary current with this method is robust even if postsynaptic currents are generated by receptors having different kinetic parameters, the case when peak-scaled non-stationary fluctuation analysis is not applicable. Thus, with the new method, routinely recorded postsynaptic currents could be used to study the properties of synaptic receptors in their native biochemical environment.

  11. Cellular normoxic biophysical markers of hydroxyurea treatment in sickle cell disease.

    Science.gov (United States)

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

    2016-08-23

    Hydroxyurea (HU) has been used clinically to reduce the frequency of painful crisis and the need for blood transfusion in sickle cell disease (SCD) patients. However, the mechanisms underlying such beneficial effects of HU treatment are still not fully understood. Studies have indicated a weak correlation between clinical outcome and molecular markers, and the scientific quest to develop companion biophysical markers have mostly targeted studies of blood properties under hypoxia. 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. Our results show that patient-specific HU effects on the cellular biophysical properties are detectable at normoxia, and that these properties are strongly correlated with the clinically measured mean cellular volume rather than fetal hemoglobin level.

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

    Science.gov (United States)

    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.

  13. Biophysical radiosensitization

    International Nuclear Information System (INIS)

    Vladescu, C.; Apetroae, M.

    1983-01-01

    Experimental studies on normal and tumor-bearing rats revealed that chronic treatment with hydroquinone (5 mg/kg/day) inhibited catalase activity in liver, spleen, blood, and H 18R tumor. 3 H-hydroquinone (1.5 μCi/g body weight) showed tumor specificity, with maximum radioactivity in the tumor at 1 h after administration. The biological half-time of 3 H-hydroquinone in the tumor was 2 h, but there seems to exist a longer component, since 24 h after administration, some 30% of the maximum radioactivity could be detected in the tumor. Hydroquinone treatment produces a specific inhibition of catalase in the tumor and a higher degree of oxygenation at this level. These findings support the assumption that the mechanism of action of hydroquinone as an anticancer agent is achieved mainly via peroxide production. The oxygenation of the hypoxic tumoral tissue is done at non-toxic levels of hydroquinone, through a natural and specific biophysical pathway, recommanding hydroquinone for combined anticancer treatment (radiotherapy and chemotherapy). (orig.)

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

    Science.gov (United States)

    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.

  15. The biophysics of renal sympathetic denervation using radiofrequency energy.

    Science.gov (United States)

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

    2014-05-01

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

  16. Raman spectroscopy reveals biophysical markers in skin cancer surgical margins

    Science.gov (United States)

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

    2018-02-01

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

  17. On the biophysics and kinetics of toehold-mediated DNA strand displacement.

    Science.gov (United States)

    Srinivas, Niranjan; Ouldridge, Thomas E; Sulc, Petr; Schaeffer, Joseph M; Yurke, Bernard; Louis, Ard A; Doye, Jonathan P K; Winfree, Erik

    2013-12-01

    Dynamic DNA nanotechnology often uses toehold-mediated strand displacement for controlling reaction kinetics. Although the dependence of strand displacement kinetics on toehold length has been experimentally characterized and phenomenologically modeled, detailed biophysical understanding has remained elusive. Here, we study strand displacement at multiple levels of detail, using an intuitive model of a random walk on a 1D energy landscape, a secondary structure kinetics model with single base-pair steps and a coarse-grained molecular model that incorporates 3D geometric and steric effects. Further, we experimentally investigate the thermodynamics of three-way branch migration. Two factors explain the dependence of strand displacement kinetics on toehold length: (i) the physical process by which a single step of branch migration occurs is significantly slower than the fraying of a single base pair and (ii) initiating branch migration incurs a thermodynamic penalty, not captured by state-of-the-art nearest neighbor models of DNA, due to the additional overhang it engenders at the junction. Our findings are consistent with previously measured or inferred rates for hybridization, fraying and branch migration, and they provide a biophysical explanation of strand displacement kinetics. Our work paves the way for accurate modeling of strand displacement cascades, which would facilitate the simulation and construction of more complex molecular systems.

  18. Chief, Structural Biophysics Laboratory | Center for Cancer Research

    Science.gov (United States)

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

  19. Developing spatial biophysical accounting for multiple ecosystem services

    NARCIS (Netherlands)

    Remme, R.P.; Schroter, M.; Hein, L.G.

    2014-01-01

    Ecosystem accounting is receiving increasing interest as a way to systematically monitor the conditions of ecosystems and the ecosystem services they provide. A critical element of ecosystem accounting is understanding spatially explicit flows of ecosystem services. We developed spatial biophysical

  20. Introducing "biophysical redundancy": the global status and past evolution of unused water, land and productivity resources for food production

    Science.gov (United States)

    Fader, Marianela

    2017-04-01

    Countries have different resilience to sudden and long-term changes in food demand and supply. An important part of this resilience is the degree of biophysical redundancy, defined as the potential food production of 'spare land', available water resources (i.e., not already used for human activities), as well as production increases through yield gap closure on cultivated areas and potential agricultural areas. The presentation will show the results of a recently published paper1 on the evolution of biophysical redundancy for agricultural production at country level, from 1992 to 2012. Results indicate that in 2012, the biophysical redundancy of 75 (48) countries, mainly in North Africa, Western Europe, the Middle East and Asia, was insufficient to produce the caloric nutritional needs for at least 50% (25%) of their population during a year. Biophysical redundancy has decreased in the last two decades in 102 out of 155 countries, 11 of these went from high to limited redundancy, and nine of these from limited to very low redundancy. Although the variability of the drivers of change across different countries is high, improvements in yield and population growth have a clear impact on the decreases of redundancy towards the very low redundancy category. We took a more detailed look at countries classified as 'Low Income Economies (LIEs)' since they are particularly vulnerable to domestic or external food supply changes, due to their limited capacity to offset for food supply decreases with higher purchasing power on the international market. Currently, nine LIEs have limited or very low biophysical redundancy. Many of these showed a decrease in redundancy over the last two decades, which is not always linked with improvements in per capita food availability.

  1. Achievements and challenges in structural bioinformatics and computational biophysics.

    Science.gov (United States)

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

    2015-01-01

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

  2. Evolution and Biophysics of the Escherichia coli lac Operon

    Science.gov (United States)

    Ray, J. Christian; Igoshin, Oleg; Quan, Selwyn; Monds, Russell; Cooper, Tim; Balázsi, Gábor

    2011-03-01

    To understand, predict, and control the evolution of living organisms, we consider biophysical effects and molecular network architectures. The lactose utilization system of E. coli is among the most well-studied molecular networks in biology, making it an ideal candidate for such studies. Simulations show how the genetic architecture of the wild-type operon attenuates large metabolic intermediate fluctuations that are predicted to occur in an equivalent system with the component genes on separate operons. Quantification of gene expression in the lac operon evolved in growth conditions containing constant lactose, alternating with glucose, or constant glucose, shows characteristic gene expression patterns depending on conditions. We are simulating these conditions to show context-dependent biophysical sources and costs of different lac operon architectures.

  3. Identifying bio-physical, social and political challenges to catchment governance for sustainable freshwater fisheries in West Africa: Systems overview through scenario development in the SUSFISH project.

    Science.gov (United States)

    Sendzimir, Jan; Slezak, Gabriele; Melcher, Andreas

    2015-04-01

    Chronic and episodic water scarcity prompted construction of 1400 reservoirs in Burkina Faso since 1950, greatly expanding fisheries production. These fisheries provided an increasingly important protein source for a population that has risen 600% since 1920, but production has plateaued, and dramatic declines in adult fish size suggest these fisheries are not sustainable. The SUSFISH project joined Austrian and Burkinabe scientists to increase local capacities to manage fisheries sustainably. SUSFISH has successfully increased capacity to monitor fish populations, identify endangered species, and use specific fish and macroinvertebrate species as bio-indicators of water and habitat quality as well as anthropogenic pressures. But projects to support sustainable development in Africa have a long history of failure if only based on transfer of technology and theory based on bio-physical sciences. This paper describes the processes and products of knowledge elicitation, scenario development and systems analysis to identify barriers and bridges to long-term sustainable fisheries development that arise from bio-physical, social, political and cultural causes, and, especially, interactions between them. Lessons learned and important on-going research questions are identified for both the natural and social sciences as they apply to managing catchments at multiple scales of governance, from local to national.

  4. Biophysical characteristics reveal neural stem cell differentiation potential.

    Directory of Open Access Journals (Sweden)

    Fatima H Labeed

    Full Text Available Distinguishing human neural stem/progenitor cell (huNSPC populations that will predominantly generate neurons from those that produce glia is currently hampered by a lack of sufficient cell type-specific surface markers predictive of fate potential. This limits investigation of lineage-biased progenitors and their potential use as therapeutic agents. A live-cell biophysical and label-free measure of fate potential would solve this problem by obviating the need for specific cell surface markers.We used dielectrophoresis (DEP to analyze the biophysical, specifically electrophysiological, properties of cortical human and mouse NSPCs that vary in differentiation potential. Our data demonstrate that the electrophysiological property membrane capacitance inversely correlates with the neurogenic potential of NSPCs. Furthermore, as huNSPCs are continually passaged they decrease neuron generation and increase membrane capacitance, confirming that this parameter dynamically predicts and negatively correlates with neurogenic potential. In contrast, differences in membrane conductance between NSPCs do not consistently correlate with the ability of the cells to generate neurons. DEP crossover frequency, which is a quantitative measure of cell behavior in DEP, directly correlates with neuron generation of NSPCs, indicating a potential mechanism to separate stem cells biased to particular differentiated cell fates.We show here that whole cell membrane capacitance, but not membrane conductance, reflects and predicts the neurogenic potential of human and mouse NSPCs. Stem cell biophysical characteristics therefore provide a completely novel and quantitative measure of stem cell fate potential and a label-free means to identify neuron- or glial-biased progenitors.

  5. CREB Overexpression Ameliorates Age-related Behavioral and Biophysical Deficits

    Science.gov (United States)

    Yu, Xiao-Wen

    Age-related cognitive deficits are observed in both humans and animals. Yet, the molecular mechanisms underlying these deficits are not yet fully elucidated. In aged animals, a decrease in intrinsic excitability of pyramidal neurons from the CA1 sub-region of hippocampus is believed to contribute to age-related cognitive impairments, but the molecular mechanism(s) that modulate both these factors has yet to be identified. Increasing activity of the transcription factor cAMP response element-binding protein (CREB) in young adult rodents has been shown to facilitate cognition, and increase intrinsic excitability of their neurons. However, how CREB changes with age, and how that impacts cognition in aged animals, is not clear. Therefore, we first systematically characterized age- and training-related changes in CREB levels in dorsal hippocampus. At a remote time point after undergoing behavioral training, levels of total CREB and activated CREB (phosphorylated at S133, pCREB) were measured in both young and aged rats. We found that pCREB, but not total CREB was significantly reduced in dorsal CA1 of aged rats. Importantly, levels of pCREB were found to be positively correlated with short-term spatial memory in both young and aged rats i.e. higher pCREB in dorsal CA1 was associated with better spatial memory. These findings indicate that an age-related deficit in CREB activity may contribute to the development of age-related cognitive deficits. However, it was still unclear if increasing CREB activity would be sufficient to ameliorate age-related cognitive, and biophysical deficits. To address this question, we virally overexpressed CREB in CA1, where we found the age-related deficit. Young and aged rats received control or CREB virus, and underwent water maze training. While control aged animals exhibited deficits in long-term spatial memory, aged animals with CREB overexpression performed at levels comparable to young animals. Concurrently, aged neurons

  6. European Union Harmonized Excise Taxation : Occasional Importation Process

    OpenAIRE

    Tanhua, Taina

    2013-01-01

    This thesis was written with the intent to compile the information related to occasional importation process and European Union harmonized taxation into a single package. The process is based on European Union legislation and the aim of it is to unify the taxation within the internal market area. The national excise duties are not part of the occasional importation process but are partly linked to it. The first part of the thesis discusses the occasional importation of goods subject to ha...

  7. Biophysical approach to low back pain: a pilot report

    Czech Academy of Sciences Publication Activity Database

    Foletti, A.; Pokorný, Jiří

    2015-01-01

    Roč. 34, č. 2 (2015), s. 156-159 ISSN 1536-8378 Institutional support: RVO:67985882 Keywords : Bioelectromagnetic medicine * Biophysical therapy * Coherence domains Subject RIV: JA - Electronics ; Optoelectronics, Electrical Engineering Impact factor: 1.208, year: 2015

  8. Cruciform structures are a common DNA feature important for regulating biological processes

    Czech Academy of Sciences Publication Activity Database

    Brázda, Václav; Laister, R.C.; Jagelská, Eva; Arrowsmith, Ch.

    2011-01-01

    Roč. 12, č. 33 (2011), s. 1-16 ISSN 1471-2199 R&D Projects: GA ČR(CZ) GAP301/10/1211; GA MŠk(CZ) LC06035 Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702 Keywords : cruciform structure * inverted repeat * protein- DNA binding Subject RIV: BO - Biophysics Impact factor: 2.857, year: 2011

  9. Biophysical modeling of in vitro and in vivo processes underlying regulated photoprotective mechanism in cyanobacteria.

    Science.gov (United States)

    Shirshin, Evgeny A; Nikonova, Elena E; Kuzminov, Fedor I; Sluchanko, Nikolai N; Elanskaya, Irina V; Gorbunov, Maxim Y; Fadeev, Victor V; Friedrich, Thomas; Maksimov, Eugene G

    2017-09-01

    Non-photochemical quenching (NPQ) is a mechanism responsible for high light tolerance in photosynthetic organisms. In cyanobacteria, NPQ is realized by the interplay between light-harvesting complexes, phycobilisomes (PBs), a light sensor and effector of NPQ, the photoactive orange carotenoid protein (OCP), and the fluorescence recovery protein (FRP). Here, we introduced a biophysical model, which takes into account the whole spectrum of interactions between PBs, OCP, and FRP and describes the experimental PBs fluorescence kinetics, unraveling interaction rate constants between the components involved and their relative concentrations in the cell. We took benefit from the possibility to reconstruct the photoprotection mechanism and its parts in vitro, where most of the parameters could be varied, to develop the model and then applied it to describe the NPQ kinetics in the Synechocystis sp. PCC 6803 mutant lacking photosystems. Our analyses revealed  that while an excess of the OCP over PBs is required to obtain substantial PBs fluorescence quenching in vitro, in vivo the OCP/PBs ratio is less than unity, due to higher local concentration of PBs, which was estimated as ~10 -5 M, compared to in vitro experiments. The analysis of PBs fluorescence recovery on the basis of the generalized model of enzymatic catalysis resulted in determination of the FRP concentration in vivo close to 10% of the OCP concentration. Finally, the possible role of the FRP oligomeric state alteration in the kinetics of PBs fluorescence was shown. This paper provides the most comprehensive model of the OCP-induced PBs fluorescence quenching to date and the results are important for better understanding of the regulatory molecular mechanisms underlying NPQ in cyanobacteria.

  10. Radiobiology, biochemistry and radiation biophysics at CYLAB

    International Nuclear Information System (INIS)

    Ftacnikova, S.

    1998-01-01

    The Cyclotron Laboratory (CYLAB) should fill the gap in the field of nuclear medicine, radiotherapy, basic research, metrology of ionizing radiation, education and implications of accelerator technology existing today in Slovak Republic. The main planned activities of this facility are in the fields of nuclear medicine (production of radioisotopes for Positron Emission Tomography - PET and for oncology) and radiotherapy (neutron capture therapy, fast neutron therapy and proton therapy). The radiobiological and biophysical research will be closely connected with medical applications, particularly with radiotherapy. Problems to be addressed include the determination of the values of Relative Biological Effectiveness (RBE) for different types of ionizing radiation involved in the therapy, microdosimetric measurements and calculations, which are indispensable in the calculation of the absorbed dose (lineal and specific energy spectra) at the cellular and macromolecular level. Radiation biophysics and medical physics help in creating therapeutic plans for radiotherapy (NCT and fast neutron therapy). In nuclear medicine, in diagnostic and therapeutical procedures it is necessary to assess the biodistribution of radiopharmaceuticals and to calculate doses in target and critical organs and to determine whole body burden - effective equivalent dose for newly developed radiopharmaceuticals

  11. The conformational stability and biophysical properties of the eukaryotic thioredoxins of Pisum sativum are not family-conserved.

    Directory of Open Access Journals (Sweden)

    David Aguado-Llera

    2011-02-01

    Full Text Available 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.

  12. A biophysical approach to the optimisation of dendritic-tumour cell electrofusion

    International Nuclear Information System (INIS)

    Sukhorukov, Vladimir L.; Reuss, Randolph; Endter, Joerg M.; Fehrmann, Steffen; Katsen-Globa, Alisa; Gessner, Petra; Steinbach, Andrea; Mueller, Kilian J.; Karpas, Abraham; Zimmermann, Ulrich; Zimmermann, Heiko

    2006-01-01

    Electrofusion of tumour and dendritic cells (DCs) is a promising approach for production of DC-based anti-tumour vaccines. Although human DCs are well characterised immunologically, little is known about their biophysical properties, including dielectric and osmotic parameters, both of which are essential for the development of efficient electrofusion protocols. In the present study, human DCs from the peripheral blood along with a tumour cell line used as a model fusion partner were examined by means of time-resolved cell volumetry and electrorotation. Based on the biophysical cell data, the electrofusion protocol could be rapidly optimised with respect to the sugar composition of the fusion medium, duration of hypotonic treatment, frequency range for stable cell alignment, and field strengths of breakdown pulses triggering membrane fusion. The hypotonic electrofusion consistently gave a tumour-DC hybrid rate of up to 19%, as determined by counting dually labelled fluorescent hybrids in a microscope. This fusion rate is nearly twice as high as that usually reported in the literature for isotonic media. The experimental findings and biophysical approach presented here are generally useful for the development of efficient electrofusion protocols, especially for rare and valuable human cells

  13. Seminal Fluid Analysis And Biophysical Profile: Findings And ...

    African Journals Online (AJOL)

    Seminal Fluid Analysis And Biophysical Profile: Findings And Relevance In Infertile Males In Ilorin, Nigeria. EK Oghagbon, AAG Jimoh, SA Adebisi. Abstract. To determine if there was a bearing of body mass index (BMI) on male infertility, a cross-sectional study of males of infertile couples, attending our infertility clinic was ...

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

    Science.gov (United States)

    Rodriguez, Idaykis

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

  15. Biophysical constraints on leaf expansion in a tall conifer.

    Science.gov (United States)

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

    2008-01-01

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

  16. 19th International School of Biophysics "Ettore Majorana"

    CERN Document Server

    Blank, M; Bioelectrochemistry III : Charge Separation across Biomembranes

    1988-01-01

    This book contains aseries of review papers related to the lectures given at the Third Course on Bioelectrochemistry held at Erice in November 1988, in the framework of the International School of Biophysics. The topics covered by this course, "Charge Separation Across Biomembranes, " deal with the electrochemical aspects of some basic phenomena in biological systems, such as transport of ions, ATP synthesis, formation and maintenance of ionic and protonic gradients. In the first part of the course some preliminary lectures introduce the students to the most basic phenomena and technical aspects of membrane bioelectrochemistry. The remaining part of the course is devoted to the description of a selected group of membrane-enzyme systems, capable of promoting, or exploiting, the processes of separation of electrically charged entities (electrons or ions) across the membrane barrier. These systems are systematically discussed both from a structural and functional point of view. The effort of the many dis...

  17. Biophysics and cancer

    CERN Document Server

    Nicolini, Claudio

    1986-01-01

    Since the early times of the Greek philosophers Leucippus and Democritus, and later of the Roman philosopher Lucretius, a simple, fundamental idea emerged that brought the life sciences into the realm of the physical sciences. Atoms, after various interactions, were assumed to acquire stable configurations that corresponded either to the living or to the inanimate world. This simple and unitary theory, which has evolved in successive steps to our present time, remarkably maintained its validity despite several centuries of alternative vicissitudes, and is the foundation of modern biophysics. Some of the recent developments of this ancient idea are the discovery of the direct relationship between spatial structures and chemical activity of such molecules as methane and benzene, and the later discovery of the three-dimensional structure of double-helical DNA, and of its relationship with biological activity. The relationship between the structure of various macromolecules and the function of living cells was on...

  18. Biophysical aspects of using liposomes as delivery vehicles.

    Science.gov (United States)

    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.

  19. Epigenetic modulation of the biophysical properties of drug-resistant cell lipids to restore drug transport and endocytic functions.

    Science.gov (United States)

    Vijayaraghavalu, Sivakumar; Peetla, Chiranjeevi; Lu, Shan; Labhasetwar, Vinod

    2012-09-04

    In our recent studies exploring the biophysical characteristics of resistant cell lipids, and the role they play in drug transport, we demonstrated the difference of drug-resistant breast cancer cells from drug-sensitive cells in lipid composition and biophysical properties, suggesting that cancer cells acquire a drug-resistant phenotype through the alteration of lipid synthesis to inhibit intracellular drug transport to protect from cytotoxic effect. In cancer cells, epigenetic changes (e.g., DNA hypermethylation) are essential to maintain this drug-resistant phenotype. Thus, altered lipid synthesis may be linked to epigenetic mechanisms of drug resistance. We hypothesize that reversing DNA hypermethylation in resistant cells with an epigenetic drug could alter lipid synthesis, changing the cell membrane's biophysical properties to facilitate drug delivery to overcome drug resistance. Herein we show that treating drug-resistant breast cancer cells (MCF-7/ADR) with the epigenetic drug 5-aza-2'-deoxycytidine (decitabine) significantly alters cell lipid composition and biophysical properties, causing the resistant cells to acquire biophysical characteristics similar to those of sensitive cell (MCF-7) lipids. Following decitabine treatment, resistant cells demonstrated increased sphingomyelinase activity, resulting in a decreased sphingomyelin level that influenced lipid domain structures, increased membrane fluidity, and reduced P-glycoprotein expression. Changes in the biophysical characteristics of resistant cell lipids facilitated doxorubicin transport and restored endocytic function for drug delivery with a lipid-encapsulated form of doxorubicin, enhancing the drug efficacy. In conclusion, we have established a new mechanism for efficacy of an epigenetic drug, mediated through changes in lipid composition and biophysical properties, in reversing cancer drug resistance.

  20. Biophysical Aspects of Radiation Quality. Second Panel Report

    International Nuclear Information System (INIS)

    1968-01-01

    If a living system is exposed to ionizing radiation a sequence of events follows. It starts with the absorption and dissipation of radiation energy, and continues through various physico-chemical and biochemical reactions up to the final biological end point observed. One of the aims of research in quantitative radiation biology is to understand the mechanism of this sequence of actions and to explore the differences in quality of different kinds of radiations. Because of its complexity, progress in this work requires the combined efforts of physicists, biochemists, biologists and physicians. It should, however, be done in very close collaboration rather than in following isolated lines in any one direction. For this reason, and because of the growing importance of the field for almost all applications of ionizing radiations, it was felt desirable to bring together a group of scientists engaged in research on radiation quality who represented a wide range of interests. The first panel on Biophysical Aspects of Radiation Quality, convened by the International Atomic Energy Agency in Vienna and held from 29 March to 2 April 1965, proved to be a successful beginning, stimulating a useful exchange of ideas and information. By this meeting, and the resulting collection of papers, published in 1966 as No. 58 of the Agency's Technical Reports Series, the importance of research on radiation quality was highlighted and the field itself became more clearly defined. The Agency held a second Panel on the same subject in Vienna from 14 to 18 April 1967. This meeting was attended by 18 experts from 10 countries, and representatives from Euratom and WHO. The Czechoslovak Socialist Republic, France, India and Poland were represented for the first time. Fourteen papers were presented and discussed in some detail. It became evident that much progress had been made since the previous meeting in certain areas such as microdosimetry, the dependence of the oxygen effect on radiation

  1. Biophysical and lipofection studies of DOTAP analogs.

    Science.gov (United States)

    Regelin, A E; Fankhaenel, S; Gürtesch, L; Prinz, C; von Kiedrowski, G; Massing, U

    2000-03-15

    In order to investigate the relationship between lipid structure and liposome-mediated gene transfer, we have studied biophysical parameters and transfection properties of monocationic DOTAP analogs, systematically modified in their non-polar hydrocarbon chains. Stability, size and (by means of anisotropy profiles) membrane fluidity of liposomes and lipoplexes were determined, and lipofection efficiency was tested in a luciferase reporter gene assay. DOTAP analogs were used as single components or combined with a helper lipid, either DOPE or cholesterol. Stability of liposomes was a precondition for formation of temporarily stable lipoplexes. Addition of DOPE or cholesterol improved liposome and lipoplex stability. Transfection efficiencies of lipoplexes based on pure DOTAP analogs could be correlated with stability data and membrane fluidity at transfection temperature. Inclusion of DOPE led to rather uniform transfection and anisotropy profiles, corresponding to lipoplex stability. Cholesterol-containing lipoplexes were generally stable, showing high transfection efficiency at low relative fluidity. Our results demonstrate that the efficiency of gene transfer mediated by monocationic lipids is greatly influenced by lipoplex biophysics due to lipid composition. The measurement of fluorescence anisotropy is an appropriate method to characterize membrane fluidity within a defined system of liposomes or lipoplexes and may be helpful to elucidate structure-activity relationships.

  2. Monitoring and ming bio-physical parameters for hypoxia hazard in a coastal sand pit

    DEFF Research Database (Denmark)

    Mariani, Patrizio; Benassai, Guido; Grieco, Luisa

    2018-01-01

    Management of coastal areas requires monitoring and modeling of the anthropogenic drivers and the bio-physical processes affecting water quality. To assess the range of hydrographic conditions controlling oxygen distribution in the bottom layers of sand pits, a multi-year oceanographic survey has...... of the sand pits is associated with higher temperatures and wind speed lower than 5 m/s, which is not infrequent during the summer season. However, the number of consecutive days of oxygen depletion can be considered lower than the danger threshold level assumed in the literature....

  3. Biophysical approach to low back pain: a pilot report.

    Science.gov (United States)

    Foletti, Alberto; Pokorný, Jiry

    2015-01-01

    Since biophysical treatment has been reported to be effective in the general management of pain, we decided to assess the specific effect and treatment duration of this therapeutic strategy in low back pain. We were interested in verifying the possibility that a single clinical procedure could reduce pain and improve patients' quality of life within a period of three months. An Electromagnetic Information Transfer Through Aqueous System was employed to record endogenous therapeutic signals from each individual using an electromagnetic recording device (Med Select 729). A highly significant reduction in the Roland Morris low back pain and disability questionnaire score was observed after 3 months following a single biophysical intervention (11.83 ± 6 at baseline versus 2.3 ± 3.25 at 3 months, p < 0.0001). This preliminary report provides further evidence of the theoretical implications and clinical applications of Quantum Electro Dynamic concepts in biology and medicine.

  4. Quantum-Sequencing: Biophysics of quantum tunneling through nucleic acids

    Science.gov (United States)

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

    2014-03-01

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

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

    Science.gov (United States)

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

    2017-11-01

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

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

    Science.gov (United States)

    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.

  7. Biophysical Characterization of α-Synuclein and Rotenone Interaction

    Directory of Open Access Journals (Sweden)

    Anthony L. Fink

    2013-09-01

    Full Text Available Previous studies revealed that pesticides interact with α-synuclein and accelerate the rate of fibrillation. These results are consistent with the prevailing hypothesis that the direct interaction of α-synuclein with pesticides is one of many suspected factors leading to α-synuclein fibrillation and ultimately to Parkinson’s disease. In this study, the biophysical properties and fibrillation kinetics of α-synuclein in the presence of rotenone were investigated and, more specifically, the effects of rotenone on the early-stage misfolded forms of α-synuclein were considered. The thioflavine T (ThT fluorescence assay studies provide evidence that early-phase misfolded α-synuclein forms are affected by rotenone and that the fibrillation process is accelerated. Further characterization by attenuated total reflectance Fourier transform infrared spectroscopy (ATR-FTIR shows that rotenone increases the amount of ordered secondary structure in this intrinsically disordered protein. Morphological characterization by transmission electron microscopy (TEM and atomic force microscopy (AFM provide visualization of the differences in the aggregated α-synuclein species developing during the early kinetics of the fibrillation process in the absence and presence of rotenone. We believe that these data provide useful information for a better understanding of the molecular basis of rotenone-induced misfolding and aggregation of α-synuclein.

  8. Developing a protocol for managing the biophysical condition of a ...

    African Journals Online (AJOL)

    Their function will focus on the overall management of water resources on a ... for the integrated management of the biophysical component of a catchment, with ... and implement a protocol which will combine and integrate the knowledge of ...

  9. Putting technology and societal dynamics within a biophysical perspective: Is more of the same a sustainable perspective?

    CERN Multimedia

    CERN. Geneva

    2015-01-01

    The wealth of a nation, as recognized in the past by Adam Smith and others, is its resource base, not its Gross National Product. "A tank of gasoline drives a car the same distance regardless of what people are willing to pay for it" (Odum, 1994). Until recently, neoclassical economics has been unsuitable for understanding the role of the biophysical support provided at no cost by the environment to the development of economic processes. In the distant past when populations were small and the extent of human use of the environment was negligible compared to the size of the environment, wealth consisted of a nation?s forests, soils, fisheries and the water and sunlight falling on its landscape. As the fossil fuels increased in amount and came to dominate the energetic base of economies, they allowed the exploitation of mineral resources, which synergistically increased the use of already scarce fossil fuels and in the long run diminished the importance of renewable resources. Our activities a...

  10. On The Development of Biophysical Models for Space Radiation Risk Assessment

    Science.gov (United States)

    Cucinotta, F. A.; Dicello, J. F.

    1999-01-01

    Experimental techniques in molecular biology are being applied to study biological risks from space radiation. The use of molecular assays presents a challenge to biophysical models which in the past have relied on descriptions of energy deposition and phenomenological treatments of repair. We describe a biochemical kinetics model of cell cycle control and DNA damage response proteins in order to model cellular responses to radiation exposures. Using models of cyclin-cdk, pRB, E2F's, p53, and GI inhibitors we show that simulations of cell cycle populations and GI arrest can be described by our biochemical approach. We consider radiation damaged DNA as a substrate for signal transduction processes and consider a dose and dose-rate reduction effectiveness factor (DDREF) for protein expression.

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

    Directory of Open Access Journals (Sweden)

    Sinjan Choudhary

    Full Text Available 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.

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

    Science.gov (United States)

    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.

  13. Effects of the strain background and autolysis process on the composition and biophysical properties of the cell wall from two different industrial yeasts.

    Science.gov (United States)

    Schiavone, Marion; Sieczkowski, Nathalie; Castex, Mathieu; Dague, Etienne; Marie François, Jean

    2015-03-01

    The Saccharomyces cerevisiae cell surface is endowed with some relevant technological properties, notably antimicrobial and biosorption activities. For these purposes, yeasts are usually processed and packaged in an 'autolysed/dried' formula, which may have some impacts on cell surface properties. In this report, we showed using a combination of biochemical, biophysical and molecular methods that the composition of the cell wall of two wine yeast strains was not altered by the autolysis process. In contrast, this process altered the nanomechanical properties as shown by a 2- to 4-fold increased surface roughness and to a higher adhesion to the atomic force microscope tips of the autolysed cells as compared to live yeast cells. Besides, we found that the two strains harboured differences in biomechanical properties that could be due in part to higher levels of mannan in one of them, and to the fact that the surface of this mannan-enriched strain is decorated with highly adhesive patches forming nanodomains. The presence of these nanodomains could be correlated with the upregulation of flocculin encoding FLO11 as well as to higher expression of few other genes encoding cell wall mannoproteins in this mannan-enriched strain as compared to the other strain. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permission@oup.com.

  14. Biophysical properties of the normal-sized aorta in patients with Marfan syndrome: evaluation with MR flow mapping

    NARCIS (Netherlands)

    Groenink, M.; de Roos, A.; Mulder, B. J.; Verbeeten, B.; Timmermans, J.; Zwinderman, A. H.; Spaan, J. A.; van der Wall, E. E.

    2001-01-01

    PURPOSE: To investigate the feasibility of magnetic resonance (MR) flow mapping in the assessment of aortic biophysical properties in patients with Marfan syndrome and to detect differences in biophysical properties in the normal-sized aorta distal to the aortic root between these patients and

  15. Review of FEWS NET Biophysical Monitoring Requirements

    Science.gov (United States)

    Ross, K. W.; Brown, Molly E.; Verdin, J.; Underwood, L. W.

    2009-01-01

    The Famine Early Warning System Network (FEWS NET) provides monitoring and early warning support to decision makers responsible for responding to famine and food insecurity. FEWS NET transforms satellite remote sensing data into rainfall and vegetation information that can be used by these decision makers. The National Aeronautics and Space Administration has recently funded activities to enhance remote sensing inputs to FEWS NET. To elicit Earth observation requirements, a professional review questionnaire was disseminated to FEWS NET expert end-users: it focused upon operational requirements to determine additional useful remote sensing data and; subsequently, beneficial FEWS NET biophysical supplementary inputs. The review was completed by over 40 experts from around the world, enabling a robust set of professional perspectives to be gathered and analyzed rapidly. Reviewers were asked to evaluate the relative importance of environmental variables and spatio-temporal requirements for Earth science data products, in particular for rainfall and vegetation products. The results showed that spatio-temporal resolution requirements are complex and need to vary according to place, time, and hazard: that high resolution remote sensing products continue to be in demand, and that rainfall and vegetation products were valued as data that provide actionable food security information.

  16. Biophysically realistic minimal model of dopamine neuron

    Science.gov (United States)

    Oprisan, Sorinel

    2008-03-01

    We proposed and studied a new biophysically relevant computational model of dopaminergic neurons. Midbrain dopamine neurons are involved in motivation and the control of movement, and have been implicated in various pathologies such as Parkinson's disease, schizophrenia, and drug abuse. The model we developed is a single-compartment Hodgkin-Huxley (HH)-type parallel conductance membrane model. The model captures the essential mechanisms underlying the slow oscillatory potentials and plateau potential oscillations. The main currents involved are: 1) a voltage-dependent fast calcium current, 2) a small conductance potassium current that is modulated by the cytosolic concentration of calcium, and 3) a slow voltage-activated potassium current. We developed multidimensional bifurcation diagrams and extracted the effective domains of sustained oscillations. The model includes a calcium balance due to the fundamental importance of calcium influx as proved by simultaneous electrophysiological and calcium imaging procedure. Although there are significant evidences to suggest a partially electrogenic calcium pump, all previous models considered only elecrtogenic pumps. We investigated the effect of the electrogenic calcium pump on the bifurcation diagram of the model and compared our findings against the experimental results.

  17. A Method Sustaining the Bioelectric, Biophysical, and Bioenergetic Function of Cultured Rabbit Atrial Cells

    OpenAIRE

    Noa Kirschner Peretz; Sofia Segal; Limor Arbel-Ganon; Ronen Ben Jehuda; Ronen Ben Jehuda; Yuval Shemer; Yuval Shemer; Binyamin Eisen; Binyamin Eisen; Moran Davoodi; Ofer Binah; Ofer Binah; Yael Yaniv

    2017-01-01

    Culturing atrial cells leads to a loss in their ability to be externally paced at physiological rates and to maintain their shape. We aim to develop a culture method that sustains the shape of atrial cells along with their biophysical and bioenergetic properties in response to physiological pacing. We hypothesize that adding 2,3-Butanedione 2-monoxime (BDM), which inhibits contraction during the culture period, will preserve these biophysical and bioenergetic properties. Rabbit atrial cells w...

  18. Studies of land-cover, land-use, and biophysical properties of vegetation in the Large Scale Biosphere Atmosphere experiment in Amazonia.

    Science.gov (United States)

    Dar A. Robertsa; Michael Keller; Joao Vianei Soares

    2003-01-01

    We summarize early research on land-cover, land-use, and biophysical properties of vegetation from the Large Scale Biosphere Atmosphere (LBA) experiment in Amazoˆnia. LBA is an international research program developed to evaluate regional function and to determine how land-use and climate modify biological, chemical and physical processes there. Remote sensing has...

  19. Unofficial Road Building in the Amazon: Socioeconomic and Biophysical Explanations

    Science.gov (United States)

    Perz, Stephen G.; Caldas, Marcellus M.; Arima, Eugenio; Walker, Robert J.

    2007-01-01

    Roads have manifold social and environmental impacts, including regional development, social conflicts and habitat fragmentation. 'Road ecology' has emerged as an approach to evaluate the various ecological and hydrological impacts of roads. This article aims to complement road ecology by examining the socio-spatial processes of road building itself. Focusing on the Brazilian Amazon, a heavily-studied context due to forest fragmentation by roads, the authors consider non-state social actors who build 'unofficial roads' for the purpose of gaining access to natural resources to support livelihoods and community development. They examine four case studies of roads with distinct histories in order to explain the socio-spatial processes behind road building in terms of profit maximization, land tenure claims, co-operative and conflictive political ecologies, and constraints as well as opportunities afforded by the biophysical environment. The study cases illustrate the need for a multi-pronged theoretical approach to understanding road building, and call for more attention to the role of non-state actors in unofficial road construction.

  20. Identifying important parameters for a continuous bioscouring process

    NARCIS (Netherlands)

    Lenting, H.B.M.; Lenting, H.B.M.; Zwier, E.; Nierstrasz, Vincent

    2002-01-01

    Compared to a bioscouring process in the batch mode, a continuously operating process requires relatively short processing steps. This study focusses on minimizing the required enzymatic incubation time. It is clear that the presence of a sufficient level of surfactant is of major importance in

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

    International Nuclear Information System (INIS)

    Liu, Miao; Zheng, Mingjing; Xu, Hanying; Liu, Lianqing; Li, Yanchun; Xiao, Wei; Li, Jianchun; Ma, Enlong

    2015-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Miao; Zheng, Mingjing; Xu, Hanying [Department of Pharmacology, Shenyang Pharmaceutical University, Shenyang, 110016 (China); Liu, Lianqing [Shenyang Institute of Automation China Academy of Sciences, Shenyang, 110016 (China); Li, Yanchun [Department of Pharmacology, Shenyang Pharmaceutical University, Shenyang, 110016 (China); Xiao, Wei [Jiangsu Kanion Pharmaceutical Co., Ltd., Nanjing, 222001 (China); Li, Jianchun, E-mail: lijianchun0317@sina.com.cn [Department of Pharmacology, Shenyang Pharmaceutical University, Shenyang, 110016 (China); Ma, Enlong, E-mail: enlong_ma2014@hotmail.com [Department of Pharmacology, Shenyang Pharmaceutical University, Shenyang, 110016 (China); Jiangsu Kanion Pharmaceutical Co., Ltd., Nanjing, 222001 (China)

    2015-12-04

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

  3. Mass spectrometry for the biophysical characterization of therapeutic monoclonal antibodies.

    Science.gov (United States)

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

    2014-01-21

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

  4. Enhancing the biophysical properties of mRFP1 through incorporation of fluoroproline

    Energy Technology Data Exchange (ETDEWEB)

    Deepankumar, Kanagavel; Nadarajan, Saravanan Prabhu; Ayyadurai, Niraikulam; Yun, Hyungdon, E-mail: hyungdon@ynu.ac.kr

    2013-11-01

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

  5. Materials science and biophysics applications at the ISOLDE radioactive ion beam facility

    Energy Technology Data Exchange (ETDEWEB)

    Wahl, U., E-mail: uwahl@itn.pt [Instituto Tecnologico e Nuclear, Estrada Nacional 10, 2686-953 Sacavem (Portugal); Centro de Fisica Nuclear da Universidade de Lisboa, Av. Prof. Gama Pinto 2, 1649-003 Lisboa (Portugal)

    2011-12-15

    The ISOLDE isotope separator facility at CERN provides a variety of radioactive ion beams, currently more than 800 different isotopes from {approx}70 chemical elements. The radioisotopes are produced on-line by nuclear reactions from a 1.4 GeV proton beam with various types of targets, outdiffusion of the reaction products and, if possible, chemically selective ionisation, followed by 60 kV acceleration and mass separation. While ISOLDE is mainly used for nuclear and atomic physics studies, applications in materials science and biophysics account for a significant part (currently {approx}15%) of the delivered beam time, requested by 18 different experiments. The ISOLDE materials science and biophysics community currently consists of {approx}80 scientists from more than 40 participating institutes and 21 countries. In the field of materials science, investigations focus on the study of semiconductors and oxides, with the recent additions of nanoparticles and metals, while the biophysics studies address the toxicity of metal ions in biological systems. The characterisation methods used are typical radioactive probe techniques such as Moessbauer spectroscopy, perturbed angular correlation, emission channeling, and tracer diffusion studies. In addition to these 'classic' methods of nuclear solid state physics, also standard semiconductor analysis techniques such as photoluminescence or deep level transient spectroscopy profit from the application of radioactive isotopes, which helps them to overcome their chemical 'blindness' since the nuclear half life of radioisotopes provides a signal that changes in time with characteristic exponential decay or saturation curves. In this presentation an overview will be given on the recent research activities in materials science and biophysics at ISOLDE, presenting some of the highlights during the last five years, together with a short outlook on the new developments under way.

