KEK digital accelerator

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T. Iwashita

2011-07-01

Full Text Available The High Energy Accelerator Research Organization KEK digital accelerator (KEK-DA is a renovation of the KEK 500 MeV booster proton synchrotron, which was shut down in 2006. The existing 40 MeV drift tube linac and rf cavities have been replaced by an electron cyclotron resonance (ECR ion source embedded in a 200 kV high-voltage terminal and induction acceleration cells, respectively. A DA is, in principle, capable of accelerating any species of ion in all possible charge states. The KEK-DA is characterized by specific accelerator components such as a permanent magnet X-band ECR ion source, a low-energy transport line, an electrostatic injection kicker, an extraction septum magnet operated in air, combined-function main magnets, and an induction acceleration system. The induction acceleration method, integrating modern pulse power technology and state-of-art digital control, is crucial for the rapid-cycle KEK-DA. The key issues of beam dynamics associated with low-energy injection of heavy ions are beam loss caused by electron capture and stripping as results of the interaction with residual gas molecules and the closed orbit distortion resulting from relatively high remanent fields in the bending magnets. Attractive applications of this accelerator in materials and biological sciences are discussed.

Biological and medical research with accelerated heavy ions at the Bevalac, 1977-1980. [Lead abstract

Energy Technology Data Exchange (ETDEWEB)

Pirruccello, M.C.; Tobias, C.A. (eds.)

1980-11-01

Separate abstracts were prepared for the 46 papers presented in this progress report. This report is a major review of studies with accelerated heavy ions carried out by the Biology and Medicine Division of Lawrence Berkeley Laboratory from 1977 to 1980. (KRM)

Accelerating and benchmarking operating system functions in a “soft” system

Directory of Open Access Journals (Sweden)

Péter Molnár

2015-06-01

Full Text Available The todays computing technology provokes serious debates whether the operating system functions are implemented in the best possible way. The suggestions range from accelerating only certain functions through providing complete real-time operating systems as coprocessors to using simultaneously hardware and software implemented threads in the operating system. The performance gain in such systems depends on many factors, so its quantification is not a simple task at all. In addition to the subtleties of operating systems, the hardware accelerators in modern processors may considerably affect the results of such measurements. The reconfigurable systems offer a platform, where even end users can carry out reliable and accurate measurements. The paper presents a hardware acceleration idea for speeding up a simple OS service, its verification setup and the measurement results.

A Unifying Theory of Biological Function.

Science.gov (United States)

van Hateren, J H

2017-01-01

A new theory that naturalizes biological function is explained and compared with earlier etiological and causal role theories. Etiological (or selected effects) theories explain functions from how they are caused over their evolutionary history. Causal role theories analyze how functional mechanisms serve the current capacities of their containing system. The new proposal unifies the key notions of both kinds of theories, but goes beyond them by explaining how functions in an organism can exist as factors with autonomous causal efficacy. The goal-directedness and normativity of functions exist in this strict sense as well. The theory depends on an internal physiological or neural process that mimics an organism's fitness, and modulates the organism's variability accordingly. The structure of the internal process can be subdivided into subprocesses that monitor specific functions in an organism. The theory matches well with each intuition on a previously published list of intuited ideas about biological functions, including intuitions that have posed difficulties for other theories.

ASPIRE: An automated sample positioning and irradiation system for radiation biology experiments at Inter University Accelerator Centre, New Delhi

International Nuclear Information System (INIS)

Kothari, Ashok; Barua, P.; Archunan, M.; Rani, Kusum; Subramanian, E.T.; Pujari, Geetanjali; Kaur, Harminder; Satyanarayanan, V.V.V.; Sarma, Asitikantha; Avasthi, D.K.

2015-01-01

An automated irradiation setup for biology samples has been built at Inter University Accelerator Centre (IUAC), New Delhi, India. It can automatically load and unload 20 biology samples in a run of experiment. It takes about 20 min [2% of the cell doubling time] to irradiate all the 20 samples. Cell doubling time is the time taken by the cells (kept in the medium) to grow double in numbers. The cells in the samples keep growing during entire of the experiment. The fluence irradiated to the samples is measured with two silicon surface barrier detectors. Tests show that the uniformity of fluence and dose of heavy ions reaches to 2% at the sample area in diameter of 40 mm. The accuracy of mean fluence at the center of the target area is within 1%. The irradiation setup can be used to the studies of radiation therapy, radiation dosimetry and molecular biology at the heavy ion accelerator. - Highlights: • Automated positioning and irradiation setup for biology samples at IUAC is built. • Loading and unloading of 20 biology samples can be automatically carried out. • Biologicals cells keep growing during entire experiment. • Fluence and dose of heavy ions are measured by two silicon barrier detectors. • Uniformity of fluence and dose of heavy ions at sample position reaches to 2%

Distribution of computer functionality for accelerator control at the Brookhaven AGS

International Nuclear Information System (INIS)

Stevens, A.; Clifford, T.; Frankel, R.

1985-01-01

A set of physical and functional system components and their interconnection protocols have been established for all controls work at the AGS. Portions of these designs were tested as part of enhanced operation of the AGS as a source of polarized protons and additional segments will be implemented during the continuing construction efforts which are adding heavy ion capability to our facility. Included in our efforts are the following computer and control system elements: a broad band local area network, which embodies MODEMS; transmission systems and branch interface units; a hierarchical layer, which performs certain data base and watchdog/alarm functions; a group of work station processors (Apollo's) which perform the function of traditional minicomputer host(s) and a layer, which provides both real time control and standardization functions for accelerator devices and instrumentation. Data base and other accelerator functionality is assigned to the most correct level within our network for both real time performance, long-term utility, and orderly growth

Distinguishing between "function" and "effect" in genome biology.

Science.gov (United States)

Doolittle, W Ford; Brunet, Tyler D P; Linquist, Stefan; Gregory, T Ryan

2014-05-09

Much confusion in genome biology results from conflation of possible meanings of the word "function." We suggest that, in this connection, attention should be paid to evolutionary biologists and philosophers who have previously dealt with this problem. We need only decide that although all genomic structures have effects, only some of them should be said to have functions. Although it will very often be difficult or impossible to establish function (strictly defined), it should not automatically be assumed. We enjoin genomicists in particular to pay greater attention to parsing biological effects. © The Author(s) 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

A Unifying Theory of Biological Function

NARCIS (Netherlands)

van Hateren, J. H.

2017-01-01

A new theory that naturalizes biological function is explained and compared with earlier etiological and causal role theories. Etiological (or selected effects) theories explain functions from how they are caused over their evolutionary history. Causal role theories analyze how functional mechanisms

A functional overview of conservation biological control

DEFF Research Database (Denmark)

Begg, Graham S; Cook, Samantha M; Dye, Richard

2017-01-01

Conservation biological control (CBC) is a sustainable approach to pest management that can contribute to a reduction in pesticide use as part of an Integrated Pest Management (IPM) strategy. CBC is based on the premise that countering habitat loss and environmental disturbance associated...... CBC prescriptions have proved elusive. To tackle this, we consolidate existing knowledge of CBC using a simple conceptual model that organises the functional elements of CBC into a common, unifying framework. We identify and integrate the key biological processes affecting natural enemies...... and their biological control function across local and regional scales, and consider the interactions, interdependencies and constraints that determine the outcome of CBC strategies. Conservation measures are often effective in supporting natural enemy populations but their success cannot be guaranteed; the greatest...

Uncovering Biological Network Function via Graphlet Degree Signatures

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Nataša Pržulj

2008-01-01

Full Text Available Motivation: Proteins are essential macromolecules of life and thus understanding their function is of great importance. The number of functionally unclassified proteins is large even for simple and well studied organisms such as baker’s yeast. Methods for determining protein function have shifted their focus from targeting specific proteins based solely on sequence homology to analyses of the entire proteome based on protein-protein interaction (PPI networks. Since proteins interact to perform a certain function, analyzing structural properties of PPI networks may provide useful clues about the biological function of individual proteins, protein complexes they participate in, and even larger subcellular machines.Results: We design a sensitive graph theoretic method for comparing local structures of node neighborhoods that demonstrates that in PPI networks, biological function of a node and its local network structure are closely related. The method summarizes a protein’s local topology in a PPI network into the vector of graphlet degrees called the signature of the protein and computes the signature similarities between all protein pairs. We group topologically similar proteins under this measure in a PPI network and show that these protein groups belong to the same protein complexes, perform the same biological functions, are localized in the same subcellular compartments, and have the same tissue expressions. Moreover, we apply our technique on a proteome-scale network data and infer biological function of yet unclassified proteins demonstrating that our method can provide valuable guidelines for future experimental research such as disease protein prediction.Availability: Data is available upon request.

Towards Integration of Biological and Physiological Functions at Multiple Levels

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Taishin eNomura

2010-12-01

Full Text Available An aim of systems physiology today can be stated as to establish logical and quantitative bridges between phenomenological attributes of physiological entities such as cells and organs and physical attributes of biological entities, i.e., biological molecules, allowing us to describe and better understand physiological functions in terms of underlying biological functions. This article illustrates possible schema that can be used for promoting systems physiology by integrating quantitative knowledge of biological and physiological functions at multiple levels of time and space with the use of information technology infrastructure. Emphasis will be made for systematic, modular, hierarchical, and standardized descriptions of mathematical models of the functions and advantages for the use of them.

Biocellion: accelerating computer simulation of multicellular biological system models.

Science.gov (United States)

Kang, Seunghwa; Kahan, Simon; McDermott, Jason; Flann, Nicholas; Shmulevich, Ilya

2014-11-01

Biological system behaviors are often the outcome of complex interactions among a large number of cells and their biotic and abiotic environment. Computational biologists attempt to understand, predict and manipulate biological system behavior through mathematical modeling and computer simulation. Discrete agent-based modeling (in combination with high-resolution grids to model the extracellular environment) is a popular approach for building biological system models. However, the computational complexity of this approach forces computational biologists to resort to coarser resolution approaches to simulate large biological systems. High-performance parallel computers have the potential to address the computing challenge, but writing efficient software for parallel computers is difficult and time-consuming. We have developed Biocellion, a high-performance software framework, to solve this computing challenge using parallel computers. To support a wide range of multicellular biological system models, Biocellion asks users to provide their model specifics by filling the function body of pre-defined model routines. Using Biocellion, modelers without parallel computing expertise can efficiently exploit parallel computers with less effort than writing sequential programs from scratch. We simulate cell sorting, microbial patterning and a bacterial system in soil aggregate as case studies. Biocellion runs on x86 compatible systems with the 64 bit Linux operating system and is freely available for academic use. Visit http://biocellion.com for additional information. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Frontier applications of electrostatic accelerators

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Liu, Ke-Xin; Wang, Yu-Gang; Fan, Tie-Shuan; Zhang, Guo-Hui; Chen, Jia-Er

2013-10-01

Electrostatic accelerator is a powerful tool in many research fields, such as nuclear physics, radiation biology, material science, archaeology and earth sciences. Two electrostatic accelerators, one is the single stage Van de Graaff with terminal voltage of 4.5 MV and another one is the EN tandem with terminal voltage of 6 MV, were installed in 1980s and had been put into operation since the early 1990s at the Institute of Heavy Ion Physics. Many applications have been carried out since then. These two accelerators are described and summaries of the most important applications on neutron physics and technology, radiation biology and material science, as well as accelerator mass spectrometry (AMS) are presented.

Microfluidic Technologies for Synthetic Biology

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Sung Kuk Lee

2011-06-01

Full Text Available Microfluidic technologies have shown powerful abilities for reducing cost, time, and labor, and at the same time, for increasing accuracy, throughput, and performance in the analysis of biological and biochemical samples compared with the conventional, macroscale instruments. Synthetic biology is an emerging field of biology and has drawn much attraction due to its potential to create novel, functional biological parts and systems for special purposes. Since it is believed that the development of synthetic biology can be accelerated through the use of microfluidic technology, in this review work we focus our discussion on the latest microfluidic technologies that can provide unprecedented means in synthetic biology for dynamic profiling of gene expression/regulation with high resolution, highly sensitive on-chip and off-chip detection of metabolites, and whole-cell analysis.

Function of dynamic models in systems biology: linking structure to behaviour.

Science.gov (United States)

Knüpfer, Christian; Beckstein, Clemens

2013-10-08

Dynamic models in Systems Biology are used in computational simulation experiments for addressing biological questions. The complexity of the modelled biological systems and the growing number and size of the models calls for computer support for modelling and simulation in Systems Biology. This computer support has to be based on formal representations of relevant knowledge fragments. In this paper we describe different functional aspects of dynamic models. This description is conceptually embedded in our "meaning facets" framework which systematises the interpretation of dynamic models in structural, functional and behavioural facets. Here we focus on how function links the structure and the behaviour of a model. Models play a specific role (teleological function) in the scientific process of finding explanations for dynamic phenomena. In order to fulfil this role a model has to be used in simulation experiments (pragmatical function). A simulation experiment always refers to a specific situation and a state of the model and the modelled system (conditional function). We claim that the function of dynamic models refers to both the simulation experiment executed by software (intrinsic function) and the biological experiment which produces the phenomena under investigation (extrinsic function). We use the presented conceptual framework for the function of dynamic models to review formal accounts for functional aspects of models in Systems Biology, such as checklists, ontologies, and formal languages. Furthermore, we identify missing formal accounts for some of the functional aspects. In order to fill one of these gaps we propose an ontology for the teleological function of models. We have thoroughly analysed the role and use of models in Systems Biology. The resulting conceptual framework for the function of models is an important first step towards a comprehensive formal representation of the functional knowledge involved in the modelling and simulation process

Fibroblast Growth Factors: Biology, Function, and Application for Tissue Regeneration

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Ye-Rang Yun

2010-01-01

Full Text Available Fibroblast growth factors (FGFs that signal through FGF receptors (FGFRs regulate a broad spectrum of biological functions, including cellular proliferation, survival, migration, and differentiation. The FGF signal pathways are the RAS/MAP kinase pathway, PI3 kinase/AKT pathway, and PLCγ pathway, among which the RAS/MAP kinase pathway is known to be predominant. Several studies have recently implicated the in vitro biological functions of FGFs for tissue regeneration. However, to obtain optimal outcomes in vivo, it is important to enhance the half-life of FGFs and their biological stability. Future applications of FGFs are expected when the biological functions of FGFs are potentiated through the appropriate use of delivery systems and scaffolds. This review will introduce the biology and cellular functions of FGFs and deal with the biomaterials based delivery systems and their current applications for the regeneration of tissues, including skin, blood vessel, muscle, adipose, tendon/ligament, cartilage, bone, tooth, and nerve tissues.

The biological function of consciousness

Directory of Open Access Journals (Sweden)

Brian eEarl

2014-08-01

Full Text Available This research is an investigation of whether consciousness—one’s ongoing experience—influences one’s behavior and, if so, how. Analysis of the components, structure, properties, and temporal sequences of consciousness has established that, (1 contrary to one’s intuitive understanding, consciousness does not have an active, executive role in determining behavior; (2 consciousness does have a biological function; and (3 consciousness is solely information in various forms. Consciousness is associated with a flexible response mechanism (FRM for decision-making, planning, and generally responding in nonautomatic ways. The FRM generates responses by manipulating information and, to function effectively, its data input must be restricted to task-relevant information. The properties of consciousness correspond to the various input requirements of the FRM; and when important information is missing from consciousness, functions of the FRM are adversely affected; both of which indicate that consciousness is the input data to the FRM. Qualitative and quantitative information (shape, size, location, etc., is incorporated into the input data by a qualia array of colors, sounds, and so on, which makes the input conscious. This view of the biological function of consciousness provides an explanation why we have experiences; why we have emotional and other feelings, and why their loss is associated with poor decision-making; why blindsight patients do not spontaneously initiate responses to events in their blind field; why counter-habitual actions are only possible when the intended action is in mind; and the reason for inattentional blindness.

Accelerating Smith-Waterman Algorithm for Biological Database Search on CUDA-Compatible GPUs

Science.gov (United States)

Munekawa, Yuma; Ino, Fumihiko; Hagihara, Kenichi

This paper presents a fast method capable of accelerating the Smith-Waterman algorithm for biological database search on a cluster of graphics processing units (GPUs). Our method is implemented using compute unified device architecture (CUDA), which is available on the nVIDIA GPU. As compared with previous methods, our method has four major contributions. (1) The method efficiently uses on-chip shared memory to reduce the data amount being transferred between off-chip video memory and processing elements in the GPU. (2) It also reduces the number of data fetches by applying a data reuse technique to query and database sequences. (3) A pipelined method is also implemented to overlap GPU execution with database access. (4) Finally, a master/worker paradigm is employed to accelerate hundreds of database searches on a cluster system. In experiments, the peak performance on a GeForce GTX 280 card reaches 8.32 giga cell updates per second (GCUPS). We also find that our method reduces the amount of data fetches to 1/140, achieving approximately three times higher performance than a previous CUDA-based method. Our 32-node cluster version is approximately 28 times faster than a single GPU version. Furthermore, the effective performance reaches 75.6 giga instructions per second (GIPS) using 32 GeForce 8800 GTX cards.

Accelerating functional verification of an integrated circuit

Science.gov (United States)

Deindl, Michael; Ruedinger, Jeffrey Joseph; Zoellin, Christian G.

2015-10-27

Illustrative embodiments include a method, system, and computer program product for accelerating functional verification in simulation testing of an integrated circuit (IC). Using a processor and a memory, a serial operation is replaced with a direct register access operation, wherein the serial operation is configured to perform bit shifting operation using a register in a simulation of the IC. The serial operation is blocked from manipulating the register in the simulation of the IC. Using the register in the simulation of the IC, the direct register access operation is performed in place of the serial operation.

Analyzing radial acceleration with a smartphone acceleration sensor

Science.gov (United States)

Vogt, Patrik; Kuhn, Jochen

2013-03-01

This paper continues the sequence of experiments using the acceleration sensor of smartphones (for description of the function and the use of the acceleration sensor, see Ref. 1) within this column, in this case for analyzing the radial acceleration.

Special conference of the American Association for Cancer Research on molecular imaging in cancer: linking biology, function, and clinical applications in vivo.

Science.gov (United States)

Luker, Gary D

2002-04-01

The AACR Special Conference on Molecular Imaging in Cancer: Linking Biology, Function, and Clinical Applications In Vivo, was held January 23-27, 2002, at the Contemporary Hotel, Walt Disney World, Orlando, FL. Co-Chairs David Piwnica-Worms, Patricia Price and Thomas Meade brought together researchers with diverse expertise in molecular biology, gene therapy, chemistry, engineering, pharmacology, and imaging to accelerate progress in developing and applying technologies for imaging specific cellular and molecular signals in living animals and humans. The format of the conference was the presentation of research that focused on basic and translational biology of cancer and current state-of-the-art techniques for molecular imaging in animal models and humans. This report summarizes the special conference on molecular imaging, highlighting the interfaces of molecular biology with animal models, instrumentation, chemistry, and pharmacology that are essential to convert the dreams and promise of molecular imaging into improved understanding, diagnosis, and management of cancer.

Mining Functional Modules in Heterogeneous Biological Networks Using Multiplex PageRank Approach.

Science.gov (United States)

Li, Jun; Zhao, Patrick X

2016-01-01

Identification of functional modules/sub-networks in large-scale biological networks is one of the important research challenges in current bioinformatics and systems biology. Approaches have been developed to identify functional modules in single-class biological networks; however, methods for systematically and interactively mining multiple classes of heterogeneous biological networks are lacking. In this paper, we present a novel algorithm (called mPageRank) that utilizes the Multiplex PageRank approach to mine functional modules from two classes of biological networks. We demonstrate the capabilities of our approach by successfully mining functional biological modules through integrating expression-based gene-gene association networks and protein-protein interaction networks. We first compared the performance of our method with that of other methods using simulated data. We then applied our method to identify the cell division cycle related functional module and plant signaling defense-related functional module in the model plant Arabidopsis thaliana. Our results demonstrated that the mPageRank method is effective for mining sub-networks in both expression-based gene-gene association networks and protein-protein interaction networks, and has the potential to be adapted for the discovery of functional modules/sub-networks in other heterogeneous biological networks. The mPageRank executable program, source code, the datasets and results of the presented two case studies are publicly and freely available at http://plantgrn.noble.org/MPageRank/.

Synthesis of Biologically Active Natural Component 4-Hydroxyderricin Through Water-Accelerated [3,3]-Sigmatropic Rearrangement

Energy Technology Data Exchange (ETDEWEB)

Kim, Sijun; Lee, Jaejun; Yoon, Hyunho; Jun, Jonggab [Hallym Univ., Chuncheon (Korea, Republic of)

2013-09-15

We report herein the practical and effective total synthesis of biologically active 4-hydroxyderricin, a poly-phenolic chalcone compound containing m-prenyl group at ring A. The key steps of the synthesis are Claisen-Schmidt condensation of the the two phenolic units 17 and 18 to chalcone 19 and the water-accelerated [3,3]-sigma-tropic rearrangement of 1,1-dimethyl-2-propenyl aryl ether 20 to introduce the m-prenyl unit in 4-hydroxyderricin. Two types of polyphenolic chalcones, 4-hydroxyderricin (1) and xanthoangelol (2), are especially rich in the plant, and the 4-hydroxyderricin exhibited the major responsibility for the various biological activities. Sugamoto reported the synthesis of 4-hydroxy-derricin via [1,3]-sigmatropic rearrangement of chalcone ether using montmorillonite K10 which showed relatively low rearrangement yield (Scheme 1), and this is the only reported total synthesis of 1 as far as we know.

Accelerator mass spectrometry and associated facilities at Inter-University Accelerator Centre, New Delhi, India

International Nuclear Information System (INIS)

Kumar, Pankaj; Bohra, Archna; Ojha, S.; Gargari, S.; Joshi, R.; Roonwal, G.S.; Chopra, S.; Pattanaik, J.K.; Balakrishnan, S.

2011-01-01

Accelerator Mass Spectrometry (AMS) facility at Inter-University Accelerator Centre (IUAC) is developed by upgrading its existing 15UD Pelletron accelerator. Since last two decades Pelletron is mainly used for nuclear physics, materials science, atomic physics, radiation biology and accelerator mass spectrometry is recent development. In addition, a chemistry laboratory in clean room for the chemical processing of samples for AMS studies has also been established. At present the AMS facility is used for 10 Be, 26 Al measurements and soon other long lived radio-isotopes will also be used

Lipid polymorphism and the functional roles of lipids in biological membranes

NARCIS (Netherlands)

Cullis, P.R.; Kruijff, B. de

1979-01-01

The reasons for the great variety of lipids found in biological membranes, and the relations between lipid composition and membrane function pose major unsolved problems in membrane biology. Perhaps the only major functional role of lipids which may be regarded as firmly established involves the

Functional biology of sympatric krill species

DEFF Research Database (Denmark)

Agersted, Mette Dalgaard; Nielsen, Torkel Gissel

2016-01-01

Here we compare the functional biology of the sympatric krill species, Meganyctiphanes norvegica and Thysanoessa inermis. For M. norvegica, we investigated functional responses on diatoms and copepods, together with prey size spectra on plankton ,400 mm and copepods in the size range 500–3220 mm....... For T. inermis, only prey size spectrum on plankton ,400 mm were investigated. The prey size ranges of both species include organisms ,400 mm, and they consequently graze on several trophic levels. However, T. inermis feed on cells ,10 mm equivalent spherical diameter (ESD), whereas M. norvegica only...

The reflection of life functional entailment and imminence in relational biology

CERN Document Server

Louie, A H

2013-01-01

A. H. Louie’s The Reflection of Life: Functional Entailment and Imminence in Relational Biology is a continuation of the exploratory journey in relational biology which began with his 2009 monograph More Than Life Itself: A Synthetic Continuation in Relational Biology. The theme of his first book was ‘What is life?’; the theme of this sequel is “How do two life forms interact?” Biology is a subject concerned with organization of relations. Relational biology is the approach that advocates ‘function dictates structure”, rather than ‘structure implies function’. It is mathematics decoded into biological realizations. The book demonstrates some of the powers of the approach of relational biology, and illustrates how pertinent problems in biology can be better addressed this way. In the first volume the theory was developed by using partially ordered sets, lattices, simulations, models, Aristotle’s four causes, graphs, categories, simple and complex systems, anticipatory systems, and metabolis...

Students' Perceptions of Long-Functioning Cooperative Teams in Accelerated Adult Degree Programs

Science.gov (United States)

Favor, Judy

2012-01-01

This study examined 718 adult students' perceptions of long-functioning cooperative study teams in accelerated associate's, bachelor's, and master's business degree programs. Six factors were examined: attraction toward team, alignment of performance expectations, intrateam conflict, workload sharing, preference for teamwork, and impact on…

Biological and medical research with accelerated heavy ions at the Bevalac, 1974--1977

International Nuclear Information System (INIS)

Elam, S.

1977-04-01

The Bevalac, a versatile high-energy heavy-ion accelerator complex, has been in operation for less than two years. A major purpose for which the Bevalac was constructed was to explore the possibility of heavy-ion teams for therapy for certain forms of cancer. Significant progress has been made in this direction. The National Cancer Institute has recognized the advantages that these and other accelerated particles offer, and heavy ions have been included in a long-term plan for particle therapy that will assess by means of controlled therapeutic tests the value of various modalities. Since accelerated heavy ions became available, the possibility of other contributions, not planned, became apparent. We are developig a new diagnostic method known as heavy-ion radiography that has greatly increased sensitivity for soft-tissue detail and that may become a powerful tool for localizing early tumors and metastases. We have discovered that radioactive beams are formed from fragmentation of stable deflected beams. Use of these autoradioactive beams is just beginning; however, we know that these beams will be helpful in localizing the region in the body where therapy is being delivered. In addition, it has been demonstrated that instant implantation of the radioactive beam allows direct measurements of blood perfusion rates in inaccessible parts of the body, and such a technique may become a new tool for the study of fast hot atom reactions in biochemistry, tracer biology and nuclear medicine. The Bevalac will also be useful for the continuation of previously developed methods for the control of acromegaly, Cushing's disease and, on a research basis, advanced diabetes mellitus with vascular disease. The ability to make small bloodless lesions in the brain and elsewhere with heavy-ion beams has great potential for nervous-system studies and perhaps later for radioneurosurgery

Pelletron accelerator at Panjab University Chandigarh

International Nuclear Information System (INIS)

Singh, Nirmal; Mehta, Devinder

2006-01-01

The purpose of pelletron accelerator at Panjab University is to develop a low-energy accelerator laboratory within the university infrastructure. It will be housing a tandem electrostatic accelerator. The facility will bring together the available scientific expertise from a wide range of applications, viz. medical, biological and physical sciences and engineering that utilize accelerator-based technologies and techniques. It will play an important role in promoting integrated research and education across scientific disciplines available in the campus. (author)

Heavy ion radiation biology research facility and ongoing activities at the Inter-University Accelerator Centre, New Delhi

International Nuclear Information System (INIS)

Sarma, Asitikantha

2014-01-01

Heavy Ion Radiation Biology is an interdisciplinary science involving use of charged particle accelerator in the study of molecular biology. It is the study of the interaction of a beam of swift heavy ions with a biological system. In contrast to the sparsely ionizing photon or electron radiation, the high velocity charged heavy ions leave a track of densely populated ionization sites resulting in clustered DNA damage. The growing interest in this field encompasses the studies in gene expression, mechanisms of cell death, DNA damage and repair, signal transduction etc. induced because of this unique assault on the genetic material. IUAC radiation biology programme is focused on the in-vitro studies of different effects of heavy ion irradiation on eukaryotic cells. The facility provides a laboratory for pre and post irradiation treatment of samples. The irradiation system called ASPIRE (Automatic Sample Positioning for Irradiation in Radiation Biology Experiments) is installed at the dedicated Radiation Biology Beam line. It produces a nearly uniform flux distribution over a irradiation field of 40 mm diameter. The particle doses can be preselected and repeated within inherent statistical accuracy. The particle energy can also be measured. The facility is at present utilized by the University researchers of India. A few results obtained by the investigators would be presented. The outcome of the research in heavy ion radiation biology would be of immense use in augmenting the efficacy of Hadron therapy of cancer. The results would also contribute to the field of space radiation protection. It would also help in understanding the phenomena subsequent to complex DNA damage. (author)

Obesity-induced oxidative stress, accelerated functional decline with age and increased mortality in mice.

Science.gov (United States)

Zhang, Yiqiang; Fischer, Kathleen E; Soto, Vanessa; Liu, Yuhong; Sosnowska, Danuta; Richardson, Arlan; Salmon, Adam B

2015-06-15

Obesity is a serious chronic disease that increases the risk of numerous co-morbidities including metabolic syndrome, cardiovascular disease and cancer as well as increases risk of mortality, leading some to suggest this condition represents accelerated aging. Obesity is associated with significant increases in oxidative stress in vivo and, despite the well-explored relationship between oxidative stress and aging, the role this plays in the increased mortality of obese subjects remains an unanswered question. Here, we addressed this by undertaking a comprehensive, longitudinal study of a group of high fat-fed obese mice and assessed both their changes in oxidative stress and in their performance in physiological assays known to decline with aging. In female C57BL/6J mice fed a high-fat diet starting in adulthood, mortality was significantly increased as was oxidative damage in vivo. High fat-feeding significantly accelerated the decline in performance in several assays, including activity, gait, and rotarod. However, we also found that obesity had little effect on other markers of function and actually improved performance in grip strength, a marker of muscular function. Together, this first comprehensive assessment of longitudinal, functional changes in high fat-fed mice suggests that obesity may induce segmental acceleration of some of the aging process. Published by Elsevier Inc.

Milk protein tailoring to improve functional and biological properties

Directory of Open Access Journals (Sweden)

JEAN-MARC CHOBERT

2012-01-01

Full Text Available Proteins are involved in every aspects of life: structure, motion, catalysis, recognition and regulation. Today's highly sophisticated science of the modifications of proteins has ancient roots. The tailoring of proteins for food and medical uses precedes the beginning of what is called biochemistry. Chemical modification of proteins was pursued early in the twentieth century as an analytical procedure for side-chain amino acids. Later, methods were developed for specific inactivation of biologically active proteins and titration of their essential groups. Enzymatic modifications were mainly developed in the seventies when many more enzymes became economically available. Protein engineering has become a valuable tool for creating or improving proteins for practical use and has provided new insights into protein structure and function. The actual and potential use of milk proteins as food ingredients has been a popular topic for research over the past 40 years. With today's sophisticated analytical, biochemical and biological research tools, the presence of compounds with biological activity has been demonstrated. Improvements in separation techniques and enzyme technology have enabled efficient and economic isolation and modification of milk proteins, which has made possible their use as functional foods, dietary supplements, nutraceuticals and medical foods. In this review, some chemical and enzymatic modifications of milk proteins are described, with particular focus on their functional and biological properties.

Diurnal rhythmicity in biological processes involved in bioavailability of functional food factors.

Science.gov (United States)

Tsurusaki, Takashi; Sakakibara, Hiroyuki; Aoshima, Yoshiki; Yamazaki, Shunsuke; Sakono, Masanobu; Shimoi, Kayoko

2013-05-01

In the past few decades, many types of functional factors have been identified in dietary foods; for example, flavonoids are major groups widely distributed in the plant kingdom. However, the absorption rates of the functional food factors are usually low, and many of these are difficult to be absorbed in the intact forms because of metabolization by biological processes during absorption. To gain adequate beneficial effects, it is therefore mandatory to know whether functional food factors are absorbed in sufficient quantity, and then reach target organs while maintaining beneficial effects. These are the reasons why the bioavailability of functional food factors has been well investigated using rodent models. Recently, many of the biological processes have been reported to follow diurnal rhythms recurring every 24 h. Therefore, absorption and metabolism of functional food factors influenced by the biological processes may vary with time of day. Consequently, the evaluation of the bioavailability of functional food factors using rodent models should take into consideration the timing of consumption. In this review, we provide a perspective overview of the diurnal rhythm of biological processes involved in the bioavailability of functional food factors, particularly flavonoids.

Biological effects of several extreme space flight factors (acceleration, magnetically activated water) on mouse natural or modified radiosensitivity

International Nuclear Information System (INIS)

Datsov, E.R.

1979-01-01

Irradiated and Adeturon-protected mice were used to assess biological effects of several static (magnetically-activated water - MW) and dynamic (acceleration) factors of space flight. The study shows that increased gravitation, 20 G, 5 min, generated by a small radius centrifuge, increases static ability to work, while the number of peripheral blood cells decreases. Continuous exposure of mice to MW induces a decrease in dynamic ability to work, in comparison with the physiological controls, without substantial changes in other indices. Extreme factors in space flight (acceleration MW, radiation, radiation protector), alone or in combination, decrease the animal's growth rate. After administration of 200 mg/kg Adeturone, mouse dynamic ability to work increases, while its capabilities for adaptation and training are lowered, and pronounced leucocytosis is observed. MW, acceleration, or Adeturone pre-treatment of mice increases their survival and dynamic ability to work, following exposure to 600 R, when compared to irradiated animals, but decreases their capabilities for adaptation and training. Acceleration and Adeturone protect peripheral blood from radiation injury, while MW alone intensifies radiation cytopenia. Irradiation does not significantly modify the static ability to work, upon preceding exposure to MW or acceleration. In this case, Adeturone exerts protective effect. ME and Adeturone combined action results in increased survival rate and mean duration of life of irradiated animals, as compared to their single administration. Acceleration reduces MW, Adeturone and MW + Adeturone effect on survival. Peripheral blood parameters do not correlate with survival rates. Combined pre-treatment with two or three of the factors studied increases dynamic ability to work following irradiation, and in many cases the static ability as well. The combination of Adeturone and MW was the only one with negative effect on the static ability to work. (A.B.)

Biological pathways and genetic mechanisms involved in social functioning.

Science.gov (United States)

Ordoñana, Juan R; Bartels, Meike; Boomsma, Dorret I; Cella, David; Mosing, Miriam; Oliveira, Joao R; Patrick, Donald L; Veenhoven, Ruut; Wagner, Gert G; Sprangers, Mirjam A G

2013-08-01

To describe the major findings in the literature regarding associations between biological and genetic factors and social functioning, paying special attention to: (1) heritability studies on social functioning and related concepts; (2) hypothesized biological pathways and genetic variants that could be involved in social functioning, and (3) the implications of these results for quality-of-life research. A search of Web of Science and PubMed databases was conducted using combinations of the following keywords: genetics, twins, heritability, social functioning, social adjustment, social interaction, and social dysfunction. Variability in the definitions and measures of social functioning was extensive. Moderate to high heritability was reported for social functioning and related concepts, including prosocial behavior, loneliness, and extraversion. Disorders characterized by impairments in social functioning also show substantial heritability. Genetic variants hypothesized to be involved in social functioning are related to the network of brain structures and processes that are known to affect social cognition and behavior. Better knowledge and understanding about the impact of genetic factors on social functioning is needed to help us to attain a more comprehensive view of health-related quality-of-life (HRQOL) and will ultimately enhance our ability to identify those patients who are vulnerable to poor social functioning.

Second International Conference on Accelerating Biopharmaceutical Development

Science.gov (United States)

2009-01-01

The Second International Conference on Accelerating Biopharmaceutical Development was held in Coronado, California. The meeting was organized by the Society for Biological Engineering (SBE) and the American Institute of Chemical Engineers (AIChE); SBE is a technological community of the AIChE. Bob Adamson (Wyeth) and Chuck Goochee (Centocor) were co-chairs of the event, which had the theme “Delivering cost-effective, robust processes and methods quickly and efficiently.” The first day focused on emerging disruptive technologies and cutting-edge analytical techniques. Day two featured presentations on accelerated cell culture process development, critical quality attributes, specifications and comparability, and high throughput protein formulation development. The final day was dedicated to discussion of technology options and new analysis methods provided by emerging disruptive technologies; functional interaction, integration and synergy in platform development; and rapid and economic purification process development. PMID:20065637

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

Science.gov (United States)

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

2015-12-01

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

Center of Mass Acceleration Feedback Control of Standing Balance by Functional Neuromuscular Stimulation against External Postural Perturbations

Science.gov (United States)

Nataraj, Raviraj; Audu, Musa L.; Triolo, Ronald J.

2013-01-01

This study investigated the use of center of mass (COM) acceleration feedback for improving performance of a functional neuromuscular stimulation (FNS) control system to restore standing function to a subject with complete, thoracic-level spinal cord injury (SCI). The approach for linearly relating changes in muscle stimulation to changes in COM acceleration was verified experimentally and subsequently produced data to create an input-output map driven by sensor feedback. The feedback gains were systematically tuned to reduce upper extremity (UE) loads applied to an instrumented support device while resisting external postural disturbances. Total body COM acceleration was accurately estimated (> 89% variance explained) using three-dimensional (3-D) outputs of two accelerometers mounted on the pelvis and torso. Compared to constant muscle stimulation employed clinically, feedback control of stimulation reduced UE loading by 33%. COM acceleration feedback is advantageous in constructing a standing neuroprosthesis since it provides the basis for a comprehensive control synergy about a global, dynamic variable and requires minimal instrumentation. Future work should include tuning and testing the feedback control system during functional reaching activity that is more indicative of activities of daily living. PMID:22987499

Advanced Accelerators for Medical Applications

Science.gov (United States)

Uesaka, Mitsuru; Koyama, Kazuyoshi

We review advanced accelerators for medical applications with respect to the following key technologies: (i) higher RF electron linear accelerator (hereafter “linac”); (ii) optimization of alignment for the proton linac, cyclotron and synchrotron; (iii) superconducting magnet; (iv) laser technology. Advanced accelerators for medical applications are categorized into two groups. The first group consists of compact medical linacs with high RF, cyclotrons and synchrotrons downsized by optimization of alignment and superconducting magnets. The second group comprises laser-based acceleration systems aimed of medical applications in the future. Laser plasma electron/ion accelerating systems for cancer therapy and laser dielectric accelerating systems for radiation biology are mentioned. Since the second group has important potential for a compact system, the current status of the established energy and intensity and of the required stability are given.

Accelerating Yeast Prion Biology using Droplet Microfluidics

Science.gov (United States)

Ung, Lloyd; Rotem, Assaf; Jarosz, Daniel; Datta, Manoshi; Lindquist, Susan; Weitz, David

2012-02-01

Prions are infectious proteins in a misfolded form, that can induce normal proteins to take the misfolded state. Yeast prions are relevant, as a model of human prion diseases, and interesting from an evolutionary standpoint. Prions may also be a form of epigenetic inheritance, which allow yeast to adapt to stressful conditions at rates exceeding those of random mutations and propagate that adaptation to their offspring. Encapsulation of yeast in droplet microfluidic devices enables high-throughput measurements with single cell resolution, which would not be feasible using bulk methods. Millions of populations of yeast can be screened to obtain reliable measurements of prion induction and loss rates. The population dynamics of clonal yeast, when a fraction of the cells are prion expressing, can be elucidated. Furthermore, the mechanism by which certain strains of bacteria induce yeast to express prions in the wild can be deduced. Integrating the disparate fields of prion biology and droplet microfluidics reveals a more complete picture of how prions may be more than just diseases and play a functional role in yeast.

Dynamic Biological Functioning Important for Simulating and Stabilizing Ocean Biogeochemistry

Science.gov (United States)

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

2018-04-01

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

Virtual Accelerator for Accelerator Optics Improvement

CERN Document Server

Yan Yi Ton; Decker, Franz Josef; Ecklund, Stanley; Irwin, John; Seeman, John; Sullivan, Michael K; Turner, J L; Wienands, Ulrich

2005-01-01

Through determination of all quadrupole strengths and sextupole feed-downs by fitting quantities derivable from precision orbit measurement, one can establish a virtual accelerator that matches the real accelerator optics. These quantities (the phase advances, the Green's functions, and the coupling eigen-plane ellipses tilt angles and axis ratios) are obtained by analyzing turn-by-turn Beam Position Monitor (BPM) data with a model-independent analysis (MIA). Instead of trying to identify magnet errors, a limited number of quadrupoles are chosen for optimized strength adjustment to improve the virtual accelerator optics and then applied to the real accelerator accordingly. These processes have been successfully applied to PEP-II rings for beta beating fixes, phase and working tune adjustments, and linear coupling reduction to improve PEP-II luminosity.

Composite Structural Motifs of Binding Sites for Delineating Biological Functions of Proteins

Science.gov (United States)

Kinjo, Akira R.; Nakamura, Haruki

2012-01-01

Most biological processes are described as a series of interactions between proteins and other molecules, and interactions are in turn described in terms of atomic structures. To annotate protein functions as sets of interaction states at atomic resolution, and thereby to better understand the relation between protein interactions and biological functions, we conducted exhaustive all-against-all atomic structure comparisons of all known binding sites for ligands including small molecules, proteins and nucleic acids, and identified recurring elementary motifs. By integrating the elementary motifs associated with each subunit, we defined composite motifs that represent context-dependent combinations of elementary motifs. It is demonstrated that function similarity can be better inferred from composite motif similarity compared to the similarity of protein sequences or of individual binding sites. By integrating the composite motifs associated with each protein function, we define meta-composite motifs each of which is regarded as a time-independent diagrammatic representation of a biological process. It is shown that meta-composite motifs provide richer annotations of biological processes than sequence clusters. The present results serve as a basis for bridging atomic structures to higher-order biological phenomena by classification and integration of binding site structures. PMID:22347478

Linking structural features of protein complexes and biological function.

Science.gov (United States)

Sowmya, Gopichandran; Breen, Edmond J; Ranganathan, Shoba

2015-09-01

Protein-protein interaction (PPI) establishes the central basis for complex cellular networks in a biological cell. Association of proteins with other proteins occurs at varying affinities, yet with a high degree of specificity. PPIs lead to diverse functionality such as catalysis, regulation, signaling, immunity, and inhibition, playing a crucial role in functional genomics. The molecular principle of such interactions is often elusive in nature. Therefore, a comprehensive analysis of known protein complexes from the Protein Data Bank (PDB) is essential for the characterization of structural interface features to determine structure-function relationship. Thus, we analyzed a nonredundant dataset of 278 heterodimer protein complexes, categorized into major functional classes, for distinguishing features. Interestingly, our analysis has identified five key features (interface area, interface polar residue abundance, hydrogen bonds, solvation free energy gain from interface formation, and binding energy) that are discriminatory among the functional classes using Kruskal-Wallis rank sum test. Significant correlations between these PPI interface features amongst functional categories are also documented. Salt bridges correlate with interface area in regulator-inhibitors (r = 0.75). These representative features have implications for the prediction of potential function of novel protein complexes. The results provide molecular insights for better understanding of PPIs and their relation to biological functions. © 2015 The Protein Society.

Building biological foundries for next-generation synthetic biology.

Science.gov (United States)

Chao, Ran; Yuan, YongBo; Zhao, HuiMin

2015-07-01

Synthetic biology is an interdisciplinary field that takes top-down approaches to understand and engineer biological systems through design-build-test cycles. A number of advances in this relatively young field have greatly accelerated such engineering cycles. Specifically, various innovative tools were developed for in silico biosystems design, DNA de novo synthesis and assembly, construct verification, as well as metabolite analysis, which have laid a solid foundation for building biological foundries for rapid prototyping of improved or novel biosystems. This review summarizes the state-of-the-art technologies for synthetic biology and discusses the challenges to establish such biological foundries.

Characterization Study of Accelerator for Application in Biotechnology

International Nuclear Information System (INIS)

Yazid-M; Muryono, H.

2000-01-01

The characterization of accelerator for application in biotechnology was studied. Accelerator is a machine to produce ion beam particles. Accelerator can be used for biotechnology experiments. Ion beam particles irradiation on the biological material will produced variabilities of genetics and induced mutations. In general, new varieties were found by hybridization method or mutation breeding method by gamma rays irradiation. Ion beam particles can be used for biological material irradiation to find variabilities of genetics and induced mutations. The high percentage of mutation rate and LET value by ion beam particles irradiation was found higher than by gamma rays irradiation. Ion beam particle irradiation can also be controlled and foewed to target in biological material. The characterization of accelerator needed for biotechnology experiments are types of accelerator (Tandem Van de Graff, AVF Cyclotron, Synchrotron, Rilac), types of ion particles (C, He, electron, Ar, Ne, Ni, Al, Xe and Au), range of energy (5 - 2.090 MeV), range of dose irradiation (10 - 250 Gy), range of ion current (0.02 - 20 nA), range of ion beam particles diameter (10 - 100 μm), range of LET value (300 - 1.800 keV/μm ) and irradiation time (5 - 30 seconds/samples). (author)

SU-E-T-54: Benefits of Biological Cost Functions

International Nuclear Information System (INIS)

Demirag, N

2014-01-01

Purpose: To verify the benefits of the biological cost functions. Methods: TG166 patients were used for the test case scenarios. Patients were planned using Monaco V5.0 (CMS/Elekta, St.Louis, MO) Monaco has 3 biological and 8 physical CFs. In this study the plans were optimized using 3 different scenarios. 1- Biological CFs only 2-Physical CFs only 3- Combination of Physical and Biological CFsMonaco has 3 biological CFs. Target EUD used for the targets, derived from the poisson cell kill model, has an α value that controls the cold spots inside the target. α values used in the optimization were 0.5 and 0.8. if cold spots needs to be penalized α value increased. Serial CF: it's called serial to mimic the behaviour of the serial organs, if a high k value like 12 or 14 is used it controls the maximum dose. Serial CF has a k parameter that is used to shape the whole dvh curve. K value ranges between 1–20. k:1 is used to control the mean dose, lower k value controls the mean dose, higher k value controls the higher dose, using 2 serial CFs with different k values controls the whole DVH. Paralel CF controls the percentage of the volume that tolerates higher doses than the reference dose to mimic the behaviour of the paralel organs. Results: It was possible to achive clinically accepted plans in all 3 scenarios. The benefit of the biological cost functions were to control the mean dose for target and OAR, to shape the DVH curve using one EUD value and one k value simplifies the optimization process. Using the biological CFs alone, it was hard to control the dose at a point. Conclusion: Biological CFs in Monaco doesn't require the ntcp/tcp values from the labs and useful to shape the whole dvh curve. I work as an applications support specialist for Elekta and I am a Ph.D. Student in Istanbul University for radiation therapy physics

Study of biological effects of accelerated heavy ions irradiation on rices: Pt. 1

International Nuclear Information System (INIS)

Liu Zhensheng; Qiu Quanfa; Huang Wenzhong; Mei Mantong; Yang, T.C.H.

1991-01-01

The dried rice seeds were irradiated with accelerated 56 Fe and 40 Ar ion beams or 60 Co γ-rays at various doses. The irradiation effects on seeding growth as well as micronuclei and chronosome aberration induction were observed. The results indicated that the seeding height raduction, frequency of micronucleated cells and frequency of chromosome aberrations all appeared to dose dependent for these three types of rediation. The RBE value for seeding height reduction, determined at fifity percent of hight inhibition level, was found to be about 6.3, 1.9 and 1 for 56 Fe, 40 Ar and 60 Co γ-ray respectively. However, the RBE values for the frequency of micronucleated cells were about 11, 4 and 1 for 56 Fe and 40 Ar particles and 60 Co γ-ray. It appeared that the effectiveness of high LET radiation in inducing biological effects at the first generation was higler than that of low LET radiation, especially in inducing the micronuclei formation

Relative biological efficiency of 592 MeV protons. Analysis of the biological effect of secondary radiation

International Nuclear Information System (INIS)

Legeay, G.; Baarli, J.

1968-01-01

The relative biological efficiency (RBE) of high energy protons is of importance because of their effects in the field of radioprotection around large accelerators and during space-flights. The nature of the interactions between 592 MeV protons and biological tissues makes it necessary to take into consideration the contribution of secondary radiation to the biological effect. Since it is not possible to obtain from a synchrotron a beam having a sufficiently large cross-section to irradiate large animals, one has to resort to certain devices concerning the mode of exposure when small laboratory animals are used. By irradiating rats individually and in groups, and by using the lethal test as a function of time, the authors show that the value of the RBE is different for animals of the same species having the same biological parameters. Thus there appears an increase in the biological effect due to secondary radiation produced in nuclear cascades which develop in a large volume, for example that of a human being. (author) [fr

Evolutionary cell biology: functional insight from "endless forms most beautiful".

Science.gov (United States)

Richardson, Elisabeth; Zerr, Kelly; Tsaousis, Anastasios; Dorrell, Richard G; Dacks, Joel B

2015-12-15

In animal and fungal model organisms, the complexities of cell biology have been analyzed in exquisite detail and much is known about how these organisms function at the cellular level. However, the model organisms cell biologists generally use include only a tiny fraction of the true diversity of eukaryotic cellular forms. The divergent cellular processes observed in these more distant lineages are still largely unknown in the general scientific community. Despite the relative obscurity of these organisms, comparative studies of them across eukaryotic diversity have had profound implications for our understanding of fundamental cell biology in all species and have revealed the evolution and origins of previously observed cellular processes. In this Perspective, we will discuss the complexity of cell biology found across the eukaryotic tree, and three specific examples of where studies of divergent cell biology have altered our understanding of key functional aspects of mitochondria, plastids, and membrane trafficking. © 2015 Richardson et al. This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication it is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

Ligand-accelerated non-directed C-H functionalization of arenes

Science.gov (United States)

Wang, Peng; Verma, Pritha; Xia, Guoqin; Shi, Jun; Qiao, Jennifer X.; Tao, Shiwei; Cheng, Peter T. W.; Poss, Michael A.; Farmer, Marcus E.; Yeung, Kap-Sun; Yu, Jin-Quan

2017-11-01

The directed activation of carbon-hydrogen bonds (C-H) is important in the development of synthetically useful reactions, owing to the proximity-induced reactivity and selectivity that is enabled by coordinating functional groups. Palladium-catalysed non-directed C-H activation could potentially enable further useful reactions, because it can reach more distant sites and be applied to substrates that do not contain appropriate directing groups; however, its development has faced substantial challenges associated with the lack of sufficiently active palladium catalysts. Currently used palladium catalysts are reactive only with electron-rich arenes, unless an excess of arene is used, which limits synthetic applications. Here we report a 2-pyridone ligand that binds to palladium and accelerates non-directed C-H functionalization with arene as the limiting reagent. This protocol is compatible with a broad range of aromatic substrates and we demonstrate direct functionalization of advanced synthetic intermediates, drug molecules and natural products that cannot be used in excessive quantities. We also developed C-H olefination and carboxylation protocols, demonstrating the applicability of our methodology to other transformations. The site selectivity in these transformations is governed by a combination of steric and electronic effects, with the pyridone ligand enhancing the influence of sterics on the selectivity, thus providing complementary selectivity to directed C-H functionalization.