  6. Enhancing the biophysical properties of mRFP1 through incorporation of fluoroproline

    International Nuclear Information System (INIS)

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

    2013-01-01

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

  7. Unveiling soil degradation and desertification risk in the Mediterranean basin: a data mining analysis of the relationships between biophysical and socioeconomic factors in agro-forest landscapes

    NARCIS (Netherlands)

    Salvati, L.; Kosmas, C.; Kairis, O.; Karavitis, C.; Hessel, R.; Ritsema, C.J.

    2015-01-01

    Soil degradation and desertification processes in the Mediterranean basin reflect the interplay between environmental and socioeconomic drivers. An approach to evaluate comparatively the multiple relationships between biophysical variables and socioeconomic factors is illustrated in the present

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

    Science.gov (United States)

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

    1996-10-01

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

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

    Science.gov (United States)

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

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

  10. Southwest Ecological Restoration Institutes (SWERI) Biophysical Monitoring Workshop Report

    Science.gov (United States)

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

    2009-01-01

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

  11. Biophysical and electrochemical studies of protein-nucleic acid interactions

    Czech Academy of Sciences Publication Activity Database

    Bowater, R. P.; Cobb, A:M.; Pivoňková, Hana; Havran, Luděk; Fojta, Miroslav

    2015-01-01

    Roč. 146, č. 5 (2015), s. 723-739 ISSN 0026-9247 R&D Projects: GA ČR(CZ) GBP206/12/G151; GA ČR(CZ) GAP301/11/2076 Institutional support: RVO:68081707 Keywords : ISOTHERMAL TITRATION CALORIMETRY * OSMIUM-TETROXIDE COMPLEXES * SURFACE-PLASMON RESONANCE Subject RIV: BO - Biophysics Impact factor: 1.131, year: 2015

  12. From hadron therapy to cosmic rays: a life in biophysics

    CERN Multimedia

    Christine Sutton

    2014-01-01

    In 1954 – the year CERN was founded – another scientific journey began at what is now the Lawrence Berkeley National Laboratory. Beams of protons from a particle accelerator were used for the first time by John Lawrence – a doctor and the brother of Ernest Lawrence, the physicist after whom the Berkeley lab is named – to treat patients with cancer. For many years, Eleanor Blakely has been one of the leaders of that journey. She visited CERN last week and spoke with the Bulletin about her life in biophysics.   Use of the cylcotron beam to mimic "shooting stars" seen by astronauts. Black hood on subject Cornelius Tobias keeps out light during neutron irradiation experiment at the 184-inch accelerator. Helping to position Tobias in the beam line are (left to right) John Lyman of Biomedical Division, and Ralph Thomas of Health Physics. (Photo courtesy of Lawrence Berkeley National Laboratory.) Interested in biophysics, which was still a new...

  13. Social and Biophysical Predictors of Public Perceptions of Extreme Fires

    Science.gov (United States)

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

    2013-12-01

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

  14. Constructing Precisely Computing Networks with Biophysical Spiking Neurons.

    Science.gov (United States)

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

    2015-07-15

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

  15. Evaluating impacts of climate change on future water scarcity in an intensively managed semi-arid region using a coupled model of biophysical processes and water rights

    Science.gov (United States)

    Han, B.; Flores, A. N.; Benner, S. G.

    2017-12-01

    In semiarid and arid regions where water supply is intensively managed, future water scarcity is a product of complex interactions between climate change and human activities. Evaluating future water scarcity under alternative scenarios of climate change, therefore, necessitates modeling approaches that explicitly represent the coupled biophysical and social processes responsible for the redistribution of water in these regions. At regional scales a particular challenge lies in adequately capturing not only the central tendencies of change in projections of climate change, but also the associated plausible range of variability in those projections. This study develops a framework that combines a stochastic weather generator, historical climate observations, and statistically downscaled General Circulation Model (GCM) projections. The method generates a large ensemble of daily climate realizations, avoiding deficiencies of using a few or mean values of individual GCM realizations. Three climate change scenario groups reflecting the historical, RCP4.5, and RCP8.5 future projections are developed. Importantly, the model explicitly captures the spatiotemporally varying irrigation activities as constrained by local water rights in a rapidly growing, semi-arid human-environment system in southwest Idaho. We use this modeling framework to project water use and scarcity patterns under the three future climate change scenarios. The model is built using the Envision alternative futures modeling framework. Climate projections for the region show future increases in both precipitation and temperature, especially under the RCP8.5 scenario. The increase of temperature has a direct influence on the increase of the irrigation water use and water scarcity, while the influence of increased precipitation on water use is less clear. The predicted changes are potentially useful in identifying areas in the watershed particularly sensitive to water scarcity, the relative importance of

  16. Urban thermal environment and its biophysical parameters derived from satellite remote sensing imagery

    Science.gov (United States)

    Zoran, Maria A.; Savastru, Roxana S.; Savastru, Dan M.; Tautan, Marina N.; Baschir, Laurentiu V.

    2013-10-01

    In frame of global warming, the field of urbanization and urban thermal environment are important issues among scientists all over the world. This paper investigated the influences of urbanization on urban thermal environment as well as the relationships of thermal characteristics to other biophysical variables in Bucharest metropolitan area of Romania based on satellite remote sensing imagery Landsat TM/ETM+, time series MODIS Terra/Aqua data and IKONOS acquired during 1990 - 2012 period. Vegetation abundances and percent impervious surfaces were derived by means of linear spectral mixture model, and a method for effectively enhancing impervious surface has been developed to accurately examine the urban growth. The land surface temperature (Ts), a key parameter for urban thermal characteristics analysis, was also retrieved from thermal infrared band of Landsat TM/ETM+, from MODIS Terra/Aqua datasets. Based on these parameters, the urban growth, urban heat island effect (UHI) and the relationships of Ts to other biophysical parameters have been analyzed. Results indicated that the metropolitan area ratio of impervious surface in Bucharest increased significantly during two decades investigated period, the intensity of urban heat island and heat wave events being most significant. The correlation analyses revealed that, at the pixel-scale, Ts possessed a strong positive correlation with percent impervious surfaces and negative correlation with vegetation abundances at the regional scale, respectively. This analysis provided an integrated research scheme and the findings can be very useful for urban ecosystem modeling.

  17. the economic importance of microorganism in food processing

    African Journals Online (AJOL)

    BSN

    This paper attempts to highlight the Economic Importance of microorganisms in food processing and manufacturing; it goes further to differentiate between the desirable ... Desirable importance are those cost saving and revenue generating activities ... Microorganism (yeast) play very useful role in the Bakery industries.

  18. Biophysical approach to chronic kidney disease management in older patients

    Directory of Open Access Journals (Sweden)

    Alberto Foletti

    2016-06-01

    Full Text Available Chronic kidney disease (CKD and its clinical progression are a critical issue in an aging population. Therefore, strategies aimed at preventing and managing the decline of renal function are warranted. Recent evidence has provided encouraging results for the improvement of renal function achieved through an integrated biophysical approach, but prospective studies on the clinical efficacy of this strategy are still lacking. This was an open-label prospective pilot study to investigate the effect of electromagnetic information transfer through the aqueous system on kidney function of older patients affected by stage 1 or 2 CKD. Patients received biophysical therapy every 3 months over a 1-year period. Estimated glomerular filtration rate (eGFR values were calculated using the CKD–Epidemiology Collaboration formula, and were recorded at baseline and at the end of treatment. Overall, 58 patients (mean age 74.8 ± 3.7 years were included in the study. At baseline, mean eGFR was 64.6 ± 15.5 mL/min, and it significantly increased to 69.9 ± 15.8 mL/min after 1 year (+5.2 ± 10 mL/min, p<0.0002. The same trend was observed among men (+5.7 ± 10.2 mL/min, p<0.0064 and women (+4.7 ± 9.9 mL/min, p<0.014. When results were analyzed by sex, no difference was found between the 2 groups. Although further and larger prospective studies are needed, our findings suggest that an integrated biophysical approach may be feasible in the management of older patients with early-stage CKD, to reduce and prevent the decline of renal function due to aging or comorbidities.

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

    Science.gov (United States)

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

    2009-03-01

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

  20. Biophysical insight into the anti-amyloidogenic behavior of taurine.

    Science.gov (United States)

    Chaturvedi, Sumit Kumar; Alam, Parvez; Khan, Javed Masood; Siddiqui, Mohd Khursheed; Kalaiarasan, Ponnusamy; Subbarao, Naidu; Ahmad, Zeeshan; Khan, Rizwan Hasan

    2015-09-01

    In this work, we investigated the inhibitory ability of taurine on the aggregation of Human serum albumin (HSA) and also examined how it controls the kinetic parameters of the aggregation process. We demonstrated the structural alterations in the HSA after binding to the taurine at 65 °C by exploiting various biophysical techniques. UV-vis spectroscopy was used to check the turbidometric changes in the protein. Thioflavin T fluorescence kinetics was subjected to explore kinetic parameters comparing the amyloid formation in the presence of varying concentration of taurine. Further, Congo red binding and ANS binding assays were performed to determine the inhibitory effect of taurine on HSA fibrillation process and surface hydrophobicity modifications occurring before and after the addition of taurine with protein, respectively. Far UV CD and Dynamic Light Scattering (DLS) confirmed that taurine stabilized the protein α-helical structure and formed complex with HSA which is further supported by differential scanning calorimetry (DSC). Moreover, microscopic imaging techniques were also done to analyze the morphology of aggregation formed. Taurine is also capable of altering the cytotoxicity of the proteinaceous aggregates. Molecular docking study also deciphered the possible residues involved in protein and drug interaction. Copyright © 2015 Elsevier B.V. All rights reserved.

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

    Directory of Open Access Journals (Sweden)

    Raymond eDe Young

    2014-11-01

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

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

    Science.gov (United States)

    De Young, Raymond

    2014-01-01

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

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

    Science.gov (United States)

    De Young, Raymond

    2014-01-01

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

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

    CERN Document Server

    Bloomfield, Victor

    2009-01-01

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

  5. Biophysical characterization of the proton-coupled oligopeptide transporter YjdL

    DEFF Research Database (Denmark)

    Jensen, Johanne Mørch; Simonsen, Fie C.; Mastali, Amir

    2012-01-01

    significantly different from prototypical POTs such as the human hPepT1. Nonetheless YjdL contains several highly conserved POT residues, which include Glu388 that is located in the putative substrate binding cavity. Here we present biophysical characterization of WT-YjdL and Glu388Gln. Isothermal titration...

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

  9. LBA-ECO ND-01 Reflectance and Biophysical Measures, Grass Pastures: Rondonia, Brazil

    Data.gov (United States)

    National Aeronautics and Space Administration — ABSTRACT: This data set provides the results of spectral reflectance (350 to 2,500 nm at 1-nm increments) and biophysical measurements on grass pastures in eight...

  10. DOE/CEC [Department of Energy/Commission of the European Communities] workshop on critical evaluation of radiobiological data to biophysical modeling

    International Nuclear Information System (INIS)

    1988-01-01

    The Department of Energy's Office of Health and Environmental Research and the Commission of the European Communities (CEC) Radiation Protection Program support the majority of Research in the Field of Radiobiological Modeling. This field of science develops models based on scientifically sound principles to predict biological response (at the cellular, molecular, and animal level) to exposure to low level ionizing radiation. Biophysical models are an important tool for estimating response of ionizing radiation at low doses and dose rates. Generally speaking, the biophysical models can be classified into two groups: (1) mechanistic models and (2) phenomenological models. Mechanistic models are based on some assumptions about the physical, chemical, or biological mechanisms of action in association with radiobiological data whereas the phenomenological models are based solely on available experimental data on radiobiological effects with less emphasis on mechanisms of action. There are a number of these models which are being developed. Since model builders rely on radiobiological data available in the literature either to develop mechanistic or phenomenological models, it is essential that a critical evaluation of existing radiobiological data be made and data that is generally considered good and most appropriate for biophysical modeling be identified. A Workshop jointly sponsored by the DOE and the CEC was held at Oak Ridge, Tennessee from June 23--25, 1988, to review the data available from physical and chemical, cellular and molecular and animal studies with ionizing radiation

  11. Assimilation of Biophysical Neuronal Dynamics in Neuromorphic VLSI.

    Science.gov (United States)

    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.

  12. Biophysics of filament length regulation by molecular motors

    International Nuclear Information System (INIS)

    Kuan, Hui-Shun; Betterton, M D

    2013-01-01

    Regulating physical size is an essential problem that biological organisms must solve from the subcellular to the organismal scales, but it is not well understood what physical principles and mechanisms organisms use to sense and regulate their size. Any biophysical size-regulation scheme operates in a noisy environment and must be robust to other cellular dynamics and fluctuations. This work develops theory of filament length regulation inspired by recent experiments on kinesin-8 motor proteins, which move with directional bias on microtubule filaments and alter microtubule dynamics. Purified kinesin-8 motors can depolymerize chemically-stabilized microtubules. In the length-dependent depolymerization model, the rate of depolymerization tends to increase with filament length, because long filaments accumulate more motors at their tips and therefore shorten more quickly. When balanced with a constant filament growth rate, this mechanism can lead to a fixed polymer length. However, the mechanism by which kinesin-8 motors affect the length of dynamic microtubules in cells is less clear. We study the more biologically realistic problem of microtubule dynamic instability modulated by a motor-dependent increase in the filament catastrophe frequency. This leads to a significant decrease in the mean filament length and a narrowing of the filament length distribution. The results improve our understanding of the biophysics of length regulation in cells. (paper)

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

    Science.gov (United States)

    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

  14. Quantum Nanobiology and Biophysical Chemistry

    DEFF Research Database (Denmark)

    2013-01-01

    An introduction was provided in the first issue by way of an Editorial to this special two issue volume of Current Physical Chemistry – “Quantum Nanobiology and Biophysical Chemistry” [1]. The Guest Editors would like to thank all the authors and referees who have contributed to this second issue....... Wu et al. use density functional theory to explore the use of Ni/Fe bimetallic nanotechnology in the bioremediation of decabromo-diphenyl esters. Araújo-Chaves et al. explore the binding and reactivity of Mn(III) porphyrins in the membrane mimetic setting of model liposomal systems. Claussen et al....... demonstrate extremely low detection performance of acyl-homoserine lactone in a biologically relevant system using surface enhanced Raman spectroscopy. Sugihara and Bondar evaluate the influence of methyl-groups and the protein environment on retinal geometries in rhodopsin and bacteriorhodopsin, two...

  15. Across Space and Time: Social Responses to Large-Scale Biophysical Systems

    Science.gov (United States)

    Macmynowski, Dena P.

    2007-06-01

    The conceptual rubric of ecosystem management has been widely discussed and deliberated in conservation biology, environmental policy, and land/resource management. In this paper, I argue that two critical aspects of the ecosystem management concept require greater attention in policy and practice. First, although emphasis has been placed on the “space” of systems, the “time”—or rates of change—associated with biophysical and social systems has received much less consideration. Second, discussions of ecosystem management have often neglected the temporal disconnects between changes in biophysical systems and the response of social systems to management issues and challenges. The empirical basis of these points is a case study of the “Crown of the Continent Ecosystem,” an international transboundary area of the Rocky Mountains that surrounds Glacier National Park (USA) and Waterton Lakes National Park (Canada). This project assessed the experiences and perspectives of 1) middle- and upper-level government managers responsible for interjurisdictional cooperation, and 2) environmental nongovernment organizations with an international focus. I identify and describe 10 key challenges to increasing the extent and intensity of transboundary cooperation in land/resource management policy and practice. These issues are discussed in terms of their political, institutional, cultural, information-based, and perceptual elements. Analytic techniques include a combination of environmental history, semistructured interviews with 48 actors, and text analysis in a systematic qualitative framework. The central conclusion of this work is that the rates of response of human social systems must be better integrated with the rates of ecological change. This challenge is equal to or greater than the well-recognized need to adapt the spatial scale of human institutions to large-scale ecosystem processes and transboundary wildlife.

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

    Science.gov (United States)

    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.

  17. The Biophysics Microgravity Initiative

    Science.gov (United States)

    Gorti, S.

    2016-01-01

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

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

    Science.gov (United States)

    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.

  19. Human Pluripotent Stem Cell Mechanobiology: Manipulating the Biophysical Microenvironment for Regenerative Medicine and Tissue Engineering Applications.

    Science.gov (United States)

    Ireland, Ronald G; Simmons, Craig A

    2015-11-01

    A stem cell in its microenvironment is subjected to a myriad of soluble chemical cues and mechanical forces that act in concert to orchestrate cell fate. Intuitively, many of these soluble and biophysical factors have been the focus of intense study to successfully influence and direct cell differentiation in vitro. Human pluripotent stem cells (hPSCs) have been of considerable interest in these studies due to their great promise for regenerative medicine. Culturing and directing differentiation of hPSCs, however, is currently extremely labor-intensive and lacks the efficiency required to generate large populations of clinical-grade cells. Improved efficiency may come from efforts to understand how the cell biophysical signals can complement biochemical signals to regulate cell pluripotency and direct differentiation. In this concise review, we explore hPSC mechanobiology and how the hPSC biophysical microenvironment can be manipulated to maintain and differentiate hPSCs into functional cell types for regenerative medicine and tissue engineering applications. © 2015 AlphaMed Press.

  20. Biophysical studies of irradiated thymocytes. 1. Surface changes

    Energy Technology Data Exchange (ETDEWEB)

    Sungurov, A Yu; Tokalov, S V; Petrov, Yu P; Sharlaeva, T M

    1985-08-15

    In order to study postirradiation changes in thymus lymphocyte surface, a number of biophysical analytical methods was used: the cell two-partition method, the physical adhesion method, fluorescence intensity and binding parameters of negatively charged ANS probe. Reduction of cell distribution factor in two-phase system and adhesion of thymocytes to cotton 1 hour after irradiation, as well as abrupt change in parameters of binding the probe in the interval of 3-4 hours after X-ray irradiation at the dose of 4 Gy are demonstrated.

  1. Biophysical processes leading to the ingress of temperate fish larvae into estuarine nursery areas: A review

    Science.gov (United States)

    Teodósio, Maria Alexandra; Paris, Claire B.; Wolanski, Eric; Morais, Pedro

    2016-12-01

    A series of complementary hypotheses have been proposed to explain the recruitment of marine and temperate pelagic fish larvae originated from pelagic eggs in coastal environments. In this review, we propose a new and complementary hypothesis describing the biophysical processes intervening in the recruitment of temperate fish larvae into estuaries. This new hypothesis, the Sense Acuity And Behavioral (SAAB) hypothesis, recognizes that recruitment is unlikely if the larvae drift passively with the water currents, and that successful recruitment requires the sense acuity of temperate fish larvae and their behavioral response to the estuarine cues present in coastal areas. We propose that temperate fish larvae use a hierarchy of sensory cues (odor, sound, visual and geomagnetic cues) to detect estuarine nursery areas and to aid during navigation towards these areas. The sensorial acuity increases along ontogeny, which coincides with increased swimming capabilities. The swimming strategies of post-flexion larvae differ from offshore areas to the tidal zone. In offshore areas, innate behavior might lead larvae towards the coast guided by a sun compass or by the earth's geomagnetic field. In areas under limited influence of estuarine plumes (either in energetic nearshore areas or offshore), post-flexion larvae display a searching swimming behavior for estuarine disconnected patches (infotaxis strategy). After finding an estuarine plume, larvae may swim along the increasing cue concentration to ingress into the estuary. Here, larvae exhibit a rheotaxis behavior and avoid displacement by longshore currents by keeping bearing during navigation. When larvae reach the vicinity of an estuary, merging diel rhythms with feeding and predator avoidance strategies with tidally induced movements is essential to increase their chances of estuarine ingress. A fish larva recruitment model developed for the Ria Formosa lagoon supports the general framework of the SAAB hypothesis. In

  2. Time-resolved biophysical approaches to nucleocytoplasmic transport

    Directory of Open Access Journals (Sweden)

    Francesco Cardarelli

    Full Text Available Molecules are continuously shuttling across the nuclear envelope barrier that separates the nucleus from the cytoplasm. Instead of being just a barrier to diffusion, the nuclear envelope is rather a complex filter that provides eukaryotes with an elaborate spatiotemporal regulation of fundamental molecular processes, such as gene expression and protein translation. Given the highly dynamic nature of nucleocytoplasmic transport, during the past few decades large efforts were devoted to the development and application of time resolved, fluorescence-based, biophysical methods to capture the details of molecular motion across the nuclear envelope. These methods are here divided into three major classes, according to the differences in the way they report on the molecular process of nucleocytoplasmic transport. In detail, the first class encompasses those methods based on the perturbation of the fluorescence signal, also known as ensemble-averaging methods, which average the behavior of many molecules (across many pores. The second class comprises those methods based on the localization of single fluorescently-labelled molecules and tracking of their position in space and time, potentially across single pores. Finally, the third class encompasses methods based on the statistical analysis of spontaneous fluorescence fluctuations out of the equilibrium or stationary state of the system. In this case, the behavior of single molecules is probed in presence of many similarly-labelled molecules, without dwelling on any of them. Here these three classes, with their respective pros and cons as well as their main applications to nucleocytoplasmic shuttling will be briefly reviewed and discussed. Keywords: Fluorescence recovery after photobleaching, Single particle tracking, Fluorescence correlation spectroscopy, Diffusion, Transport, GFP, Nuclear pore complex, Live cell, Confocal microscopy

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

    Science.gov (United States)

    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.

  4. Using Biophysical Models to Understand the Effect of tDCS on Neurorehabilitation: Searching for Optimal Covariates to Enhance Poststroke Recovery.

    Science.gov (United States)

    Malerba, Paola; Straudi, Sofia; Fregni, Felipe; Bazhenov, Maxim; Basaglia, Nino

    2017-01-01

    Stroke is a leading cause of worldwide disability, and up to 75% of survivors suffer from some degree of arm paresis. Recently, rehabilitation of stroke patients has focused on recovering motor skills by taking advantage of use-dependent neuroplasticity, where high-repetition of goal-oriented movement is at times combined with non-invasive brain stimulation, such as transcranial direct current stimulation (tDCS). Merging the two approaches is thought to provide outlasting clinical gains, by enhancing synaptic plasticity and motor relearning in the motor cortex primary area. However, this general approach has shown mixed results across the stroke population. In particular, stroke location has been found to correlate with the likelihood of success, which suggests that different patients might require different protocols. Understanding how motor rehabilitation and stimulation interact with ongoing neural dynamics is crucial to optimize rehabilitation strategies, but it requires theoretical and computational models to consider the multiple levels at which this complex phenomenon operate. In this work, we argue that biophysical models of cortical dynamics are uniquely suited to address this problem. Specifically, biophysical models can predict treatment efficacy by introducing explicit variables and dynamics for damaged connections, changes in neural excitability, neurotransmitters, neuromodulators, plasticity mechanisms, and repetitive movement, which together can represent brain state, effect of incoming stimulus, and movement-induced activity. In this work, we hypothesize that effects of tDCS depend on ongoing neural activity and that tDCS effects on plasticity may be also related to enhancing inhibitory processes. We propose a model design for each step of this complex system, and highlight strengths and limitations of the different modeling choices within our approach. Our theoretical framework proposes a change in paradigm, where biophysical models can contribute

  5. Salicylic acid and nitric oxide alleviate high temperature induced oxidative damage in Lablab purpureus L plants by regulating bio-physical processes and DNA methylation.

    Science.gov (United States)

    Rai, Krishna Kumar; Rai, Nagendra; Rai, Shashi Pandey

    2018-07-01

    Salicylic acid (SA) and sodium nitroprusside (SNP, NO donor) modulates plant growth and development processes and recent findings have also revealed their involvement in the regulation of epigenetic factors under stress condition. In the present study, some of these factors were comparatively studied in hyacinth bean plants subjected to high temperature (HT) environment (40-42 °C) with and without exogenous application of SA and SNP under field condition. Exogenous application of SA and SNP substantially modulated the growth and biophysical process of hyacinth bean plants under HT environment. Exogenous application of SA and SNP also remarkably regulated the activities of antioxidant enzymes, modulated mRNA level of certain enzymes, improves plant water relation, enhance photosynthesis and thereby increasing plant defence under HT. Coupled restriction enzyme digestion-random amplification (CRED-RA) technique revealed that many methylation changes were "dose dependent" and HT significantly increased DNA damages as evidenced by both increase and decrease in bands profiles, methylation and de-methylation pattern. Thus, the result of the present study clearly shows that exogenous SA and SNP regulates DNA methylation pattern, modulates stress-responsive genes and can impart transient HT tolerance by synchronizing growth and physiological acclimatization of plants, thus narrowing the gaps between physio-biochemical and molecular events in addressing HT tolerance. Copyright © 2018 Elsevier Masson SAS. All rights reserved.

  6. Integrating biophysical and socioeconomic information for prioritizing watersheds in a Kashmir Himalayan lake: a remote sensing and GIS approach.

    Science.gov (United States)

    Badar, Bazigha; Romshoo, Shakil A; Khan, M A

    2013-08-01

    Dal Lake, a cradle of Kashmiri civilization has strong linkage with socioeconomics of the state of Jammu and Kashmir. During last few decades, anthropogenic pressures in Dal Lake Catchment have caused environmental deterioration impairing, inter-alia, sustained biotic communities and water quality. The present research was an integrated impact analysis of socioeconomic and biophysical processes at the watershed level on the current status of Dal Lake using multi-sensor and multi-temporal satellite data, simulation modelling together with field data verification. Thirteen watersheds (designated as 'W1-W13') were identified and investigated for land use/land cover change detection, quantification of erosion and sediment loads and socioeconomic analysis (total population, total households, literacy rate and economic development status). All the data for the respective watersheds was integrated into the GIS environment based upon multi-criteria analysis and knowledge-based weightage system was adopted for watershed prioritization based on its factors and after carefully observing the field situation. The land use/land cover change detection revealed significant changes with a uniform trend of decreased vegetation and increased impervious surface cover. Increased erosion and sediment loadings were recorded for the watersheds corresponding to their changing land systems, with bare and agriculture lands being the major contributors. The prioritization analysis revealed that W5 > W2 > W6 > W8 > W1 ranked highest in priority and W13 > W3 > W4 > W11 > W7 under medium priority. W12 > W9 > W10 belonged to low-priority category. The integration of the biophysical and the socioeconomic environment at the watershed level using modern geospatial tools would be of vital importance for the conservation and management strategies of Dal Lake ecosystem.

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

    Science.gov (United States)

    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

  8. The water-food-energy nexus in Pakistan: a biophysical and socio-economic challenge

    Science.gov (United States)

    Grigg, Nicola; Foran, Tira; Darbas, Toni; Kirby, Mac; Colloff, Matthew J.; Ahmad, Mobin-ud-Din; Podger, Geoff

    2018-02-01

    We draw on previous work examining historical trends, likely future water use and food availability in Pakistan and extend the analysis to consider interactions with hydropower generation and the energy demand in food production due to pumping of groundwater for irrigation. Business-as-usual scenarios suggest growing demands for groundwater and energy use for food production as population grows rapidly. However, groundwater use is already unsustainable in many areas, and energy supply is failing to keep up with demand. Quantifying material linkages between water, food and energy provides a means to explore biophysical constraints. Characterising institutional constraints is equally important, as they can be significant barriers to effective stewardship of water, energy and food resources. The experience in Pakistan reinforces this finding, and we discuss the implications for hydrologists.

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

    Science.gov (United States)

    Liu, Miao; Zheng, Mingjing; Xu, Hanying; Liu, Lianqing; Li, Yanchun; Xiao, Wei; Li, Jianchun; Ma, Enlong

    Various methods have been used to evaluate anti-fibrotic activity of drugs. However, most of them are complicated, labor-intensive and lack of efficiency. This study was intended to develop a rapid method for anti-fibrotic drugs screening based on biophysical properties. A549 cells in vitro were stimulated with transforming growth factor-β1 (TGF-β1), and fibrogenesis was confirmed by conventional immunological assays. Meanwhile, the alterations of cyto-biophysical properties including morphology, roughness and stiffness were measured utilizing atomic force microscopy (AFM). It was found that fibrogenesis was accompanied with changes of cellular biophysical properties. TGF-β1-stimulated A549 cells became remarkably longer, rougher and stiffer than the control. Then, the effect of N-acetyl-L-cysteine (NAC) as a positive drug on ameliorating fibrogenesis in TGF-β1-stimulated A549 cells was verified respectively by immunological and biophysical markers. The result of Principal Component Analysis showed that stiffness was a leading index among all biophysical markers during fibrogenesis. Salvianolic acid B (SalB), a natural anti-oxidant, was detected by AFM to protect TGF-β1-stimulated A549 cells against stiffening. Then, SalB treatment was provided in preventive mode on a rat model of bleomycin (BLM) -induced pulmonary fibrosis. The results showed that SalB treatment significantly ameliorated BLM-induced histological alterations, blocked collagen accumulations and reduced α-SMA expression in lung tissues. All these results revealed the anti-pulmonary fibrotic activity of SalB. Detection of cyto-biophysical properties were therefore recommended as a rapid method for anti-pulmonary fibrotic drugs screening. Copyright © 2015 Elsevier Inc. All rights reserved.

  10. Biophysical characterisation of calumenin as a charged F508del-CFTR folding modulator.

    Directory of Open Access Journals (Sweden)

    Rashmi Tripathi

    Full Text Available The cystic fibrosis transmembrane regulator (CFTR is a cyclic-AMP dependent chloride channel expressed at the apical surface of epithelial cells lining various organs such as the respiratory tract. Defective processing and functioning of this protein caused by mutations in the CFTR gene results in loss of ionic balance, defective mucus clearance, increased proliferation of biofilms and inflammation of human airways observed in cystic fibrosis (CF patients. The process by which CFTR folds and matures under the influence of various chaperones in the secretory pathway remains incompletely understood. Recently, calumenin, a secretory protein, belonging to the CREC family of low affinity calcium binding proteins has been identified as a putative CFTR chaperone whose biophysical properties and functions remain uncharacterized. We compared hydropathy, instability, charge, unfoldability, disorder and aggregation propensity of calumenin and other CREC family members with CFTR associated chaperones and calcium binding proteins, wild-type and mutant CFTR proteins and intrinsically disordered proteins (IDPs. We observed that calumenin, along with other CREC proteins, was significantly more charged and less folded compared to CFTR associated chaperones. Moreover like IDPs, calumenin and other CREC proteins were found to be less hydrophobic and aggregation prone. Phylogenetic analysis revealed a close link between calumenin and other CREC proteins indicating how evolution might have shaped their similar biophysical properties. Experimentally, calumenin was observed to significantly reduce F508del-CFTR aggregation in a manner similar to AavLEA1, a well-characterized IDP. Fluorescence microscopy based imaging analysis also revealed altered trafficking of calumenin in bronchial cells expressing F508del-CFTR, indicating its direct role in the pathophysiology of CF. In conclusion, calumenin is characterized as a charged protein exhibiting close similarity with

  11. 6th international conference on biophysics and synchrotron radiation. Program/Abstracts

    International Nuclear Information System (INIS)

    Pittroff, Connie; Strasser, Susan Barr

    1999-01-01

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

  12. 6th international conference on biophysics and synchrotron radiation. Program/Abstracts

    Energy Technology Data Exchange (ETDEWEB)

    Pittroff, Connie; Strasser, Susan Barr [lead editors

    1999-08-03

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

  13. IS THERE ANY ASSOCIATION BETWEEN MATERNAL DEPRESSION AND BIOPHYSICAL PROFILE?

    Directory of Open Access Journals (Sweden)

    M Z Pezeshki

    2008-11-01

    Full Text Available "nMother's mental health status during pregnancy has important effects on fetal growth and development. However, there are few studies concerning association of maternal depression and biophysical profile (BPP of the fetus. We performed this research to know if maternal depression has any association with fetal BPP score. For measuring depression, Farsi version of Patient Health Questionnaire-9 (PHQ-9 was completed. A total of 100 pregnant women in their third trimester (>24 weeks who had not hyperthyroidism, hypothyroidism, eclampsia and preeclampsia, fever, infection, diabetes or a fetus with intrauterine growth retardation (IUGR and were not using any medication entered the study. Spearman correlation coefficient between the score of PHQ-9 questionnaire and BPP score was -0.08 (P = 0.43. Based on Kruskal Wallis test, there was no difference in BPP score of depressed and nondepressed women (P = 0.65. We found no relationship between maternal depression and BPP score in third trimester of pregnancy. Further studies for elucidating neuro-hormonal mechanisms related to the result of our study are suggested

  14. Interplay of mycolic acids, antimycobacterial compounds and pulmonary surfactant membrane: a biophysical approach to disease.

    Science.gov (United States)

    Pinheiro, Marina; Giner-Casares, Juan J; Lúcio, Marlene; Caio, João M; Moiteiro, Cristina; Lima, José L F C; Reis, Salette; Camacho, Luis

    2013-02-01

    This work focuses on the interaction of mycolic acids (MAs) and two antimycobacterial compounds (Rifabutin and N'-acetyl-Rifabutin) at the pulmonary membrane level to convey a biophysical perspective of their role in disease. For this purpose, accurate biophysical techniques (Langmuir isotherms, Brewster angle microscopy, and polarization-modulation infrared reflection spectroscopy) and lipid model systems were used to mimic biomembranes: MAs mimic bacterial lipids of the Mycobacterium tuberculosis (MTb) membrane, whereas Curosurf® was used as the human pulmonary surfactant (PS) membrane model. The results obtained show that high quantities of MAs are responsible for significant changes on PS biophysical properties. At the dynamic inspiratory surface tension, high amounts of MAs decrease the order of the lipid monolayer, which appears to be a concentration dependent effect. These results suggest that the amount of MAs might play a critical role in the initial access of the bacteria to their targets. Both molecules also interact with the PS monolayer at the dynamic inspiratory surface. However, in the presence of higher amounts of MAs, both compounds improve the phospholipid packing and, therefore, the order of the lipid surfactant monolayer. In summary, this work discloses the putative protective effects of antimycobacterial compounds against the MAs induced biophysical impairment of PS lipid monolayers. These protective effects are most of the times overlooked, but can constitute an additional therapeutic value in the treatment of pulmonary tuberculosis (Tb) and may provide significant insights for the design of new and more efficient anti-Tb drugs based on their behavior as membrane ordering agents. Copyright © 2012 Elsevier B.V. All rights reserved.

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

    Science.gov (United States)

    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.

  16. Ecosystem biophysical memory in the southwestern North America climate system

    International Nuclear Information System (INIS)

    Forzieri, G; Feyen, L; Vivoni, E R

    2013-01-01

    To elucidate the potential role of vegetation to act as a memory source in the southwestern North America climate system, we explore correlation structures of remotely sensed vegetation dynamics with precipitation, temperature and teleconnection indices over 1982–2006 for six ecoregions. We found that lagged correlations between vegetation dynamics and climate variables are modulated by the dominance of monsoonal or Mediterranean regimes and ecosystem-specific physiological processes. Subtropical and tropical ecosystems exhibit a one month lag positive correlation with precipitation, a zero- to one-month lag negative correlation with temperature, and modest negative effects of sea surface temperature (SST). Mountain forests have a zero month lag negative correlation with precipitation, a zero–one month lag negative correlation with temperature, and no significant correlation with SSTs. Deserts show a strong one–four month lag positive correlation with precipitation, a low zero–two month lag negative correlation with temperature, and a high four–eight month lag positive correlation with SSTs. The ecoregion-specific biophysical memories identified offer an opportunity to improve the predictability of land–atmosphere interactions and vegetation feedbacks onto climate. (letter)

  17. Indoor Fast Neutron Generator for Biophysical and Electronic Applications

    Science.gov (United States)

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

    2018-05-01

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

  18. Modern nuclear medicine methods as a topic of biophysics in veterinary training at UVM in Kosice

    International Nuclear Information System (INIS)

    Stanicova, J.; Lohajova, L.

    2004-01-01

    Diagnostic and therapeutic application of ionising radiation is very important in all of branches of medicine including veterinary medicine. In veterinary training at University of Veterinary Medicine in Kosice (UVM), biophysics is a basic subject and it grants physical basis necessary for understanding subsequent subjects such as veterinary surgery, roentgenology, orthopedics. In view of this, traditional methods of radiology such as fluoroscopy, skiagraphy and tomography are explaining. The appearance and application of the theory so called reconstruction of image and also computers led to qualitatively new solutions via the development of modern methods in radiology. Explaining of physical principles, advantages or disadvantages of these new methods is also important in veterinary training although some of them do not use in veterinary practice yet. Two modern methods of nuclear medicine using in diagnostic (SPECT and PET) are discussed bellow. (authors)

  19. Epigenetic Modulation of the Biophysical Properties of Drug-Resistant Cell Lipids to Restore Drug Transport and Endocytic Functions

    OpenAIRE

    Vijayaraghavalu, Sivakumar; Peetla, Chiranjeevi; Lu, Shan; Labhasetwar, Vinod

    2012-01-01

    In our recent studies exploring the biophysical characteristics of resistant cell lipids, and the role they play in drug transport, we demonstrated the difference of drug-resistant breast cancer cells from drug-sensitive cells in lipid composition and biophysical properties, suggesting that cancer cells acquire a drug-resistant phenotype through the alteration of lipid synthesis to inhibit intracellular drug transport to protect from cytotoxic effect. In cancer cells, epigenetic changes (e.g....

  20. Applications of the BIOPHYS Algorithm for Physically-Based Retrieval of Biophysical, Structural and Forest Disturbance Information

    Science.gov (United States)

    Peddle, Derek R.; Huemmrich, K. Fred; Hall, Forrest G.; Masek, Jeffrey G.; Soenen, Scott A.; Jackson, Chris D.

    2011-01-01

    Canopy reflectance model inversion using look-up table approaches provides powerful and flexible options for deriving improved forest biophysical structural information (BSI) compared with traditional statistical empirical methods. The BIOPHYS algorithm is an improved, physically-based inversion approach for deriving BSI for independent use and validation and for monitoring, inventory and quantifying forest disturbance as well as input to ecosystem, climate and carbon models. Based on the multiple-forward mode (MFM) inversion approach, BIOPHYS results were summarized from different studies (Minnesota/NASA COVER; Virginia/LEDAPS; Saskatchewan/BOREAS), sensors (airborne MMR; Landsat; MODIS) and models (GeoSail; GOMS). Applications output included forest density, height, crown dimension, branch and green leaf area, canopy cover, disturbance estimates based on multi-temporal chronosequences, and structural change following recovery from forest fires over the last century. Good correspondences with validation field data were obtained. Integrated analyses of multiple solar and view angle imagery further improved retrievals compared with single pass data. Quantifying ecosystem dynamics such as the area and percent of forest disturbance, early regrowth and succession provide essential inputs to process-driven models of carbon flux. BIOPHYS is well suited for large-area, multi-temporal applications involving multiple image sets and mosaics for assessing vegetation disturbance and quantifying biophysical structural dynamics and change. It is also suitable for integration with forest inventory, monitoring, updating, and other programs.

  1. Risk Importance Determination Process of CANDU Maintenance Rule Function

    International Nuclear Information System (INIS)

    Seo, Mi Ro; Jo, Ha Yan; Hwang, Mi Jeong

    2009-01-01

    In Korea, Maintenance Rule (MR) programs development for all PWR were completed. However, in case of PHWR (CANDU type, Wolsong Unit 1,2,3,4), the study of MR program was delayed, since the design concepts and operating experiences are different from those of PWR. This paper describes the process and results for the risk importance determination process of functions in scope. The risk importance was determined by PSA Basic Event Mapping and Delphi method. For Delphi evaluation, Delphi evaluation item for CANDU need to be developed because the design and normal operation functions are different from PWR

  2. Adaptive multiple importance sampling for Gaussian processes

    Czech Academy of Sciences Publication Activity Database

    Xiong, X.; Šmídl, Václav; Filippone, M.

    2017-01-01

    Roč. 87, č. 8 (2017), s. 1644-1665 ISSN 0094-9655 R&D Projects: GA MŠk(CZ) 7F14287 Institutional support: RVO:67985556 Keywords : Gaussian Process * Bayesian estimation * Adaptive importance sampling Subject RIV: BB - Applied Statistics, Operational Research OBOR OECD: Statistics and probability Impact factor: 0.757, year: 2016 http://library.utia.cas.cz/separaty/2017/AS/smidl-0469804.pdf

  3. Biophysical and structural considerations for protein sequence evolution

    Directory of Open Access Journals (Sweden)

    Grahnen Johan A

    2011-12-01

    Full Text Available Abstract Background Protein sequence evolution is constrained by the biophysics of folding and function, causing interdependence between interacting sites in the sequence. However, current site-independent models of sequence evolutions do not take this into account. Recent attempts to integrate the influence of structure and biophysics into phylogenetic models via statistical/informational approaches have not resulted in expected improvements in model performance. This suggests that further innovations are needed for progress in this field. Results Here we develop a coarse-grained physics-based model of protein folding and binding function, and compare it to a popular informational model. We find that both models violate the assumption of the native sequence being close to a thermodynamic optimum, causing directional selection away from the native state. Sampling and simulation show that the physics-based model is more specific for fold-defining interactions that vary less among residue type. The informational model diffuses further in sequence space with fewer barriers and tends to provide less support for an invariant sites model, although amino acid substitutions are generally conservative. Both approaches produce sequences with natural features like dN/dS Conclusions Simple coarse-grained models of protein folding can describe some natural features of evolving proteins but are currently not accurate enough to use in evolutionary inference. This is partly due to improper packing of the hydrophobic core. We suggest possible improvements on the representation of structure, folding energy, and binding function, as regards both native and non-native conformations, and describe a large number of possible applications for such a model.

  4. Microwave Tissue Ablation: Biophysics, Technology and Applications

    Science.gov (United States)

    2010-01-01

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

  5. Abstracts of the 9. Brazilian Congress of Biophysics, 2. Brazilian Congress of Pharmacology and Experimental Therapeutics and 19. Brazilian Congress of Physiology

    International Nuclear Information System (INIS)

    1984-01-01

    Abstracts about biophysics, pharmacology, experimental therapeutics and physiology are presented. The use of radioisotopes in radioassays involve topics like biophysics and renal physiology; central nervous system; endocrinology; animal and comparative physiology; general physiology, digestion and nutrition; general pharmacology. (M.A.C.) [pt

  6. Canopy-scale biophysical controls on transpiration and evaporation in the Amazon Basin

    DEFF Research Database (Denmark)

    Mallick, Kaniska; Trebs, Ivonne; Bøgh, Eva

    2016-01-01

    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...

  7. Investigation of the Effects of Irrigation and Nutrient Treatments on Biophysical and Biomechanical Properties of Safflower Seed

    Directory of Open Access Journals (Sweden)

    M Feyzollahzadeh

    2013-02-01

    Full Text Available Safflower is a strategic plant regarding to its valuable nutrition value (45% extractable oil and industrial uses. Due to massive import of edible oil to the country as well as high potential for safflower cultivation, the research on production of safflower for oil extrusion purpose is of remarkable importance. The design of various processing and oil extraction units and also their optimization which are in relation to seed attributes is essential. In this paper the effects of different irrigation and nutrient treatments on some important physical and mechanical properties of IL111 varieties of safflower seed were investigated. The measured properties included size, mass, volume, surface area, arithmetic and geometric mean diameter, sphericity, bulk and true densities, porosity, static and dynamic coefficient of friction, rupture force, deformation at rupture point, rupture energy, modulus of elasticity and seed hardness. The results indicated a significant effect of treatments on the biophysical and biomechanical properties at p ≤ 0.01. The maximum seed mass, geometric mean diameter and rupture energy were obtained when the (cg treatment applied i.e. “Cut-off irrigation at the growth stage and bio sulfur nutrition”. Seed mass was found to be 0.040 gr to 0.055 gr. Results also showed a significant effect of geometric mean diameter on mass and rupture energy and also mass on seed hardness. Direct correlations observed between seed mass and rupture energy, which indicates that for larger and heavier seeds, much more energy required for oil extraction. The maximum rupture energy was measured as 0.033 J.

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

    Energy Technology Data Exchange (ETDEWEB)

    Hansmann, Ulrich H.E.

    2012-07-02

    This report summarizes the outcome of the international workshop From Computational Biophysics to Systems Biology (CBSB12) which was held June 3-5, 2012, at the University of Tennessee Conference Center in Knoxville, TN, and supported by DOE through the Conference Support Grant 120174. The purpose of CBSB12 was to provide a forum for the interaction between a data-mining interested systems biology community and a simulation and first-principle oriented computational biophysics/biochemistry community. CBSB12 was the sixth in a series of workshops of the same name organized in recent years, and the second that has been held in the USA. As in previous years, it gave researchers from physics, biology, and computer science an opportunity to acquaint each other with current trends in computational biophysics and systems biology, to explore venues of cooperation, and to establish together a detailed understanding of cells at a molecular level. The conference grant of $10,000 was used to cover registration fees and provide travel fellowships to selected students and postdoctoral scientists. By educating graduate students and providing a forum for young scientists to perform research into the working of cells at a molecular level, the workshop adds to DOE's mission of paving the way to exploit the abilities of living systems to capture, store and utilize energy.

  9. Thermal and chemical denaturation of Bacillus circulans xylanase: A biophysical chemistry laboratory module.

    Science.gov (United States)

    Raabe, Richard; Gentile, Lisa

    2008-11-01

    A number of institutions have been, or are in the process of, modifying their biochemistry major to include some emphasis on the quantitative physical chemistry of biomolecules. Sometimes this is done as a replacement for part for the entire physical chemistry requirement, while at other institutions this is incorporated as a component into the traditional two-semester biochemistry series. The latter is the model used for biochemistry and molecular biology majors at the University of Richmond, whose second semester of biochemistry is a course entitled Proteins: Structure, Function, and Biophysics. What is described herein is a protein thermodynamics laboratory module, using the protein Bacillus circulans xylanase, which reinforces many lecture concepts, including: (i) the denatured (D) state ensemble of a protein can be different, depending on how it was populated; (ii) intermediate states may be detected by some spectroscopic techniques but not by others; (iii) the use and assumptions of the van't Hoff approach to calculate ΔH(o) , ΔS(o) , and ΔG(o) (T) for thermal protein unfolding transitions; and (iv) the use and assumptions of an approach that allows determination of the Gibb's free energy of a protein unfolding transition based on the linear dependence of ΔG(o) on the concentration of denaturant used. This module also requires students to design their own experimental protocols and spend time in the primary literature, both important parts of an upper division lab. Copyright © 2008 International Union of Biochemistry and Molecular Biology, Inc.

  10. Developing a physics expert identity in a biophysics research group

    Science.gov (United States)

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

    2015-06-01

    We investigate the development of expert identities through the use of the sociocultural perspective of learning as participating in a community of practice. An ethnographic case study of biophysics graduate students focuses on the experiences the students have in their research group meetings. The analysis illustrates how the communities of practice-based identity constructs of competencies characterize student expert membership. A microanalysis of speech, sound, tones, and gestures in video data characterize students' social competencies in the physics community of practice. Results provide evidence that students at different stages of their individual projects have opportunities to develop social competencies such as mutual engagement, negotiability of the repertoire, and accountability to the enterprises as they interact with group members. The biophysics research group purposefully designed a learning trajectory including conducting research and writing it for publication in the larger community of practice as a pathway to expertise. The students of the research group learn to become socially competent as specific experts of their project topic and methodology, ensuring acceptance, agency, and membership in their community of practice. This work expands research on physics expertise beyond the cognitive realm and has implications for how to design graduate learning experiences to promote expert identity development.

  11. Biophysically inspired rational design of structured chimeric substrates for DNAzyme cascade engineering.

    Directory of Open Access Journals (Sweden)

    Matthew R Lakin

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

  12. Novel biophysical determination of miRNAs related to prostate and head and neck cancers

    Czech Academy of Sciences Publication Activity Database

    Hudcová, K.; Trnková, L.; Kejnovská, Iva; Vorlíčková, Michaela; Gumulec, J.; Kizek, R.; Masarik, M.

    2015-01-01

    Roč. 44, č. 3 (2015), s. 131-138 ISSN 0175-7571 Institutional support: RVO:68081707 Keywords : SQUAMOUS-CELL CARCINOMA * ELIMINATION VOLTAMMETRY * CYTOSINE SIGNALS Subject RIV: BO - Biophysics Impact factor: 1.444, year: 2015

  13. Radiation fields, dosimetry, biokinetics and biophysical models for cancer induction by ionising radiation 1996-1999. Executive summary

    International Nuclear Information System (INIS)

    Jacob, P.; Paretzke, H.G.; Roth, P.

    2000-01-01

    The Association Contract covers a range of research domains that are important to the Radiation Protection Research Action, especially in the areas 'Evaluation of Radiation Risks' and 'Understanding Radiation Mechanisms and Epidemiology'. Three research projects concentrate on radiation dosimetry research and two projects on the modelling of radiation carcinogenesis. The following list gives an overview on the topics and responsible scientific project leaders of the Association Contract: Study of radiation fields and dosimetry at aviation altitudes. Biokinetics and dosimetry of incorporated radionuclides. Dose reconstruction. Biophysical models for the induction of cancer by radiation. Experimental data for the induction of cancer by radiation of different qualities. (orig.)

  14. Biophysical studies related to energy generation: Progress report

    International Nuclear Information System (INIS)

    Green, A.E.S.

    1988-01-01

    This report covers work subsequent to our previous report of December 24, 1986. At that time we were groping to find relationships between vibrational and rotational electron impact cross sections in the vapor and liquid phases of water. Having reached an impass within the radiological literature, we drew upon the atmospheric, oceanographic and flame radiation literatures. Here a much broader body of excitation energy and intensity data related to the vibrational and rotational excitation of water in the vapor phases and liquid phases enabled us to identify certain ''big bands'' of H 2 O. These bands account for the major infrared absorption features observed in atmospheric transmission studies as well as important spectral radiation features observed in hydrocarbon combustion. Related liquid phase-gas phase involvement also entered our work on co-combustion of biomass and waste, and natural gas in studies directed toward contributing to the solution of national energy-environmental and economic problems. Attachments to this report include our published works, submitted works, and in complete studies related to radiological, atmospheric, and combustion studies which encompass biophysical studies related to energy generation and which have a common thread involving water in liquid and vapor form. These works are tied together in this brief report, along with some comments on trends in science and technology which they might illustrate

  15. Ground-and satellite-based evidence of the biophysical mechanisms behind the greening Sahel

    DEFF Research Database (Denmark)

    Brandt, Martin Stefan; Mbow, Cheikh; Diouf, Abdoul A.

    2015-01-01

    After a dry period with prolonged droughts in the 1970s and 1980s, recent scientific outcome suggests that the decades of abnormally dry conditions in the Sahel have been reversed by positive anomalies in rainfall. Various remote sensing studies observed a positive trend in vegetation greenness...... over the last decades which is known as the re-greening of the Sahel. However, little investment has been made in including long-term ground-based data collections to evaluate and better understand the biophysical mechanisms behind these findings. Thus, deductions on a possible increment in biomass...... remain speculative. Our aim is to bridge these gaps and give specifics on the biophysical background factors of the re-greening Sahel. Therefore, a trend analysis was applied on long time series (1987-2013) of satellite-based vegetation and rainfall data, as well as on ground-observations of leaf biomass...

  16. Affinity-based, biophysical methods to detect and analyze ligand binding to recombinant proteins: matching high information content with high throughput.

    Science.gov (United States)

    Holdgate, Geoff A; Anderson, Malcolm; Edfeldt, Fredrik; Geschwindner, Stefan

    2010-10-01

    Affinity-based technologies have become impactful tools to detect, monitor and characterize molecular interactions using recombinant target proteins. This can aid the understanding of biological function by revealing mechanistic details, and even more importantly, enables the identification of new improved ligands that can modulate the biological activity of those targets in a desired fashion. The selection of the appropriate technology is a key step in that process, as each one of the currently available technologies offers a characteristic type of biophysical information about the ligand-binding event. Alongside the indisputable advantages of each of those technologies they naturally display diverse restrictions that are quite frequently related to the target system to be studied but also to the affinity, solubility and molecular size of the ligands. This paper discusses some of the theoretical and experimental aspects of the most common affinity-based methods, what type of information can be gained from each one of those approaches, and what requirements as well as limitations are expected from working with recombinant proteins on those platforms and how those can be optimally addressed.

  17. Importance of the hexagonal lipid phase in biological membrane organisation

    Directory of Open Access Journals (Sweden)

    Juliette eJouhet

    2013-12-01

    Full Text Available Abstract:Domains are present in every natural membrane. They are characterised by a distinctive protein and/or lipid composition. Their size is highly variable from the nano- to the micrometer scale. The domains confer specific properties to the membrane leading to original structure and function. The determinants leading to domain organisation are therefore important but remain obscure. This review presents how the ability of lipids to organize into hexagonal II or lamellar phases can promote particular local structures within membranes. Since biological membranes are composed of a mixture of lipids, each with distinctive biophysical properties, lateral and transversal sorting of lipids can promote creation of domains inside the membrane through local modulation of the lipid phase. Lipid biophysical properties have been characterized for long based on in vitro analyses using non-natural lipid molecules; their re-examinations using natural lipids might open interesting perspectives on membrane architecture occurring in vivo in various cellular and physiological contexts.

  18. Importance of the hexagonal lipid phase in biological membrane organization.

    Science.gov (United States)

    Jouhet, Juliette

    2013-01-01

    Domains are present in every natural membrane. They are characterized by a distinctive protein and/or lipid composition. Their size is highly variable from the nano- to the micrometer scale. The domains confer specific properties to the membrane leading to original structure and function. The determinants leading to domain organization are therefore important but remain obscure. This review presents how the ability of lipids to organize into hexagonal II or lamellar phases can promote particular local structures within membranes. Since biological membranes are composed of a mixture of lipids, each with distinctive biophysical properties, lateral and transversal sorting of lipids can promote creation of domains inside the membrane through local modulation of the lipid phase. Lipid biophysical properties have been characterized for long based on in vitro analyses using non-natural lipid molecules; their re-examinations using natural lipids might open interesting perspectives on membrane architecture occurring in vivo in various cellular and physiological contexts.

  19. Biophysical-and socioeconomic aspects of land degradation in the Guadalentin (SE-Spain): towards understanding and effective soil conservation

    International Nuclear Information System (INIS)

    Vente, J. de; Sole-Benet, A.; Boix-Fayos, C.; Nainggolan, D.; Romero-Diaz, A.

    2009-01-01

    Desertification and land degradation have been widely studied in the Guadalentin basin (SE Spain) through various national and international research projects. Most important identified degradation types are due to soil erosion, soil surface crusting, aridity, soil organic matter decline and salinisation. On the one hand, political and socioeconomic drivers have caused important land use and management changes, which have formed an important driver for further land degradation. On the other hand, soil conservation practice were initiated by the government and by individual land users, although there is very limited knowledge on their effectiveness. the objective of this work is to provide and overview of previous studies that addressed land degradation in the Guadalentin and to present an integrated synthesis of the main biophysical and socioeconomic factors identifies in these studies as being responsible for land degradation, with a focus on feasible soil conservation strategies. (Author) 18 refs.

  20. Biophysical-and socioeconomic aspects of land degradation in the Guadalentin (SE-Spain): towards understanding and effective soil conservation

    Energy Technology Data Exchange (ETDEWEB)

    Vente, J. de; Sole-Benet, A.; Boix-Fayos, C.; Nainggolan, D.; Romero-Diaz, A.

    2009-07-01

    Desertification and land degradation have been widely studied in the Guadalentin basin (SE Spain) through various national and international research projects. Most important identified degradation types are due to soil erosion, soil surface crusting, aridity, soil organic matter decline and salinisation. On the one hand, political and socioeconomic drivers have caused important land use and management changes, which have formed an important driver for further land degradation. On the other hand, soil conservation practice were initiated by the government and by individual land users, although there is very limited knowledge on their effectiveness. the objective of this work is to provide and overview of previous studies that addressed land degradation in the Guadalentin and to present an integrated synthesis of the main biophysical and socioeconomic factors identifies in these studies as being responsible for land degradation, with a focus on feasible soil conservation strategies. (Author) 18 refs.

  1. An introduction to environmental biophysics

    CERN Document Server

    Campbell, Gaylon S

    1977-01-01

    The study of environmental biophysics probably began earlier in man's history than that of any other science. The study of organism-environment interaction provided a key to survival and progress. Systematic study of the science and recording of experimental results goes back many hundreds of years. Ben­ jamin Franklin, the early American statesman, inventor, printer, and scientist studied conduction, evaporation, and radiation. One of his observations is as follows: My desk on which I now write, and the lock of my desk, are both exposed to the same temperature of the air, and have therefore the same degree of heat or cold; yet if I lay my hand successively on the wood and on the metal, the latter feels much the coldest, not that it is really so, but being a better conductor, it more readily than the wood takes away and draws into itself the fire that was in my skin. 1 Franklin probably was not the first to discover this principle, and certainly was not the last. Modem researchers rediscover this principle f...

  2. Efficacy of betamethasone on the fetal motion and biophysical profile and amniotic fluid index in preterm fetuses.

    Science.gov (United States)

    Abbasalizadeh, Shamsi; Pharabar, Zahra Neghadan; Abbasalizadeh, Fatmeh; Ghojazadeh, Morteza; Goldust, Mohamad

    2013-11-15

    The term ofpreterm birth is used to define the premature neonates considering pregnancy age. In less than 34 week pregnancies, corticosteroids are prescribed to promote embryos' lung maturity. The presents study aimed at evaluating effects of betamethasone injection on feeling embryo motion by mother and index and biophysical profile in preterm pregnancies. In a descriptive-analytical study, 40 pregnant women with the pregnancy age of 30-34 weeks were evaluated. Embryo motion and index and biophysical profile of the amniotic fluid were checked before prescription of double dosage of muscular betamethasone (12 mg) at a 24 h time interval. The injection was repeated for 24 and 48 h after the first injection. The resulted outcomes were compared with those results related to before betamethasone injection. In this study, there was statistically meaningful relationship between embryo motions before injection of betamethasone and 12 h after its injection (p = 0.03). Also, there was a significant relationship between embryo motions 24 and 48 h after injection of betamethasone (p = 0.001). In other words, the embryo motions decreased 12 h after injection of betamethasone. They were improved 48 h after betamethasone injection. But, index and biophysical profile results of amniotic fluid were left unchanged. Application of betamethasone leads to evident but transient decrease in embryo motions. Although motion element of index and biophysical profile of amniotic fluid which is one of the tests used in evaluating the embryo health is fixed and normal, it can be concluded that injection of betamethasone may not affect embryo health.

  3. LFPy: A tool for biophysical simulation of extracellular potentials generated by detailed model neurons

    Directory of Open Access Journals (Sweden)

    Henrik eLindén

    2014-01-01

    Full Text Available Electrical extracellular recordings, i.e., recordings of the electrical potentials in the extracellular medium between cells, have been a main work-horse in electrophysiology for almost a century. The high-frequency part of the signal (>=500 Hz, i.e., themulti-unit activity (MUA, contains information about the firing of action potentials in surrounding neurons, while the low-frequency part, the local field potential (LFP, contains information about how these neurons integrate synaptic inputs. As the recorded extracellular signals arise from multiple neural processes, their interpretation is typically ambiguous and difficult. Fortunately, a precise biophysical modeling scheme linking activity at the cellular level and the recorded signal has been established: the extracellular potential can be calculated as a weighted sum of all transmembrane currents in all cells located in the vicinity of the electrode. This computational scheme can considerably aid the modeling and analysis of MUA and LFP signals.Here, we describe LFPy, an open source Python package for numerical simulations of extracellular potentials. LFPy consists of a set of easy-to-use classes for defining cells, synapses and recording electrodes as Python objects, implementing this biophysical modeling scheme. It runs on top of the widely used NEURON simulation environment, which allows for flexible usage of both new and existing cell models.Further, calculation of extracellular potentials using the line-source-method is efficiently implemented.We describe the theoretical framework underlying the extracellular potential calculations and illustrate by examples how LFPy can be used both for simulating LFPs, i.e., synaptic contributions from single cells as well a populations of cells, and MUAs, i.e., extracellular signatures of action potentials.

  4. LFPy: a tool for biophysical simulation of extracellular potentials generated by detailed model neurons.

    Science.gov (United States)

    Lindén, Henrik; Hagen, Espen; Lęski, Szymon; Norheim, Eivind S; Pettersen, Klas H; Einevoll, Gaute T

    2013-01-01

    Electrical extracellular recordings, i.e., recordings of the electrical potentials in the extracellular medium between cells, have been a main work-horse in electrophysiology for almost a century. The high-frequency part of the signal (≳500 Hz), i.e., the multi-unit activity (MUA), contains information about the firing of action potentials in surrounding neurons, while the low-frequency part, the local field potential (LFP), contains information about how these neurons integrate synaptic inputs. As the recorded extracellular signals arise from multiple neural processes, their interpretation is typically ambiguous and difficult. Fortunately, a precise biophysical modeling scheme linking activity at the cellular level and the recorded signal has been established: the extracellular potential can be calculated as a weighted sum of all transmembrane currents in all cells located in the vicinity of the electrode. This computational scheme can considerably aid the modeling and analysis of MUA and LFP signals. Here, we describe LFPy, an open source Python package for numerical simulations of extracellular potentials. LFPy consists of a set of easy-to-use classes for defining cells, synapses and recording electrodes as Python objects, implementing this biophysical modeling scheme. It runs on top of the widely used NEURON simulation environment, which allows for flexible usage of both new and existing cell models. Further, calculation of extracellular potentials using the line-source-method is efficiently implemented. We describe the theoretical framework underlying the extracellular potential calculations and illustrate by examples how LFPy can be used both for simulating LFPs, i.e., synaptic contributions from single cells as well a populations of cells, and MUAs, i.e., extracellular signatures of action potentials.

  5. Biophysical analysis of HTLV-1 particles reveals novel insights into particle morphology and Gag stochiometry

    Directory of Open Access Journals (Sweden)

    Fogarty Keir H

    2010-09-01

    Full Text Available Abstract Background Human T-lymphotropic virus type 1 (HTLV-1 is an important human retrovirus that is a cause of adult T-cell leukemia/lymphoma. While an important human pathogen, the details regarding virus replication cycle, including the nature of HTLV-1 particles, remain largely unknown due to the difficulties in propagating the virus in tissue culture. In this study, we created a codon-optimized HTLV-1 Gag fused to an EYFP reporter as a model system to quantitatively analyze HTLV-1 particles released from producer cells. Results The codon-optimized Gag led to a dramatic and highly robust level of Gag expression as well as virus-like particle (VLP production. The robust level of particle production overcomes previous technical difficulties with authentic particles and allowed for detailed analysis of particle architecture using two novel methodologies. We quantitatively measured the diameter and morphology of HTLV-1 VLPs in their native, hydrated state using cryo-transmission electron microscopy (cryo-TEM. Furthermore, we were able to determine HTLV-1 Gag stoichiometry as well as particle size with the novel biophysical technique of fluorescence fluctuation spectroscopy (FFS. The average HTLV-1 particle diameter determined by cryo-TEM and FFS was 71 ± 20 nm and 75 ± 4 nm, respectively. These values are significantly smaller than previous estimates made of HTLV-1 particles by negative staining TEM. Furthermore, cryo-TEM reveals that the majority of HTLV-1 VLPs lacks an ordered structure of the Gag lattice, suggesting that the HTLV-1 Gag shell is very likely to be organized differently compared to that observed with HIV-1 Gag in immature particles. This conclusion is supported by our observation that the average copy number of HTLV-1 Gag per particle is estimated to be 510 based on FFS, which is significantly lower than that found for HIV-1 immature virions. Conclusions In summary, our studies represent the first quantitative biophysical

  6. Biophysical influence of airborne carbon nanomaterials on natural pulmonary surfactant.

    Science.gov (United States)

    Valle, Russell P; Wu, Tony; Zuo, Yi Y

    2015-05-26

    Inhalation of nanoparticles (NP), including lightweight airborne carbonaceous nanomaterials (CNM), poses a direct and systemic health threat to those who handle them. Inhaled NP penetrate deep pulmonary structures in which they first interact with the pulmonary surfactant (PS) lining at the alveolar air-water interface. In spite of many research efforts, there is a gap of knowledge between in vitro biophysical study and in vivo inhalation toxicology since all existing biophysical models handle NP-PS interactions in the liquid phase. This technical limitation, inherent in current in vitro methodologies, makes it impossible to simulate how airborne NP deposit at the PS film and interact with it. Existing in vitro NP-PS studies using liquid-suspended particles have been shown to artificially inflate the no-observed adverse effect level of NP exposure when compared to in vivo inhalation studies and international occupational exposure limits (OELs). Here, we developed an in vitro methodology called the constrained drop surfactometer (CDS) to quantitatively study PS inhibition by airborne CNM. We show that airborne multiwalled carbon nanotubes and graphene nanoplatelets induce a concentration-dependent PS inhibition under physiologically relevant conditions. The CNM aerosol concentrations controlled in the CDS are comparable to those defined in international OELs. Development of the CDS has the potential to advance our understanding of how submicron airborne nanomaterials affect the PS lining of the lung.

  7. Marine resources, biophysical processes, and environmental management of a tropical shelf seaway: Torres Strait, Australia Introduction to the special issue

    Science.gov (United States)

    Harris, P. T.; Butler, A. J.; Coles, R. G.

    2008-09-01

    This special issue of Continental Shelf Research contains 20 papers giving research results produced as part of Australia's Torres Strait Co-operative Research Centre (CRC) Program, which was funded over a three-year period during 2003-2006. Marine biophysical, fisheries, socioeconomic-cultural and extension research in the Torres Strait region of northeastern Australia was carried out to meet three aims: 1) support the sustainable development of marine resources and minimize impacts of resource use in Torres Strait; 2) enhance the conservation of the marine environment and the social, cultural and economic well being of all stakeholders, particularly the Torres Strait peoples; and 3) contribute to effective policy formulation and management decision making. Subjects covered, including commercial and traditional fisheries management, impacts of anthropogenic sediment inputs on seagrass meadows and communication of science results to local communities, have broad applications to other similar environments.

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

    NARCIS (Netherlands)

    Denning, Denise; Roos, Wouter H

    2016-01-01

    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

  9. Nonparametric Inference of Doubly Stochastic Poisson Process Data via the Kernel Method.

    Science.gov (United States)

    Zhang, Tingting; Kou, S C

    2010-01-01

    Doubly stochastic Poisson processes, also known as the Cox processes, frequently occur in various scientific fields. In this article, motivated primarily by analyzing Cox process data in biophysics, we propose a nonparametric kernel-based inference method. We conduct a detailed study, including an asymptotic analysis, of the proposed method, and provide guidelines for its practical use, introducing a fast and stable regression method for bandwidth selection. We apply our method to real photon arrival data from recent single-molecule biophysical experiments, investigating proteins' conformational dynamics. Our result shows that conformational fluctuation is widely present in protein systems, and that the fluctuation covers a broad range of time scales, highlighting the dynamic and complex nature of proteins' structure.

  10. Exploring the biophysical properties of phytosterols in the plasma membrane for novel cancer prevention strategies.

    Science.gov (United States)

    Fakih, Omar; Sanver, Didem; Kane, David; Thorne, James L

    2018-05-03

    Cancer is a global problem with no sign that incidences are reducing. The great costs associated with curing cancer, through developing novel treatments and applying patented therapies, is an increasing burden to developed and developing nations alike. These financial and societal problems will be alleviated by research efforts into prevention, or treatments that utilise off-patent or repurposed agents. Phytosterols are natural components of the diet found in an array of seeds, nuts and vegetables and have been added to several consumer food products for the management of cardio-vascular disease through their ability to lower LDL-cholesterol levels. In this review, we provide a connected view between the fields of structural biophysics and cellular and molecular biology to evaluate the growing evidence that phytosterols impair oncogenic pathways in a range of cancer types. The current state of understanding of how phytosterols alter the biophysical properties of plasma membrane is described, and the potential for phytosterols to be repurposed from cardio-vascular to oncology therapeutics. Through an overview of the types of biophysical and molecular biology experiments that have been performed to date, this review informs the reader of the molecular and biophysical mechanisms through which phytosterols could have anti-cancer properties via their interactions with the plasma cell membrane. We also outline emerging and under-explored areas such as computational modelling, improved biomimetic membranes and ex vivo tissue evaluation. Focus of future research in these areas should improve understanding, not just of phytosterols in cancer cell biology but also to give insights into the interaction between the plasma membrane and the genome. These fields are increasingly providing meaningful biological and clinical data but iterative experiments between molecular biology assays, biosynthetic membrane studies and computational membrane modelling improve and refine our

  11. Biophysical mechanisms of endotoxin neutralization by cationic amphiphilic peptides.

    Science.gov (United States)

    Kaconis, Yani; Kowalski, Ina; Howe, Jörg; Brauser, Annemarie; Richter, Walter; Razquin-Olazarán, Iosu; Iñigo-Pestaña, Melania; Garidel, Patrick; Rössle, Manfred; Martinez de Tejada, Guillermo; Gutsmann, Thomas; Brandenburg, Klaus

    2011-06-08

    Bacterial endotoxins (lipopolysaccharides (LPS)) are strong elicitors of the human immune system by interacting with serum and membrane proteins such as lipopolysaccharide-binding protein (LBP) and CD14 with high specificity. At LPS concentrations as low as 0.3 ng/ml, such interactions may lead to severe pathophysiological effects, including sepsis and septic shock. One approach to inhibit an uncontrolled inflammatory reaction is the use of appropriate polycationic and amphiphilic antimicrobial peptides, here called synthetic anti-LPS peptides (SALPs). We designed various SALP structures and investigated their ability to inhibit LPS-induced cytokine secretion in vitro, their protective effect in a mouse model of sepsis, and their cytotoxicity in physiological human cells. Using a variety of biophysical techniques, we investigated selected SALPs with considerable differences in their biological responses to characterize and understand the mechanism of LPS inactivation by SALPs. Our investigations show that neutralization of LPS by peptides is associated with a fluidization of the LPS acyl chains, a strong exothermic Coulomb interaction between the two compounds, and a drastic change of the LPS aggregate type from cubic into multilamellar, with an increase in the aggregate sizes, inhibiting the binding of LBP and other mammalian proteins to the endotoxin. At the same time, peptide binding to phospholipids of human origin (e.g., phosphatidylcholine) does not cause essential structural changes, such as changes in membrane fluidity and bilayer structure. The absence of cytotoxicity is explained by the high specificity of the interaction of the peptides with LPS. Copyright © 2011 Biophysical Society. Published by Elsevier Inc. All rights reserved.

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

    Science.gov (United States)

    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

  13. Biomechanical and biophysical environment of bone from the macroscopic to the pericellular and molecular level.

    Science.gov (United States)

    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

  14. Biophysical and biomathematical adventures in radiobiology

    International Nuclear Information System (INIS)

    Scott, B.R.

    1991-01-01

    Highlights of my biophysical and biomathematical adventures in radiobiology is presented. Early adventures involved developing ''state-vector models'' for specific harmful effects (cell killing, life shortening) of exposure to radiation. More recent adventures led to developing ''hazard-function models'' for predicting biological effects (e.g., cell killing, mutations, tumor induction) of combined exposure to different toxicants. Hazard-function models were also developed for predicting harm to man from exposure to large radiation doses. Major conclusions derived from the modeling adventures are as follows: (1) synergistic effects of different genotoxic agents should not occur at low doses; (2) for exposure of the lung or bone marrow to large doses of photon radiation, low rates of exposure should be better tolerated than high rates; and (3) for some types of radiation (e.g., alpha particles and fission neutrons), moderate doses delivered at a low rate may be more harmful than the same dose given at a high rate. 53 refs., 7 figs

  15. A Diagnosis of Biophysical and Socio-Economic Factors Influencing Farmers' Choice to Adopt Organic or Conventional Farming Systems for Cotton Production.

    Science.gov (United States)

    Riar, Amritbir; Mandloi, Lokendra S; Poswal, Randhir S; Messmer, Monika M; Bhullar, Gurbir S

    2017-01-01

    Organic agriculture is one of the most widely known alternative production systems advocated for its benefits to soil, environment, health and economic well-being of farming communities. Rapid increase in the market demand for organic products presents a remarkable opportunity for expansion of organic agriculture. A thorough understanding of the context specific motivations of farmers for adoption of organic farming systems is important so that appropriate policy measures are put in place. With an aim of understanding the social and biophysical motivations of organic and conventional cotton farmers for following their respective farming practices, a detailed farm survey was conducted in Nimar valley of Madhya Pradesh state in central India. The study area was chosen for being an important region for cotton production, where established organic and conventional farms operate under comparable circumstances. We found considerable variation among organic and conventional farmers for their social and biophysical motivations. Organic farmers were motivated by the sustainability of cotton production and growing safer food without pesticides, whereas conventional farmers were sensitive about their reputation in community. Organic farmers with larger holdings were more concerned about closed nutrient cycles and reducing their dependence on external inputs, whereas medium and small holding organic farmers were clearly motivated by the premium price of organic cotton. Higher productivity was the only important motivation for conventional farmers with larger land holdings. We also found considerable yield gaps among different farms, both under conventional and organic management, that need to be addressed through extension and training. Our findings suggest that research and policy measures need to be directed toward strengthening of extension services, local capacity building, enhancing availability of suitable inputs and market access for organic farmers.

  16. Fragility of complexity biophysical systems by neutron scattering

    Energy Technology Data Exchange (ETDEWEB)

    Magazu, Salvatore [Dipartimento di Fisica, Universita di Messina, P.O. Box 55, I-98166 Messina (Italy)]. E-mail: smagazu@unime.it; Migliardo, Federica [Dipartimento di Fisica, Universita di Messina, P.O. Box 55, I-98166 Messina (Italy); Bellocco, Ersilia [Dipartimento di Chimica Organica e Biologica, Universita di Messina, I-98166 Messina (Italy); Lagana, Giuseppina [Dipartimento di Chimica Organica e Biologica, Universita di Messina, I-98166 Messina (Italy); Mondelli, Claudia [CNR-INFM OGG and CRS-SOFT, c/o ILL, 6 Jules Horowitz, BP 156, 38042 Grenoble Cedex 9 (France)

    2006-11-15

    Neutron scattering is an exceptional tool to investigate structural and dynamical properties of systems of biophysical interest, such as proteins, enzymes, lipids and sugars. Moreover, elastic neutron scattering enhances the investigation of atomic motions in hydrated proteins in a wide temperature range and on the picosecond timescale. Homologous disaccharides, such as trehalose, maltose and sucrose, are cryptobiotic substances, since they allow to many organisms to undergo in a 'suspended life' state, known as cryptobiosis in extreme environmental conditions. The present paper is aimed to discuss the fragility degree of disaccharides, as evaluated of the temperature dependence of the mean square displacement by elastic neutron scattering, in order to link this feature with their bioprotective functions.

  17. 24 CFR 3282.53 - Service of process on foreign manufacturers and importers.

    Science.gov (United States)

    2010-04-01

    ... 24 Housing and Urban Development 5 2010-04-01 2010-04-01 false Service of process on foreign manufacturers and importers. 3282.53 Section 3282.53 Housing and Urban Development Regulations Relating to... REGULATIONS Formal Procedures § 3282.53 Service of process on foreign manufacturers and importers. The...

  18. Expert evaluation in NPP safety important systems licensing process

    International Nuclear Information System (INIS)

    Mikhail, A Yastrebenetsky; Vasilchenko, V.N.

    2001-01-01

    Expert evaluation of nuclear power plant safety important systems modernization is an integral part of these systems licensing process. The paper contains some aspects of this evaluation which are based on Ukrainian experience of VVER-1000 and VVER-440 modernization. (authors)

  19. Expert evaluation in NPP safety important systems licensing process

    Energy Technology Data Exchange (ETDEWEB)

    Mikhail, A Yastrebenetsky; Vasilchenko, V.N. [Ukrainian State Scientific Technical Center of Nuclear and Radiation Safety (Ukraine)

    2001-07-01

    Expert evaluation of nuclear power plant safety important systems modernization is an integral part of these systems licensing process. The paper contains some aspects of this evaluation which are based on Ukrainian experience of VVER-1000 and VVER-440 modernization. (authors)

  20. Binaural processing by the gecko auditory periphery

    DEFF Research Database (Denmark)

    Christensen-Dalsgaard, Jakob; Tang, Ye Zhong; Carr, Catherine E

    2011-01-01

    Lizards have highly directional ears, owing to strong acoustical coupling of the eardrums and almost perfect sound transmission from the contralateral ear. To investigate the neural processing of this remarkable tympanic directionality, we combined biophysical measurements of eardrum motion in th...