Source-to-accelerator quadrupole matching section for a compact linear accelerator

Science.gov (United States)

Seidl, P. A.; Persaud, A.; Ghiorso, W.; Ji, Q.; Waldron, W. L.; Lal, A.; Vinayakumar, K. B.; Schenkel, T.

2018-05-01

Recently, we presented a new approach for a compact radio-frequency (RF) accelerator structure and demonstrated the functionality of the individual components: acceleration units and focusing elements. In this paper, we combine these units to form a working accelerator structure: a matching section between the ion source extraction grids and the RF-acceleration unit and electrostatic focusing quadrupoles between successive acceleration units. The matching section consists of six electrostatic quadrupoles (ESQs) fabricated using 3D-printing techniques. The matching section enables us to capture more beam current and to match the beam envelope to conditions for stable transport in an acceleration lattice. We present data from an integrated accelerator consisting of the source, matching section, and an ESQ doublet sandwiched between two RF-acceleration units.

Chemically-functionalized microcantilevers for detection of chemical, biological and explosive material

Science.gov (United States)

Pinnaduwage, Lal A [Knoxville, TN; Thundat, Thomas G [Knoxville, TN; Brown, Gilbert M [Knoxville, TN; Hawk, John Eric [Olive Branch, MS; Boiadjiev, Vassil I [Knoxville, TN

2007-04-24

A chemically functionalized cantilever system has a cantilever coated on one side thereof with a reagent or biological species which binds to an analyte. The system is of particular value when the analyte is a toxic chemical biological warfare agent or an explosive.

Heavy water effects on the structure, functions and behavior of biological systems

International Nuclear Information System (INIS)

Buzgariu, Wanda; Caloianu, Maria; Moldovan, Lucia; Titescu, G.

2003-01-01

The H 2 O substitution for D 2 O either in environment or in the culture medium of the living systems generates changes in their main functions and composition. In this paper some of the heavy water effects in biological systems such as structural and functional changes were reviewed: normal cell architecture alterations, cell division and membrane functions disturbance, muscular contractility and the perturbations of biological oscillators such as circadian rhythm, heart rate, respiratory cycle, tidal and ultradian rhythm. (authors)

Medical uses of accelerators

International Nuclear Information System (INIS)

Bradbury, J.N.

1981-01-01

A variety of particle accelerators have either potential or already demonstrated uses in connection with medically-related research, diagnosis, and treatment. For cancer radiotherapy, nuclear particles including protons, neutrons, heavy ions, and negative pi mesons have advantages compared to conventional radiations in terms of dose localization and/or biological effectiveness. Clinical evaluations of these particles are underway at a number of institutions. Accelerator-produced radionuclides are in widespread use for research and routine diagnostic purposes. Elemental analysis techniques with charged particles and neutrons are being applied to bone, blood, and other tissues. Finally, low-dose medical imaging can be accomplished with accelerated protons and heavy ions. The status and future of these programs are discussed

The Automatic Radiation Control System Of The Inr Linear Accelerator (troitsk).

CERN Document Server

Grachev, M I; Kuptsov, S I; Peleshko, V N; Shishkin, K I; Shmelev, M O; Skorkin, V M

2004-01-01

The radiation monitor system (RMS) at accelerator INR is a part of radiation safety system of experimental complex INR. RMS is intended for continuous monitoring of radiation field behind biological protection of linear accelerator INR with the personnel dose control and alarm purposes. Three-level system RMS consists of the operator computer, microprocessor data acquisition modules and networks of UDBN-02R neutron detectors and BDRC-01P photon detectors, located inside and behind biological protection of the accelerator (fig. 1).

Correction of dispersion and the betatron functions in the CEBAF accelerator

International Nuclear Information System (INIS)

Lebedev, V.A.; Bickley, M.; Schaffner, S.; Zeijts, J. van; Krafft, G.A.; Watson, C.

1996-01-01

During the commissioning of the CEBAF accelerator, correction of dispersion and momentum compaction, and, to a lesser extent, transverse transfer matrices were essential for robust operation. With changing machine conditions, repeated correction was found necessary. To speed the diagnostic process the authors developed a method which allows one to rapidly track the machine optics. The method is based on measuring the propagation of 30 Hz modulated betatron oscillations downstream of a point of perturbation. Compared to the usual methods of dispersion or difference orbit measurement, synchronous detection of the beam displacement, as measured by beam position monitors, offers significantly improved speed and accuracy of the measurements. The beam optics of the accelerator was altered to decrease lattice sensitivity at critical points and to simplify control of the betatron function match. The calculation of the Courant-Snyder invariant from signals of each pair of nearby beam position monitors has allowed one to perform on-line measurement and correction of the lattice properties

The Bevalac accelerator

International Nuclear Information System (INIS)

Dacal, A.

1989-01-01

Presented are the characteristics of the Bevatron and SuperHilac heavy ion accelerators in a very general manner. Some aspects of their application in the field of biological medicine and some of the interesting results obtained in experiments on nuclear physics are mentioned. (Author). 20 refs, 2 figs, 2 tabs

Sharing Structure and Function in Biological Design with SBOL 2.0.

Science.gov (United States)

Roehner, Nicholas; Beal, Jacob; Clancy, Kevin; Bartley, Bryan; Misirli, Goksel; Grünberg, Raik; Oberortner, Ernst; Pocock, Matthew; Bissell, Michael; Madsen, Curtis; Nguyen, Tramy; Zhang, Michael; Zhang, Zhen; Zundel, Zach; Densmore, Douglas; Gennari, John H; Wipat, Anil; Sauro, Herbert M; Myers, Chris J

2016-06-17

The Synthetic Biology Open Language (SBOL) is a standard that enables collaborative engineering of biological systems across different institutions and tools. SBOL is developed through careful consideration of recent synthetic biology trends, real use cases, and consensus among leading researchers in the field and members of commercial biotechnology enterprises. We demonstrate and discuss how a set of SBOL-enabled software tools can form an integrated, cross-organizational workflow to recapitulate the design of one of the largest published genetic circuits to date, a 4-input AND sensor. This design encompasses the structural components of the system, such as its DNA, RNA, small molecules, and proteins, as well as the interactions between these components that determine the system's behavior/function. The demonstrated workflow and resulting circuit design illustrate the utility of SBOL 2.0 in automating the exchange of structural and functional specifications for genetic parts, devices, and the biological systems in which they operate.

Nonlinear transport of accelerator beam phase space

International Nuclear Information System (INIS)

Xie Xi; Xia Jiawen

1995-01-01

Based on the any order analytical solution of accelerator beam dynamics, the general theory for nonlinear transport of accelerator beam phase space is developed by inverse transformation method. The method is general by itself, and hence can also be applied to the nonlinear transport of various dynamic systems in physics, chemistry and biology

Averaged Propulsive Body Acceleration (APBA Can Be Calculated from Biologging Tags That Incorporate Gyroscopes and Accelerometers to Estimate Swimming Speed, Hydrodynamic Drag and Energy Expenditure for Steller Sea Lions.

Directory of Open Access Journals (Sweden)

Colin Ware

Full Text Available Forces due to propulsion should approximate forces due to hydrodynamic drag for animals horizontally swimming at a constant speed with negligible buoyancy forces. Propulsive forces should also correlate with energy expenditures associated with locomotion-an important cost of foraging. As such, biologging tags containing accelerometers are being used to generate proxies for animal energy expenditures despite being unable to distinguish rotational movements from linear movements. However, recent miniaturizations of gyroscopes offer the possibility of resolving this shortcoming and obtaining better estimates of body accelerations of swimming animals. We derived accelerations using gyroscope data for swimming Steller sea lions (Eumetopias jubatus, and determined how well the measured accelerations correlated with actual swimming speeds and with theoretical drag. We also compared dive averaged dynamic body acceleration estimates that incorporate gyroscope data, with the widely used Overall Dynamic Body Acceleration (ODBA metric, which does not use gyroscope data. Four Steller sea lions equipped with biologging tags were trained to swim alongside a boat cruising at steady speeds in the range of 4 to 10 kph. At each speed, and for each dive, we computed a measure called Gyro-Informed Dynamic Acceleration (GIDA using a method incorporating gyroscope data with accelerometer data. We derived a new metric-Averaged Propulsive Body Acceleration (APBA, which is the average gain in speed per flipper stroke divided by mean stroke cycle duration. Our results show that the gyro-based measure (APBA is a better predictor of speed than ODBA. We also found that APBA can estimate average thrust production during a single stroke-glide cycle, and can be used to estimate energy expended during swimming. The gyroscope-derived methods we describe should be generally applicable in swimming animals where propulsive accelerations can be clearly identified in the signal

The auroral electron accelerator

International Nuclear Information System (INIS)

Bryant, D.A.; Hall, D.S.

1989-01-01

A model of the auroral electron acceleration process is presented in which the electrons are accelerated resonantly by lower-hybrid waves. The essentially stochastic acceleration process is approximated for the purposes of computation by a deterministic model involving an empirically derived energy transfer function. The empirical function, which is consistent with all that is known of electron energization by lower-hybrid waves, allows many, possibly all, observed features of the electron distribution to be reproduced. It is suggested that the process occurs widely in both space and laboratory plasmas. (author)

Construction of Biologically Functional Bacterial Plasmids In Vitro

Science.gov (United States)

Cohen, Stanley N.; Chang, Annie C. Y.; Boyer, Herbert W.; Helling, Robert B.

1973-01-01

The construction of new plasmid DNA species by in vitro joining of restriction endonuclease-generated fragments of separate plasmids is described. Newly constructed plasmids that are inserted into Escherichia coli by transformation are shown to be biologically functional replicons that possess genetic properties and nucleotide base sequences from both of the parent DNA molecules. Functional plasmids can be obtained by reassociation of endonuclease-generated fragments of larger replicons, as well as by joining of plasmid DNA molecules of entirely different origins. Images PMID:4594039

Delivery of single accelerated particles

International Nuclear Information System (INIS)

McNulty, P.J.; Pease, V.P.; Bond, V.P.; Schimmerling, W.; Vosburgh, K.G.; Crebbin, K.; Everette, W.; Howard, J.

1978-01-01

It is desirable for certain experiments involving accelerators to have the capability of delivering just a single beam particle to the target area. The essential features of such a one-at-a-time facility are discussed. Two such facilities are described which were implemented at high-energy heavy ion accelerators without having to make major structural changes in the existing beam lines or substantially interfering with other accelerator uses. Two accelerator facilities are described which had the capability of delivering a single beam particle to the target area. This feature is necessary in certain experiments investigating visual phenomena induced by charged particles, other single particle interactions in biology, and other experiments in which the low intensities of cosmic rays need to be simulated. Both facilities were implemented without having to make structural changes in the existing beam lines or substantially interfering with other accelerator uses. (Auth.)

Accelerator microanalysis

International Nuclear Information System (INIS)

Tuniz, C.

1997-01-01

Particle accelerators have been developed more than sixty years ago to investigate nuclear and atomic phenomena. A major shift toward applications of accelerators in the study of materials structure and composition in inter-disciplinary projects has been witnessed in the last two decades. The Australian Nuclear Science and Technology Organisation (ANSTO) has developed advanced research programs based on the use of particle and photon beams. Atmospheric pollution problems are investigated at the 3 MV Van de Graff accelerator using ion beam analysis techniques to detect toxic elements in aerosol particles. High temperature superconductor and semiconductor materials are characterised using the recoil of iodine and other heavy ions produced at ANTARES, the 10-MV Tandem accelerator. A heavy-ion microprobe is presently being developed at ANTARES to map elemental concentrations of specific elements with micro-size resolution. An Accelerator mass Spectrometry (AMS) system has been developed at ANSTO for the ultra-sensitive detection of Carbon-14, Iodine-129 and other long-lived radioisotopes. This AMS spectrometer is a key instrument for climate change studies and international safeguards. ANSTO is also managing the Australian Synchrotron Research program based on facilities developed at the Photon Factory (Japan) and at the Advanced Photon Source (USA). Advanced projects in biology, materials chemistry, structural condensed matter and other disciplines are being promoted by a consortium involving Australian universities and research institutions. This paper will review recent advances in the use of particle accelerators, with a particular emphasis on applications developed at ANSTO and related to problems of international concern, such as global environmental change, public health and nuclear proliferation

Ion beams provided by small accelerators for material synthesis and characterization

Science.gov (United States)

Mackova, Anna; Havranek, Vladimir

2017-06-01

The compact, multipurpose electrostatic tandem accelerators are extensively used for production of ion beams with energies in the range from 400 keV to 24 MeV of almost all elements of the periodic system for the trace element analysis by means of nuclear analytical methods. The ion beams produced by small accelerators have a broad application, mainly for material characterization (Rutherford Back-Scattering spectrometry, Particle Induced X ray Emission analysis, Nuclear Reaction Analysis and Ion-Microprobe with 1 μm lateral resolution among others) and for high-energy implantation. Material research belongs to traditionally progressive fields of technology. Due to the continuous miniaturization, the underlying structures are far beyond the analytical limits of the most conventional methods. Ion Beam Analysis (IBA) techniques provide this possibility as they use probes of similar or much smaller dimensions (particles, radiation). Ion beams can be used for the synthesis of new progressive functional nanomaterials for optics, electronics and other applications. Ion beams are extensively used in studies of the fundamental energetic ion interaction with matter as well as in the novel nanostructure synthesis using ion beam irradiation in various amorphous and crystalline materials in order to get structures with extraordinary functional properties. IBA methods serve for investigation of materials coming from material research, industry, micro- and nano-technology, electronics, optics and laser technology, chemical, biological and environmental investigation in general. Main research directions in laboratories employing small accelerators are also the preparation and characterization of micro- and nano-structured materials which are of interest for basic and oriented research in material science, and various studies of biological, geological, environmental and cultural heritage artefacts are provided too.

Marine Carotenoids: Biological Functions and Commercial Applications

Science.gov (United States)

Vílchez, Carlos; Forján, Eduardo; Cuaresma, María; Bédmar, Francisco; Garbayo, Inés; Vega, José M.

2011-01-01

Carotenoids are the most common pigments in nature and are synthesized by all photosynthetic organisms and fungi. Carotenoids are considered key molecules for life. Light capture, photosynthesis photoprotection, excess light dissipation and quenching of singlet oxygen are among key biological functions of carotenoids relevant for life on earth. Biological properties of carotenoids allow for a wide range of commercial applications. Indeed, recent interest in the carotenoids has been mainly for their nutraceutical properties. A large number of scientific studies have confirmed the benefits of carotenoids to health and their use for this purpose is growing rapidly. In addition, carotenoids have traditionally been used in food and animal feed for their color properties. Carotenoids are also known to improve consumer perception of quality; an example is the addition of carotenoids to fish feed to impart color to farmed salmon. PMID:21556162

Cognitive and functional correlates of accelerated long-term forgetting in temporal lobe epilepsy.

Science.gov (United States)

Audrain, Samantha; McAndrews, Mary P

2018-03-30

While we know that hippocampal dysfunction is responsible for the memory deficits that patients with temporal lobe epilepsy exhibit at relatively short study-test delays, the role of this region in accelerated long-term forgetting (ALF) is not yet clear. In the present study, we probed the role of the hippocampus in ALF by directly comparing memory for associations to memory that could be supported by item recognition during a forced choice recognition task over delays ranging from 15-min to 72-h. We additionally examined resting-state functional connectivity between the hippocampus and cortical regions known to be involved in processing these types of stimuli, as well as the relationship between ALF and various clinical variables including structural abnormality in the hippocampus, lateralization of epileptic focus, presence of seizures across the retention period, and standardized composite memory scores. We found evidence of accelerated forgetting for item stimuli (but not associative stimuli) by 6 h post-learning, which became statistically reliable by 72-h. This finding suggests that unlike controls, patients were unable to utilize novelty to reject the incorrect object-scene pair. While none of the examined clinical variables were related to long-term forgetting, reduced resting-state functional connectivity between the affected anterior hippocampus and unaffected lateral temporal cortex predicted forgetting of item stimuli over the 72-h delay. Implications for the role of the hippocampus in accelerated long-term forgetting, and existing theories of systems consolidation in this context are discussed. Crown Copyright © 2018. Published by Elsevier Ltd. All rights reserved.

Protein aggregates as depots for the release of biologically active compounds.

Science.gov (United States)

Artemova, Natalya V; Kasakov, Alexei S; Bumagina, Zoya M; Lyutova, Elena M; Gurvits, Bella Ya

2008-12-12

Protein misfolding and aggregation is one of the most serious problems in cell biology, molecular medicine, and biotechnology. Misfolded proteins interact with each other or with other proteins in non-productive or damaging ways. However, a new paradigm arises that protein aggregation may be exploited by nature to perform specific functions in different biological contexts. From this consideration, acceleration of stress-induced protein aggregation triggered by any factor resulting in the formation of soluble aggregates may have paradoxical positive consequences. Here, we suggest that amorphous aggregates can act as a source for the release of biologically active proteins after removal of stress conditions. To address this concept, we investigated the kinetics of thermal aggregation in vitro of yeast alcohol dehydrogenase (ADH) as a model substrate in the presence of two amphiphilic peptides: Arg-Phe or Ala-Phe-Lys. Using dynamic light scattering (DLS) and turbidimetry, we have demonstrated that under mild stress conditions the concentration-dependent acceleration of ADH aggregation by these peptides results in formation of large but soluble complexes of proteins prone to refolding.

Testing the hypothesis of accelerated cerebral white matter aging in schizophrenia and major depression.

Science.gov (United States)

Kochunov, Peter; Glahn, David C; Rowland, Laura M; Olvera, Rene L; Winkler, Anderson; Yang, Yi-Hong; Sampath, Hemalatha; Carpenter, Will T; Duggirala, Ravindranath; Curran, Joanne; Blangero, John; Hong, L Elliot

2013-03-01

Elevated rate of aging-related biological and functional decline, termed "accelerated aging," is reported in patients with schizophrenia (SCZ) and major depressive disorder (MDD). We used diffusion tensor imaging derived fractional anisotropy (FA) as a biomarker of aging-related decline in white matter (WM) integrity to test the hypotheses of accelerated aging in SCZ and MDD. The SCZ cohort comprised 58 SCZ patients and 60 controls (aged 20-60 years). The MDD cohort comprised 136 MDD patients and 351 controls (aged 20-79 years). The main outcome measures were the diagnosis-by-age interaction on whole-brain-averaged WM FA values and FA values from 12 major WM tracts. Diagnosis-by-age interaction for the whole-brain average FA was significant for the SCZ (p = .04) but not the MDD (p = .80) cohort. Diagnosis-by-age interaction was nominally significant (paccelerated aging in SCZ but not in MDD, suggesting some difference in the pathophysiology underlying their WM aging changes. Tract-specific heterochronicity of WM development modulated presentation of accelerated aging in SCZ: WM tracts that matured later in life appeared more sensitive to the pathophysiology of SCZ and demonstrated more susceptibility to disorder-related accelerated decline in FA values with age. This trend was not observed in MDD cohort. Copyright © 2013 Society of Biological Psychiatry. Published by Elsevier Inc. All rights reserved.

Biological properties of extracellular vesicles and their physiological functions

Directory of Open Access Journals (Sweden)

María Yáñez-Mó

2015-05-01

Full Text Available In the past decade, extracellular vesicles (EVs have been recognized as potent vehicles of intercellular communication, both in prokaryotes and eukaryotes. This is due to their capacity to transfer proteins, lipids and nucleic acids, thereby influencing various physiological and pathological functions of both recipient and parent cells. While intensive investigation has targeted the role of EVs in different pathological processes, for example, in cancer and autoimmune diseases, the EV-mediated maintenance of homeostasis and the regulation of physiological functions have remained less explored. Here, we provide a comprehensive overview of the current understanding of the physiological roles of EVs, which has been written by crowd-sourcing, drawing on the unique EV expertise of academia-based scientists, clinicians and industry based in 27 European countries, the United States and Australia. This review is intended to be of relevance to both researchers already working on EV biology and to newcomers who will encounter this universal cell biological system. Therefore, here we address the molecular contents and functions of EVs in various tissues and body fluids from cell systems to organs. We also review the physiological mechanisms of EVs in bacteria, lower eukaryotes and plants to highlight the functional uniformity of this emerging communication system.

Biological properties of extracellular vesicles and their physiological functions

Science.gov (United States)

Yáñez-Mó, María; Siljander, Pia R.-M.; Andreu, Zoraida; Zavec, Apolonija Bedina; Borràs, Francesc E.; Buzas, Edit I.; Buzas, Krisztina; Casal, Enriqueta; Cappello, Francesco; Carvalho, Joana; Colás, Eva; Silva, Anabela Cordeiro-da; Fais, Stefano; Falcon-Perez, Juan M.; Ghobrial, Irene M.; Giebel, Bernd; Gimona, Mario; Graner, Michael; Gursel, Ihsan; Gursel, Mayda; Heegaard, Niels H. H.; Hendrix, An; Kierulf, Peter; Kokubun, Katsutoshi; Kosanovic, Maja; Kralj-Iglic, Veronika; Krämer-Albers, Eva-Maria; Laitinen, Saara; Lässer, Cecilia; Lener, Thomas; Ligeti, Erzsébet; Linē, Aija; Lipps, Georg; Llorente, Alicia; Lötvall, Jan; Manček-Keber, Mateja; Marcilla, Antonio; Mittelbrunn, Maria; Nazarenko, Irina; Hoen, Esther N.M. Nolte-‘t; Nyman, Tuula A.; O'Driscoll, Lorraine; Olivan, Mireia; Oliveira, Carla; Pállinger, Éva; del Portillo, Hernando A.; Reventós, Jaume; Rigau, Marina; Rohde, Eva; Sammar, Marei; Sánchez-Madrid, Francisco; Santarém, N.; Schallmoser, Katharina; Ostenfeld, Marie Stampe; Stoorvogel, Willem; Stukelj, Roman; Van der Grein, Susanne G.; Vasconcelos, M. Helena; Wauben, Marca H. M.; De Wever, Olivier

2015-01-01

In the past decade, extracellular vesicles (EVs) have been recognized as potent vehicles of intercellular communication, both in prokaryotes and eukaryotes. This is due to their capacity to transfer proteins, lipids and nucleic acids, thereby influencing various physiological and pathological functions of both recipient and parent cells. While intensive investigation has targeted the role of EVs in different pathological processes, for example, in cancer and autoimmune diseases, the EV-mediated maintenance of homeostasis and the regulation of physiological functions have remained less explored. Here, we provide a comprehensive overview of the current understanding of the physiological roles of EVs, which has been written by crowd-sourcing, drawing on the unique EV expertise of academia-based scientists, clinicians and industry based in 27 European countries, the United States and Australia. This review is intended to be of relevance to both researchers already working on EV biology and to newcomers who will encounter this universal cell biological system. Therefore, here we address the molecular contents and functions of EVs in various tissues and body fluids from cell systems to organs. We also review the physiological mechanisms of EVs in bacteria, lower eukaryotes and plants to highlight the functional uniformity of this emerging communication system. PMID:25979354

Assessment of left ventricular function with single breath-hold highly accelerated cine MRI combined with guide-point modeling

International Nuclear Information System (INIS)

Heilmaier, Christina; Nassenstein, Kai; Nielles-Vallespin, Sonia; Zuehlsdorff, Sven; Hunold, Peter; Barkhausen, Joerg

2010-01-01

Purpose: To prospectively assess the performance of highly accelerated cine MRI in multi-orientations combined with a new guide-point modeling post-processing technique (GPM approach) for assessment of left ventricular (LV) function compared to the standard summation of slices method based on a stack of short axis views (SoS approach). Materials and methods: 33 consecutive patients were examined on a 1.5 T scanner with a standard steady state free precession (SSFP) sequence (TR, 3.0 ms; TE, 1.5 m; flip angle (FA), 60 o ; acceleration factor (AF), 2) analyzed with the SoS method and a highly accelerated, single breath-hold temporal parallel acquisition SSFP sequence (TR, 4.6 ms; TE, 1.1 ms; AF, 3) post-processed with the GPM method. LV function values were measured by two independent readers with different experience in cardiac MRI and compared by using the paired t-test and F-test. Inter- and intraobserver agreements were calculated using Bland-Altman-Plots. Results: Mean acquisition and post-processing time was significantly shorter with the GPM approach (15 s/3 min versus 360 s/6 min). For all LV function parameters interobserver agreement between the experienced and non-experienced reader was significantly improved when the GPM approach was used. However, end-diastolic and end-systolic volumes were larger for the GPM technique when compared to the SoS method (P 0.121). In both readers and for all parameters variances did not differ significantly (P ≥ 0.409) and the two approaches showed an excellent linear correlation (r > 0.951). Conclusion: Due to its accurate, fast and reproducible assessment of LV function parameters highly accelerated MRI combined with the GPM technique may become the technique of first choice for assessment of LV function in clinical routine.

The functioning and behaviour of biological parents of children ...

African Journals Online (AJOL)

Parenting a child with ADHD may intensify parental stress through functional impairment notwithstanding the diagnosis of ADHD. Methods: Eighty-one biological parents of children diagnosed with attention-deficit/ hyperactivity disorder were screened using self-reporting measurements. ADHD self-report scale (ASRS-V 1.1) ...

N-acylation of phosphatidylethanolamine and its biological functions in mammals

DEFF Research Database (Denmark)

Wellner, Niels; Diep, Thi Ai; Janfelt, Christian

2013-01-01

N-acylphosphatidylethanolamine (NAPE) and N-acylplasmenylethanolamine (pNAPE) are widely found phospholipids, and they are precursors for N-acylethanolamines, a group of compounds that has a variety of biological effects and encompasses the endocannabinoid anandamide. NAPE and pNAPE are synthesiz...... reviews the metabolism, occurrence and assay of NAPE and pNAPE, and discusses the putative biological functions in mammals of these phospholipids. This article is part of a Special Issue entitled Phospholipids and Phospholipid Metabolism....

Functional imaging of murine hearts using accelerated self-gated UTE cine MRI.

Science.gov (United States)

Motaal, Abdallah G; Noorman, Nils; de Graaf, Wolter L; Hoerr, Verena; Florack, Luc M J; Nicolay, Klaas; Strijkers, Gustav J

2015-01-01

We introduce a fast protocol for ultra-short echo time (UTE) Cine magnetic resonance imaging (MRI) of the beating murine heart. The sequence involves a self-gated UTE with golden-angle radial acquisition and compressed sensing reconstruction. The self-gated acquisition is performed asynchronously with the heartbeat, resulting in a randomly undersampled kt-space that facilitates compressed sensing reconstruction. The sequence was tested in 4 healthy rats and 4 rats with chronic myocardial infarction, approximately 2 months after surgery. As a control, a non-accelerated self-gated multi-slice FLASH sequence with an echo time (TE) of 2.76 ms, 4.5 signal averages, a matrix of 192 × 192, and an acquisition time of 2 min 34 s per slice was used to obtain Cine MRI with 15 frames per heartbeat. Non-accelerated UTE MRI was performed with TE = 0.29 ms, a reconstruction matrix of 192 × 192, and an acquisition time of 3 min 47 s per slice for 3.5 averages. Accelerated imaging with 2×, 4× and 5× undersampled kt-space data was performed with 1 min, 30 and 15 s acquisitions, respectively. UTE Cine images up to 5× undersampled kt-space data could be successfully reconstructed using a compressed sensing algorithm. In contrast to the FLASH Cine images, flow artifacts in the UTE images were nearly absent due to the short echo time, simplifying segmentation of the left ventricular (LV) lumen. LV functional parameters derived from the control and the accelerated Cine movies were statistically identical.

Revealing complex function, process and pathway interactions with high-throughput expression and biological annotation data.

Science.gov (United States)

Singh, Nitesh Kumar; Ernst, Mathias; Liebscher, Volkmar; Fuellen, Georg; Taher, Leila

2016-10-20

The biological relationships both between and within the functions, processes and pathways that operate within complex biological systems are only poorly characterized, making the interpretation of large scale gene expression datasets extremely challenging. Here, we present an approach that integrates gene expression and biological annotation data to identify and describe the interactions between biological functions, processes and pathways that govern a phenotype of interest. The product is a global, interconnected network, not of genes but of functions, processes and pathways, that represents the biological relationships within the system. We validated our approach on two high-throughput expression datasets describing organismal and organ development. Our findings are well supported by the available literature, confirming that developmental processes and apoptosis play key roles in cell differentiation. Furthermore, our results suggest that processes related to pluripotency and lineage commitment, which are known to be critical for development, interact mainly indirectly, through genes implicated in more general biological processes. Moreover, we provide evidence that supports the relevance of cell spatial organization in the developing liver for proper liver function. Our strategy can be viewed as an abstraction that is useful to interpret high-throughput data and devise further experiments.

Heavy accelerated nuclei in biomedical research

International Nuclear Information System (INIS)

Tobias, C.A.

1987-01-01

Accelerated atomic nuclei in physics accelerators have been used in basic biological research and in applied medical diagnostic and therapeutic studies for the past 50 years. The passage of single heavy particles through the cell nucleus is capable of producing multiple DNA double-strand scission and chromatin breaks. According to the Repair-Misrepair model, the high biological effectiveness of high-LET particles is due to misrepair and misrejoining of the breaks. The Bragg depth ionization effect allows heavy particles to deposit considerably more energy deep in tissue than at the surface, and this property has been used for great improvements in the radiation therapy of localized tumors. Recent advances in producing radioactive beams will allow verification of therapeutic administration of such beams. The radioactive beams also open a new field of Nuclear Medicine. There is increasing interest in building special biomedical light and heavy-ion accelerators. These will be used not only for therapy but also for diagnosis, for the study of radiation hazards in space flight, and for basic molecular and cellular understanding of the mechanisms of radiation effect

Accelerator breeder concept

International Nuclear Information System (INIS)

Bartholomew, G.A.; Fraser, J.S.; Garvey, P.M.

1978-10-01

The principal components and functions of an accelerator breeder are described. The role of the accelerator breeder as a possible long-term fissile production support facility for CANDU (Canada Deuterium Uranium) thorium advanced fuel cycles and the Canadian research and development program leading to such a facility are outlined. (author)

Optimizing accelerator technology

CERN Multimedia

Katarina Anthony

2012-01-01

A new EU-funded research and training network, oPAC, is bringing together 22 universities, research centres and industry partners to optimize particle accelerator technology. CERN is one of the network’s main partners and will host 5 early-stage researchers in the BE department.   A diamond detector that will be used for novel beam diagnostics applications in the oPAC project based at CIVIDEC. (Image courtesy of CIVIDEC.) As one of the largest Marie Curie Initial Training Networks ever funded by the EU – to the tune of €6 million – oPAC extends well beyond the particle physics community. “Accelerator physics has become integral to research in almost every scientific discipline – be it biology and life science, medicine, geology and material science, or fundamental physics,” explains Carsten P. Welsch, oPAC co-ordinator based at the University of Liverpool. “By optimizing the operation of accelerators, all of these...

Metabolomics for functional genomics, systems biology, and biotechnology.

Science.gov (United States)

Saito, Kazuki; Matsuda, Fumio

2010-01-01

Metabolomics now plays a significant role in fundamental plant biology and applied biotechnology. Plants collectively produce a huge array of chemicals, far more than are produced by most other organisms; hence, metabolomics is of great importance in plant biology. Although substantial improvements have been made in the field of metabolomics, the uniform annotation of metabolite signals in databases and informatics through international standardization efforts remains a challenge, as does the development of new fields such as fluxome analysis and single cell analysis. The principle of transcript and metabolite cooccurrence, particularly transcriptome coexpression network analysis, is a powerful tool for decoding the function of genes in Arabidopsis thaliana. This strategy can now be used for the identification of genes involved in specific pathways in crops and medicinal plants. Metabolomics has gained importance in biotechnology applications, as exemplified by quantitative loci analysis, prediction of food quality, and evaluation of genetically modified crops. Systems biology driven by metabolome data will aid in deciphering the secrets of plant cell systems and their application to biotechnology.

Accelerated ion beam research at ATOMKI

International Nuclear Information System (INIS)

Kiss, A.Z.

2009-01-01

The paper summarizes the studies on accelerated ion beams at ATOMKI and their technical background, their use from chemical analysis to biological, medical, geological, archaeological applications, their advance from material science to micromachining. (TRA)

MicroRNA functional network in pancreatic cancer: From biology to ...

Indian Academy of Sciences (India)

[Wang J and Sen S 2011 MicroRNA functional network in pancreatic cancer: From biology to biomarkers of disease. ... growth factor type I receptor; INSR, insulin receptor; IPA, Ingenuity Pathway Analysis; IPMN, ..... Prostate cancer signalling.

Unexpected functional similarities between gatekeeper tumour suppressor genes and proto-oncogenes revealed by systems biology.

Science.gov (United States)

Zhao, Yongzhong; Epstein, Richard J

2011-05-01

Familial tumor suppressor genes comprise two subgroups: caretaker genes (CTs) that repair DNA, and gatekeeper genes (GKs) that trigger cell death. Since GKs may also induce cell cycle delay and thus enhance cell survival by facilitating DNA repair, we hypothesized that the prosurvival phenotype of GKs could be selected during cancer progression, and we used a multivariable systems biology approach to test this. We performed multidimensional data analysis, non-negative matrix factorization and logistic regression to compare the features of GKs with those of their putative antagonists, the proto-oncogenes (POs), as well as with control groups of CTs and functionally unrelated congenital heart disease genes (HDs). GKs and POs closely resemble each other, but not CTs or HDs, in terms of gene structure (Pexpression level and breadth (Pimplied suggest a common functional attribute that is strongly negatively selected-that is, a shared phenotype that enhances cell survival. The counterintuitive finding of similar evolutionary pressures affecting GKs and POs raises an intriguing possibility: namely, that cancer microevolution is accelerated by an epistatic cascade in which upstream suppressor gene defects subvert the normal bifunctionality of wild-type GKs by constitutively shifting the phenotype away from apoptosis towards survival. If correct, this interpretation would explain the hitherto unexplained phenomenon of frequent wild-type GK (for example, p53) overexpression in tumors.

Laser-driven particle acceleration towards radiobiology and medicine

CERN Document Server

2016-01-01

This book deals with the new method of laser-driven acceleration for application to radiation biophysics and medicine. It provides multidisciplinary contributions from world leading scientist in order to assess the state of the art of innovative tools for radiation biology research and medical applications of ionizing radiation. The book contains insightful contributions on highly topical aspects of spatio-temporal radiation biophysics, evolving over several orders of magnitude, typically from femtosecond and sub-micrometer scales. Particular attention is devoted to the emerging technology of laser-driven particle accelerators and their applicatio to spatio-temporal radiation biology and medical physics, customization of non-conventional and selective radiotherapy and optimized radioprotection protocols.

The bottom-up approach to defining life : deciphering the functional organization of biological cells via multi-objective representation of biological complexity from molecules to cells

Directory of Open Access Journals (Sweden)

Sathish ePeriyasamy

2013-12-01

Full Text Available In silico representation of cellular systems needs to represent the adaptive dynamics of biological cells, recognizing a cell’s multi-objective topology formed by spatially and temporally cohesive intracellular structures. The design of these models needs to address the hierarchical and concurrent nature of cellular functions and incorporate the ability to self-organise in response to transitions between healthy and pathological phases, and adapt accordingly. The functions of biological systems are constantly evolving, due to the ever changing demands of their environment. Biological systems meet these demands by pursuing objectives, aided by their constituents, giving rise to biological functions. A biological cell is organised into an objective/task hierarchy. These objective hierarchy corresponds to the nested nature of temporally cohesive structures and representing them will facilitate in studying pleiotropy and polygeny by modeling causalities propagating across multiple interconnected intracellular processes. Although biological adaptations occur in physiological, developmental and reproductive timescales, the paper is focused on adaptations that occur within physiological timescales, where the biomolecular activities contributing to functional organisation, play a key role in cellular physiology. The paper proposes a multi-scale and multi-objective modelling approach from the bottom-up by representing temporally cohesive structures for multi-tasking of intracellular processes. Further the paper characterises the properties and constraints that are consequential to the organisational and adaptive dynamics in biological cells.

Functional Data Analysis of Spaceflight-Induced Changes in Coordination and Phase in Head Pitch Acceleration During Treadmill Walking

Science.gov (United States)

Miller, Christopher; Peters, Brian; Feiveson, Alan; Bloomberg, Jacob

2011-01-01

Astronauts returning from spaceflight experience neurovestibular disturbances during head movements and attempt to mitigate them by limiting head motion. Analyses to date of the head movements made during walking have concentrated on amplitude and variability measures extracted from ensemble averages of individual gait cycles. Phase shifts within each gait cycle can be determined by functional data analysis through the computation of time-warping functions. Large, localized variations in the timing of peaks in head kinematics may indicate changes in coordination. The purpose of this study was to determine timing changes in head pitch acceleration of astronauts during treadmill walking before and after flight. Six astronauts (5M/1F; age = 43.5+/-6.4yr) participated in the study. Subjects walked at 1.8 m/sec (4 mph) on a motorized treadmill while reading optotypes displayed on a computer screen 4 m in front of their eyes. Three-dimensional motion of the subject s head was recorded with an Inertial Measurement Unit (IMU) device. Data were recorded twice before flight and four times after landing. The head pitch acceleration was calculated by taking the time derivative of the pitch velocity data from the IMU. Data for each session with each subject were time-normalized into gait cycles, then registered to align significant features and create a mean curve. The mean curves of each postflight session for each subject were re-registered based on their preflight mean curve to create time-warping functions. The root mean squares (RMS) of these warping functions were calculated to assess the deviation of head pitch acceleration mean curves in each postflight session from the preflight mean curve. After landing, most crewmembers exhibited localized shifts within their head pitch acceleration regimes, with the greatest deviations in RMS occurring on landing day or 1 day after landing. These results show that the alteration of head pitch coordination due to spaceflight may be

Bioimaging of cells and tissues using accelerator-based sources.

Science.gov (United States)

Petibois, Cyril; Cestelli Guidi, Mariangela

2008-07-01

A variety of techniques exist that provide chemical information in the form of a spatially resolved image: electron microprobe analysis, nuclear microprobe analysis, synchrotron radiation microprobe analysis, secondary ion mass spectrometry, and confocal fluorescence microscopy. Linear (LINAC) and circular (synchrotrons) particle accelerators have been constructed worldwide to provide to the scientific community unprecedented analytical performances. Now, these facilities match at least one of the three analytical features required for the biological field: (1) a sufficient spatial resolution for single cell (pros and cons of the most popular techniques that have been implemented on accelerator-based sources to address analytical issues on biological specimens.

Virtual Agonist-antagonist Mechanisms Produce Biological Muscle-like Functions: An Application for Robot Joint Control

DEFF Research Database (Denmark)

Xiong, Xiaofeng; Wörgötter, Florentin; Manoonpong, Poramate

2014-01-01

Purpose – Biological muscles of animals have a surprising variety of functions, i.e., struts, springs, and brakes. According to this, the purpose of this paper is to apply virtual agonist-antagonist mechanisms to robot joint control allowing for muscle-like functions and variably compliant joint......, variably compliant joint motions can be produced without mechanically bulky and complex mechanisms or complex force/toque sensing at each joint. Moreover, through tuning the damping coefficient of the VAAM, the functions of the VAAM are comparable to biological muscles. Originality/value – The model (i.......e., VAAM) provides a way forward to emulate muscle-like functions that are comparable to those found in physiological experiments of biological muscles. Based on these muscle-like functions, the robotic joints can easily achieve variable compliance that does not require complex physical components...

Ion accelerator applications in medicine and cultural heritage

International Nuclear Information System (INIS)

Denker, A.; Cordini, D.; Heufelder, J.; Homeyer, H.; Kluge, H.; Simiantonakis, I.; Stark, R.; Weber, A.

2007-01-01

Formerly, accelerator laboratories were mainly dedicated to nuclear physics. Today, they are used in up-coming research fields and applications like material analysis and material science as well as biology, medicine or archaeology. Practical applications have been developed, involving hospitals, industry and even humanists in the use of accelerators. This paper focuses on some medical and analytical applications of the HMI accelerator facility, especially for eye tumour therapy and archaeology. The innovation of techniques to measure the dose distribution, the development of an automated monitoring procedure allowing an improved and accelerated patient positioning, and the implementation of a modern treatment planning system will be presented first. In the second part, the employment of accelerators in better understanding of our cultural heritage will be shown

Scavenger Receptor CD163 and Its Biological Functions

Directory of Open Access Journals (Sweden)

Gabriela Onofre

2009-01-01

Full Text Available CD163 is a member of scavenger receptor super family class B of the first subgroup. It is mapped to the region p13 on chromosome 12. Five different isoforms of CD163 have been described, which differ in the structure of their cytoplasmic domains and putative phosporylation sites. This scavenger receptor is selectively expressed on cells of monocytes and macrophages lineage exclusively. CD163 immunological function is essentially homeostatic. It also has other functions because participates in adhesion to endothelial cells, in tolerance induction and tissues regeneration. Other very important function of CD163 is the clearance of hemoglobin in its cell-free form and participation in anti-inflammation in its soluble form, exhibiting cytokine-like functions. We review the biological functions of CD163 which have been discovered until now. It seems apparent from this review that CD163 scavenger receptor can be used as biomarker in different diseases and as a valuable diagnostic parameter for prognosis of many diseases especially inflammatory disorders and sepsis.

Carotenoids from Marine Organisms: Biological Functions and Industrial Applications

Directory of Open Access Journals (Sweden)

Christian Galasso

2017-11-01

Full Text Available As is the case for terrestrial organisms, carotenoids represent the most common group of pigments in marine environments. They are generally biosynthesized by all autotrophic marine organisms, such as bacteria and archaea, algae and fungi. Some heterotrophic organisms also contain carotenoids probably accumulated from food or partly modified through metabolic reactions. These natural pigments are divided into two chemical classes: carotenes (such as lycopene and α- and β-carotene that are composed of hydrogen and carbon; xanthophylls (such as astaxanthin, fucoxanthin and lutein, which are constituted by hydrogen, carbon and oxygen. Carotenoids, as antioxidant compounds, assume a key role in the protection of cells. In fact, quenching of singlet oxygen, light capture and photosynthesis protection are the most relevant biological functions of carotenoids. The present review aims at describing (i the biological functions of carotenoids and their benefits for human health, (ii the most common carotenoids from marine organisms and (iii carotenoids having large success in pharmaceutical, nutraceutical and cosmeceutical industries, highlighting the scientific progress in marine species cultivation for natural pigments production.

Damage limits of accelerator equipment

CERN Document Server

Rosell, Gemma

2014-01-01

Beam losses occur in particle accelerators for various reasons. The effect of lost particles on accelerator equipment becomes more severe with the increasing energies and intensities. The present study is focused on the damage potential of the proton beam as a function of particle energy and beam size. Injection and extraction energies of different accelerators at CERN were considered.

Neurotrophin Propeptides: Biological Functions and Molecular Mechanisms.

Science.gov (United States)

Rafieva, Lola M; Gasanov, Eugene V

2016-01-01

Neurotrophins constitute a family of growth factors that play a key role in the regulation of the development and function of the central and peripheral nervous systems. A common feature of all the neurotrophins is their synthesis in cells as long precursors (pre-pro-neurotrophins) that contain an N-terminal signal peptide, a following propeptide and the mature neurotrophin. Although the signal peptide functions have been well studied, the role of neurotrophin propeptides is not so clear. Here, we briefly summarize the biochemistry of neurotrophin propeptides, including their role as folding-assistants for the mature factor and their role in processing and in secretion of neurotrophins. In the main part of the review we summarize our current state of knowledge of the biological activity of neurotrophin propeptides, their possible mechanisms of action, and their potential influence on the activity of the mature neurotrophins.

Basis of medical accelerator. Synchrotron

International Nuclear Information System (INIS)

Kawachi, Kiyomitsu

2014-01-01

On the synchrotron as a medical accelerator, this paper introduces the basic principle, basic techniques and the like. The accelerator, when synchrotron is adopted as an ion beam radiotherapy system, is the composite accelerator composed of ion sources, injector, and synchrotron. This paper introduces the overall structure of synchrotron, and conceptually explains the basic behavior of high-frequency waves and magnetic field of synchrotron, as well as the deflection electromagnet of medical synchrotron and the operation pattern of high-frequency acceleration system. The types of synchrotron can be classified to the function combination type and function separation type, and this paper introduces the features of each type and various types of synchrotrons. It also explains beam dynamics important for ensuring the stability of beams, with a focus on the coordinate system, vertical movement, and lateral movement. In addition, it explains the incidence and outgoing of beams that are important for properly operating the accelerator, with a focus on their techniques. (A.O.)

Accelerated cardiovascular magnetic resonance of the mouse heart using self-gated parallel imaging strategies does not compromise accuracy of structural and functional measures

Directory of Open Access Journals (Sweden)

Dörries Carola

2010-07-01

Full Text Available Abstract Background Self-gated dynamic cardiovascular magnetic resonance (CMR enables non-invasive visualization of the heart and accurate assessment of cardiac function in mouse models of human disease. However, self-gated CMR requires the acquisition of large datasets to ensure accurate and artifact-free reconstruction of cardiac cines and is therefore hampered by long acquisition times putting high demands on the physiological stability of the animal. For this reason, we evaluated the feasibility of accelerating the data collection using the parallel imaging technique SENSE with respect to both anatomical definition and cardiac function quantification. Results Findings obtained from accelerated data sets were compared to fully sampled reference data. Our results revealed only minor differences in image quality of short- and long-axis cardiac cines: small anatomical structures (papillary muscles and the aortic valve and left-ventricular (LV remodeling after myocardial infarction (MI were accurately detected even for 3-fold accelerated data acquisition using a four-element phased array coil. Quantitative analysis of LV cardiac function (end-diastolic volume (EDV, end-systolic volume (ESV, stroke volume (SV, ejection fraction (EF and LV mass in healthy and infarcted animals revealed no substantial deviations from reference (fully sampled data for all investigated acceleration factors with deviations ranging from 2% to 6% in healthy animals and from 2% to 8% in infarcted mice for the highest acceleration factor of 3.0. CNR calculations performed between LV myocardial wall and LV cavity revealed a maximum CNR decrease of 50% for the 3-fold accelerated data acquisition when compared to the fully-sampled acquisition. Conclusions We have demonstrated the feasibility of accelerated self-gated retrospective CMR in mice using the parallel imaging technique SENSE. The proposed method led to considerably reduced acquisition times, while preserving high

Re-evaluating concepts of biological function in clinical medicine: towards a new naturalistic theory of disease.

Science.gov (United States)

Chin-Yee, Benjamin; Upshur, Ross E G

2017-08-01

Naturalistic theories of disease appeal to concepts of biological function, and use the notion of dysfunction as the basis of their definitions. Debates in the philosophy of biology demonstrate how attributing functions in organisms and establishing the function-dysfunction distinction is by no means straightforward. This problematization of functional ascription has undermined naturalistic theories and led some authors to abandon the concept of dysfunction, favoring instead definitions based in normative criteria or phenomenological approaches. Although this work has enhanced our understanding of disease and illness, we need not necessarily abandon naturalistic concepts of function and dysfunction in the disease debate. This article attempts to move towards a new naturalistic theory of disease that overcomes the limitations of previous definitions and offers advantages in the clinical setting. Our approach involves a re-evaluation of concepts of biological function employed by naturalistic theories. Drawing on recent insights from the philosophy of biology, we develop a contextual and evaluative account of function that is better suited to clinical medicine and remains consistent with contemporary naturalism. We also show how an updated naturalistic view shares important affinities with normativist and phenomenological positions, suggesting a possibility for consilience in the disease debate.

Active Interaction Mapping as a tool to elucidate hierarchical functions of biological processes.

Science.gov (United States)

Farré, Jean-Claude; Kramer, Michael; Ideker, Trey; Subramani, Suresh

2017-07-03

Increasingly, various 'omics data are contributing significantly to our understanding of novel biological processes, but it has not been possible to iteratively elucidate hierarchical functions in complex phenomena. We describe a general systems biology approach called Active Interaction Mapping (AI-MAP), which elucidates the hierarchy of functions for any biological process. Existing and new 'omics data sets can be iteratively added to create and improve hierarchical models which enhance our understanding of particular biological processes. The best datatypes to further improve an AI-MAP model are predicted computationally. We applied this approach to our understanding of general and selective autophagy, which are conserved in most eukaryotes, setting the stage for the broader application to other cellular processes of interest. In the particular application to autophagy-related processes, we uncovered and validated new autophagy and autophagy-related processes, expanded known autophagy processes with new components, integrated known non-autophagic processes with autophagy and predict other unexplored connections.

The relationship between oral health status and biological and psychosocial function in the bedridden elderly.

Science.gov (United States)

Hanada, N; Tada, A

2001-01-01

The present study was conducted in order to determine what item of biological and psychosocial function is related to oral health status in the bedridden elderly. The subjects were 94 elderly individuals (30 males, 64 females) who had been admitted to a nursing home in Chiba city, Japan. We assessed the number of remaining teeth and the number of functional teeth as oral health status variables. Biological and psychosocial function levels were determined using the functional independence measure method developed by the State University of New York at Buffalo. More than 70% of subjects had less than ten remaining teeth. Almost all subjects needed prosthesis treatment. More than 50% of subjects had 27 or less functional teeth. Mann-Whitney U-test and logistic regression models showed that 'expression' was concerned with the number of remaining teeth and 'bladder management', 'locomotion', 'transfers' were related to the number of functional teeth. These data suggest close relation between oral health status and biological and psychosocial function levels in the bedridden elderly.

Accelerated Testing and Modeling of Potential-Induced Degradation as a Function of Temperature and Relative Humidity

DEFF Research Database (Denmark)

Hacke, Peter; Spataru, Sergiu; Terwilliger, Kent

2015-01-01

An acceleration model based on the Peck equation was applied to power performance of crystalline silicon cell modules as a function of time and of temperature and humidity, which are the two main environmental stress factors that promote potential-induced degradation (PID). This model was derived...

Accelerated Testing and Modeling of Potential-Induced Degradation as a Function of Temperature and Relative Humidity

DEFF Research Database (Denmark)

Hacke, Peter; Spataru, Sergiu; Terwilliger, Kent

2015-01-01

An acceleration model based on the Peck equation was applied to power performance of crystalline silicon cell modules as a function of time and of temperature and humidity, the two main environmental stress factors that promote potential-induced degradation. This model was derived from module pow...

A periodic plasma waveguide accelerator

International Nuclear Information System (INIS)

Cole, F.T.

1985-01-01

The increasing cost of synchrotrons and storage rings has given new interest in the search for new methods of acceleration. The primary goal of this search is very large accelerating fields, because the cost of an accelerator to reach TeV energies is dominated by costs that scale with length. Very large electric fields are possible in plasmas and in lasers and many geometries are being studied that make use of plasmas, lasers, or combinations of them. In a plasma accelerator, the plasma can have several different functions. It may act as a medium for the propagation of accelerating electric-field waves. In addition, these waves may also act as a source of the energy needed to accelerate particles. Accelerators using various waves in plasmas have been built and studied in many laboratories. The device proposed here is an attempt to separate the two functions of providing a medium and providing an energy source. A relatively low-energy electron beam is used as a non-neutral plasma only to make a slow-wave medium for the propagation of an externally generated wave. The wave is a TM electromagnetic wave and the device may be thought of as a conventional electron linear accelerator with the evacuated volume and metallic envelope replaced by the electron beam. A separate second beam, which may be electrons or heavier particles, is accelerated. The application in mind here is a single-pass collider

Radiation protection and dosimetry problems around medium energy accelerators

Energy Technology Data Exchange (ETDEWEB)

Pavlovic, R; Pavlovic, S; Markovic, S [Inst. of Nuclear Sciences Vinca, Belgrade (Yugoslavia); Boreli, F [Fac. of Electrical Engineering, Belgrade (Yugoslavia)

1996-12-31

In the Institute of Nuclear Sciences `VINCA`, the Accelerator Installation `TESLA`, which is an ion accelerator facility consisting of an isochronous cyclotron `VINCY`, a heavy ion source, a D{sup -} / H{sup -} ion source, three low energy and five high energy experimental channels is now under construction. The Tesla Accelerator Installation should by the principal facility for basic and applied research in physics, chemistry, biology, and material science, as well as for production of radioisotopes, medical diagnostics and therapy with radioisotopes and accelerated particle beams. Some problems in defining radiation protection and safety programme, particularly problems in construction appropriate shielding barriers at the Accelerator Installation `TESLA` are discussed in this paper. (author) 1 fig., 9 refs.

Paul Langerhans: a prilgrim "traveling" from functional histology to marine biology.

Science.gov (United States)

Raica, Marius; Cimpean, Anca Maria

2017-06-01

The nineteenth century was the time of a real revolution in science and medicine. A lot of seminal discoveries in medicine and biology were done in this time, and many of them were coincident with the introduction of the compound microscope by Hermann van Deijl and the standard histological technique by Paul Ehrlich. The main tissue types and individual cells were characterized and originally classified more than hundred years ago, although less attention was paid to their basic functions. This was mainly due to the modality of tissue specimen processing that allowed particularly detailed descriptive studies. Even so, we can notice some attempts to correlate the structure with the function. The German scientist Paul Langerhans, well-known for the discovery of Langerhans islets of the pancreas and Langerhans cells from the epidermis, tried to change the conventional fate of morphological studies introducing in his works functional hypothesis based on traditional microscopic observations even from the beginning of his scientific career. Paul Langerhans was a complex personality of the second half of the nineteenth century, not only in medicine, but also in other fields of biology. In the present review, presented is the life and research activity of Paul Langerhans, not only because of the importance of his discoveries, but also for perspectives that were opened by these findings in unexpected fields of medicine and biology.

Particle acceleration in the interplanetary space

International Nuclear Information System (INIS)

Tverskoj, B.A.

1983-01-01

A review on the problem of particle acceleration in the interplanetary space is given. The main lationship attention is paid to the problem of the re/ between the impact- and turbulent acceleration when an undisturbed magnetic field forms not too small angle THETA > 10 deg with the shock wave front. The following conclusions are drawn. Particle acceleration at the shock wave front is manifested in the explicit form, if the shock wave propagates along a homogeneous (in the 11 cm range) solar wind. The criterion of such an acceleration is the exponential distribution function F approximately vsup(-ν) (v is the particle velocity and ν is the accelerated particle spectrum index) in the low energy range and the conservation of this function at considerable distances behind the front. The presence of an additional turbulent acceleration behind the front is manifested in decreasing ν down to approximately 3.5 in the low energy range and in the spectrum evolution behind the front

Neurotrophin-3 accelerates wound healing in diabetic mice by promoting a paracrine response in mesenchymal stem cells.

Science.gov (United States)

Shen, Lei; Zeng, Wen; Wu, Yang-Xiao; Hou, Chun-Li; Chen, Wen; Yang, Ming-Can; Li, Li; Zhang, Ya-Fang; Zhu, Chu-Hong

2013-01-01

Angiogenesis is a major obstacle for wound healing in patients with diabetic foot wounds. Mesenchymal stem cells (MSCs) have an important function in wound repair, and neurotrophin-3 (NT-3) can promote nerve regeneration and angiogenesis. We investigated the effect of NT-3 on accelerating wound healing in the diabetic foot by improving human bone marrow MSC (hMSC) activation. In vitro, NT-3 significantly promoted VEGF, NGF, and BDNF secretion in hMSCs. NT-3 improved activation of the hMSC conditioned medium, promoted human umbilical vein endothelial cell (HUVEC) proliferation and migration, and significantly improved the closure rate of HUVEC scratches. In addition, we produced nanofiber mesh biological tissue materials through the electrospinning technique using polylactic acid, mixed silk, and collagen. The hMSCs stimulated by NT-3 were implanted into the material. Compared with the control group, the NT-3-stimulated hMSCs in the biological tissue material significantly promoted angiogenesis in the feet of diabetic C57BL/6J mice and accelerated diabetic foot wound healing. These results suggest that NT-3 significantly promotes hMSC secretion of VEGF, NGF, and other vasoactive factors and that it accelerates wound healing by inducing angiogenesis through improved activation of vascular endothelial cells. The hMSCs stimulated by NT-3 can produce materials that accelerate wound healing in the diabetic foot and other ischemic ulcers.

Collective ion acceleration

International Nuclear Information System (INIS)

Godfrey, B.B.; Faehl, R.J.; Newberger, B.S.; Shanahan, W.R.; Thode, L.E.

1977-01-01

Progress achieved in the understanding and development of collective ion acceleration is presented. Extensive analytic and computational studies of slow cyclotron wave growth on an electron beam in a helix amplifier were performed. Research included precise determination of linear coupling between beam and helix, suppression of undesired transients and end effects, and two-dimensional simulations of wave growth in physically realizable systems. Electrostatic well depths produced exceed requirements for the Autoresonant Ion Acceleration feasibility experiment. Acceleration of test ions to modest energies in the troughs of such waves was also demonstrated. Smaller efforts were devoted to alternative acceleration mechanisms. Langmuir wave phase velocity in Converging Guide Acceleration was calculated as a function of the ratio of electron beam current to space-charge limiting current. A new collective acceleration approach, in which cyclotron wave phase velocity is varied by modulation of electron beam voltage, is proposed. Acceleration by traveling Virtual Cathode or Localized Pinch was considered, but appears less promising. In support of this research, fundamental investigations of beam propagation in evacuated waveguides, of nonneutral beam linear eigenmodes, and of beam stability were carried out. Several computer programs were developed or enhanced. Plans for future work are discussed

Knowledge base and functionality of concepts of some Filipino biology teachers in five biology topics

Science.gov (United States)

Barquilla, Manuel B.

2018-01-01

This mixed research, is a snapshot of some Filipino Biology teachers' knowledge structure and how their concepts of the five topics in Biology (Photosynthesis, Cellular Respiration, human reproductive system, Mendelian genetics and NonMendelian genetics) functions and develops inside a biology classroom. The study focuses on the six biology teachers and a total of 222 students in their respective classes. Of the Six (6) teachers, three (3) are under the Science curriculum and the other three (3) are under regular curriculum in both public and private schools in Iligan city and Lanao del Norte, Philippines. The study utilized classroom discourses, concept maps, interpretative case-study method, bracketing method, and concept analysis for qualitative part; the quantitative part uses a nonparametric statistical tool, Kendall's tau Coefficient for determining relationship and congruency while measures of central tendencies and dispersion (mean, and standard deviation) for concept maps scores interpretation. Knowledge Base of Biology teachers were evaluated by experts in field of specialization having a doctorate program (e.g. PhD in Genetics) and PhD Biology candidates. The data collection entailed seven (7) months immersion: one (1) month for preliminary phase for the researcher to gain teachers' and students' confidence and the succeeding six (6) months for main observation and data collection. The evaluation of teachers' knowledge base by experts indicated that teachers' knowledge of (65%) is lower than the minimum (75%) recommended by ABD-el-Khalick and Boujaoude (1997). Thus, the experts believe that content knowledge of the teachers is hardly adequate for their teaching assignment. Moreover, the teachers in this study do not systematically use reallife situation to apply the concepts they teach. They can identify concepts too abstract for their student; however, they seldom use innovative ways to bring the discussion to their students' level of readiness and

Combined small-molecule inhibition accelerates the derivation of functional, early-born, cortical neurons from human pluripotent stem cells

Science.gov (United States)

Qi, Yuchen; Zhang, Xin-Jun; Renier, Nicolas; Wu, Zhuhao; Atkin, Talia; Sun, Ziyi; Ozair, M. Zeeshan; Tchieu, Jason; Zimmer, Bastian; Fattahi, Faranak; Ganat, Yosif; Azevedo, Ricardo; Zeltner, Nadja; Brivanlou, Ali H.; Karayiorgou, Maria; Gogos, Joseph; Tomishima, Mark; Tessier-Lavigne, Marc; Shi, Song-Hai; Studer, Lorenz

2017-01-01

Considerable progress has been made in converting human pluripotent stem cells (hPSCs) into functional neurons. However, the protracted timing of human neuron specification and functional maturation remains a key challenge that hampers the routine application of hPSC-derived lineages in disease modeling and regenerative medicine. Using a combinatorial small-molecule screen, we previously identified conditions for the rapid differentiation of hPSCs into peripheral sensory neurons. Here we generalize the approach to central nervous system (CNS) fates by developing a small-molecule approach for accelerated induction of early-born cortical neurons. Combinatorial application of 6 pathway inhibitors induces post-mitotic cortical neurons with functional electrophysiological properties by day 16 of differentiation, in the absence of glial cell co-culture. The resulting neurons, transplanted at 8 days of differentiation into the postnatal mouse cortex, are functional and establish long-distance projections, as shown using iDISCO whole brain imaging. Accelerated differentiation into cortical neuron fates should facilitate hPSC-based strategies for disease modeling and cell therapy in CNS disorders. PMID:28112759

The SARAF Project - Soreq Applied Research Accelerator Facility

International Nuclear Information System (INIS)

Nagler, A.; Mardor, I.; Berkovits, D.; Piel, C.

2004-01-01

The relevance of particle accelerators to society, in the use of their primary and secondary beams for the analysis of physical, chemical and biological samples and for modification of properties of materials, is well recognized and documented. Nevertheless, apart of the construction of small accelerators for nuclear research in the 1960's and 70's, Israel has so far neglected this important and growing field. Furthermore, there is an urgent need in Israel for a state of the art research facility to attract and introduce students to current advanced physics techniques and technologies and to train the next generation of experimental scientists in various branches and disciplines. Therefore, Soreq NRC recently initiated the establishment of a new accelerator facility, named SARAF Soreq Applied Research Accelerator Facility. SARAF will be a continuous wave (CW), proton and deuteron RF superconducting linear accelerator with variable energy (5 - 40 MeV) and current (0.04 -2 mA). SARAF is designed to enable hands-on maintenance, which means that its beam loss will be below 10 -5 for the entire accelerator. These specifications will place SARAF in line with the next generation of accelerators world wide. Soreq expects that this fact will attract the Israeli and international research communities to use this facility extensively. Soreq NRC intends to use SARAF for basic, medical and biological research, and non-destructive testing (NDT). Another major activity will be the research and development of radio-isotopes production techniques. Given the availability of high current (up to 2 mA) protons and deuterons, a major activity will be research and development of high power density (up to 80 kW on a few cm 2 ) irradiation targets

Progress in the biological function of alpha-enolase

Directory of Open Access Journals (Sweden)

Hong Ji

2016-03-01

Full Text Available Alpha-enolase (ENO1, also known as 2-phospho-D-glycerate hydrolase, is a metalloenzyme that catalyzes the conversion of 2-phosphoglyceric acid to phosphoenolpyruvic acid in the glycolytic pathway. It is a multifunctional glycolytic enzyme involved in cellular stress, bacterial and fungal infections, autoantigen activities, the occurrence and metastasis of cancer, parasitic infections, and the growth, development and reproduction of organisms. This article mainly reviews the basic characteristics and biological functions of ENO1.

Role of accelerated segment switch in exons to alter targeting (ASSET in the molecular evolution of snake venom proteins

Directory of Open Access Journals (Sweden)

Kini R Manjunatha

2009-06-01

Full Text Available Abstract Background Snake venom toxins evolve more rapidly than other proteins through accelerated changes in the protein coding regions. Previously we have shown that accelerated segment switch in exons to alter targeting (ASSET might play an important role in its functional evolution of viperid three-finger toxins. In this phenomenon, short sequences in exons are radically changed to unrelated sequences and hence affect the folding and functional properties of the toxins. Results Here we analyzed other snake venom protein families to elucidate the role of ASSET in their functional evolution. ASSET appears to be involved in the functional evolution of three-finger toxins to a greater extent than in several other venom protein families. ASSET leads to replacement of some of the critical amino acid residues that affect the biological function in three-finger toxins as well as change the conformation of the loop that is involved in binding to specific target sites. Conclusion ASSET could lead to novel functions in snake venom proteins. Among snake venom serine proteases, ASSET contributes to changes in three surface segments. One of these segments near the substrate binding region is known to affect substrate specificity, and its exchange may have significant implications for differences in isoform catalytic activity on specific target protein substrates. ASSET therefore plays an important role in functional diversification of snake venom proteins, in addition to accelerated point mutations in the protein coding regions. Accelerated point mutations lead to fine-tuning of target specificity, whereas ASSET leads to large-scale replacement of multiple functionally important residues, resulting in change or gain of functions.

Experiments on heat pipes submitted to strong accelerations; Experimentation de caloducs soumis a de fortes accelerations

Energy Technology Data Exchange (ETDEWEB)

Labuthe, A [Dassault Aviation, 92 - Saint Cloud (France)

1997-12-31

In order to evaluate the possibility to use heat pipes as efficient heat transfer devices in aircrafts, a study of their behaviour during strong accelerations is necessary. This study has been jointly carried out by the Laboratory of Thermal Studies of Poitiers (France) and Dassault Aviation company. It is based on a series of tests performed with an experimental apparatus that uses the centrifugal effect to simulate the acceleration fields submitted to the heat pipe. Un-priming - priming cycles have been performed under different power and acceleration levels and at various functioning temperatures in order to explore the behaviour of heat pipes: rate of un-priming and re-priming, functioning in blocked mode etc.. This preliminary study demonstrates the rapid re-priming of the tested heat pipes when submitted to favourable acceleration situations and the possibility to use them under thermosyphon conditions despite the brief unfavourable acceleration periods encountered. (J.S.)

Experiments on heat pipes submitted to strong accelerations; Experimentation de caloducs soumis a de fortes accelerations

Energy Technology Data Exchange (ETDEWEB)

Labuthe, A. [Dassault Aviation, 92 - Saint Cloud (France)

1996-12-31

In order to evaluate the possibility to use heat pipes as efficient heat transfer devices in aircrafts, a study of their behaviour during strong accelerations is necessary. This study has been jointly carried out by the Laboratory of Thermal Studies of Poitiers (France) and Dassault Aviation company. It is based on a series of tests performed with an experimental apparatus that uses the centrifugal effect to simulate the acceleration fields submitted to the heat pipe. Un-priming - priming cycles have been performed under different power and acceleration levels and at various functioning temperatures in order to explore the behaviour of heat pipes: rate of un-priming and re-priming, functioning in blocked mode etc.. This preliminary study demonstrates the rapid re-priming of the tested heat pipes when submitted to favourable acceleration situations and the possibility to use them under thermosyphon conditions despite the brief unfavourable acceleration periods encountered. (J.S.)

Biological markers for kidney injury and renal function in the intensive care unit

NARCIS (Netherlands)

Royakkers, A.A.N.M.

2014-01-01

The purpose of the investigations described in this thesis was to seek for answers to two relevant questions in ICUs in resource-rich settings, i.e., can new biological markers play a role in early recognition of AKI, and can new biological markers predict recovery of renal function in patients who

Synthetic biology for microbial heavy metal biosensors.

Science.gov (United States)

Kim, Hyun Ju; Jeong, Haeyoung; Lee, Sang Jun

2018-02-01

Using recombinant DNA technology, various whole-cell biosensors have been developed for detection of environmental pollutants, including heavy metal ions. Whole-cell biosensors have several advantages: easy and inexpensive cultivation, multiple assays, and no requirement of any special techniques for analysis. In the era of synthetic biology, cutting-edge DNA sequencing and gene synthesis technologies have accelerated the development of cell-based biosensors. Here, we summarize current technological advances in whole-cell heavy metal biosensors, including the synthetic biological components (bioparts), sensing and reporter modules, genetic circuits, and chassis cells. We discuss several opportunities for improvement of synthetic cell-based biosensors. First, new functional modules must be discovered in genome databases, and this knowledge must be used to upgrade specific bioparts through molecular engineering. Second, modules must be assembled into functional biosystems in chassis cells. Third, heterogeneity of individual cells in the microbial population must be eliminated. In the perspectives, the development of whole-cell biosensors is also discussed in the aspects of cultivation methods and synthetic cells.

Accelerator boom hones China's engineering expertise

Science.gov (United States)

Normile, Dennis

2018-02-01

In raising the curtain on the China Spallation Neutron Source, China has joined just four other nations in having mastered the technology of accelerating and controlling beams of protons. The $277 million facility, set to open to users this spring in Dongguan, is expected to yield big dividends in materials science, chemistry, and biology. More world class machines are on the way, as China this year starts construction on four other major accelerator facilities. The building boom is prompting a scramble to find enough engineers and technicians to finish the projects. But if they all come off as planned, the facilities would position China to tackle the next global megaproject: a giant accelerator that would pick up where Europe's Large Hadron Collider leaves off.

Functional anthology of intrinsic disorder. 1. Biological processes and functions of proteins with long disordered regions.

Science.gov (United States)

Xie, Hongbo; Vucetic, Slobodan; Iakoucheva, Lilia M; Oldfield, Christopher J; Dunker, A Keith; Uversky, Vladimir N; Obradovic, Zoran

2007-05-01

Identifying relationships between function, amino acid sequence, and protein structure represents a major challenge. In this study, we propose a bioinformatics approach that identifies functional keywords in the Swiss-Prot database that correlate with intrinsic disorder. A statistical evaluation is employed to rank the significance of these correlations. Protein sequence data redundancy and the relationship between protein length and protein structure were taken into consideration to ensure the quality of the statistical inferences. Over 200,000 proteins from the Swiss-Prot database were analyzed using this approach. The predictions of intrinsic disorder were carried out using PONDR VL3E predictor of long disordered regions that achieves an accuracy of above 86%. Overall, out of the 710 Swiss-Prot functional keywords that were each associated with at least 20 proteins, 238 were found to be strongly positively correlated with predicted long intrinsically disordered regions, whereas 302 were strongly negatively correlated with such regions. The remaining 170 keywords were ambiguous without strong positive or negative correlation with the disorder predictions. These functions cover a large variety of biological activities and imply that disordered regions are characterized by a wide functional repertoire. Our results agree well with literature findings, as we were able to find at least one illustrative example of functional disorder or order shown experimentally for the vast majority of keywords showing the strongest positive or negative correlation with intrinsic disorder. This work opens a series of three papers, which enriches the current view of protein structure-function relationships, especially with regards to functionalities of intrinsically disordered proteins, and provides researchers with a novel tool that could be used to improve the understanding of the relationships between protein structure and function. The first paper of the series describes our

[Recent advances of synthetic biology for production of functional ingredients in Chinese materia medica].

Science.gov (United States)

Su, Xin-Yao; Xue, Jian-Ping; Wang, Cai-Xia

2016-11-01

The functional ingredients in Chinese materia medica are the main active substance for traditional Chinese medicine and most of them are secondary metabolites derivatives. Until now,the main method to obtain those functional ingredients is through direct extraction from the Chinese materia medica. However, the income is very low because of the high extraction costs and the decreased medicinal plants. Synthetic biology technology, as a new and microbial approach, can be able to carry out large-scale production of functional ingredients and greatly ease the shortage of traditional Chinese medicine ingredients. This review mainly focused on the recent advances in synthetic biology for the functional ingredients production. Copyright© by the Chinese Pharmaceutical Association.

Advanced Accelerator Applications in Medicine

International Nuclear Information System (INIS)

Rimjiaem, Sakhorn

2015-01-01

besides the original purpose on development of particle acceleratora as research tools in nuclear and high-energy physics, there are large variety of accelerators used in various fileds from fundamental research to industrial usesand applications chemistry, biology and medicine. Pratical accelators used in various field of medical applications since serveral decades. Even through, a large fraction of applications is emphasized on cancer therappy, the number of accelerators used in midicine for other diagnostics and treatments has increased steady over the years. Several types of accelerated particles are used including electron, proton, neutron and ions. Presently, relativistic electron beams and radiation from linear accelerators (linas) are widely used. A combination of positron emission tomography (PRT) and radiotherapy is an example of excellent invention early detection and treat of cancer tumors. The most developments for proton and heavy ion therapy as well as a modern boron neutron capture therapy (BNCT) are also great incoming effective systems. This talk will focus on developments of the accelrator systems as well as overview on biophysical properties and medical aspects of the diacnostics and treatments.

Mediating objects: scientific and public functions of models in nineteenth-century biology.

Science.gov (United States)

Ludwig, David

2013-01-01

The aim of this article is to examine the scientific and public functions of two- and three-dimensional models in the context of three episodes from nineteenth-century biology. I argue that these models incorporate both data and theory by presenting theoretical assumptions in the light of concrete data or organizing data through theoretical assumptions. Despite their diverse roles in scientific practice, they all can be characterized as mediators between data and theory. Furthermore, I argue that these different mediating functions often reflect their different audiences that included specialized scientists, students, and the general public. In this sense, models in nineteenth-century biology can be understood as mediators between theory, data, and their diverse audiences.

Biomarkers of Aging: From Function to Molecular Biology

Directory of Open Access Journals (Sweden)

Karl-Heinz Wagner

2016-06-01

Full Text Available Aging is a major risk factor for most chronic diseases and functional impairments. Within a homogeneous age sample there is a considerable variation in the extent of disease and functional impairment risk, revealing a need for valid biomarkers to aid in characterizing the complex aging processes. The identification of biomarkers is further complicated by the diversity of biological living situations, lifestyle activities and medical treatments. Thus, there has been no identification of a single biomarker or gold standard tool that can monitor successful or healthy aging. Within this short review the current knowledge of putative biomarkers is presented, focusing on their application to the major physiological mechanisms affected by the aging process including physical capability, nutritional status, body composition, endocrine and immune function. This review emphasizes molecular and DNA-based biomarkers, as well as recent advances in other biomarkers such as microRNAs, bilirubin or advanced glycation end products.

Automated quantitative assessment of proteins' biological function in protein knowledge bases.

Science.gov (United States)

Mayr, Gabriele; Lepperdinger, Günter; Lackner, Peter

2008-01-01

Primary protein sequence data are archived in databases together with information regarding corresponding biological functions. In this respect, UniProt/Swiss-Prot is currently the most comprehensive collection and it is routinely cross-examined when trying to unravel the biological role of hypothetical proteins. Bioscientists frequently extract single entries and further evaluate those on a subjective basis. In lieu of a standardized procedure for scoring the existing knowledge regarding individual proteins, we here report about a computer-assisted method, which we applied to score the present knowledge about any given Swiss-Prot entry. Applying this quantitative score allows the comparison of proteins with respect to their sequence yet highlights the comprehension of functional data. pfs analysis may be also applied for quality control of individual entries or for database management in order to rank entry listings.

Automated Quantitative Assessment of Proteins' Biological Function in Protein Knowledge Bases

Directory of Open Access Journals (Sweden)

Gabriele Mayr

2008-01-01

Full Text Available Primary protein sequence data are archived in databases together with information regarding corresponding biological functions. In this respect, UniProt/Swiss-Prot is currently the most comprehensive collection and it is routinely cross-examined when trying to unravel the biological role of hypothetical proteins. Bioscientists frequently extract single entries and further evaluate those on a subjective basis. In lieu of a standardized procedure for scoring the existing knowledge regarding individual proteins, we here report about a computer-assisted method, which we applied to score the present knowledge about any given Swiss-Prot entry. Applying this quantitative score allows the comparison of proteins with respect to their sequence yet highlights the comprehension of functional data. pfs analysis may be also applied for quality control of individual entries or for database management in order to rank entry listings.

Exploring candidate biological functions by Boolean Function Networks for Saccharomyces cerevisiae.

Directory of Open Access Journals (Sweden)

Maria Simak

Full Text Available The great amount of gene expression data has brought a big challenge for the discovery of Gene Regulatory Network (GRN. For network reconstruction and the investigation of regulatory relations, it is desirable to ensure directness of links between genes on a map, infer their directionality and explore candidate biological functions from high-throughput transcriptomic data. To address these problems, we introduce a Boolean Function Network (BFN model based on techniques of hidden Markov model (HMM, likelihood ratio test and Boolean logic functions. BFN consists of two consecutive tests to establish links between pairs of genes and check their directness. We evaluate the performance of BFN through the application to S. cerevisiae time course data. BFN produces regulatory relations which show consistency with succession of cell cycle phases. Furthermore, it also improves sensitivity and specificity when compared with alternative methods of genetic network reverse engineering. Moreover, we demonstrate that BFN can provide proper resolution for GO enrichment of gene sets. Finally, the Boolean functions discovered by BFN can provide useful insights for the identification of control mechanisms of regulatory processes, which is the special advantage of the proposed approach. In combination with low computational complexity, BFN can serve as an efficient screening tool to reconstruct genes relations on the whole genome level. In addition, the BFN approach is also feasible to a wide range of time course datasets.

Reviews of accelerator science and technology

CERN Document Server

Chou, Weiren

2008-01-01

Particle accelerators are a major invention of the 20th century. In the last eight decades, they have evolved enormously and have fundamentally changed the way we live, think and work. Accelerators are the most powerful microscopes for viewing the tiniest inner structure of cells, genes, molecules, atoms and their constituents such as protons, neutrons, electrons, neutrinos and quarks. This opens up a whole new world for materials science, chemistry and molecular biology.Accelerators with megawatt beam power may ultimately solve a critical problem faced by our society, namely, the treatment of nuclear waste and the supply of an alternative type of energy. There are also tens of thousands of small accelerators all over the world. They are used every day for medical imaging, cancer therapy, radioisotope production, high-density chip-making, mass spectrometry, cargo x-ray/gamma-ray imaging, detection of explosives and illicit drugs, and weapons. This volume provides a comprehensive review of this driving and fas...

Parotid gland function following accelerated and conventionally fractionated radiotherapy

International Nuclear Information System (INIS)

Leslie, M.D.; Dische, S.

1991-01-01

The function of parotid glands in patients treated by 3 different schedules of radiotherapy was studied 9 months or more after its conclusion. All had received radiotherapy for a malignancy confined to 1 side of the head and neck region and only the gland on the side of the lesion was in the treatment volume; the contralateral gland acted as an internal control. Saliva was selectively collected from the parotid glands and the stimulated flow rate and pH of the saliva determined. Flow rates were expressed in each case as a percentage of that of the contralateral ('untreated') gland. Twelve glands that had received conventionally fractionated radiotherapy to a dose of 60-66 Gy showed a mean percentage flow of 20 percent and a significant fall in the pH of the saliva produced. Six glands that had received CHART (Continuous Hyperfractionated Accelerated RadioTherapy) and 8 conventionally fractionated radiotherapy to a dose of 35-40 Gy showed mean percentage flows of 57 and 65 percent respectively, with only slight and non-significant falls in saliva pH. The results show that in the treatment of squamous cell carcinoma in the head and neck the use of CHART can lead to considerable less late change in the function of the parotid gland. (author). 26 refs.; 5 figs.; 2 tabs

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

Mathematical simulation of biologically equivalent doses for LDR-HDR

International Nuclear Information System (INIS)

Slosarek, K.; Zajusz, A.

1996-01-01

Based on the LQ model examples of biologically equivalent doses LDR, HDR and external beams were calculated. The biologically equivalent doses for LDR were calculated by appending to the LQ model the corrector for the time of repair of radiation sublethal damages. For radiation continuously delivered at a low dose rate the influence of sublethal damage repair time changes on biologically equivalent doses were analysed. For fractionated treatment with high dose rate the biologically equivalent doses were calculated by adding to the LQ model the formula of accelerated repopulation. For total biologically equivalent dose calculation for combine LDR-HDR-Tele irradiation examples are presented with the use of different parameters of the time of repair of sublethal damages and accelerated repopulation. The calculations performed show, that the same biologically equivalent doses can be obtained for different parameters of cell kinetics changes during radiation treatment. It also shows, that during biologically equivalent dose calculations for different radiotherapy schedules, ignorance of cell kinetics parameters can lead to relevant errors

Form and function: Perspectives on structural biology and resources for the future

International Nuclear Information System (INIS)

Vaughan, D.

1990-12-01

The purpose of this study is largely to explore and expand on the thesis that biological structures and their functions are suited to. Form indeed follows function and if we are to understand the workings of a living system, with all that such an understanding promises, we must first seek to describe the structure of its parts. Descriptions of a few achievements of structural biology lay the groundwork, but the substance of this booklet is a discussion of important questions yet unanswered and opportunities just beyond our grasp. The concluding pages then outline a course of action in which the Department of Energy would exercise its responsibility to develop the major resources needed to extend our reach and to answer some of those unanswered questions. 22 figs

Form and function: Perspectives on structural biology and resources for the future

Energy Technology Data Exchange (ETDEWEB)

Vaughan, D. (ed.)

1990-12-01

The purpose of this study is largely to explore and expand on the thesis that biological structures and their functions are suited to. Form indeed follows function and if we are to understand the workings of a living system, with all that such an understanding promises, we must first seek to describe the structure of its parts. Descriptions of a few achievements of structural biology lay the groundwork, but the substance of this booklet is a discussion of important questions yet unanswered and opportunities just beyond our grasp. The concluding pages then outline a course of action in which the Department of Energy would exercise its responsibility to develop the major resources needed to extend our reach and to answer some of those unanswered questions. 22 figs.

The spinning disc: studying radial acceleration and its damping process with smartphone acceleration sensors

Science.gov (United States)

Hochberg, K.; Gröber, S.; Kuhn, J.; Müller, A.

2014-03-01

Here, we show the possibility of analysing circular motion and acceleration using the acceleration sensors of smartphones. For instance, the known linear dependence of the radial acceleration on the distance to the centre (a constant angular frequency) can be shown using multiple smartphones attached to a revolving disc. As a second example, the decrease of the radial acceleration and the rotation frequency due to friction can be measured and fitted with a quadratic function, in accordance with theory. Finally, because the disc is not set up exactly horizontal, each smartphone measures a component of the gravitational acceleration that adds to the radial acceleration during one half of the period and subtracts from the radial acceleration during the other half. Hence, every graph shows a small modulation, which can be used to determine the rotation frequency, thus converting a ‘nuisance effect’ into a source of useful information, making additional measurements with stopwatches or the like unnecessary.

Annual report of Tandem Accelerator Center, University of Tsukuba, for fiscal 1976

International Nuclear Information System (INIS)

1977-01-01

A research center of the University of Tsukuba, Tandem Accelerator Center (TAC) has a 12 UD Pelletron tandem accelerator as its principal apparatus; of which acceptance test was finished in July 1976. Activities of the TAC for the period of April 1976 to March 1977 are reported: accelerator and beam transport system, general equipments, equipment development, nuclear physics, chemistry, and biological and medical Science. (Mori, K.)

Auroral electron acceleration

International Nuclear Information System (INIS)

Bryant, D.A.

1989-10-01

Two theories of auroral electron acceleration are discussed. Part 1 examines the currently widely held view that the acceleration is an ordered process in a quasi-static electric field. It is suggested that, although there are many factors seeming to support this theory, the major qualifications and uncertainties that have been identified combine to cast serious doubt over its validity. Part 2 is devoted to a relatively new interpretation in terms of stochastic acceleration in turbulent electric fields. This second theory, which appears to account readily for most known features of the electron distribution function, is considered to provide a more promising approach to this central question in magnetospheric plasma physics. (author)

Wavelet approach to accelerator problems. 3: Melnikov functions and symplectic topology

International Nuclear Information System (INIS)

Fedorova, A.; Zeitlin, M.; Parsa, Z.

1997-05-01

This is the third part of a series of talks in which the authors present applications of methods of wavelet analysis to polynomial approximations for a number of accelerator physics problems. They consider the generalization of the variational wavelet approach to nonlinear polynomial problems to the case of Hamiltonian systems for which they need to preserve underlying symplectic or Poissonian or quasicomplex structures in any type of calculations. They use the approach for the problem of explicit calculations of Arnold-Weinstein curves via Floer variational approach from symplectic topology. The loop solutions are parameterized by the solutions of reduced algebraical problem--matrix Quadratic Mirror Filters equations. Also they consider wavelet approach to the calculations of Melnikov functions in the theory of homoclinic chaos in perturbed Hamiltonian systems

Event-based text mining for biology and functional genomics

Science.gov (United States)

Thompson, Paul; Nawaz, Raheel; McNaught, John; Kell, Douglas B.

2015-01-01

The assessment of genome function requires a mapping between genome-derived entities and biochemical reactions, and the biomedical literature represents a rich source of information about reactions between biological components. However, the increasingly rapid growth in the volume of literature provides both a challenge and an opportunity for researchers to isolate information about reactions of interest in a timely and efficient manner. In response, recent text mining research in the biology domain has been largely focused on the identification and extraction of ‘events’, i.e. categorised, structured representations of relationships between biochemical entities, from the literature. Functional genomics analyses necessarily encompass events as so defined. Automatic event extraction systems facilitate the development of sophisticated semantic search applications, allowing researchers to formulate structured queries over extracted events, so as to specify the exact types of reactions to be retrieved. This article provides an overview of recent research into event extraction. We cover annotated corpora on which systems are trained, systems that achieve state-of-the-art performance and details of the community shared tasks that have been instrumental in increasing the quality, coverage and scalability of recent systems. Finally, several concrete applications of event extraction are covered, together with emerging directions of research. PMID:24907365

Stimulation of biological N2-fixation to accelerate the microbial remediation of soil contaminated by petroleum hydrocarbons

International Nuclear Information System (INIS)

Tereshenko, N.N.; Lushnikov, S.V.

2005-01-01

All remediation projects are comprised at least in accelerating the processes of the self-cleaning and self-restoration of biocenose which is led to increasing the functional activity of hydrocarbon-oxidizing microflora (HOM). Some of experts are carefully relate to introducing the commercial cultures of active hydrocarbon-consuming microbes into soils. They are afraid of unpredictable behavior of the cultures in soils. That why the stimulation of metabolic activity of indigenous soil microflora seems to be most preferable. In fact, contamination of soil with low nitrogen capacity by oil spills leads to significant deficient of nitrogen for HOM. Nitrogen content limits the soil self-restoration. Inorganic nitrogen fertilizers are supplied to recover the balance. The study of the microbial destruction of petroleum-hydrocarbons in association with biochemical transformation of nitrogen was carried out in lab and field experiments during 2000-2004. Study showed the activity of HOM correlates with rate of microbial fixing atmospheric nitrogen. Activity of biological N 2 -fixation significantly depends on supplying fertilizers (dose, date and kind). General practice of remediation of hydrocarbon-contaminated soils applies high initial doses of nitrogen-fertilizers (0.5-1 t per ha). Such practice leads to inhibition of N 2 -fixation processes, decreasing rate of oil destruction and loosing nitrogen due to activation of microbial denitrification. In opposition to that, the fractioned and advanced supplying mineral nitrogen fertilizers with aluminosilicate is the cost-effective approach to remediation of hydrocarbon-contaminated soils. Field experiments showed that the approach allows to increase efficiency of treatment up to 70-75% and to decrease operational expenses 2-3 times at least. (authors)

Functional Anthology of Intrinsic Disorder. I. Biological Processes and Functions of Proteins with Long Disordered Regions

Science.gov (United States)

Xie, Hongbo; Vucetic, Slobodan; Iakoucheva, Lilia M.; Oldfield, Christopher J.; Dunker, A. Keith; Uversky, Vladimir N.; Obradovic, Zoran

2008-01-01

Identifying relationships between function, amino acid sequence and protein structure represents a major challenge. In this study we propose a bioinformatics approach that identifies functional keywords in the Swiss-Prot database that correlate with intrinsic disorder. A statistical evaluation is employed to rank the significance of these correlations. Protein sequence data redundancy and the relationship between protein length and protein structure were taken into consideration to ensure the quality of the statistical inferences. Over 200,000 proteins from Swiss-Prot database were analyzed using this approach. The predictions of intrinsic disorder were carried out using PONDR VL3E predictor of long disordered regions that achieves an accuracy of above 86%. Overall, out of the 710 Swiss-Prot functional keywords that were each associated with at least 20 proteins, 238 were found to be strongly positively correlated with predicted long intrinsically disordered regions, whereas 302 were strongly negatively correlated with such regions. The remaining 170 keywords were ambiguous without strong positive or negative correlation with the disorder predictions. These functions cover a large variety of biological activities and imply that disordered regions are characterized by a wide functional repertoire. Our results agree well with literature findings, as we were able to find at least one illustrative example of functional disorder or order shown experimentally for the vast majority of keywords showing the strongest positive or negative correlation with intrinsic disorder. This work opens a series of three papers, which enriches the current view of protein structure-function relationships, especially with regards to functionalities of intrinsically disordered proteins and provides researchers with a novel tool that could be used to improve the understanding of the relationships between protein structure and function. The first paper of the series describes our statistical

Accelerator shield design of KIPT neutron source facility

International Nuclear Information System (INIS)

Zhong, Z.; Gohar, Y.

2013-01-01

Argonne National Laboratory (ANL) of the United States and Kharkov Institute of Physics and Technology (KIPT) of Ukraine have been collaborating on the design development of a neutron source facility at KIPT utilizing an electron-accelerator-driven subcritical assembly. Electron beam power is 100 kW, using 100 MeV electrons. The facility is designed to perform basic and applied nuclear research, produce medical isotopes, and train young nuclear specialists. The biological shield of the accelerator building is designed to reduce the biological dose to less than 0.5-mrem/hr during operation. The main source of the biological dose is the photons and the neutrons generated by interactions of leaked electrons from the electron gun and accelerator sections with the surrounding concrete and accelerator materials. The Monte Carlo code MCNPX serves as the calculation tool for the shield design, due to its capability to transport electrons, photons, and neutrons coupled problems. The direct photon dose can be tallied by MCNPX calculation, starting with the leaked electrons. However, it is difficult to accurately tally the neutron dose directly from the leaked electrons. The neutron yield per electron from the interactions with the surrounding components is less than 0.01 neutron per electron. This causes difficulties for Monte Carlo analyses and consumes tremendous computation time for tallying with acceptable statistics the neutron dose outside the shield boundary. To avoid these difficulties, the SOURCE and TALLYX user subroutines of MCNPX were developed for the study. The generated neutrons are banked, together with all related parameters, for a subsequent MCNPX calculation to obtain the neutron and secondary photon doses. The weight windows variance reduction technique is utilized for both neutron and photon dose calculations. Two shielding materials, i.e., heavy concrete and ordinary concrete, were considered for the shield design. The main goal is to maintain the total

Proteome-wide Structural Analysis of PTM Hotspots Reveals Regulatory Elements Predicted to Impact Biological Function and Disease.

Science.gov (United States)

Torres, Matthew P; Dewhurst, Henry; Sundararaman, Niveda

2016-11-01

Post-translational modifications (PTMs) regulate protein behavior through modulation of protein-protein interactions, enzymatic activity, and protein stability essential in the translation of genotype to phenotype in eukaryotes. Currently, less than 4% of all eukaryotic PTMs are reported to have biological function - a statistic that continues to decrease with an increasing rate of PTM detection. Previously, we developed SAPH-ire (Structural Analysis of PTM Hotspots) - a method for the prioritization of PTM function potential that has been used effectively to reveal novel PTM regulatory elements in discrete protein families (Dewhurst et al., 2015). Here, we apply SAPH-ire to the set of eukaryotic protein families containing experimental PTM and 3D structure data - capturing 1,325 protein families with 50,839 unique PTM sites organized into 31,747 modified alignment positions (MAPs), of which 2010 (∼6%) possess known biological function. Here, we show that using an artificial neural network model (SAPH-ire NN) trained to identify MAP hotspots with biological function results in prediction outcomes that far surpass the use of single hotspot features, including nearest neighbor PTM clustering methods. We find the greatest enhancement in prediction for positions with PTM counts of five or less, which represent 98% of all MAPs in the eukaryotic proteome and 90% of all MAPs found to have biological function. Analysis of the top 1092 MAP hotspots revealed 267 of truly unknown function (containing 5443 distinct PTMs). Of these, 165 hotspots could be mapped to human KEGG pathways for normal and/or disease physiology. Many high-ranking hotspots were also found to be disease-associated pathogenic sites of amino acid substitution despite the lack of observable PTM in the human protein family member. Taken together, these experiments demonstrate that the functional relevance of a PTM can be predicted very effectively by neural network models, revealing a large but testable

Acceleration Modes and Transitions in Pulsed Plasma Accelerators

Science.gov (United States)

Polzin, Kurt A.; Greve, Christine M.

2018-01-01

accelerators was developed by Cheng, et al. The Coaxial High ENerGy (CHENG) thruster operated on the 10-microseconds timescales of pulsed plasma thrusters, but claimed high thrust density, high efficiency and low electrode erosion rates, which are more consistent with the deflagration mode of acceleration. Separate work on gas-fed pulsed plasma thrusters (PPTs) by Ziemer, et al. identified two separate regimes of performance. The regime at higher mass bits (termed Mode I in that work) possessed relatively constant thrust efficiency (ratio of jet kinetic energy to input electrical energy) as a function of mass bit. In the second regime at very low mass bits (termed Mode II), the efficiency increased with decreasing mass bit. Work by Poehlmann et al. and by Sitaraman and Raja sought to understand the performance of the CHENG thruster and the Mode I / Mode II performance in PPTs by modeling the acceleration using the Hugoniot Relation, with the detonation and deflagration modes representing two distinct sets of solutions to the relevant conservation laws. These works studied the proposal that, depending upon the values of the various controllable parameters, the accelerator would operate in either the detonation or deflagration mode. In the present work, we propose a variation on the explanation for the differences in performance between the various pulsed plasma accelerators. Instead of treating the accelerator as if it were only operating in one mode or the other during a pulse, we model the initial stage of the discharge in all cases as an accelerating current sheet (detonation mode). If the current sheet reaches the exit of the accelerator before the discharge is completed, the acceleration mode transitions to the deflagration mode type found in the quasi-steady MPD thrusters. This modeling method is used to demonstrate that standard gas-fed pulsed plasma accelerators, the CHENG thruster, and the quasi-steady MPD accelerator are variations of the same device, with the overall

Distribution uniformity of laser-accelerated proton beams

Science.gov (United States)

Zhu, Jun-Gao; Zhu, Kun; Tao, Li; Xu, Xiao-Han; Lin, Chen; Ma, Wen-Jun; Lu, Hai-Yang; Zhao, Yan-Ying; Lu, Yuan-Rong; Chen, Jia-Er; Yan, Xue-Qing

2017-09-01

Compared with conventional accelerators, laser plasma accelerators can generate high energy ions at a greatly reduced scale, due to their TV/m acceleration gradient. A compact laser plasma accelerator (CLAPA) has been built at the Institute of Heavy Ion Physics at Peking University. It will be used for applied research like biological irradiation, astrophysics simulations, etc. A beamline system with multiple quadrupoles and an analyzing magnet for laser-accelerated ions is proposed here. Since laser-accelerated ion beams have broad energy spectra and large angular divergence, the parameters (beam waist position in the Y direction, beam line layout, drift distance, magnet angles etc.) of the beamline system are carefully designed and optimised to obtain a radially symmetric proton distribution at the irradiation platform. Requirements of energy selection and differences in focusing or defocusing in application systems greatly influence the evolution of proton distributions. With optimal parameters, radially symmetric proton distributions can be achieved and protons with different energy spread within ±5% have similar transverse areas at the experiment target. Supported by National Natural Science Foundation of China (11575011, 61631001) and National Grand Instrument Project (2012YQ030142)

Salivary gland function of nasopharyngeal cancer patients treated by simultaneous modulated accelerated radiation therapy

International Nuclear Information System (INIS)

Zhang Qi; Li Huanbin; Wang Ling

2007-01-01

The work was to study protective effect of simultaneous modulated accelerated radiation therapy (SMART) on salivary function of nasopharyngeal cancer patients. Forty-six patients were treated by SMART with 2.5Gy/fraction at gross tumor volume to a total does of 70 Gy, and 2.0 Gy/fraction at the clinical treatment volume to a total does of 56 Gy. The SMART was practiced in step-and-shoot mode, one time a day, and five times each week. Fourteen patients were treated by conventional radiation therapy. All the patients received salivary gland function imaging for their uptake index, excretive index and excretive speed, so as to evaluate their degree of salivary function injury. Meanwhile, the dry discomfort in mouth of the patients was recorded and classified. The results showed that the functional indexes of the SMART group were significantly higher than those of the conventional radiation therapy group (P 2 =23.52, P<0.005). Therefore, SMART can play a key role in protecting salivary gland function of naso- pharyngeal cancer patients. (authors)

Muon acceleration in cosmic-ray sources

International Nuclear Information System (INIS)

Klein, Spencer R.; Mikkelsen, Rune E.; Becker Tjus, Julia

2013-01-01

Many models of ultra-high energy cosmic-ray production involve acceleration in linear accelerators located in gamma-ray bursts, magnetars, or other sources. These transient sources have short lifetimes, which necessitate very high accelerating gradients, up to 10 13 keV cm –1 . At gradients above 1.6 keV cm –1 , muons produced by hadronic interactions undergo significant acceleration before they decay. This muon acceleration hardens the neutrino energy spectrum and greatly increases the high-energy neutrino flux. Using the IceCube high-energy diffuse neutrino flux limits, we set two-dimensional limits on the source opacity and matter density, as a function of accelerating gradient. These limits put strong constraints on different models of particle acceleration, particularly those based on plasma wake-field acceleration, and limit models for sources like gamma-ray bursts and magnetars.

The functional biology of human milk oligosaccharides.

Science.gov (United States)

Bode, Lars

2015-11-01

Human milk oligosaccharides (HMOs) are a group of complex sugars that are highly abundant in human milk, but currently not present in infant formula. More than a hundred different HMOs have been identified so far. The amount and composition of HMOs are highly variable between women, and each structurally defined HMO might have a distinct functionality. HMOs are not digested by the infant and serve as metabolic substrates for select microbes, contributing to shape the infant gut microbiome. HMOs act as soluble decoy receptors that block the attachment of viral, bacterial or protozoan parasite pathogens to epithelial cell surface sugars, which may help prevent infectious diseases in the gut and also the respiratory and urinary tracts. HMOs are also antimicrobials that act as bacteriostatic or bacteriocidal agents. In addition, HMOs alter host epithelial and immune cell responses with potential benefits for the neonate. The article reviews current knowledge as well as future challenges and opportunities related to the functional biology of HMOs. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Venomics-Accelerated Cone Snail Venom Peptide Discovery

Science.gov (United States)

Himaya, S. W. A.

2018-01-01

Cone snail venoms are considered a treasure trove of bioactive peptides. Despite over 800 species of cone snails being known, each producing over 1000 venom peptides, only about 150 unique venom peptides are structurally and functionally characterized. To overcome the limitations of the traditional low-throughput bio-discovery approaches, multi-omics systems approaches have been introduced to accelerate venom peptide discovery and characterisation. This “venomic” approach is starting to unravel the full complexity of cone snail venoms and to provide new insights into their biology and evolution. The main challenge for venomics is the effective integration of transcriptomics, proteomics, and pharmacological data and the efficient analysis of big datasets. Novel database search tools and visualisation techniques are now being introduced that facilitate data exploration, with ongoing advances in related omics fields being expected to further enhance venomics studies. Despite these challenges and future opportunities, cone snail venomics has already exponentially expanded the number of novel venom peptide sequences identified from the species investigated, although most novel conotoxins remain to be pharmacologically characterised. Therefore, efficient high-throughput peptide production systems and/or banks of miniaturized discovery assays are required to overcome this bottleneck and thus enhance cone snail venom bioprospecting and accelerate the identification of novel drug leads. PMID:29522462

Venomics-Accelerated Cone Snail Venom Peptide Discovery

Directory of Open Access Journals (Sweden)

S. W. A. Himaya

2018-03-01

Full Text Available Cone snail venoms are considered a treasure trove of bioactive peptides. Despite over 800 species of cone snails being known, each producing over 1000 venom peptides, only about 150 unique venom peptides are structurally and functionally characterized. To overcome the limitations of the traditional low-throughput bio-discovery approaches, multi-omics systems approaches have been introduced to accelerate venom peptide discovery and characterisation. This “venomic” approach is starting to unravel the full complexity of cone snail venoms and to provide new insights into their biology and evolution. The main challenge for venomics is the effective integration of transcriptomics, proteomics, and pharmacological data and the efficient analysis of big datasets. Novel database search tools and visualisation techniques are now being introduced that facilitate data exploration, with ongoing advances in related omics fields being expected to further enhance venomics studies. Despite these challenges and future opportunities, cone snail venomics has already exponentially expanded the number of novel venom peptide sequences identified from the species investigated, although most novel conotoxins remain to be pharmacologically characterised. Therefore, efficient high-throughput peptide production systems and/or banks of miniaturized discovery assays are required to overcome this bottleneck and thus enhance cone snail venom bioprospecting and accelerate the identification of novel drug leads.

Applied Physics Research at the Idaho Accelerator Center

International Nuclear Information System (INIS)

Date, D. S.; Hunt, A. W.; Chouffani, K.; Wells, D. P.

2011-01-01

The Idaho Accelerator Center, founded in 1996 and based at Idaho State University, supports research, education, and high technology economic development in the United States. The research center currently has eight electron linear accelerators ranging in energy from 6 to 44 MeV with the latter linear accelerator capable of picosecond pulses, a 2 MeV positive-ion Van de Graaff, a 4 MV Nec tandem Pelletron, and a pulsed-power 8 k A, 10 MeV electron induction accelerator. Current research emphases include, accelerator physics research, accelerator based medical isotope production, active interrogation techniques for homeland security and nuclear nonproliferation applications, non destructive testing and materials science studies in support of industry as well as the development of advanced nuclear fuels, pure and applied radio-biology, and medical physics. This talk will highlight three of these areas including the production of the isotopes 99 Tc and 67 Cu for medical diagnostics and therapy, as well as two new technologies currently under development for nuclear safeguards and homeland security - namely laser Compton scattering and the polarized photofission of actinides

Utilization of electron beam accelerators for polymer processing

International Nuclear Information System (INIS)

Sarma, K.S.S.