  1. Mechanoresponsive stem cells to target cancer metastases through biophysical cues.

    Science.gov (United States)

    Liu, Linan; Zhang, Shirley X; Liao, Wenbin; Farhoodi, Henry P; Wong, Chi W; Chen, Claire C; Ségaliny, Aude I; Chacko, Jenu V; Nguyen, Lily P; Lu, Mengrou; Polovin, George; Pone, Egest J; Downing, Timothy L; Lawson, Devon A; Digman, Michelle A; Zhao, Weian

    2017-07-26

    Despite decades of effort, little progress has been made to improve the treatment of cancer metastases. To leverage the central role of the mechanoenvironment in cancer metastasis, we present a mechanoresponsive cell system (MRCS) to selectively identify and treat cancer metastases by targeting the specific biophysical cues in the tumor niche in vivo. Our MRCS uses mechanosensitive promoter-driven mesenchymal stem cell (MSC)-based vectors, which selectively home to and target cancer metastases in response to specific mechanical cues to deliver therapeutics to effectively kill cancer cells, as demonstrated in a metastatic breast cancer mouse model. Our data suggest a strong correlation between collagen cross-linking and increased tissue stiffness at the metastatic sites, where our MRCS is specifically activated by the specific cancer-associated mechano-cues. MRCS has markedly reduced deleterious effects compared to MSCs constitutively expressing therapeutics. MRCS indicates that biophysical cues, specifically matrix stiffness, are appealing targets for cancer treatment due to their long persistence in the body (measured in years), making them refractory to the development of resistance to treatment. Our MRCS can serve as a platform for future diagnostics and therapies targeting aberrant tissue stiffness in conditions such as cancer and fibrotic diseases, and it should help to elucidate mechanobiology and reveal what cells "feel" in the microenvironment in vivo. Copyright © 2017 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

  2. Evaluation of biophysical skin parameters and assessment of hair growth in patients with acne treated with isotretinoin.

    Science.gov (United States)

    Kmieć, Małgorzata L; Pajor, Anna; Broniarczyk-Dyła, Grażyna

    2013-12-01

    Treatment of the severe forms of acne vulgaris remains a challenge. Isotretinoin is a drug often used in these cases. Retinoids affect the mechanisms that play a role in the pathogenesis of acne, reduce the production of sebum and sizes of the sebaceous glands. However, isotretinoin appears to have undesirable side effects in the skin, mucous membranes and hair. THE AIM OF THIS STUDY WAS TO ASSESS THE EFFECT OF ACNE VULGARIS TREATMENT WITH ISOTRETINOIN ON BIOPHYSICAL SKIN PARAMETERS: skin sebum and stratum corneum hydration levels, transepidermal water loss values, pH, erythema and hair growth parameters: total number, density and proportion of anagen hair. THE STUDY INCLUDED THIRTY PATIENTS WITH ACNE TYPES: papulopustular, conglobata and phlegmonosa. Patients were treated with isotretinoin at a dose of 0.5-1.0 mg/kg/day for a period of 4-7 months. The measurements of skin biophysical parameters were performed before and after the treatment using Sebumeter SM815, Corneometer CM825, Tewameter TM300, MX Mexameter MX18 and Skin-pH-Meter PH908. Hair growth parameters were evaluated with FotoFinder Dermoscope using the TrichoScan Professional V3.0.8.76 software. The results of biophysical skin parameter measurements after the treatment showed a reduction in the severity of seborrhea. However, the skin was dry, which confirmed a lowered degree of stratum corneum hydration and an increase in transepidermal water loss values. Moreover, severity of erythema, an increase in pH value, and variations in selected hair growth parameters: decrease in total count, density and proportion of anagen hair were demonstrated. The reduction in the skin sebum levels was observed after the treatment. There was dryness of the skin, which was confirmed by biophysical skin parameter measurements. Changes in the hair growth parameters showed telogen effluvium hair loss.

  3. Summaries of fiscal year 1994 projects in medical applications and biophysical research

    International Nuclear Information System (INIS)

    1995-04-01

    This report provides information on the research supported in Fiscal Year 1994 by the Medical Applications and Biophysical Research Division of the Office of Health and Environmental Research. A brief statement of the scope of the following areas is presented: dosimetry; measurement science; radiological and chemical physics; structural biology; human genome; and medical applications. Summaries of the research projects in these categories are presented

  4. Importance and process of feedback in undergraduate medical education in Saudi Arabia.

    Science.gov (United States)

    Alhaqwi, Ali I

    2012-09-01

    Feedback is an essential element in the process of students' learning and development. This study aimed to explore the views of medical students regarding the importance and process of feedback in their medical education. A cross-sectional questionnaire-based study was conducted in our college of medicine. The questionnaire included questions to assess the students' views about the importance and the need of feedback in the learning process and whether feed-back should follow certain or all forms of assessment. In addition, the questionnaire contained questions that aimed to explore students' views about the contents and process of feedback. One hundred and eighty-six male medical students participated in this study. While the majority of students (85%) indicated that feedback was important for their learning and expressed their need for regular feedback during their study, only about 20% of them indicated receiving regular feed-back. Senior students perceived that they received feedback less frequently than their junior colleagues' (P importance and should be considered for planning and implementing an effective feedback system.

  5. Unraveling biophysical interactions of radiation pneumonitis in non-small-cell lung cancer via Bayesian network analysis.

    Science.gov (United States)

    Luo, Yi; El Naqa, Issam; McShan, Daniel L; Ray, Dipankar; Lohse, Ines; Matuszak, Martha M; Owen, Dawn; Jolly, Shruti; Lawrence, Theodore S; Kong, Feng-Ming Spring; Ten Haken, Randall K

    2017-04-01

    In non-small-cell lung cancer radiotherapy, radiation pneumonitis≥grade 2 (RP2) depends on patients' dosimetric, clinical, biological and genomic characteristics. We developed a Bayesian network (BN) approach to explore its potential for interpreting biophysical signaling pathways influencing RP2 from a heterogeneous dataset including single nucleotide polymorphisms, micro RNAs, cytokines, clinical data, and radiation treatment plans before and during the course of radiotherapy. Model building utilized 79 patients (21 with RP2) with complete data, and model testing used 50 additional patients with incomplete data. A developed large-scale Markov blanket approach selected relevant predictors. Resampling by k-fold cross-validation determined the optimal BN structure. Area under the receiver-operating characteristics curve (AUC) measured performance. Pre- and during-treatment BNs identified biophysical signaling pathways from the patients' relevant variables to RP2 risk. Internal cross-validation for the pre-BN yielded an AUC=0.82 which improved to 0.87 by incorporating during treatment changes. In the testing dataset, the pre- and during AUCs were 0.78 and 0.82, respectively. Our developed BN approach successfully handled a high number of heterogeneous variables in a small dataset, demonstrating potential for unraveling relevant biophysical features that could enhance prediction of RP2, although the current observations would require further independent validation. Copyright © 2017 Elsevier B.V. All rights reserved.

  6. Determination of import process during Yucca Mountain Site characterization

    International Nuclear Information System (INIS)

    Hastings, P.S.; Gwyn, D.W.; Wemheuer, R.F.

    1996-01-01

    Construction of an underground Exploratory Studies Facility (ESF) for characterizing the Yucca Mountain site precedes the design of a potential repository, with site characterization testing and ESF construction conducted as parallel activities. As a result of this fact, a program is required to: (1) provide for inclusion of the underground excavation into a potential repository, (2) minimize the potential impact of ESF construction on site characterization test results, and (3) minimize the potential impact of ESF construction and site characterization testing on the waste isolation capabilities of the site. At Yucca Mountain, the Determination of Importance (DI) process fulfills these goals. This paper addresses the evolution of the DI process; describes how the DI process fits into design, testing, and construction programs: and discusses how the process is implemented through specification requirements

  7. Importance of neutral processes varies in time and space: Evidence from dryland stream ecosystems.

    Directory of Open Access Journals (Sweden)

    Xiaoli Dong

    Full Text Available Many ecosystems experience strong temporal variability in environmental conditions; yet, a clear picture of how niche and neutral processes operate to determine community assembly in temporally variable systems remains elusive. In this study, we constructed neutral metacommunity models to assess the relative importance of neutral processes in a spatially and temporally variable ecosystem. We analyzed macroinvertebrate community data spanning multiple seasons and years from 20 sites in a Sonoran Desert river network in Arizona. The model goodness-of-fit was used to infer the importance of neutral processes. Averaging over eight stream flow conditions across three years, we found that neutral processes were more important in perennial streams than in non-perennial streams (intermittent and ephemeral streams. Averaging across perennial and non-perennial streams, we found that neutral processes were more important during very high flow and in low flow periods; whereas, at very low flows, the relative importance of neutral processes varied greatly. These findings were robust to the choice of model parameter values. Our study suggested that the net effect of disturbance on the relative importance of niche and neutral processes in community assembly varies non-monotonically with the severity of disturbance. In contrast to the prevailing view that disturbance promotes niche processes, we found that neutral processes could become more important when the severity of disturbance is beyond a certain threshold such that all organisms are adversely affected regardless of their biological traits and strategies.

  8. Biophysical processes affecting DOM dynamics at the Arno river mouth (Tyrrhenian Sea).

    Science.gov (United States)

    Retelletti Brogi, S; Gonnelli, M; Vestri, S; Santinelli, C

    2015-02-01

    Dissolved organic carbon (DOC) and optical properties (absorption and fluorescence) of chromophoric dissolved organic matter (CDOM) were measured in October 2012, at the Arno river mouth and in a coastal station close to it. The data reported indicates that the Arno river represents an important source of DOC and CDOM to this coastal area, with a total DOC flux of 11.23-12.04 · 10(9)g C · y(-1). Moving from the river to the sea, CDOM absorption and fluorescence decreased, while the spectral slope increased, suggesting a change in the molecular properties of CDOM. Mineralization experiments were carried out in order to investigate the main processes of DOM removal and/or transformation in riverine and coastal water. DOC removal rates were 20 μM · month(-1) in the river and 3 μM · month(-1) in the seawater, while CDOM was released during the first 30 days and removed in the following 40 days. Copyright © 2014 Elsevier B.V. All rights reserved.

  9. Investigating Irregularly Patterned Deep Brain Stimulation Signal Design Using Biophysical Models

    Directory of Open Access Journals (Sweden)

    Samantha Rose Summerson

    2015-06-01

    Full Text Available Parkinson’s disease (PD is a neurodegenerative disorder which follows from cell loss of dopaminergic neurons in the substantia nigra pars compacta (SNc, a nucleus in the basal ganglia (BG. Deep brain stimulation (DBS is an electrical therapy that modulates the pathological activity to treat the motor symptoms of PD. Although this therapy is currently used in clinical practice, the sufficient conditions for therapeutic efficacy are unknown. In this work we develop a model of critical motor circuit structures in the brain using biophysical cell models as the base components and then evaluate performance of different DBS signals in this model to perform comparative studies of their efficacy. Biological models are an important tool for gaining insights into neural function and, in this case, serve as effective tools for investigating innovative new DBS paradigms. Experiments were performed using the hemi-parkinsonian rodent model to test the same set of signals, verifying the obedience of the model to physiological trends. We show that antidromic spiking from DBS of the subthalamic nucleus (STN has a significant impact on cortical neural activity, which is frequency dependent and additionally modulated by the regularity of the stimulus pulse train used. Irregular spacing between stimulus pulses, where the amount of variability added is bounded, is shown to increase diversification of response of basal ganglia neurons and reduce entropic noise in cortical neurons, which may be fundamentally important to restoration of information flow in the motor circuit.

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

    Science.gov (United States)

    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.

  11. PyFolding: Open-Source Graphing, Simulation, and Analysis of the Biophysical Properties of Proteins.

    Science.gov (United States)

    Lowe, Alan R; Perez-Riba, Albert; Itzhaki, Laura S; Main, Ewan R G

    2018-02-06

    For many years, curve-fitting software has been heavily utilized to fit simple models to various types of biophysical data. Although such software packages are easy to use for simple functions, they are often expensive and present substantial impediments to applying more complex models or for the analysis of large data sets. One field that is reliant on such data analysis is the thermodynamics and kinetics of protein folding. Over the past decade, increasingly sophisticated analytical models have been generated, but without simple tools to enable routine analysis. Consequently, users have needed to generate their own tools or otherwise find willing collaborators. Here we present PyFolding, a free, open-source, and extensible Python framework for graphing, analysis, and simulation of the biophysical properties of proteins. To demonstrate the utility of PyFolding, we have used it to analyze and model experimental protein folding and thermodynamic data. Examples include: 1) multiphase kinetic folding fitted to linked equations, 2) global fitting of multiple data sets, and 3) analysis of repeat protein thermodynamics with Ising model variants. Moreover, we demonstrate how PyFolding is easily extensible to novel functionality beyond applications in protein folding via the addition of new models. Example scripts to perform these and other operations are supplied with the software, and we encourage users to contribute notebooks and models to create a community resource. Finally, we show that PyFolding can be used in conjunction with Jupyter notebooks as an easy way to share methods and analysis for publication and among research teams. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  12. A Diagnosis of Biophysical and Socio-Economic Factors Influencing Farmers’ Choice to Adopt Organic or Conventional Farming Systems for Cotton Production

    Directory of Open Access Journals (Sweden)

    Amritbir Riar

    2017-07-01

    Full Text Available Organic agriculture is one of the most widely known alternative production systems advocated for its benefits to soil, environment, health and economic well-being of farming communities. Rapid increase in the market demand for organic products presents a remarkable opportunity for expansion of organic agriculture. A thorough understanding of the context specific motivations of farmers for adoption of organic farming systems is important so that appropriate policy measures are put in place. With an aim of understanding the social and biophysical motivations of organic and conventional cotton farmers for following their respective farming practices, a detailed farm survey was conducted in Nimar valley of Madhya Pradesh state in central India. The study area was chosen for being an important region for cotton production, where established organic and conventional farms operate under comparable circumstances. We found considerable variation among organic and conventional farmers for their social and biophysical motivations. Organic farmers were motivated by the sustainability of cotton production and growing safer food without pesticides, whereas conventional farmers were sensitive about their reputation in community. Organic farmers with larger holdings were more concerned about closed nutrient cycles and reducing their dependence on external inputs, whereas medium and small holding organic farmers were clearly motivated by the premium price of organic cotton. Higher productivity was the only important motivation for conventional farmers with larger land holdings. We also found considerable yield gaps among different farms, both under conventional and organic management, that need to be addressed through extension and training. Our findings suggest that research and policy measures need to be directed toward strengthening of extension services, local capacity building, enhancing availability of suitable inputs and market access for organic farmers.

  13. Tool for assessment of process importance at the groundwater/surface water interface.

    Science.gov (United States)

    Palakodeti, Ravi C; LeBoeuf, Eugene J; Clarke, James H

    2009-10-01

    The groundwater/surface water interface (GWSWI) represents an important transition zone between groundwater and surface water environments that potentially changes the nature and flux of contaminants exchanged between the two systems. Identifying dominant and rate-limiting contaminant transformation processes is critically important for estimating contaminant fluxes and compositional changes across the GWSWI. A new, user-friendly, spreadsheet- and Visual Basic-based analytical screening tool that assists in evaluating the dominance of controlling kinetic processes across the GWSWI is presented. Based on contaminant properties, first-order processes that may play a significant role in solute transport/transformation are evaluated in terms of a ratio of process importance (P(i)) that relates the process rate to the rate of fluid transfer. Besides possessing several useful compilations of contaminant and process data, the screening tool also includes 1-D analytical models that assist users in evaluating contaminant transport across the GWSWI. The tool currently applies to 29 organics and 10 inorganics of interest within the context of the GWSWI. Application of the new screening tool is demonstrated through an evaluation of natural attenuation at a site with trichloroethylene and 1,1,2,2-tetrachloroethane contaminated groundwater discharging into wetlands.

  14. Cellular Biophysics During Freezing of Rat and Mouse Sperm Predicts Post-thaw Motility1

    Science.gov (United States)

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

    2009-01-01

    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°C/min and 20°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 Lpg and ELp. A “combined fit” (to 5°C/min and 20°C/min data) for rat sperm in Biggers-Whitten-Whittingham media yielded Lpg = 0.007 μm min−1 atm−1 and ELp = 17.8 kcal/mol, and in egg yolk cryopreservation media yielded Lpg = 0.005 μm min−1 atm−1 and ELp = 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°C during freezing in cryopreservation media. These predicted rates range from 53°C/min to 70°C/min and from 28°C/min to 36°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°C/min and 80

  15. Conceptual approach to the development of an active process of import substitution

    Directory of Open Access Journals (Sweden)

    Yu. A. Salikov

    2018-01-01

    Full Text Available In the current political and economic situation, the process of import substitution is of particular importance. Modern processes of social globalization involve the expansion of cooperation and integration of all levels and types of social production. However, there is a risk of increasing risks in the areas of economic and defense security, openness of new technologies, consumer (food and commodity dependence, that is, increasing the risk of loss of stability of the socio-economic system. It is obvious that the main strategic objectives for socio-economic systems are different for each hierarchical level. At the macroeconomic level, these tasks are related not only to the formation of a system of priorities and incentives for the reorientation of the national reproductive complex to the production of import-substituting products, but also to the development of an institutional framework for initiating and launching import-substitution processes.. Import substitution is an active process of replacing imported goods with domestic analogues. It is important to note that for the Russian Federation import substitution is forced, because the beginning of the policy of substitution of foreign goods for goods produced domestically against Russia was introduced a number of trade and economic sanctions imposed by the countries of Europe and the United States. In addition, it should be emphasized that the process of import substitution in the domestic economy should a priori have realistic and objectively marked borders, as the the task of ensuring that excessive (as a limit – one hundred percent of replacement itself is not only achievable in principle, but requiring undue effort and material costs, can cause considerable damage to the national economy. The analysis of the theories of foreign direct investment. The scheme of construction of production on the basis of active import substitution was built. Thus, it is necessary to note the importance of

  16. Gradient models in molecular biophysics: progress, challenges, opportunities

    Science.gov (United States)

    Bardhan, Jaydeep P.

    2013-12-01

    In the interest of developing a bridge between researchers modeling materials and those modeling biological molecules, we survey recent progress in developing nonlocal-dielectric continuum models for studying the behavior of proteins and nucleic acids. As in other areas of science, continuum models are essential tools when atomistic simulations (e.g., molecular dynamics) are too expensive. Because biological molecules are essentially all nanoscale systems, the standard continuum model, involving local dielectric response, has basically always been dubious at best. The advanced continuum theories discussed here aim to remedy these shortcomings by adding nonlocal dielectric response. We begin by describing the central role of electrostatic interactions in biology at the molecular scale, and motivate the development of computationally tractable continuum models using applications in science and engineering. For context, we highlight some of the most important challenges that remain, and survey the diverse theoretical formalisms for their treatment, highlighting the rigorous statistical mechanics that support the use and improvement of continuum models. We then address the development and implementation of nonlocal dielectric models, an approach pioneered by Dogonadze, Kornyshev, and their collaborators almost 40 years ago. The simplest of these models is just a scalar form of gradient elasticity, and here we use ideas from gradient-based modeling to extend the electrostatic model to include additional length scales. The review concludes with a discussion of open questions for model development, highlighting the many opportunities for the materials community to leverage its physical, mathematical, and computational expertise to help solve one of the most challenging questions in molecular biology and biophysics.

  17. Biophysics of skin and its treatments structural, nanotribological, and nanomechanical studies

    CERN Document Server

    Bhushan, Bharat

    2017-01-01

    This book provides a comprehensive overview of the structural, nanotribological and nanomechanical properties of skin with and without cream treatment as a function of operating environment. The biophysics of skin as the outer layer covering human or animal body is discussed as a complex biological structure. Skin cream is used to improve skin health and create a smooth, soft, and flexible surface with moist perception by altering the surface roughness, friction, adhesion, elastic modulus, and surface charge of the skin surface. .

  18. An allosteric gating model recapitulates the biophysical properties of IK,L expressed in mouse vestibular type I hair cells.

    Science.gov (United States)

    Spaiardi, Paolo; Tavazzani, Elisa; Manca, Marco; Milesi, Veronica; Russo, Giancarlo; Prigioni, Ivo; Marcotti, Walter; Magistretti, Jacopo; Masetto, Sergio

    2017-11-01

    Vestibular type I and type II hair cells and their afferent fibres send information to the brain regarding the position and movement of the head. The characteristic feature of type I hair cells is the expression of a low-voltage-activated outward rectifying K + current, I K,L , whose biophysical properties and molecular identity are still largely unknown. In vitro, the afferent nerve calyx surrounding type I hair cells causes unstable intercellular K + concentrations, altering the biophysical properties of I K,L . We found that in the absence of the calyx, I K,L in type I hair cells exhibited unique biophysical activation properties, which were faithfully reproduced by an allosteric channel gating scheme. These results form the basis for a molecular and pharmacological identification of I K,L . Type I and type II hair cells are the sensory receptors of the mammalian vestibular epithelia. Type I hair cells are characterized by their basolateral membrane being enveloped in a single large afferent nerve terminal, named the calyx, and by the expression of a low-voltage-activated outward rectifying K + current, I K,L . The biophysical properties and molecular profile of I K,L are still largely unknown. By using the patch-clamp whole-cell technique, we examined the voltage- and time-dependent properties of I K,L in type I hair cells of the mouse semicircular canal. We found that the biophysical properties of I K,L were affected by an unstable K + equilibrium potential (V eq K + ). Both the outward and inward K + currents shifted V eq K + consistent with K + accumulation or depletion, respectively, in the extracellular space, which we attributed to a residual calyx attached to the basolateral membrane of the hair cells. We therefore optimized the hair cell dissociation protocol in order to isolate mature type I hair cells without their calyx. In these cells, the uncontaminated I K,L showed a half-activation at -79.6 mV and a steep voltage dependence (2.8 mV). I K,L also

  19. Understanding the biophysical effects of transcranial magnetic stimulation on brain tissue: the bridge between brain stimulation and cognition.

    Science.gov (United States)

    Neggers, Sebastiaan F W; Petrov, Petar I; Mandija, Stefano; Sommer, Iris E C; van den Berg, Nico A T

    2015-01-01

    Transcranial magnetic stimulation (TMS) is rapidly being adopted in neuroscience, medicine, psychology, and biology, for basic research purposes, diagnosis, and therapy. However, a coherent picture of how TMS affects neuronal processing, and especially how this in turn influences behavior, is still largely unavailable despite several studies that investigated aspects of the underlying neurophysiological effects of TMS. Perhaps as a result from this "black box approach," TMS studies show a large interindividual variability in applied paradigms and TMS treatment outcome can be quite variable, hampering its general efficacy and introduction into the clinic. A better insight into the biophysical, neuronal, and cognitive mechanisms underlying TMS is crucial in order to apply it effectively in the clinic and to increase our understanding of brain-behavior relationship. Therefore, computational and experimental efforts have been started recently to understand and control the effect TMS has on neuronal functioning. Especially, how the brain shapes magnetic fields induced by a TMS coil, how currents are generated locally in the cortical surface, and how they interact with complex functional neuronal circuits within and between brain areas are crucial to understand the observed behavioral changes and potential therapeutic effects resulting from TMS. Here, we review the current knowledge about the biophysical underpinnings of single-pulse TMS and argue how to move forward to fully understand and exploit the powerful technique that TMS can be. © 2015 Elsevier B.V. All rights reserved.

  20. Novel physical chemistry approaches in biophysical researches with advanced application of lasers: Detection and manipulation.

    Science.gov (United States)

    Iwata, Koichi; Terazima, Masahide; Masuhara, Hiroshi

    2018-02-01

    Novel methodologies utilizing pulsed or intense CW irradiation obtained from lasers have a major impact on biological sciences. In this article, recent development in biophysical researches fully utilizing the laser irradiation is described for three topics, time-resolved fluorescence spectroscopy, time-resolved thermodynamics, and manipulation of the biological assemblies by intense laser irradiation. First, experimental techniques for time-resolved fluorescence spectroscopy are concisely explained in Section 2. As an example of the recent application of time-resolved fluorescence spectroscopy to biological systems, evaluation of the viscosity of lipid bilayer membranes is described. The results of the spectroscopic experiments strongly suggest the presence of heterogeneous membrane structure with two different viscosity values in liposomes formed by a single phospholipid. Section 3 covers the time-resolved thermodynamics. Thermodynamical properties are important to characterize biomolecules. However, measurement of these quantities for short-lived intermediate species has been impossible by traditional thermodynamical techniques. Recently, development of a spectroscopic method based on the transient grating method enables us to measure these quantities and also to elucidate reaction kinetics which cannot be detected by other spectroscopic methods. The principle of the measurements and applications to some protein reactions are reviewed. Manipulation and fabrication of supramolecues, amino acids, proteins, and living cells by intense laser irradiation are described in Section 4. Unconventional assembly, crystallization and growth, amyloid fibril formation, and living cell manipulation are achieved by CW laser trapping and femtosecond laser-induced cavitation bubbling. Their spatio-temporal controllability is opening a new avenue in the relevant molecular and bioscience research fields. This article is part of a Special Issue entitled "Biophysical Exploration of

  1. Climate Change Effects on Agriculture: Economic Responses to Biophysical Shocks

    Science.gov (United States)

    Nelson, Gerald C.; Valin, Hugo; Sands, Ronald D.; Havlik, Petr; Ahammad, Helal; Deryng, Delphine; Elliott, Joshua; Fujimori, Shinichiro; Hasegawa, Tomoko; Heyhoe, Edwina

    2014-01-01

    Agricultural production is sensitive to weather and thus directly affected by climate change. Plausible estimates of these climate change impacts require combined use of climate, crop, and economic models. Results from previous studies vary substantially due to differences in models, scenarios, and data. This paper is part of a collective effort to systematically integrate these three types of models. We focus on the economic component of the assessment, investigating how nine global economic models of agriculture represent endogenous responses to seven standardized climate change scenarios produced by two climate and five crop models. These responses include adjustments in yields, area, consumption, and international trade. We apply biophysical shocks derived from the Intergovernmental Panel on Climate Change's representative concentration pathway with end-of-century radiative forcing of 8.5 W/m(sup 2). The mean biophysical yield effect with no incremental CO2 fertilization is a 17% reduction globally by 2050 relative to a scenario with unchanging climate. Endogenous economic responses reduce yield loss to 11%, increase area of major crops by 11%, and reduce consumption by 3%. Agricultural production, cropland area, trade, and prices show the greatest degree of variability in response to climate change, and consumption the lowest. The sources of these differences include model structure and specification; in particular, model assumptions about ease of land use conversion, intensification, and trade. This study identifies where models disagree on the relative responses to climate shocks and highlights research activities needed to improve the representation of agricultural adaptation responses to climate change.

  2. Improving evapotranspiration in a land surface model using biophysical variables derived from MSG/SEVIRI satellite

    Directory of Open Access Journals (Sweden)

    N. Ghilain

    2012-08-01

    Full Text Available Monitoring evapotranspiration over land is highly dependent on the surface state and vegetation dynamics. Data from spaceborn platforms are desirable to complement estimations from land surface models. The success of daily evapotranspiration monitoring at continental scale relies on the availability, quality and continuity of such data. The biophysical variables derived from SEVIRI on board the geostationary satellite Meteosat Second Generation (MSG and distributed by the Satellite Application Facility on Land surface Analysis (LSA-SAF are particularly interesting for such applications, as they aimed at providing continuous and consistent daily time series in near-real time over Africa, Europe and South America. In this paper, we compare them to monthly vegetation parameters from a database commonly used in numerical weather predictions (ECOCLIMAP-I, showing the benefits of the new daily products in detecting the spatial and temporal (seasonal and inter-annual variability of the vegetation, especially relevant over Africa. We propose a method to handle Leaf Area Index (LAI and Fractional Vegetation Cover (FVC products for evapotranspiration monitoring with a land surface model at 3–5 km spatial resolution. The method is conceived to be applicable for near-real time processes at continental scale and relies on the use of a land cover map. We assess the impact of using LSA-SAF biophysical variables compared to ECOCLIMAP-I on evapotranspiration estimated by the land surface model H-TESSEL. Comparison with in-situ observations in Europe and Africa shows an improved estimation of the evapotranspiration, especially in semi-arid climates. Finally, the impact on the land surface modelled evapotranspiration is compared over a north–south transect with a large gradient of vegetation and climate in Western Africa using LSA-SAF radiation forcing derived from remote sensing. Differences are highlighted. An evaluation against remote sensing derived land

  3. Surface enhanced raman spectroscopy analytical, biophysical and life science applications

    CERN Document Server

    Schlücker, Sebastian

    2013-01-01

    Covering everything from the basic theoretical and practical knowledge to new exciting developments in the field with a focus on analytical and life science applications, this monograph shows how to apply surface-enhanced Raman scattering (SERS) for solving real world problems. From the contents: * Theory and practice of SERS * Analytical applications * SERS combined with other analytical techniques * Biophysical applications * Life science applications including various microscopies Aimed at analytical, surface and medicinal chemists, spectroscopists, biophysicists and materials scientists. Includes a Foreword by the renowned Raman spectroscopist Professor Wolfgang Kiefer, the former Editor-in-Chief of the Journal of Raman Spectroscopy.

  4. Hydrophobic ampersand hydrophilic: Theoretical models of solvation for molecular biophysics

    International Nuclear Information System (INIS)

    Pratt, L.R.; Tawa, G.J.; Hummer, G.; Garcia, A.E.; Corcelli, S.A.

    1996-01-01

    Molecular statistical thermodynamic models of hydration for chemistry and biophysics have advanced abruptly in recent years. With liquid water as solvent, salvation phenomena are classified as either hydrophobic or hydrophilic effects. Recent progress in treatment of hydrophilic effects have been motivated by continuum dielectric models interpreted as a modelistic implementation of second order perturbation theory. New results testing that perturbation theory of hydrophilic effects are presented and discussed. Recent progress in treatment of hydrophobic effects has been achieved by applying information theory to discover models of packing effects in dense liquids. The simplest models to which those ideas lead are presented and discussed

  5. The Multistream Self: Biophysical, Mental, Social, and Existential

    Directory of Open Access Journals (Sweden)

    Vinod D. Deshmukh

    2008-01-01

    Full Text Available Self is difficult to define because of its multiple, constitutive streams of functional existence. A more comprehensive and expanded definition of self is proposed. The standard bio-psycho-social model of psyche is expanded to biophysical-mental-social and existential self. The total human experience is better understood and explained by adding the existential component. Existential refers to lived human experience, which is firmly rooted in reality. Existential living is the capacity to live fully in the present, and respond freely and flexibly to new experience without fear. Four common fears of isolation, insecurity, insignificance, and death can be overcome by developing a lifestyle of whole-hearted engagement in the present reality, creative problem solving, self-actualization, and altruism. Such integrative living creates a sense of presence with self-awareness, understanding, and existential well-being. Well-being is defined as a life of happiness, contentment, low distress, and good health with positive outlook. Self is a complex, integrative process of living organisms. It organizes, coordinates, and integrates energy-information within and around itself, spontaneously, unconsciously, and consciously. Self-process is understood in terms of synergetics, coordination dynamics, and energy-information–directed self-organization. It is dynamic, composite, ever renewing, and enduring. It can be convergent or divergent, and can function as the source or target of its own behavior-mentation. The experience of self is continuously generated by spontaneous activation of neural networks in the cerebral neocortex by the brainstem-diencephalic arousal system. The multiple constitutive behavioral-mental streams develop concurrently into a unique experience of self, specific for a person at his/her developmental stage. The chronological neuro-behavioral-mental development of self is described in detail from embryonic stage to old age. Self can be

  6. Polish Academy of Sciences. Institute of Biochemistry and Biophysics. Research Report 1998-1999

    International Nuclear Information System (INIS)

    2000-01-01

    The report presented research activities of the Institute of Biochemistry and Biophysics, Polish Academy of Sciences, in 1998-1999. Research interests focus on: replication, mutagenesis and repair of DNA, regulation of gene expression, biosynthesis and post-translational modifications of proteins, gene sequencing and functional gene analysis, structure and function of enzymes, conformation of proteins and peptides, modeling of structures and prediction of function of proteins

  7. Polish Academy of Sciences. Institute of Biochemistry and Biophysics. Research Report 1998-1999

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2000-07-01

    The report presented research activities of the Institute of Biochemistry and Biophysics, Polish Academy of Sciences, in 1998-1999. Research interests focus on: replication, mutagenesis and repair of DNA, regulation of gene expression, biosynthesis and post-translational modifications of proteins, gene sequencing and functional gene analysis, structure and function of enzymes, conformation of proteins and peptides, modeling of structures and prediction of function of proteins.

  8. Biophysical properties of membrane lipids of anammox bacteria : I. Ladderane phospholipids form highly organized fluid membranes

    NARCIS (Netherlands)

    Boumann, Henry A.; Longo, Marjorie L.; Stroeve, Pieter; Poolman, Bert; Hopmans, Ellen C.; Stuart, Marc C. A.; Damste, Jaap S. Sinninghe; Schouten, Stefan

    Anammox bacteria that are capable of anaerobically oxidizing ammonium (anammox) with nitrite to nitrogen gas produce unique membrane phospholipids that comprise hydrocarbon chains with three or five linearly condensed cyclobutane rings. To gain insight into the biophysical properties of these

  9. 7 CFR 361.8 - Cleaning of imported seed and processing of certain Canadian-origin screenings.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 5 2010-01-01 2010-01-01 false Cleaning of imported seed and processing of certain... SCREENINGS UNDER THE FEDERAL SEED ACT § 361.8 Cleaning of imported seed and processing of certain Canadian... compliance agreement for the cleaning of imported seed or processing of otherwise prohibited screenings from...

  10. The Analytic Hierarchy Process and Participatory Decisionmaking

    Science.gov (United States)

    Daniel L. Schmoldt; Daniel L. Peterson; Robert L. Smith

    1995-01-01

    Managing natural resource lands requires social, as well as biophysical, considerations. Unfortunately, it is extremely difficult to accurately assess and quantify changing social preferences, and to aggregate conflicting opinions held by diverse social groups. The Analytic Hierarchy Process (AHP) provides a systematic, explicit, rigorous, and robust mechanism for...

  11. Fluctuation theory of solutions applications in chemistry, chemical engineering, and biophysics

    CERN Document Server

    Smith, Paul E

    2013-01-01

    There are essentially two theories of solutions that can be considered exact: the McMillan-Mayer theory and Fluctuation Solution Theory (FST). The first is mostly limited to solutes at low concentrations, while FST has no such issue. It is an exact theory that can be applied to any stable solution regardless of the number of components and their concentrations, and the types of molecules and their sizes. Fluctuation Theory of Solutions: Applications in Chemistry, Chemical Engineering, and Biophysics outlines the general concepts and theoretical basis of FST and provides a range of applications

  12. The biophysical perspective of a middle income economy. Material flows in Mexico

    International Nuclear Information System (INIS)

    Gonzalez-Martinez, Ana Citlalic; Schandl, Heinz

    2008-01-01

    We analyse natural resource use dynamics in the Mexican economy during the last three decades. Despite low and uneven economic growth, the extraction and use of materials in the Mexican economy has continuously increased during the last 30 years. In this period, population growth rather than economic growth was the main driving force for biophysical growth. In addition, fundamental changes have taken place in the primary sectors, in manufacturing, and in household consumption and these are reflected in an increasing emphasis on the use of fossil fuels and construction materials. Mexico's economy has been strongly influenced by international trade since the country commenced competing in international markets. In the 1970s, Mexico mainly exported primary resources. This pattern has changed and manufactured goods now have a much greater importance due to a boom in assembling industries. In contrast with other Latin American countries, Mexico has achieved a diversification of production, moving towards technology-intensive products and a better mix in its export portfolio. However, crude oil exports still represent the single most important export good. Mexico's material consumption is still well below the OECD average but is growing fast and the current resource use patterns may well present serious social and environmental problems to the medium and long-term sustainability of Mexico's economy and community. Information on natural resource use and resource productivity could provide valuable guidance for economic policy planning in Mexico. (author)

  13. Modelling interactions and feedback mechanisms between land use change and landscape processes

    NARCIS (Netherlands)

    Claessens, L.; Schoorl, J.M.; Verburg, P.H.; Geraedts, L.; Veldkamp, A.

    2009-01-01

    Land use changes and landscape processes are interrelated and influenced by multiple bio-physical and socio-economic driving factors, resulting in a complex, multi-scale system. Consequently in landscapes with active landscape processes such as erosion, land use changes should not be analysed in

  14. Gradient Models in Molecular Biophysics: Progress, Challenges, Opportunities.

    Science.gov (United States)

    Bardhan, Jaydeep P

    2013-12-01

    In the interest of developing a bridge between researchers modeling materials and those modeling biological molecules, we survey recent progress in developing nonlocal-dielectric continuum models for studying the behavior of proteins and nucleic acids. As in other areas of science, continuum models are essential tools when atomistic simulations (e.g. molecular dynamics) are too expensive. Because biological molecules are essentially all nanoscale systems, the standard continuum model, involving local dielectric response, has basically always been dubious at best. The advanced continuum theories discussed here aim to remedy these shortcomings by adding features such as nonlocal dielectric response, and nonlinearities resulting from dielectric saturation. We begin by describing the central role of electrostatic interactions in biology at the molecular scale, and motivate the development of computationally tractable continuum models using applications in science and engineering. For context, we highlight some of the most important challenges that remain and survey the diverse theoretical formalisms for their treatment, highlighting the rigorous statistical mechanics that support the use and improvement of continuum models. We then address the development and implementation of nonlocal dielectric models, an approach pioneered by Dogonadze, Kornyshev, and their collaborators almost forty years ago. The simplest of these models is just a scalar form of gradient elasticity, and here we use ideas from gradient-based modeling to extend the electrostatic model to include additional length scales. The paper concludes with a discussion of open questions for model development, highlighting the many opportunities for the materials community to leverage its physical, mathematical, and computational expertise to help solve one of the most challenging questions in molecular biology and biophysics.

  15. Gradient Models in Molecular Biophysics: Progress, Challenges, Opportunities

    Science.gov (United States)

    Bardhan, Jaydeep P.