2013-01-01

During the last decade, electron beam processing has been amply demonstrated to the Indian cable industry by BARC using 2 MeV/20 kW electron beam (EB) accelerator (ILU-6 EBA facility) located at BARC-BRIT complex, Vashi. The electron beam accelerator is a machine producing high energy electrons which are made to impinge on the materials for inducing physical, chemical and biological modifications. The process is carried out at room temperature and in ambient atmospheric conditions. Lately, quite a few numbers of accelerators have been installed by the private cable industry and carrying out cross-linking of cable insulations for high performance viz. high temperature stability, good flame retardancy, lesser solvent-swelling, thinner insulations etc. The indigenously made accelerators at EB centre, particularly the 3 MeV/30 kW accelerator will be of much help for Indian industry for polymer processing as the market is poised to grow by adapting the technology

Accelerated Recovery of Endothelium Function after Stent Implantation with the Use of a Novel Systemic Nanoparticle Curcumin

Directory of Open Access Journals (Sweden)

Qi Lu

2015-01-01

Full Text Available Curcumin was reported to exhibit a wide range of pharmacological effects including antioxidant, anti-inflammatory, and antiproliferative activities and significantly prevent smooth muscle cells migration. In the present study, a novel kind of curcumin loaded nanoparticles (Cur-NP has been prepared and characterized with the aim of inhibiting inflammation formation and accelerating the healing process of the stented arteries. Cur-NP was administrated intravenously after stent implantation twice a week and detailed tissue responses were evaluated. The results demonstrated that intravenous administration of Cur-NP after stent implantation accelerated endothelial cells restoration and endothelium function recovery and may potentially be an effective therapeutic alternative to reduce adverse events for currently available drug eluting stents.

Effects of Physical Exercise on Cognitive Functioning and Wellbeing: Biological and Psychological Benefits

Directory of Open Access Journals (Sweden)

Laura Mandolesi

2018-04-01

Full Text Available Much evidence shows that physical exercise (PE is a strong gene modulator that induces structural and functional changes in the brain, determining enormous benefit on both cognitive functioning and wellbeing. PE is also a protective factor for neurodegeneration. However, it is unclear if such protection is granted through modifications to the biological mechanisms underlying neurodegeneration or through better compensation against attacks. This concise review addresses the biological and psychological positive effects of PE describing the results obtained on brain plasticity and epigenetic mechanisms in animal and human studies, in order to clarify how to maximize the positive effects of PE while avoiding negative consequences, as in the case of exercise addiction.

Second International Conference on Accelerating Biopharmaceutical Development: March 9-12, 2009, Coronado, CA, USA.

Science.gov (United States)

Reichert, Janice M; Jacob, Nitya M; Amanullah, Ashraf

2009-01-01

The Second International Conference on Accelerating Biopharmaceutical Development was held in Coronado, California. The meeting was organized by the Society for Biological Engineering (SBE) and the American Institute of Chemical Engineers (AIChE); SBE is a technological community of the AIChE. Bob Adamson (Wyeth) and Chuck Goochee (Centocor) were co-chairs of the event, which had the theme "Delivering cost-effective, robust processes and methods quickly and efficiently." The first day focused on emerging disruptive technologies and cutting-edge analytical techniques. Day two featured presentations on accelerated cell culture process development, critical quality attributes, specifications and comparability, and high throughput protein formulation development. The final day was dedicated to discussion of technology options and new analysis methods provided by emerging disruptive technologies; functional interaction, integration and synergy in platform development; and rapid and economic purification process development.

Relating Time-Dependent Acceleration and Height Using an Elevator

Science.gov (United States)

Kinser, Jason M.

2015-01-01

A simple experiment in relating a time-dependent linear acceleration function to height is explored through the use of a smartphone and an elevator. Given acceleration as a function of time, a(t), the velocity function and position functions are determined through integration as in v(t)=? a(t) dt (1) and x(t)=? v(t) dt. Mobile devices such as…

Exercise enhances cognitive function and neurotrophin expression in the hippocampus accompanied by changes in epigenetic programming in senescence-accelerated mice.

Science.gov (United States)

Maejima, Hiroshi; Kanemura, Naohiko; Kokubun, Takanori; Murata, Kenji; Takayanagi, Kiyomi

2018-02-05

Aerobic exercise is known to increase expression of neurotrophins, particularly brain-derived neurotrophic factor (BDNF), in the hippocampus and to improve cognitive function. Exercise exerts neuroprotective effects in the hippocampus by inducing epigenetic changes, which play crucial roles in aging and neurodegenerative diseases. Specifically, the activity levels of histone acetyltransferases (HATs) and histone deacetylases (HDACs) regulate histone acetylation and modulate gene transcription. The objective of the present study was to assess the interactive effects of exercise and aging on cognitive function, expression of neurotrophins (BDNF and neurotrophin-4) and their receptors (tyrosine receptor kinase B and p75), and epigenetic regulations, including the activity of HATs and HADCs in the hippocampus. We used the senescence-accelerated mouse (SAM) model, specifically 13-month-old SAM resistant 1(SAMR1) and SAM prone 1 (SAMP1) lines. Mice were distributed into four groups based on accelerated senescence and exercise status. Mice in the exercise groups exercised on a treadmill for approximately 60min a day, 5days a week. Aerobic exercise for 4 weeks improved cognitive function, accompanied by an increase in BDNF expression and a decrease in p75 transcription in both SAMR1 and SAMP1. In addition, the exercise regimen activated both HAT and HDAC in the hippocampus. Therefore, the present study reveals that despite accelerated senescence, long-term exercise improved cognitive function, upregulated the expression of BDNF, and downregulated p75, a receptor involved in apoptotic signaling. Furthermore, long-term exercise enhanced activity of both HAT and HDAC, which may contribute to the transcriptional regulation underlying the improvement of cognitive function. Copyright © 2017 Elsevier B.V. All rights reserved.

Accelerator tube construction and characterization for a tandem-electrostatic-quadrupole for accelerator-based boron neutron capture therapy

International Nuclear Information System (INIS)

Cartelli, D.; Thatar Vento, V.; Castell, W.; Di Paolo, H.; Kesque, J.M.; Bergueiro, J.; Valda, A.A.

2011-01-01

The accelerator tubes are essential components of the accelerator. Their function is to transport and accelerate a very intense proton or deuteron beam through the machine, from the ion source to the neutron production target, without significant losses. In this contribution, we discuss materials selected for the tube construction, the procedures used for their assembly and the testing performed to meet the stringent requirements to which it is subjected.

Accelerator Based Neutron Beams for Neutron Capture Therapy

International Nuclear Information System (INIS)

Yanch, Jacquelyn C.

2003-01-01

The DOE-funded accelerator BNCT program at the Massachusetts Institute of Technology has resulted in the only operating accelerator-based epithermal neutron beam facility capable of generating significant dose rates in the world. With five separate beamlines and two different epithermal neutron beam assemblies installed, we are currently capable of treating patients with rheumatoid arthritis in less than 15 minutes (knee joints) or 4 minutes (finger joints) or irradiating patients with shallow brain tumors to a healthy tissue dose of 12.6 Gy in 3.6 hours. The accelerator, designed by Newton scientific Incorporated, is located in dedicated laboratory space that MIT renovated specifically for this project. The Laboratory for Accelerator Beam Applications consists of an accelerator room, a control room, a shielded radiation vault, and additional laboratory space nearby. In addition to the design, construction and characterization of the tandem electrostatic accelerator, this program also resulted in other significant accomplishments. Assemblies for generating epithermal neutron beams were designed, constructed and experimentally evaluated using mixed-field dosimetry techniques. Strategies for target construction and target cooling were implemented and tested. We demonstrated that the method of submerged jet impingement using water as the coolant is capable of handling power densities of up to 6 x 10(sup 7) W/m(sup 2) with heat transfer coefficients of 10(sup 6)W/m(sup 2)-K. Experiments with the liquid metal gallium demonstrated its superiority compared with water with little effect on the neutronic properties of the epithermal beam. Monoenergetic proton beams generated using the accelerator were used to evaluate proton RBE as a function of LET and demonstrated a maximum RBE at approximately 30-40 keV/um, a finding consistent with results published by other researchers. We also developed an experimental approach to biological intercomparison of epithermal beams and

Pulsed radiobiology with laser-driven plasma accelerators

Science.gov (United States)

Giulietti, Antonio; Grazia Andreassi, Maria; Greco, Carlo

2011-05-01

Recently, a high efficiency regime of acceleration in laser plasmas has been discovered, allowing table top equipment to deliver doses of interest for radiotherapy with electron bunches of suitable kinetic energy. In view of an R&D program aimed to the realization of an innovative class of accelerators for medical uses, a radiobiological validation is needed. At the present time, the biological effects of electron bunches from the laser-driven electron accelerator are largely unknown. In radiobiology and radiotherapy, it is known that the early spatial distribution of energy deposition following ionizing radiation interactions with DNA molecule is crucial for the prediction of damages at cellular or tissue levels and during the clinical responses to this irradiation. The purpose of the present study is to evaluate the radio-biological effects obtained with electron bunches from a laser-driven electron accelerator compared with bunches coming from a IORT-dedicated medical Radio-frequency based linac's on human cells by the cytokinesis block micronucleus assay (CBMN). To this purpose a multidisciplinary team including radiotherapists, biologists, medical physicists, laser and plasma physicists is working at CNR Campus and University of Pisa. Dose on samples is delivered alternatively by the "laser-linac" operating at ILIL lab of Istituto Nazionale di Ottica and an RF-linac operating for IORT at Pisa S. Chiara Hospital. Experimental data are analyzed on the basis of suitable radiobiological models as well as with numerical simulation based on Monte Carlo codes. Possible collective effects are also considered in the case of ultrashort, ultradense bunches of ionizing radiation.

Survey of teaching experiments with small accelerators

International Nuclear Information System (INIS)

Treado, P.A.; Lambert, J.M.

1974-01-01

Accelerator facilities are being used to provide an educational experience to undergraduate students, both science and non-science majors, and to graduate students. Nuclear physics, accelerator physics, atomic physics, chemistry, materials science, and some nuclear techniques applied to biology, medicine and energy/environmental problems are components of various courses. Previously published experiments are the ones most frequently used, but societal needs have caused some recent, interesting experiments to be adopted. A brief outline of a number of conventional and interesting experiments, and a tabulation of reference materials pertinent to such experiments is given. Experimental science can be presented to students in a dramatic and an exciting manner with an accelerator and readily available, but quite inexpensive, ancillary equipment. Lectures, discussions, demonstrations, and the collection and analysis of data provide a well-rounded educational experience

Role of accelerator mass spectrometry in biological dosimetry

International Nuclear Information System (INIS)

Felton, J.S.; Turteltaub, K.W.; Frantz, C.; Vogel, J.S.; Gledhill, B.L.

1992-01-01

Understanding risks from exposures to carcinogens and other chemicals depends upon measurement of their dose to target tissues and their reactivity with critical macromolecules. The authors have used AMS detection of radio-isotopes to assess doses and reactivities at low, environmentally relevant doses. Several biomedical investigations show the effectiveness of quantification of biologically important events at extremely high sensitivity with AMS. Specifically, they have measured the addition of environmental carcinogens such as 2-amino-3,8-dimethylimidazo[4,5-f]-quinoaxaline (MelQx), a chemical found in cooked food, to DNA at concentrations relevant to human exposure. Other low level detection problems in biology, such as immunoassay assessment of small environmental chemicals, is being developed with attomole sensitivity. AMS also aids the assessment of genotoxic risks from chemicals by quantifying the binding of labeled chemicals to DNA. The very toxic and potent carcinogen, tetrachlorodibenzo-p-dioxin (TCDD) was assessed for DNA binding, but no detectable radiocarbon-labeled TCDD was found associated with mouse liver DNA at less than systematically toxic levels. The data indicate that a mutation mechanism does not mediate TCDD carcinogenesis

Induction of the Tn10 Precise Excision in E. coli Cells after Accelerated Heavy Ions Irradiation

CERN Document Server

Zhuravel, D V

2003-01-01

The influence of the irradiation of different kinds on the indication of the structural mutations in the bacteria Escherichia coli is considered. The regularities of the Tn10 precise excision after accelerated ^{4}He and ^{12}C ions irradiations with different linear energy transfer (LET) were investigated. Dose dependences of the survival and relative frequency of the Tn10 precise excision were obtained. It was shown, that the relative frequency of the Tn10 precise excision is the exponential function from the irradiation dose. Relative biological efficiency (RBE), and relative genetic efficiency (RGE) were calculated, and were treated as the function of the LET.

Biological Effects of Particles with Very High Energy Deposition on Mammalian Cells Utilizing the Brookhaven Tandem Van de Graaff Accelerator

Science.gov (United States)

Saha, Janapriya; Cucinotta, Francis A.; Wang, Minli

2013-01-01

High LET radiation from GCR (Galactic Cosmic Rays) consisting mainly of high charge and energy (HZE) nuclei and secondary protons and neutrons, and secondaries from protons in SPE (Solar Particle Event) pose a major health risk to astronauts due to induction of DNA damage and oxidative stress. Experiments with high energy particles mimicking the space environment for estimation of radiation risk are being performed at NASA Space Radiation Laboratory at BNL. Experiments with low energy particles comparing to high energy particles of similar LET are of interest for investigation of the role of track structure on biological effects. For this purpose, we report results utilizing the Tandem Van de Graaff accelerator at BNL. The primary objective of our studies is to elucidate the influence of high vs low energy deposition on track structure, delta ray contribution and resulting biological responses. These low energy ions are of special relevance as these energies may occur following absorption through the spacecraft and shielding materials in human tissues and nuclear fragments produced in tissues by high energy protons and neutrons. This study will help to verify the efficiency of these low energy particles and better understand how various cell types respond to them.

A Synthetic Biology Framework for Programming Eukaryotic Transcription Functions

Science.gov (United States)

Khalil, Ahmad S.; Lu, Timothy K.; Bashor, Caleb J.; Ramirez, Cherie L.; Pyenson, Nora C.; Joung, J. Keith; Collins, James J.

2013-01-01

SUMMARY Eukaryotic transcription factors (TFs) perform complex and combinatorial functions within transcriptional networks. Here, we present a synthetic framework for systematically constructing eukaryotic transcription functions using artificial zinc fingers, modular DNA-binding domains found within many eukaryotic TFs. Utilizing this platform, we construct a library of orthogonal synthetic transcription factors (sTFs) and use these to wire synthetic transcriptional circuits in yeast. We engineer complex functions, such as tunable output strength and transcriptional cooperativity, by rationally adjusting a decomposed set of key component properties, e.g., DNA specificity, affinity, promoter design, protein-protein interactions. We show that subtle perturbations to these properties can transform an individual sTF between distinct roles (activator, cooperative factor, inhibitory factor) within a transcriptional complex, thus drastically altering the signal processing behavior of multi-input systems. This platform provides new genetic components for synthetic biology and enables bottom-up approaches to understanding the design principles of eukaryotic transcriptional complexes and networks. PMID:22863014

AFM imaging of functionalized carbon nanotubes on biological membranes

International Nuclear Information System (INIS)

Lamprecht, C; Danzberger, J; Rangl, M; Gruber, H J; Hinterdorfer, P; Kienberger, F; Ebner, A; Liashkovich, I; Neves, V; Heister, E; Coley, H M; McFadden, J; Flahaut, E

2009-01-01

Multifunctional carbon nanotubes are promising for biomedical applications as their nano-size, together with their physical stability, gives access into the cell and various cellular compartments including the nucleus. However, the direct and label-free detection of carbon nanotube uptake into cells is a challenging task. The atomic force microscope (AFM) is capable of resolving details of cellular surfaces at the nanometer scale and thus allows following of the docking of carbon nanotubes to biological membranes. Here we present topographical AFM images of non-covalently functionalized single walled (SWNT) and double walled carbon nanotubes (DWNT) immobilized on different biological membranes, such as plasma membranes and nuclear envelopes, as well as on a monolayer of avidin molecules. We were able to visualize DWNT on the nuclear membrane while at the same time resolving individual nuclear pore complexes. Furthermore, we succeeded in localizing individual SWNT at the border of incubated cells and in identifying bundles of DWNT on cell surfaces by AFM imaging.

Proteome-wide Structural Analysis of PTM Hotspots Reveals Regulatory Elements Predicted to Impact Biological Function and Disease*

Science.gov (United States)

Dewhurst, Henry; Sundararaman, Niveda

2016-01-01

Post-translational modifications (PTMs) regulate protein behavior through modulation of protein-protein interactions, enzymatic activity, and protein stability essential in the translation of genotype to phenotype in eukaryotes. Currently, less than 4% of all eukaryotic PTMs are reported to have biological function - a statistic that continues to decrease with an increasing rate of PTM detection. Previously, we developed SAPH-ire (Structural Analysis of PTM Hotspots) - a method for the prioritization of PTM function potential that has been used effectively to reveal novel PTM regulatory elements in discrete protein families (Dewhurst et al., 2015). Here, we apply SAPH-ire to the set of eukaryotic protein families containing experimental PTM and 3D structure data - capturing 1,325 protein families with 50,839 unique PTM sites organized into 31,747 modified alignment positions (MAPs), of which 2010 (∼6%) possess known biological function. Here, we show that using an artificial neural network model (SAPH-ire NN) trained to identify MAP hotspots with biological function results in prediction outcomes that far surpass the use of single hotspot features, including nearest neighbor PTM clustering methods. We find the greatest enhancement in prediction for positions with PTM counts of five or less, which represent 98% of all MAPs in the eukaryotic proteome and 90% of all MAPs found to have biological function. Analysis of the top 1092 MAP hotspots revealed 267 of truly unknown function (containing 5443 distinct PTMs). Of these, 165 hotspots could be mapped to human KEGG pathways for normal and/or disease physiology. Many high-ranking hotspots were also found to be disease-associated pathogenic sites of amino acid substitution despite the lack of observable PTM in the human protein family member. Taken together, these experiments demonstrate that the functional relevance of a PTM can be predicted very effectively by neural network models, revealing a large but testable

On the application of accelerated molecular dynamics to liquid water simulations.

Science.gov (United States)

de Oliveira, César Augusto F; Hamelberg, Donald; McCammon, J Andrew

2006-11-16

Our group recently proposed a robust bias potential function that can be used in an efficient all-atom accelerated molecular dynamics (MD) approach to simulate the transition of high energy barriers without any advance knowledge of the potential-energy landscape. The main idea is to modify the potential-energy surface by adding a bias, or boost, potential in regions close to the local minima, such that all transitions rates are increased. By applying the accelerated MD simulation method to liquid water, we observed that this new simulation technique accelerates the molecular motion without losing its microscopic structure and equilibrium properties. Our results showed that the application of a small boost energy on the potential-energy surface significantly reduces the statistical inefficiency of the simulation while keeping all the other calculated properties unchanged. On the other hand, although aggressive acceleration of the dynamics simulation increases the self-diffusion coefficient of water molecules greatly and dramatically reduces the correlation time of the simulation, configurations representative of the true structure of liquid water are poorly sampled. Our results also showed the strength and robustness of this simulation technique, which confirm this approach as a very useful and promising tool to extend the time scale of the all-atom simulations of biological system with explicit solvent models. However, we should keep in mind that there is a compromise between the strength of the boost applied in the simulation and the reproduction of the ensemble average properties.

Preferential acceleration in collisionless supernova shocks

International Nuclear Information System (INIS)

Hainebach, K.; Eichler, D.; Schramm, D.

1979-01-01

The preferential acceleration and resulting cosmic ray abundance enhancements of heavy elements (relative to protons) are calculated in the collisionless supernova shock acceleration model described by Eichler in earlier work. Rapidly increasing enhancements up to several tens times solar ratios are obtained as a function of atomic weight over charge at the time of acceleration. For material typical of hot phase interstellar medium, good agreement is obtained with the observed abundance enhancements

Biological activity of lactoferrin-functionalized biomimetic hydroxyapatite nanocrystals

Directory of Open Access Journals (Sweden)

Nocerino N

2014-03-01

Full Text Available Nunzia Nocerino,1 Andrea Fulgione,1 Marco Iannaccone,1 Laura Tomasetta,1 Flora Ianniello,1 Francesca Martora,1 Marco Lelli,2 Norberto Roveri,2 Federico Capuano,3 Rosanna Capparelli1 1Department of Agriculture Special Biotechnology Center Federico II, CeBIOTEC Biotechnology, University of Naples Federico II, Naples, 2Department of Chemistry, G Ciamician, Alma Mater Studiorum, University of Bologna, Bologna, 3Department of Food Inspection IZS ME, Naples, Italy Abstract: The emergence of bacterial strains resistant to antibiotics is a general public health problem. Progress in developing new molecules with antimicrobial properties has been made. In this study, we evaluated the biological activity of a hybrid nanocomposite composed of synthetic biomimetic hydroxyapatite surface-functionalized by lactoferrin (LF-HA. We evaluated the antimicrobial, anti-inflammatory, and antioxidant properties of LF-HA and found that the composite was active against both Gram-positive and Gram-negative bacteria, and that it modulated proinflammatory and anti-inflammatory responses and enhanced antioxidant properties as compared with LF alone. These results indicate the possibility of using LF-HA as an antimicrobial system and biomimetic hydroxyapatite as a candidate for innovative biomedical applications. Keywords: lactoferrin, hydroxyapatite nanocrystals, biomimetism, biological activity, drug delivery

Cyclic-glycine-proline accelerates mammary involution by promoting apoptosis and inhibiting IGF-1 function.

Science.gov (United States)

Singh-Mallah, Gagandeep; McMahon, Christopher D; Guan, Jian; Singh, Kuljeet

2017-12-01

In rodents, post-lactational involution of mammary glands is characterized by the loss of mammary epithelial cells via apoptosis, which is associated with a decline in the expression of insulin-like growth factor-1 (IGF-1). Overexpression of IGF-1 delays involution by inhibiting apoptosis of epithelial cells and preserving the remaining secretory alveoli. Cyclic-glycine-proline (cGP), a metabolite of IGF-1, normalizes IGF-1 function under pathological conditions by regulating the bioavailability of IGF-1. The present study investigated the effect of cGP on the physiological decline in IGF-1 function during post-lactational mammary involution. Rat dams were gavaged with either cGP (3 mg/kg) or saline once per day from post-natal d8-22. Before collecting tissue on post-natal d23, a pair of mammary glands were sealed on d20 (72 hr-engorgement, thus representative of late-involution) and d22 (24 hr-engorgement, thus representative of mid-involution), while the remaining glands were allowed to involute naturally (early-involution). During early-involution, cGP accelerated the loss of mammary cells through apoptosis, resulting in an earlier clearance of intact secretory alveoli compared with the control group. This coincided with an earlier up-regulation of the cell survival factors, Bcl-xl and IGF-1R, in the early-involution cGP glands compared with the control glands. During late-involution, cGP reduced the bioactivity of IGF-1, which was evident through decreased phosphorylation of IGF-1R in the regressed alveoli. Maternal administration of cGP did not alter milk production and composition during early-, peak-, or late-stage of lactation. These data show that cGP accelerates post-lactational involution by promoting apoptosis and the physiological decline in IGF-1 function. © 2017 Wiley Periodicals, Inc.

Dysregulated physiological stress systems and accelerated cellular aging

NARCIS (Netherlands)

Révész, D.; Verhoeven, J.; Milaneschi, Y.; de Geus, E.J.C.; Wolkowitz, O.M.; Penninx, B.W.J.H.

2014-01-01

Exposure to chronic stressors is associated with accelerated biological aging as indicated by reduced leukocyte telomere length (LTL). This impact could be because of chronic overactivation of the body's physiological stress systems. This study examined the associations between LTL and the immune

An improved ashing procedure for biologic sample

Energy Technology Data Exchange (ETDEWEB)

Zongmei, Wu [Zhejiang Province Enviromental Radiation Monitoring Centre (China)

1992-07-01

The classical ashing procedure in muffle was modified for biologic samples. In the modified procedure the door of muffle was open in the duration of ashing process, the ashing was accelerated and the ashing product quality was comparable to that the classical procedure. The modified procedure is suitable for ashing biologic samples in large batches.

An improved ashing procedure for biologic sample

International Nuclear Information System (INIS)

Wu Zongmei

1992-01-01

The classical ashing procedure in muffle was modified for biologic samples. In the modified procedure the door of muffle was open in the duration of ashing process, the ashing was accelerated and the ashing product quality was comparable to that the classical procedure. The modified procedure is suitable for ashing biologic samples in large batches

Principles of laser-plasma accelerators

International Nuclear Information System (INIS)

Malka, V.; Mora, P.

2009-01-01

The continuing development of powerful laser systems has permitted to extend the interaction of laser beams with matter far into the relativistic domain in which extremely high electric and magnetic fields are generated. Thanks to these tremendous fields, that only plasma can support and sustain, new and compact approaches for producing energetic particle beams have been recently achieved (for example the bubble regime and the colliding laser pulses scheme). The incredible progress of these laser-plasma accelerators has allowed physicists to produce high quality beams of energetic radiation and particles. These beams have interesting properties such as shortness, brightness and spatial quality, and could lend themselves to applications in many fields, including medicine (radiotherapy, proton therapy, imaging), radiation biology (short-time-scale), chemistry (radiolysis), physics and material science (radiography, electron and photon diffraction), security (material inspection), and of course accelerator science. Stimulated by the advent of compact and powerful lasers, with moderate costs and high repetition rate, this research field has witnessed considerable growth in the past few years, and the promises of laser-plasma accelerators are in tremendous progress. The recent years in particular have seen spectacular progress in the acceleration of electrons and of ions, both in terms of energy and in terms of quality of the beams. (authors)

CAS CERN Accelerator School. Measurement and alignment of accelerator and detector magnets. Proceedings

International Nuclear Information System (INIS)

Turner, S.

1998-01-01

These proceedings present the lectures given at the eleventh specialised course organised by the CERN Accelerator School (CAS), the topic this time being 'Measurement and Alignment of Accelerator and Detector Magnets'. A similar course was already presented at Montreux, Switzerland in 1992 and its proceedings published as CERN 92-05. However recent progress in the field, especially in the use of superconducting magnets, has been so rapid that a revised course had become imperative. The lectures start with basic magnet theory and the motivation for magnet measurements followed by a review of superconducting magnets and their field dynamics. After a review of measurement methods, the details of search and harmonic coils, magnetic resonance techniques and Hall generators are given followed by methods to minimise errors in mechanical equipment, series production and detector magnet measurements. Turning to magnet metrology and alignment, first data quality control is explained followed by the setting of reference targets, and the alignment methods for accelerators and experiments including alignment by feedback. Finally seminars are presented on the biological effects of magnetic fields and on superconducting magnet fabrication and quality control. (orig.)

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

Science.gov (United States)

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

2005-03-01

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

Accelerated ageing and renal dysfunction links lower socioeconomic status and dietary phosphate intake.

Science.gov (United States)

McClelland, Ruth; Christensen, Kelly; Mohammed, Suhaib; McGuinness, Dagmara; Cooney, Josephine; Bakshi, Andisheh; Demou, Evangelia; MacDonald, Ewan; Caslake, Muriel; Stenvinkel, Peter; Shiels, Paul G

2016-05-01

We have sought to explore the impact of dietary Pi intake on human age related health in the pSoBid cohort (n=666) to explain the disparity between health and deprivation status in this cohort. As hyperphosphataemia is a driver of accelerated ageing in rodent models of progeria we tested whether variation in Pi levels in man associate with measures of biological ageing and health. We observed significant relationships between serum Pi levels and markers of biological age (telomere length (p=0.040) and DNA methylation content (p=0.028), gender and chronological age (p=0.032). When analyses were adjusted for socio-economic status and nutritional factors, associations were observed between accelerated biological ageing (telomere length, genomic methylation content) and dietary derived Pi levels among the most deprived males, directly related to the frequency of red meat consumption. Accelerated ageing is associated with high serum Pi levels and frequency of red meat consumption. Our data provide evidence for a mechanistic link between high intake of Pi and age-related morbidities tied to socio-economic status.

Comparing joint kinematics and center of mass acceleration as feedback for control of standing balance by functional neuromuscular stimulation.

Science.gov (United States)

Nataraj, Raviraj; Audu, Musa L; Triolo, Ronald J

2012-05-06

The purpose of this study was to determine the comparative effectiveness of feedback control systems for maintaining standing balance based on joint kinematics or total body center of mass (COM) acceleration, and assess their clinical practicality for standing neuroprostheses after spinal cord injury (SCI). In simulation, controller performance was measured according to the upper extremity effort required to stabilize a three-dimensional model of bipedal standing against a variety of postural disturbances. Three cases were investigated: proportional-derivative control based on joint kinematics alone, COM acceleration feedback alone, and combined joint kinematics and COM acceleration feedback. Additionally, pilot data was collected during external perturbations of an individual with SCI standing with functional neuromuscular stimulation (FNS), and the resulting joint kinematics and COM acceleration data was analyzed. Compared to the baseline case of maximal constant muscle excitations, the three control systems reduced the mean upper extremity loading by 51%, 43% and 56%, respectively against external force-pulse perturbations. Controller robustness was defined as the degradation in performance with increasing levels of input errors expected with clinical deployment of sensor-based feedback. At error levels typical for body-mounted inertial sensors, performance degradation due to sensor noise and placement were negligible. However, at typical tracking error levels, performance could degrade as much as 86% for joint kinematics feedback and 35% for COM acceleration feedback. Pilot data indicated that COM acceleration could be estimated with a few well-placed sensors and efficiently captures information related to movement synergies observed during perturbed bipedal standing following SCI. Overall, COM acceleration feedback may be a more feasible solution for control of standing with FNS given its superior robustness and small number of inputs required.

Nerve Regeneration: Understanding Biology and Its Influence on Return of Function After Nerve Transfers.

Science.gov (United States)

Gordon, Tessa

2016-05-01

Poor functional outcomes are frequent after peripheral nerve injuries despite the regenerative support of Schwann cells. Motoneurons and, to a lesser extent, sensory neurons survive the injuries but outgrowth of axons across the injury site is slow. The neuronal regenerative capacity and the support of regenerating axons by the chronically denervated Schwann cells progressively declines with time and distance of the injury from the denervated targets. Strategies, including brief low-frequency electrical stimulation that accelerates target reinnervation and functional recovery, and the insertion of cross-bridges between a donor nerve and a recipient denervated nerve stump, are effective in promoting functional outcomes after complete and incomplete injuries. Copyright © 2016 Elsevier Inc. All rights reserved.

The functional and biological properties of whey proteins: prospects for the development of functional foods

Directory of Open Access Journals (Sweden)

H. J. T. KORHONEN

2008-12-01

Full Text Available Advances in processing technologies and the accumulation of scientific data on the functional and biological properties of whey components have contributed to the growing commercial valuation of cheese whey over the last decade. New membrane separation and chromatographic techniques have made it possible to fractionate and enrich various components of whey more efficiently than before. The specific properties of these components can now be examined in greater detail and new applications developed accordingly. The utilisation of cheese whey is evolving into a new industry producing a multitude of purified ingredients for numerous purposes. The most significant areas of R&D related to whey proteins include functional foods, the rheological properties of foodstuffs, and biopharmaceuticals.

The Scanning Electron Microscope As An Accelerator For The Undergraduate Advanced Physics Laboratory

International Nuclear Information System (INIS)

Peterson, Randolph S.; Berggren, Karl K.; Mondol, Mark

2011-01-01

Few universities or colleges have an accelerator for use with advanced physics laboratories, but many of these institutions have a scanning electron microscope (SEM) on site, often in the biology department. As an accelerator for the undergraduate, advanced physics laboratory, the SEM is an excellent substitute for an ion accelerator. Although there are no nuclear physics experiments that can be performed with a typical 30 kV SEM, there is an opportunity for experimental work on accelerator physics, atomic physics, electron-solid interactions, and the basics of modern e-beam lithography.

Development of aluminium-26 accelerator mass spectrometry for biological and toxicological applications

Science.gov (United States)

Barker, James

Aluminium is now recognised as a toxic element. Its accumulation in the body leads to serious conditions in renal failure patients on haemodialysis, and there is suspected involvement in the aetiology of Alzheimer's Disease. Although uptake from food and water are important exposure pathways, there is so far little quantitative knowledge about gastrointestinal absorption of aluminium, its general speciation in the blood or its metabolism. This is partly because seven of aluminium's eight radioisotopes have half-lives too short to conduct accurate biochemical studies. The use of [67]Ga as a tracer for aluminium begs the question of its biochemical similarity. Radiotracer studies on aluminium are possible with [26]Al (T[2] = 716,000 years), but a comparatively large amount of this scarce and expensive radioisotope (price ca. 50 pence per Bq) would be needed to measure by normal counting techniques. Use of conventional mass spectrometry is impracticable due to [26]Mg interference (comprises 11 % of total stable Mg and inherent in all biological or environmental samples), but high energy Accelerator Mass Spectrometry (A.M.S.), resulting in some fully-stripped ions (Al[13+], Mg[12+]) , potentially overcomes this problem. [26]Al is particularly attractive in human toxicology because of its negligible natural abundance and low radiological hazard. We have used the 20 MV tandem Van De Graaff accelerator (S.E.R.C. Daresbury) to conduct 1A1 A.M.S. measurements in biological media. Stable currents of ALQ[-](100 nA for > 5 hours) were obtained from a modified Middleton ion source, using alumina/silver ion source preparations of 50 mug Al. [26]Al is unambiguously identified from and [26]Mg [27]AlO[-] is repeatedly measured on a Faray Cup placed in the beamline after adjusting the ion source magnet. Linear calibration (C.V. range tested ([26]Al/[27]Al ratios from 10[-6] to 10[-11]) and a detection limit (2?) of ca. 7 x 10[-18]g (5 nBq) [26]Al ratio [26]Al/[27]Al limit of 1.4 x

Accelerator tube construction and characterization for a tandem-electrostatic-quadrupole for accelerator-based boron neutron capture therapy.

Science.gov (United States)

Cartelli, D; Vento, V Thatar; Castell, W; Di Paolo, H; Kesque, J M; Bergueiro, J; Valda, A A; Erhardt, J; Kreiner, A J

2011-12-01

The accelerator tubes are essential components of the accelerator. Their function is to transport and accelerate a very intense proton or deuteron beam through the machine, from the ion source to the neutron production target, without significant losses. In this contribution, we discuss materials selected for the tube construction, the procedures used for their assembly and the testing performed to meet the stringent requirements to which it is subjected. Copyright © 2011 Elsevier Ltd. All rights reserved.

Electrical stimulation accelerates axonal and functional peripheral nerve regeneration across long gaps.

Science.gov (United States)

Haastert-Talini, Kirsten; Schmitte, Ruth; Korte, Nele; Klode, Dorothee; Ratzka, Andreas; Grothe, Claudia

2011-04-01

Short-term low-frequency electrical stimulation (ESTIM) of proximal peripheral nerve stumps prior to end-to-end coaptation or tubular bridging of small distances has been reported to increase preferential motor reinnervation and functional motor recovery in animal models and human patients undergoing carpal tunnel release surgery. We investigated the effects of ESTIM on regeneration across rat sciatic nerve gaps, which exceed distances that allow spontaneous regeneration. Three different reconstruction approaches were combined with ESTIM in the experimental groups. Nerve gaps (13 mm) were bridged using (I) nerve autotransplantation, (II) transplantation of differentially filled silicone tubes, or (III) transplantation of tubular grafts containing fibroblast growth factor-2 overexpressing Schwann cells (SCs) for gene therapy. The regeneration outcome was followed for up to 8 weeks, and functionally as well as histomorphometrically analyzed in comparison to non-stimulated control groups. Combining ESTIM with nerve autotransplantation significantly increased the nerve fiber density in the regenerated nerve, and the grade of functional recovery as detected by electrodiagnostic recordings from the gastrocnemius muscle. The combination of ESTIM with transplantation of naïve SCs increased the regeneration of gap-bridging nerve tissue. Although macroscopic tissue regeneration was not further improved after combining ESTIM with FGF-2(21/23-kD) gene therapy, the latter resulted in a high rate of regenerated nerves that functionally reconnected to the target muscle. Based on our results, brief ESTIM shows high potential to accelerate axonal as well as functional (motor and sensory) outcomes in the clinical setting of peripheral nerve gap reconstruction in human patients.

Light Ion Biomedical Research Accelerator LIBRA

International Nuclear Information System (INIS)

Gough, R.A.

1987-01-01

LIBRA is a concept to place a light-ion, charged-particle facility in a hospital environment, and to dedicate it to applications in biology and medicine. There are two aspects of the program envisaged for LIBRA: a basic research effort coupled with a program in clinical applications of accelerated charged particles. The operational environment to be provided for LIBRA is one in which both of these components can coexist and flourish, and one that will promote the transfer of technology and knowledge from one to the other. In order to further investigate the prospects for a Light Ion Biomedical Research Accelerator (LIBRA), discussions are underway with the Merritt Peralta Medical Center MPMC) in Oakland CA, and the University of California at San Francisco (UCSF). In this paper, a brief discussion of the technical requirements for such a facility is given, together with an outline of the accelerator technology required. While still in a preliminary stage, it is possible nevertheless to develop an adequate working description of the type, size, performance and cost of the accelerator facilities required to meet the preliminary goals for LIBRA

Particle acceleration in modified shocks

Energy Technology Data Exchange (ETDEWEB)

Drury, L.O' C. (Max-Planck-Institut fuer Kernphysik, Heidelberg (Germany, F.R.)); Axford, W.I. (Max-Planck-Institut fuer Aeronomie, Katlenburg-Lindau (Germany, F.R.)); Summers, D. (Memorial Univ. of Newfoundland, St. John' s (Canada))

1982-03-01

Efficient particle acceleration in shocks must modify the shock structure with consequent changes in the particle acceleration. This effect is studied and analytic solutions are found describing the diffusive acceleration of particles with momentum independent diffusion coefficients in hyperbolic tangent type velocity transitions. If the input particle spectrum is a delta function, the shock smoothing replaces the truncated power-law downstream particle spectrum by a more complicated form, but one which has a power-law tail at high momenta. For a cold plasma this solution can be made completely self-consistent. Some problems associated with momentum dependent diffusion coefficients are discussed.

Particle acceleration in modified shocks

International Nuclear Information System (INIS)

Drury, L.O'C.; Axford, W.I.; Summers, D.

1982-01-01

Efficient particle acceleration in shocks must modify the shock structure with consequent changes in the particle acceleration. This effect is studied and analytic solutions are found describing the diffusive acceleration of particles with momentum independent diffusion coefficients in hyperbolic tangent type velocity transitions. If the input particle spectrum is a delta function, the shock smoothing replaces the truncated power-law downstream particle spectrum by a more complicated form, but one which has a power-law tail at high momenta. For a cold plasma this solution can be made completely self-consistent. Some problems associated with momentum dependent diffusion coefficients are discussed. (author)

Effect of biological factors during functional scintigraphy of the heart

Energy Technology Data Exchange (ETDEWEB)

Breuel, H P; Emrich, D; Luig, H [Goettingen Univ. (F.R. Germany). Abt. fuer Nuklearmedizin

1976-07-01

The parameters relating to functional scintigraphy of the heart (average circulation time, peak time) depend not only on the method (injection technique, radiopharmaceutical), but also on biological factors. Failure to take these into consideration may result in an erroneous interpretation of the findings. Circulation time in normal children aged 6 to 14 years, as determined by isotope methods is significantly shorter than in normal adults. Patients with compensated heart disease, as well trained athletes, show significant increase in all portions of the circulation time, when compared with normals of similar ages. This indicates that deviation in the haemodynamics of the circulation as shown by functional scintigraphy, can only be interpreted in the light of clinical findings.

Accelerator and Fusion Research Division: 1987 summary of activities

International Nuclear Information System (INIS)

1988-04-01

An overview of the design and the initial studies for the Advanced Light Source is given. The research efforts for the Center for X-Ray Optics include x-ray imaging, multilayer mirror technology, x-ray sources and detectors, spectroscopy and scattering, and synchrotron radiation projects. The Accelerator Operations highlights include the research by users in nuclear physics, biology and medicine. The upgrade of the Bevalac is also discussed. The High Energy Physics Technology review includes the development of superconducting magnets and superconducting cables. A review of the Heavy-Ion Fusion Accelerator Research is also presented. The Magnetic Fusion Energy research included the development of ion sources, accelerators for negative ions, diagnostics, and theoretical plasma physics

Accelerator and Fusion Research Division: 1987 summary of activities

Energy Technology Data Exchange (ETDEWEB)

1988-04-01

An overview of the design and the initial studies for the Advanced Light Source is given. The research efforts for the Center for X-Ray Optics include x-ray imaging, multilayer mirror technology, x-ray sources and detectors, spectroscopy and scattering, and synchrotron radiation projects. The Accelerator Operations highlights include the research by users in nuclear physics, biology and medicine. The upgrade of the Bevalac is also discussed. The High Energy Physics Technology review includes the development of superconducting magnets and superconducting cables. A review of the Heavy-Ion Fusion Accelerator Research is also presented. The Magnetic Fusion Energy research included the development of ion sources, accelerators for negative ions, diagnostics, and theoretical plasma physics. (WRF)

Tongue and Taste Organ Biology and Function: Homeostasis Maintained by Hedgehog Signaling.

Science.gov (United States)

Mistretta, Charlotte M; Kumari, Archana

2017-02-10

The tongue is an elaborate complex of heterogeneous tissues with taste organs of diverse embryonic origins. The lingual taste organs are papillae, composed of an epithelium that includes specialized taste buds, the basal lamina, and a lamina propria core with matrix molecules, fibroblasts, nerves, and vessels. Because taste organs are dynamic in cell biology and sensory function, homeostasis requires tight regulation in specific compartments or niches. Recently, the Hedgehog (Hh) pathway has emerged as an essential regulator that maintains lingual taste papillae, taste bud and progenitor cell proliferation and differentiation, and neurophysiological function. Activating or suppressing Hh signaling, with genetic models or pharmacological agents used in cancer treatments, disrupts taste papilla and taste bud integrity and can eliminate responses from taste nerves to chemical stimuli but not to touch or temperature. Understanding Hh regulation of taste organ homeostasis contributes knowledge about the basic biology underlying taste disruptions in patients treated with Hh pathway inhibitors.

Transiently disordered tails accelerate folding of globular proteins.

Science.gov (United States)

Mallik, Saurav; Ray, Tanaya; Kundu, Sudip

2017-07-01

Numerous biological proteins exhibit intrinsic disorder at their termini, which are associated with multifarious functional roles. Here, we show the surprising result that an increased percentage of terminal short transiently disordered regions with enhanced flexibility (TstDREF) is associated with accelerated folding rates of globular proteins. Evolutionary conservation of predicted disorder at TstDREFs and drastic alteration of folding rates upon point-mutations suggest critical regulatory role(s) of TstDREFs in shaping the folding kinetics. TstDREFs are associated with long-range intramolecular interactions and the percentage of native secondary structural elements physically contacted by TstDREFs exhibit another surprising positive correlation with folding kinetics. These results allow us to infer probable molecular mechanisms behind the TstDREF-mediated regulation of folding kinetics that challenge protein biochemists to assess by direct experimental testing. © 2017 Federation of European Biochemical Societies.

PMS2 endonuclease activity has distinct biological functions and is essential for genome maintenance.

Science.gov (United States)

van Oers, Johanna M M; Roa, Sergio; Werling, Uwe; Liu, Yiyong; Genschel, Jochen; Hou, Harry; Sellers, Rani S; Modrich, Paul; Scharff, Matthew D; Edelmann, Winfried

2010-07-27

The DNA mismatch repair protein PMS2 was recently found to encode a novel endonuclease activity. To determine the biological functions of this activity in mammals, we generated endonuclease-deficient Pms2E702K knock-in mice. Pms2EK/EK mice displayed increased genomic mutation rates and a strong cancer predisposition. In addition, class switch recombination, but not somatic hypermutation, was impaired in Pms2EK/EK B cells, indicating a specific role in Ig diversity. In contrast to Pms2-/- mice, Pms2EK/EK male mice were fertile, indicating that this activity is dispensable in spermatogenesis. Therefore, the PMS2 endonuclease activity has distinct biological functions and is essential for genome maintenance and tumor suppression.

Functions of MicroRNAs in Cardiovascular Biology and Disease

Science.gov (United States)

Hata, Akiko

2015-01-01

In 1993, lin-4 was discovered as a critical modulator of temporal development in Caenorhabditis elegans and, most notably, as the first in the class of small, single-stranded noncoding RNAs now defined as microRNAs (miRNAs). Another eight years elapsed before miRNA expression was detected in mammalian cells. Since then, explosive advancements in the field of miRNA biology have elucidated the basic mechanism of miRNA biogenesis, regulation, and gene-regulatory function. The discovery of this new class of small RNAs has augmented the complexity of gene-regulatory programs as well as the understanding of developmental and pathological processes in the cardiovascular system. Indeed, the contributions of miRNAs in cardiovascular development and function have been widely explored, revealing the extensive role of these small regulatory RNAs in cardiovascular physiology. PMID:23157557

Exogenous endothelial cells as accelerators of hematopoietic reconstitution

Directory of Open Access Journals (Sweden)

Mizer J

2012-11-01

Full Text Available Abstract Despite the successes of recombinant hematopoietic-stimulatory factors at accelerating bone marrow reconstitution and shortening the neutropenic period post-transplantation, significant challenges remain such as cost, inability to reconstitute thrombocytic lineages, and lack of efficacy in conditions such as aplastic anemia. A possible means of accelerating hematopoietic reconstitution would be administration of cells capable of secreting hematopoietic growth factors. Advantages of this approach would include: a ability to regulate secretion of cytokines based on biological need; b long term, localized production of growth factors, alleviating need for systemic administration of factors that possess unintended adverse effects; and c potential to actively repair the hematopoietic stem cell niche. Here we overview the field of hematopoietic growth factors, discuss previous experiences with mesenchymal stem cells (MSC in accelerating hematopoiesis, and conclude by putting forth the rationale of utilizing exogenous endothelial cells as a novel cellular therapy for acceleration of hematopoietic recovery.

Damage-free vibrational spectroscopy of biological materials in the electron microscope.

Science.gov (United States)

Rez, Peter; Aoki, Toshihiro; March, Katia; Gur, Dvir; Krivanek, Ondrej L; Dellby, Niklas; Lovejoy, Tracy C; Wolf, Sharon G; Cohen, Hagai

2016-03-10

Vibrational spectroscopy in the electron microscope would be transformative in the study of biological samples, provided that radiation damage could be prevented. However, electron beams typically create high-energy excitations that severely accelerate sample degradation. Here this major difficulty is overcome using an 'aloof' electron beam, positioned tens of nanometres away from the sample: high-energy excitations are suppressed, while vibrational modes of energies electron energy loss spectra from biogenic guanine crystals in their native state, resolving their characteristic C-H, N-H and C=O vibrational signatures with no observable radiation damage. The technique opens up the possibility of non-damaging compositional analyses of organic functional groups, including non-crystalline biological materials, at a spatial resolution of ∼10 nm, simultaneously combined with imaging in the electron microscope.

Comparing joint kinematics and center of mass acceleration as feedback for control of standing balance by functional neuromuscular stimulation

Directory of Open Access Journals (Sweden)

Nataraj Raviraj

2012-05-01

Full Text Available Abstract Background The purpose of this study was to determine the comparative effectiveness of feedback control systems for maintaining standing balance based on joint kinematics or total body center of mass (COM acceleration, and assess their clinical practicality for standing neuroprostheses after spinal cord injury (SCI. Methods In simulation, controller performance was measured according to the upper extremity effort required to stabilize a three-dimensional model of bipedal standing against a variety of postural disturbances. Three cases were investigated: proportional-derivative control based on joint kinematics alone, COM acceleration feedback alone, and combined joint kinematics and COM acceleration feedback. Additionally, pilot data was collected during external perturbations of an individual with SCI standing with functional neuromuscular stimulation (FNS, and the resulting joint kinematics and COM acceleration data was analyzed. Results Compared to the baseline case of maximal constant muscle excitations, the three control systems reduced the mean upper extremity loading by 51%, 43% and 56%, respectively against external force-pulse perturbations. Controller robustness was defined as the degradation in performance with increasing levels of input errors expected with clinical deployment of sensor-based feedback. At error levels typical for body-mounted inertial sensors, performance degradation due to sensor noise and placement were negligible. However, at typical tracking error levels, performance could degrade as much as 86% for joint kinematics feedback and 35% for COM acceleration feedback. Pilot data indicated that COM acceleration could be estimated with a few well-placed sensors and efficiently captures information related to movement synergies observed during perturbed bipedal standing following SCI. Conclusions Overall, COM acceleration feedback may be a more feasible solution for control of standing with FNS given its

Biological effects induced by the inner-target reaction of accelerated 7Li+3 ions with wheat embryo

International Nuclear Information System (INIS)

Yang Juncheng; Pan Wei; Zheng Qicheng; Liu Luxiang; Wang Jing; Zhao Linshu; Yu Weixiang; Zhao Wenrong; Bai Xixiang

2004-01-01

Using the mechanism of the nuclear reaction of accelerated 7 Li +3 ions with the inner target in mutant material i.e 1 H( 7 Li, 7 Be)n, the biological effects were studied. The wheat seeds were irradiated with the doses ranged from 1.416 x 10 10 ions/cm 2 to 1.416 x 10 12 ions/cm 2 . It was found that the cell membrane ruptured, the plasmolysis occurred, the nucleus shape changed. The serious changes of the chloroplast were as follows: the membrane protuberance, the grand disorder, the membrane disappearance, crista of mitochondrion rupture etc. by checking of the sub-microstructure of leaf cell. The single micronucleus and multi-micronucleus were observed at the interphase. The chromosome aberrational cells including chromosome fragment, lagging chromosome, chromosome bridge and circular chromosome were found during the mitosis. RAPD analysis of seedling genomic DNA variation in M 2 generation of three mutants showed their DNA sequences had changed. The result confirmed that the implantation of 7 Li +3 ions could induce genetic mutation in wheat

Status of MAPA (Modular Accelerator Physics Analysis) and the Tech-X Object-Oriented Accelerator Library

Science.gov (United States)

Cary, J. R.; Shasharina, S.; Bruhwiler, D. L.

1998-04-01

The MAPA code is a fully interactive accelerator modeling and design tool consisting of a GUI and two object-oriented C++ libraries: a general library suitable for treatment of any dynamical system, and an accelerator library including many element types plus an accelerator class. The accelerator library inherits directly from the system library, which uses hash tables to store any relevant parameters or strings. The GUI can access these hash tables in a general way, allowing the user to invoke a window displaying all relevant parameters for a particular element type or for the accelerator class, with the option to change those parameters. The system library can advance an arbitrary number of dynamical variables through an arbitrary mapping. The accelerator class inherits this capability and overloads the relevant functions to advance the phase space variables of a charged particle through a string of elements. Among other things, the GUI makes phase space plots and finds fixed points of the map. We discuss the object hierarchy of the two libraries and use of the code.

Report of the consultant's meeting on applications of accelerator based analysis

International Nuclear Information System (INIS)

1998-07-01

At the present meeting, applications of accelerator based analytical methods, often referred as ion beam analysis (IBA) methods, to the following areas have been discussed: materials (including thin films), Earth sciences (including environmental studies), biology and medicine, art and archaeology (cultural heritage), and other applications (including forensic applications). This report gives brief overview of IBA applications in these areas, with short background about accelerators needed and corresponding analytical techniques

Effector genomics accelerates discovery and functional profiling of potato disease resistance and phytophthora infestans avirulence genes.

Directory of Open Access Journals (Sweden)

Vivianne G A A Vleeshouwers

Full Text Available Potato is the world's fourth largest food crop yet it continues to endure late blight, a devastating disease caused by the Irish famine pathogen Phytophthora infestans. Breeding broad-spectrum disease resistance (R genes into potato (Solanum tuberosum is the best strategy for genetically managing late blight but current approaches are slow and inefficient. We used a repertoire of effector genes predicted computationally from the P. infestans genome to accelerate the identification, functional characterization, and cloning of potentially broad-spectrum R genes. An initial set of 54 effectors containing a signal peptide and a RXLR motif was profiled for activation of innate immunity (avirulence or Avr activity on wild Solanum species and tentative Avr candidates were identified. The RXLR effector family IpiO induced hypersensitive responses (HR in S. stoloniferum, S. papita and the more distantly related S. bulbocastanum, the source of the R gene Rpi-blb1. Genetic studies with S. stoloniferum showed cosegregation of resistance to P. infestans and response to IpiO. Transient co-expression of IpiO with Rpi-blb1 in a heterologous Nicotiana benthamiana system identified IpiO as Avr-blb1. A candidate gene approach led to the rapid cloning of S. stoloniferum Rpi-sto1 and S. papita Rpi-pta1, which are functionally equivalent to Rpi-blb1. Our findings indicate that effector genomics enables discovery and functional profiling of late blight R genes and Avr genes at an unprecedented rate and promises to accelerate the engineering of late blight resistant potato varieties.

Characterization of the radiation environment at the UNLV accelerator facility during operation of the Varian M6 linac

International Nuclear Information System (INIS)

Hodges, M.; Barzilov, A.; Chen, Y.; Lowe, D.

2016-01-01

The bremsstrahlung photon flux from the UNLV particle accelerator (Varian M6 model) was determined using MCNP5 code for 3 MeV and 6 MeV incident electrons. Human biological equivalent dose rates due to accelerator operation were evaluated using the photon flux with the flux-to-dose conversion factors. Dose rates were computed for the accelerator facility for M6 linac use under different operating conditions. The results showed that the use of collimators and linac internal shielding significantly reduced the dose rates throughout the facility. It was shown that the walls of the facility, in addition to the earthen berm enveloping the building, provide equivalent shielding to reduce dose rates outside to below the 2 mrem/h limit. - Highlights: • A 3/6 MeV electron accelerator equipped with a high energy x-ray target was studied. • Monte Carlo modeling of photon flux was carried out for three accelerator configurations. • Human biological equivalent doses were evaluated within the accelerator facility building.

The formation of kappa-distribution accelerated electron populations in solar flares

Energy Technology Data Exchange (ETDEWEB)

Bian, Nicolas H.; Stackhouse, Duncan J.; Kontar, Eduard P. [School of Physics and Astronomy, University of Glasgow, Glasgow G12 8QQ (United Kingdom); Emslie, A. Gordon, E-mail: n.bian@physics.gla.ac.uk, E-mail: d.stackhouse.1@research.gla.ac.uk, E-mail: eduard@astro.gla.ac.uk, E-mail: emslieg@wku.edu [Department of Physics and Astronomy, Western Kentucky University, Bowling Green, KY 42101 (United States)

2014-12-01

Driven by recent RHESSI observations of confined loop-top hard X-ray sources in solar flares, we consider stochastic acceleration of electrons in the presence of Coulomb collisions. If electron escape from the acceleration region can be neglected, the electron distribution function is determined by a balance between diffusive acceleration and collisions. Such a scenario admits a stationary solution for the electron distribution function that takes the form of a kappa distribution. We show that the evolution toward this kappa distribution involves a 'wave front' propagating forward in velocity space, so that electrons of higher energy are accelerated later; the acceleration timescales with energy according to τ{sub acc} ∼ E {sup 3/2}. At sufficiently high energies escape from the finite-length acceleration region will eventually dominate. For such energies, the electron velocity distribution function is obtained by solving a time-dependent Fokker-Planck equation in the 'leaky-box' approximation. Solutions are obtained in the limit of a small escape rate from an acceleration region that can effectively be considered a thick target.

Electron accelerators for environmental protection

International Nuclear Information System (INIS)

Zimek, Z.

1998-01-01

The primary objective of this publication is to provide information suitable for electron accelerators implementation in facilities applying radiation technology for environmental protection. It should be noticed that radiation processing has been successfully used in the fields of crosslinking polymer curing and medical products sterilization for more than 40 years. Practical application of radiation technology today extends on SO 2 and NO x removal from the flue gas (one of major power intensive radiation processing), destruction and removal of organic chemicals from water, decreasing bacteria content in the irradiated sludge and waste water. On the other hand the increased awareness of environmental pollution hazards and more stringent waste regulations in many countries may open stronger support for environmentally oriented technologies. This publication provides an evaluation of electron accelerators capabilities in respect of environmental applications where technological and economical criteria are now well defined. In order to determine the potential of electron accelerators, the literature data were examined as well visits and meetings with various accelerator manufacturers were performed by the author. Experience of the author in accelerator facilities construction and exploitation including those which were used for environmental protection are significant part of this publication. The principle of accelerator action was described in Chapter 1. Early development, accelerator classification and fields of accelerators application were included to this chapter as well. Details of accelerator construction was described in Chapter 2 to illustrate physical capability of accelerators to perform the function of ionizing radiation source. Electron beam extraction devices, under beam equipment, electron beam parameters and measuring methods were characterized in this chapter as well. Present studies of accelerator technology was described in Chapter 3, where

Pulsed-focusing recirculating linacs for muon acceleration

Energy Technology Data Exchange (ETDEWEB)

Johnson, Rolland [Muons, Inc., Batavia, IL (United States)

2014-12-31

Since the muon has a short lifetime, fast acceleration is essential for high-energy applications such as muon colliders, Higgs factories, or neutrino factories. The best one can do is to make a linear accelerator with the highest possible accelerating gradient to make the accelerating time as short as possible. However, the cost of such a single linear accelerator is prohibitively large due to expensive power sources, cavities, tunnels, and related infrastructure. As was demonstrated in the Thomas Jefferson Accelerator Facility (Jefferson Lab) Continuous Electron Beam Accelerator Facility (CEBAF), an elegant solution to reduce cost is to use magnetic return arcs to recirculate the beam through the accelerating RF cavities many times, where they gain energy on each pass. In such a Recirculating Linear Accelerator (RLA), the magnetic focusing strength diminishes as the beam energy increases in a conventional linac that has constant strength quadrupoles. After some number of passes the focusing strength is insufficient to keep the beam from going unstable and being lost. In this project, the use of fast pulsed quadrupoles in the linac sections was considered for stronger focusing as a function of time to allow more successive passes of a muon beam in a recirculating linear accelerator. In one simulation, it was shown that the number of passes could be increased from 8 to 12 using pulsed magnet designs that have been developed and tested. This could reduce the cost of linac sections of a muon RLA by 8/12, where more improvement is still possible. The expense of a greater number of passes and corresponding number of return arcs was also addressed in this project by exploring the use of ramped or FFAG-style magnets in the return arcs. A better solution, invented in this project, is to use combined-function dipole-quadrupole magnets to simultaneously transport two beams of different energies through one magnet string to reduce costs of return arcs by almost a factor of

Medical Proton Accelerator Project

International Nuclear Information System (INIS)

Comsan, M.N.H.

2008-01-01

A project for a medical proton accelerator for cancer treatment is outlined. The project is motivated by the need for a precise modality for cancer curing especially in children. Proton therapy is known by its superior radiation and biological effectiveness as compared to photon or electron therapy. With 26 proton and 3 heavy-ion therapy complexes operating worldwide only one (p) exists in South Africa, and none in south Asia and the Middle East. The accelerator of choice should provide protons with energy 75 MeV for eye treatment and 250 MeV for body treatment. Four treatment rooms are suggested: two with isocentric gantries, one with fixed beams and one for development. Passive scanning is recommended. The project can serve Middle East and North Africa with ∼ 400 million populations. The annual capacity of the project is estimated as 1,100 to be compared with expected radiation cases eligible for proton cancer treatment of not less than 200,000

Production of radioisotopes using accelerators

International Nuclear Information System (INIS)

Qaim, S.M.

1990-01-01

Accelerator produced radioisotopes find applications in many fields. Most of them are ideally suited for in-vivo studies of physiological functions. A brief review of various types of accelerators used for radioisotope production is given. The 'state of art' technology relevant to the production of radioisotopes is briefly discussed. Some of the recent advances in nuclear data measurements, target development, chemical processing and quality control are described. There appears to be a definite shift from multipurpose accelerators to dedicated machines, and greater emphasis is placed now on the production of radioisotopes with high radionuclidic purity by choosing a suitable nuclear reaction in a proper energy range. (author)

Characteristics of microbial community functional structure of a biological coking wastewater treatment system.

Science.gov (United States)

Joshi, Dev Raj; Zhang, Yu; Zhang, Hong; Gao, Yingxin; Yang, Min

2018-01-01

Nitrogenous heterocyclic compounds are key pollutants in coking wastewater; however, the functional potential of microbial communities for biodegradation of such contaminants during biological treatment is still elusive. Herein, a high throughput functional gene array (GeoChip 5.0) in combination with Illumina HiSeq2500 sequencing was used to compare and characterize the microbial community functional structure in a long run (500days) bench scale bioreactor treating coking wastewater, with a control system treating synthetic wastewater. Despite the inhibitory toxic pollutants, GeoChip 5.0 detected almost all key functional gene (average 61,940 genes) categories in the coking wastewater sludge. With higher abundance, aromatic ring cleavage dioxygenase genes including multi ring1,2diox; one ring2,3diox; catechol represented significant functional potential for degradation of aromatic pollutants which was further confirmed by Illumina HiSeq2500 analysis results. Response ratio analysis revealed that three nitrogenous compound degrading genes- nbzA (nitro-aromatics), tdnB (aniline), and scnABC (thiocyanate) were unique for coking wastewater treatment, which might be strong cause to increase ammonia level during the aerobic process. Additionally, HiSeq2500 elucidated carbozole and isoquinoline degradation genes in the system. These findings expanded our understanding on functional potential of microbial communities to remove organic nitrogenous pollutants; hence it will be useful in optimization strategies for biological treatment of coking wastewater. Copyright © 2017. Published by Elsevier B.V.

Spallator - accelerator breeder

International Nuclear Information System (INIS)

Steinberg, M.

1985-01-01

The concept involves the use of spallation neutrons produced by interaction of a high energy proton (1 to 2 GeV) from a linear accelerator (LINAC) with a heavy metal target (uranium). The principal spallator concept is based on generating fissile fuel for use in LWR nuclear power plants. The spallator functions in conjunction with a reprocessing plant to regenerate and produce the Pu-239 or U-233 for fabrication into fresh LWR reactor fuel elements. Advances in proton accelerator technology has provided a solid base for predicting performance and optimizing the design of a reliable, continuous wave, high-current LINAC required by a fissile fuel production machine

RIKEN accelerator progress report, vol. 36. January - December 2002

International Nuclear Information System (INIS)

Asahi, K.; Abe, T.; Ichihara, T.

2003-03-01

This issue of RIKEN Accelerator Progress Report reports research activities of the RIKEN Accelerator Research Facility (RARF) during the calendar year of 2002. The research programs have been coordinated in the framework of the project entitled Multidisciplinary Researches on Heavy Ion Science. The project involves a variety of fields such as: nuclear physics, nuclear astrophysics, atomic physics, nuclear chemistry, radiation biology, condensed matter physics in terms of accelerator or radiation application, plant mutation, material characterization, application to space science, accelerator physics and engineering, laser technology, and computational technology. These activities involved ten laboratories, five Centers involving seven divisions, the RIKEN-RAL (Rutherford-Appleton Laboratory) Center, and the RBRC (RIKEN-Brookhaven Research Center at Brookhaven National Laboratory), and more than 350 researchers from domestic and foreign institutions. Thirty-six universities and institutes from within Japan and 33 institutes from 10 countries are involved. (J.P.N.)

Neural computation and particle accelerators research, technology and applications

CERN Document Server

D'Arras, Horace

2010-01-01

This book discusses neural computation, a network or circuit of biological neurons and relatedly, particle accelerators, a scientific instrument which accelerates charged particles such as protons, electrons and deuterons. Accelerators have a very broad range of applications in many industrial fields, from high energy physics to medical isotope production. Nuclear technology is one of the fields discussed in this book. The development that has been reached by particle accelerators in energy and particle intensity has opened the possibility to a wide number of new applications in nuclear technology. This book reviews the applications in the nuclear energy field and the design features of high power neutron sources are explained. Surface treatments of niobium flat samples and superconducting radio frequency cavities by a new technique called gas cluster ion beam are also studied in detail, as well as the process of electropolishing. Furthermore, magnetic devises such as solenoids, dipoles and undulators, which ...

Measurement and correction of accelerator optics

International Nuclear Information System (INIS)

Zimmerman, F.

1998-06-01

This report reviews procedures and techniques for measuring, correcting and controlling various optics parameters of an accelerator, including the betatron tune, beta function, betatron coupling, dispersion, chromaticity, momentum compaction factor, and beam orbit. The techniques described are not only indispensable for the basic set-up of an accelerator, but in addition the same methods can be used to study more esoteric questions as, for instance, dynamic aperture limitations or wakefield effects. The different procedures are illustrated by examples from several accelerators, storage rings, as well as linacs and transport lines

Wake fields and wake field acceleration

International Nuclear Information System (INIS)

Bane, K.L.F.; Wilson, P.B.; Weiland, T.

1984-12-01

In this lecture we introduce the concepts of wake fields and wake potentials, examine some basic properties of these functions, show how they can be calculated, and look briefly at a few important applications. One such application is wake field acceleration. The wake field accelerator is capable of producing the high gradients required for future very high energy e + e - linear colliders. The principles of wake field acceleration, and a brief description of experiments in progress in this area, are presented in the concluding section. 40 references, 27 figures

A Gaussian mixture model based cost function for parameter estimation of chaotic biological systems

Science.gov (United States)

Shekofteh, Yasser; Jafari, Sajad; Sprott, Julien Clinton; Hashemi Golpayegani, S. Mohammad Reza; Almasganj, Farshad

2015-02-01

As we know, many biological systems such as neurons or the heart can exhibit chaotic behavior. Conventional methods for parameter estimation in models of these systems have some limitations caused by sensitivity to initial conditions. In this paper, a novel cost function is proposed to overcome those limitations by building a statistical model on the distribution of the real system attractor in state space. This cost function is defined by the use of a likelihood score in a Gaussian mixture model (GMM) which is fitted to the observed attractor generated by the real system. Using that learned GMM, a similarity score can be defined by the computed likelihood score of the model time series. We have applied the proposed method to the parameter estimation of two important biological systems, a neuron and a cardiac pacemaker, which show chaotic behavior. Some simulated experiments are given to verify the usefulness of the proposed approach in clean and noisy conditions. The results show the adequacy of the proposed cost function.

Electron accelerator shielding design of KIPT neutron source facility

Energy Technology Data Exchange (ETDEWEB)

Zhong, Zhao Peng; Gohar, Yousry [Argonne National Laboratory, Argonne (United States)

2016-06-15

The Argonne National Laboratory of the United States and the Kharkov Institute of Physics and Technology of the Ukraine have been collaborating on the design, development and construction of a neutron source facility at Kharkov Institute of Physics and Technology utilizing an electron-accelerator-driven subcritical assembly. The electron beam power is 100 kW using 100-MeV electrons. The facility was designed to perform basic and applied nuclear research, produce medical isotopes, and train nuclear specialists. The biological shield of the accelerator building was designed to reduce the biological dose to less than 5.0e-03 mSv/h during operation. The main source of the biological dose for the accelerator building is the photons and neutrons generated from different interactions of leaked electrons from the electron gun and the accelerator sections with the surrounding components and materials. The Monte Carlo N-particle extended code (MCNPX) was used for the shielding calculations because of its capability to perform electron-, photon-, and neutron-coupled transport simulations. The photon dose was tallied using the MCNPX calculation, starting with the leaked electrons. However, it is difficult to accurately tally the neutron dose directly from the leaked electrons. The neutron yield per electron from the interactions with the surrounding components is very small, ∼0.01 neutron for 100-MeV electron and even smaller for lower-energy electrons. This causes difficulties for the Monte Carlo analyses and consumes tremendous computation resources for tallying the neutron dose outside the shield boundary with an acceptable accuracy. To avoid these difficulties, the SOURCE and TALLYX user subroutines of MCNPX were utilized for this study. The generated neutrons were banked, together with all related parameters, for a subsequent MCNPX calculation to obtain the neutron dose. The weight windows variance reduction technique was also utilized for both neutron and photon dose

Theoretical evaluation of the biological shielding sufficiency for the Pelletron NEC Particle Accelerator at the Ghana Atomic Energy Commission

International Nuclear Information System (INIS)

Amoah, P. A.

2012-01-01

Theoretical evaluation of the biological shielding sufficiency provided for 1.7MV Pelletron NEC Particle Accelerator yet to be installed at the Accelerator Research Centre of the Ghana Atomic Energy Commission (GAEC) has been done. Using the Beer Lambert law attenuation of radiation dose outside the walls of the facility was made for protons of energy 1.7MeV. Simulation of charged particle-matter interactions leading to bremsstrahlung radiation using Monte Carlo code (MCNP5) have been carried out. Neutron Activation Analysis (NAA) technique has also been used to identify the composition of the concrete material used during the construction of the Accelerator Research Centre (ARC) building. The NAA analysis revealed that the elemental constituents of the ordinary concrete of density 2.3g/cm 3 used for the construction of the walls included Na, Al, and Ca. Background radiation levels within and outside the facility was measured with the aid of a Sodium Iodide (NaI) identifinder and a Rados detector so as to have a practical reference datum. The weekly background radiation measurements yielded an average dose rate value of 0.05μSv/hr from recorded value range of 0.01μSv/hr to 0.07μSv/hr for an eight month period. Modeling and simulation of charged particle-matter interactions at different beam energies using Monte Carlo code (MCNP5) have yielded the dose rate of 1.58E-07μSv/hr, 1.98E-07μSv/h and 2.20E-05μSv/h outside the 22.86cm (9.0 inch) thick wall of the accelerator facility, for the beam energy range of 0.5-3.0MeV for Titanium, iron and Zirconium target samples respectively. From the Beer-Lambert law, the operational energy of 1.7MeV was used to evaluate theoretically the radiation dose rate of 1.178E-05μSv/hr, 2.656E-05μSv/hr and 4.787E-05μSv/hr outside the 22.86cm thick wall of the accelerator facility for Titanium, Iron and Zirconium targets respectively. At the operational energy energy of 3.0 MeV, the dose rate values obtained were 4.382E-05μSv/h, 9

Click Chemistry Mediated Functionalization of Vertical Nanowires for Biological Applications.

Science.gov (United States)

Vutti, Surendra; Schoffelen, Sanne; Bolinsson, Jessica; Buch-Månson, Nina; Bovet, Nicolas; Nygård, Jesper; Martinez, Karen L; Meldal, Morten

2016-01-11

Semiconductor nanowires (NWs) are gaining significant importance in various biological applications, such as biosensing and drug delivery. Efficient and controlled immobilization of biomolecules on the NW surface is crucial for many of these applications. Here, we present for the first time the use of the Cu(I) -catalyzed alkyne-azide cycloaddition and its strain-promoted variant for the covalent functionalization of vertical NWs with peptides and proteins. The potential of the approach was demonstrated in two complementary applications of measuring enzyme activity and protein binding, which is of general interest for biological studies. The attachment of a peptide substrate provided NW arrays for the detection of protease activity. In addition, green fluorescent protein was immobilized in a site-specific manner and recognized by antibody binding to demonstrate the proof-of-concept for the use of covalently modified NWs for diagnostic purposes using minute amounts of material. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Simbios: an NIH national center for physics-based simulation of biological structures.

Science.gov (United States)

Delp, Scott L; Ku, Joy P; Pande, Vijay S; Sherman, Michael A; Altman, Russ B

2012-01-01

Physics-based simulation provides a powerful framework for understanding biological form and function. Simulations can be used by biologists to study macromolecular assemblies and by clinicians to design treatments for diseases. Simulations help biomedical researchers understand the physical constraints on biological systems as they engineer novel drugs, synthetic tissues, medical devices, and surgical interventions. Although individual biomedical investigators make outstanding contributions to physics-based simulation, the field has been fragmented. Applications are typically limited to a single physical scale, and individual investigators usually must create their own software. These conditions created a major barrier to advancing simulation capabilities. In 2004, we established a National Center for Physics-Based Simulation of Biological Structures (Simbios) to help integrate the field and accelerate biomedical research. In 6 years, Simbios has become a vibrant national center, with collaborators in 16 states and eight countries. Simbios focuses on problems at both the molecular scale and the organismal level, with a long-term goal of uniting these in accurate multiscale simulations.

The Light Ion Biomedical Research Accelerator (LIBRA)

International Nuclear Information System (INIS)

Gough, R.A.

1987-03-01

LIBRA is a concept to place a light-ion, charged-particle facility in a hospital environment, and to dedicate it to applications in biology and medicine. There are two aspects of the program envisaged for LIBRA: a basic research effort coupled with a program in clinical applications of accelerated charged particles. The operational environment to be provided for LIBRA is one in which both of these components can coexist and flourish, and one that will promote the transfer of technology and knowledge from one to the other. In order to further investigate the prospects for a Light Ion Biomedical Research Accelerator (LIBRA), discussions are underway with the Merritt Peralta Medical Center (MPMC) in Oakland, California, and the University of California at San Francisco (UCSF). In this paper, a brief discussion of the technical requirements for such a facility is given, together with an outline of the accelerator technology required. While still in a preliminary stage, it is possible nevertheless to develop an adequate working description of the type, size, performance and cost of the accelerator facilities required to meet the preliminary goals for LIBRA

Quality of Graphite Target for Biological/Biomedical/Environmental Applications of 14C-Accelerator Mass Spectrometry

Science.gov (United States)

2010-01-01

Catalytic graphitization for 14C-accelerator mass spectrometry (14C-AMS) produced various forms of elemental carbon. Our high-throughput Zn reduction method (C/Fe = 1:5, 500 °C, 3 h) produced the AMS target of graphite-coated iron powder (GCIP), a mix of nongraphitic carbon and Fe3C. Crystallinity of the AMS targets of GCIP (nongraphitic carbon) was increased to turbostratic carbon by raising the C/Fe ratio from 1:5 to 1:1 and the graphitization temperature from 500 to 585 °C. The AMS target of GCIP containing turbostratic carbon had a large isotopic fractionation and a low AMS ion current. The AMS target of GCIP containing turbostratic carbon also yielded less accurate/precise 14C-AMS measurements because of the lower graphitization yield and lower thermal conductivity that were caused by the higher C/Fe ratio of 1:1. On the other hand, the AMS target of GCIP containing nongraphitic carbon had higher graphitization yield and better thermal conductivity over the AMS target of GCIP containing turbostratic carbon due to optimal surface area provided by the iron powder. Finally, graphitization yield and thermal conductivity were stronger determinants (over graphite crystallinity) for accurate/precise/high-throughput biological, biomedical, and environmental14C-AMS applications such as absorption, distribution, metabolism, elimination (ADME), and physiologically based pharmacokinetics (PBPK) of nutrients, drugs, phytochemicals, and environmental chemicals. PMID:20163100

FY 1999 report on the results on analysis of protein functions; 1999 nendo tanpakushitsu kino kaiseki seika hokokusho

Energy Technology Data Exchange (ETDEWEB)

NONE

2001-03-01

This project is aimed at construction of the intellectual infrastructures for biotechnologies, in order to accelerate development of the Japanese technologies and activate their application to industries. Described herein are the FY 1999 results. These infrastructures are for functional analysis of protein which will be one of the key issues in genome analysis, and collection and analysis of biological information. This project includes a total of 9 research and development themes for four research categories: frequency analysis of gene expression (development of the gene expression profile database system for functional analysis of human genome, and analysis of the gene expression and protein functions by the ECA chip technology), function analysis by the biological model (high-performance analysis by the bio-project, database system for drug metabolizing enzymes, analysis of gene functions using mutant mice, and simple genome function analysis of murine individuals using the RNAi effect), protein expression (function validation of unknown human genes based on the useful biological model, and protein function analysis using multi-purpose destination vectors), and protein function prediction by the information science method. (NEDO)

CAS Accelerators for Medical Applications in Vösendorf, Austria

CERN Multimedia

CERN Accelerator School

2015-01-01

The CERN Accelerator School (CAS) and MedAustron jointly organised a course on Accelerators for Medical Applications in Vösendorf, Austria between 26 May and 5 June 2015. The course was held at the Eventhotel Pyramide on the outskirts of Vienna, and was attended by 76 participants from 29 countries, coming from as far away as Canada, China, Lithuania, Thailand, Ukraine and Russia.       The intensive programme comprised 37 lectures. The emphasis was on using charged particle beams for cancer therapy and the programme began by covering the way in which particles interact with biological material, how this translates into the dose needed for treatment and how this dose is best delivered. The different accelerator options for providing the particles needed were then presented in some detail. The production of radioisotopes and how these are used for diagnostics and therapy was also covered, together with a look at novel acceleration techniques that may play a role i...

Pulsed high field magnets. An efficient way of shaping laser accelerated proton beams for application

Energy Technology Data Exchange (ETDEWEB)

Kroll, Florian; Schramm, Ulrich [Helmholtz-Zentrum Dresden - Rossendorf, 01328 Dresden (Germany); Technische Universitaet Dresden, 01062 Dresden (Germany); Bagnoud, Vincent; Blazevic, Abel; Busold, Simon [GSI Helmholtzzentrum fuer Schwerionenforschung, 64291 Darmstadt (Germany); Helmholtz Institut Jena, 07734 Jena (Germany); Brabetz, Christian; Schumacher, Dennis [GSI Helmholtzzentrum fuer Schwerionenforschung, 64291 Darmstadt (Germany); Deppert, Oliver; Jahn, Diana; Roth, Markus [Technische Universitaet Darmstadt, 64289 Darmstadt (Germany); Karsch, Leonhard; Masood, Umar [OncoRay-National Center for Radiation Research in Oncology, TU Dresden, 01307 Dresden (Germany); Kraft, Stephan [Helmholtz-Zentrum Dresden - Rossendorf, 01328 Dresden (Germany)

2015-07-01

Compact laser-driven proton accelerators are a potential alternative to complex, expensive conventional accelerators, enabling unique beam properties, like ultra-high pulse dose. Nevertheless, they still require substantial development in reliable beam generation and transport. We present experimental studies on capture, shape and transport of laser and conventionally accelerated protons via pulsed high-field magnets. These magnets, common research tools in the fields of solid state physics, have been adapted to meet the demands of laser acceleration experiments.Our work distinctively shows that pulsed magnet technology makes laser acceleration more suitable for application and can facilitate compact and efficient accelerators, e.g. for material research as well as medical and biological purposes.

[The hyperiricosuria as an indicator of derangement of biologic functions of endoecology and adaptation, biologic reactions of excretion, inflammation and arterial tension].

Science.gov (United States)

Titov, V N; Oshchepkova, E V; Dmitriev, V A; Gushchina, O V; Shiriaeva, Iu K; Iashin, A Ia

2012-04-01

During millions years in all animals allantoine (oxidized by uricase uric acid) was catabolite of purines and ascorbic acid was an acceptor of active forms of oxygen. The proximal tubules of nephron reabsorbed the trace amounts of uric acid Then during phylogenesis the primates had a mutation of ascorbic acid gen minus. Later on occurred a second spontaneous mutation and uricase gen minus and uric acid became catabolites of purines. In absence of ascorbic acid synthesis ions of urates became a major capturers of active forms of oxygen and all uric acid as before underwent the reabsorption. Later the carriers were formed which began in epithelium of proximal tubules to secrete all uric acid into urine. At every incident of "littering" of intercellular medium with endogenic flogogens (impairment of biologic function of endoecology) under compensatory development of biologic reaction of inflammation the need in inactivation of active forms of oxygen increases. Hence later on in phylogenesis one more stage was formed--post secretory reabsorption of uric acid In the biologic reaction of inflammation epithelium of proximal tubules initiates retentional hyperiricosuria. The general antioxidant activity of human blood plasma in 60% is presented by urates' ions. The excretion of uric acid includes 4 stages: filtration, full reabsorption, secretion and post secretory reabsorption. In phylogenesis these stages formed in sequence. The mild hyperiricosuria is most frequently considered as a non-specific indicator of activation of biologic reaction of inflammation. The productive hyperiricosuria develops more infrequently under surplus of meat food and cytolysis syndrome (intensification of cell loss in vivo). Under concentration of uric acid more than 400 mkmol/l part of urates circulates in intercellular medium in the form of crystals. The microcrystals of uric acid (biologic "litter") initiate the syndrome of systemic inflammatory response as an endogenic flogogen

Industrial applications of electron accelerators

CERN Document Server

Cleland, M R

2006-01-01

This paper addresses the industrial applications of electron accelerators for modifying the physical, chemical or biological properties of materials and commercial products by treatment with ionizing radiation. Many beneficial effects can be obtained with these methods, which are known as radiation processing. The earliest practical applications occurred during the 1950s, and the business of radiation processing has been expanding since that time. The most prevalent applications are the modification of many different plastic and rubber products and the sterilization of single-use medical devices. Emerging applications are the pasteurization and preservation of foods and the treatment of toxic industrial wastes. Industrial accelerators can now provide electron energies greater than 10 MeV and average beam powers as high as 700 kW. The availability of high-energy, high-power electron beams is stimulating interest in the use of X-rays (bremsstrahlung) as an alternative to gamma rays from radioactive nuclides.

Multistage charged particle accelerator, with high-vacuum insulation

International Nuclear Information System (INIS)

Holl, P.

1976-01-01

A multistage charged-particle accelerator for operating with accelerating voltages higher than 150 kV is described. The device consists essentially of a high-voltage insulator, a source for producing charged particles, a Wehnelt cylinder, an anode, and a post-accelerating tube containing stack-wise positioned post-accelerating electrodes. A high vacuum is used for insulating the parts carrying the high voltages, and at least one cylindrical screen surrounding these parts is interposed between them and the vacuum vessel, which can itself also function as a cylindrical screen

Cellular Basis for ADT-Induced Acceleration of Sarcopenia

Science.gov (United States)

2015-10-01

1 AWARD NUMBER: W81XWH-14-1-0454 TITLE: Cellular Basis for ADT-Induced Acceleration of Sarcopenia PRINCIPAL INVESTIGATOR: Joe V...AND SUBTITLE Cellular Basis for ADT-Induced Acceleration of Sarcopenia 5a. CONTRACT NUMBER 5b. GRANT NUMBER W81XWH-14-1-0454 5c. PROGRAM...cell function and thereby regenerative capability contribute to the acceleration of sarcopenia observed in prostate cancer patients undergoing ADT

FUNCTION IN BIOLOGY: ETIOLOGICAL AND ORGANIZATIONAL PERSPECTIVES

Directory of Open Access Journals (Sweden)

Charbel Niño El-Hani

2009-10-01

Full Text Available ABSTRACT. In this paper, we argue for a taxonomy of approaches to function based on different epistemological perspectives assumed with regard to the treatment of this central concept in the life sciences. We distinguish between etiological and organizational perspectives on function, analyzing two distinct theories related to each perspective: Wright’s selectionist etiological approach and Godfrey-Smith’s modern history theory of functions, in the case of the etiological perspective; and Cummins’ functional analysis and Collier’s interactivist approach to function, among organizational accounts. We explain differences and similarities between these theories and the broader perspectives on function, arguing for a particular way of understanding the consensus without unity in debates about function. While explaining the accounts of function, we also deal with the relationship between this concept and other important biological concepts, such as adaptation, selection, complexity, and autonomy. We also advance an argument for the limits and prospects of the explanatory role of function in evolution. By arguing that changes in functionality are always grounded on changes in systems’ organization, we show that function can never explain the origins of traits. Nevertheless, it can explain the spread of traits in populations, but only when we are dealing with functionally novel traits. Finally, we stress that organizational accounts of function are needed to understand how new functions appear by means of changes in systems’ organization. KEYWORDS: Function; Teleology; Explanation; Etiology; Organization.   RESUMEN. En este artículo, argumentamos a favor de una taxonomía de abordajes sobre función basada en diferentes perspectivas epistemológicas a cerca del tratamiento de este concepto central en las ciencias de la vida. Distinguimos entre perspectivas etiológicas y organizacionales sobre función, analizando dos teorías distintas

Enzymes for ecdysteroid biosynthesis: their biological functions in insects and beyond.

Science.gov (United States)

Niwa, Ryusuke; Niwa, Yuko S

2014-01-01

Steroid hormones are responsible for the coordinated regulation of many aspects of biological processes in multicellular organisms. Since the last century, many studies have identified and characterized steroidogenic enzymes in vertebrates, including mammals. However, much less is known about invertebrate steroidogenic enzymes. In the last 15 years, a number of steroidogenic enzymes and their functions have been characterized in ecdysozoan animals, especially in the fruit fly Drosophila melanogaster. In this review, we summarize the latest knowledge of enzymes crucial for synthesizing ecdysteroids, the principal insect steroid hormones. We also discuss the functional conservation and diversity of ecdysteroidogenic enzymes in other insects and even non-insect species, such as nematodes, vertebrates, and lower eukaryotes.

Effects of acceleration through the Dirac sea

International Nuclear Information System (INIS)

Hacyan, S.

1986-01-01

The effects of acceleration through massive scalar and spin-1/2 fields are investigated. It is shown that the density-of-states factor in a uniformly accelerated frame takes a complicated form, but the energy spectrum exhibits a Bose-Einstein or Fermi-Dirac distribution function. In particular, the Dirac sea shows thermal-like effects

Echocardiographic assessment with right ventricular function improvement following ultrasound-accelerated catheter-directed thrombolytic therapy in submassive pulmonary embolism.

Science.gov (United States)

Doheny, Charles; Gonzalez, Lorena; Duchman, Stanley M; Varon, Joseph; Bechara, Carlos F; Cheung, Mathew; Lin, Peter H

2018-06-01

Introduction The objective of this study was to evaluate the efficacy of ultrasound-accelerated catheter-directed thrombolytic therapy in patients with submassive pulmonary embolism. Methods Clinical records of 46 patients with submassive pulmonary embolism who underwent ultrasound-accelerated catheter-directed pulmonary thrombolysis using tissue plasminogen activator, from 2007 to 2017, were analyzed. All patients experienced clinical symptoms with computed tomography evidence of pulmonary thrombus burden. Right ventricular dysfunction was present in all patients by echocardiographic finding of right ventricle-to-left ventricle ratio > 0.9. Treatment outcome, procedural complications, right ventricular pressures, and thrombus clearance were evaluated. Follow-up evaluation included echocardiographic assessment of right ventricle-to-left ventricle ratio at one month, six months, and one year. Results Technical success was achieved in all patients ( n = 46, 100%). Our patients received an average of 18.4 ± 4.7 mg of tissue plasminogen activator using ultrasound-accelerated thrombolytic catheter with an average infusion time of 16.5± 5.4 h. Clinical success was achieved in all patients (100%). Significant reduction of mean pulmonary artery pressure occurred following the treatment, which decreased from 36 ± 8 to 21 ± 5 mmHg ( p right ventricular dysfunction based on echocardiographic assessment. The right ventricle-to-left ventricle ratio decreased from 1.32 ± 0.18 to 0.91 ± 0.13 at the time of hospital discharge ( p right ventricular function remained improved at 6 months and 12 months of follow-up, as right ventricle-to-left ventricle ratio were 0.92 ± 0.14 ( p right ventricular function in patients with submassive pulmonary embolism.

The functional biology and trophic role of krill (Thysanoessa raschii) in a Greenlandic fjord

DEFF Research Database (Denmark)

Agersted, Mette Dalgaard; Nielsen, Torkel Gissel; Munk, Peter

2011-01-01

Despite being a key zooplankton group, knowledge on krill biology from the Arctic is inadequate. The present study examine the functional biology and evaluate the trophic role of krill in the GodthAyenbsfjord (64 degrees N, 51 degrees W) SW Greenland, through a combination of fieldwork...... and laboratory experiments. Krill biomass was highest in the middle fjord and inner fjord, whereas no krill was found offshore. The dominating species Thysanoessa raschii revealed a type III functional response when fed with the diatom Thalassiosira weissflogii. At food saturation, T. raschii exhibited a daily...... ration of 1% body C d(-1). Furthermore, T. raschii was capable of exploiting plankton cells from 5 to 400 mu m, covering several trophic levels of the pelagic food web. The calculated grazing impact by T. raschii on the fjord plankton community was negligible. However, the schooling and migratory...

PreproVIP-derived peptides in the human female genital tract: expression and biological function

DEFF Research Database (Denmark)

Bredkjoer, H E; Palle, C; Ekblad, E

1997-01-01

The aim of the study was to elucidate the localization, distribution, colocalization and biological effect of preproVIP-derived peptides in the human female genital tract. Radioimmunoassays applying antisera against the five functional domains of the VIP precursor in combination with immunohistoc......The aim of the study was to elucidate the localization, distribution, colocalization and biological effect of preproVIP-derived peptides in the human female genital tract. Radioimmunoassays applying antisera against the five functional domains of the VIP precursor in combination...... with immunohistochemistry were used. The effect of preproVIP 22-79, preproVIP 111-122 and preproVIP 156-170 on genital smooth muscle activity in the Fallopian tube was investigated in vitro and compared to that of VIP. All the preproVIP-derived peptides were expressed throughout the genital tract in neuronal elements...

Linking biological soil crust diversity to ecological functions

Science.gov (United States)

Glaser, Karin; Borchhardt, Nadine; Schulz, Karoline; Mikhailyuk, Tatiana; Baumann, Karen; Leinweber, Peter; Ulf, Karsten

2016-04-01

Biological soil crusts (BSCs) are an association of different microorganisms and soil particles in the top millimeters of the soil. They are formed by algae, cyanobacteria, microfungi, bacteria, bryophytes and lichens in various compositions. Our aim was to determine and compare the biodiversity of all occurring organisms in biogeographically different habitats, ranging from polar (both Arctic and Antarctic), subpolar (Scandinavia), temperate (Germany) to dry regions (Chile). The combination of microscopy and molecular techniques (next-generation sequencing) revealed highly diverse crust communities, whose composition clustered by region and correlates with habitat characteristics such as water content. The BSC biodiversity was then linked to the ecological function of the crusts. The functional role of the BSCs in the biogeochemical cycles of carbon, nitrogen and phosphorous is evaluated using an array of state of the art soil chemistry methods including Py-FIMS (pyrolysis field ionization mass spectrometry) and XANES (x-ray absorbance near edge structure). Total P as well as P fractions were quantified in all BSCs, adjacent soil underneath and comparable nearby soil of BSC-free areas revealing a remarkable accumulation of total phosphorous and a distinct pattern of P fractions in the crust. Further, we observed an indication of a different P-speciation composition in the crust compared with BSC-free soil. The data allow answering the question whether BSCs act as sink or source for these compounds, and how biodiversity controls the biogeochemical function of BSCs.

Photochemical Acceleration of DNA Strand Displacement by Using Ultrafast DNA Photo-crosslinking.

Science.gov (United States)

Nakamura, Shigetaka; Hashimoto, Hirokazu; Kobayashi, Satoshi; Fujimoto, Kenzo

2017-10-18

DNA strand displacement is an essential reaction in genetic recombination, biological processes, and DNA nanotechnology. In particular, various DNA nanodevices enable complicated calculations. However, it takes time before the output is obtained, so acceleration of DNA strand displacement is required for a rapid-response DNA nanodevice. Herein, DNA strand displacement by using DNA photo-crosslinking to accelerate this displacement is evaluated. The DNA photo-crosslinking of 3-cyanovinylcarbazole ( CNV K) was accelerated at least 20 times, showing a faster DNA strand displacement. The rate of photo-crosslinking is a key factor and the rate of DNA strand displacement is accelerated through ultrafast photo-crosslinking. The rate of DNA strand displacement was regulated by photoirradiation energy. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Function behavior of a gas-operated accelerator for kinetic energy projectiles

International Nuclear Information System (INIS)

Heine, H.

1979-01-01

The test facility - presented here - was designed and constructed in order to make investigations on the load case 'airplane crash'. The facility consists mainly of the accelerator on a rail track, an abutment, a control centre, and a measuring-bunker.To perform a test the two parts of the accelerator - a compression chamber and an expansion tube (diameter 613 mm) - are strongly connected after the projectile has been inserted into the tube. The chamber - closed by a steel membrane - is filled with a mixture of methane and compressed air. The mixture is ignited and expands. The membrane opens and the projectile is accelerated. The velocity range can be varied between 80 and 300 m/s.The reinforced concrete slabs that are impacted during the main test series have the dimensions of 6.00 m by 6.50 m and a maximum thickness of 90 cm. During the test the slab hangs at a cross beam so that there is no friction between the specimen and the abutment. (orig.)

FUNCTIONAL OUTCOME OF ACCELERATED REHABILITATION IN ARTHROSCOPIC ANTERIOR CRUCIATE LIGAMENT RECONSTRUCTION WITH BONE PATELLAR TENDON BONE GRAFT A PROSPECTIVE STUDY

Directory of Open Access Journals (Sweden)

Hiranyakumar

2016-03-01

Full Text Available INTRODUCTION An ideal rehabilitation program post anterior cruciate ligament reconstruction enables an individual to return to pre injury levels at a faster rate with minimal to no risk of reinjury to the graft. Rehabilitation protocols have changed considerably over time in the past. It has become “aggressive”, meaning an intensive rehabilitation which includes greater variety of exercises and sports related training. AIM OF THE STUDY The aim of our study is to assess the outcome of accelerated rehabilitation post anterior cruciate ligament (ACL reconstruction. METHODOLOGY 106 patients were operated by a single surgeon underwent arthroscopic anterior cruciate ligament reconstruction using bone patella tendon bone graft and partial meniscectomy for associated meniscal tear. Patients were put on an accelerated rehabilitation protocol designed in our institute on first post-operative day, under the guidance of a physical therapist in consultation with the operated surgeon. Patients were followed up at 3 weeks, 6 months and 9 months, post onset of rehabilitation, patients were assessed using KT1000 Arthrometer and Lysholm knee scoring system. RESULTS Out of 106 patients, who were selected, 96(91% were males and 10(9% were females. The mean pre-operative Lysholm score was 55.09. Post operatively, while on accelerated rehabilitation program the Lysholm scores were 69.73 at 3 weeks, 89.13 at 6 months and 89.19 at 9 months. In our pre-operative evaluation mean KT 1000 arthrometer score was 10.53 and post-operative at six months was 3.49. At nine months 105 patients had excellent results whereas 1 patient had good result. CONCLUSION Accelerated rehabilitation protocol enables the patient to functionally recover faster to pre injury levels. A rehabilitation protocol for 6 months is sufficient in enabling a patient to get back to pre-injury levels. Functional outcome is the same with or without associated meniscal injuries.

MUON ACCELERATION WITH THE RACETRACK FFAG

International Nuclear Information System (INIS)

TRBOJEVIC, D.; EBERHARD, K.; SESSLER, A.

2007-01-01

Muon acceleration for muon collider or neutrino factory is still in a stage where further improvements are likely as a result of further study. This report presents a design of the racetrack non-scaling Fixed Field Alternating Gradient (NS-FFAG) accelerator to allow fast muon acceleration in small number of turns. The racetrack design is made of four arcs: two arcs at opposite sides have a smaller radius and are made of closely packed combined function magnets, while two additional arcs, with a very large radii, are used for muon extraction, injection, and RF accelerating cavities. The ends of the large radii arcs are geometrically matched at the connections to the arcs with smaller radii. The dispersion and both horizontal and vertical amplitude fictions are matched at the central energy

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

Science.gov (United States)

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

2017-11-01

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

Accelerating the design of biomimetic materials by integrating RNA-seq with proteomics and materials science.

Science.gov (United States)

Guerette, Paul A; Hoon, Shawn; Seow, Yiqi; Raida, Manfred; Masic, Admir; Wong, Fong T; Ho, Vincent H B; Kong, Kiat Whye; Demirel, Melik C; Pena-Francesch, Abdon; Amini, Shahrouz; Tay, Gavin Z; Ding, Dawei; Miserez, Ali

2013-10-01

Efforts to engineer new materials inspired by biological structures are hampered by the lack of genomic data from many model organisms studied in biomimetic research. Here we show that biomimetic engineering can be accelerated by integrating high-throughput RNA-seq with proteomics and advanced materials characterization. This approach can be applied to a broad range of systems, as we illustrate by investigating diverse high-performance biological materials involved in embryo protection, adhesion and predation. In one example, we rapidly engineer recombinant squid sucker ring teeth proteins into a range of structural and functional materials, including nanopatterned surfaces and photo-cross-linked films that exceed the mechanical properties of most natural and synthetic polymers. Integrating RNA-seq with proteomics and materials science facilitates the molecular characterization of natural materials and the effective translation of their molecular designs into a wide range of bio-inspired materials.

Biological effects of simple changes in functionality on rhodium metalloinsertors

Science.gov (United States)

Weidmann, Alyson G.; Komor, Alexis C.; Barton, Jacqueline K.

2013-01-01

DNA mismatch repair (MMR) is crucial to ensuring the fidelity of the genome. The inability to correct single base mismatches leads to elevated mutation rates and carcinogenesis. Using metalloinsertors–bulky metal complexes that bind with high specificity to mismatched sites in the DNA duplex–our laboratory has adopted a new chemotherapeutic strategy through the selective targeting of MMR-deficient cells, that is, those that have a propensity for cancerous transformation. Rhodium metalloinsertors display inhibitory effects selectively in cells that are deficient in the MMR machinery, consistent with this strategy. However, a highly sensitive structure–function relationship is emerging with the development of new complexes that highlights the importance of subcellular localization. We have found that small structural modifications, for example a hydroxyl versus a methyl functional group, can yield profound differences in biological function. Despite similar binding affinities and selectivities for DNA mismatches, only one metalloinsertor shows selective inhibition of cellular proliferation in MMR-deficient versus -proficient cells. Studies of whole-cell, nuclear and mitochondrial uptake reveal that this selectivity depends upon targeting DNA mismatches in the cell nucleus. PMID:23776288

Structure, function, and behaviour of computational models in systems biology.

Science.gov (United States)

Knüpfer, Christian; Beckstein, Clemens; Dittrich, Peter; Le Novère, Nicolas

2013-05-31

Systems Biology develops computational models in order to understand biological phenomena. The increasing number and complexity of such "bio-models" necessitate computer support for the overall modelling task. Computer-aided modelling has to be based on a formal semantic description of bio-models. But, even if computational bio-models themselves are represented precisely in terms of mathematical expressions their full meaning is not yet formally specified and only described in natural language. We present a conceptual framework - the meaning facets - which can be used to rigorously specify the semantics of bio-models. A bio-model has a dual interpretation: On the one hand it is a mathematical expression which can be used in computational simulations (intrinsic meaning). On the other hand the model is related to the biological reality (extrinsic meaning). We show that in both cases this interpretation should be performed from three perspectives: the meaning of the model's components (structure), the meaning of the model's intended use (function), and the meaning of the model's dynamics (behaviour). In order to demonstrate the strengths of the meaning facets framework we apply it to two semantically related models of the cell cycle. Thereby, we make use of existing approaches for computer representation of bio-models as much as possible and sketch the missing pieces. The meaning facets framework provides a systematic in-depth approach to the semantics of bio-models. It can serve two important purposes: First, it specifies and structures the information which biologists have to take into account if they build, use and exchange models. Secondly, because it can be formalised, the framework is a solid foundation for any sort of computer support in bio-modelling. The proposed conceptual framework establishes a new methodology for modelling in Systems Biology and constitutes a basis for computer-aided collaborative research.

TCA Cycle and Mitochondrial Membrane Potential Are Necessary for Diverse Biological Functions.

Science.gov (United States)

Martínez-Reyes, Inmaculada; Diebold, Lauren P; Kong, Hyewon; Schieber, Michael; Huang, He; Hensley, Christopher T; Mehta, Manan M; Wang, Tianyuan; Santos, Janine H; Woychik, Richard; Dufour, Eric; Spelbrink, Johannes N; Weinberg, Samuel E; Zhao, Yingming; DeBerardinis, Ralph J; Chandel, Navdeep S

2016-01-21

Mitochondrial metabolism is necessary for the maintenance of oxidative TCA cycle function and mitochondrial membrane potential. Previous attempts to decipher whether mitochondria are necessary for biological outcomes have been hampered by genetic and pharmacologic methods that simultaneously disrupt multiple functions linked to mitochondrial metabolism. Here, we report that inducible depletion of mitochondrial DNA (ρ(ο) cells) diminished respiration, oxidative TCA cycle function, and the mitochondrial membrane potential, resulting in diminished cell proliferation, hypoxic activation of HIF-1, and specific histone acetylation marks. Genetic reconstitution only of the oxidative TCA cycle function specifically in these inducible ρ(ο) cells restored metabolites, resulting in re-establishment of histone acetylation. In contrast, genetic reconstitution of the mitochondrial membrane potential restored ROS, which were necessary for hypoxic activation of HIF-1 and cell proliferation. These results indicate that distinct mitochondrial functions associated with respiration are necessary for cell proliferation, epigenetics, and HIF-1 activation. Copyright © 2016 Elsevier Inc. All rights reserved.