    2014-01-01

    In the interest of developing a bridge between researchers modeling materials and those modeling biological molecules, we survey recent progress in developing nonlocal-dielectric continuum models for studying the behavior of proteins and nucleic acids. As in other areas of science, continuum models are essential tools when atomistic simulations (e.g. molecular dynamics) are too expensive. Because biological molecules are essentially all nanoscale systems, the standard continuum model, involving local dielectric response, has basically always been dubious at best. The advanced continuum theories discussed here aim to remedy these shortcomings by adding features such as nonlocal dielectric response, and nonlinearities resulting from dielectric saturation. We begin by describing the central role of electrostatic interactions in biology at the molecular scale, and motivate the development of computationally tractable continuum models using applications in science and engineering. For context, we highlight some of the most important challenges that remain and survey the diverse theoretical formalisms for their treatment, highlighting the rigorous statistical mechanics that support the use and improvement of continuum models. We then address the development and implementation of nonlocal dielectric models, an approach pioneered by Dogonadze, Kornyshev, and their collaborators almost forty years ago. The simplest of these models is just a scalar form of gradient elasticity, and here we use ideas from gradient-based modeling to extend the electrostatic model to include additional length scales. The paper concludes with a discussion of open questions for model development, highlighting the many opportunities for the materials community to leverage its physical, mathematical, and computational expertise to help solve one of the most challenging questions in molecular biology and biophysics. PMID:25505358

  16. The physics, biophysics and technology of photodynamic therapy

    International Nuclear Information System (INIS)

    Wilson, Brian C; Patterson, Michael S

    2008-01-01

    Photodynamic therapy (PDT) uses light-activated drugs to treat diseases ranging from cancer to age-related macular degeneration and antibiotic-resistant infections. This paper reviews the current status of PDT with an emphasis on the contributions of physics, biophysics and technology, and the challenges remaining in the optimization and adoption of this treatment modality. A theme of the review is the complexity of PDT dosimetry due to the dynamic nature of the three essential components-light, photosensitizer and oxygen. Considerable progress has been made in understanding the problem and in developing instruments to measure all three, so that optimization of individual PDT treatments is becoming a feasible target. The final section of the review introduces some new frontiers of research including low dose rate (metronomic) PDT, two-photon PDT, activatable PDT molecular beacons and nanoparticle-based PDT. (topical review)

  17. The physics, biophysics and technology of photodynamic therapy.

    Science.gov (United States)

    Wilson, Brian C; Patterson, Michael S

    2008-05-07

    Photodynamic therapy (PDT) uses light-activated drugs to treat diseases ranging from cancer to age-related macular degeneration and antibiotic-resistant infections. This paper reviews the current status of PDT with an emphasis on the contributions of physics, biophysics and technology, and the challenges remaining in the optimization and adoption of this treatment modality. A theme of the review is the complexity of PDT dosimetry due to the dynamic nature of the three essential components -- light, photosensitizer and oxygen. Considerable progress has been made in understanding the problem and in developing instruments to measure all three, so that optimization of individual PDT treatments is becoming a feasible target. The final section of the review introduces some new frontiers of research including low dose rate (metronomic) PDT, two-photon PDT, activatable PDT molecular beacons and nanoparticle-based PDT.

  18. The physics, biophysics and technology of photodynamic therapy

    Energy Technology Data Exchange (ETDEWEB)

    Wilson, Brian C [Division of Biophysics and Bioimaging, Ontario Cancer Institute and Department of Medical Biophysics, University of Toronto, 610 University Avenue, Toronto, ON M5G 2M9 (Canada); Patterson, Michael S [Department of Medical Physics, Juravinski Cancer Centre and Department of Medical Physics and Applied Radiation Sciences, McMaster University, 699 Concession Street, Hamilton, ON L8V 5C2 (Canada)], E-mail: wilson@uhnres.utoronto.ca, E-mail: mike.patterson@jcc.hhsc.ca

    2008-05-07

    Photodynamic therapy (PDT) uses light-activated drugs to treat diseases ranging from cancer to age-related macular degeneration and antibiotic-resistant infections. This paper reviews the current status of PDT with an emphasis on the contributions of physics, biophysics and technology, and the challenges remaining in the optimization and adoption of this treatment modality. A theme of the review is the complexity of PDT dosimetry due to the dynamic nature of the three essential components-light, photosensitizer and oxygen. Considerable progress has been made in understanding the problem and in developing instruments to measure all three, so that optimization of individual PDT treatments is becoming a feasible target. The final section of the review introduces some new frontiers of research including low dose rate (metronomic) PDT, two-photon PDT, activatable PDT molecular beacons and nanoparticle-based PDT. (topical review)

  19. ''Spinolaminar breach'': an important sign in cervical spinous process fractures

    International Nuclear Information System (INIS)

    Matar, L.D.; Helms, C.A.

    2000-01-01

    Objective. To report the sign of ''spinolaminar breach'' and its likely importance in fractures of the cervical spinous processes.Design. Six cases of spinous process fractures demonstrating disruption of the spinolaminar line or ''spinolaminar breach'' were analyzed. Lateral and anteroposterior radiographs (n=6), CT scans (n=3) and MRI scans (n=1) were reviewed together by the authors, with consensus being reached as to the radiographic findings. Clinical records were also reviewed.Results. The levels of injury were C6 (n=5) and C5 (n=2). Injuries were associated with delayed anterior subluxation (n=4) and neurological deficit (n=2). Five patients were male and one was female with a mean age of 31 years (range 8-59 years). Injuries resulted from motor vehicle accidents (n=4), a motor cycle accident (n=1) and a fall (n=1).Conclusion. ''Spinolaminar breach'', or disruption of the spinolaminar line, indicates a complex spinous process fracture with extension into the lamina and spinal canal. Spinous process fractures with spinolaminar breach may have associated posterior ligamentous injury with potential for delayed instability and neurological deficit. It is important that radiologists and physicians caring for the trauma patient be aware of this sign in order to avoid misdiagnosis as a ''clay shoveler's fracture'', which can lead to adverse outcome. (orig.)

  20. How important is vehicle safety in the new vehicle purchase process?

    Science.gov (United States)

    Koppel, Sjaanie; Charlton, Judith; Fildes, Brian; Fitzharris, Michael

    2008-05-01

    Whilst there has been a significant increase in the amount of consumer interest in the safety performance of privately owned vehicles, the role that it plays in consumers' purchase decisions is poorly understood. The aims of the current study were to determine: how important vehicle safety is in the new vehicle purchase process; what importance consumers place on safety options/features relative to other convenience and comfort features, and how consumers conceptualise vehicle safety. In addition, the study aimed to investigate the key parameters associated with ranking 'vehicle safety' as the most important consideration in the new vehicle purchase. Participants recruited in Sweden and Spain completed a questionnaire about their new vehicle purchase. The findings from the questionnaire indicated that participants ranked safety-related factors (e.g., EuroNCAP (or other) safety ratings) as more important in the new vehicle purchase process than other vehicle factors (e.g., price, reliability etc.). Similarly, participants ranked safety-related features (e.g., advanced braking systems, front passenger airbags etc.) as more important than non-safety-related features (e.g., route navigation systems, air-conditioning etc.). Consistent with previous research, most participants equated vehicle safety with the presence of specific vehicle safety features or technologies rather than vehicle crash safety/test results or crashworthiness. The key parameters associated with ranking 'vehicle safety' as the most important consideration in the new vehicle purchase were: use of EuroNCAP, gender and education level, age, drivers' concern about crash involvement, first vehicle purchase, annual driving distance, person for whom the vehicle was purchased, and traffic infringement history. The findings from this study are important for policy makers, manufacturers and other stakeholders to assist in setting priorities with regard to the promotion and publicity of vehicle safety features

  1. REMOTE-SENSING-BASED BIOPHYSICAL MODELS FOR ESTIMATING LAI OF IRRIGATED CROPS IN MURRY DARLING BASIN

    Directory of Open Access Journals (Sweden)

    I. Wittamperuma

    2012-07-01

    Full Text Available Remote sensing is a rapid and reliable method for estimating crop growth data from individual plant to crops in irrigated agriculture ecosystem. The LAI is one of the important biophysical parameter for determining vegetation health, biomass, photosynthesis and evapotranspiration (ET for the modelling of crop yield and water productivity. Ground measurement of this parameter is tedious and time-consuming due to heterogeneity across the landscape over time and space. This study deals with the development of remote-sensing based empirical relationships for the estimation of ground-based LAI (LAIG using NDVI, modelled with and without atmospheric correction models for three irrigated crops (corn, wheat and rice grown in irrigated farms within Coleambally Irrigation Area (CIA which is located in southern Murray Darling basin, NSW in Australia. Extensive ground truthing campaigns were carried out to measure crop growth and to collect field samples of LAI using LAI- 2000 Plant Canopy Analyser and reflectance using CROPSCAN Multi Spectral Radiometer at several farms within the CIA. A Set of 12 cloud free Landsat 5 TM satellite images for the period of 2010-11 were downloaded and regression analysis was carried out to analyse the co-relationships between satellite and ground measured reflectance and to check the reliability of data sets for the crops. Among all the developed regression relationships between LAI and NDVI, the atmospheric correction process has significantly improved the relationship between LAI and NDVI for Landsat 5 TM images. The regression analysis also shows strong correlations for corn and wheat but weak correlations for rice which is currently being investigated.

  2. Biophysical detector for definition of anomalies in Semipalatinsk nuclear test site zone

    International Nuclear Information System (INIS)

    Sokolovskaya, E.V.; Inyushin, V.M.; Kalieva, Zh.A.

    2000-01-01

    With help of space aero-survey of thermodynamical anomaly (increase of land surface temperature) in Semipalatinsk test site zone is revealed. It was suggested that it is a result of recombination processes of Earth's plasma due to entropy increase in result of plasma fluctuations called by underground nuclear explosions. This hypothesis was checked by means of territory scanning around Semipalatinsk test site with help of biophysical detectors representing isolate fragments of bio-plasma of animal and vegetation origin. It was revealed that there are anomalies in Almaty-Semipalatinsk cities' beam of Ayaguz-Semipalatinsk zone and on Omsk-Semipalatinsk beam on Semenovka-Semipalatinsk section. During passing of areas in close proximity to the nuclear site an increase of micro-currents amplitude in 4-5 μA as well as irregular amplitude change are registered. Although anomalies make up 10 % from geo-plasma's micro-currents initial values, and this value can exert significant influence on human plasma homeostasis for persons living in anomalous regions. It is concluded that it is necessary research of non-radiation effects nature of underground nuclear explosions and its action on biological status of men, animals, plants and soils

  3. Community Earth System Model Simulations Reveal the Relative Importance of Afforestation and Forest Management to Surface Temperature in Eastern North America

    Directory of Open Access Journals (Sweden)

    Benjamin J. Ahlswede

    2017-12-01

    Full Text Available Afforestation changes the land surface energy balance, though the effects on climate in temperate regions is uncertain, particularly the changes associated with forest management. In this study, we used idealized Community Earth System Model simulations to assess the influence of afforestation and afforestation management in eastern North America on climate via changes in the biophysics of the land surface. Afforestation using broadleaf deciduous trees maintained at high leaf area index (LAI in the southern part of the study region provided the greatest climate benefit by cooling summer surface air temperatures (Tsa. In contrast, the greatest warming occurred in the northern extent of the study region when afforesting with needleleaf evergreen trees maintained at high LAI. Forest management had an equal or greater influence on Tsa than the overall decision to afforest land in the southern extent of the region. Afforestation had a greater influence on Tsa than forest management in the northern extent. Integrating our results, focused on biophysical processes, with other research quantifying carbon cycle sensitivity to management can help guide the use of temperate afforestation to optimize climate benefits. Further, our results highlight the potential importance of including forest management in simulations of past and future climate.

  4. Biophysical analysis of water filtration phenomenon in the roots of halophytes

    Science.gov (United States)

    Kim, Kiwoong; Lee, Sang Joon

    2015-11-01

    The water management systems of plants, such as water collection and water filtration have been optimized through a long history. In this point of view, new bio-inspired technologies can be developed by mimicking the nature's strategies for the survival of the fittest. In this study, the biophysical characteristics of water filtration process in the roots of halophytes are experimentally investigated in the plant hydrodynamic point of view. To understand the functional features of the halophytes 3D morphological structure of their roots are analyzed using advanced bioimaging techniques. The surface properties of the roots of halophytes are also examined Based on the quantitatively analyzed information, water filtration phenomenon in the roots is examined. Sodium treated mangroves are soaked in sodium acting fluorescent dye solution to trace sodium ions in the roots. In addition, in vitroexperiment is carried out by using the roots. As a result, the outermost layer of the roots filters out continuously most of sodium ions. This study on developing halophytes would be helpful for understanding the water filtration mechanism of the roots of halophytes and developing a new bio inspired desalination system. This research was financially supported by the National Research Foundation (NRF) of Korea (Contract grant number: 2008-0061991).

  5. Signal processing for molecular and cellular biological physics: an emerging field.

    Science.gov (United States)

    Little, Max A; Jones, Nick S

    2013-02-13

    Recent advances in our ability to watch the molecular and cellular processes of life in action--such as atomic force microscopy, optical tweezers and Forster fluorescence resonance energy transfer--raise challenges for digital signal processing (DSP) of the resulting experimental data. This article explores the unique properties of such biophysical time series that set them apart from other signals, such as the prevalence of abrupt jumps and steps, multi-modal distributions and autocorrelated noise. It exposes the problems with classical linear DSP algorithms applied to this kind of data, and describes new nonlinear and non-Gaussian algorithms that are able to extract information that is of direct relevance to biological physicists. It is argued that these new methods applied in this context typify the nascent field of biophysical DSP. Practical experimental examples are supplied.

  6. [Correlation analysis between biochemical and biophysical markers of endothelium damage in children with diabetes type 1].

    Science.gov (United States)

    Głowińska-Olszewska, Barbara; Urban, Mirosława; Tołwińska, Joanna; Peczyńska, Jadwiga; Florys, Bozena

    2005-01-01

    Endothelial damage is one of the earliest stages in the atherosclerosis process. Adhesion molecules, secreted from dysfunctional endothelial cells are considered as early markers of atherosclerotic disease. Ultrasonographic evaluation of brachial arteries serves to detect biophysical changes in endothelial function, and evaluation of carotid arteries intima-media thickness allows to evaluate the earliest structural changes in the vessels. The aim of the study was to the evaluate levels of selected adhesion molecules (sICAM-1, sVCAM-1, sE-selectin, sP-selectin) and endothelial function with use of brachial artery dilatation study (flow mediated dilation--FMD, nitroglycerine mediated dilation--NTGMD) and IMT in carotid arteries in children and adolescents with diabetes type 1, as well as the correlation analysis between biochemical and biophysical markers of endothelial dysfunction. We studied 76 children and adolescents, with mean age--15.6+/-2.5 years, suffering from diabetes mean 7.8+/-2.8 years, mean HbA1c--8.4+/-1.5%. Control group consisted of 33 healthy children age and gender matched. Adhesion molecules levels were estimated with the use of immunoenzymatic methods (R&D Systems). Endothelial function was evaluated by study of brachial arteries dilation--FMD, NTGMD, with ultrasonographic evaluation (Hewlett Packard Sonos 4500) after Celermajer method, and IMT after Pignoli method. In the study group we found elevated levels of sICAM-1: 309.54+/-64 vs. 277.85+/-52 ng/ml in the control group (p<00.05) and elevated level of sE-selectin: 87.81+/-35 vs. 66.21+/-22 ng/ml (p<00.05). We found significantly impaired FMD in brachial arteries in the study group--7.51+/-4.52 vs. 12.61+/-4.65% (p<00.05) and significantly higher IMT value: 0.51+/-0.07 vs. 0.42+/-0.05 mm (p<00.001). Correlation analysis revealed a significant negative correlation between sE-selectin and FMD - r=-0.33 (p=0.004), and a positive correlation between E-selectin and IMT: r=0.32 (p=0.005). 1. In

  7. A new theoretical approach to analyze complex processes in cytoskeleton proteins.

    Science.gov (United States)

    Li, Xin; Kolomeisky, Anatoly B

    2014-03-20

    Cytoskeleton proteins are filament structures that support a large number of important biological processes. These dynamic biopolymers exist in nonequilibrium conditions stimulated by hydrolysis chemical reactions in their monomers. Current theoretical methods provide a comprehensive picture of biochemical and biophysical processes in cytoskeleton proteins. However, the description is only qualitative under biologically relevant conditions because utilized theoretical mean-field models neglect correlations. We develop a new theoretical method to describe dynamic processes in cytoskeleton proteins that takes into account spatial correlations in the chemical composition of these biopolymers. Our approach is based on analysis of probabilities of different clusters of subunits. It allows us to obtain exact analytical expressions for a variety of dynamic properties of cytoskeleton filaments. By comparing theoretical predictions with Monte Carlo computer simulations, it is shown that our method provides a fully quantitative description of complex dynamic phenomena in cytoskeleton proteins under all conditions.

  8. Biophysical Properties of Cultivated Pastures in the Brazilian Savanna Biome: An Analysis in the Spatial-Temporal Domains Based on Ground and Satellite Data

    Directory of Open Access Journals (Sweden)

    Fernando M. Araújo

    2013-01-01

    Full Text Available Brazil has the largest commercial beef cattle herd in the world, with cattle ranching being particularly prominent in the 200-million ha, Brazilian neotropical moist savanna biome, known as Cerrado, one of the world’s hotspots for biodiversity conservation. As decreasing productivity is a major concern affecting the Cerrado pasturelands, evaluation of pasture conditions through the determination of biophysical parameters is instrumental for more effective management practices and herd occupation strategies. Within this context, the primary goal of this study was the regional assessment of pasture biophysical properties, through the scaling of wet- and dry-season ground truth data (total biomass, green biomass, and % green cover via the combined use of high (Landsat-TM and moderate (MODIS spatial resolution vegetation index images. Based on the high correlation found between NDVI (normalized difference vegetation index and % green cover (r = 0.95, monthly MODIS-based % green cover images were derived for the 2009–2010 hydrological cycle, which were able to capture major regional patterns and differences in pasture biophysical responses, including the increasing greenness values towards the southern portions of the biome, due to both local conditions (e.g., more fertile soils and management practices. These results corroborate the development of biophysically-based landscape degradation indices, in support of improved land use governance and natural area conservation in the Cerrado.

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

    Science.gov (United States)

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

    2014-12-01

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

  10. Derivation of global vegetation biophysical parameters from EUMETSAT Polar System

    Science.gov (United States)

    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

  11. The importance of information goods abstraction levels for information commerce process models

    NARCIS (Netherlands)

    Wijnhoven, Alphonsus B.J.M.

    2002-01-01

    A process model, in the context of e-commerce, is an organized set of activities for the creation, (re-)production, trade and delivery of goods. Electronic commerce studies have created important process models for the trade of physical goods via Internet. These models are not easily suitable for

  12. The importance of understanding during the teaching process

    Directory of Open Access Journals (Sweden)

    Dubljanin Saša

    2015-01-01

    Full Text Available Learning in the teaching process often goes on without proper understanding which is one of important problems that modern didactics tries to solve. In order to direct the totality of teaching towards understanding it is necessary to answer the question what understanding is, which is why we analysed different philosophical views on the concept of understanding and stressed their semblance to pedagogic explanations. Different kinds of understanding were analyzed as well as their role and contribution in different teaching situations, especially in the context of problem solving. As an alternative to the teaching based on accumulation of knowledge the characteristics and some principles of teaching focused on understanding are described, and the need for stimulating and developing understanding as an important goal of education. The results of our research unequivocally show that learning with understanding enables students to memorize the teaching material better, as well as to understand the whole teaching subject and efficiently apply the acquired knowledge out of school, and leads to more flexible behaviour and better coping in everyday life.

  13. Effect of biophysical therapy on articular pain in a primary care setting compared to ibuprofen and placebo: a randomized controlled trial.

    Science.gov (United States)

    Foletti, A; Egan, C G; Baron, P

    2018-01-01

    Articular pain is one of the most frequent complaints practitioners face in their daily work. With an aging population, many patients have multiple comorbidities that are associated with the presence of chronic diseases, while others experience allergies, side effects or do not respond to standard medications or procedures. Therefore, there is an urgent need for new effective and safe strategies to manage articular pain, especially in its chronic manifestations. This randomized controlled trial was designed to assess the efficacy of a single therapy session using a biophysical procedure matched with a common non-steroidal anti-inflammatory drug (ibuprofen) and placebo. Biophysical therapy was performed using a Med Select 729 device. One hundred fifty patients (mean age 56±15.6 years) diagnosed with acute or chronic articular pain at different locations were randomized into 3 groups and the Numeric Pain Rating Score (NPRS) was used to measure pain at baseline, after one week, one month, and three months. While no difference in NPRS was observed at baseline among the 3 groups, a statistically significant difference was observed at all subsequent time points, respectively, after one week (p less than 0.05), one month (p less than 0.001), and three months (p less than 0.01), for both ibuprofen and biophysical groups vs placebo. Biophysical treatment of articular pain was shown to be as effective as a conventional non-steroidal anti-inflammatory treatment over a period of 3 months compared to placebo and could, therefore, represent an integrative, safe and long-lasting therapy to be considered for the management of acute and particularly chronic articular pain in current medical practice.

  14. Perspective: On the importance of hydrodynamic interactions in the subcellular dynamics of macromolecules

    Science.gov (United States)

    Skolnick, Jeffrey

    2016-09-01

    An outstanding challenge in computational biophysics is the simulation of a living cell at molecular detail. Over the past several years, using Stokesian dynamics, progress has been made in simulating coarse grained molecular models of the cytoplasm. Since macromolecules comprise 20%-40% of the volume of a cell, one would expect that steric interactions dominate macromolecular diffusion. However, the reduction in cellular diffusion rates relative to infinite dilution is due, roughly equally, to steric and hydrodynamic interactions, HI, with nonspecific attractive interactions likely playing rather a minor role. HI not only serve to slow down long time diffusion rates but also cause a considerable reduction in the magnitude of the short time diffusion coefficient relative to that at infinite dilution. More importantly, the long range contribution of the Rotne-Prager-Yamakawa diffusion tensor results in temporal and spatial correlations that persist up to microseconds and for intermolecular distances on the order of protein radii. While HI slow down the bimolecular association rate in the early stages of lipid bilayer formation, they accelerate the rate of large scale assembly of lipid aggregates. This is suggestive of an important role for HI in the self-assembly kinetics of large macromolecular complexes such as tubulin. Since HI are important, questions as to whether continuum models of HI are adequate as well as improved simulation methodologies that will make simulations of more complex cellular processes practical need to be addressed. Nevertheless, the stage is set for the molecular simulations of ever more complex subcellular processes.

  15. Evaluation of changes in skin biophysical parameters and appearance after pneumatic injections of non-cross-linked hyaluronic acid in the face.

    Science.gov (United States)

    Cheng, Hai-Yan; Chen, Yu-Xin; Wang, Mei-Fang; Zhao, Jun-Ying; Li, Lin-Feng

    2018-03-15

    Pneumatic injections of non-cross-linked hyaluronic acid are effective in skin rejuvenation, however, the associated biophysical parameters and appearance have not been evaluated. To determine the changes in skin biophysical parameters after facial pneumatic injections of non-cross-linked hyaluronic acid. Twenty-eight healthy female volunteers received pneumatic injections of non-cross-linked hyaluronic acid into the face for consecutive 5 weeks. Skin biophysical parameter assessment and clinical evaluation were performed using the CK Multi-Probe Adapter and Visia system. Five of the volunteers also underwent retroauricular skin biopsy before and after the last treatment. The skin tissues were all stained with Masson-trichrome, Verhoeff-van Gieson stain, and hematoxylin-eosin to evaluate the changes in collagen, elastic fibers, and the epidermis, before and after the last treatment. Transepidermal water loss was significantly lower in week 4 (18.46 ± 4.70 g/h/m 2 ) than at the baseline (22.03 ± 7.15 g/h/m 2 , p pores also improved significantly at week 4 (934.07 ± 458.78) compared to the baseline (1024.57 ± 415.31, p pores, and wrinkles.

  16. Importance and variability in processes relevant to environmental tritium ingestion dose models

    International Nuclear Information System (INIS)

    Raskob, W.; Barry, P.

    1997-01-01

    The Aiken List was devised in 1990 to help decide which transport processes should be investigated experimentally so as to derive the greatest improvement in performance of environmental tritium assessment models. Each process was rated high, medium and low on each of two criteria. These were ''Importance'', which rated processes by how much each contributed to ingestion doses, and ''State of Modelling'', which rated the adequacy of the knowledge base on which models were built. Ratings, though unanimous, were, nevertheless, qualitative and subjective opinions. This paper describes how we have tried to quantify the ratings. To do this, we use, as measures of ''Importance'', sensitivities of predicted ingestion doses to changes in values of parameters in mathematical descriptions of individual processes. Measures of ''ModellinStatus'' were taken from a recently completed BIOMOVS study of HTO transport model performance and based either on by how much predicted transport by individual processes differed amongst participating modellers or by the variety of different ways that modellers chose to describe individual processes. The tritium transport model UFOTRI was used, and because environmental transport of HTO varies according to the weather at and after release time, sensitivities were measured in a sample of all conditions likely to arise in central Europe. (Author)

  17. Biophysical Assessment of Single Cell Cytotoxicity: Diesel Exhaust Particle-Treated Human Aortic Endothelial Cells

    OpenAIRE

    Wu, Yangzhe; Yu, Tian; Gilbertson, Timothy A.; Zhou, Anhong; Xu, Hao; Nguyen, Kytai Truong

    2012-01-01

    Exposure to diesel exhaust particles (DEPs), a major source of traffic-related air pollution, has become a serious health concern due to its adverse influences on human health including cardiovascular and respiratory disorders. To elucidate the relationship between biophysical properties (cell topography, cytoskeleton organizations, and cell mechanics) and functions of endothelial cells exposed to DEPs, atomic force microscope (AFM) was applied to analyze the toxic effects of DEPs on a model ...

  18. Coexistence between silent and bursting states in a biophysical Hodgkin-Huxley-type of model

    DEFF Research Database (Denmark)

    Stankevich, Nataliya; Mosekilde, Erik

    2017-01-01

    in a slightly modified, biophysical model that describe the dynamics of pancreatic beta-cells. To realize this form of coexistence, we have introduced an additional voltage-dependent potassium current that is activated in the region around the original, unstable equilibrium point. It is interesting to note...... that this modification also leads the model to display a blue-sky catastrophe in the transition region between chaotic and bursting states....

  19. Importance of isotopes for understanding the sedimentation processes

    International Nuclear Information System (INIS)

    Manjunatha, B.R.

    2012-01-01

    Isotopes of either radioactive or stable depending upon radiation emitted or not respectively which have wide applications in understanding not only the history of sedimentation, but also provide information about paleoclimate. Stable isotope mass difference occurs due to changes in physicochemical conditions of the ambient environment, for instance temperature, evaporation, precipitation, redox processes, and changes in the mobility of elements during weathering processes, biological uptake, metabolism, re-mineralization of biogenic material, etc. In contrast, radionuclides emit radiation because of excess of neutrons present in the nucleus when compared to protons of an atom. The decay of radioactive isotopes is unaffected despite changes in physicochemical variations; hence, they are useful for determining ages of different types of materials on earth. The radioisotopes can be classified based on origin and half life into primordial or long-lived, cosmogenic and artificial radionuclides or fission products. In this study, the importance of 137 Cs artificial radionuclides will be highlighted to understand short-term sedimentation processes, particularly in estuaries, deltas/continental shelf of west coast of India. The distribution of 137 Cs in sediments of south-western continental margin of India indicates that coastal marginal environments are filters or sinks for fall-out radionuclides. The sparse of 137 Cs in the open continental shelf environment indicates that most of sediments are either older or sediments being diluted by components generated in the marine environment

  20. Planning for sustainable tourism in southern Pulau Banggi: an assessment of biophysical conditions and their implications for future tourism development.

    Science.gov (United States)

    Teh, Lydia; Cabanban, Annadel S

    2007-12-01

    A priori assessments of a site's biophysical and socio-economic capacity for accommodating tourism are less common than tourism impact studies. A priori evaluations can provide a contextual understanding of ecological, economic and socio-cultural forces, which shape the prospects for sustainable tourism development at the host destination, and can avert adverse impacts of tourism. We conduct an a priori assessment of the biophysical environment of Pulau Banggi, in the Malaysian state of Sabah for sustainable tourism development. We characterise baseline conditions of the island's marine biodiversity, seasonality, and infrastructure. We then evaluate how existing biophysical conditions will influence options for sustainable tourism development. In particular, we suggest conditions, if there are any, which constitute a limit to future tourism development in terms of compatibility for recreation and resilience to visitor impacts. We find that the biggest constraint is the lack of adequate water and sanitation infrastructure. Blast fishing, although occurring less than once per hour, can potentially destroy the major attraction for tourists. We conclude that while Pulau Banggi possesses natural qualities that are attractive for ecotourism, financial and institutional support must be made available to provide facilities and services that will enable local participation in environmental protection and enhance prospects for future sustainable tourism.

  1. Symposium on Biophysics and Physiology of Biological Transport

    CERN Document Server

    Capraro, V; Porter, K; Robertson, J

    1967-01-01

    The study of cell membranes began to attract increasing interest before the turn of the present century with the observations of 0 verton. Since that time many investigators have become interested in the broad problem of structure and function of the membrane and today we find ourselVes at a stage in which several branches of research, particularly physical chemistry, biochemistry, biophysics, physiology and pharmacology have come together, leading to the possibility of obtaining a better perspective of the overall problems. The purpose of this Symposium was to assemble in an orderly sequence representations of the knowledge of membranes achieved to date in the areas of the various disciplines. It was thought that to bring together many points of view on a problem should allow the conferees to see better what had been accomplished, what has been overlooked and what needs further development. It is to be hoped that efforts of this type have and will fulfill the desired purpose. This volume contains the majorit...

  2. Simulation of Tillage Systems Impact on Soil Biophysical Properties Using the SALUS Model

    Directory of Open Access Journals (Sweden)

    Luigi Sartori

    2011-02-01

    Full Text Available A sustainable land management has been defined as the management system that allows for production, while minimizing risk, maintaining quality of soil and water. Tillage systems can significantly decrease soil carbon storage and influence the soil environment of a crop. Crop growth models can be useful tools in evaluating the impact of different tillage systems on soil biophysical properties and on the growth and final yield of the crops. The objectives of this paper were i to illustrate the SALUS model and its tillage component; ii to evaluate the effects of different tillage systems on water infiltration and time to ponding, iii to simulate the effect of tillage systems on some soil biophysical properties. The SALUS (System Approach to Land Use Sustainability model is designed to simulate continuous crop, soil, water and nutrient conditions under different tillage and crop residues management strategies for multiple years. Predictions of changes in surface residue, bulk density, runoff, drainage and evaporation were consistent with expected behaviours of these parameters as described in the literature. The experiment to estimate the time to ponding curve under different tillage system confirmed the theory and showed the beneficial effects of the residue on soil surface with respect to water infiltration. It also showed that the no-tillage system is a more appropriate system to adopt in areas characterized by high intensity rainfall.

  3. Simulation of Tillage Systems Impact on Soil Biophysical Properties Using the SALUS Model

    Directory of Open Access Journals (Sweden)

    Bruno Basso

    2006-12-01

    Full Text Available A sustainable land management has been defined as the management system that allows for production, while minimizing risk, maintaining quality of soil and water. Tillage systems can significantly decrease soil carbon storage and influence the soil environment of a crop. Crop growth models can be useful tools in evaluating the impact of different tillage systems on soil biophysical properties and on the growth and final yield of the crops. The objectives of this paper were i to illustrate the SALUS model and its tillage component; ii to evaluate the effects of different tillage systems on water infiltration and time to ponding, iii to simulate the effect of tillage systems on some soil biophysical properties. The SALUS (System Approach to Land Use Sustainability model is designed to simulate continuous crop, soil, water and nutrient conditions under different tillage and crop residues management strategies for multiple years. Predictions of changes in surface residue, bulk density, runoff, drainage and evaporation were consistent with expected behaviours of these parameters as described in the literature. The experiment to estimate the time to ponding curve under different tillage system confirmed the theory and showed the beneficial effects of the residue on soil surface with respect to water infiltration. It also showed that the no-tillage system is a more appropriate system to adopt in areas characterized by high intensity rainfall.

  4. Micro-morphologic changes around biophysically-stimulated titanium implants in ovariectomized rats

    Directory of Open Access Journals (Sweden)

    Chang Ting-Ling

    2007-07-01

    Full Text Available Abstract Background Osteoporosis may present a risk factor in achievement of osseointegration because of its impact on bone remodeling properties of skeletal phsiology. The purpose of this study was to evaluate micro-morphological changes in bone around titanium implants exposed to mechanical and electrical-energy in osteoporotic rats. Methods Fifteen 12-week old sprague-dowley rats were ovariectomized to develop osteoporosis. After 8 weeks of healing period, two titanium implants were bilaterally placed in the proximal metaphyses of tibia. The animals were randomly divided into a control group and biophysically-stimulated two test groups with five animals in each group. In the first test group, a pulsed electromagnetic field (PEMF stimulation was administrated at a 0.2 mT 4 h/day, whereas the second group received low-magnitude high-frequency mechanical vibration (MECHVIB at 50 Hz 14 min/day. Following completion of two week treatment period, all animals were sacrificed. Bone sites including implants were sectioned, removed en bloc and analyzed using a microCT unit. Relative bone volume and bone micro-structural parameters were evaluated for 144 μm wide peri-implant volume of interest (VOI. Results Mean relative bone volume in the peri-implant VOI around implants PEMF and MECHVIB was significantly higher than of those in control (P P > .05 while the difference in trabecular-number among test and control groups was significant in all VOIs (P Conclusion Biophysical stimulation remarkably enhances bone volume around titanium implants placed in osteoporotic rats. Low-magnitude high-frequency MECHVIB is more effective than PEMF on bone healing in terms of relative bone volume.

  5. New generation non-stationary portable neutron generators for biophysical applications of Neutron Activation Analysis.

    Science.gov (United States)

    Marchese, N; Cannuli, A; Caccamo, M T; Pace, C

    2017-01-01

    Neutron sources are increasingly employed in a wide range of research fields. For some specific purposes an alternative to existing large-scale neutron scattering facilities, can be offered by the new generation of portable neutron devices. This review reports an overview for such recently available neutron generators mainly addressed to biophysics applications with specific reference to portable non-stationary neutron generators applied in Neutron Activation Analysis (NAA). The review reports a description of a typical portable neutron generator set-up addressed to biophysics applications. New generation portable neutron devices, for some specific applications, can constitute an alternative to existing large-scale neutron scattering facilities. Deuterium-Deuterium pulsed neutron sources able to generate 2.5MeV neutrons, with a neutron yield of 1.0×10 6 n/s, a pulse rate of 250Hz to 20kHz and a duty factor varying from 5% to 100%, when combined with solid-state photon detectors, show that this kind of compact devices allow rapid and user-friendly elemental analysis. "This article is part of a Special Issue entitled "Science for Life" Guest Editor: Dr. Austen Angell, Dr. Salvatore Magazù and Dr. Federica Migliardo". Copyright © 2016 Elsevier B.V. All rights reserved.

  6. Biophysical characterization data on Aβ soluble oligomers produced through a method enabling prolonged oligomer stability and biological buffer conditions

    Directory of Open Access Journals (Sweden)

    Amanda C. Crisostomo

    2015-09-01

    Aβ1-40 soluble oligomers are produced that are suitable for biophysical studies requiring sufficient transient stability to exist in their “native” conformation in biological phosphate-saline buffers for extended periods of time. The production involves an initial preparation of highly monomeric Aβ in a phosphate saline buffer that transitions to fibrils and oligomers through time incubation alone, without added detergents or non-aqueous chemicals. This criteria ensures that the only difference between initial monomeric Aβ reactant and subsequent Aβ oligomer products is their degree of peptide assembly. A number of chemical and biophysical methods were used to characterize the monomeric reactants and soluble oligomer and amyloid fibril products, including chemical cross-linking, Western blots, fraction solubility, thioflvain T binding, size exclusion chromatography, transmission electron micrscopy, circular dichroism spectroscopy, and fluorescence resonance energy transfer.

  7. Simulated Local and Remote Biophysical Effects of Afforestation over the Southeast United States in Boreal Summer

    Science.gov (United States)

    Guang-Shan Chen; Michael Notaro; Zhengyu Liu; Yongqiang Liu

    2012-01-01

    Afforestation has been proposed as a climate change mitigation strategy by sequestrating atmospheric carbon dioxide. With the goal of increasing carbon sequestration, a Congressional project has been planned to afforest about 18 million acres by 2020 in the Southeast United States (SEUS), the Great Lake states, and the Corn Belt states. However, biophysical feedbacks...

  8. Biophysical characterisation of GlycoPEGylated recombinant human factor VIIa

    DEFF Research Database (Denmark)

    Plesner, Bitten; Westh, Peter; Nielsen, Anders D.

    2011-01-01

    The effects of GlycoPEGylation on the structural, kinetic and thermal stability of recombinant human FVIIa were investigated using rFVIIa and linear 10 kDa and branched 40 kDa GlycoPEGylated® recombinant human FVIIa derivatives. The secondary and tertiary structure of rFVIIa measured by circular...... dichroism (CD) was maintained upon PEGylation. In contrast, the thermal and kinetic stability of rFVIIa was affected by GlycoPEGylation, as the apparent unfolding temperature Tm measured by differential scanning calorimetry (DSC) and the temperature of aggregation, Tagg, measured by light scattering (LS......) both increased with GlycoPEGylation. Both Tm and Tagg were independent of the molecular weight and the shape of the PEG chain. From the present biophysical characterisation it is concluded that after GlycoPEGylation, rFVIIa appears to be unaffected structurally (secondary and tertiary structure...

  9. PGAA method for control of the technologically important elements at processing of sulfide ores

    International Nuclear Information System (INIS)

    Kurbanov, B.I.; Aripov, G.A.; Allamuratova, G.; Umaraliev, M.

    2006-01-01

    Full text: Many precious elements (Au, Re, Pt, Pd, Ag, Cu, Ni, Co, Mo) in ores mainly exist in the form of sulfide minerals and the flotation method is often used for processing of such kind of ores. To enhance the efficiency of the process it is very important to carry out the operative control of the elements of interest at various stages of ore processing. In this work the results of studies for developing methods for control of technologically important elements at processing and enrichment sulfide ores, which content the gold, copper, nickel, molybdenum in the ore-processing plants of Uzbekistan. The design of transportable experimental PGAA device on the basis of low-power radionuclide neutron source ( 252 Cf) with neutrons of 2x10 7 neutr/sec allowing to determine element content of the above named ores and their processing products is offered. It is shown that the use of the thermal neutron capture gamma-ray spectrometry in real samples and technological products allows prompt determination of such elements as S, Cu, Ti and others, which are important for flotation of sulfide ores. Efficiency control of the flotation processing of sulfide ores is based on quick determination of the content of sulfur and some other important elements at different stages of the process. It was found that to determine elements the following gamma lines are the most suitable - 840.3 keV for sulfur, 609 keV and 7307 keV for copper and 1381.5 keV, 1498.3 keV and 1585.3 keV for titanium. Based on the measurements of original ores, concentrates of various stages of flotation and flotation slime the possibility for prompt determination of S, Cu and Ti content and thus to get necessary information on the efficiency of the flotation process was shown. (author)

  10. Emergy analysis of a farm biogas project in China: A biophysical perspective of agricultural ecological engineering

    Science.gov (United States)

    Zhou, S. Y.; Zhang, B.; Cai, Z. F.

    2010-05-01

    This paper aims to present a biophysical understanding of the agricultural ecological engineering by emergy analysis for a farm biogas project in China as a representative case. Accounting for the resource inputs into and accumulation within the project, as well as the outputs to the social system, emergy analysis provides an empirical study in the biophysical dimension of the agricultural ecological engineering. Economic benefits and ecological economic benefits of the farm biogas project indicated by market value and emergy monetary value are discussed, respectively. Relative emergy-based indices such as renewability (R%), emergy yield ratio (EYR), environmental load ratio (ELR) and environmental sustainability index (ESI) are calculated to evaluate the environmental load and local sustainability of the concerned biogas project. The results show that the farm biogas project has more reliance on the local renewable resources input, less environmental pressure and higher sustainability compared with other typical agricultural systems. In addition, holistic evaluation and its policy implications for better operation and management of the biogas project are presented.