A compact, repetitive accelerator for military and industrial applications

International Nuclear Information System (INIS)

Zutavern, F.J.; O'Malley, M.W.; Ruebush, M.H.; Rinehart, L.F.; Loubriel, G.M.; Babcock, S.R.; Denison, G.J.

1998-04-01

A compact, short pulse, repetitive accelerator has many useful military and commercial applications in biological counter proliferation, materials processing, radiography, and sterilization (medical instruments, waste, and food). The goal of this project was to develop and demonstrate a small, 700 kV accelerator, which can produce 7 kA particle beams with pulse lengths of 10--30 ns at rates up to 50 Hz. At reduced power levels, longer pulses or higher repetition rates (up to 10 kHz) could be achieved. Two switching technologies were tested: (1) spark gaps, which have been used to build low repetition rate accelerators for many years; and (2) high gain photoconductive semiconductor switches (PCSS), a new solid state switching technology. This plan was economical, because it used existing hardware for the accelerator, and the PCSS material and fabrication for one module was relatively inexpensive. It was research oriented, because it provided a test bed to examine the utility of other emerging switching technologies, such as magnetic switches. At full power, the accelerator will produce 700 kV and 7 kA with either the spark gap or PCSS pulser

Present status of TIARA electrostatic accelerator facility

Energy Technology Data Exchange (ETDEWEB)

Tajima, Satoshi; Takada, Isao; Mizuhashi, Kiyoshi; Saito, Yuichi; Uno, Sadanori; Okoshi, Kiyonori; Ishii, Yasuyuki; Nakajima, Yoshinori; Sakai, Takuro [Japan Atomic Energy Research Inst., Takasaki, Gunma (Japan). Takasaki Radiation Chemistry Research Establishment

1996-12-01

The electrostatic accelerator, 3 MV tandem accelerator, 3 MV single end accelerator and 400 kV ion implantation equipment, which were installed in Takasaki Ion Irradiation Research Facility (TIARA) of Japan Atomic Energy Research Institute, have been used for the research on the advanced utilization of radiation mainly in material science by ion beam. The utilization is open to other researchers, and in fiscal year 1995, about 40% was the utilization by outsiders. The number of the experimental subjects adopted in fiscal year 1995 was 47, and the fields of research were space and environment materials, nuclear fusion reactor materials, new functional materials, biotechnology and base technology. The operation time in fiscal year 1995 was 1201, 1705 and 1505 hours for the tandem accelerator, single end accelerator and ion implantation equipment, respectively. The methods of experiment are reported. The troubles occurred in the tandem accelerator and single end accelerator are reported. As the diversification of beam utilization in the tandem accelerator, the utilizations of high energy molecular ions, low energy negative ions, multivalent ions by post stripper and low intensity ions by mesh attenuator have been attempted. These utilizations are described. (K.I.)

Indian participation in FAIR accelerator facility

International Nuclear Information System (INIS)

Sur, Amitava

2015-01-01

India is a founder member of the FAIR-GmbH, the upcoming International Accelerator Facility at Darmstadt, Germany. Indian participation at FAIR is being funded jointly by the Department of Science and Technology (DST) and the Department of Atomic Energy (DAE). Indo- FAIR Coordination Centre at Bose Institute (BI-IFCC) is coordinating the Indian efforts of both in-kind contribution as well as experimental programmes at FAIR. FAIR aims for beams of stable and unstable nuclei as well as antiprotons in a wide range of intensities and energies. A superconducting double-synchrotron SIS100/300 with a circumference of 1,100 meters and with magnetic rigidities of 100 and 300 Tm, respectively, is at the heart of the FAIR accelerator facility. The existing GSI accelerators UNILAC and SIS18 will serve as an injector. Adjacent to the large double- synchrotron is a complex system of storage- cooler rings and experiment stations, including a superconducting nuclear fragment separator (Super-FRS) and an antiproton production target. FAIR will supply rare isotope beams (RIBs) and antiproton beams. In FAIR accelerator facility up to four research programs can be run in a parallel mode. The multidisciplinary research program covers the fields of QCD studies with cooled beams of antiprotons, nucleus nucleus collisions at highest baryon density, nuclear structure and nuclear astrophysics investigations with nuclei far off stability, high density plasma physics, atomic and material science studies, radio-biological and other application-oriented studies will contribute in providing in-kind items both for the accelerator and the experiments. As per current plans Indian in kind contributions include: Power Converters, Superconducting Magnets, Beam Stopper, Vacuum Chamber. A short sample from an Indian Industry has been tested successfully at FAIR. Indian participation in building the accelerator components for FAIR is presented

Role of soil biology and soil functions in relation to land use intensity.

Science.gov (United States)

Bondi, Giulia; Wall, David; Bacher, Matthias; Emmet-Booth, Jeremy; Graça, Jessica; Marongiu, Irene; Creamer, Rachel

2017-04-01

The delivery of the ecosystem's functions is predominantly controlled by soil biology. The biology found in a gram of soil contains more than ten thousand individual species of bacteria and fungi (Torsvik et al., 1990). Understanding the role and the requirements of these organisms is essential for the protection and the sustainable use of soils. Soil biology represents the engine of all the processes occurring in the soil and it supports the ecosystem services such as: 1) nutrient mineralisation 2) plant production 3) water purification and regulation and 4) carbon cycling and storage. During the last years land management type and intensity have been identified as major drivers for microbial performance in soil. For this reason land management needs to be appropriately studied to understand the role of soil biology within this complex interplay of functions. We aimed to study whether and how land management drives soil biological processes and related functions. To reach this objective we built a land use intensity index (LUI) able to quantify the impact of the common farming practices carried out in Irish grassland soils. The LUI is derived from a detailed farmer questionnaire on grassland management practices at 38 farms distributed in the five major agro-climatic regions of Ireland defined by Holden and Brereton (2004). Soils were classified based on their drainage status according to the Irish Soil Information System by Creamer et al. (2014). This detailed questionnaire is then summarised into 3 management intensity components: (i) intensity of Fertilisation (Fi), (ii) frequency of Mowing (Mi) and (iii) intensity of Livestock Grazing (Gi). Sites were sampled to assess the impact of land management intensity on microbial community structure and enzyme behaviour in relation to nitrogen, phosphorus and carbon cycling. Preliminary results for enzymes linked to C and N cycles showed higher activity in relation to low grazing pressure (low Gi). Enzymes linked to P

Electron acceleration by turbulent plasmoid reconnection

Science.gov (United States)

Zhou, X.; Büchner, J.; Widmer, F.; Muñoz, P. A.

2018-04-01

In space and astrophysical plasmas, like in planetary magnetospheres, as that of Mercury, energetic electrons are often found near current sheets, which hint at electron acceleration by magnetic reconnection. Unfortunately, electron acceleration by reconnection is not well understood yet, in particular, acceleration by turbulent plasmoid reconnection. We have investigated electron acceleration by turbulent plasmoid reconnection, described by MHD simulations, via test particle calculations. In order to avoid resolving all relevant turbulence scales down to the dissipation scales, a mean-field turbulence model is used to describe the turbulence of sub-grid scales and their effects via a turbulent electromotive force (EMF). The mean-field model describes the turbulent EMF as a function of the mean values of current density, vorticity, magnetic field as well as of the energy, cross-helicity, and residual helicity of the turbulence. We found that, mainly around X-points of turbulent reconnection, strongly enhanced localized EMFs most efficiently accelerated electrons and caused the formation of power-law spectra. Magnetic-field-aligned EMFs, caused by the turbulence, dominate the electron acceleration process. Scaling the acceleration processes to parameters of the Hermean magnetotail, electron energies up to 60 keV can be reached by turbulent plasmoid reconnection through the thermal plasma.

Microstructure, mechanical properties, and biological response to functionally graded HA coatings

International Nuclear Information System (INIS)

Rabiei, Afsaneh; Blalock, Travis; Thomas, Brent; Cuomo, Jerry; Yang, Y.; Ong, Joo

2007-01-01

Hydroxyapatite (HA) [Ca 10 (PO 4 ) 6 (OH) 2 ] is the primary mineral content, representing 43% by weight, of bone. Applying a thin layer of HA, to the surface of a metal implant, can promote osseointegration and increase the mechanical stability of the implant. In this study, a biocompatible coating comprising an HA film with functionally graded crystallinity is being deposited on a heated substrate in an Ion Beam Assisted Deposition (IBAD) system. The microstructure of the film was studied using Transmission Electron Microscopy techniques. Finally, initial cell adhesion and cell differentiation on the coating was evaluated using ATCC CRL 1486 human embryonic palatal mesenchymal cell, an osteoblast precursor cell line. The results have shown superior mechanical properties and biological response to the functionally graded HA film

The Widespread Prevalence and Functional Significance of Silk-Like Structural Proteins in Metazoan Biological Materials.

Directory of Open Access Journals (Sweden)

Carmel McDougall

Full Text Available In nature, numerous mechanisms have evolved by which organisms fabricate biological structures with an impressive array of physical characteristics. Some examples of metazoan biological materials include the highly elastic byssal threads by which bivalves attach themselves to rocks, biomineralized structures that form the skeletons of various animals, and spider silks that are renowned for their exceptional strength and elasticity. The remarkable properties of silks, which are perhaps the best studied biological materials, are the result of the highly repetitive, modular, and biased amino acid composition of the proteins that compose them. Interestingly, similar levels of modularity/repetitiveness and similar bias in amino acid compositions have been reported in proteins that are components of structural materials in other organisms, however the exact nature and extent of this similarity, and its functional and evolutionary relevance, is unknown. Here, we investigate this similarity and use sequence features common to silks and other known structural proteins to develop a bioinformatics-based method to identify similar proteins from large-scale transcriptome and whole-genome datasets. We show that a large number of proteins identified using this method have roles in biological material formation throughout the animal kingdom. Despite the similarity in sequence characteristics, most of the silk-like structural proteins (SLSPs identified in this study appear to have evolved independently and are restricted to a particular animal lineage. Although the exact function of many of these SLSPs is unknown, the apparent independent evolution of proteins with similar sequence characteristics in divergent lineages suggests that these features are important for the assembly of biological materials. The identification of these characteristics enable the generation of testable hypotheses regarding the mechanisms by which these proteins assemble and direct the

The Structure and Function of Biological Networks

Science.gov (United States)

Wu, Daniel Duanqing

2010-01-01

Biology has been revolutionized in recent years by an explosion in the availability of data. Transforming this new wealth of data into meaningful biological insights and clinical breakthroughs requires a complete overhaul both in the questions being asked and the methodologies used to answer them. A major challenge in organizing and understanding…

Biological applications of ultraviolet free-electron lasers

International Nuclear Information System (INIS)

Sutherland, J.C.

1997-10-01

This review examines the possibilities for biological research using the three ultraviolet free-electron lasers that are nearing operational status in the US. The projected operating characteristics of major interest in biological research of the free-electron lasers at Brookhaven National Laboratory, the Thomas Jefferson National Accelerator Facility, and Duke University are presented. Experimental applications in the areas of far- and vacuum ultraviolet photophysics and photochemistry, structural biology, environmental photobiology, and medical research are discussed and the prospects for advances in these areas, based upon the characteristics of the new ultraviolet free-electron lasers, are evaluated

Plant Metabolomics: An Indispensable System Biology Tool for Plant Science

Directory of Open Access Journals (Sweden)

Jun Hong

2016-06-01

Full Text Available As genomes of many plant species have been sequenced, demand for functional genomics has dramatically accelerated the improvement of other omics including metabolomics. Despite a large amount of metabolites still remaining to be identified, metabolomics has contributed significantly not only to the understanding of plant physiology and biology from the view of small chemical molecules that reflect the end point of biological activities, but also in past decades to the attempts to improve plant behavior under both normal and stressed conditions. Hereby, we summarize the current knowledge on the genetic and biochemical mechanisms underlying plant growth, development, and stress responses, focusing further on the contributions of metabolomics to practical applications in crop quality improvement and food safety assessment, as well as plant metabolic engineering. We also highlight the current challenges and future perspectives in this inspiring area, with the aim to stimulate further studies leading to better crop improvement of yield and quality.

Plant Metabolomics: An Indispensable System Biology Tool for Plant Science

Science.gov (United States)

Hong, Jun; Yang, Litao; Zhang, Dabing; Shi, Jianxin

2016-01-01

As genomes of many plant species have been sequenced, demand for functional genomics has dramatically accelerated the improvement of other omics including metabolomics. Despite a large amount of metabolites still remaining to be identified, metabolomics has contributed significantly not only to the understanding of plant physiology and biology from the view of small chemical molecules that reflect the end point of biological activities, but also in past decades to the attempts to improve plant behavior under both normal and stressed conditions. Hereby, we summarize the current knowledge on the genetic and biochemical mechanisms underlying plant growth, development, and stress responses, focusing further on the contributions of metabolomics to practical applications in crop quality improvement and food safety assessment, as well as plant metabolic engineering. We also highlight the current challenges and future perspectives in this inspiring area, with the aim to stimulate further studies leading to better crop improvement of yield and quality. PMID:27258266

Pectin: cell biology and prospects for functional analysis.

Science.gov (United States)

Willats, W G; McCartney, L; Mackie, W; Knox, J P

2001-09-01

Pectin is a major component of primary cell walls of all land plants and encompasses a range of galacturonic acid-rich polysaccharides. Three major pectic polysaccharides (homogalacturonan, rhamnogalacturonan-I and rhamnogalacturonan-II) are thought to occur in all primary cell walls. This review surveys what is known about the structure and function of these pectin domains. The high degree of structural complexity and heterogeneity of the pectic matrix is produced both during biosynthesis in the endomembrane system and as a result of the action of an array of wall-based pectin-modifying enzymes. Recent developments in analytical techniques and in the generation of anti-pectin probes have begun to place the structural complexity of pectin in cell biological and developmental contexts. The in muro de-methyl-esterification of homogalacturonan by pectin methyl esterases is emerging as a key process for the local modulation of matrix properties. Rhamnogalacturonan-I comprises a highly diverse population of spatially and developmentally regulated polymers, whereas rhamnogalacturonan-II appears to be a highly conserved and stable pectic domain. Current knowledge of biosynthetic enzymes, plant and microbial pectinases and the interactions of pectin with other cell wall components and the impact of molecular genetic approaches are reviewed in terms of the functional analysis of pectic polysaccharides in plant growth and development.

Electronics around the accelerators- mathematical recalls

International Nuclear Information System (INIS)

Le Meur, G.

1992-02-01

The author presents the main mathematical tools used in electronics and in particular in accelerator electronics: complex functions, distributions, Fourier series, Laplace transformation, Fourier transformation and probabilities

Biological adaptations for functional features of language in the face of cultural evolution.

Science.gov (United States)

Christiansen, Morten H; Reali, Florencia; Chater, Nick

2011-04-01

Although there may be no true language universals, it is nonetheless possible to discern several family resemblance patterns across the languages of the world. Recent work on the cultural evolution of language indicates the source of these patterns is unlikely to be an innate universal grammar evolved through biological adaptations for arbitrary linguistic features. Instead, it has been suggested that the patterns of resemblance emerge because language has been shaped by the brain, with individual languages representing different but partially overlapping solutions to the same set of nonlinguistic constraints. Here, we use computational simulations to investigate whether biological adaptation for functional features of language, deriving from cognitive and communicative constraints, may nonetheless be possible alongside rapid cultural evolution. Specifically, we focus on the Baldwin effect as an evolutionary mechanism by which previously learned linguistic features might become innate through natural selection across many generations of language users. The results indicate that cultural evolution of language does not necessarily prevent functional features of language from becoming genetically fixed, thus potentially providing a particularly informative source of constraints on cross-linguistic resemblance patterns.

Assessment of the setup dependence of detector response functions for mega-voltage linear accelerators

Energy Technology Data Exchange (ETDEWEB)

Fox, Christopher; Simon, Tom; Simon, Bill; Dempsey, James F.; Kahler, Darren; Palta, Jatinder R.; Liu Chihray; Yan Guanghua [Sun Nuclear Inc., 425-A Pineda Court, Melbourne, Florida 32940 and Department of Radiation Oncology, University of Florida, P.O. Box 100385, Gainesville, Florida 32610-0385 (United States); NRE, 202 Nuclear Science Building, University of Florida, P.O. Box 118300, Gainesville, Florida 32611-8300 and Sun Nuclear Inc., 425-A Pineda Court, Melbourne, Florida 32940 (United States); Sun Nuclear Inc., 425-A Pineda Court, Melbourne, Florida 32940 (United States); ViewRay Inc., 2 Thermo Fisher Way, Oakwood Village, Ohio 44146 (United States); Department of Radiation Oncology, University of Florida, P.O. Box 100385, Gainesville, Florida 32610-0385 (United States)

2010-02-15

Purpose: Accurate modeling of beam profiles is important for precise treatment planning dosimetry. Calculated beam profiles need to precisely replicate profiles measured during machine commissioning. Finite detector size introduces perturbations into the measured profiles, which, in turn, impact the resulting modeled profiles. The authors investigate a method for extracting the unperturbed beam profiles from those measured during linear accelerator commissioning. Methods: In-plane and cross-plane data were collected for an Elekta Synergy linac at 6 MV using ionization chambers of volume 0.01, 0.04, 0.13, and 0.65 cm{sup 3} and a diode of surface area 0.64 mm{sup 2}. The detectors were orientated with the stem perpendicular to the beam and pointing away from the gantry. Profiles were measured for a 10x10 cm{sup 2} field at depths ranging from 0.8 to 25.0 cm and SSDs from 90 to 110 cm. Shaping parameters of a Gaussian response function were obtained relative to the Edge detector. The Gaussian function was deconvolved from the measured ionization chamber data. The Edge detector profile was taken as an approximation to the true profile, to which deconvolved data were compared. Data were also collected with CC13 and Edge detectors for additional fields and energies on an Elekta Synergy, Varian Trilogy, and Siemens Oncor linear accelerator and response functions obtained. Response functions were compared as a function of depth, SSD, and detector scan direction. Variations in the shaping parameter were introduced and the effect on the resulting deconvolution profiles assessed. Results: Up to 10% setup dependence in the Gaussian shaping parameter occurred, for each detector for a particular plane. This translated to less than a {+-}0.7 mm variation in the 80%-20% penumbral width. For large volume ionization chambers such as the FC65 Farmer type, where the cavity length to diameter ratio is far from 1, the scan direction produced up to a 40% difference in the shaping

Assessment of the setup dependence of detector response functions for mega-voltage linear accelerators

International Nuclear Information System (INIS)

Fox, Christopher; Simon, Tom; Simon, Bill; Dempsey, James F.; Kahler, Darren; Palta, Jatinder R.; Liu Chihray; Yan Guanghua

2010-01-01

Purpose: Accurate modeling of beam profiles is important for precise treatment planning dosimetry. Calculated beam profiles need to precisely replicate profiles measured during machine commissioning. Finite detector size introduces perturbations into the measured profiles, which, in turn, impact the resulting modeled profiles. The authors investigate a method for extracting the unperturbed beam profiles from those measured during linear accelerator commissioning. Methods: In-plane and cross-plane data were collected for an Elekta Synergy linac at 6 MV using ionization chambers of volume 0.01, 0.04, 0.13, and 0.65 cm 3 and a diode of surface area 0.64 mm 2 . The detectors were orientated with the stem perpendicular to the beam and pointing away from the gantry. Profiles were measured for a 10x10 cm 2 field at depths ranging from 0.8 to 25.0 cm and SSDs from 90 to 110 cm. Shaping parameters of a Gaussian response function were obtained relative to the Edge detector. The Gaussian function was deconvolved from the measured ionization chamber data. The Edge detector profile was taken as an approximation to the true profile, to which deconvolved data were compared. Data were also collected with CC13 and Edge detectors for additional fields and energies on an Elekta Synergy, Varian Trilogy, and Siemens Oncor linear accelerator and response functions obtained. Response functions were compared as a function of depth, SSD, and detector scan direction. Variations in the shaping parameter were introduced and the effect on the resulting deconvolution profiles assessed. Results: Up to 10% setup dependence in the Gaussian shaping parameter occurred, for each detector for a particular plane. This translated to less than a ±0.7 mm variation in the 80%-20% penumbral width. For large volume ionization chambers such as the FC65 Farmer type, where the cavity length to diameter ratio is far from 1, the scan direction produced up to a 40% difference in the shaping parameter between in

Accelerator mass spectrometry for measurement of long-lived radioisotopes.

Science.gov (United States)

Elmore, D; Phillips, F M

1987-05-01

Particle accelerators, such as those built for research in nuclear physics, can also be used together with magnetic and electrostatic mass analyzers to measure rare isotopes at very low abundance ratios. All molecular ions can be eliminated when accelerated to energies of millions of electron volts. Some atomic isobars can be eliminated with the use of negative ions; others can be separated at high energies by measuring their rate of energy loss in a detector. The long-lived radioisotopes (10)Be, (14)C,(26)A1, 36Cl, and (129)1 can now be measured in small natural samples having isotopic abundances in the range 10(-12) to 10(- 5) and as few as 10(5) atoms. In the past few years, research applications of accelerator mass spectrometry have been concentrated in the earth sciences (climatology, cosmochemistry, environmental chemistry, geochronology, glaciology, hydrology, igneous petrogenesis, minerals exploration, sedimentology, and volcanology), in anthropology and archeology (radiocarbon dating), and in physics (searches for exotic particles and measurement of halflives). In addition, accelerator mass spectrometry may become an important tool for the materials and biological sciences.

Proceedings of the 3rd workshop on ion-beam-applied biology

International Nuclear Information System (INIS)

Matsuhashi, Shinpei; Suzui, Nobuo; Ishioka, Noriko S.

2005-09-01

In order to encourage research on biological application using ion beam at TIARA, we have had the workshop on ion beam applied biology at JAERI Takasaki every year since 2002. The 3rd workshop titled 'Future development of plant research using the positron imaging method - Understanding the plant functions through visualization images-' is held this year. The main topics of this workshop are introduction of the latest studies on the assimilation and transportation of nutrients by plant using positron imaging method. Further, related technologies of the positron imaging and prospect of positron imaging for is discussed. We hope this workshop popularizes positron imaging technology for plants, accelerates cooperation between industries, universities and governmental institutes and contributes future projects of understanding of the physiological functions of plants using the positron imaging method. This workshop was held on September 29th 2004, hosted by JAERI Takasaki and cooperated by The Japan Radioisotope Association, Japanese Society of Soil Science and Plant Nutrition. The Japanese Society of Plant Physiologists, Atomic Energy Society of Japan, The Japanese Society of Nuclear and Radiochemical Science and The Ion Beam Breeding Society. There were 85 participants from not only universities and laboratories but also private company developing the environment conservation technology, so on. Highly qualified presentations were given on biological studies with ion beam, on analysis of plant functions using the positron imaging method and on supporting technology for the positron imaging monitoring. Progress in the elucidation of plant functions is expected to develop the technologies for production of safe provisions and conservation of environment with plant. The 14 of the presented papers are indexed individually. (J.P.N.)

A living foundry for Synthetic Biological Materials: A synthetic biology roadmap to new advanced materials.

Science.gov (United States)

Le Feuvre, Rosalind A; Scrutton, Nigel S

2018-06-01

Society is on the cusp of harnessing recent advances in synthetic biology to discover new bio-based products and routes to their affordable and sustainable manufacture. This is no more evident than in the discovery and manufacture of Synthetic Biological Materials , where synthetic biology has the capacity to usher in a new Materials from Biology era that will revolutionise the discovery and manufacture of innovative synthetic biological materials. These will encompass novel, smart, functionalised and hybrid materials for diverse applications whose discovery and routes to bio-production will be stimulated by the fusion of new technologies positioned across physical, digital and biological spheres. This article, which developed from an international workshop held in Manchester, United Kingdom, in 2017 [1], sets out to identify opportunities in the new materials from biology era. It considers requirements, early understanding and foresight of the challenges faced in delivering a Discovery to Manufacturing Pipeline for synthetic biological materials using synthetic biology approaches. This challenge spans the complete production cycle from intelligent and predictive design, fabrication, evaluation and production of synthetic biological materials to new ways of bringing these products to market. Pathway opportunities are identified that will help foster expertise sharing and infrastructure development to accelerate the delivery of a new generation of synthetic biological materials and the leveraging of existing investments in synthetic biology and advanced materials research to achieve this goal.

Development Biology Worksheet Oriented Accelerated Learning on Plantae and Ecosystems for 10th-Grade Senior High School Students

Science.gov (United States)

Dipuja, D. A.; Lufri, L.; Ahda, Y.

2018-04-01

The problem that found are learning outcomes student is low on the plantae and ecosystems. Students less motivated and passive learning because learning is teacher center and teaching materials not facilitate student. Therefore, it is necessary to design a worksheet oriented accelerated learning. Accelerated learning approach that can improve motivation and learning activities. The purpose of the research was to produce worksheet oriented accelerated learning on plantae and ecosystems. This research is designed as a research and development by using Plomp model, consists of the preliminary, prototyping, and assessment phase. Data was collected through questionnaires, observation sheet, test, and documentation. The results of the research was worksheet oriented accelerated learning on plantae and ecosystems is very valid.

Huntington's disease accelerates epigenetic aging of human brain and disrupts DNA methylation levels.

Science.gov (United States)

Horvath, Steve; Langfelder, Peter; Kwak, Seung; Aaronson, Jeff; Rosinski, Jim; Vogt, Thomas F; Eszes, Marika; Faull, Richard L M; Curtis, Maurice A; Waldvogel, Henry J; Choi, Oi-Wa; Tung, Spencer; Vinters, Harry V; Coppola, Giovanni; Yang, X William

2016-07-01

Age of Huntington's disease (HD) motoric onset is strongly related to the number of CAG trinucleotide repeats in the huntingtin gene, suggesting that biological tissue age plays an important role in disease etiology. Recently, a DNA methylation based biomarker of tissue age has been advanced as an epigenetic aging clock. We sought to inquire if HD is associated with an accelerated epigenetic age. DNA methylation data was generated for 475 brain samples from various brain regions of 26 HD cases and 39 controls. Overall, brain regions from HD cases exhibit a significant epigenetic age acceleration effect (p=0.0012). A multivariate model analysis suggests that HD status increases biological age by 3.2 years. Accelerated epigenetic age can be observed in specific brain regions (frontal lobe, parietal lobe, and cingulate gyrus). After excluding controls, we observe a negative correlation (r=-0.41, p=5.5×10-8) between HD gene CAG repeat length and the epigenetic age of HD brain samples. Using correlation network analysis, we identify 11 co-methylation modules with a significant association with HD status across 3 broad cortical regions. In conclusion, HD is associated with an accelerated epigenetic age of specific brain regions and more broadly with substantial changes in brain methylation levels.

Cosmic-ray shock acceleration in oblique MHD shocks

Science.gov (United States)

Webb, G. M.; Drury, L. OC.; Volk, H. J.

1986-01-01

A one-dimensional, steady-state hydrodynamical model of cosmic-ray acceleration at oblique MHD shocks is presented. Upstream of the shock the incoming thermal plasma is subject to the adverse pressure gradient of the accelerated particles, the J x B force, as well as the thermal gas pressure gradient. The efficiency of the acceleration of cosmic-rays at the shock as a function of the upstream magnetic field obliquity and upstream plasma beta is investigated. Astrophysical applications of the results are briefly discussed.

A theoretical response of the electrostatic parallel plate to constant and low-frequency accelerations

International Nuclear Information System (INIS)

Lee, Ki Bang

2009-01-01

A theoretical response of an electrostatic gap-closing actuator based on parallel plates to constant and low-frequency accelerations has been derived as a function of the applied acceleration and voltage. The nonlinear equation of motion is obtained in a dimensionless form from the fact that the inertial and damping forces are neglected at a frequency much less than the resonant frequency of the parallel plate, and thereafter the nonlinear equation is solved for the stable inter-plate gap at the acceleration and voltage. From the derived solution, the pull-in acceleration is obtained as a function of the applied voltage, and the pull-in voltage is also expressed as a function of the acceleration. The closed-form solution is validated by comparison with a numerical solution. The theoretical solution is in excellent agreement with the numerical results when the actuator is exposed to a constant acceleration as well as a low-frequency acceleration. The theoretical solution and pull-in acceleration and voltage thus provide guidance to prescribe operational constraints for devices that use the parallel plate actuator and to predict the response of the electrostatic gap-closing parallel plates to constant and low-frequency acceleration

Current-voltage relationship in the auroral particle acceleration region

Directory of Open Access Journals (Sweden)

M. Morooka

2004-11-01

Full Text Available The current-voltage relationship in the auroral particle acceleration region has been studied statistically by the Akebono (EXOS-D satellite in terms of the charge carriers of the upward field-aligned current. The Akebono satellite often observed field-aligned currents which were significantly larger than the model value predicted by Knight (1973. We compared the upward field-aligned current estimated by three different methods, and found that low-energy electrons often play an important role as additional current carriers, together with the high-energy primary electrons which are expected from Knight's relation. Such additional currents have been observed especially at high and middle altitudes of the particle acceleration region. Some particular features of electron distribution functions, such as "cylindrical distribution functions" and "electron conics", have often been observed coinciding with the additional currents. They indicated time variability of the particle acceleration region. Therefore, we have concluded that the low-energy electrons within the "forbidden" region of electron phase space in the stationary model often contribute to charge carriers of the current because of the rapid time variability of the particle acceleration region. "Cylindrical distribution functions" are expected to be found below the time-varying potential difference. We statistically examined the locations of "cylindrical distribution function", and found that their altitudes are related to the location where the additional currents have been observed. This result is consistent with the idea that the low-energy electrons can also carry significant current when the acceleration region changes in time.

A protection system for picosecond accelerator

International Nuclear Information System (INIS)

Cao Hongping; Chinese Academy of Sciences, Beijing; Chen Huanguang; Xu Ruinian; Tang Junlong; Li Deming

2006-01-01

A personnel and machine protection system for the picosecond accelerator has been built. The key of the system is to send on/off of three triggering signals which are those of electron gun, 2856 MHz and 476 MHz, respectively, to ensure the safety of users and the accelerator. This paper describes the emergencies interlocked by ADAM5511 and timing trigger processor, and some secondary functions which improve the efficiency of the protection system completed in upper layer software. (authors)

Maintenance of systemic immune functions prevents accelerated presbycusis.

Science.gov (United States)

Iwai, Hiroshi; Baba, Susumu; Omae, Mariko; Lee, Shinryu; Yamashita, Toshio; Ikehara, Susumu

2008-05-07

There is no effective therapy for progressive hearing loss such as presbycusis, the causes of which remain poorly understood because of the difficulty of separating genetic and environmental contributions. In the present study, we show that the age-related dysfunctions of the systemic immune system in an animal model of accelerated presbycusis (SAMP1, senescence-accelerated mouse P1) can be corrected by allogeneic bone marrow transplantation (BMT). We also demonstrate that this presbycusis can be prevented; BMT protects the recipients from age-related hearing impairment and the degeneration of spiral ganglion cells (SGCs) as well as the dysfunctions of T lymphocytes, which have a close relation to immune senescence. No donor cells are infiltrated to the spiral ganglia, confirming that this experimental system using BMT is connected to the systemic immune system and does not contribute to transdifferentiation or fusion by donor hematopoietic stem cells (HSCs), or to the direct maintenance of ganglion cells by locally infiltrated donor immunocompetent cells. Therefore, another procedure which attempts to prevent the age-related dysfunctions of the recipient immune system is the inoculation of syngeneic splenocytes from young donors. These mice show no development of hearing loss, compared with the recipient mice with inoculation of saline or splenocytes from old donors. Our studies on the relationship between age-related systemic immune dysfunctions and neurodegeneration mechanisms open up new avenues of treatment for presbycusis, for which there is no effective therapy.

Precise isotope analysis. Application of accelerator mass spectrometry to human sample

International Nuclear Information System (INIS)

Tokanai, Fuyuki

2016-01-01

Isotope 14 C is a radioisotope with a half-life of 5,730 years, and the measurement of its concentration makes it possible to calculate 'carbon 14 age.' This paper introduces up-to-date accelerator mass spectrometry (AMS), which is used in 14 C concentration measurement, and outlines its applied researches in pharmaceutical and medical fields. AMS technique has been applied in Europe and the United States to microdose clinical tests. In Japan, implementation foundation has been ready through the guidelines of the Ministry of Health, Labour and Welfare, five years behind Europe and the United States. Although conventional AMS measurement of 14 C required an acceleration voltage of 3 million volts or more, technological development has enabled a high accuracy of 14 C concentration measurement with the low acceleration voltage of about 400,000 volts. A sample for AMS method is graphitized, transformed to carbon ions ( 12 C-, 13 C-, and 14 C-) through negative ionization with cesium irradiation, accelerated under 450 kV, bombarded with argon gas, charge-converted to 12 C+, 13 C+, and 14 C+, and measured. Biological samples for microdose study are plasma, urine, feces, and biological tissue. Model tests showed a very good linearity between the concentrations of 14 C-containing compounds and 14 C concentrations. Applied research on microdose clinical tests is expected to increase its usability in the future, as an effective means of drug development. (A.O.)

Accuracy of accelerated cine MR imaging at 3 Tesla in longitudinal follow-up of cardiac function

International Nuclear Information System (INIS)

Sandner, Torleif A.; Huber, Armin M.; Theisen, Daniel; Reiser, Maximilian F.; Wintersperger, Bernd J.; Houck, Philip; Runge, Val M.; Sincleair, Spencer

2008-01-01

The ability of fast, parallel-imaging-based cine magnetic resonance (MR) to monitor global cardiac function in longitudinal exams at 3 Tesla was evaluated. Seventeen patients with chronic cardiac disease underwent serial cine MR imaging exams (n=3) at 3 Tesla. Data were acquired in short-axis orientation using cine steady-state free precession (SSFP) with a spatial resolution of 2.5 x 1.9 mm 2 at 45 ms temporal resolution. Multislice imaging (three slices/breath-hold) was performed using TSENSE acceleration (R=3) and standard single-slice cine (non-TSENSE) was performed at identical locations in consecutive breath-holds. End-diastolic volume (EDV), end-systolic volume (ESV), ejection fraction (EF) and myocardial mass (MM) of both cine approaches were compared for individual time-points as well as for longitudinal comparison. TSENSE-cine did not show significant differences for EDV (2.6 ml; P=.79), ESV (2.2 ml; P=0.81), EF (-0.3%; P=0.95) and MM (2.4 g; P=0.72) in comparison with non-TSENSE. Longitudinal ANOVA analysis did not reveal significant differences for any parameter, neither for non-TSENSE data (all P>0.7) nor for TSENSE data (all P>0.9). Multifactorial ANOVA showed non-significant differences (all P>0.7) at comparable data variances. Data acquisition was significantly shortened using TSENSE. Threefold accelerated multislice cine at 3 Tesla allows accurate assessment of volumetric LV data and accurate longitudinal monitoring of global LV function at a substantially shorter overall examination time. (orig.)

Accelerator physics experiments at Aladdin

International Nuclear Information System (INIS)

Chattopadhyay, S.; Cornacchia, M.; Jackson, A.; Zisman, M.S.

1985-07-01

The Aladdin accelerator is a 1 GeV synchrotron light source located at the University of Wisconsin. The results of experimental studies of the Aladdin accelerator are described. The primary purpose of the experiments reported was to investigate reported anomalies in the behavior of the linear lattice, particularly in the vertical plane. A second goal was to estimate the ring broadband impedance. Experimental observations and interpretation of the linear properties of the Aladdin ring are described, including the beta function and dispersion measurements. Two experiments are described to measure the ring impedance, the first a measurement of the parasitic mode loss, and the second a measurement of the beam transfer function. Measurements of the longitudinal and transverse emittance at 100 and 200 MeV are described and compared with predictions. 10 refs., 24 figs., 2 tabs

FPGA Acceleration of the phylogenetic likelihood function for Bayesian MCMC inference methods

Directory of Open Access Journals (Sweden)

Bakos Jason D

2010-04-01

Full Text Available Abstract Background Likelihood (ML-based phylogenetic inference has become a popular method for estimating the evolutionary relationships among species based on genomic sequence data. This method is used in applications such as RAxML, GARLI, MrBayes, PAML, and PAUP. The Phylogenetic Likelihood Function (PLF is an important kernel computation for this method. The PLF consists of a loop with no conditional behavior or dependencies between iterations. As such it contains a high potential for exploiting parallelism using micro-architectural techniques. In this paper, we describe a technique for mapping the PLF and supporting logic onto a Field Programmable Gate Array (FPGA-based co-processor. By leveraging the FPGA's on-chip DSP modules and the high-bandwidth local memory attached to the FPGA, the resultant co-processor can accelerate ML-based methods and outperform state-of-the-art multi-core processors. Results We use the MrBayes 3 tool as a framework for designing our co-processor. For large datasets, we estimate that our accelerated MrBayes, if run on a current-generation FPGA, achieves a 10× speedup relative to software running on a state-of-the-art server-class microprocessor. The FPGA-based implementation achieves its performance by deeply pipelining the likelihood computations, performing multiple floating-point operations in parallel, and through a natural log approximation that is chosen specifically to leverage a deeply pipelined custom architecture. Conclusions Heterogeneous computing, which combines general-purpose processors with special-purpose co-processors such as FPGAs and GPUs, is a promising approach for high-performance phylogeny inference as shown by the growing body of literature in this field. FPGAs in particular are well-suited for this task because of their low power consumption as compared to many-core processors and Graphics Processor Units (GPUs 1.

FADTTSter: accelerating hypothesis testing with functional analysis of diffusion tensor tract statistics

Science.gov (United States)

Noel, Jean; Prieto, Juan C.; Styner, Martin

2017-03-01

Functional Analysis of Diffusion Tensor Tract Statistics (FADTTS) is a toolbox for analysis of white matter (WM) fiber tracts. It allows associating diffusion properties along major WM bundles with a set of covariates of interest, such as age, diagnostic status and gender, and the structure of the variability of these WM tract properties. However, to use this toolbox, a user must have an intermediate knowledge in scripting languages (MATLAB). FADTTSter was created to overcome this issue and make the statistical analysis accessible to any non-technical researcher. FADTTSter is actively being used by researchers at the University of North Carolina. FADTTSter guides non-technical users through a series of steps including quality control of subjects and fibers in order to setup the necessary parameters to run FADTTS. Additionally, FADTTSter implements interactive charts for FADTTS' outputs. This interactive chart enhances the researcher experience and facilitates the analysis of the results. FADTTSter's motivation is to improve usability and provide a new analysis tool to the community that complements FADTTS. Ultimately, by enabling FADTTS to a broader audience, FADTTSter seeks to accelerate hypothesis testing in neuroimaging studies involving heterogeneous clinical data and diffusion tensor imaging. This work is submitted to the Biomedical Applications in Molecular, Structural, and Functional Imaging conference. The source code of this application is available in NITRC.

A living foundry for Synthetic Biological Materials: A synthetic biology roadmap to new advanced materials

Directory of Open Access Journals (Sweden)

Rosalind A. Le Feuvre

2018-06-01

Full Text Available Society is on the cusp of harnessing recent advances in synthetic biology to discover new bio-based products and routes to their affordable and sustainable manufacture. This is no more evident than in the discovery and manufacture of Synthetic Biological Materials, where synthetic biology has the capacity to usher in a new Materials from Biology era that will revolutionise the discovery and manufacture of innovative synthetic biological materials. These will encompass novel, smart, functionalised and hybrid materials for diverse applications whose discovery and routes to bio-production will be stimulated by the fusion of new technologies positioned across physical, digital and biological spheres. This article, which developed from an international workshop held in Manchester, United Kingdom, in 2017 [1], sets out to identify opportunities in the new materials from biology era. It considers requirements, early understanding and foresight of the challenges faced in delivering a Discovery to Manufacturing Pipeline for synthetic biological materials using synthetic biology approaches. This challenge spans the complete production cycle from intelligent and predictive design, fabrication, evaluation and production of synthetic biological materials to new ways of bringing these products to market. Pathway opportunities are identified that will help foster expertise sharing and infrastructure development to accelerate the delivery of a new generation of synthetic biological materials and the leveraging of existing investments in synthetic biology and advanced materials research to achieve this goal. Keywords: Synthetic biology, Materials, Biological materials, Biomaterials, Advanced materials

A magnetorheological haptic cue accelerator for manual transmission vehicles

International Nuclear Information System (INIS)

Han, Young-Min; Noh, Kyung-Wook; Choi, Seung-Bok; Lee, Yang-Sub

2010-01-01

This paper proposes a new haptic cue function for manual transmission vehicles to achieve optimal gear shifting. This function is implemented on the accelerator pedal by utilizing a magnetorheological (MR) brake mechanism. By combining the haptic cue function with the accelerator pedal, the proposed haptic cue device can transmit the optimal moment of gear shifting for manual transmission to a driver without requiring the driver's visual attention. As a first step to achieve this goal, a MR fluid-based haptic device is devised to enable rotary motion of the accelerator pedal. Taking into account spatial limitations, the design parameters are optimally determined using finite element analysis to maximize the relative control torque. The proposed haptic cue device is then manufactured and its field-dependent torque and time response are experimentally evaluated. Then the manufactured MR haptic cue device is integrated with the accelerator pedal. A simple virtual vehicle emulating the operation of the engine of a passenger vehicle is constructed and put into communication with the haptic cue device. A feed-forward torque control algorithm for the haptic cue is formulated and control performances are experimentally evaluated and presented in the time domain

The effect of acceleration on turbulent entrainment

International Nuclear Information System (INIS)

Breidenthal, Robert E

2008-01-01

A new class of self-similar turbulent flows is proposed, which exhibits dramatically reduced entrainment rates. Under strong acceleration, the rotation period of the large-scale vortices is forced to decrease linearly in time. In ordinary unforced turbulence, the rotation period always increases linearly with time, at least in the mean. However, by imposing an exponential acceleration on the flow, the vortex rotation period is forced to become the e-folding timescale of the acceleration. If the e-folding timescale itself decreases linearly in time, the forcing is 'super-exponential', characterized by an acceleration parameter α. Based on dimensional and heuristic arguments, a model suggests that the dissipation rate is an exponential function of α and the dimensions of the conserved quantity of the flow. Acceleration decreases the dissipation and entrainment rates in all canonical laboratory flows except for Rayleigh-Taylor. Experiments of exponential jets and super-exponential transverse jets are in accord with the model. As noted by Johari, acceleration is the only known means of affecting the entrainment rate of the far-field jet. Numerical simulations of Rayleigh-Taylor flow by Cook and Greenough are also consistent. In the limit of large acceleration, vortices do not move far before their rotation period changes substantially. In this sense, extreme acceleration corresponds to stationary vortices.

Importance of N-Glycosylation on CD147 for Its Biological Functions

Science.gov (United States)

Bai, Yang; Huang, Wan; Ma, Li-Tian; Jiang, Jian-Li; Chen, Zhi-Nan

2014-01-01

Glycosylation of glycoproteins is one of many molecular changes that accompany malignant transformation. Post-translational modifications of proteins are closely associated with the adhesion, invasion, and metastasis of tumor cells. CD147, a tumor-associated antigen that is highly expressed on the cell surface of various tumors, is a potential target for cancer diagnosis and therapy. A significant biochemical property of CD147 is its high level of glycosylation. Studies on the structure and function of CD147 glycosylation provide valuable clues to the development of targeted therapies for cancer. Here, we review current understanding of the glycosylation characteristics of CD147 and the glycosyltransferases involved in the biosynthesis of CD147 N-glycans. Finally, we discuss proteins regulating CD147 glycosylation and the biological functions of CD147 glycosylation. PMID:24739808

Importance of N-Glycosylation on CD147 for Its Biological Functions

Directory of Open Access Journals (Sweden)

Yang Bai

2014-04-01

Full Text Available Glycosylation of glycoproteins is one of many molecular changes that accompany malignant transformation. Post-translational modifications of proteins are closely associated with the adhesion, invasion, and metastasis of tumor cells. CD147, a tumor-associated antigen that is highly expressed on the cell surface of various tumors, is a potential target for cancer diagnosis and therapy. A significant biochemical property of CD147 is its high level of glycosylation. Studies on the structure and function of CD147 glycosylation provide valuable clues to the development of targeted therapies for cancer. Here, we review current understanding of the glycosylation characteristics of CD147 and the glycosyltransferases involved in the biosynthesis of CD147 N-glycans. Finally, we discuss proteins regulating CD147 glycosylation and the biological functions of CD147 glycosylation.

Functionalized gold nanoparticle supported sensory mechanisms applied in detection of chemical and biological threat agents: A review

International Nuclear Information System (INIS)

Upadhyayula, Venkata K.K.

2012-01-01

Highlights: ► Smart sensors are needed for detection of chemical and biological threat agents. ► Smart sensors detect analytes with rapid speed, high sensitivity and selectivity. ► Functionalized gold nanoparticles (GNPs) can potentially smart sense threat agents. ► Functionalized GNPs support multiple analytical methods for sensing threat agents. ► Threat agents of all types can be detected using functionalized GNPs. - Abstract: There is a great necessity for development of novel sensory concepts supportive of smart sensing capabilities in defense and homeland security applications for detection of chemical and biological threat agents. A smart sensor is a detection device that can exhibit important features such as speed, sensitivity, selectivity, portability, and more importantly, simplicity in identifying a target analyte. Emerging nanomaterial based sensors, particularly those developed by utilizing functionalized gold nanoparticles (GNPs) as a sensing component potentially offer many desirable features needed for threat agent detection. The sensitiveness of physical properties expressed by GNPs, e.g. color, surface plasmon resonance, electrical conductivity and binding affinity are significantly enhanced when they are subjected to functionalization with an appropriate metal, organic or biomolecular functional groups. This sensitive nature of functionalized GNPs can be potentially exploited in the design of threat agent detection devices with smart sensing capabilities. In the presence of a target analyte (i.e., a chemical or biological threat agent) a change proportional to concentration of the analyte is observed, which can be measured either by colorimetric, fluorimetric, electrochemical or spectroscopic means. This article provides a review of how functionally modified gold colloids are applied in the detection of a broad range of threat agents, including radioactive substances, explosive compounds, chemical warfare agents, biotoxins, and

Functionalized gold nanoparticle supported sensory mechanisms applied in detection of chemical and biological threat agents: A review

Energy Technology Data Exchange (ETDEWEB)

Upadhyayula, Venkata K.K., E-mail: Upadhyayula.Venkata@epa.gov [Oak Ridge Institute of Science and Education (ORISE), MC-100-44, PO Box 117, Oak Ridge, TN 37831 (United States)

2012-02-17

Highlights: Black-Right-Pointing-Pointer Smart sensors are needed for detection of chemical and biological threat agents. Black-Right-Pointing-Pointer Smart sensors detect analytes with rapid speed, high sensitivity and selectivity. Black-Right-Pointing-Pointer Functionalized gold nanoparticles (GNPs) can potentially smart sense threat agents. Black-Right-Pointing-Pointer Functionalized GNPs support multiple analytical methods for sensing threat agents. Black-Right-Pointing-Pointer Threat agents of all types can be detected using functionalized GNPs. - Abstract: There is a great necessity for development of novel sensory concepts supportive of smart sensing capabilities in defense and homeland security applications for detection of chemical and biological threat agents. A smart sensor is a detection device that can exhibit important features such as speed, sensitivity, selectivity, portability, and more importantly, simplicity in identifying a target analyte. Emerging nanomaterial based sensors, particularly those developed by utilizing functionalized gold nanoparticles (GNPs) as a sensing component potentially offer many desirable features needed for threat agent detection. The sensitiveness of physical properties expressed by GNPs, e.g. color, surface plasmon resonance, electrical conductivity and binding affinity are significantly enhanced when they are subjected to functionalization with an appropriate metal, organic or biomolecular functional groups. This sensitive nature of functionalized GNPs can be potentially exploited in the design of threat agent detection devices with smart sensing capabilities. In the presence of a target analyte (i.e., a chemical or biological threat agent) a change proportional to concentration of the analyte is observed, which can be measured either by colorimetric, fluorimetric, electrochemical or spectroscopic means. This article provides a review of how functionally modified gold colloids are applied in the detection of a broad

A portable accelerator control toolkit

Energy Technology Data Exchange (ETDEWEB)

Watson, W.A. III

1997-06-01

In recent years, the expense of creating good control software has led to a number of collaborative efforts among laboratories to share this cost. The EPICS collaboration is a particularly successful example of this trend. More recently another collaborative effort has addressed the need for sophisticated high level software, including model driven accelerator controls. This work builds upon the CDEV (Common DEVice) software framework, which provides a generic abstraction of a control system, and maps that abstraction onto a number of site-specific control systems including EPICS, the SLAC control system, CERN/PS and others. In principle, it is now possible to create portable accelerator control applications which have no knowledge of the underlying and site-specific control system. Applications based on CDEV now provide a growing suite of tools for accelerator operations, including general purpose displays, an on-line accelerator model, beamline steering, machine status displays incorporating both hardware and model information (such as beam positions overlaid with beta functions) and more. A survey of CDEV compatible portable applications will be presented, as well as plans for future development.

A portable accelerator control toolkit

International Nuclear Information System (INIS)

Watson, W.A. III.

1997-01-01

In recent years, the expense of creating good control software has led to a number of collaborative efforts among laboratories to share this cost. The EPICS collaboration is a particularly successful example of this trend. More recently another collaborative effort has addressed the need for sophisticated high level software, including model driven accelerator controls. This work builds upon the CDEV (Common DEVice) software framework, which provides a generic abstraction of a control system, and maps that abstraction onto a number of site-specific control systems including EPICS, the SLAC control system, CERN/PS and others. In principle, it is now possible to create portable accelerator control applications which have no knowledge of the underlying and site-specific control system. Applications based on CDEV now provide a growing suite of tools for accelerator operations, including general purpose displays, an on-line accelerator model, beamline steering, machine status displays incorporating both hardware and model information (such as beam positions overlaid with beta functions) and more. A survey of CDEV compatible portable applications will be presented, as well as plans for future development

Biological response to purification and acid functionalization of carbon nanotubes

Science.gov (United States)

Figarol, Agathe; Pourchez, Jérémie; Boudard, Delphine; Forest, Valérie; Tulliani, Jean-Marc; Lecompte, Jean-Pierre; Cottier, Michèle; Bernache-Assollant, Didier; Grosseau, Philippe

2014-07-01

Acid functionalization has been considered as an easy way to enhance the dispersion and biodegradation of carbon nanotubes (CNT). However, inconsistencies between toxicity studies of acid functionalized CNT remain unexplained. This could be due to a joint effect of the main physicochemical modifications resulting from an acid functionalization: addition of surface acid groups and purification from catalytic metallic impurities. In this study, the impact on CNT biotoxicity of these two physiochemical features was assessed separately. The in vitro biological response of RAW 264.7 macrophages was evaluated after exposure to 15-240 µg mL-1 of two types of multi-walled CNT. For each type of CNT (small: 20 nm diameter, and big: 90 nm diameter), three different surface chemical properties were studied (total of six CNT samples): pristine, acid functionalized and desorbed. Desorbed CNT were purified by the acid functionalization but presented a very low amount of surface acid groups due to a thermal treatment under vacuum. A Janus effect of acid functionalization with two opposite impacts is highlighted. The CNT purification decreased the overall toxicity, while the surface acid groups intensified it when present at a specific threshold. These acid groups especially amplified the pro-inflammatory response. The threshold mechanism which seemed to regulate the impact of acid groups should be further studied to determine its value and potential link to the other physicochemical state of the CNT. The results suggest that, for a safer-design approach, the benefit-risk balance of an acid functionalization has to be considered, depending on the CNT primary state of purification. Further research should be conducted in this direction.

An Accelerator Control Middle Layer Using MATLAB

International Nuclear Information System (INIS)

Portmann, Gregory J.; Corbett, Jeff; Terebilo, Andrei

2005-01-01

Matlab is a matrix manipulation language originally developed to be a convenient language for using the LINPACK and EISPACK libraries. What makes Matlab so appealing for accelerator physics is the combination of a matrix oriented programming language, an active workspace for system variables, powerful graphics capability, built-in math libraries, and platform independence. A number of software toolboxes for accelerators have been written in Matlab--the Accelerator Toolbox (AT) for machine simulations, LOCO for accelerator calibration, Matlab Channel Access Toolbox (MCA) for EPICS connections, and the Middle Layer. This paper will describe the ''middle layer'' software toolbox that resides between the high-level control applications and the low-level accelerator control system. This software was a collaborative effort between ALS (LBNL) and SPEAR3 (SSRL) but easily ports to other machines. Five accelerators presently use this software. The high-level Middle Layer functionality includes energy ramp, configuration control (save/restore), global orbit correction, local photon beam steering, insertion device compensation, beam-based alignment, tune correction, response matrix measurement, and script-based programs for machine physics studies

STAT6: its role in interleukin 4-mediated biological functions.

Science.gov (United States)

Takeda, K; Kishimoto, T; Akira, S

1997-05-01

Interleukin (IL) 4 is known to be a cytokine which plays a central role in the regulation of immune response. Studies on cytokine signal transduction have clarified the mechanism by which IL4 exerts its functions. Two cytoplasmic proteins, signal transducer and activator of transcription (STAT) 6 and IL4-induced phosphotyrosine substrate/insulin receptor substrate 2 (4PS/IRS2), are activated in IL4 signal transduction. Recent studies from STAT6-deficient mice have revealed the essential role of STAT6 in IL4-mediated biological actions. In addition, STAT6 has also been demonstrated to be important for the functions mediated by IL13, which is related to IL4. IL4 and IL13 have been shown to induce the production of IgE, which is a major mediator in an allergic response. These findings indicate that STAT6 activation is involved in IL4- and IL13-mediated disorders such as allergy.

Aging in a Relativistic Biological Space-Time

Directory of Open Access Journals (Sweden)

Davide Maestrini

2018-05-01

Full Text Available Here we present a theoretical and mathematical perspective on the process of aging. We extend the concepts of physical space and time to an abstract, mathematically-defined space, which we associate with a concept of “biological space-time” in which biological dynamics may be represented. We hypothesize that biological dynamics, represented as trajectories in biological space-time, may be used to model and study different rates of biological aging. As a consequence of this hypothesis, we show how dilation or contraction of time analogous to relativistic corrections of physical time resulting from accelerated or decelerated biological dynamics may be used to study precipitous or protracted aging. We show specific examples of how these principles may be used to model different rates of aging, with an emphasis on cancer in aging. We discuss how this theory may be tested or falsified, as well as novel concepts and implications of this theory that may improve our interpretation of biological aging.

Extensions of MAD Version 8 to Include Beam Acceleration

International Nuclear Information System (INIS)

Raubenheimer, Tor O

2000-01-01

In this paper, the authors describe modifications to MAD version 8.23 to include linear accelerator cavities and beam acceleration. An additional energy variable has been added which is modified as the beam passes through LCAV elements (linear accelerator cavities) and can be used as a constraint in matching commands. The calculation of the beta functions and phase advance is consistent with that in other codes that treat acceleration such as TRANSPORT or DIMAD. These modifications allow this version of MAD to be used for the design and modeling of linacs and the authors present examples from the Next Linear Collider design as well as a muon acceleration complex. The code is available from CERN or SLAC

The functionality of biological knowledge in the workplace. Integrating school and workplace learning about reproduction

NARCIS (Netherlands)

Mazereeuw, M.

2013-01-01

This thesis reports on a design research project about a learning, supervising and teaching strategy to enable students in agricultural preparatory vocational secondary education (VMBO) to recognize the functionality of biological knowledge of reproduction in work placement sites. Although

Next-generation mammalian genetics toward organism-level systems biology.

Science.gov (United States)

Susaki, Etsuo A; Ukai, Hideki; Ueda, Hiroki R

2017-01-01

Organism-level systems biology in mammals aims to identify, analyze, control, and design molecular and cellular networks executing various biological functions in mammals. In particular, system-level identification and analysis of molecular and cellular networks can be accelerated by next-generation mammalian genetics. Mammalian genetics without crossing, where all production and phenotyping studies of genome-edited animals are completed within a single generation drastically reduce the time, space, and effort of conducting the systems research. Next-generation mammalian genetics is based on recent technological advancements in genome editing and developmental engineering. The process begins with introduction of double-strand breaks into genomic DNA by using site-specific endonucleases, which results in highly efficient genome editing in mammalian zygotes or embryonic stem cells. By using nuclease-mediated genome editing in zygotes, or ~100% embryonic stem cell-derived mouse technology, whole-body knock-out and knock-in mice can be produced within a single generation. These emerging technologies allow us to produce multiple knock-out or knock-in strains in high-throughput manner. In this review, we discuss the basic concepts and related technologies as well as current challenges and future opportunities for next-generation mammalian genetics in organism-level systems biology.

Spatial Structures and Regulation in Biological Systems

DEFF Research Database (Denmark)

Yde, Pernille

, and the other is the spatial regulation of biological systems, here related to different aspects of the inflammatory response. All systems are studied using computational modelling and mathematical analysis. The first part of the thesis explores different protein aggregation scenarios. In Chapter 1, we consider...... a previously studied and very general aggregation model describing frangible linear filaments. This model is especially relevant for the growth of amyloid fibres, that have been related to a number of serious human diseases, and which are known to grow in an accelerated self-enhanced manner.We derive...... model of the tissue and show how coupled cells are able to function as an excitable medium and propagate waves of high cytokine concentration through the tissue. If the internal regulation in the cells is over-productive, the model predicts a continuous amplification of cytokines, which spans the entire...

Systems Biology and Stem Cell Pluripotency

DEFF Research Database (Denmark)

Mashayekhi, Kaveh; Hall, Vanessa Jane; Freude, Kristine

2016-01-01

Recent breakthroughs in stem cell biology have accelerated research in the area of regenerative medicine. Over the past years, it has become possible to derive patient-specific stem cells which can be used to generate different cell populations for potential cell therapy. Systems biological...... modeling of stem cell pluripotency and differentiation have largely been based on prior knowledge of signaling pathways, gene regulatory networks, and epigenetic factors. However, there is a great need to extend the complexity of the modeling and to integrate different types of data, which would further...... improve systems biology and its uses in the field. In this chapter, we first give a general background on stem cell biology and regenerative medicine. Stem cell potency is introduced together with the hierarchy of stem cells ranging from pluripotent embryonic stem cells (ESCs) and induced pluripotent stem...

SIS: an accelerator installation for heavy ions of high energy

International Nuclear Information System (INIS)

The two major sections of the report cover the scientific experimental program and the accelerator installation. Topics covered in the first include: heavy ion physics in the medium energy region; nuclear physics at relativistic energies; atomic physics loss and capture cross sections for electrons; spectroscopy of few-electron systems; atomic collision processes; biological experiments; nuclear track techniques in biology; and experiments with protons and secondary radiation. The second includes: concept for the total installation; technical description of the SIS 12; technical description of the SIS 100; status of the UNILAC injector; development options for the SIS installations; properties of the heavy ion beam; and structural work and technical supply provisions. In this SIS project proposal, an accelerator installation based on two synchrotrons is described with which atomic nuclei up to uranium can be accelerated to energies of more than 10 GeV/μ. With the SIS 12, which is the name of the first stage, heavy ion physics at intermediate energies can be pursued up to 500 MeV/μ. The second stage, a larger synchrotron, the SIS 100, has a diameter of 250 m. With this device, it is proposed to open up the domain of relativistic heavy ion physics up to 14 GeV/μ (for intermediate mass particles) and 10 GeV/μ (for uranium)

Heuristic Strategies in Systems Biology

Directory of Open Access Journals (Sweden)

Fridolin Gross

2016-06-01

Full Text Available Systems biology is sometimes presented as providing a superior approach to the problem of biological complexity. Its use of ‘unbiased’ methods and formal quantitative tools might lead to the impression that the human factor is effectively eliminated. However, a closer look reveals that this impression is misguided. Systems biologists cannot simply assemble molecular information and compute biological behavior. Instead, systems biology’s main contribution is to accelerate the discovery of mechanisms by applying models as heuristic tools. These models rely on a variety of idealizing and simplifying assumptions in order to be efficient for this purpose. The strategies of systems biologists are similar to those of experimentalists in that they attempt to reduce the complexity of the discovery process. Analyzing and comparing these strategies, or ‘heuristics’, reveals the importance of the human factor in computational approaches and helps to situate systems biology within the epistemic landscape of the life sciences.

Late time solution for interacting scalar in accelerating spaces

Energy Technology Data Exchange (ETDEWEB)

Prokopec, Tomislav, E-mail: t.prokopec@uu.nl [Institute for Theoretical Physics, Spinoza Institute and EMME$\\Phi$, Utrecht University, Postbus 80.195, Utrecht, 3508 TD The Netherlands (Netherlands)

2015-11-01

We consider stochastic inflation in an interacting scalar field in spatially homogeneous accelerating space-times with a constant principal slow roll parameter ε. We show that, if the scalar potential is scale invariant (which is the case when scalar contains quartic self-interaction and couples non-minimally to gravity), the late-time solution on accelerating FLRW spaces can be described by a probability distribution function (PDF) ρ which is a function of φ/H only, where φ=φ( x-vector ) is the scalar field and H=H(t) denotes the Hubble parameter. We give explicit late-time solutions for ρarrow ρ{sub ∞}(φ/H), and thereby find the order ε corrections to the Starobinsky-Yokoyama result. This PDF can then be used to calculate e.g. various n-point functions of the (self-interacting) scalar field, which are valid at late times in arbitrary accelerating space-times with ε= constant.

Accelerating Climate Simulations Through Hybrid Computing

Science.gov (United States)

Zhou, Shujia; Sinno, Scott; Cruz, Carlos; Purcell, Mark

2009-01-01

Unconventional multi-core processors (e.g., IBM Cell B/E and NYIDIDA GPU) have emerged as accelerators in climate simulation. However, climate models typically run on parallel computers with conventional processors (e.g., Intel and AMD) using MPI. Connecting accelerators to this architecture efficiently and easily becomes a critical issue. When using MPI for connection, we identified two challenges: (1) identical MPI implementation is required in both systems, and; (2) existing MPI code must be modified to accommodate the accelerators. In response, we have extended and deployed IBM Dynamic Application Virtualization (DAV) in a hybrid computing prototype system (one blade with two Intel quad-core processors, two IBM QS22 Cell blades, connected with Infiniband), allowing for seamlessly offloading compute-intensive functions to remote, heterogeneous accelerators in a scalable, load-balanced manner. Currently, a climate solar radiation model running with multiple MPI processes has been offloaded to multiple Cell blades with approx.10% network overhead.

Major depressive disorder mediates accelerated aging in rats subjected to chronic mild stress.

Science.gov (United States)

Xie, Xiaoxian; Chen, Yangyang; Ma, Lingyan; Shen, Qichen; Huang, Liangfeng; Zhao, Binggong; Wu, Tao; Fu, Zhengwei

2017-06-30

Major depressive disorder (MDD) has a complex etiology and is characterized by a change in mood and psychophysiological state. MDD has been shown to mediate accelerated biological aging in patients, although the underlying mechanism is not well understood. In the present study, we used a chronic mild stress (CMS) paradigm to induce anhedonia, one of the main symptoms of MDD. CMS induced depression-like symptoms in rats, including reduced sucrose preference and increased immobility time in the forced swim test. Moreover, stressed rats travelled a shorter total distance, had fewer grid line crossings, and spent less time in the outer zone in the open field test than controls. CMS altered the levels of 5-hydroxytryptophan, dopamine, and corticosterone in the serum and hippocampus (P<0.05); these rats also exhibited impaired liver function, decreased telomerase activity, and telomere shortening, which was associated with increased oxidative damage along with decreased superoxide dismutase and glutathione reductase activities. Mitochondria in CMS-treated rats showed ultrastructural damage as well as reduced DNA content and integrity. These findings provide physiological and cellular evidence that the MDD can mediate accelerated aging in rats. Copyright © 2017 Elsevier B.V. All rights reserved.

Single bunch beam loading on the SLAC three-kilometer accelerator

International Nuclear Information System (INIS)

Koontz, R.F.; Loew, G.A.; Miller, R.H.; Wilson, P.B.

1977-03-01

Since the report on single bunch beam loading experiments at SLAC at the 1975 Particle Accelerator Conference, it has been possible to obtain a much better understanding and agreement of theoretical and experimental results related to this problem. These improvements were made possible by two developments: the generation of a ''wake-field'' function for the SLAC 3-km slow-wave structure and the use of this function to calculate single bunch energy spectra. The wake-field function which gives the time decay of the fields generated by the passage of a delta-function beam was derived by summing all the TM cylindrically symmetrical modes of an equivalent accelerator cavity. By multiplying this wake-field function by a measured bunch density function and integrating along the bunch, it is possible to calculate the energy of each electron in the bunch. This in turn enables one to predict the energy spectrum for any given phase angle of the bunch with respect to the crest of the rf accelerating wave. Agreement between these calculations and experimental measurements is very good. These results are presented, and the possible sources of some of the remaining discrepancies are discussed

Single bunch beam loading on the SLAC three-kilometer accelerator

International Nuclear Information System (INIS)

Koontz, R.F.; Loew, G.A.; Miller, R.H.; Wilson, P.B.

1977-01-01

Since the report on single bunch beam loading experiments at SLAC at the 1975 Particle Accelerator Conference, it has been possible to obtain a much better understanding and agreement of theoretical and experimental results related to this problem. These improvements have been made possible by two developments: the generation of a ''wake-field'' function for the SLAC 3-km slow-wave structure and the use of this function to calculate single bunch energy spectra. The wake-field function which gives the time decay of the fields generated by the passage of a delta-function beam was derived by summing all the TM cylindrically symmetrical modes of an equivalent accelerator cavity. By multiplying this wake-field function by a measured bunch density function and integrating along the bunch, it is possible to calculate the energy of each electron in the bunch. This in turn enables one to predict the energy spectrum for any given phase angle of the bunch with respect to the crest of the rf accelerating wave. Agreement between these calculations and experimental measurements is very good. These results are presented and the possible sources of some of the remaining discrepancies are discussed

Plasma accelerators

International Nuclear Information System (INIS)

Bingham, R.; Angelis, U. de; Johnston, T.W.

1991-01-01

Recently attention has focused on charged particle acceleration in a plasma by a fast, large amplitude, longitudinal electron plasma wave. The plasma beat wave and plasma wakefield accelerators are two efficient ways of producing ultra-high accelerating gradients. Starting with the plasma beat wave accelerator (PBWA) and laser wakefield accelerator (LWFA) schemes and the plasma wakefield accelerator (PWFA) steady progress has been made in theory, simulations and experiments. Computations are presented for the study of LWFA. (author)

Genome-scale biological models for industrial microbial systems.

Science.gov (United States)

Xu, Nan; Ye, Chao; Liu, Liming

2018-04-01

The primary aims and challenges associated with microbial fermentation include achieving faster cell growth, higher productivity, and more robust production processes. Genome-scale biological models, predicting the formation of an interaction among genetic materials, enzymes, and metabolites, constitute a systematic and comprehensive platform to analyze and optimize the microbial growth and production of biological products. Genome-scale biological models can help optimize microbial growth-associated traits by simulating biomass formation, predicting growth rates, and identifying the requirements for cell growth. With regard to microbial product biosynthesis, genome-scale biological models can be used to design product biosynthetic pathways, accelerate production efficiency, and reduce metabolic side effects, leading to improved production performance. The present review discusses the development of microbial genome-scale biological models since their emergence and emphasizes their pertinent application in improving industrial microbial fermentation of biological products.

PANTHER version 6: protein sequence and function evolution data with expanded representation of biological pathways

OpenAIRE

Mi, Huaiyu; Guo, Nan; Kejariwal, Anish; Thomas, Paul D.

2006-01-01

PANTHER is a freely available, comprehensive software system for relating protein sequence evolution to the evolution of specific protein functions and biological roles. Since 2005, there have been three main improvements to PANTHER. First, the sequences used to create evolutionary trees are carefully selected to provide coverage of phylogenetic as well as functional information. Second, PANTHER is now a member of the InterPro Consortium, and the PANTHER hidden markov Models (HMMs) are distri...

Bomb pulse biology

Energy Technology Data Exchange (ETDEWEB)

Falso, Miranda J. Sarachine [Center for Accelerator Mass Spectrometry, Mail Stop L-397, Lawrence Livermore National Laboratory, P.O. Box 808, Livermore, CA 94551 (United States); Buchholz, Bruce A., E-mail: buchholz2@llnl.gov [Center for Accelerator Mass Spectrometry, Mail Stop L-397, Lawrence Livermore National Laboratory, P.O. Box 808, Livermore, CA 94551 (United States)

2013-01-15

The past decade has seen an explosion in use of the {sup 14}C bomb pulse to do fundamental cell biology. Studies in the 1960s used decay counting to measure tissue turnover when the atmospheric {sup 14}C/C concentration was changing rapidly. Today bulk tissue measurements are of marginal interest since most of the carbon in the tissue resides in proteins, lipids and carbohydrates that turn over rapidly. Specific cell types with specialized functions are the focus of cell turnover investigations. Tissue samples need to be fresh or frozen. Fixed or preserved samples contain petroleum-derived carbon that has not been successfully removed. Cell or nuclear surface markers are used to sort specific cell types, typically by fluorescence-activated cell sorting (FACS). Specific biomolecules need to be isolated with high purity and accelerator mass spectrometry (AMS) measurements must accommodate samples that generally contain less than 40 {mu}g of carbon. Furthermore, all separations must not add carbon to the sample. Independent means such as UV absorbance must be used to confirm molecule purity. Approaches for separating specific proteins and DNA and combating contamination of undesired molecules are described.

Towards MRI-guided linear accelerator control: gating on an MRI accelerator.

Science.gov (United States)

Crijns, S P M; Kok, J G M; Lagendijk, J J W; Raaymakers, B W

2011-08-07

To boost the possibilities of image guidance in radiotherapy by providing images with superior soft-tissue contrast during treatment, we pursue diagnostic quality MRI functionality integrated with a linear accelerator. Large respiration-induced semi-periodic target excursions hamper treatment of cancer of the abdominal organs. Methods to compensate in real time for such motion are gating and tracking. These strategies are most effective in cases where anatomic motion can be visualized directly, which supports the use of an integrated MRI accelerator. We establish here an infrastructure needed to realize gated radiation delivery based on MR feedback and demonstrate its potential as a first step towards more advanced image guidance techniques. The position of a phantom subjected to one-dimensional periodic translation is tracked with the MR scanner. Real-time communication with the MR scanner and control of the radiation beam are established. Based on the time-resolved position of the phantom, gated radiation delivery to the phantom is realized. Dose distributions for dynamic delivery conditions with varying gating windows are recorded on gafchromic film. The similarity between dynamically and statically obtained dose profiles gradually increases as the gating window is decreased. With gating windows of 5 mm, we obtain sharp dose profiles. We validate our gating implementation by comparing measured dose profiles to theoretical profiles calculated using the knowledge of the imposed motion pattern. Excellent correspondence is observed. At the same time, we show that real-time on-line reconstruction of the accumulated dose can be performed using time-resolved target position information. This facilitates plan adaptation not only on a fraction-to-fraction scale but also during one fraction, which is especially valuable in highly accelerated treatment strategies. With the currently established framework and upcoming improvements to our prototype-integrated MRI accelerator

Acceleration of O+ from the cusp to the plasma sheet

Science.gov (United States)

Liao, J.; Kistler, L. M.; Mouikis, C. G.; Klecker, B.; Dandouras, I.

2015-02-01

Heavy ions from the ionosphere that are accelerated in the cusp/cleft have been identified as a direct source for the hot plasma in the plasma sheet. However, the details of the acceleration and transport that transforms the originally cold ions into the hot plasma sheet population are not fully understood. The polar orbit of the Cluster satellites covers the main transport path of the O+ from the cusp to the plasma sheet, so Cluster is ideal for tracking its velocity changes. However, because the cusp outflow is dispersed according to its velocity as it is transported to the tail, due to the velocity filter effect, the observed changes in beam velocity over the Cluster orbit may simply be the result of the spacecraft accessing different spatial regions and not necessarily evidence of acceleration. Using the Cluster Ion Spectrometry/Composition Distribution Function instrument onboard Cluster, we compare the distribution function of streaming O+ in the tail lobes with the initial distribution function observed over the cusp and reveal that the observations of energetic streaming O+ in the lobes around -20 RE are predominantly due to the velocity filter effect during nonstorm times. During storm times, the cusp distribution is further accelerated. In the plasma sheet boundary layer, however, the average O+ distribution function is above the upper range of the outflow distributions at the same velocity during both storm and nonstorm times, indicating that acceleration has taken place. Some of the velocity increase is in the direction perpendicular to the magnetic field, indicating that the E × B velocity is enhanced. However, there is also an increase in the parallel direction, which could be due to nonadiabatic acceleration at the boundary or wave heating.

Innovative applications of genetic algorithms to problems in accelerator physics

Directory of Open Access Journals (Sweden)

Alicia Hofler

2013-01-01

Full Text Available The genetic algorithm (GA is a powerful technique that implements the principles nature uses in biological evolution to optimize a multidimensional nonlinear problem. The GA works especially well for problems with a large number of local extrema, where traditional methods (such as conjugate gradient, steepest descent, and others fail or, at best, underperform. The field of accelerator physics, among others, abounds with problems which lend themselves to optimization via GAs. In this paper, we report on the successful application of GAs in several problems related to the existing Continuous Electron Beam Accelerator Facility nuclear physics machine, the proposed Medium-energy Electron-Ion Collider at Jefferson Lab, and a radio frequency gun-based injector. These encouraging results are a step forward in optimizing accelerator design and provide an impetus for application of GAs to other problems in the field. To that end, we discuss the details of the GAs used, include a newly devised enhancement which leads to improved convergence to the optimum, and make recommendations for future GA developments and accelerator applications.

MODERN TECHNOLOGICAL SOLUTIONS USED IN THE PRODUCTION OF BAKERY PRODUCTS WITH HIGH BIOLOGICAL VALUE

Directory of Open Access Journals (Sweden)

Marta Brodowska

2014-06-01

Full Text Available Biological value of the food products is a result of the presence of bioactive substances and the proportions of the components. Technological development allows to optimize and accelerate the processes of bread production and increase value of food. Bakery industry used whole grains and pseudocereals as additional source of active compounds, biotechnological techniques as using appropriate yeast strain and encapsulation, which provide protection of substance and their controlled release in production of functional bread. The adding to bread fruits, vegetables and condiments may increase content of vitamin, minerals, dietary fiber and other bioactive compounds.

The effect of blood acceleration on the ultrasound power Doppler spectrum

Science.gov (United States)

Matchenko, O. S.; Barannik, E. A.

2017-09-01

The purpose of the present work was to study the influence of blood acceleration and time window length on the power Doppler spectrum for Gaussian ultrasound beams. The work has been carried out on the basis of continuum model of the ultrasound scattering from inhomogeneities in fluid flow. Correlation function of fluctuations has been considered for uniformly accelerated scatterers, and the resulting power Doppler spectra have been calculated. It is shown that within the initial phase of systole uniformly accelerated slow blood flow in pulmonary artery and aorta tends to make the correlation function about 4.89 and 7.83 times wider, respectively, than the sensitivity function of typical probing system. Given peak flow velocities, the sensitivity function becomes, vice versa, about 4.34 and 3.84 times wider, respectively, then the correlation function. In these limiting cases, the resulting spectra can be considered as Gaussian. The optimal time window duration decreases with increasing acceleration of blood flow and equals to 11.62 and 7.54 ms for pulmonary artery and aorta, respectively. The width of the resulting power Doppler spectrum is shown to be defined mostly by the wave vector of the incident field, the duration of signal and the acceleration of scatterers in the case of low flow velocities. In the opposite case geometrical properties of probing field and the average velocity itself are more essential. In the sense of signal-noise ratio, the optimal duration of time window can be found. Abovementioned results may contribute to the improved techniques of Doppler ultrasound diagnostics of cardiovascular system.

Structure and function in biology

International Nuclear Information System (INIS)

Hirs, C.H.W.

1976-01-01

A summary is given of the history of the developments of structural chemistry in biology beginning with the work of the bacteriologist Ehrlich leading to a comprehensive examination of the influence of size and configuration on the interaction between specific antibodies and side-chain determinants. Recent developments include the recognition of a higher order of specificity in the interaction of proteins with one another

Low-dose neutron dose response of zebrafish embryos obtained from the Neutron exposure Accelerator System for Biological Effect Experiments (NASBEE) facility

International Nuclear Information System (INIS)

Ng, C.Y.P.; Kong, E.Y.; Konishi, T.; Kobayashi, A.; Suya, N.; Cheng, S.H.; Yu, K.N.

2015-01-01

The dose response of embryos of the zebrafish, Danio rerio, irradiated at 5 h post fertilization (hpf) by 2-MeV neutrons with ≤100 mGy was determined. The neutron irradiations were made at the Neutron exposure Accelerator System for Biological Effect Experiments (NASBEE) facility in the National Institute of Radiological Sciences (NIRS), Chiba, Japan. A total of 10 neutron doses ranging from 0.6 to 100 mGy were employed (with a gamma-ray contribution of 14% to the total dose), and the biological effects were studied through quantification of apoptosis at 25 hpf. The responses for neutron doses of 10, 20, 25, and 50 mGy approximately fitted on a straight line, while those for neutron doses of 0.6, 1 and 2.5 mGy exhibited neutron hormetic effects. As such, hormetic responses were generically developed by different kinds of ionizing radiations with different linear energy transfer (LET) values. The responses for neutron doses of 70 and 100 mGy were significantly below the lower 95% confidence band of the best-fit line, which strongly suggested the presence of gamma-ray hormesis. - Highlights: • Neutron dose response was determined for embryos of the zebrafish, Danio rerio. • Neutron doses of 0.6, 1 and 2.5 mGy led to neutron hormetic effects. • Neutron doses of 70 and 100 mGy accompanied by gamma rays led to gamma-ray hormesis

Biological effects of high-energy radiation

International Nuclear Information System (INIS)

Curtis, S.B.

1976-01-01

The biological effects of high-energy radiation are reviewed, with emphasis on the effects of the hadronic component. Proton and helium ion effects are similar to those of the more conventional and sparsely ionizing x- and γ-radiation. Heavy-ions are known to be more biologically effective, but the long term hazard from accumulated damage has yet to be assessed. Some evidence of widely varying but dramatically increased effectiveness of very high-energy (approximately 70 GeV) hadron beams is reviewed. Finally, the importance of the neutron component in many situations around high-energy accelerators is pointed out

Decreased proteasomal function accelerates cigarette smoke-induced pulmonary emphysema in mice.

Science.gov (United States)

Yamada, Yosuke; Tomaru, Utano; Ishizu, Akihiro; Ito, Tomoki; Kiuchi, Takayuki; Ono, Ayako; Miyajima, Syota; Nagai, Katsura; Higashi, Tsunehito; Matsuno, Yoshihiro; Dosaka-Akita, Hirotoshi; Nishimura, Masaharu; Miwa, Soichi; Kasahara, Masanori

2015-06-01

Chronic obstructive pulmonary disease (COPD) is a disease common in elderly people, characterized by progressive destruction of lung parenchyma and chronic inflammation of the airways. The pathogenesis of COPD remains unclear, but recent studies suggest that oxidative stress-induced apoptosis in alveolar cells contributes to emphysematous lung destruction. The proteasome is a multicatalytic enzyme complex that plays a critical role in proteostasis by rapidly destroying misfolded and modified proteins generated by oxidative and other stresses. Proteasome activity decreases with aging in many organs including lungs, and an age-related decline in proteasomal function has been implicated in various age-related pathologies. However, the role of the proteasome system in the pathogenesis of COPD has not been investigated. Recently, we have established a transgenic (Tg) mouse model with decreased proteasomal chymotrypsin-like activity, showing age-related phenotypes. Using this model, we demonstrate here that decreased proteasomal function accelerates cigarette smoke (CS)-induced pulmonary emphysema. CS-exposed Tg mice showed remarkable airspace enlargement and increased foci of inflammation compared with wild-type controls. Importantly, apoptotic cells were found in the alveolar walls of the affected lungs. Impaired proteasomal activity also enhanced apoptosis in cigarette smoke extract (CSE)-exposed fibroblastic cells derived from mice and humans in vitro. Notably, aggresome formation and prominent nuclear translocation of apoptosis-inducing factor were observed in CSE-exposed fibroblastic cells isolated from Tg mice. Collective evidence suggests that CS exposure and impaired proteasomal activity coordinately enhance apoptotic cell death in the alveolar walls that may be involved in the development and progression of emphysema in susceptible individuals such as the elderly.

Commissioning the GTA accelerator

International Nuclear Information System (INIS)

Sander, O.R.; Atkins, W.H.; Bolme, G.O.; Bowling, S.; Brown, S.; Cole, R.; Gilpatrick, J.D.; Garnett, R.; Guy, F.W.; Ingalls, W.B.; Johnson, K.F.; Kerstiens, D.; Little, C.; Lohsen, R.A.; Lloyd, S.; Lysenko, W.P.; Mottershead, C.T.; Neuschaefer, G.; Power, J.; Rusthoi, D.P.; Sandoval, D.P. Stevens, R.R. Jr.; Vaughn, G.; Wadlinger, E.A.; Yuan, V.; Connolly, R.; Weiss, R.; Saadatmand, K.

1992-01-01

The Ground Test Accelerator (GTA) is supported by the Strategic Defense command as part of their Neutral Particle Beam (NPB) program. Neutral particles have the advantage that in space they are unaffected by the earth's magnetic field and travel in straight lines unless they enter the earth's atmosphere and become charged by stripping. Heavy particles are difficult to stop and can probe the interior of space vehicles; hence, NPB can function as a discriminator between warheads and decoys. We are using GTA to resolve the physics and engineering issues related to accelerating, focusing, and steering a high-brightness, high-current H - beam and then neutralizing it. Our immediate goal is to produce a 24-MeV, 50mA device with a 2% duty factor

First muon acceleration using a radio-frequency accelerator

Directory of Open Access Journals (Sweden)

S. Bae

2018-05-01

Full Text Available Muons have been accelerated by using a radio-frequency accelerator for the first time. Negative muonium atoms (Mu^{-}, which are bound states of positive muons (μ^{+} and two electrons, are generated from μ^{+}’s through the electron capture process in an aluminum degrader. The generated Mu^{-}’s are initially electrostatically accelerated and injected into a radio-frequency quadrupole linac (RFQ. In the RFQ, the Mu^{-}’s are accelerated to 89 keV. The accelerated Mu^{-}’s are identified by momentum measurement and time of flight. This compact muon linac opens the door to various muon accelerator applications including particle physics measurements and the construction of a transmission muon microscope.

Accelerator mass spectrometry of ultra-small samples with applications in the biosciences

International Nuclear Information System (INIS)

Salehpour, Mehran; Håkansson, Karl; Possnert, Göran

2013-01-01

An overview is presented covering the biological accelerator mass spectrometry activities at Uppsala University. The research utilizes the Uppsala University Tandem laboratory facilities, including a 5 MV Pelletron tandem accelerator and two stable isotope ratio mass spectrometers. In addition, a dedicated sample preparation laboratory for biological samples with natural activity is in use, as well as another laboratory specifically for 14 C-labeled samples. A variety of ongoing projects are described and presented. Examples are: (1) Ultra-small sample AMS. We routinely analyze samples with masses in the 5–10 μg C range. Data is presented regarding the sample preparation method, (2) bomb peak biological dating of ultra-small samples. A long term project is presented where purified and cell-specific DNA from various part of the human body including the heart and the brain are analyzed with the aim of extracting regeneration rate of the various human cells, (3) biological dating of various human biopsies, including atherosclerosis related plaques is presented. The average built up time of the surgically removed human carotid plaques have been measured and correlated to various data including the level of insulin in the human blood, and (4) In addition to standard microdosing type measurements using small pharmaceutical drugs, pre-clinical pharmacokinetic data from a macromolecular drug candidate are discussed.

Accelerator mass spectrometry of ultra-small samples with applications in the biosciences

Energy Technology Data Exchange (ETDEWEB)

Salehpour, Mehran, E-mail: mehran.salehpour@physics.uu.se [Department of Physics and Astronomy, Ion Physics, PO Box 516, SE-751 20 Uppsala (Sweden); Hakansson, Karl; Possnert, Goeran [Department of Physics and Astronomy, Ion Physics, PO Box 516, SE-751 20 Uppsala (Sweden)

2013-01-15

An overview is presented covering the biological accelerator mass spectrometry activities at Uppsala University. The research utilizes the Uppsala University Tandem laboratory facilities, including a 5 MV Pelletron tandem accelerator and two stable isotope ratio mass spectrometers. In addition, a dedicated sample preparation laboratory for biological samples with natural activity is in use, as well as another laboratory specifically for {sup 14}C-labeled samples. A variety of ongoing projects are described and presented. Examples are: (1) Ultra-small sample AMS. We routinely analyze samples with masses in the 5-10 {mu}g C range. Data is presented regarding the sample preparation method, (2) bomb peak biological dating of ultra-small samples. A long term project is presented where purified and cell-specific DNA from various part of the human body including the heart and the brain are analyzed with the aim of extracting regeneration rate of the various human cells, (3) biological dating of various human biopsies, including atherosclerosis related plaques is presented. The average built up time of the surgically removed human carotid plaques have been measured and correlated to various data including the level of insulin in the human blood, and (4) In addition to standard microdosing type measurements using small pharmaceutical drugs, pre-clinical pharmacokinetic data from a macromolecular drug candidate are discussed.

6 MV Folded Tandem Ion Accelerator facility at BARC

International Nuclear Information System (INIS)

Gupta, S.K.

2010-01-01

The 6 MV Folded Tandem Ion Accelerator (FOTIA) facility is operational round the clock and accelerated beams of both light and heavy ions are being used extensively by various divisions of BARC, Universities, lIT Bombay and other R and D labs across the country. The FOTIA is an upgraded version of the old 5.5 MV single stage Van-de-Graaff accelerator (1962-1992). Since its commissioning in the year 2000, the poor beam transmission through the 180 deg folding magnet was a matter of concern. A systematic study for beam transmission through the accelerator was carried out and progressive modifications in folding magnet chamber, foil stripper holder and improvement in average vacuum level through the accelerator have resulted in large improvement of beam transmission leading to up to 2.0 micro-amp analyzed proton beams on target. Now the utilization of the beams from the accelerator has increased many folds for basic and applied research in the fields of atomic and nuclear physics, material science and radiation biology etc. Few new beam lines after the indigenously developed 5-port switching magnet are added and the experimental setup for PIXE, PIGE, External PIXE, 4 neutron detector, Proton Induced Positron Annihilation Spectroscopy (PIPAS) setup and the general purpose scattering chamber etc have been commissioned in the beam hall. The same team has developed a Low Energy Accelerator Facility (LEAF) which delivers negative ions of light and heavy ions for application in implantation, irradiation damage studies in semiconductor devices and testing of new beam line components being developed for Low Energy High Intensity Proton Accelerator (LEHIPA) programme at BARC. The LEAF has been developed as stand alone facility and can deliver beam quickly with minimum intervention of the operator. Few more features are being planned to deliver uniform scanned beams on large targets. (author)

Accelerator development

International Nuclear Information System (INIS)

Anon.

1975-01-01

Because the use of accelerated heavy ions would provide many opportunities for new and important studies in nuclear physics and nuclear chemistry, as well as other disciplines, both the Chemistry and Physics Divisions are supporting the development of a heavy-ion accelerator. The design of greatest current interest includes a tandem accelerator with a terminal voltage of approximately 25 MV injecting into a linear accelerator with rf superconducting resonators. This combined accelerator facility would be capable of accelerating ions of masses ranging over the entire periodic table to an energy corresponding to approximately 10 MeV/nucleon. This approach, as compared to other concepts, has the advantages of lower construction costs, lower operating power, 100 percent duty factor, and high beam quality (good energy resolution, good timing resolution, small beam size, and small beam divergence). The included sections describe the concept of the proposed heavy-ion accelerator, and the development program aiming at: (1) investigation of the individual questions concerning the superconducting accelerating resonators; (2) construction and testing of prototype accelerator systems; and (3) search for economical solutions to engineering problems. (U.S.)

The planned replacement of a functioning control system on the CERN 28 GEV accelerator

International Nuclear Information System (INIS)

Carpenter, B.E.; Daneels, A.; Perriollat, F.

1979-01-01

The subject is discussed under the following headings: the accelerators (in the 28 GeV accelerator complex) and the old control system; goals of the new control system; constraints (involved in planning a replacement for the control system); a pilot project; major software issues in the system design; portability; parallelism; transition; conclusion. (U.K.)

Late-stage diversification of biologically active pyridazinones via a direct C-H functionalization strategy.

Science.gov (United States)

Li, Wei; Fan, Zhoulong; Geng, Kaijun; Xu, Youjun; Zhang, Ao

2015-01-14

Divergent C-H functionalization reactions (arylation, carboxylation, olefination, thiolation, acetoxylation, halogenation, naphthylation) using a pyridazinone moiety as an internal directing group were successfully established. This approach offers a late-stage, ortho-selective diversification of a biologically active pyridazinone scaffold. Seven series of novel pyridazinone analogues were synthesized conveniently as the synthetic precursors of potential sortase A (SrtA) inhibitors.

Development of an automated system for the operation of an electron beam accelerator

International Nuclear Information System (INIS)

Somessari, Samir L.; Moura, João A.; Calvo, Wilson Ap. Parejo

2017-01-01

Electron beam accelerators are used in many applications, such as basic physical research, chemistry, medicine, molecular biology, microelectronics, agriculture and industry, among others. The majority of the accelerators have electrons from a hot tungsten filament and their energy is increased as it passes through an electric field in the vacuum chamber. For industrial purposes, the most common model is Dynamitrons®. At IPEN-CNEN/SP, there is an electron beam accelerator Dynamitron® Type (Manufactured by RDI- Radiation Dynamics Inc., 1978) model DC1500/25/4. The technology applied was available in the 60's and 70's, but, nowadays is obsolete. Moreover, there are not original spare parts for this equipment any longer. The aim of this work is to develop a nationalized automated operation system for the accelerator, to replace the old equipment. (author)

Development of an automated system for the operation of an electron beam accelerator

Energy Technology Data Exchange (ETDEWEB)

Somessari, Samir L.; Moura, João A.; Calvo, Wilson Ap. Parejo, E-mail: somessar@ipen.br [Instituto de Pesquisas Energeticas e Nucleares (IPEN/CNEN-SP), Sao Paulo, SP (Brazil)

2017-11-01

Electron beam accelerators are used in many applications, such as basic physical research, chemistry, medicine, molecular biology, microelectronics, agriculture and industry, among others. The majority of the accelerators have electrons from a hot tungsten filament and their energy is increased as it passes through an electric field in the vacuum chamber. For industrial purposes, the most common model is Dynamitrons®. At IPEN-CNEN/SP, there is an electron beam accelerator Dynamitron® Type (Manufactured by RDI- Radiation Dynamics Inc., 1978) model DC1500/25/4. The technology applied was available in the 60's and 70's, but, nowadays is obsolete. Moreover, there are not original spare parts for this equipment any longer. The aim of this work is to develop a nationalized automated operation system for the accelerator, to replace the old equipment. (author)

Accelerator Technology: Geodesy and Alignment for Particle Accelerators

CERN Document Server

Missiaen, D

2013-01-01

This document is part of Subvolume C 'Accelerators and Colliders' of Volume 21 'Elementary Particles' of Landolt-Börnstein - Group I 'Elementary Particles, Nuclei and Atoms'. It contains the the Section '8.9 Geodesy and Alignment for Particle Accelerators' of the Chapter '8 Accelerator Technology' with the content: 8.9 Geodesy and Alignment for Particle Accelerators 8.9.1 Introduction 8.9.2 Reference and Co-ordinate Systems 8.9.3 Definition of the Beam Line on the Accelerator Site 8.9.4 Geodetic Network 8.9.5 Tunnel Preliminary Works 8.9.6 The Alignment References 8.9.7 Alignment of Accelerator Components 8.9.8 Permanent Monitoring and Remote Alignment of Low Beta Quadrupoles 8.9.9 Alignment of Detector Components

Rayleigh-Taylor mixing with time-dependent acceleration

Science.gov (United States)

Abarzhi, Snezhana

2016-10-01

We extend the momentum model to describe Rayleigh-Taylor (RT) mixing driven by a time-dependent acceleration. The acceleration is a power-law function of time, similarly to astrophysical and plasma fusion applications. In RT flow the dynamics of a fluid parcel is driven by a balance per unit mass of the rates of momentum gain and loss. We find analytical solutions in the cases of balanced and imbalanced gains and losses, and identify their dependence on the acceleration exponent. The existence is shown of two typical regimes of self-similar RT mixing-acceleration-driven Rayleigh-Taylor-type and dissipation-driven Richtymer-Meshkov-type with the latter being in general non-universal. Possible scenarios are proposed for transitions from the balanced dynamics to the imbalanced self-similar dynamics. Scaling and correlations properties of RT mixing are studied on the basis of dimensional analysis. Departures are outlined of RT dynamics with time-dependent acceleration from canonical cases of homogeneous turbulence as well as blast waves with first and second kind self-similarity. The work is supported by the US National Science Foundation.

Biological intercomparison using gut crypt survivals for proton and carbon ions

International Nuclear Information System (INIS)

Uzawa, Akiko; Ando, Koichi; Furusawa, Yoshiya

2006-01-01

Charged particle therapy depends on biological information for the dose prescription. Relative biological effectiveness or relative biological effectiveness (RBE) for this requirement could basically be provided by experimental data. As RBE values of protons and carbon ions depend on several factors such as cell/tissue type, endpoint, dose and fractionation schedule, a single RBE value could not function as a master key to open all rooms filled with guests of different radiosensitivities. However, any biological model with accurate reproducibility is useful for comparing biological effectiveness between different facilities. We used mouse gut crypt survivals as endpoint, and compared the cell killing efficiency of proton beams at three Japanese facilities. Three Linac X-ray machines with 4 and 6 MeV were used as reference beams, and there was only a small variation (coefficient of variance <2%) in biological effectiveness among them. The RBE values of protons relative to Linac X-rays ranged from 1.0 to 1.11 at the middle of a 6-cm SOBP (spread-out Bragg peak) and from 0.96 to 1.01 at the entrance plateau. The coefficient of variance for protons ranged between 4.0 and 5.1%. The biological comparison of carbon ions showed fairly good agreement in that the difference in biological effectiveness between National Institute of Radiological Sciences (NIRS)/Heavy Ion Medical Accelerator in Chiba (HIMAC) and Gesellschaft fur Schwerionenforschung (GSI)/Heavy Ion Synchrotron (SIS) was 1% for three positions within the 6-cm SOBP. The coefficient of variance was <1.7, <0.6 and <1.6% for proximal, middle and distal SOBP, respectively. We conclude that the inter-institutional variation of biological effectiveness is smaller for carbon ions than protons, and that beam-spreading methods of carbon ions do not critically influence gut crypt survival. (author)

2014 CERN Accelerator Schools: Plasma Wake Acceleration

CERN Multimedia

2014-01-01

A specialised school on Plasma Wake Acceleration will be held at CERN, Switzerland from 23-29 November, 2014.   This course will be of interest to staff and students in accelerator laboratories, university departments and companies working in or having an interest in the field of new acceleration techniques. Following introductory lectures on plasma and laser physics, the course will cover the different components of a plasma wake accelerator and plasma beam systems. An overview of the experimental studies, diagnostic tools and state of the art wake acceleration facilities, both present and planned, will complement the theoretical part. Topical seminars and a visit of CERN will complete the programme. Further information can be found at: http://cas.web.cern.ch/cas/PlasmaWake2014/CERN-advert.html http://indico.cern.ch/event/285444/

Symplectic maps for accelerator lattices

International Nuclear Information System (INIS)

Warnock, R.L.; Ruth, R.; Gabella, W.

1988-05-01

We describe a method for numerical construction of a symplectic map for particle propagation in a general accelerator lattice. The generating function of the map is obtained by integrating the Hamilton-Jacobi equation as an initial-value problem on a finite time interval. Given the generating function, the map is put in explicit form by means of a Fourier inversion technique. We give an example which suggests that the method has promise. 9 refs., 9 figs

Accelerated Evolution and Functional Divergence of the Dim Light Visual Pigment Accompanies Cichlid Colonization of Central America.

Science.gov (United States)

Hauser, Frances E; Ilves, Katriina L; Schott, Ryan K; Castiglione, Gianni M; López-Fernández, Hernán; Chang, Belinda S W

2017-10-01

Cichlids encompass one of the most diverse groups of fishes in South and Central America, and show extensive variation in life history, morphology, and colouration. While studies of visual system evolution in cichlids have focussed largely on the African rift lake species flocks, Neotropical cichlids offer a unique opportunity to investigate visual system evolution at broader temporal and geographic scales. South American cichlid colonization of Central America has likely promoted accelerated rates of morphological evolution in Central American lineages as they encountered reduced competition, renewed ecological opportunity, and novel aquatic habitats. To investigate whether such transitions have influenced molecular evolution of vision in Central American cichlids, we sequenced the dim-light rhodopsin gene in 101 Neotropical cichlid species, spanning the diversity of the clade. We find strong evidence for increased rates of evolution in Central American cichlid rhodopsin relative to South American lineages, and identify several sites under positive selection in rhodopsin that likely contribute to adaptation to different photic environments. We expressed a Neotropical cichlid rhodopsin protein invitro for the first time, and found that while its spectral tuning properties were characteristic of typical vertebrate rhodopsin pigments, the rate of decay of its active signalling form was much slower, consistent with dim light adaptation in other vertebrate rhodopsins. Using site-directed mutagenesis combined with spectroscopic assays, we found that a key amino acid substitution present in some Central American cichlids accelerates the rate of decay of active rhodopsin, which may mediate adaptation to clear water habitats. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Genetic mitigation strategies to tackle agricultural GHG emissions: The case for biological nitrification inhibition technology.

Science.gov (United States)

Subbarao, G V; Arango, J; Masahiro, K; Hooper, A M; Yoshihashi, T; Ando, Y; Nakahara, K; Deshpande, S; Ortiz-Monasterio, I; Ishitani, M; Peters, M; Chirinda, N; Wollenberg, L; Lata, J C; Gerard, B; Tobita, S; Rao, I M; Braun, H J; Kommerell, V; Tohme, J; Iwanaga, M

2017-09-01

Accelerated soil-nitrifier activity and rapid nitrification are the cause of declining nitrogen-use efficiency (NUE) and enhanced nitrous oxide (N 2 O) emissions from farming. Biological nitrification inhibition (BNI) is the ability of certain plant roots to suppress soil-nitrifier activity, through production and release of nitrification inhibitors. The power of phytochemicals with BNI-function needs to be harnessed to control soil-nitrifier activity and improve nitrogen-cycling in agricultural systems. Transformative biological technologies designed for genetic mitigation are needed, so that BNI-enabled crop-livestock and cropping systems can rein in soil-nitrifier activity, to help reduce greenhouse gas (GHG) emissions and globally make farming nitrogen efficient and less harmful to environment. This will reinforce the adaptation or mitigation impact of other climate-smart agriculture technologies. Copyright © 2017 Elsevier B.V. All rights reserved.

Beam Spot Measurement on a 400 keV Electron Accelerator

DEFF Research Database (Denmark)

Miller, Arne

1979-01-01

A line probe is used to measure the beam spot radius and beam divergence at a 400 keV ICT electron accelerator, and a method is shown for reducing the line probe data in order to get the radial function.......A line probe is used to measure the beam spot radius and beam divergence at a 400 keV ICT electron accelerator, and a method is shown for reducing the line probe data in order to get the radial function....

Finding an acceleration function for calculating the reliability of redundant systems - Application to common mode failures

International Nuclear Information System (INIS)

Gonnot, R.

1975-01-01

While it may be reasonable to assume that the reliability of a system - the design of which is perfectly known - can be evaluated, it seems less easy to be sure that overall reliability is correctly estimated in the case of multiple redundancies arranged in sequence. Framatome is trying to develop a method of evaluating overall reliability correctly for its installations. For example, the protection systems in its power stations considered as a whole are such that several scram signals may be relayed in sequence when an incident occurs. These signals all involve the same components for a given type of action, but the components themselves are in fact subject to different stresses and constraints, which tend to reduce their reliability. Whatever the sequence in which these signals are transmitted (in a fast-developing accident, for example), it is possible to evaluate the actual reliability of a given system (or component) for different constraints, as the latter are generally obtained via the transient codes. By applying the so-called ''equal probability'' hypothesis one can estimate a reliability acceleration function taking into account the constraints imposed. This function is linear for the principal failure probability distribution laws. By generalizing such a method one can: (1) Perform failure calculations for redundant systems (or components) in a more general way than is possible with event trees, since one of the main parameters is the constraint exercised on that system (or component); (2) Determine failure rates of components on the basis of accelerated tests (up to complete failure of the component) which are quicker than the normal long-term tests (statistical results of operation); (3) Evaluate the multiplication factor for the reliability of a system or component in the case of common mode failures. The author presents the mathematical tools required for such a method and described their application in the cases mentioned above

Primer on theory and operation of linear accelerators in radiation therapy

International Nuclear Information System (INIS)

Karzmark, C.J.; Morton, R.J.