  11. How radiation influences atherosclerotic plaque development. A biophysical approach in ApoE{sup -/-} mice

    Energy Technology Data Exchange (ETDEWEB)

    Kloosterman, Astrid; Dillen, Teun van; Dekkers, Fieke [National Institute for Public Health and the Environment (RIVM), Centre for Environmental Safety and Security, Bilthoven (Netherlands); Bijwaard, Harmen [National Institute for Public Health and the Environment (RIVM), Centre for Environmental Safety and Security, Bilthoven (Netherlands); Inholland University of Applied Sciences, Medical Technology Research Group, Haarlem (Netherlands); Heeneman, Sylvia [Maastricht University Medical Center, Experimental Vascular Pathology group, Department of Pathology, Cardiovascular Research Institute Maastricht (CARIM), Maastricht (Netherlands); Hoving, Saske; Stewart, Fiona A. [Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Division of Biological Stress Response (H3), Amsterdam (Netherlands)

    2017-11-15

    Atherosclerosis is the development of lipid-laden plaques in arteries and is nowadays considered as an inflammatory disease. It has been shown that high doses of ionizing radiation, as used in radiotherapy, can increase the risk of development or progression of atherosclerosis. To elucidate the effects of radiation on atherosclerosis, we propose a mathematical model to describe radiation-promoted plaque development. This model distinguishes itself from other models by combining plaque initiation and plaque growth, and by incorporating information from biological experiments. It is based on two consecutive processes: a probabilistic dose-dependent plaque initiation process, followed by deterministic plaque growth. As a proof of principle, experimental plaque size data from carotid arteries from irradiated ApoE{sup -/-} mice was used to illustrate how this model can provide insight into the underlying biological processes. This analysis supports the promoting role for radiation in plaque initiation, but the model can easily be extended to include dose-related effects on plaque growth if available experimental data would point in that direction. Moreover, the model could assist in designing future biological experiments on this research topic. Additional biological data such as plaque size data from chronically-irradiated mice or experimental data sets with a larger variety in biological parameters can help to further unravel the influence of radiation on plaque development. To the authors' knowledge, this is the first biophysical model that combines probabilistic and mechanistic modeling which uses experimental data to investigate the influence of radiation on plaque development. (orig.)

  12. A biophysical analysis of mitochondrial movement: differences between transport in neuronal cell bodies versus processes.

    Science.gov (United States)

    Narayanareddy, Babu Reddy Janakaloti; Vartiainen, Suvi; Hariri, Neema; O'Dowd, Diane K; Gross, Steven P

    2014-07-01

    There is an increasing interest in factors that can impede cargo transport by molecular motors inside the cell. Although potentially relevant (Yi JY, Ori-McKenney KM, McKenney RJ, Vershinin M, Gross SP, Vallee RB. High-resolution imaging reveals indirect coordination of opposite motors and a role for LIS1 in high-load axonal transport. J Cell Biol 2011;195:193-201), the importance of cargo size and subcellular location has received relatively little attention. Here we address these questions taking advantage of the fact that mitochondria - a common cargo - in Drosophila neurons exhibit a wide distribution of sizes. In addition, the mitochondria can be genetically marked with green fluorescent protein (GFP) making it possible to visualize and compare their movement in the cell bodies and in the processes of living cells. Using total internal reflection microscopy coupled with particle tracking and analysis, we quantified the transport properties of GFP-positive mitochondria as a function of their size and location. In neuronal cell bodies, we find little evidence for significant opposition to motion, consistent with a previous study on lipid droplets (Shubeita GT, Tran SL, Xu J, Vershinin M, Cermelli S, Cotton SL, Welte MA, Gross SP. Consequences of motor copy number on the intracellular transport of kinesin-1-driven lipid droplets. Cell 2008;135:1098-1107). However, in the processes, we observe an inverse relationship between the mitochondrial size and velocity and the run distances. This can be ameliorated via hypotonic treatment to increase process size, suggesting that motor-mediated movement is impeded in this more-confined environment. Interestingly, we also observe local mitochondrial accumulations in processes but not in cell bodies. Such accumulations do not completely block the transport but do increase the probability of mitochondria-mitochondria interactions. They are thus particularly interesting in relation to mitochondrial exchange of elements.

  13. Adjusting policy to institutional, cultural and biophysical context conditions: The case of conservation banking in California

    Science.gov (United States)

    Carsten Mann; James D. Absher

    2013-01-01

    This paper examines the political construction of a policy instrument for matching particular institutional, biophysical and cultural context conditions in a social–ecological system, using the case of conservation banking in California as an example. The guiding research question is: How is policy design negotiated between various actors on its way from early...

  14. ON THE ISSUE OF IMPORT SUBSTITUTION OF DEEP PROCESSING PRODUCTS FROM GRAIN AND POTATO

    Directory of Open Access Journals (Sweden)

    N. R. Andreev

    2014-01-01

    Full Text Available Summary. The analysis of structure of starch containing raw materials processing in Russia Federation is provided in the article. There was noted an increase in volumes of corn and wheat processing, however the share of processed potato is still low (below 4%. It was established that Russian starch products and starch sweeteners are on the same level on quality as best European samples and they are very competitive. Market demand in crystalline glucose for food and medical purposes (over 30 thous. tons is fully covered by import. The volume of import of modified starches exceeds 80 % of total consumption. The biggest volume of import among native starches belongs to potato starch – over 60 %. The article provides suggestions on import substitution of mentioned starch products. The growth of starch production in Russia was accompanied by concentration of production at large enterprises. So, in 2013 over 90 % of glucose syrup was produced at six enterprises, over 80 % of dry starch – at five enterprises. Efficiency of corn and wheat processing into starch and starch products is achieved by production and selling of co-products (dry gluten, gluten, corn germ or corn oil, corn extract, feed products.Development of starch sweeteners production from starch could be achieved by expanding the consumption areas of different kinds of glucose syrup and production of glucose-fructose syrups as full substitute of sugar, providing import substitution of sugar, crystalline glucose of food and medicine purpose, deep processing of glucose into polyols (sorbit, maltit, polylactites, aminoacids.

  15. Fab-based bispecific antibody formats with robust biophysical properties and biological activity.

    Science.gov (United States)

    Wu, Xiufeng; Sereno, Arlene J; Huang, Flora; Lewis, Steven M; Lieu, Ricky L; Weldon, Caroline; Torres, Carina; Fine, Cody; Batt, Micheal A; Fitchett, Jonathan R; Glasebrook, Andrew L; Kuhlman, Brian; Demarest, Stephen J

    2015-01-01

    A myriad of innovative bispecific antibody (BsAb) platforms have been reported. Most require significant protein engineering to be viable from a development and manufacturing perspective. Single-chain variable fragments (scFvs) and diabodies that consist only of antibody variable domains have been used as building blocks for making BsAbs for decades. The drawback with Fv-only moieties is that they lack the native-like interactions with CH1/CL domains that make antibody Fab regions stable and soluble. Here, we utilize a redesigned Fab interface to explore 2 novel Fab-based BsAbs platforms. The redesigned Fab interface designs limit heavy and light chain mixing when 2 Fabs are co-expressed simultaneously, thus allowing the use of 2 different Fabs within a BsAb construct without the requirement of one or more scFvs. We describe the stability and activity of a HER2×HER2 IgG-Fab BsAb, and compare its biophysical and activity properties with those of an IgG-scFv that utilizes the variable domains of the same parental antibodies. We also generated an EGFR × CD3 tandem Fab protein with a similar format to a tandem scFv (otherwise known as a bispecific T cell engager or BiTE). We show that the Fab-based BsAbs have superior biophysical properties compared to the scFv-based BsAbs. Additionally, the Fab-based BsAbs do not simply recapitulate the activity of their scFv counterparts, but are shown to possess unique biological activity.

  16. Contribution to researches in biophysics and biology

    International Nuclear Information System (INIS)

    Luccioni, Catherine

    2000-01-01

    In this accreditation to supervise research, the author indicates its curriculum and scientific works which mainly dealt with the different agents used in chemotherapy. Scientific works addressed anti-carcinogenic pharmacology, applied biophysics, and researches in oncology and radiobiology. Current research projects deal with mechanisms of cellular transformation and the implication of the anti-oxidising metabolism and of nucleotide metabolism in cell radio-sensitivity. Teaching and research supervising activities are also indicated. Several articles are proposed in appendix: Average quality factor and dose equivalent meter based on microdosimetry techniques; Activity of thymidylate synthetase, thymidine kinase and galactokinase in primary and xenografted human colorectal cancers in relation to their chromosomal patterns; Nucleotide metabolism in human gliomas, relation to the chromosomal profile; Pyrimidine nucleotide metabolism in human colon carcinomas: comparison of normal tissues, primary tumors and xenografts; Modifications of the antioxidant metabolism during proliferation and differentiation of colon tumours cell lines; Modulation of the antioxidant enzymes, p21 and p53 expression during proliferation and differentiation of human melanoma cell lines; Purine metabolism in 2 human melanoma cell lines, relation with proliferation and differentiation; Radiation-induced changes in nucleotide metabolism of 2 colon cancer cell lines with different radio-sensitivities

  17. High-field 1H NMR microscopy for fundamental biophysical research

    International Nuclear Information System (INIS)

    Haddad, D.

    2003-01-01

    This work has a biophysical background and uses different examples to demonstrate the practical applicability of NMR-Microscopy in the medical and biological sector. Therefore, the different projects are feasibility studies which are used to compare the possibilities and advantages of NMR-Microscopy with other, established examination techniques. In detail, using MR-Microscopy, different living and fixed biological samples have been visualized non-invasively with high spatial resolution. The specific purpose of the studies ranged from the visualization of the invasion of tumor-spheroids into cell aggregates using T2 parameter maps (time constant of the spin-spin relaxation) to the three-dimensional display of the honey bee brain in the intact head capsule and the non-invasive visualization of the anatomy of prenatal dolphins. For all these projects, the non-invasive character of MR-experiments was of utmost importance. The tumor invasion was not to be disturbed by the measurements, the bee brain should be visualized as close to its true natural shape as possible and the examined dolphins represent rare museum specimens which should not be destroyed. The different samples were all imaged with the best possible spatial resolution which was either limited by the necessary signal-to-noise ratio (SNR) or the available scan time. In order to resolve single details and fine structures in the images, it was necessary to optimize the SNR as well as the contrast-to-noise ratio. To guarantee the necessary SNR, the measurements were performed on high field MR-spectrometers with resonance frequencies of 500 and 750 MHz

  18. Biophysical controls on soil respiration in the dominant patch types of an old-growth, mixed-conifer forest

    Science.gov (United States)

    Siyan Ma; Jiquan Chen; John R. Butnor; Malcolm North; Eugénie S. Euskirchen; Brian Oakley

    2005-01-01

    Little is known about biophysical controls on soil respiration in California's Sierra Nevada old-growth, mixed-conifer forests. Using portable and automated soil respiration sampling units, we measured soil respiration rate (SRR) in three dominant patch types: closed canopy (CC), ceanothus-dominated patches (CECO), and open canopy (OC). SRR varied significantly...

  19. Assessing the Importance of Treatment Goals in Patients with Psoriasis: Analytic Hierarchy Process vs. Likert Scales.

    Science.gov (United States)

    Gutknecht, Mandy; Danner, Marion; Schaarschmidt, Marthe-Lisa; Gross, Christian; Augustin, Matthias

    2018-02-15

    To define treatment benefit, the Patient Benefit Index contains a weighting of patient-relevant treatment goals using the Patient Needs Questionnaire, which includes a 5-point Likert scale ranging from 0 ("not important at all") to 4 ("very important"). These treatment goals have been assigned to five health dimensions. The importance of each dimension can be derived by averaging the importance ratings on the Likert scales of associated treatment goals. As the use of a Likert scale does not allow for a relative assessment of importance, the objective of this study was to estimate relative importance weights for health dimensions and associated treatment goals in patients with psoriasis by using the analytic hierarchy process and to compare these weights with the weights resulting from the Patient Needs Questionnaire. Furthermore, patients' judgments on the difficulty of the methods were investigated. Dimensions of the Patient Benefit Index and their treatment goals were mapped into a hierarchy of criteria and sub-criteria to develop the analytic hierarchy process questionnaire. Adult patients with psoriasis starting a new anti-psoriatic therapy in the outpatient clinic of the Institute for Health Services Research in Dermatology and Nursing at the University Medical Center Hamburg (Germany) were recruited and completed both methods (analytic hierarchy process, Patient Needs Questionnaire). Ratings of treatment goals on the Likert scales (Patient Needs Questionnaire) were summarized within each dimension to assess the importance of the respective health dimension/criterion. Following the analytic hierarchy process approach, consistency in judgments was assessed using a standardized measurement (consistency ratio). At the analytic hierarchy process level of criteria, 78 of 140 patients achieved the accepted consistency. Using the analytic hierarchy process, the dimension "improvement of physical functioning" was most important, followed by "improvement of social

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

    Science.gov (United States)

    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.

  1. 7 CFR 319.56-11 - Importation of dried, cured, or processed fruits, vegetables, nuts, and legumes.

    Science.gov (United States)

    2010-01-01

    ... QUARANTINE NOTICES Fruits and Vegetables § 319.56-11 Importation of dried, cured, or processed fruits, vegetables, nuts, and legumes. (a) Dried, cured, or processed fruits and vegetables (except frozen fruits and... 7 Agriculture 5 2010-01-01 2010-01-01 false Importation of dried, cured, or processed fruits...

  2. Combining Biophysical and Price Simulations to Assess the Economics of Long-Term Crop Rotations

    OpenAIRE

    Murray-Prior, Roy B.; Whish, J.; Carberry, Peter S.; Dalgleish, N.

    2003-01-01

    Biophysical simulation models (e.g. APSIM) using historical rainfall data are increasingly being used to provide yield and other data on crop rotations in various regions of Australia. However, to analyse the economics of these rotations it is desirable to incorporate the other main driver of profitability, price variation. Because the context was that APSIM was being used to simulate an existing trial site being monitored by a farmer group Gross Margin output was considered most appropriate....

  3. Improving the spatial representation of soil properties and hydrology using topographically derived initialization processes in the SWAT model

    Science.gov (United States)

    Topography exerts critical controls on many hydrologic, geomorphologic, and environmental biophysical processes. Unfortunately many watershed modeling systems use topography only to define basin boundaries and stream channels and do not explicitly account for the topographic controls on processes su...

  4. EFFECTS OF ACOUSTIC STIMULATION ON BIOPHYSICAL PROFILE TESTING TIME

    Directory of Open Access Journals (Sweden)

    M. Pourissa

    2008-04-01

    Full Text Available Biophysical profile (BPP test is the most commonly used antenatal test of fetal well-being. Purpose of this study is determining the influence of acoustic stimulation (AS on BPP testing time. About 55 pregnant women at 35 to 42 weeks who referred to department of Obstetric & Gynecology at university of medical sciences, Tabriz, Iran, were selected randomly. We used abdominal ultrasound guidance to place buzzer like device with power of 110 dB at the skin surface of the maternal abdomen, close to the fetal head. BPP test performed and BPP mean testing time calculated before and after AS. Data compared and analyzed by paired t-test. The results showed that fetal AS reduces the overall mean testing time from 24 minutes to 5 minutes. This clinical application can be helpful in busy clinics when rapid assessment of fetal health is required.

  5. Apocynin: Chemical and Biophysical Properties of a NADPH Oxidase Inhibitor

    Directory of Open Access Journals (Sweden)

    Valdecir F. Ximenes

    2013-03-01

    Full Text Available Apocynin is the most employed inhibitor of NADPH oxidase (NOX, a multienzymatic complex capable of catalyzing the one-electron reduction of molecular oxygen to the superoxide anion. Despite controversies about its selectivity, apocynin has been used as one of the most promising drugs in experimental models of inflammatory and neurodegenerative diseases. Here, we aimed to study the chemical and biophysical properties of apocynin. The oxidation potential was determined by cyclic voltammetry (Epa = 0.76V, the hydrophobicity index was calculated (logP = 0.83 and the molar absorption coefficient was determined (e275nm = 1.1 × 104 M−1 cm−1. Apocynin was a weak free radical scavenger (as measured using the DPPH, peroxyl radical and nitric oxide assays when compared to protocatechuic acid, used here as a reference antioxidant. On the other hand, apocynin was more effective than protocatechuic acid as scavenger of the non-radical species hypochlorous acid. Apocynin reacted promptly with the non-radical reactive species H2O2 only in the presence of peroxidase. This finding is relevant, since it represents a new pathway for depleting H2O2 in cellular experimental models, besides the direct inhibition of NADPH oxidase. This could be relevant for its application as an inhibitor of NOX4, since this isoform produces H2O2 and not superoxide anion. The binding parameters calculated by fluorescence quenching showed that apocynin binds to human serum albumin (HSA with a binding affinity of 2.19 × 104 M−1. The association did not alter the secondary and tertiary structure of HSA, as verified by synchronous fluorescence and circular dichroism. The displacement of fluorescent probes suggested that apocynin binds to site I and site II of HSA. Considering the current biomedical applications of this phytochemical, the dissemination of these chemical and biophysical properties can be very helpful for scientists and physicians interested in the use of apocynin.

  6. Distribution and biophysical processes of beaded streams in Arctic permafrost landscapes

    Science.gov (United States)

    Arp, Christopher D.; Whitman, Matthew S.; Jones, Benjamin M.; Grosse, Guido; Gaglioti, Benjamin V.; Heim, Kurt C.

    2015-01-01

    Beaded streams are widespread in permafrost regions and are considered a common thermokarst landform. However, little is known about their distribution, how and under what conditions they form, and how their intriguing morphology translates to ecosystem functions and habitat. Here we report on a Circum-Arctic survey of beaded streams and a watershed-scale analysis in northern Alaska using remote sensing and field studies. We mapped over 400 channel networks with beaded morphology throughout the continuous permafrost zone of northern Alaska, Canada, and Russia and found the highest abundance associated with medium- to high- ground ice content permafrost in moderately sloping terrain. In the Fish Creek watershed, beaded streams accounted for half of the drainage density, occurring primarily as low-order channels initiating from lakes and drained lake basins. Beaded streams predictably transition to alluvial channels with increasing drainage area and decreasing channel slope, although this transition is modified by local controls on water and sediment delivery. Comparison of one beaded channel using repeat photography between 1948 and 2013 indicate a relatively stable landform and 14C dating of basal sediments suggest channel formation may be as early as the Pleistocene-Holocene transition. Contemporary processes, such as deep snow accumulation in riparian zones effectively insulates channel ice and allows for perennial liquid water below most beaded stream pools. Because of this, mean annual temperatures in pool beds are greater than 2°C, leading to the development of perennial thaw bulbs or taliks underlying these thermokarst features. In the summer, some pools thermally stratify, which reduces permafrost thaw and maintains coldwater habitats. Snowmelt generated peak-flows decrease rapidly by two or more orders of magnitude to summer low flows with slow reach-scale velocity distributions ranging from 0.1 to 0.01 m/s, yet channel runs still move water rapidly

  7. Copper complexes containing thiosemicarbazones derived from 6-nitropiperonal: Antimicrobial and biophysical properties

    Science.gov (United States)

    Beckford, Floyd A.; Webb, Kelsey R.

    2017-08-01

    A series of four thiosemicarbazones from 6-nitropiperonal along with the corresponding copper complexes were synthesized. The biophysical characteristics of the complexes were investigated by the binding to DNA and human serum albumin. The binding to DNA is moderate; the binding constants run from (0.49-7.50) × 104 M- 1. In relation to HSA, the complexes interact strongly with binding constants on the order of 105 M- 1. The complexes also display antioxidant behavior as determined by the ability to scavenge diphenylpicrylhydrazyl (dpph) and nitric oxide radicals. The antimicrobial profiles of the compounds, tested against a panel of microbes including five of the ESKAPE pathogens (Staphylococcus aureus, MRSA, Escherichia coli, Klebsiella pneumoniae, MDR, Acinetobacter baumannii, Pseudomonas aeruginosa) and two yeasts (Candida albicans and Cryptococcus neoformans var. grubii), are also described. The compounds contain a core moiety that is similar to oxolinic acid, a quinolone antibiotic that targets DNA gyrase and topoisomerase (IV). The binding interaction between the complexes and these important antibacterial targets were studied by computational methods, chiefly docking studies. The calculated dissociation constants for the interaction with DNA gyrase B (from Staphylococcus aureus) range from 4.32 to 24.65 μM; the binding was much stronger to topoisomerase IV, with dissociation constants ranging from 0.37 to 1.27 μM.

  8. Insulin amyloid fibrillation studied by terahertz spectroscopy and other biophysical methods

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Rui [State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072 (China); He, Mingxia [College of Precision Instrument and Optoelectronics Engineering, Tianjin University, Tianjin 300072 (China); Su, Rongxin, E-mail: surx@tju.edu.cn [State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072 (China); Tianjin Key Laboratory of Membrane Science and Desalination Technology, Tianjin University, Tianjin 300072 (China); Yu, Yanjun [State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072 (China); Qi, Wei; He, Zhimin [State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072 (China); Tianjin Key Laboratory of Membrane Science and Desalination Technology, Tianjin University, Tianjin 300072 (China)

    2010-01-01

    Assembly and fibrillation of amyloid proteins are believed to play a key role in the etiology of various human diseases, including Alzheimer's, Parkinson's, Huntington's and type II diabetes. Insights into conformational changes and formation processes during amyloid fibrillation are essential for the clinical diagnosis and drug discovery. To study the changes in secondary, tertiary, quaternary structures, and the alteration in the collective vibrational mode density of states during the amyloid fibrillation, bovine insulin in 20% acetic acid was incubated at 60 {sup o}C, and its multi-level structures were followed by various biophysical techniques, including circular dichroism (CD), thioflavin T fluorescence (ThT), dynamic light scattering (DLS), electron microscopy, and terahertz (THz) absorption spectroscopy. The experimental data demonstrated a transformation of {alpha}-helix into {beta}-sheet starting at 26 h. This was followed by the aggregation of insulin, as shown by ThT binding, with a transition midpoint at 41 h, and by the bulk formation of mature aggregates after about 71 h. THz is a quick and non-invasive technique, which has the advantage of allowing the study of the conformational state of biomolecules and tissues. We first applied THz spectroscopy to study the amyloid fibrillation. At the terahertz frequency range of 0.2-2.0 THz, there was an apparent increase in both the absorbance and refractive index in THz spectra. Thus, THz is expected to provide a new way of looking into amyloid fibrillation.

  9. The importance of sensory integration processes for action cascading

    Science.gov (United States)

    Gohil, Krutika; Stock, Ann-Kathrin; Beste, Christian

    2015-01-01

    Dual tasking or action cascading is essential in everyday life and often investigated using tasks presenting stimuli in different sensory modalities. Findings obtained with multimodal tasks are often broadly generalized, but until today, it has remained unclear whether multimodal integration affects performance in action cascading or the underlying neurophysiology. To bridge this gap, we asked healthy young adults to complete a stop-change paradigm which presented different stimuli in either one or two modalities while recording behavioral and neurophysiological data. Bimodal stimulus presentation prolonged response times and affected bottom-up and top-down guided attentional processes as reflected by the P1 and N1, respectively. However, the most important effect was the modulation of response selection processes reflected by the P3 suggesting that a potentially different way of forming task goals operates during action cascading in bimodal vs. unimodal tasks. When two modalities are involved, separate task goals need to be formed while a conjoint task goal may be generated when all stimuli are presented in the same modality. On a systems level, these processes seem to be related to the modulation of activity in fronto-polar regions (BA10) as well as Broca's area (BA44). PMID:25820681

  10. The importance of ethics in the process of education in today globalised society

    Directory of Open Access Journals (Sweden)

    Josefová Alena

    2016-01-01

    Full Text Available The events of the recent past show fluctuating structure of today world which is characterized on one hand as multicultural cooperation of people from various cultures and ethnic groups, and on the other hand seen with many conflicts and misunderstandings. Therefore ethical behavior becomes more important, which creates our humanity. The paper focuses on the importance of ethics in the process of education in today globalized world with the aim of leading the students to multicultural perception of the society and the world. To understand the world in European and globalized consequences will lead to reduction or eradication of religious intolerance. The paper describes the changes in education system in the Czech Republic in the past years and focuses on the importance of ethics in the process during primary, secondary and university education.

  11. From dating to biophysics -- 20 years of progress in applied ESR spectroscopy

    International Nuclear Information System (INIS)

    Regulla, Dieter

    2000-01-01

    ESR spectroscopy represents a tool for quantitative radiation analysis that was developed somehow simultaneously for dating purposes in Japan and in Germany for high-level standardization, in the mid-seventies. Meanwhile, ESR dosimetry has reached an established metrology level. Present research fields of ESR dosimetry consider post-accident dose reconstruction in the environment, and biophysical dosimetry using human tissues. The latter promises a re-definition of radiation risk for chronicle exposure to be derived from individuals of the early nuclear facilities in Russia, and hopefully United States in the future. An attempt is made to sketch development and potential future of the ESR technique

  12. How important is vehicle safety for older consumers in the vehicle purchase process?

    Science.gov (United States)

    Koppel, Sjaan; Clark, Belinda; Hoareau, Effie; Charlton, Judith L; Newstead, Stuart V

    2013-01-01

    This study aimed to investigate the importance of vehicle safety to older consumers in the vehicle purchase process. Older (n = 102), middle-aged (n = 791), and younger (n = 109) participants throughout the eastern Australian states of Victoria, New South Wales, and Queensland who had recently purchased a new or used vehicle completed an online questionnaire about their vehicle purchase process. When asked to list the 3 most important considerations in the vehicle purchase process (in an open-ended format), older consumers were mostly likely to list price as their most important consideration (43%). Similarly, when presented with a list of vehicle factors (such as price, design, Australasian New Car Assessment Program [ANCAP] rating), older consumers were most likely to identify price as the most important vehicle factor (36%). When presented with a list of vehicle features (such as automatic transmission, braking, air bags), older consumers in the current study were most likely to identify an antilock braking system (41%) as the most important vehicle feature, and 50 percent of older consumers identified a safety-related vehicle feature as the highest priority vehicle feature (50%). When asked to list up to 3 factors that make a vehicle safe, older consumers in the current study were most likely to list braking systems (35%), air bags (22%), and the driver's behavior or skill (11%). When asked about the influence of safety in the new vehicle purchase process, one third of older consumers reported that all new vehicles are safe (33%) and almost half of the older consumers rated their vehicle as safer than average (49%). A logistic regression model was developed to predict the profile of older consumers more likely to assign a higher priority to safety features in the vehicle purchasing process. The model predicted that the importance of safety-related features was influenced by several variables, including older consumers' beliefs that they could protect themselves

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

    Science.gov (United States)

    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.

  14. The effect of sugar and processed food imports on the prevalence of overweight and obesity in 172 countries.

    Science.gov (United States)

    Lin, Tracy Kuo; Teymourian, Yasmin; Tursini, Maitri Shila

    2018-04-14

    Studies find that economic, political, and social globalization - as well as trade liberalization specifically - influence the prevalence of overweight and obesity in countries through increasing the availability and affordability of unhealthful food. However, what are the mechanisms that connect globalization, trade liberalization, and rising average body mass index (BMI)? We suggest that the various sub-components of globalization interact, leading individuals in countries that experience higher levels of globalization to prefer, import, and consume more imported sugar and processed food products than individuals in countries that experience lower levels of globalization. This study codes the amount of sugar and processed food imports in 172 countries from 1995 to 2010 using the United Nations Comtrade dataset. We employ country-specific fixed effects (FE) models, with robust standard errors, to examine the relationship between sugar and processed foods imports, globalization, and average BMI. To highlight further the relationship between the sugar and processed food import and average BMI, we employ a synthetic control method to calculate a counterfactual average BMI in Fiji. We find that sugar and processed food imports are part of the explanation to increasing average BMI in countries; after controlling for globalization and general imports and exports, sugar and processed food imports have a statistically and substantively significant effect in increasing average BMI. In the case of Fiji, the increased prevalence of obesity is associated with trade agreements and increased imports of sugar and processed food. The counterfactual estimates suggest that sugar and processed food imports are associated with a 0.5 increase in average BMI in Fiji.

  15. Biophysical constraints on the computational capacity of biochemical signaling networks

    Science.gov (United States)

    Wang, Ching-Hao; Mehta, Pankaj

    Biophysics fundamentally constrains the computations that cells can carry out. Here, we derive fundamental bounds on the computational capacity of biochemical signaling networks that utilize post-translational modifications (e.g. phosphorylation). To do so, we combine ideas from the statistical physics of disordered systems and the observation by Tony Pawson and others that the biochemistry underlying protein-protein interaction networks is combinatorial and modular. Our results indicate that the computational capacity of signaling networks is severely limited by the energetics of binding and the need to achieve specificity. We relate our results to one of the theoretical pillars of statistical learning theory, Cover's theorem, which places bounds on the computational capacity of perceptrons. PM and CHW were supported by a Simons Investigator in the Mathematical Modeling of Living Systems Grant, and NIH Grant No. 1R35GM119461 (both to PM).

  16. Important to investigate the dynamics of the stigma process.

    Science.gov (United States)

    Angermeyer, Matthias

    2004-01-01

    Studies have shown that the stigma of the most common mental disorder, namely depression, expose people with these disorders to a substantial amount of stigmatization in the workplace. Apart from the descriptive assessment of the magnitude of stigma, it is also important to investigate the dynamics of the stigma process. Agreeing with Dr. Stuart, three approaches to research on stigma and the workplace are proposed. The first is the dimension of social stigma, i.e., knowledge, attitudes and practices of employers. The second is the perspectives of the patients, i.e., self- stigmatization. The third is legal and policy frameworks, i.e., structural discrimination.

  17. Biophysical properties and cellular toxicity of covalent crosslinked oligomers of α-synuclein formed by photoinduced side-chain tyrosyl radicals

    Czech Academy of Sciences Publication Activity Database

    Borsarelli, C.D.; Falomir-Lockhart, L.J.; Ostatná, Veronika; Fauerbach, J.A.; Hsiao, H.-H.; Urlaub, H.; Paleček, Emil; Jares-Erijman, E.A.; Jovin, T.M.

    2012-01-01

    Roč. 53, č. 4 (2012), s. 1004-1015 ISSN 0891-5849 R&D Projects: GA AV ČR(CZ) KJB100040901 Institutional research plan: CEZ:AV0Z50040702 Keywords : Parkinson's disease * neurodegeneration * oxidative stress Subject RIV: BO - Biophysics Impact factor: 5.271, year: 2012

  18. Biophysical and biochemical strategies to understand membrane binding and pore formation by sticholysins, pore-forming proteins from a sea anemone.

    Science.gov (United States)

    Alvarez, Carlos; Ros, Uris; Valle, Aisel; Pedrera, Lohans; Soto, Carmen; Hervis, Yadira P; Cabezas, Sheila; Valiente, Pedro A; Pazos, Fabiola; Lanio, Maria E

    2017-10-01

    Actinoporins constitute a unique class of pore-forming toxins found in sea anemones that are able to bind and oligomerize in membranes, leading to cell swelling, impairment of ionic gradients and, eventually, to cell death. In this review we summarize the knowledge generated from the combination of biochemical and biophysical approaches to the study of sticholysins I and II (Sts, StI/II), two actinoporins largely characterized by the Center of Protein Studies at the University of Havana during the last 20 years. These approaches include strategies for understanding the toxin structure-function relationship, the protein-membrane association process leading to pore formation and the interaction of toxin with cells. The rational combination of experimental and theoretical tools have allowed unraveling, at least partially, of the complex mechanisms involved in toxin-membrane interaction and of the molecular pathways triggered upon this interaction. The study of actinoporins is important not only to gain an understanding of their biological roles in anemone venom but also to investigate basic molecular mechanisms of protein insertion into membranes, protein-lipid interactions and the modulation of protein conformation by lipid binding. A deeper knowledge of the basic molecular mechanisms involved in Sts-cell interaction, as described in this review, will support the current investigations conducted by our group which focus on the design of immunotoxins against tumor cells and antigen-releasing systems to cell cytosol as Sts-based vaccine platforms.

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

    Science.gov (United States)

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

    2018-02-13

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

  20. Biophysics environmental conditions of swamp buffalo Bubalus bubalis Pampangan in district Rambutan South Sumatera

    Directory of Open Access Journals (Sweden)

    Yuanita Windusari

    2015-06-01

    Full Text Available Swamp buffalo (Bubalus bubalis is a germ plasm specific of Pampangan and endemic in South Sumatera with low productivity and limited distribution. The aims of this study was to obtain information regarding biophysical conditions in the central areas of swamp buffalo in South Sumatera. The method used is purposive sampling method. Data collected in the form of quantitative and qualitative. Primary data were obtained through direct observation, interviews breeders selected as respondents while secondary data obtained from various related. The data obtained are presented descriptively and data tabulation. Productivity of swamp buffalo Pampangan can be increased by managing and maintaining habitat conditions although traditional maintenance. The results of observations of the biophysical condition of swamp buffalo (B. bubalis Pampangan showed that habitat of swamp buffalo Pampangan consists of dominated by lowland swamp area is overgrown with shrubs and grass. The conclution of the research are productivity and population of swamp buffalo (B. bubalis pampangan as specific plasma nutfah of South Sumatra can be improved by studying the characteristics and preferred habitat of the buffalo, although developed in a traditional farms but is good enough and so need to be developed, grass is most preferred by swamp buffalo Pampangan derived from ‘Kumpai’ grass group, and ‘Kasur’grass and ‘Kumpai’ grass is the dominant grass type found in habitat swamp buffalo Pampangan.

  1. 40 CFR 761.187 - Reporting importers and by persons generating PCBs in excluded manufacturing processes.

    Science.gov (United States)

    2010-07-01

    ...) MANUFACTURING, PROCESSING, DISTRIBUTION IN COMMERCE, AND USE PROHIBITIONS General Records and Reports § 761.187 Reporting importers and by persons generating PCBs in excluded manufacturing processes. In addition to... generating PCBs in excluded manufacturing processes. 761.187 Section 761.187 Protection of Environment...

  2. Biophysical Insights into the Inhibitory Mechanism of Non-Nucleoside HIV-1 Reverse Transcriptase Inhibitors

    Directory of Open Access Journals (Sweden)

    Nicolas Sluis-Cremer

    2013-11-01

    Full Text Available HIV-1 reverse transcriptase (RT plays a central role in HIV infection. Current United States Federal Drug Administration (USFDA-approved antiretroviral therapies can include one of five approved non-nucleoside RT inhibitors (NNRTIs, which are potent inhibitors of RT activity. Despite their crucial clinical role in treating and preventing HIV-1 infection, their mechanism of action remains elusive. In this review, we introduce RT and highlight major advances from experimental and computational biophysical experiments toward an understanding of RT function and the inhibitory mechanism(s of NNRTIs.

  3. Biophysical induction of vascular smooth muscle cell podosomes.

    Directory of Open Access Journals (Sweden)

    Na Young Kim

    Full Text Available Vascular smooth muscle cell (VSMC migration and matrix degradation occurs with intimal hyperplasia associated with atherosclerosis, vascular injury, and restenosis. One proposed mechanism by which VSMCs degrade matrix is through the use of podosomes, transient actin-based structures that are thought to play a role in extracellular matrix degradation by creating localized sites of matrix metalloproteinase (MMP secretion. To date, podosomes in VSMCs have largely been studied by stimulating cells with phorbol esters, such as phorbol 12,13-dibutyrate (PDBu, however little is known about the physiological cues that drive podosome formation. We present the first evidence that physiological, physical stimuli mimicking cues present within the microenvironment of diseased arteries can induce podosome formation in VSMCs. Both microtopographical cues and imposed pressure mimicking stage II hypertension induce podosome formation in A7R5 rat aortic smooth muscle cells. Moreover, wounding using a scratch assay induces podosomes at the leading edge of VSMCs. Notably the effect of each of these biophysical stimuli on podosome stimulation can be inhibited using a Src inhibitor. Together, these data indicate that physical cues can induce podosome formation in VSMCs.

  4. Use of Unpalatable Forages by Ruminants: The Influence of Experience with the Biophysical and Social Environment

    Directory of Open Access Journals (Sweden)

    Roberto A. Distel

    2018-04-01

    Full Text Available Unpalatable forage resources (low nutrient density, potentially toxic metabolites are widespread and represent a challenge for ruminant nutrition, health, and welfare. Our objective was to synthesize the role of biophysical and social experience on the use of unpalatable forages by ruminants, and highlight derived behavioural solutions for the well-being of soils, plants, and animals. Environmental experiences early in life modulate gene expression and promote learning, which alters morpho-physiological and psychological mechanisms that modify behavioural responses and change food and habitat selection. In this process, ruminants can become better adapted to the habitat where they are reared. Moreover, experiential learning provides flexibility in diet selection, which is critical for changing foraging environments. Learned associations between unpalatable and palatable foods, if ingested in appropriate amounts, sequence, and close temporal association, induce the development of preference for the former type of food. In this way, a more uniform use of resources can be achieved from the landscape level down to the individual plant, with the associated benefits to ecosystem integrity and stability. Ruminants can also learn the medicinal benefits of ingesting foods with toxins (e.g., condensed tannins and saponins with antiparasitic properties. This knowledge on behavioural processes can be translated into behavioural applications that provide low-cost solutions to many challenges that producers face in managing sustainable livestock production systems.

  5. Combining biophysical methods to analyze the disulfide bond in SH2 domain of C-terminal Src kinase.

    Science.gov (United States)

    Liu, Dongsheng; Cowburn, David

    2016-01-01

    The Src Homology 2 (SH2) domain is a structurally conserved protein domain that typically binds to a phosphorylated tyrosine in a peptide motif from the target protein. The SH2 domain of C-terminal Src kinase (Csk) contains a single disulfide bond, which is unusual for most SH2 domains. Although the global motion of SH2 domain regulates Csk function, little is known about the relationship between the disulfide bond and binding of the ligand. In this study, we combined X-ray crystallography, solution NMR, and other biophysical methods to reveal the interaction network in Csk. Denaturation studies have shown that disulfide bond contributes significantly to the stability of SH2 domain, and crystal structures of the oxidized and C122S mutant showed minor conformational changes. We further investigated the binding of SH2 domain to a phosphorylated peptide from Csk-binding protein upon reduction and oxidation using both NMR and fluorescence approaches. This work employed NMR, X-ray cryptography, and other biophysical methods to study a disulfide bond in Csk SH2 domain. In addition, this work provides in-depth understanding of the structural dynamics of Csk SH2 domain.

  6. Single amino acid substitution in important hemoglobinopathies does not disturb molecular function and biological process

    Directory of Open Access Journals (Sweden)

    Viroj Wiwanitkit

    2008-06-01

    Full Text Available Viroj WiwanitkitDepartment of Laboratory Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, ThailandAbstract: Hemoglobin is an important protein found in the red cells of many animals. In humans, the hemoglobin is mainly distributed in the red blood cell. Single amino acid substitution is the main pathogenesis of most hemoglobin disorders. Here, the author used a new gene ontology technology to predict the molecular function and biological process of four important hemoglobin disorders with single substitution. The four studied important abnormal hemoglobins (Hb with single substitution included Hb S, Hb E, Hb C, and Hb J-Baltimore. Using the GoFigure server, the molecular function and biological process in normal and abnormal hemoglobins was predicted. Compared with normal hemoglobin, all studied abnormal hemoglobins had the same function and biological process. This indicated that the overall function of oxygen transportation is not disturbed in the studied hemoglobin disorders. Clinical findings of oxygen depletion in abnormal hemoglobin should therefore be due to the other processes rather than genomics, proteomics, and expression levels.Keywords: hemoglobin, amino acid, substitution, function

  7. [Biophysical principles of collagen cross-linking].

    Science.gov (United States)

    Spörl, E; Raiskup-Wolf, F; Pillunat, L E

    2008-02-01

    The reduced mechanical stability of the cornea in keratoconus or in keratectasia after Lasik may be increased by photooxidative cross-linking of corneal collagen. The biophysical principles are compiled for the safe and effective application of this new treatment method. The setting of the therapy parameters should be elucidated from the absorption behaviour of the cornea. The safety of the method for the endothelium cells and the lens will be discussed. The induced cross-links are shown to be the result of changes in the physico-chemical properties of the cornea. To reach a high absorption of the irradiation energy in the cornea, riboflavin of a concentration of 0.1% and UV light of a wavelength of 370 nm, corresponding to the relative maximum of absorption of riboflavin, were used. An irradiance of 3 mW/cm(2) and an irradiation time of 30 min lead to an increase of the mechanical stiffness. The endothelium cells will be protected due to the high absorption within the cornea, that means the damaging threshold of the endothelium cells will not be reached in a 400 microm thick stroma. As evidence for cross-links we can consider the increase of the biomechanical stiffness, the increased resistance against enzymatic degradation, a higher shrinkage temperature, a lower swelling rate and an increased diameter of collagen fibres. The therapy parameters were tested experimentally and have been proven clinically in the corneal collagen cross-linking. These parameters should be respected to reach a safe cross-linking effect without damage of the adjacent tissues.

  8. Modeling the effects of noninvasive transcranial brain stimulation at the biophysical, network, and cognitive Level

    DEFF Research Database (Denmark)

    Hartwigsen, Gesa; Bergmann, Til Ole; Herz, Damian Marc

    2015-01-01

    these approaches advance the scientific potential of NTBS as an interventional tool in cognitive neuroscience. (i) Leveraging the anatomical information provided by structural imaging, the electric field distribution in the brain can be modeled and simulated. Biophysical modeling approaches generate testable...... predictions regarding the impact of interindividual variations in cortical anatomy on the injected electric fields or the influence of the orientation of current flow on the physiological stimulation effects. (ii) Functional brain mapping of the spatiotemporal neural dynamics during cognitive tasks can...

  9. Coupling the Biophysical and Social Dimensions of Wildfire Risk to Improve Wildfire Mitigation Planning.

    Science.gov (United States)

    Ager, Alan A; Kline, Jeffrey D; Fischer, A Paige

    2015-08-01

    We describe recent advances in biophysical and social aspects of risk and their potential combined contribution to improve mitigation planning on fire-prone landscapes. The methods and tools provide an improved method for defining the spatial extent of wildfire risk to communities compared to current planning processes. They also propose an expanded role for social science to improve understanding of community-wide risk perceptions and to predict property owners' capacities and willingness to mitigate risk by treating hazardous fuels and reducing the susceptibility of dwellings. In particular, we identify spatial scale mismatches in wildfire mitigation planning and their potential adverse impact on risk mitigation goals. Studies in other fire-prone regions suggest that these scale mismatches are widespread and contribute to continued wildfire dwelling losses. We discuss how risk perceptions and behavior contribute to scale mismatches and how they can be minimized through integrated analyses of landscape wildfire transmission and social factors that describe the potential for collaboration among landowners and land management agencies. These concepts are then used to outline an integrated socioecological planning framework to identify optimal strategies for local community risk mitigation and improve landscape-scale prioritization of fuel management investments by government entities. © 2015 Society for Risk Analysis.

  10. Incorporating Modeling and Simulations in Undergraduate Biophysical Chemistry Course to Promote Understanding of Structure-Dynamics-Function Relationships in Proteins

    Science.gov (United States)

    Hati, Sanchita; Bhattacharyya, Sudeep

    2016-01-01

    A project-based biophysical chemistry laboratory course, which is offered to the biochemistry and molecular biology majors in their senior year, is described. In this course, the classroom study of the structure-function of biomolecules is integrated with the discovery-guided laboratory study of these molecules using computer modeling and…

  11. Possible etiology of calculi formation in salivary glands: biophysical analysis of calculus.

    Science.gov (United States)

    Mimura, Masafumi; Tanaka, Nobuyuki; Ichinose, Shizuko; Kimijima, Yutaka; Amagasa, Teruo

    2005-09-01

    Sialolithiasis is one of the common diseases of the salivary glands. It was speculated that, in the process of calculi formation, degenerative substances are emitted by saliva and calcification then occurs around these substances, and finally calculi are formed. However, the exact mechanism of the formation of calculi is still unclear. In this study, we identify some possible etiologies of calculi formation in salivary glands through biophysical analysis. Calculi from 13 patients with submandibular sialolithiasis were investigated by transmission electron microscopy, scanning electron microscopy, X-ray microanalyzer, and electron diffraction. Transmission electron microscopic observation of calculi was performed in the submandibular gland (n = 13). In 3 of the 13 cases, a number of mitochondria-like structures and lysosomes were found near calcified materials. Scanning electron microscopic examination of these materials revealed that there were lamellar and concentric structures and that the degree of calcification was different among the calculi. X-ray microanalysis disclosed the component elements in the calculi to be Ca, P, S, Na, etc., and the main constituents were Ca and P. The calcium-to-phosphorus ratio was 1.60-1.89. Analysis of the area including mitochondria-like structures, lysosomes, and the fibrous structures by electron diffraction revealed the presence of hydroxyapatite and calcified materials. It is speculated that mitochondria and lysosomal bodies from the ductal system of the submandibular gland are an etiological source for calcification in the salivary gland.

  12. Cholesterol oxidation products and their biological importance

    Czech Academy of Sciences Publication Activity Database

    Kulig, W.; Cwiklik, Lukasz; Jurkiewicz, P.; Rog, T.; Vattulainen, I.

    2016-01-01

    Roč. 199, Sep (2016), s. 144-160 ISSN 0009-3084 R&D Projects: GA ČR(CZ) GBP208/12/G016 Institutional support: RVO:61388963 Keywords : cholesterol * oxidation * oxysterols * biological membranes * biophysical properties Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.361, year: 2016

  13. Resolving the biophysics of axon transmembrane polarization in a single closed-form description

    Energy Technology Data Exchange (ETDEWEB)

    Melendy, Robert F., E-mail: rfmelendy@liberty.edu [School of Engineering and Computational Sciences, Liberty University, Lynchburg, Virginia 24515 (United States)

    2015-12-28

    When a depolarizing event occurs across a cell membrane there is a remarkable change in its electrical properties. A complete depolarization event produces a considerably rapid increase in voltage that propagates longitudinally along the axon and is accompanied by changes in axial conductance. A dynamically changing magnetic field is associated with the passage of the action potential down the axon. Over 75 years of research has gone into the quantification of this phenomenon. To date, no unified model exist that resolves transmembrane polarization in a closed-form description. Here, a simple but formative description of propagated signaling phenomena in the membrane of an axon is presented in closed-form. The focus is on using both biophysics and mathematical methods for elucidating the fundamental mechanisms governing transmembrane polarization. The results presented demonstrate how to resolve electromagnetic and thermodynamic factors that govern transmembrane potential. Computational results are supported by well-established quantitative descriptions of propagated signaling phenomena in the membrane of an axon. The findings demonstrate how intracellular conductance, the thermodynamics of magnetization, and current modulation function together in generating an action potential in a unified closed-form description. The work presented in this paper provides compelling evidence that three basic factors contribute to the propagated signaling in the membrane of an axon. It is anticipated this work will compel those in biophysics, physical biology, and in the computational neurosciences to probe deeper into the classical and quantum features of membrane magnetization and signaling. It is hoped that subsequent investigations of this sort will be advanced by the computational features of this model without having to resort to numerical methods of analysis.

  14. Ground- and satellite-based evidence of the biophysical mechanisms behind the greening Sahel.

    Science.gov (United States)

    Brandt, Martin; Mbow, Cheikh; Diouf, Abdoul A; Verger, Aleixandre; Samimi, Cyrus; Fensholt, Rasmus

    2015-04-01

    After a dry period with prolonged droughts in the 1970s and 1980s, recent scientific outcome suggests that the decades of abnormally dry conditions in the Sahel have been reversed by positive anomalies in rainfall. Various remote sensing studies observed a positive trend in vegetation greenness over the last decades which is known as the re-greening of the Sahel. However, little investment has been made in including long-term ground-based data collections to evaluate and better understand the biophysical mechanisms behind these findings. Thus, deductions on a possible increment in biomass remain speculative. Our aim is to bridge these gaps and give specifics on the biophysical background factors of the re-greening Sahel. Therefore, a trend analysis was applied on long time series (1987-2013) of satellite-based vegetation and rainfall data, as well as on ground-observations of leaf biomass of woody species, herb biomass, and woody species abundance in different ecosystems located in the Sahel zone of Senegal. We found that the positive trend observed in satellite vegetation time series (+36%) is caused by an increment of in situ measured biomass (+34%), which is highly controlled by precipitation (+40%). Whereas herb biomass shows large inter-annual fluctuations rather than a clear trend, leaf biomass of woody species has doubled within 27 years (+103%). This increase in woody biomass did not reflect on biodiversity with 11 of 16 woody species declining in abundance over the period. We conclude that the observed greening in the Senegalese Sahel is primarily related to an increasing tree cover that caused satellite-driven vegetation indices to increase with rainfall reversal. © 2014 John Wiley & Sons Ltd.

  15. DEPENDENCE OF THE SPECKLE-PATTERNS SIZE AND THEIR CONTRAST ON THE BIOPHYSICAL AND STRUCTURAL PARAMETERS OF BIOLOGICAL TISSUES

    Directory of Open Access Journals (Sweden)

    N. D. Abramovich

    2017-01-01

    Full Text Available Speckle fields are widely used in optical diagnostics of biotissues and evaluation of the functional state of bioobjects. The speckle field is formed by laser radiation scattered from the object under study. It bears information about the average dimensions of the scatterers, the degree of surface roughness makes it possible to judge the structural and biophysical characteristics of individual tissue cells (particles, on the one hand, and the integral optical characteristics of the entire biological tissue. The aim of the study was – the determination of connections between the biophysical and structural characteristics of the biotissue and the light fields inside the biotissues.The model developed of the medium gives a direct relationship between the optical and biophysical parameters of the biotissue. Calculations were carried out using known solutions of the radiation transfer equation, taking into account the multilayer structure of the tissue, multiple scattering in the medium, and multiple reflection of irradiation between the layers.With the increase wavelength, the size of speckles formed by the non-scattered component (direct light of laser radiation increases by a factor of 2 from 400 to 800 μm in the stratum corneum and 5 times from 0.6 to 3 μm for the epidermis and from 0.27 to 1.4 μm to the dermis. Typical values of sizes of speckles formed by the diffraction component of laser radiation for the stratum corneum and epidermis range from 0.02 to 0.15 μm. For the dermis typical spot sizes are up to 0.03 μm. The speckle-spot size of the diffusion component in the dermis can vary from ±10 % at 400 nm and up to ±23 % for 800 nm when the volume concentration of blood capillaries changes. Characteristic dependencies are obtained and biophysical factors associated with the volume concentration of blood and the degree of it’s oxygenation that affect the contrast of the speckle structure in the dermis are discussed.The of speckles

  16. Modern licensing approaches for analysis of important to safety processes in Nuclear Power Plants

    International Nuclear Information System (INIS)

    Andreeva, M.; Groudev, P.; Pavlova, M.; Stoyanov, S.

    2008-01-01

    It is presented within the paper the modern approaches for analysis of important to safety assessment processes in Nuclear Power Plants, included Bulgarian Regulatory Agency's requirements for quantity assessment of these processes applying deterministic and probabilistic approaches for establishing and confirming the design basis and defence-in-depth effectiveness. (authors)

  17. The design and analysis of a teaching and learning strategy in Biophysics Course

    Directory of Open Access Journals (Sweden)

    Beatriz Aiziczon

    2010-01-01

    Full Text Available This work presents the design and analysis of a teaching and learning strategy of Biophysics in the Medical career, in the mark of the Ausubelian Significant Learning Model, to overtake the Model of Transmission-Reception of knowledge. It is an integrative Module constructed from our previous theoretical Model and based on the authors' previous works (AIZICZON; CUDMANI, 2004, 2005, 2007. We analyze applications of conceptual maps strategy and the previous organizing in Medical Education (AUSUBEL, 1981; MOREIRA, 1983, 1999 promoting the integration of concepts allowing the progressive differentiation and the integrative reorganization as well as the formative evaluation. In this work we analyze the experience with teachers.

  18. A conceptual framework for coupling the biophysical and social dimensions of wildfire to improve fireshed planning and risk mitigation

    Science.gov (United States)

    Jeff Kline; Alan A. Ager; Paige Fischer

    2015-01-01

    The need for improved methods for managing wildfire risk is becoming apparent as uncharacteristically large wildfires in the western US and elsewhere exceed government capacities for their control and suppression. We propose a coupled biophysical-social framework to managing wildfire risk that relies on wildfire simulation to identify spatial patterns of wildfire risk...

  19. The Importance of Endospore-Forming Bacteria Originating from Soil for Contamination of Industrial Food Processing

    International Nuclear Information System (INIS)

    Heyndrickx, M

    2011-01-01

    Specific endo spore formers have become important contaminants in industrial food processing. The direct or indirect soil route of contamination or dispersal is the start of events or processes in the agrofood chain that eventually leads to important problems or concerns for food safety and/or quality. Three important food sectors are discussed in this paper. In the dairy sector, Bacillus cereus, the most important pathogen or spoilage organism in this sector, and Clostridium tyrobutyricum, the most important spoiler in certain cheeses, both contaminate pasteurized milk through the faecal and/or (at least for B. cereus) the direct soil route. In the fruit juice industry, Alicyclobacillus acidoterrestris, present on raw fruits, has become a major quality-target organism. In the ready-to-eat food sector, B. cereus and other aerobic endo spore formers are introduced via vegetables, fruits, or herbs and spices, while anaerobic spore formers like non proteolytic Clostridium botulinum and Clostridium estertheticum pose safety and spoilage risks in chilled packaged foods, respectively

  20. The Importance of Endospore-Forming Bacteria Originating from Soil for Contamination of Industrial Food Processing

    Directory of Open Access Journals (Sweden)

    Marc Heyndrickx

    2011-01-01

    Full Text Available Specific endospore formers have become important contaminants in industrial food processing. The direct or indirect soil route of contamination or dispersal is the start of events or processes in the agrofood chain that eventually leads to important problems or concerns for food safety and/or quality. Three important food sectors are discussed in this paper. In the dairy sector, Bacillus cereus, the most important pathogen or spoilage organism in this sector, and Clostridium tyrobutyricum, the most important spoiler in certain cheeses, both contaminate pasteurized milk through the faecal and/or (at least for B. cereus the direct soil route. In the fruit juice industry, Alicyclobacillus acidoterrestris, present on raw fruits, has become a major quality-target organism. In the ready-to-eat food sector, B. cereus and other aerobic endospore formers are introduced via vegetables, fruits, or herbs and spices, while anaerobic spore formers like nonproteolytic Clostridium botulinum and Clostridium estertheticum pose safety and spoilage risks in chilled packaged foods, respectively.

  1. Membrane Biophysics

    CERN Document Server

    Ashrafuzzaman, Mohammad

    2013-01-01

    Physics, mathematics and chemistry all play a vital role in understanding the true nature and functioning of biological membranes, key elements of living processes. Besides simple spectroscopic observations and electrical measurements of membranes we address in this book the phenomena of coexistence and independent existence of different membrane components using various theoretical approaches. This treatment will be helpful for readers who want to understand biological processes by applying both simple observations and fundamental scientific analysis. It provides a deep understanding of the causes and effects of processes inside membranes, and will thus eventually open new doors for high-level pharmaceutical approaches towards fighting membrane- and cell-related diseases.

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

    International Nuclear Information System (INIS)

    Zhao, Huaying; Schuck, Peter

    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 biophysical 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

  3. Ref2RIS: Importing Word-Processed Bibliographies into Bibliographic Management Software

    OpenAIRE

    Deborah Fitchett

    2012-01-01

    Many who would benefit the most from timesaving bibliographic managers hesitate to adopt the technology due to the difficulties in importing legacy bibliographies developed over years. Existing shortcuts rely on manual reformatting or on re-searching online databases for the records - often almost as laborious as retyping the references. Ref2RIS was developed to automate the task of converting a bibliography in specific citation styles from common word processing document formats into the wid...

  4. Toward Biophysical Probes for the 5-HT3 Receptor: Structure−Activity Relationship Study of Granisetron Derivatives

    Science.gov (United States)

    2010-01-01

    This report describes the synthesis and biological characterization of novel granisetron derivatives that are antagonists of the human serotonin (5-HT3A) receptor. Some of these substituted granisetron derivatives showed low nanomolar binding affinity and allowed the identification of positions on the granisetron core that might be used as attachment points for biophysical tags. A BODIPY fluorophore was appended to one such position and specifically bound to 5-HT3A receptors in mammalian cells. PMID:20146481

  5. Toward biophysical probes for the 5-HT3 receptor: structure-activity relationship study of granisetron derivatives.

    Science.gov (United States)

    Vernekar, Sanjeev Kumar V; Hallaq, Hasan Y; Clarkson, Guy; Thompson, Andrew J; Silvestri, Linda; Lummis, Sarah C R; Lochner, Martin

    2010-03-11

    This report describes the synthesis and biological characterization of novel granisetron derivatives that are antagonists of the human serotonin (5-HT(3)A) receptor. Some of these substituted granisetron derivatives showed low nanomolar binding affinity and allowed the identification of positions on the granisetron core that might be used as attachment points for biophysical tags. A BODIPY fluorophore was appended to one such position and specifically bound to 5-HT(3)A receptors in mammalian cells.

  6. Microspectroscopic Confocal Raman and Macroscopic Biophysical Measurements in the in vivo Assessment of the Skin Barrier: Perspective for Dermatology and Cosmetic Sciences

    NARCIS (Netherlands)

    Falcone, D.; Uzunbajakava, N.E.; Varghese, B.; Aquino Santos, G.R. de; Richters, R.J.H.; Kerkhof, P.C.M. van de; Erp, P.E.J. van

    2015-01-01

    Skin barrier function, confined to the stratum corneum, is traditionally evaluated using established, noninvasive biophysical methods like transepidermal water loss, capacitance and conductance. However, these methods neither measure skin molecular composition nor its structure, hindering the actual

  7. Comparison of Cold Weather Clothing Biophysical Properties: US Army, Canadian Department of National Defence, and Norwegian Military

    Science.gov (United States)

    2018-03-01

    Natick, MA 2 Rutgers University, School of Biomedical and Health Sciences, Newark, NJ 3 Research Support Division, USARIEM, Natick, MA 4 Toronto...issue for the U.S. military, as they routinely travel and conduct a range of physical activities around the world within the full spectrum of extreme...level of physical analysis (level 1), for example, clothing can be weighed and inspected for physical attributes. Biophysical analysis (level 2

  8. Biophysical information in asymmetric and symmetric diurnal bidirectional canopy reflectance

    Science.gov (United States)

    Vanderbilt, Vern C.; Caldwell, William F.; Pettigrew, Rita E.; Ustin, Susan L.; Martens, Scott N.; Rousseau, Robert A.; Berger, Kevin M.; Ganapol, B. D.; Kasischke, Eric S.; Clark, Jenny A.

    1991-01-01

    The authors present a theory for partitioning the information content in diurnal bidirectional reflectance measurements in order to detect differences potentially related to biophysical variables. The theory, which divides the canopy reflectance into asymmetric and symmetric functions of solar azimuth angle, attributes asymmetric variation to diurnal changes in the canopy biphysical properties. The symmetric function is attributed to the effects of sunlight interacting with a hypothetical average canopy which would display the average diurnal properties of the actual canopy. The authors analyzed radiometer data collected diurnally in the Thematic Mapper wavelength bands from two walnut canopies that received differing irrigation treatments. The reflectance of the canopies varied with sun and view angles and across seven bands in the visible, near-infrared, and middle infrared wavelength regions. Although one of the canopies was permanently water stressed and the other was stressed in mid-afternoon each day, no water stress signature was unambiguously evident in the reflectance data.

  9. Molecular, biophysical, and pharmacological properties of calcium-activated chloride channels.

    Science.gov (United States)

    Kamaleddin, Mohammad Amin

    2018-02-01

    Calcium-activated chloride channels (CaCCs) are a family of anionic transmembrane ion channels. They are mainly responsible for the movement of Cl - and other anions across the biological membranes, and they are widely expressed in different tissues. Since the Cl - flow into or out of the cell plays a crucial role in hyperpolarizing or depolarizing the cells, respectively, the impact of intracellular Ca 2+ concentration on these channels is attracting a lot of attentions. After summarizing the molecular, biophysical, and pharmacological properties of CaCCs, the role of CaCCs in normal cellular functions will be discussed, and I will emphasize how dysregulation of CaCCs in pathological conditions can account for different diseases. A better understanding of CaCCs and a pivotal regulatory role of Ca 2+ can shed more light on the therapeutic strategies for different neurological disorders that arise from chloride dysregulation, such as asthma, cystic fibrosis, and neuropathic pain. © 2017 Wiley Periodicals, Inc.

  10. Lessons from the biophysics of interfaces: Lung surfactant and tear fluid

    DEFF Research Database (Denmark)

    Rantamaki, A.; Telenius, J.; Koivuniemi, A.

    2011-01-01

    The purpose of this review is to provide insight into the biophysical properties and functions of tear fluid and lung surfactant - two similar fluids covering the epithelium of two distinctive organs. Both fluids form a layer-like structure that essentially comprise of an aqueous layer next......-active function of the fluid film. The lipid layer of lung surfactant comprises mainly of phospholipids, especially phosphatidylcholines, and only small amounts of non-polar lipids, mainly cholesterol. In contrast, tear fluid lipid layer comprises of a mixture of polar and non-polar lipids. However, the relative...... proportion and the spectrum of different polar and non-polar lipids seem to be more extensive in tear fluid than in lung surfactant. The differing lipid compositions generate distinctive lipid layer structures. Despite the structural differences, these lipid layers decrease the surface tension of the air...

  11. Electron paramagnetic resonance biophysical radiation dosimetry with tooth enamel

    International Nuclear Information System (INIS)

    Khan, Rao F.H.

    2003-01-01

    This thesis deals with the advancements made in the field of Electron Paramagnetic Resonance (EPR) for biophysical dosimetry with tooth enamel for accident, emergency, and retrospective radiation dose reconstruction. A methodology has been developed to measure retrospective radiation exposures in human tooth enamel. This entails novel sample preparation procedures with minimum mechanical treatment to reduce the preparation induced uncertainties, establish optimum measurement conditions inside the EPR cavity, post-process the measured spectrum with functional simulation of dosimetric and other interfering signals, and reconstruct dose. By using this technique, retrospective gamma exposures as low as 80±30 mGy have been successfully deciphered. The notion of dose modifier was introduced in EPR biodosimetry for low dose measurements. It has been demonstrated that by using the modified zero added dose (MZAD) technique for low radiation exposures, doses in 100 mGy ranges can be easily reconstructed in teeth that were previously thought useless for EPR dosimetry. Also, the use of a dose modifier makes robust dose reconstruction possible for higher radiation exposures. The EPR dosimetry technique was also developed for tooth samples extracted from rodents, which represent small tooth sizing. EPR doses in the molars, extracted from the mice irradiated with whole body exposures, were reassessed and shown to be correct within the experimental uncertainty. The sensitivity of human tooth enamel for neutron irradiation, obtained from the 3 MV McMaster K.N. Van de Graaff accelerator, was also studied. For the first time this work has shown that the neutron sensitivity of the tooth enamel is approximately 1/10th of the equivalent gamma sensitivity. Parametric studies for neutron dose rate and neutron energy within the available range of the accelerator, showed no impact on the sensitivity of the tooth enamel. Therefore, tooth enamel can be used as a dosimeter for both neutrons

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

    Science.gov (United States)

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

    1992-01-01

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

  13. Theoretical Insights into the Biophysics of Protein Bi-stability and Evolutionary Switches.

    Directory of Open Access Journals (Sweden)

    Tobias Sikosek

    2016-06-01

    Full Text Available Deciphering the effects of nonsynonymous mutations on protein structure is central to many areas of biomedical research and is of fundamental importance to the study of molecular evolution. Much of the investigation of protein evolution has focused on mutations that leave a protein's folded structure essentially unchanged. However, to evolve novel folds of proteins, mutations that lead to large conformational modifications have to be involved. Unraveling the basic biophysics of such mutations is a challenge to theory, especially when only one or two amino acid substitutions cause a large-scale conformational switch. Among the few such mutational switches identified experimentally, the one between the GA all-α and GB α+β folds is extensively characterized; but all-atom simulations using fully transferrable potentials have not been able to account for this striking switching behavior. Here we introduce an explicit-chain model that combines structure-based native biases for multiple alternative structures with a general physical atomic force field, and apply this construct to twelve mutants spanning the sequence variation between GA and GB. In agreement with experiment, we observe conformational switching from GA to GB upon a single L45Y substitution in the GA98 mutant. In line with the latent evolutionary potential concept, our model shows a gradual sequence-dependent change in fold preference in the mutants before this switch. Our analysis also indicates that a sharp GA/GB switch may arise from the orientation dependence of aromatic π-interactions. These findings provide physical insights toward rationalizing, predicting and designing evolutionary conformational switches.

  14. The Importance of Recognition for Equal Representation in Participatory Processes: Lessons from Husby

    Directory of Open Access Journals (Sweden)

    Karin Hansson

    2014-08-01

    Full Text Available Despite the ambition to involve people on more equal terms, participation often still means that the audience is involved in clearly demarcated parts of the process and attempts to develop more deliberative democratic processes in urban planning often fail due to unequal representation in the participatory process.While sharing the general idea of the value of participatory processes, we will investigate some problematic features involved and suggest how some of these can be remedied. We employ the concept of recognition to analyse the conditions for public participation in a recent case of urban planning in the Stockholm suburb of Husby. This case is particularly interesting as it clearly demonstrates the impact of globalisation on local participatory processes.The results show the importance of broad recognition for equal representation in participatory processes, and the need for a plurality of public spheres to support long-term participation in the development of the common urban space.

  15. Perturbations of Native Membrane Protein Structure in Alkyl Phosphocholine Detergents: A Critical Assessment of NMR and Biophysical Studies

    Science.gov (United States)

    2018-01-01

    Membrane proteins perform a host of vital cellular functions. Deciphering the molecular mechanisms whereby they fulfill these functions requires detailed biophysical and structural investigations. Detergents have proven pivotal to extract the protein from its native surroundings. Yet, they provide a milieu that departs significantly from that of the biological membrane, to the extent that the structure, the dynamics, and the interactions of membrane proteins in detergents may considerably vary, as compared to the native environment. Understanding the impact of detergents on membrane proteins is, therefore, crucial to assess the biological relevance of results obtained in detergents. Here, we review the strengths and weaknesses of alkyl phosphocholines (or foscholines), the most widely used detergent in solution-NMR studies of membrane proteins. While this class of detergents is often successful for membrane protein solubilization, a growing list of examples points to destabilizing and denaturing properties, in particular for α-helical membrane proteins. Our comprehensive analysis stresses the importance of stringent controls when working with this class of detergents and when analyzing the structure and dynamics of membrane proteins in alkyl phosphocholine detergents. PMID:29488756

  16. Radiation dose responses for chemoradiation therapy of pancreatic cancer: an analysis of compiled clinical data using biophysical models.

    Science.gov (United States)

    Moraru, Ion C; Tai, An; Erickson, Beth; Li, X Allen

    2014-01-01

    We analyzed recent clinical data obtained from chemoradiation of unresectable, locally advanced pancreatic cancer (LAPC) in order to examine possible benefits from radiation therapy dose escalation. A modified linear quadratic model was used to fit clinical tumor response and survival data of chemoradiation treatments for LAPC reported from 20 institutions. Biophysical radiosensitivity parameters were extracted from the fits. Examination of the clinical data demonstrated an enhancement in tumor response with higher irradiation dose, an important clinical result for palliation and quality of life. Little indication of improvement in 1-year survival with increased radiation dose was observed. Possible dose escalation schemes are proposed based on calculations of the biologically effective dose required for a 50% tumor response rate. Based on the evaluation of tumor response data, the escalation of radiation dose presents potential clinical benefits which when combined with normal tissue complication analyses may result in improved treatment outcome for locally advanced pancreatic cancer patients. Copyright © 2014 American Society for Radiation Oncology. Published by Elsevier Inc. All rights reserved.

  17. Functional and biophysical studies on four ceratoplatanins from the fungus Moniliophthora perniciosa, causal agent of the Witche's broom disease

    International Nuclear Information System (INIS)

    Barsottini, M.; Zaparoli, G.; Garcia, O.; Pereira, G.A.G.; Oliveira, J.F.; Tiezzi, H.O.; Ambrosio, A.L.B.; Dias, S.M.G.

    2012-01-01

    Full text: Ceratoplatanin (CP) is a secreted protein of 12.4 kDa initially identified in culture filtrates of the disease ascomycete Ceratocystis fimbriata f. sp. platani, etiological agent of the canker stain disease. CP is also the founding member of the namesake protein family, which contains fungal-secreted proteins involved in various stages of the host-fungus interaction and may act as phytotoxins or elicitors of defense response. Besides the low molecular weight, CPs have a high percentage of hydrophobic residues and share two conserved intramolecular disulfide bonds. It has been suggested that CPs have important physiological functions, including interaction with cell wall or cell membrane and manipulation of the host's defense system. Furthermore, a recent work showed that the ceratoplatanin from C. fimbriata has some degree of affinity for the saccharide 4-N-acetylglucosamine. However, its precise molecular function remains elusive. Five putative CPs have been identified in Moniliophthora perniciosa a basidiomycete fungus responsible for great economic losses in cocoa industry in the form of Witches' broom disease (WBD) , four of which had their crystal structures resolved by our group. In this work we report biophysical and functional studies on these MpCPs aiming at understanding their role and importance during the WBD progression. (author)

  18. Study of a methodology of identifying important research problems by the PIRT process

    International Nuclear Information System (INIS)

    Aoki, Takayuki; Takagi, Toshiyuki; Urayama, Ryoichi; Komura, Ichiro; Furukawa, Takashi; Yusa, Noritaka

    2014-01-01

    In this paper, we propose a new methodology of identifying important research problems to be solved to improve the performance of some specific scientific technologies by the phenomena identification and ranking table (PIRT) process which has been used as a methodology for demonstrating the validity of the best estimate simulation codes in US Nuclear Regulatory Commission (USNRC) licensing of nuclear power plants. The new methodology makes it possible to identify important factors affecting the performance of the technologies from the viewpoint of the figure of merit and problems associated with them while it keeps the fundamental concepts of the original PIRT process. Also in this paper, we demonstrate the effectiveness of the new methodology by applying it to a task of extracting research problems for improving an inspection accuracy of ultrasonic testing or eddy current testing in the inspection of objects having cracks due to fatigue or stress corrosion cracking. (author)

  19. Study of a methodology of identifying important research problems by the PIRT process

    International Nuclear Information System (INIS)

    Aoki, Takayuki; Takagi, Toshiyuki; Urayama, Ryoichi; Komura, Ichiro; Furukawa, Takashi; Yusa, Noritaka

    2013-01-01

    In this paper, we propose a new methodology of identifying important research problems to be solved to improve the performance of some specific scientific technologies by the phenomena identification and ranking table (PIRT) process, which has been used as a methodology for demonstrating the validity of the best estimate simulation codes in USNRC licensing of nuclear power plants. It keeps the fundamental concepts of the original PIRT process but makes it possible to identify important factors affecting the performance of the technologies from the viewpoint of the figure of merit and problems associated with them, which need to be solved to improve the performance. Also in this paper, we demonstrate the effectiveness of the developed method by showing a specific example of the application to physical events or phenomena in objects having fatigue or SCC crack(s) under ultrasonic testing and eddy current testing. (author)

  20. Ammonium hydroxide treatment of A? produces an aggregate free solution suitable for biophysical and cell culture characterization

    OpenAIRE

    Ryan, Timothy M.; Caine, Joanne; Mertens, Haydyn D.T.; Kirby, Nigel; Nigro, Julie; Breheney, Kerry; Waddington, Lynne J.; Streltsov, Victor A.; Curtain, Cyril; Masters, Colin L.; Roberts, Blaine R.

    2013-01-01

    Alzheimer’s disease is the leading cause of dementia in the elderly. Pathologically it is characterized by the presence of amyloid plaques and neuronal loss within the brain tissue of affected individuals. It is now widely hypothesised that fibrillar structures represent an inert structure. Biophysical and toxicity assays attempting to characterize the formation of both the fibrillar and the intermediate oligomeric structures of Aβ typically involves preparing samples which are largely monome...

  1. Chemical and Biophysical Modulation of Cas9 for Tunable Genome Engineering.

    Science.gov (United States)

    Nuñez, James K; Harrington, Lucas B; Doudna, Jennifer A

    2016-03-18

    The application of the CRISPR-Cas9 system for genome engineering has revolutionized the ability to interrogate genomes of mammalian cells. Programming the Cas9 endonuclease to induce DNA breaks at specified sites is achieved by simply modifying the sequence of its cognate guide RNA. Although Cas9-mediated genome editing has been shown to be highly specific, cleavage events at off-target sites have also been reported. Minimizing, and eventually abolishing, unwanted off-target cleavage remains a major goal of the CRISPR-Cas9 technology before its implementation for therapeutic use. Recent efforts have turned to chemical biology and biophysical approaches to engineer inducible genome editing systems for controlling Cas9 activity at the transcriptional and protein levels. Here, we review recent advancements to modulate Cas9-mediated genome editing by engineering split-Cas9 constructs, inteins, small molecules, protein-based dimerizing domains, and light-inducible systems.

  2. submitter Next generation multi-scale biophysical characterization of high precision cancer particle radiotherapy using clinical proton, helium-, carbon- and oxygen ion beams

    CERN Document Server

    Dokic, Ivana; Niklas, Martin; Zimmermann, Ferdinand; Chaudhri, Naved; Krunic, Damir; Tessonnier, Thomas; Ferrari, Alfredo; Parodi, Katia; Jäkel, Oliver; Debus, Jürgen; Haberer, Thomas; Abdollahi, Amir

    2016-01-01

    The growing number of particle therapy facilities worldwide landmarks a novel era of precision oncology. Implementation of robust biophysical readouts is urgently needed to assess the efficacy of different radiation qualities. This is the first report on biophysical evaluation of Monte Carlo simulated predictive models of prescribed dose for four particle qualities i.e., proton, helium-, carbon- or oxygen ions using raster-scanning technology and clinical therapy settings at HIT. A high level of agreement was found between the in silico simulations, the physical dosimetry and the clonogenic tumor cell survival. The cell fluorescence ion track hybrid detector (Cell-Fit-HD) technology was employed to detect particle traverse per cell nucleus. Across a panel of radiobiological surrogates studied such as late ROS accumulation and apoptosis (caspase 3/7 activation), the relative biological effectiveness (RBE) chiefly correlated with the radiation species-specific spatio-temporal pattern of DNA double strand break ...

  3. Universal buffers for use in biochemistry and biophysical experiments

    Directory of Open Access Journals (Sweden)

    Dewey Brooke

    2015-08-01

    Full Text Available The use of buffers that mimic biological solutions is a foundation of biochemical and biophysical studies. However, buffering agents have both specific and nonspecific interactions with proteins. Buffer molecules can induce changes in conformational equilibria, dynamic behavior, and catalytic properties merely by their presence in solution. This effect is of concern because many of the standard experiments used to investigate protein structure and function involve changing solution conditions such as pH and/or temperature. In experiments in which pH is varied, it is common practice to switch buffering agents so that the pH is within the working range of the weak acid and conjugate base. If multiple buffers are used, it is not always possible to decouple buffer induced change from pH or temperature induced change. We have developed a series of mixed biological buffers for protein analysis that can be used across a broad pH range, are compatible with biologically relevant metal ions, and avoid complications that may arise from changing the small molecule composition of buffers when pH is used as an experimental variable.

  4. A Biophysical Neural Model To Describe Spatial Visual Attention

    International Nuclear Information System (INIS)

    Hugues, Etienne; Jose, Jorge V.

    2008-01-01

    Visual scenes have enormous spatial and temporal information that are transduced into neural spike trains. Psychophysical experiments indicate that only a small portion of a spatial image is consciously accessible. Electrophysiological experiments in behaving monkeys have revealed a number of modulations of the neural activity in special visual area known as V4, when the animal is paying attention directly towards a particular stimulus location. The nature of the attentional input to V4, however, remains unknown as well as to the mechanisms responsible for these modulations. We use a biophysical neural network model of V4 to address these issues. We first constrain our model to reproduce the experimental results obtained for different external stimulus configurations and without paying attention. To reproduce the known neuronal response variability, we found that the neurons should receive about equal, or balanced, levels of excitatory and inhibitory inputs and whose levels are high as they are in in vivo conditions. Next we consider attentional inputs that can induce and reproduce the observed spiking modulations. We also elucidate the role played by the neural network to generate these modulations

  5. 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

    Science.gov (United States)

    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

  6. Biophysical Insights into How Spike Threshold Depends on the Rate of Membrane Potential Depolarization in Type I and Type II Neurons.

    Directory of Open Access Journals (Sweden)

    Guo-Sheng Yi

    Full Text Available Dynamic spike threshold plays a critical role in neuronal input-output relations. In many neurons, the threshold potential depends on the rate of membrane potential depolarization (dV/dt preceding a spike. There are two basic classes of neural excitability, i.e., Type I and Type II, according to input-output properties. Although the dynamical and biophysical basis of their spike initiation has been established, the spike threshold dynamic for each cell type has not been well described. Here, we use a biophysical model to investigate how spike threshold depends on dV/dt in two types of neuron. It is observed that Type II spike threshold is more depolarized and more sensitive to dV/dt than Type I. With phase plane analysis, we show that each threshold dynamic arises from the different separatrix and K+ current kinetics. By analyzing subthreshold properties of membrane currents, we find the activation of hyperpolarizing current prior to spike initiation is a major factor that regulates the threshold dynamics. The outward K+ current in Type I neuron does not activate at the perithresholds, which makes its spike threshold insensitive to dV/dt. The Type II K+ current activates prior to spike initiation and there is a large net hyperpolarizing current at the perithresholds, which results in a depolarized threshold as well as a pronounced threshold dynamic. These predictions are further attested in several other functionally equivalent cases of neural excitability. Our study provides a fundamental description about how intrinsic biophysical properties contribute to the threshold dynamics in Type I and Type II neurons, which could decipher their significant functions in neural coding.

  7. Mesenchymal stem cells as therapeutic target of biophysical stimulation for the treatment of musculoskeletal disorders.

    Science.gov (United States)

    Viganò, Marco; Sansone, Valerio; d'Agostino, Maria Cristina; Romeo, Pietro; Perucca Orfei, Carlotta; de Girolamo, Laura

    2016-12-16

    Musculoskeletal disorders are regarded as a major cause of worldwide morbidity and disability, and they result in huge costs for national health care systems. Traditional therapies frequently turned out to be poorly effective in treating bone, cartilage, and tendon disorders or joint degeneration. As a consequence, the development of novel biological therapies that can treat more effectively these conditions should be the highest priority in regenerative medicine. Mesenchymal stem cells (MSCs) represent one of the most promising tools in musculoskeletal tissue regenerative medicine, thanks to their proliferation and differentiation potential and their immunomodulatory and trophic ability. Indeed, MSC-based approaches have been proposed for the treatment of almost all orthopedic conditions, starting from different cell sources, alone or in combination with scaffolds and growth factors, and in one-step or two-step procedures. While all these approaches would require cell harvesting and transplantation, the possibility to stimulate the endogenous MSCs to enhance their tissue homeostasis activity represents a less-invasive and cost-effective therapeutic strategy. Nowadays, the role of tissue-specific resident stem cells as possible therapeutic target in degenerative pathologies is underinvestigated. Biophysical stimulations, and in particular extracorporeal shock waves treatment and pulsed electromagnetic fields, are able to induce proliferation and support differentiation of MSCs from different origins and affect their paracrine production of growth factors and cytokines. The present review reports the attempts to exploit the resident stem cell potential in musculoskeletal pathologies, highlighting the role of MSCs as therapeutic target of currently applied biophysical treatments.

  8. Contribution of human, climate and biophysical drivers to the spatial distribution of wildfires in a French Mediterranean area: where do wildfires start and spread?

    Science.gov (United States)

    Ruffault, Julien; Mouillot, Florent; Moebius, Flavia

    2013-04-01

    Understanding the contribution of biophysical and human drivers to the spatial distribution of fires at regional scale has many ecological and economical implications in a context of on-going global changes. However these fire drivers often interact in complex ways, such that disentangling and assessing the relative contribution of human vs. biophysical factors remains a major challenge. Indeed, the identification of biophysical conditions that promote fires are confused by the inherent stochasticity in fire occurrences and fire spread on the one hand and, by the influence of human factors -through both fire ignition and suppression - on the other. Moreover, different factors may drive fire ignition and fire spread, in such a way that the areas with the highest density of ignitions may not coincide with those where large fires occur. In the present study, we investigated the drivers of fires ignition and spread in a Mediterranean area of southern France. We used a 17 years fire database (the PROMETHEE database from 1989-2006) combined with a set of 8 explanatory variables describing the spatial pattern in ignitions, vegetation and fire weather. We first isolated the weather conditions affecting the fire occurrence and their spread using a statistical model of the weather/fuel water status for each fire event.. The results of these statistical models were used to map the fire weather in terms of average number of days with suitable conditions for burning. Then, we used Boosted regression trees (BRT) models to assess the relative importance of the different variables on the distribution of wildfire with different sizes and to assess the relationship between each variables and fire occurrence and spread probabilities. We found that human activities explained up to 50 % of the spatial distribution of fire ignitions (SDI). The distribution of large fire was chiefly explained by fuel characteristics (about 40%). Surprisingly, the weather indices explained only 20 % of

  9. Symbolic Numerical Magnitude Processing Is as Important to Arithmetic as Phonological Awareness Is to Reading.

    Directory of Open Access Journals (Sweden)

    Kiran Vanbinst

    Full Text Available In this article, we tested, using a 1-year longitudinal design, whether symbolic numerical magnitude processing or children's numerical representation of Arabic digits, is as important to arithmetic as phonological awareness is to reading. Children completed measures of symbolic comparison, phonological awareness, arithmetic, reading at the start of third grade and the latter two were retested at the start of fourth grade. Cross-sectional and longitudinal correlations indicated that symbolic comparison was a powerful domain-specific predictor of arithmetic and that phonological awareness was a unique predictor of reading. Crucially, the strength of these independent associations was not significantly different. This indicates that symbolic numerical magnitude processing is as important to arithmetic development as phonological awareness is to reading and suggests that symbolic numerical magnitude processing is a good candidate for screening children at risk for developing mathematical difficulties.

  10. How trees uptake carbon, release water and cool themselves in air: a marriage between biophysics and turbulent fluid dynamics

    Science.gov (United States)

    Banerjee, Tirtha; Linn, Rodman

    2017-11-01

    Resolving the role of the biosphere as a terrestrial carbon sink and the nature of nonlinear couplings between carbon and water cycles across a very wide range of spatiotemporal scales constitute the scope of this work. To achieve this goal, plant physiology models are coupled with atmospheric turbulence simulations. The plant biophysics code is based on the following principles: (1) a model for photosynthesis; (2) a mass transfer model through the laminar boundary layer on leaves; (3) an optimal leaf water use strategy regulated by stomatal aperture variation; (4) a leaf-level energy balance to accommodate evaporative cooling. Leaf-level outputs are upscaled to plant, canopy and landscape scales using HIGRAD/FIRETEC, a high fidelity large eddy simulation (LES) framework developed at LANL. The coupled biophysics-CFD code can take inputs such as wind speed, light availability, ambient CO2 concentration, air temperature, site characteristics etc. and can deliver predictions for leaf temperature, transpiration, carbon assimilation, sensible and latent heat flux, which is used to illustrate the complex the complex interaction between trees and their surrounding environments. These simulation capabilities are being used to study climate feedbacks of forests and agroecosystems.

  11. Curricular Revision and Reform: The Process, What Was Important, and Lessons Learned.

    Science.gov (United States)

    Ilkiw, Jan E; Nelson, Richard W; Watson, Johanna L; Conley, Alan J; Raybould, Helen E; Chigerwe, Munashe; Boudreaux, Karen

    Beginning in 2005, the Doctor of Veterinary Medicine program at the University of California underwent major curricular review and reform. To provide information for others that follow, we have documented our process and commented on factors that were critical to success, as well as factors we found surprising, difficult, or problematic. The review and reform were initiated by the Executive Committee, who led the process and commissioned the committees. The planning stage took 6 years and involved four faculty committees, while the implementation stage took 5 years and was led by the Curriculum Committee. We are now in year 2 of the institutionalizing stage and no longer refer to our reform as the "new curriculum." The change was driven by a desire to improve the curriculum and the learning environment of the students by aligning the delivery of information with current teaching methodologies and implementing adult learning strategies. We moved from a department- and discipline-based curriculum to a school-wide integrated block curriculum that emphasized student-centered, inquiry-based learning. A limit was placed on in-class time to allow students to apply classroom knowledge by solving problems and cases. We found the journey long and arduous, requiring tremendous commitment and effort. In the change process, we learned the importance of adequate planning, leadership, communication, and a reward structure for those doing the "heavy lifting." Specific to our curricular design, we learned the importance of the block leader role, of setting clear expectations for students, and of partnering with students on the journey.

  12. The Importance of Barley Varieties in terms of Production, Marketing and Processing

    Directory of Open Access Journals (Sweden)

    Rahmi Taşcı

    2017-08-01

    Full Text Available In this study, it is aimed to investigate the criteria affecting the marketing of barley in the stages of barley production, marketing and processing in Konya province. In the study; survey results were used which get from mixed feed (37 items and malt factory (1 item, traders (50 items purchasing and selling barley, and agricultural enterprises (107 items including barley production in agricultural activities operating in Konya province. It was determined that barley varieties were not an important criterion in the selling price, while the hectoliter and other plant species do not mix into barley are the main criteria considered by agricultural enterprises to affect the sale of barley. The most important criteria that traders keep in mind when buying barley is hectoliter of barley, which is followed by moisture, colour and foreign matter confusion rate of barley. The most important criteria that factories take into consideration when purchasing barley is determined as the moisture content of the barley, followed by the hectoliter of barley and the rate of foreign matter contamination. For the malt industry; Barley variety is a very important factor in the purchase criteria, followed by barley humidity and colour.

  13. Importance of Cognitive and Affective Processes when Working with a Computer

    Directory of Open Access Journals (Sweden)

    Blaž Trbižan

    2013-06-01

    Full Text Available Research Question (RQ: Why and how to measure human emotions when working and learning with a computer? Are machines (computers, robots implementing such binary records, where there is a simulation of cognitive phenomena and their processes, or do they actually reflect, therefore, able to think?Purpose: Show the importance of cognitive and affective processes of computer and ICT usage, both in learning and in daily work tasks.Method: Comparative method, where scientific findings were compared and based on these conclusions were drawn.Results: An individual has an active role and the use of ICT enables, through the processes of reflection and exchanges of views, for an individual to resolve problems and consequently is able to achieve excellent results at both the personal (educational level and in business. In learning and working with computers, individuals needinternal motivation. Internal motivation can be increased with positive affective processes that also positively influence cognitive processes.Organization:Knowledge of generational characteristics is currently becoming a competitive advantage of organizations. Younger generations are growing up with computers and both teachers and managers have to beaware and accommodate their teaching and business processes to the requirements of ICT.Society: In the 21st century we live in a knowledge society that is unconditionally connected and dependent on the development of information technology. Digital literacy is an everyday concept that society also is aware of and training programmes are being offered on computer literacy for all generations.Originality: The paper presents a concise synthesis of research and authors points of views recorded over the last 25 years and these are combined with our own conclusions based on observations.Limitations/Future Research:The fundamental limitation is that this is a comparative research study that compares the views and conclusions of different authors

  14. Biophysical analysis of natural, double-helical DNA modified by anticancer heterocyclic complexes of ruthenium(III) in cell-free media

    Czech Academy of Sciences Publication Activity Database

    Malina, Jaroslav; Nováková, Olga; Keppler, B. K.; Alessio, E.; Brabec, Viktor

    2001-01-01

    Roč. 6, č. 4 (2001), s. 435-445 ISSN 0949-8257 R&D Projects: GA ČR GA305/99/0695; GA ČR GA204/97/P028; GA MZd NL6058; GA MZd NL6069; GA MŠk OC D8.50 Institutional research plan: CEZ:AV0Z5004920 Keywords : DNA * ruthenium * cisplatin Subject RIV: BO - Biophysics Impact factor: 3.392, year: 2001

  15. Biophysics of cancer progression and high-throughput mechanical characterization of biomaterials

    Science.gov (United States)

    Osborne, Lukas Dylan

    Cancer metastasis involves a series of events known as the metastatic cascade. In this complex progression, cancer cells detach from the primary tumor, invade the surrounding stromal space, transmigrate the vascular system, and establish secondary tumors at distal sites. Specific mechanical phenotypes are likely adopted to enable cells to successfully navigate the mechanical environments encountered during metastasis. To examine the role of cell mechanics in cancer progression, I employed force-consistent biophysical and biochemical assays to characterize the mechanistic links between stiffness, stiffness response and cell invasion during the epithelial to mesenchymal transition (EMT). EMT is an essential physiological process, whose abnormal reactivation has been implicated in the detachment of cancer cells from epithelial tissue and their subsequent invasion into stromal tissue. I demonstrate that epithelial-state cells respond to force by evoking a stiffening response, and that after EMT, mesenchymal-state cells have reduced stiffness but also lose the ability to increase their stiffness in response to force. Using loss and gain of function studies, two proteins are established as functional connections between attenuated stiffness and stiffness response and the increased invasion capacity acquired after EMT. To enable larger scale assays to more fully explore the connection between biomechanics and cancer, I discuss the development of an automated array high throughput (AHT) microscope. The AHT system is shown to implement passive microbead rheology to accurately characterize the mechanical properties of biomaterials. Compared to manually performed mechanical characterizations, the AHT system executes experiments in two orders of magnitude less time. Finally, I use the AHT microscope to study the effect of gain of function oncogenic molecules on cell stiffness. I find evidence that our assay can identify alterations in cell stiffness due to constitutive

  16. The importance of middlings in the beneficiation technology of Polish copper ore and new possibilities of their processing

    Directory of Open Access Journals (Sweden)

    Skorupska Bozena

    2017-01-01

    Full Text Available In the paper, the middlings (tailings of I cleaner flotation were characterized, and new possibilities of their processing were presented. The advantages of introducing a separate circuit for middlings processing were emphasized. This circuit should be adapted to the properties of the processed middlings and characterized by relative simplicity. An important element of the separate processing of middlings is grinding. The paper presents the advantages of the grinding process in the magnetic mill (MM, which has not been used until now in the enrichment of mineral raw materials. The importance of introducing for the difficult to treat middlings a separate flotation in a flotation machine characterized by a high dynamics of the process was emphasized.

  17. Functional imaging in oncology. Biophysical basis and technical approaches. Vol. 1

    Energy Technology Data Exchange (ETDEWEB)

    Luna, Antonio [Health Time Group, Jaen (Spain); University Hospitals, Case Western Reserve Univ., Cleveland, OH (United States). Dept. of Radiology; Vilanova, Joan C. [Clinica Girona - Hospital Sta. Caterina, Girona (Spain); Hygino da Cruz, L. Celso Jr. [CDPI and IRM, Rio de Janeiro, RJ (Brazil). Dept. of Radiology; Rossi, Santiago E. (ed.) [Centro de Diagnostico, Buenos Aires (Argentina)

    2014-07-01

    Easy-to-read manual on new functional imaging techniques in oncology. Explains current clinical applications and outlines future avenues. Includes numerous high-quality illustrations to highlight the major teaching points. In the new era of functional and molecular imaging, both currently available imaging biomarkers and biomarkers under development are expected to lead to major changes in the management of oncological patients. This well-illustrated two-volume book is a practical manual on the various imaging techniques capable of delivering functional information on cancer, including preclinical and clinical imaging techniques, based on US, CT, MRI, PET and hybrid modalities. This first volume explains the biophysical basis for these functional imaging techniques and describes the techniques themselves. Detailed information is provided on the imaging of cancer hallmarks, including angiogenesis, tumor metabolism, and hypoxia. The techniques and their roles are then discussed individually, covering the full range of modalities in clinical use as well as new molecular and functional techniques. The value of a multiparametric approach is also carefully considered.

  18. Structure-function relationships in pulmonary surfactant membranes: from biophysics to therapy.

    Science.gov (United States)

    Lopez-Rodriguez, Elena; Pérez-Gil, Jesús

    2014-06-01

    Pulmonary surfactant is an essential lipid-protein complex to maintain an operative respiratory surface at the mammalian lungs. It reduces surface tension at the alveolar air-liquid interface to stabilise the lungs against physical forces operating along the compression-expansion breathing cycles. At the same time, surfactant integrates elements establishing a primary barrier against the entry of pathogens. Lack or deficiencies of the surfactant system are associated with respiratory pathologies, which treatment often includes supplementation with exogenous materials. The present review summarises current models on the molecular mechanisms of surfactant function, with particular emphasis in its biophysical properties to stabilise the lungs and the molecular alterations connecting impaired surfactant with diseased organs. It also provides a perspective on the current surfactant-based strategies to treat respiratory pathologies. This article is part of a Special Issue entitled: Membrane Structure and Function: Relevance in the Cell's Physiology, Pathology and Therapy. Copyright © 2014 Elsevier B.V. All rights reserved.

  19. Functional imaging in oncology. Biophysical basis and technical approaches. Vol. 1

    International Nuclear Information System (INIS)

    Luna, Antonio; Hygino da Cruz, L. Celso Jr.

    2014-01-01

    Easy-to-read manual on new functional imaging techniques in oncology. Explains current clinical applications and outlines future avenues. Includes numerous high-quality illustrations to highlight the major teaching points. In the new era of functional and molecular imaging, both currently available imaging biomarkers and biomarkers under development are expected to lead to major changes in the management of oncological patients. This well-illustrated two-volume book is a practical manual on the various imaging techniques capable of delivering functional information on cancer, including preclinical and clinical imaging techniques, based on US, CT, MRI, PET and hybrid modalities. This first volume explains the biophysical basis for these functional imaging techniques and describes the techniques themselves. Detailed information is provided on the imaging of cancer hallmarks, including angiogenesis, tumor metabolism, and hypoxia. The techniques and their roles are then discussed individually, covering the full range of modalities in clinical use as well as new molecular and functional techniques. The value of a multiparametric approach is also carefully considered.

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

    International Nuclear Information System (INIS)

    Rizos, Apostolos K.; Baritaki, Stavroula; Tsikalas, Ioannis; Doetschman, David C.; Spandidos, Demetrios A.; Krambovitis, Elias

    2007-01-01

    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 production 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

  1. Exploring the biophysical option space for feeding the world without deforestation.

    Science.gov (United States)

    Erb, Karl-Heinz; Lauk, Christian; Kastner, Thomas; Mayer, Andreas; Theurl, Michaela C; Haberl, Helmut

    2016-04-19

    Safeguarding the world's remaining forests is a high-priority goal. We assess the biophysical option space for feeding the world in 2050 in a hypothetical zero-deforestation world. We systematically combine realistic assumptions on future yields, agricultural areas, livestock feed and human diets. For each scenario, we determine whether the supply of crop products meets the demand and whether the grazing intensity stays within plausible limits. We find that many options exist to meet the global food supply in 2050 without deforestation, even at low crop-yield levels. Within the option space, individual scenarios differ greatly in terms of biomass harvest, cropland demand and grazing intensity, depending primarily on the quantitative and qualitative aspects of human diets. Grazing constraints strongly limit the option space. Without the option to encroach into natural or semi-natural land, trade volumes will rise in scenarios with globally converging diets, thereby decreasing the food self-sufficiency of many developing regions.

  2. Cerebellar supervised learning revisited: biophysical modeling and degrees-of-freedom control.

    Science.gov (United States)

    Kawato, Mitsuo; Kuroda, Shinya; Schweighofer, Nicolas

    2011-10-01

    The biophysical models of spike-timing-dependent plasticity have explored dynamics with molecular basis for such computational concepts as coincidence detection, synaptic eligibility trace, and Hebbian learning. They overall support different learning algorithms in different brain areas, especially supervised learning in the cerebellum. Because a single spine is physically very small, chemical reactions at it are essentially stochastic, and thus sensitivity-longevity dilemma exists in the synaptic memory. Here, the cascade of excitable and bistable dynamics is proposed to overcome this difficulty. All kinds of learning algorithms in different brain regions confront with difficult generalization problems. For resolution of this issue, the control of the degrees-of-freedom can be realized by changing synchronicity of neural firing. Especially, for cerebellar supervised learning, the triangle closed-loop circuit consisting of Purkinje cells, the inferior olive nucleus, and the cerebellar nucleus is proposed as a circuit to optimally control synchronous firing and degrees-of-freedom in learning. Copyright © 2011 Elsevier Ltd. All rights reserved.

  3. Biophysical Stimuli: A Review of Electrical and Mechanical Stimulation in Hyaline Cartilage.

    Science.gov (United States)

    Vaca-González, Juan J; Guevara, Johana M; Moncayo, Miguel A; Castro-Abril, Hector; Hata, Yoshie; Garzón-Alvarado, Diego A

    2017-09-01

    Objective Hyaline cartilage degenerative pathologies induce morphologic and biomechanical changes resulting in cartilage tissue damage. In pursuit of therapeutic options, electrical and mechanical stimulation have been proposed for improving tissue engineering approaches for cartilage repair. The purpose of this review was to highlight the effect of electrical stimulation and mechanical stimuli in chondrocyte behavior. Design Different information sources and the MEDLINE database were systematically revised to summarize the different contributions for the past 40 years. Results It has been shown that electric stimulation may increase cell proliferation and stimulate the synthesis of molecules associated with the extracellular matrix of the articular cartilage, such as collagen type II, aggrecan and glycosaminoglycans, while mechanical loads trigger anabolic and catabolic responses in chondrocytes. Conclusion The biophysical stimuli can increase cell proliferation and stimulate molecules associated with hyaline cartilage extracellular matrix maintenance.

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

    Science.gov (United States)

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

    2018-02-01

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

  5. Immunomodulatory Potency of Microcystin, an Important Water-Polluting Cyanobacterial Toxin

    Czech Academy of Sciences Publication Activity Database

    Adamovský, O.; Moosová, Z.; Pekarová, Michaela; Basu, A.; Babica, P.; Šindlerová, Lenka; Kubala, Lukáš; Blaha, L.

    2015-01-01

    Roč. 49, č. 20 (2015), s. 12457-12464 ISSN 0013-936X Institutional support: RVO:68081707 Keywords : NF-KAPPA-B * NECROSIS-FACTOR-ALPHA * TOLL-LIKE RECEPTORS Subject RIV: BO - Biophysics Impact factor: 5.393, year: 2015

  6. Specificity and the importance of the process of education of socially maladjusted

    Directory of Open Access Journals (Sweden)

    Justyna Siemionow

    2013-06-01

    Full Text Available The school and related activities is the dominant activity in the lives of students aged 12–18 years. Part of these students for various reasons do not deal with learning , come to this educational problems appear abnormal behavior, the difficult situation in the family. This group of students requires specific approaches and different ways of working with them. Part of the students of socially maladjusted goes to educational centers. The school in the institution works according to different rules in and at the same time has the same objectives as the general school. The most important task is to prepare students to function in an environment, further learning or work. Educational activities are one of the most important elements of the process of reintegration.

  7. PHWR fuel fabrication with imported uranium - procedures and processes

    International Nuclear Information System (INIS)

    Rao, R.V.R.L.V.; Rameswara Rao, A.; Hemantha Rao, G.V.S.; Jayaraj, R.N.

    2010-01-01

    Following the 123 agreement and subsequent agreements with IAEA & NSG, Government of India has entered into bilateral agreements with different countries for nuclear trade. Department of Atomic Energy (DAE), Government of India, has entered into contract with few countries for supply of uranium material for use in the safeguarded PHWRs. Nuclear Fuel Complex (NFC), an industrial unit of DAE, established in the early seventies, is engaged in the production of Nuclear Fuel and Zircaloy items required for Nuclear Power Reactors operating in the country. NFC has placed one of its fuel fabrication facilities (NFC, Block-A, INE-) under safeguards. DAE has opted to procure uranium material in the form of ore concentrate and fuel pellets. Uranium ore concentrate was procured as per the ASTM specifications. Since no international standards are available for PHWR fuel pellets, Specifications have to be finalized based on the present fabrication and operating experience. The process steps have to be modified and fine tuned for handling the imported uranium material especially for ore concentrate. Different transportation methods are to be employed for transportation of uranium material to the facility. Cost of the uranium material imported and the recoveries at various stages of fuel fabrication have impact on the fuel pricing and in turn the unit energy costs. Similarly the operating procedures have to be modified for safeguards inspections by IAEA. NFC has successfully manufactured and supplied fuel bundles for the three 220 MWe safeguarded PHWRs. The paper describes various issues encountered while manufacturing fuel bundles with different types of nuclear material. (author)

  8. Unexplored biophysical problem of manned flight to Mars

    Science.gov (United States)

    Avakyan, Sergey; Voronin, Nikolai; Kovalenok, Vladimir; Trchounian, Armen

    The presentation discusses so far unexplored biophysical problem of manned flight to the Mars, scheduled for the next decade. In long-term manned space flights on the orbital stations "Salyut-6" Soviet cosmonaut crews under the command of one of the co-authors (cosmonaut V.V. Kovalenok) had repeatedly observed the effect of certain geophysical conditions on the psychological state of each crew. These effects were coinciding with the increased intensity of global illumination in the upper ionosphere space on flight altitudes (300-360 km). It is important that, during all these periods, the geomagnetic pulsation's were completely absent. Previously a new but very important for long interplanetary expeditions problem of psychophysical state of the crew in the absence of alternating electromagnetic fields and radiation, including the ionosphere one, was first raised for evolutionarily adapted humanity. However, up to date, this subject, particularly during the long simulation experiments such as "Mars 500", which eliminates much of their value and contribution to the Mars mission, has almost no attention. Indeed, the obtained results have clearly shown that the cosmonaut crews in orbital flight, even deep one within geomagnetic sphere, might experience severe psychological discomfort, the nature of which is fully defined. This is the appearance of such rather unusual geophysical periods of different durations (from minutes to days) those are in the form of an almost complete lack of geomagnetic pulsations on the Earth. The aim is to confirm the need of considering possible pathological effects of the complete lack of rhythm forming, inherent for terrestrial environment geomagnetic pulsation's on psychological and physical state of the cosmonaut crew. This is important for the preparation and conducting the manned flights beyond the Earth's magnetosphere, particularly to the Mars. The influence of the presence of different types of geomagnetic pulsation's recorded by

  9. Folding of multidomain proteins: biophysical consequences of tethering even in apparently independent folding.

    Science.gov (United States)

    Arviv, Oshrit; Levy, Yaakov

    2012-12-01

    Most eukaryotic and a substantial fraction of prokaryotic proteins are composed of more than one domain. The tethering of these evolutionary, structural, and functional units raises, among others, questions regarding the folding process of conjugated domains. Studying the folding of multidomain proteins in silico enables one to identify and isolate the tethering-induced biophysical determinants that govern crosstalks generated between neighboring domains. For this purpose, we carried out coarse-grained and atomistic molecular dynamics simulations of two two-domain constructs from the immunoglobulin-like β-sandwich fold. Each of these was experimentally shown to behave as the "sum of its parts," that is, the thermodynamic and kinetic folding behavior of the constituent domains of these constructs seems to occur independently, with the folding of each domain uncoupled from the folding of its partner in the two-domain construct. We show that the properties of the individual domains can be significantly affected by conjugation to another domain. The tethering may be accompanied by stabilizing as well as destabilizing factors whose magnitude depends on the size of the interface, the length, and the flexibility of the linker, and the relative stability of the domains. Accordingly, the folding of a multidomain protein should not be viewed as the sum of the folding patterns of each of its parts, but rather, it involves abrogating several effects that lead to this outcome. An imbalance between these effects may result in either stabilization or destabilization owing to the tethering. Copyright © 2012 Wiley Periodicals, Inc.

  10. Biophysical model of prokaryotic diversity in geothermal hot springs.

    Science.gov (United States)

    Klales, Anna; Duncan, James; Nett, Elizabeth Janus; Kane, Suzanne Amador

    2012-02-01

    Recent studies of photosynthetic bacteria living in geothermal hot spring environments have revealed surprisingly complex ecosystems with an unexpected level of genetic diversity. One case of particular interest involves the distribution along hot spring thermal gradients of genetically distinct bacterial strains that differ in their preferred temperatures for reproduction and photosynthesis. In such systems, a single variable, temperature, defines the relevant environmental variation. In spite of this, each region along the thermal gradient exhibits multiple strains of photosynthetic bacteria adapted to several distinct thermal optima, rather than a single thermal strain adapted to the local environmental temperature. Here we analyze microbiology data from several ecological studies to show that the thermal distribution data exhibit several universal features independent of location and specific bacterial strain. These include the distribution of optimal temperatures of different thermal strains and the functional dependence of the net population density on temperature. We present a simple population dynamics model of these systems that is highly constrained by biophysical data and by physical features of the environment. This model can explain in detail the observed thermal population distributions, as well as certain features of population dynamics observed in laboratory studies of the same organisms. © 2012 American Physical Society

  11. Impact of bio-physical feedbacks on the tropical climate in coupled and uncoupled GCMs

    Science.gov (United States)

    Park, Jong-Yeon; Kug, Jong-Seong; Seo, Hyodae; Bader, Jürgen

    2014-10-01

    The bio-physical feedback process between the marine ecosystem and the tropical climate system is investigated using both an ocean circulation model and a fully-coupled ocean-atmosphere circulation model, which interact with a biogeochemical model. We found that the presence of chlorophyll can have significant impact on the characteristics of the El Niño-Southern Oscillation (ENSO), including its amplitude and asymmetry, as well as on the mean state. That is, chlorophyll generally increases mean sea surface temperature (SST) due to the direct biological heating. However, SST in the eastern equatorial Pacific decreases due to the stronger indirect dynamical response to the biological effects outweighing the direct thermal response. It is demonstrated that this biologically-induced SST cooling is intensified and conveyed to other tropical-ocean basins when atmosphere-ocean coupling is taken into account. It is also found that the presence of chlorophyll affects the magnitude of ENSO by two different mechanisms; one is an amplifying effect by the mean chlorophyll, which is associated with shoaling of the mean thermocline depth, and the other is a damping effect derived from the interactively-varying chlorophyll coupled with the physical model. The atmosphere-ocean coupling reduces the biologically-induced ENSO amplifying effect through the weakening of atmospheric feedback. Lastly, there is also a biological impact on ENSO which enhances the positive skewness. This skewness change is presumably caused by the phase dependency of thermocline feedback which affects the ENSO magnitude.

  12. Biophysical, Socioeconomic, and Geopolitical Vulnerabilities to Hydropower Development on the Nu River, China

    Directory of Open Access Journals (Sweden)

    Desiree D. Tullos

    2013-09-01

    Full Text Available Rapid hydropower development is occurring in China's Yunnan province in response to increasing clean energy demands, exposing potential vulnerabilities of the area's ecosystems, communities, and geopolitical systems. Here, we present original data on the cultures, economics, hydro-politics, and environments of the Nu River basin, based on household surveys, analysis of geopolitical events, and hydrological, hydraulic, and landscape modeling. We identify sources of vulnerability and investigate relationships among biophysical, socioeconomic, and geopolitical elements that contribute to vulnerability. Our results illustrate the role of geographic isolation in intensifying vulnerability to hydropower development and how access to information, data uncertainty, and geopolitics influence the vulnerability of people and the environment. We emphasize specific needs for developing support mechanisms for social, ecological, and political groups that are vulnerable to hydropower development.

  13. Antimicrobial and biophysical properties of surfactant supplemented with an antimicrobial peptide for treatment of bacterial pneumonia.

    Science.gov (United States)

    Banaschewski, Brandon J H; Veldhuizen, Edwin J A; Keating, Eleonora; Haagsman, Henk P; Zuo, Yi Y; Yamashita, Cory M; Veldhuizen, Ruud A W

    2015-01-01

    Antibiotic-resistant bacterial infections represent an emerging health concern in clinical settings, and a lack of novel developments in the pharmaceutical pipeline is creating a "perfect storm" for multidrug-resistant bacterial infections. Antimicrobial peptides (AMPs) have been suggested as future therapeutics for these drug-resistant bacteria, since they have potent broad-spectrum activity, with little development of resistance. Due to the unique structure of the lung, bacterial pneumonia has the additional problem of delivering antimicrobials to the site of infection. One potential solution is coadministration of AMPs with exogenous surfactant, allowing for distribution of the peptides to distal airways and opening of collapsed lung regions. The objective of this study was to test various surfactant-AMP mixtures with regard to maintaining pulmonary surfactant biophysical properties and bactericidal functions. We compared the properties of four AMPs (CATH-1, CATH-2, CRAMP, and LL-37) suspended in bovine lipid-extract surfactant (BLES) by assessing surfactant-AMP mixture biophysical and antimicrobial functions. Antimicrobial activity was tested against methillicin-resistant Staphylococcus aureus and Pseudomonas aeruginosa. All AMP/surfactant mixtures exhibited an increase of spreading compared to a BLES control. BLES+CATH-2 mixtures had no significantly different minimum surface tension versus the BLES control. Compared to the other cathelicidins, CATH-2 retained the most bactericidal activity in the presence of BLES. The BLES+CATH-2 mixture appears to be an optimal surfactant-AMP mixture based on in vitro assays. Future directions involve investigating the potential of this mixture in animal models of bacterial pneumonia. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  14. Functional and biophysical studies on four ceratoplatanins from the fungus Moniliophthora perniciosa, causal agent of the Witche's broom disease

    Energy Technology Data Exchange (ETDEWEB)

    Barsottini, M.; Zaparoli, G.; Garcia, O.; Pereira, G.A.G. [Universidade Estadual de Campinas (UNICAMP), SP (Brazil); Oliveira, J.F.; Tiezzi, H.O.; Ambrosio, A.L.B.; Dias, S.M.G. [Laboratorio Nacional de Biociencias - LNBIO, Campinas, SP (Brazil)

    2012-07-01

    Full text: Ceratoplatanin (CP) is a secreted protein of 12.4 kDa initially identified in culture filtrates of the disease ascomycete Ceratocystis fimbriata f. sp. platani, etiological agent of the canker stain disease. CP is also the founding member of the namesake protein family, which contains fungal-secreted proteins involved in various stages of the host-fungus interaction and may act as phytotoxins or elicitors of defense response. Besides the low molecular weight, CPs have a high percentage of hydrophobic residues and share two conserved intramolecular disulfide bonds. It has been suggested that CPs have important physiological functions, including interaction with cell wall or cell membrane and manipulation of the host's defense system. Furthermore, a recent work showed that the ceratoplatanin from C. fimbriata has some degree of affinity for the saccharide 4-N-acetylglucosamine. However, its precise molecular function remains elusive. Five putative CPs have been identified in Moniliophthora perniciosa a basidiomycete fungus responsible for great economic losses in cocoa industry in the form of Witches' broom disease (WBD) , four of which had their crystal structures resolved by our group. In this work we report biophysical and functional studies on these MpCPs aiming at understanding their role and importance during the WBD progression. (author)

  15. Simulating the effect of conditioning on the drying of cut grass

    NARCIS (Netherlands)

    Lorenzi, de F.; Bosma, A.H.; Stanghellini, C.

    1996-01-01

    Field wilting and drying of hay is an important agricultural process upon which the quality of material subsequently conserved is dependent. The research described here aims at translating the biophysical processes that affect field drying of grass into parameters sets to be used for decision

  16. Process industry energy retrofits: the importance of emission baselines for greenhouse gas reductions

    International Nuclear Information System (INIS)

    Aadahl, Anders; Harvey, Simon; Berntsson, Thore

    2004-01-01

    Fuel combustion for heat and/or electric power production is often the largest contributor of greenhouse gas (GHG) emissions from an industrial process plant. Economically feasible options to reduce these emissions include fuel switching and retrofitting the plant's energy system. Process integration methods and tools can be used to evaluate potential retrofit measures. For assessing the GHG emissions reduction potential for the measures considered, it is also necessary to define appropriate GHG emission baselines. This paper presents a systematic GHG emission calculation method for retrofit situations including improved heat exchange, integration of combined heat and power (CHP) units, and combinations of both. The proposed method is applied to five different industrial processes in order to compare the impact of process specific parameters and energy market specific parameters. For potential GHG emission reductions the results from the applied study reveal that electricity grid emissions are significantly more important than differences between individual processes. Based on the results of the study, it is suggested that for sustainable investment decision considerations a conservative emission baseline is most appropriate. Even so, new industrial CHP in the Northern European energy market could play a significant role in the common effort to decrease GHG emissions

  17. From seed production to seedling establishment: Important steps in an invasive process

    Science.gov (United States)

    Ferreras, Ana Elisa; Galetto, Leonardo

    2010-03-01

    It is widely accepted that exotic invasive species are one of the most important ecological and economic problems. Reproductive and establishment traits are considered key features of a population expansion process, but few works have studied many of these simultaneously. This work examines how large the differences are in reproductive and establishment traits between two Fabaceae, the exotic invasive, Gleditsia triacanthos and the native, Acacia aroma. Gleditsia is a serious leguminous woody invader in various parts of the world and Acacia is a common native tree of Argentina. Both species have similar dispersal mechanisms and their reproductive phenology overlaps. We chose 17 plants of each species in a continuous forest of the Chaco Serrano Forest of Córdoba, Argentina. In each plant we measured fruit production, fruit removal (exclusion experiments), seed predation (pre- and post-dispersal), seed germination, seed bank (on each focal tree, three sampling periods during the year), and density of seedlings (around focal individuals and randomly in the study site). Gleditsia presented some traits that could favour the invasion process, such as a higher number of seeds per plant, percentage of scarified seed germination and density of seedlings around the focal individuals, than Acacia. On the other hand, Gleditsia presented a higher percentage of seed predation. The seed bank was persistent in both species and no differences were observed in fruit removal. This work highlights the importance of simultaneously studying reproductive and establishment variables involved in the spreading of an exotic invasive species. It also gives important insight into the variables to be considered when planning management strategies. The results are discussed from the perspective of some remarkable hypotheses on invasive species and may contribute to rethinking some aspects of the theory on invasive species.

  18. The Physics of Proteins An Introduction to Biological Physics and Molecular Biophysics

    CERN Document Server

    Frauenfelder, Hans; Chan, Winnie S

    2010-01-01

    Physics and the life sciences have established new connections within the past few decades, resulting in biological physics as an established subfield with strong groups working in many physics departments. These interactions between physics and biology form a two-way street with physics providing new tools and concepts for understanding life, while biological systems can yield new insights into the physics of complex systems. To address the challenges of this interdisciplinary area, The Physics of Proteins: An Introduction to Biological Physics and Molecular Biophysics is divided into three interconnected sections. In Parts I and II, early chapters introduce the terminology and describe the main biological systems that physicists will encounter. Similarities between biomolecules, glasses, and solids are stressed with an emphasis on the fundamental concepts of living systems. The central section (Parts III and IV) delves into the dynamics of complex systems. A main theme is the realization that biological sys...

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

    Energy Technology Data Exchange (ETDEWEB)

    Lisenko, S A; Kugeiko, M M [Belarusian State University, Minsk (Belarus)

    2013-07-31

    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. (laser applications in biology and medicine)

  20. The Activity of the Neutral Sphingomyelinase Is Important in T Cell Recruitment and Directional Migration

    Directory of Open Access Journals (Sweden)

    Lena Collenburg

    2017-08-01

    Full Text Available Breakdown of sphingomyelin as catalyzed by the activity of sphingomyelinases profoundly affects biophysical properties of cellular membranes which is particularly important with regard to compartmentalization of surface receptors and their signaling relay. As it is activated both upon TCR ligation and co-stimulation in a spatiotemporally controlled manner, the neutral sphingomyelinase (NSM has proven to be important in T cell activation, where it appears to play a particularly important role in cytoskeletal reorganization and cell polarization. Because these are important parameters in directional T cell migration and motility in tissues, we analyzed the role of the NSM in these processes. Pharmacological inhibition of NSM interfered with early lymph node homing of T cells in vivo indicating that the enzyme impacts on endothelial adhesion, transendothelial migration, sensing of chemokine gradients or, at a cellular level, acquisition of a polarized phenotype. NSM inhibition reduced adhesion of T cells to TNF-α/IFN-γ activated, but not resting endothelial cells, most likely via inhibiting high-affinity LFA-1 clustering. NSM activity proved to be highly important in directional T cell motility in response to SDF1-α, indicating that their ability to sense and translate chemokine gradients might be NSM dependent. In fact, pharmacological or genetic NSM ablation interfered with T cell polarization both at an overall morphological level and redistribution of CXCR4 and pERM proteins on endothelial cells or fibronectin, as well as with F-actin polymerization in response to SDF1-α stimulation, indicating that efficient directional perception and signaling relay depend on NSM activity. Altogether, these data support a central role of the NSM in T cell recruitment and migration both under homeostatic and inflamed conditions by regulating polarized redistribution of receptors and their coupling to the cytoskeleton.