1981-12-01

This primer is part of an educational package that also includes a series of 3 videotapes entitled Theory and Operation of Linear Accelerators in Radiation Therapy, Parts I, II, and III. This publication provides an overview of the components of the linear accelerator and how they function and interrelate. The auxiliary systems necessary to maintain the operation of the linear accelerator are also described

Functional soil microbial diversity across Europe estimated by EEA, MicroResp and BIOLOG

DEFF Research Database (Denmark)

Winding, Anne; Rutgers, Michiel; Creamer, Rachel

consisting of 81 soil samples covering five Biogeograhical Zones and three land-uses in order to test the sensitivity, ease and cost of performance and biological significance of the data output. The techniques vary in how close they are to in situ functions; dependency on growth during incubation......Soil microorganisms are abundant and essential for the bio-geochemical processes of soil, soil quality and soil ecosystem services. All this is dependent on the actual functions the microbial communities are performing in the soil. Measuring soil respiration has for many years been the basis...... of estimating soil microbial activity. However, today several techniques are in use for determining microbial functional diversity and assessing soil biodiversity: Methods based on CO2 development by the microbes such as substrate induced respiration (SIR) on specific substrates have lead to the development...

Generation and transport of laser accelerated ion beams

Energy Technology Data Exchange (ETDEWEB)

Schmidt, Peter; Boine-Frankenheim, Oliver [Technische Univ. Darmstadt (Germany); GSI Helmholtzzentrum fuer Schwerionenforschung GmbH, Darmstadt (Germany); Kornilov, Vladimir; Spaedtke, Peter [GSI Helmholtzzentrum fuer Schwerionenforschung GmbH, Darmstadt (Germany); Collaboration: LIGHT-Collaboration

2013-07-01

Currently the LIGHT- Project (Laser Ion Generation, Handling and Transport) is performed at the GSI Helmholtzzentrum fuer Schwerionenforschung GmbH Darmstadt. Within this project, intense proton beams are generated by laser acceleration, using the TNSA mechanism. After the laser acceleration the protons are transported through the beam pipe by a pulsed power solenoid. To study the transport a VORPAL 3D simulation is compared with CST simulation. A criterion as a function of beam parameters was worked out, to rate the importance of space charge. Furthermore, an exemplary comparison of the solenoid with a magnetic quadrupole-triplet was carried out. In the further course of the LIGHT-Project, it is planned to generate ion beams with higher kinetic energies, using ultra-thin targets. The acceleration processes that can appear are: RPA (Radiation Pressure Acceleration) and BOA (Break-Out Afterburner). Therefore the transport of an ion distribution will be studied, as it emerges from a RPA acceleration.

Development of a fast voltage control method for electrostatic accelerators

International Nuclear Information System (INIS)

Lobanov, Nikolai R.; Linardakis, Peter; Tsifakis, Dimitrios

2014-01-01

The concept of a novel fast voltage control loop for tandem electrostatic accelerators is described. This control loop utilises high-frequency components of the ion beam current intercepted by the image slits to generate a correction voltage that is applied to the first few gaps of the low- and high-energy acceleration tubes adjoining the high voltage terminal. New techniques for the direct measurement of the transfer function of an ultra-high impedance structure, such as an electrostatic accelerator, have been developed. For the first time, the transfer function for the fast feedback loop has been measured directly. Slow voltage variations are stabilised with common corona control loop and the relationship between transfer functions for the slow and new fast control loops required for optimum operation is discussed. The main source of terminal voltage instabilities, which are due to variation of the charging current caused by mechanical oscillations of charging chains, has been analysed

Adaptive control for accelerators

International Nuclear Information System (INIS)

Eaton, L.E.; Jachim, S.P.; Natter, E.F.

1991-01-01

This patent describes an adaptive feedforward control loop is provided to stabilize accelerator beam loading of the radio frequency field in an accelerator cavity during successive pulses of the beam into the cavity. A digital signal processor enables an adaptive algorithm to generate a feedforward error correcting signal functionally determined by the feedback error obtained by a beam pulse loading the cavity after the previous correcting signal was applied to the cavity. Each cavity feedforward correcting signal is successively stored in the digital processor and modified by the feedback error resulting from its application to generate the next feedforward error correcting signal. A feedforward error correcting signal is generated by the digital processor in advance of the beam pulse to enable a composite correcting signal and the beam pulse to arrive concurrently at the cavity

Adaptive control for accelerators

Science.gov (United States)

Eaton, Lawrie E.; Jachim, Stephen P.; Natter, Eckard F.

1991-01-01

An adaptive feedforward control loop is provided to stabilize accelerator beam loading of the radio frequency field in an accelerator cavity during successive pulses of the beam into the cavity. A digital signal processor enables an adaptive algorithm to generate a feedforward error correcting signal functionally determined by the feedback error obtained by a beam pulse loading the cavity after the previous correcting signal was applied to the cavity. Each cavity feedforward correcting signal is successively stored in the digital processor and modified by the feedback error resulting from its application to generate the next feedforward error correcting signal. A feedforward error correcting signal is generated by the digital processor in advance of the beam pulse to enable a composite correcting signal and the beam pulse to arrive concurrently at the cavity.

Radiological Research Accelerator Facility. Progress report, April 1, 1984-March 31, 1985

International Nuclear Information System (INIS)

Rossi, H.H.

1985-01-01

The aim of the Radiological Research Accelerator Facility (RARAF) was to provide a source of monoenergetic neutrons for studies in radiation biology, dosimetry and microdosimetry. The research has provided insight into the biological action of radiation and its relation to energy distribution in the cell as described by the theory of dual radiation action. This status report on the facility includes descriptions of the capabilities and layout, staffing, radiation safety, and a chronological account of the development and use of the facilities. 5 references, 2 figures

Traumatic stress and accelerated DNA methylation age: A meta-analysis.

Science.gov (United States)

Wolf, Erika J; Maniates, Hannah; Nugent, Nicole; Maihofer, Adam X; Armstrong, Don; Ratanatharathorn, Andrew; Ashley-Koch, Allison E; Garrett, Melanie; Kimbrel, Nathan A; Lori, Adriana; Va Mid-Atlantic Mirecc Workgroup; Aiello, Allison E; Baker, Dewleen G; Beckham, Jean C; Boks, Marco P; Galea, Sandro; Geuze, Elbert; Hauser, Michael A; Kessler, Ronald C; Koenen, Karestan C; Miller, Mark W; Ressler, Kerry J; Risbrough, Victoria; Rutten, Bart P F; Stein, Murray B; Ursano, Robert J; Vermetten, Eric; Vinkers, Christiaan H; Uddin, Monica; Smith, Alicia K; Nievergelt, Caroline M; Logue, Mark W

2018-06-01

Recent studies examining the association between posttraumatic stress disorder (PTSD) and accelerated aging, as defined by DNA methylation-based estimates of cellular age that exceed chronological age, have yielded mixed results. We conducted a meta-analysis of trauma exposure and PTSD diagnosis and symptom severity in association with accelerated DNA methylation age using data from 9 cohorts contributing to the Psychiatric Genomics Consortium PTSD Epigenetics Workgroup (combined N = 2186). Associations between demographic and cellular variables and accelerated DNA methylation age were also examined, as was the moderating influence of demographic variables. Meta-analysis of regression coefficients from contributing cohorts revealed that childhood trauma exposure (when measured with the Childhood Trauma Questionnaire) and lifetime PTSD severity evidenced significant, albeit small, meta-analytic associations with accelerated DNA methylation age (ps = 0.028 and 0.016, respectively). Sex, CD4T cell proportions, and natural killer cell proportions were also significantly associated with accelerated DNA methylation age (all ps age. There was no evidence of moderation of the trauma or PTSD variables by demographic factors. Results suggest that traumatic stress is associated with advanced epigenetic age and raise the possibility that cells integral to immune system maintenance and responsivity play a role in this. This study highlights the need for additional research into the biological mechanisms linking traumatic stress to accelerated DNA methylation age and the importance of furthering our understanding of the neurobiological and health consequences of PTSD. Published by Elsevier Ltd.

Elements in biological AMS

International Nuclear Information System (INIS)

Vogel, J.S.; McAninch, J.; Freeman, S.

1996-08-01

AMS (Accelerator Mass Spectrometry) provides high detection sensitivity for isotopes whose half-lives are between 10 years and 100 million years. 14 C is the most developed of such isotopes and is used in tracing natural and anthropogenic organic compounds in the Earth's biosphere. Thirty-three elements in the main periodic table and 17 lanthanides or actinides have long lived isotopes, providing potential tracers for research in elemental biochemistry. Overlap of biologically interesting heavy elements and possible AMS tracers is discussed

The grating as an accelerating structure

International Nuclear Information System (INIS)

Fernow, R.C.

1991-02-01

This report considers the use of a diffraction grating as an accelerating structure for charged particle beams. We examine the functional dependence of the electromagnetic fields above the surface of a grating. Calculations are made of the strength of the accelerating modes for structures with π and 2π phase advance per period and for incident waves polarized with either the E or H vector along the grooves of the grating. We consider examples of using gratings in a laser linac and in a grating lens. We also briefly examine previous results published about this subject. 36 refs

The emerging molecular biology toolbox for the study of long noncoding RNA biology.

Science.gov (United States)

Fok, Ezio T; Scholefield, Janine; Fanucchi, Stephanie; Mhlanga, Musa M

2017-10-01

Long noncoding RNAs (lncRNAs) have been implicated in many biological processes. However, due to the unique nature of lncRNAs and the consequential difficulties associated with their characterization, there is a growing disparity between the rate at which lncRNAs are being discovered and the assignment of biological function to these transcripts. Here we present a molecular biology toolbox equipped to help dissect aspects of lncRNA biology and reveal functionality. We outline an approach that begins with a broad survey of genome-wide, high-throughput datasets to identify potential lncRNA candidates and then narrow the focus on specific methods that are well suited to interrogate the transcripts of interest more closely. This involves the use of imaging-based strategies to validate these candidates and observe the behaviors of these transcripts at single molecule resolution in individual cells. We also describe the use of gene editing tools and interactome capture techniques to interrogate functionality and infer mechanism, respectively. With the emergence of lncRNAs as important molecules in healthy and diseased cellular function, it remains crucial to deepen our understanding of their biology.

Electrostatic Plasma Accelerator (EPA)

Science.gov (United States)

Brophy, John R.; Aston, Graeme

1995-01-01

The application of electric propulsion to communications satellites, however, has been limited to the use of hydrazine thrusters with electric heaters for thrust and specific impulse augmentation. These electrothermal thrusters operate at specific impulse levels of approximately 300 s with heater powers of about 500 W. Low power arcjets (1-3 kW) are currently being investigated as a way to increase specific impulse levels to approximately 500 s. Ion propulsion systems can easily produce specific impulses of 3000 s or greater, but have yet to be applied to communications satellites. The reasons most often given for not using ion propulsion systems are their high level of overall complexity, low thrust with long burn times, and the difficulty of integrating the propulsion system into existing commercial spacecraft busses. The Electrostatic Plasma Accelerator (EPA) is a thruster concept which promises specific impulse levels between low power arcjets and those of the ion engine while retaining the relative simplicity of the arcjet. The EPA thruster produces thrust through the electrostatic acceleration of a moderately dense plasma. No accelerating electrodes are used and the specific impulse is a direct function of the applied discharge voltage and the propellant atomic mass.

A Tricky Trait: Applying the Fruits of the "Function Debate" in the Philosophy of Biology to the "Venom Debate" in the Science of Toxinology.

Science.gov (United States)

Jackson, Timothy N W; Fry, Bryan G

2016-09-07

The "function debate" in the philosophy of biology and the "venom debate" in the science of toxinology are conceptually related. Venom systems are complex multifunctional traits that have evolved independently numerous times throughout the animal kingdom. No single concept of function, amongst those popularly defended, appears adequate to describe these systems in all their evolutionary contexts and extant variations. As such, a pluralistic view of function, previously defended by some philosophers of biology, is most appropriate. Venom systems, like many other functional traits, exist in nature as points on a continuum and the boundaries between "venomous" and "non-venomous" species may not always be clearly defined. This paper includes a brief overview of the concept of function, followed by in-depth discussion of its application to venom systems. A sound understanding of function may aid in moving the venom debate forward. Similarly, consideration of a complex functional trait such as venom may be of interest to philosophers of biology.

Perchlorate exposure and association with iron homeostasis and other biological functions among NHANES 2005-2008 subjects

Science.gov (United States)

Perchlorate exposure and association with iron homeostasis and other biological functions among NHANES 2005-2008 subjects Schreinemachers DM, Ghio AJ, Cascio WE, Sobus JR. U.S. EPA, RTP, NC, USA Perchlorate (ClO4-), an environmental pollutant, is a known thyroid toxicant and...

TL Dosimetry on the Tandetron Ion Accelerator area of the ININ

International Nuclear Information System (INIS)

Valdovinos A, M.A.; Gonzalez M, P.R.

2000-01-01

For the fulfilment of the operation tests of the Positive Ions type Tandetron 4120 MC, 2 MV, it was obtained the permission consented by the National Commission of Nuclear safety and safeguards (CNSNS). During the stage of tests were arranged Tl dosemeters in the Tandetron Accelerator area, as well as toward to the beam exit. In this work, it was presented the results obtained of the measurement of radiation levels, as much in the area as in the beam exit. This Accelerator is useful in different fields of science such as: biology, radiochemistry, materials, solid state physics, archaeology and environmental sciences between others. (Author)

Systems biology solutions for biochemical production challenges

DEFF Research Database (Denmark)

Hansen, Anne Sofie Lærke; Lennen, Rebecca M; Sonnenschein, Nikolaus

2017-01-01

There is an urgent need to significantly accelerate the development of microbial cell factories to produce fuels and chemicals from renewable feedstocks in order to facilitate the transition to a biobased society. Methods commonly used within the field of systems biology including omics...... characterization, genome-scale metabolic modeling, and adaptive laboratory evolution can be readily deployed in metabolic engineering projects. However, high performance strains usually carry tens of genetic modifications and need to operate in challenging environmental conditions. This additional complexity...... compared to basic science research requires pushing systems biology strategies to their limits and often spurs innovative developments that benefit fields outside metabolic engineering. Here we survey recent advanced applications of systems biology methods in engineering microbial production strains...

Electron bulk acceleration and thermalization at Earth's quasi-perpendicular bow shock

Science.gov (United States)

Chen, L.-J.; Wang, S.; Wilson, L. B., III; Schwartz, S. J.; Bessho, N.; Moore, T. E.; Gershman, D. J.; Giles, B. L.; Malaspina, D. M.; Wilder, F. D.; Ergun, R. E.; Hesse, M.; Lai, H.; Russell, C. T.; Strangeway, R. J.; Torbert, R. B.; Vinas, A. F.-; Burch, J. L.; Lee, S.; Pollock, C.; Dorelli, J.; Paterson, W. R.; Ahmadi, N.; Goodrich, K. A.; Lavraud, B.; Le Contel, O.; Khotyaintsev, Yu. V.; Lindqvist, P.-A.; Boardsen, S.; Wei, H.; Le, A.; Avanov, L. A.

2018-05-01

Electron heating at Earth's quasiperpendicular bow shock has been surmised to be due to the combined effects of a quasistatic electric potential and scattering through wave-particle interaction. Here we report the observation of electron distribution functions indicating a new electron heating process occurring at the leading edge of the shock front. Incident solar wind electrons are accelerated parallel to the magnetic field toward downstream, reaching an electron-ion relative drift speed exceeding the electron thermal speed. The bulk acceleration is associated with an electric field pulse embedded in a whistler-mode wave. The high electron-ion relative drift is relaxed primarily through a nonlinear current-driven instability. The relaxed distributions contain a beam traveling toward the shock as a remnant of the accelerated electrons. Similar distribution functions prevail throughout the shock transition layer, suggesting that the observed acceleration and thermalization is essential to the cross-shock electron heating.

Community Petascale Project for Accelerator Science and Simulation: Advancing Computational Science for Future Accelerators and Accelerator Technologies

Energy Technology Data Exchange (ETDEWEB)

Spentzouris, P.; /Fermilab; Cary, J.; /Tech-X, Boulder; McInnes, L.C.; /Argonne; Mori, W.; /UCLA; Ng, C.; /SLAC; Ng, E.; Ryne, R.; /LBL, Berkeley

2011-11-14

The design and performance optimization of particle accelerators are essential for the success of the DOE scientific program in the next decade. Particle accelerators are very complex systems whose accurate description involves a large number of degrees of freedom and requires the inclusion of many physics processes. Building on the success of the SciDAC-1 Accelerator Science and Technology project, the SciDAC-2 Community Petascale Project for Accelerator Science and Simulation (ComPASS) is developing a comprehensive set of interoperable components for beam dynamics, electromagnetics, electron cooling, and laser/plasma acceleration modelling. ComPASS is providing accelerator scientists the tools required to enable the necessary accelerator simulation paradigm shift from high-fidelity single physics process modeling (covered under SciDAC1) to high-fidelity multiphysics modeling. Our computational frameworks have been used to model the behavior of a large number of accelerators and accelerator R&D experiments, assisting both their design and performance optimization. As parallel computational applications, the ComPASS codes have been shown to make effective use of thousands of processors. ComPASS is in the first year of executing its plan to develop the next-generation HPC accelerator modeling tools. ComPASS aims to develop an integrated simulation environment that will utilize existing and new accelerator physics modules with petascale capabilities, by employing modern computing and solver technologies. The ComPASS vision is to deliver to accelerator scientists a virtual accelerator and virtual prototyping modeling environment, with the necessary multiphysics, multiscale capabilities. The plan for this development includes delivering accelerator modeling applications appropriate for each stage of the ComPASS software evolution. Such applications are already being used to address challenging problems in accelerator design and optimization. The ComPASS organization

Electron pulse shaping in the FELIX RF accelerator

International Nuclear Information System (INIS)

Weits, H.H.; Geer, C.A.J. van der; Oepts, D.; Meer, A.F.G. van der

1999-01-01

The FELIX free-electron laser uses short pulses of relativistic electrons produced by an RF accelerator. The design target for the duration of these electron bunches was around 3 ps. In experiments we observed that the bunches emit coherently enhanced spontaneous emission (CSE) when they travel through an undulator. It was demonstrated that the power level of the CSE critically depends on the settings of the accelerator. In this article we seek to explain these observations by studying the length and shape of the electron bunches as a function of the settings of the accelerator. A particle-tracking model was used to simulate the acceleration and transport processes. These include bunch compression in a 14-cell travelling wave buncher cavity, acceleration in a travelling wave linear accelerator, and passage through a (dispersive) chicane structure. The effect of the phase setting of the RF accelerating field with respect to the arrival time of the electron bunch in each accelerator structure was studied. The parameter range of the simulations is related to that of an actual free-electron laser experiment using these bunches. We find that, for specific settings of the accelerating system, electron pulses with a length of 350 μm FWHM (1 ps) are produced. The charge in the bunch rises steeply within a distance of 25 μm. This bunch shape explains the high level of coherently enhanced spontaneous emission observed in the FELIX laser. (author)

Accelerator Service

International Nuclear Information System (INIS)

Champelovier, Y.; Ferrari, M.; Gardon, A.; Hadinger, G.; Martin, J.; Plantier, A.

1998-01-01

Since the cessation of the operation of hydrogen cluster accelerator in July 1996, four electrostatic accelerators were in operation and used by the peri-nuclear teams working in multidisciplinary collaborations. These are the 4 MV Van de Graaff accelerator, 2,5 MV Van de Graaff accelerator, 400 kV ion implanter as well as the 120 kV isotope separator

Biology of bone and how it orchestrates the form and function of the skeleton

Science.gov (United States)

Sommerfeldt, D. W.; Rubin, C. T.

2001-01-01

The principal role of the skeleton is to provide structural support for the body. While the skeleton also serves as the body's mineral reservoir, the mineralized structure is the very basis of posture, opposes muscular contraction resulting in motion, withstands functional load bearing, and protects internal organs. Although the mass and morphology of the skeleton is defined, to some extent, by genetic determinants, it is the tissue's ability to remodel--the local resorption and formation of bone--which is responsible for achieving this intricate balance between competing responsibilities. The aim of this review is to address bone's form-function relationship, beginning with extensive research in the musculoskeletal disciplines, and focusing on several recent cellular and molecular discoveries which help understand the complex interdependence of bone cells, growth factors, physical stimuli, metabolic demands, and structural responsibilities. With a clinical and spine-oriented audience in mind, the principles of bone cell and molecular biology and physiology are presented, and an attempt has been made to incorporate epidemiologic data and therapeutic implications. Bone research remains interdisciplinary by nature, and a deeper understanding of bone biology will ultimately lead to advances in the treatment of diseases and injuries to bone itself.

The Biological Effectiveness of Accelerated Particles for the Induction of Chromosome Damage: Track Structure Effects and Cytogenetic Signatures of High-LET Exposure

Science.gov (United States)

George, K.; Hada, M.; Chappell, L.; Cucinotta, F. A.

2012-01-01

Track structure models predict that at a fixed value of LET, particles with lower charge number, Z will have a higher biological effectiveness compared to particles with a higher Z. In this report we investigated how track structure effects induction of chromosomal aberration in human cells. Human lymphocytes were irradiated in vitro with various energies of accelerated iron, silicon, neon, or titanium ions and chromosome damage was assessed in using three color FISH chromosome painting in chemically induced PCC samples collected a first cell division post irradiation. The LET values for these ions ranged from 30 to 195 keV/micrometers. Of the particles studied, Neon ions have the highest biological effectiveness for induction of total chromosome damage, which is consistent with track structure model predictions. For complex-type exchanges 64 MeV/ u Neon and 450 MeV/u Iron were equally effective and induced the most complex damage. In addition we present data on chromosomes exchanges induced by six different energies of protons (5 MeV/u to 2.5 GeV/u). The linear dose response term was similar for all energies of protons suggesting that the effect of the higher LET at low proton energies is balanced by the production of nuclear secondaries from the high energy protons. All energies of protons have a much higher percentage of complex-type chromosome exchanges than gamma rays, signifying a cytogenetic signature for proton exposures.

Department of Accelerator Physics And Technology - Overview

International Nuclear Information System (INIS)

Plawski, E.

2009-01-01

Full text: The activity of department P-10 is focused on the development of new acceleration techniques and technology, as well as on applications of particle accelerators. In 2008, the following topics were investigated and/or realized: 1. A linear accelerator for protons called TOP (Terapia Oncologica con Protoni, Oncological Proton Therapy). Basically a proton linac of modified Alvarez type working at 3000 MHz frequency and delivering beams in the energy range from 65 MeV to 200 MeV. In 2005, a contract was signed between ENEA and SINS-Swierk for the design, manufacture and delivery to Frascati of the input section of a 65 MeV linac. This section of SCDTL type will increase the proton energy from 7 to 16 MeV. In 2008, the field distribution in the manufactured structure was measured and optimized using available universal test stand. Measurements were also performed in ENEA/Frascati in October; a small difference in results, around 0.25%, is under investigation. Beam dynamics calculations using 3D codes have been started in parallel. 2. Preparation for participation in the international X-FEL project. Calculations of the parasitic Higher Order Modes (HOMs) induced in superconducting accelerating structures by very short electron bunches have been continued. Thanks to the special research grant received by department P-10 the design and completion of the HOM elements has been started for two accelerating modules, where each module consists of eight superconducting accelerating structures and focusing/correcting elements. 3. Superconducting layers; studies in INFN-Roma. Within the European CARE/JRA1/WP4-2 project, serious modification of the Nb-coating stand for the 1.3 GHz single-cell copper resonators using a vacuum arc was performed. Thanks to this stand the internal surface of the resonator was successfully coated. 4. TiN coating vacuum stand for RF components. At this stand the analysis of the TiN layer thickness as a function of reactive atmosphere pressure

Biological and medical research with accelerated heavy ions at the Bevalac, 1974--1977. [Planning for use for radiotherapy and as radiation source for diagnostic radiography

Energy Technology Data Exchange (ETDEWEB)

Elam, S. (ed.)

1977-04-01

The Bevalac, a versatile high-energy heavy-ion accelerator complex, has been in operation for less than two years. A major purpose for which the Bevalac was constructed was to explore the possibility of heavy-ion teams for therapy for certain forms of cancer. Significant progress has been made in this direction. The National Cancer Institute has recognized the advantages that these and other accelerated particles offer, and heavy ions have been included in a long-term plan for particle therapy that will assess by means of controlled therapeutic tests the value of various modalities. Since accelerated heavy ions became available, the possibility of other contributions, not planned, became apparent. We are developig a new diagnostic method known as heavy-ion radiography that has greatly increased sensitivity for soft-tissue detail and that may become a powerful tool for localizing early tumors and metastases. We have discovered that radioactive beams are formed from fragmentation of stable deflected beams. Use of these autoradioactive beams is just beginning; however, we know that these beams will be helpful in localizing the region in the body where therapy is being delivered. In addition, it has been demonstrated that instant implantation of the radioactive beam allows direct measurements of blood perfusion rates in inaccessible parts of the body, and such a technique may become a new tool for the study of fast hot atom reactions in biochemistry, tracer biology and nuclear medicine. The Bevalac will also be useful for the continuation of previously developed methods for the control of acromegaly, Cushing's disease and, on a research basis, advanced diabetes mellitus with vascular disease. The ability to make small bloodless lesions in the brain and elsewhere with heavy-ion beams has great potential for nervous-system studies and perhaps later for radioneurosurgery.

Community petascale project for accelerator science and simulation: Advancing computational science for future accelerators and accelerator technologies

International Nuclear Information System (INIS)

Spentzouris, P.; Cary, J.; McInnes, L.C.; Mori, W.; Ng, C.; Ng, E.; Ryne, R.

2008-01-01

The design and performance optimization of particle accelerators are essential for the success of the DOE scientific program in the next decade. Particle accelerators are very complex systems whose accurate description involves a large number of degrees of freedom and requires the inclusion of many physics processes. Building on the success of the SciDAC-1 Accelerator Science and Technology project, the SciDAC-2 Community Petascale Project for Accelerator Science and Simulation (ComPASS) is developing a comprehensive set of interoperable components for beam dynamics, electromagnetics, electron cooling, and laser/plasma acceleration modelling. ComPASS is providing accelerator scientists the tools required to enable the necessary accelerator simulation paradigm shift from high-fidelity single physics process modeling (covered under SciDAC1) to high-fidelity multiphysics modeling. Our computational frameworks have been used to model the behavior of a large number of accelerators and accelerator R and D experiments, assisting both their design and performance optimization. As parallel computational applications, the ComPASS codes have been shown to make effective use of thousands of processors.

Rayleigh-Taylor mixing with space-dependent acceleration

Science.gov (United States)

Abarzhi, Snezhana

2016-11-01

We extend the momentum model to describe Rayleigh-Taylor (RT) mixing driven by a space-dependent acceleration. The acceleration is a power-law function of space coordinate, similarly to astrophysical and plasma fusion applications. In RT flow the dynamics of a fluid parcel is driven by a balance per unit mass of the rates of momentum gain and loss. We find analytical solutions in the cases of balanced and imbalanced gains and losses, and identify their dependence on the acceleration exponent. The existence is shown of two typical sub-regimes of self-similar RT mixing - the acceleration-driven Rayleigh-Taylor-type mixing and dissipation-driven Richtymer-Meshkov-type mixing with the latter being in general non-universal. Possible scenarios are proposed for transitions from the balanced dynamics to the imbalanced self-similar dynamics. Scaling and correlations properties of RT mixing are studied on the basis of dimensional analysis. Departures are outlined of RT dynamics with space-dependent acceleration from canonical cases of homogeneous turbulence as well as blast waves with first and second kind self-similarity. The work is supported by the US National Science Foundation.

Multilevel functional genomics data integration as a tool for understanding physiology: a network biology perspective.

Science.gov (United States)

Davidsen, Peter K; Turan, Nil; Egginton, Stuart; Falciani, Francesco

2016-02-01

The overall aim of physiological research is to understand how living systems function in an integrative manner. Consequently, the discipline of physiology has since its infancy attempted to link multiple levels of biological organization. Increasingly this has involved mathematical and computational approaches, typically to model a small number of components spanning several levels of biological organization. With the advent of "omics" technologies, which can characterize the molecular state of a cell or tissue (intended as the level of expression and/or activity of its molecular components), the number of molecular components we can quantify has increased exponentially. Paradoxically, the unprecedented amount of experimental data has made it more difficult to derive conceptual models underlying essential mechanisms regulating mammalian physiology. We present an overview of state-of-the-art methods currently used to identifying biological networks underlying genomewide responses. These are based on a data-driven approach that relies on advanced computational methods designed to "learn" biology from observational data. In this review, we illustrate an application of these computational methodologies using a case study integrating an in vivo model representing the transcriptional state of hypoxic skeletal muscle with a clinical study representing muscle wasting in chronic obstructive pulmonary disease patients. The broader application of these approaches to modeling multiple levels of biological data in the context of modern physiology is discussed. Copyright © 2016 the American Physiological Society.

From transcriptome to biological function: environmental stress in an ectothermic vertebrate, the coral reef fish Pomacentrus moluccensis

Directory of Open Access Journals (Sweden)

Ward Alister C

2007-10-01

Full Text Available Abstract Background Our understanding of the importance of transcriptional regulation for biological function is continuously improving. We still know, however, comparatively little about how environmentally induced stress affects gene expression in vertebrates, and the consistency of transcriptional stress responses to different types of environmental stress. In this study, we used a multi-stressor approach to identify components of a common stress response as well as components unique to different types of environmental stress. We exposed individuals of the coral reef fish Pomacentrus moluccensis to hypoxic, hyposmotic, cold and heat shock and measured the responses of approximately 16,000 genes in liver. We also compared winter and summer responses to heat shock to examine the capacity for such responses to vary with acclimation to different ambient temperatures. Results We identified a series of gene functions that were involved in all stress responses examined here, suggesting some common effects of stress on biological function. These common responses were achieved by the regulation of largely independent sets of genes; the responses of individual genes varied greatly across different stress types. In response to heat exposure over five days, a total of 324 gene loci were differentially expressed. Many heat-responsive genes had functions associated with protein turnover, metabolism, and the response to oxidative stress. We were also able to identify groups of co-regulated genes, the genes within which shared similar functions. Conclusion This is the first environmental genomic study to measure gene regulation in response to different environmental stressors in a natural population of a warm-adapted ectothermic vertebrate. We have shown that different types of environmental stress induce expression changes in genes with similar gene functions, but that the responses of individual genes vary between stress types. The functions of heat

Functional profiles reveal unique ecological roles of various biological soil crust organisms

Science.gov (United States)

Bowker, M.A.; Mau, R.L.; Maestre, F.T.; Escolar, C.; Castillo-Monroy, A. P.

2011-01-01

1. At the heart of the body of research on biodiversity effects on ecosystem function is the debate over whether different species tend to be functionally singular or redundant. When we consider ecosystem multi-function, the provision of multiple ecosystem functions simultaneously, we may find that seemingly redundant species may in fact play unique roles in ecosystems. 2. Over the last few decades, the significance of biological soil crusts (BSCs) as ecological boundaries and ecosystem engineers, and their multi-functional nature, has become increasingly well documented. We compiled 'functional profiles' of the organisms in this understudied community, to determine whether functional singularity emerges when multiple ecosystem functions are considered. 3. In two data sets, one representing multiple sites around the semi-arid regions of Spain (regional scale), and another from a single site in central Spain (local scale), we examined correlations between the abundance or frequency of BSC species in a community, and multiple surrogates of ecosystem functioning. There was a wide array of apparent effects of species on specific functions. 4. Notably, in gypsiferous soils and at regional scale, we found that indicators of carbon (C) and phosphorus cycling were apparently suppressed and promoted by the lichens Diploschistes diacapsis and Squamarina lentigera, respectively. The moss Pleurochaete squarrosa appears to promote C cycling in calcareous soils at this spatial scale. At the local scale in gypsiferous soils, D. diacapsis positively correlated with carbon cycling, but negatively with nitrogen cycling, whereas numerous lichens exhibited the opposite profile. 5. We found a high degree of functional singularity, i.e. that species were highly individualistic in their effects on multiple functions. Many functional attributes were not easily predictable from existing functional grouping systems based primarily on morphology. 6. Our results suggest that maintaining

Function-Based Algorithms for Biological Sequences

Science.gov (United States)

Mohanty, Pragyan Sheela P.

2015-01-01

Two problems at two different abstraction levels of computational biology are studied. At the molecular level, efficient pattern matching algorithms in DNA sequences are presented. For gene order data, an efficient data structure is presented capable of storing all gene re-orderings in a systematic manner. A common characteristic of presented…

Annual Report of the Tandem Accelerator Center, Nuclear and Solid State Research Project, University of Tsukuba

International Nuclear Information System (INIS)

1978-01-01

In 1977, 12 UD Pelletron tandem accelerator has been operated by the University's researchers and engineers. Except for the tank opening for regular inspection we met twice the troubles which forced to change the accelerating tube. The experiences teach us that it needs about 20 days to finish the conditioning after changing the accelerating tube. A sputter ion source of new version is now being installed on the top floor. Two devices for the detection of X-rays were tested. An apparatus for bombardment of samples in air for biological and medical sciences has been successfully used. The subjects of researches on nuclear physics cover the light-ion reactions, heavy-ion reactions and nuclear spectroscopy. A special emphasis has been put on the measurements on vector- and tensor-analyzing powers in the light-ion reactions, because of a higher efficiency of the polarized ion source. Elaborate works on the heavy-ion reactions including the angular correlation patterns and excitation functions have been made in parallel. Papers of these works are now being prepared, a few having been published already. Moreover, in the University of Tsukuba, a new research system, called Special Research Project on Nuclear and Solid State Sciences Using Accelerated Beams (Nuclear and Solid State Research Project) started in 1978 and will continue for five years. In this research project, researchers from various Institutes in the University of Tsukuba, as well as visiting researchers from other institutions in Japan and from abroad, participate. Using a variety of accelerated beams, i.e. of heavy, light and polarized beams, this research project aims mainly at the high excitation, short life, transient and inhomogeneous states both in nuclear and extra-nuclear world. It covers both fundamental research in nuclear, atomic and solid state sciences as well as their application in various fields. (J.P.N.)

Advanced concepts for acceleration

International Nuclear Information System (INIS)

Keefe, D.

1986-07-01

Selected examples of advanced accelerator concepts are reviewed. Such plasma accelerators as plasma beat wave accelerator, plasma wake field accelerator, and plasma grating accelerator are discussed particularly as examples of concepts for accelerating relativistic electrons or positrons. Also covered are the pulsed electron-beam, pulsed laser accelerator, inverse Cherenkov accelerator, inverse free-electron laser, switched radial-line accelerators, and two-beam accelerator. Advanced concepts for ion acceleration discussed include the electron ring accelerator, excitation of waves on intense electron beams, and two-wave combinations

Determining the impacts of trawling on benthic function in European waters : a biological traits approach

DEFF Research Database (Denmark)

Bolam, Stefan; Kenny, Andrew; Garcia, Clement

characteristics, have allowed us to better understand the interactions between the benthic fauna and their environment at a functional level. We present the initial findings of work conducted under the auspices of the EU-funded project ‘BENTHIS’ which aims to improve our understanding of the impacts of trawling...... on benthic ecosystem functioning over much larger spatial scales than previously undertaken. Biological traits information from 887 stations across European waters (Norwegian, UK, Belgian, Dutch, Danish waters, the Mediterranean and Black Sea) were analysed to: i) quantify the relationships between infaunal...

A promising future for integrative biodiversity research: an increased role of scale-dependency and functional biology

Science.gov (United States)

Schmitz, L.

2016-01-01

Studies into the complex interaction between an organism and changes to its biotic and abiotic environment are fundamental to understanding what regulates biodiversity. These investigations occur at many phylogenetic, temporal and spatial scales and within a variety of biological and geological disciplines but often in relative isolation. This issue focuses on what can be achieved when ecological mechanisms are integrated into analyses of deep-time biodiversity patterns through the union of fossil and extant data and methods. We expand upon this perspective to argue that, given its direct relevance to the current biodiversity crisis, greater integration is needed across biodiversity research. We focus on the need to understand scaling effects, how lower-level ecological and evolutionary processes scale up and vice versa, and the importance of incorporating functional biology. Placing function at the core of biodiversity research is fundamental, as it establishes how an organism interacts with its abiotic and biotic environment and it is functional diversity that ultimately determines important ecosystem processes. To achieve full integration, concerted and ongoing efforts are needed to build a united and interactive community of biodiversity researchers, with education and interdisciplinary training at its heart. PMID:26977068

A promising future for integrative biodiversity research: an increased role of scale-dependency and functional biology.

Science.gov (United States)

Price, S A; Schmitz, L

2016-04-05

Studies into the complex interaction between an organism and changes to its biotic and abiotic environment are fundamental to understanding what regulates biodiversity. These investigations occur at many phylogenetic, temporal and spatial scales and within a variety of biological and geological disciplines but often in relative isolation. This issue focuses on what can be achieved when ecological mechanisms are integrated into analyses of deep-time biodiversity patterns through the union of fossil and extant data and methods. We expand upon this perspective to argue that, given its direct relevance to the current biodiversity crisis, greater integration is needed across biodiversity research. We focus on the need to understand scaling effects, how lower-level ecological and evolutionary processes scale up and vice versa, and the importance of incorporating functional biology. Placing function at the core of biodiversity research is fundamental, as it establishes how an organism interacts with its abiotic and biotic environment and it is functional diversity that ultimately determines important ecosystem processes. To achieve full integration, concerted and ongoing efforts are needed to build a united and interactive community of biodiversity researchers, with education and interdisciplinary training at its heart. © 2016 The Author(s).

The role of ontologies in biological and biomedical research: a functional perspective

KAUST Repository

Hoehndorf, Robert

2015-04-10

Ontologies are widely used in biological and biomedical research. Their success lies in their combination of four main features present in almost all ontologies: provision of standard identifiers for classes and relations that represent the phenomena within a domain; provision of a vocabulary for a domain; provision of metadata that describes the intended meaning of the classes and relations in ontologies; and the provision of machine-readable axioms and definitions that enable computational access to some aspects of the meaning of classes and relations. While each of these features enables applications that facilitate data integration, data access and analysis, a great potential lies in the possibility of combining these four features to support integrative analysis and interpretation of multimodal data. Here, we provide a functional perspective on ontologies in biology and biomedicine, focusing on what ontologies can do and describing how they can be used in support of integrative research. We also outline perspectives for using ontologies in data-driven science, in particular their application in structured data mining and machine learning applications.

The role of ontologies in biological and biomedical research: a functional perspective

KAUST Repository

Hoehndorf, Robert; Schofield, P. N.; Gkoutos, G. V.

2015-01-01

Ontologies are widely used in biological and biomedical research. Their success lies in their combination of four main features present in almost all ontologies: provision of standard identifiers for classes and relations that represent the phenomena within a domain; provision of a vocabulary for a domain; provision of metadata that describes the intended meaning of the classes and relations in ontologies; and the provision of machine-readable axioms and definitions that enable computational access to some aspects of the meaning of classes and relations. While each of these features enables applications that facilitate data integration, data access and analysis, a great potential lies in the possibility of combining these four features to support integrative analysis and interpretation of multimodal data. Here, we provide a functional perspective on ontologies in biology and biomedicine, focusing on what ontologies can do and describing how they can be used in support of integrative research. We also outline perspectives for using ontologies in data-driven science, in particular their application in structured data mining and machine learning applications.

Bio-templated CdSe quantum dots green synthesis in the functional protein, lysozyme, and biological activity investigation

International Nuclear Information System (INIS)

Wang, Qisui; Li, Song; Liu, Peng; Min, Xinmin

2012-01-01

Bifunctional fluorescence (CdSe Quantum Dots) – protein (Lysozyme) nanocomposites were synthesized at room temperature by a protein-directed, solution-phase, green-synthetic method. Fluorescence (FL) and absorption spectra showed that CdSe QDs were prepared successfully with Lyz. The average particle size and crystalline structure of QDs were investigated by high-resolution transmission electron microscopy (HRTEM) and X-ray diffraction (XRD), respectively. With attenuated total reflection-fourier transform infrared (ATR-FTIR) spectra and thermogravimetric (TG) analysis, it was confirmed that there is interaction between QDs and amide I, amide II groups in Lyz. FL polarization was measured and FL imaging was done to monitor whether QDs could be responsible for possible changes in the conformation and activity of Lyz. Interestingly, the results showed Lyz still retain the biological activity after formation of QDs, but the secondary structure of the Lyz was changed. And the advantage of this synthesis method is producing excellent fluorescent QDs with specifically biological function. -- Highlights: ► Lysozyme-directed green synthesis of CdSe quantum dots. ► Lysozyme still retain the biological activity after formation of CdSe. ► The method is the production of fluorescent QDs with highly specific and functions.

The impact of new accelerator control software on LEP performance

International Nuclear Information System (INIS)

Bailey, R.; Belk, A.; Collier, P.; Lamont, M.; Rigk, G. de; Tarrant, M.

1993-01-01

After the first year of running LEP, it became apparent that a new generation of application software would be required for efficient long term exploitation of the accelerator. In response to this need, a suite of accelerator control software has been developed, which is new both in style and functionality. During 1992 this software has been extensively used for driving LEP in many different operational modes, which include several different optics, polarisation runs at different energies and 8 bunch operation with Pretzels. The software has performed well and has undoubtedly enhanced the efficiency of accelerator operations. In particular the turnaround time has been significantly reduced, giving an increase of around 20% in the integrated luminosity for the year. Furthermore the software has made the accelerator accessible to less experienced operators. After outlining the development strategy, the overall functionality and performance of the software is discussed, with particular emphasis on improvements in operating efficiency. Some evaluation of the performance and reliability of ORACLE as an on-line database is also given

Accelerating tube for the ''EG-1'' electrostatic accelerator

International Nuclear Information System (INIS)

Romanov, V.A.; Ivanov, V.V.; Krupnov, E.P.; Debin, V.K.; Dudkin, N.I.; Volodin, V.I.

1980-01-01

A design of an accelerating tube (AT) for an electrostatic accelerator of the EG-1 type is described. Primary consideration in the development of the AT has been given to increasing the electric strength of accelerating gaps, the vacuum conductivity and better insulator screening from charged particles. After AT vacuum and high-voltage ageing in the accelerator, a hydrogen ions beam of up to 80 μA has been produced. The beam was adequately shaped in the energy range from 1.8 to 5.0 MeV [ru

Embryonic stem cell interactomics: the beginning of a long road to biological function.

Science.gov (United States)

Yousefi, Maram; Hajihoseini, Vahid; Jung, Woojin; Hosseinpour, Batol; Rassouli, Hassan; Lee, Bonghee; Baharvand, Hossein; Lee, KiYoung; Salekdeh, Ghasem Hosseini

2012-12-01

Embryonic stem cells (ESCs) are capable of unlimited self-renewal while maintaining pluripotency. They are of great interest in regenerative medicine due to their ability to differentiate into all cell types of the three embryonic germ layers. Recently, induced pluripotent stem cells (iPSCs) have shown similarities to ESCs and thus promise great therapeutic potential in regenerative medicine. Despite progress in stem cell biology, our understanding of the exact mechanisms by which pluripotency and self-renewal are established and maintained is largely unknown. A better understanding of these processes may lead to discovery of alternative ways for reprogramming, differentiation and more reliable applications of stem cells in therapies. It has become evident that proteins generally function as members of large complexes that are part of a more complex network. Therefore, the identification of protein-protein interactions (PPI) is an efficient strategy for understanding protein function and regulation. Systematic genome-wide and pathway-specific PPI analysis of ESCs has generated a network of ESC proteins, including major transcription factors. These PPI networks of ESCs may contribute to a mechanistic understanding of self-renewal and pluripotency. In this review we describe different experimental approaches for the identification of PPIs along with various databases. We discuss biological findings and technical challenges encountered with interactome studies of pluripotent stem cells, and provide insight into how interactomics is likely to develop.

Generic device controller for accelerator control systems

International Nuclear Information System (INIS)

Mariotti, R.; Buxton, W.; Frankel, R.; Hoff, L.

1987-01-01

A new distributed intelligence control system has become operational at the AGS for transport, injection, and acceleration of heavy ions. A brief description of the functionality of the physical devices making up the system is given. An attempt has been made to integrate the devices for accelerator specific interfacing into a standard microprocessor system, namely, the Universal Device Controller (UDC). The main goals for such a generic device controller are to provide: local computing power; flexibility to configure; and real time event handling. The UDC assemblies and software are described

Accessing Intel FPGAs for Acceleration

CERN Multimedia

CERN. Geneva

2018-01-01

In this presentation, we will discuss the latest tools and products from Intel that enables FPGAs to be deployed as Accelerators. We will first talk about the Acceleration Stack for Intel Xeon CPU with FPGAs which makes it easy to create, verify, and execute functions on the Intel Programmable Acceleration Card in a Data Center. We will then talk about the OpenCL flow which allows parallel software developers to create FPGA systems and deploy them using the OpenCL standard. Next, we will talk about the Intel High-Level Synthesis compiler which can convert C++ code into custom RTL code optimized for Intel FPGAs. Lastly, we will focus on the task of running Machine Learning inference on the FPGA leveraging some of the tools we discussed. About the speaker Karl Qi is Sr. Staff Applications Engineer, Technical Training. He has been with the Customer Training department at Altera/Intel for 8 years. Most recently, he is responsible for all training content relating to High-Level Design tools, including the OpenCL...

Present SLAC accelerator computer control system features

International Nuclear Information System (INIS)

Davidson, V.; Johnson, R.

1981-02-01

The current functional organization and state of software development of the computer control system of the Stanford Linear Accelerator is described. Included is a discussion of the distribution of functions throughout the system, the local controller features, and currently implemented features of the touch panel portion of the system. The functional use of our triplex of PDP11-34 computers sharing common memory is described. Also included is a description of the use of pseudopanel tables as data tables for closed loop control functions

The Convergence Acceleration of Two-Dimensional Fourier Interpolation

Directory of Open Access Journals (Sweden)

Anry Nersessian

2008-07-01

Full Text Available Hereby, the convergence acceleration of two-dimensional trigonometric interpolation for a smooth functions on a uniform mesh is considered. Together with theoretical estimates some numerical results are presented and discussed that reveal the potential of this method for application in image processing. Experiments show that suggested algorithm allows acceleration of conventional Fourier interpolation even for sparse meshes that can lead to an efficient image compression/decompression algorithms and also to applications in image zooming procedures.

Model-based accelerator controls: What, why and how

International Nuclear Information System (INIS)

Sidhu, S.S.

1987-01-01

Model-based control is defined as a gamut of techniques whose aim is to improve the reliability of an accelerator and enhance the capabilities of the operator, and therefore of the whole control system. The aim of model-based control is seen as gradually moving the function of model-reference from the operator to the computer. The role of the operator in accelerator control and the need for and application of model-based control are briefly summarized

The Four Lives of a Nuclear Accelerator

Science.gov (United States)

Wiescher, Michael

2017-06-01

Electrostatic accelerators have emerged as a major tool in research and industry in the second half of the twentieth century. In particular in low energy nuclear physics they have been essential for addressing a number of critical research questions from nuclear structure to nuclear astrophysics. This article describes this development on the example of a single machine which has been used for nearly sixty years at the forefront of scientific research in nuclear physics. The article summarizes the concept of electrostatic accelerators and outlines how this accelerator developed from a bare support function to an independent research tool that has been utilized in different research environments and institutions and now looks forward to a new life as part of the experiment CASPAR at the 4,850" level of the Sanford Underground Research Facility.

Laser technologies for laser accelerators. Annual report

International Nuclear Information System (INIS)

1985-01-01

The primary result of the work reported is the determination of laser system architectures that satsify the requirements of high luminosity, high energy (about 1 TeV), electron accelerators. It has been found that high laser efficiency is a very hard driver for these accelerators as the total average laser output optical power is likely to fall above 10 MW. The luminosity requires rep rates in the kHz range, and individual pulse lengths in the 1-10 psec range are required to satisfy acceleration gradient goals. CO 2 and KrF lasers were chosen for study because of their potential to simultaneously satisfy the given requirements. Accelerator luminosity is reviewed, and requirements on laser system average power and rep rate are determined as a function of electron beam bunch parameters. Laser technologies are reviewed, including CO 2 , excimers, solid state, and free electron lasers. The proposed accelerator mechanisms are summarized briefly. Work on optical transport geometries for near and far field accelerators are presented. Possible exploitation of the CO 2 and DrF laser technology to generate the required pulse lengths, rep rates, and projected efficiencies is illustrated and needed development work is suggested. Initial efforts at developing a 50 GeV benchmark conceptual design and a 100 MeV demonstration experiment conceptual design are presented

CAS CERN Accelerator School superconductivity in particle accelerators

International Nuclear Information System (INIS)

Turner, S.

1989-01-01

One of the objectives of the CERN Accelerator School is to run courses on specialised topics in the particle accelerator field. The present volume contains the proceedings of one such course, this time organized in conjunction with the Deutsches Elektronen Synchrotron (DESY) on the subject of superconductivity in particle accelerators. This course reflects the very considerable progress made over the last few years in the use of the technology for the magnet and radio-frequency systems of many large and small accelerators already in use or nearing completion, while also taking account of the development work now going on for future machines. The lectures cover the theory of superconductivity, cryogenics and accelerator magnets and cavities, while the seminars include superfluidity, superconductors, special magnets and the prospects for high-temperature superconductors. (orig.)

Accelerator and Ion Beam Tradeoffs for Studies of Warm Dense Matter

CERN Document Server

Barnard, John J; Callahan, Debra; Davidson, Ronald C; Friedman, Alex; Grant-Logan, B; Grisham, Larry; Lee, Edward; Lee, Richard; Olson, Craig; Rose, David; Santhanam, Parthiban; Sessler, Andrew M; Staples, John W; Tabak, Max; Welch, Dale; Wurtele, Jonathan; Yu, Simon

2005-01-01

One approach to heat a target to "Warm Dense Matter" conditions (similar, for example, to the interiors of giant planets or certain stages in Inertial Confinement Fusion targets), is to use intense ion beams as the heating source. By consideration of ion beam phase space constraints, both at the injector, and at the final focus, and consideration of simple equations of state, approximate conditions at a target foil may be calculated. Thus target temperature and pressure may be calculated as a function of ion mass, ion energy, pulse duration, velocity tilt, and other accelerator parameters. We examine the variation in target performance as a function of various beam and accelerator parameters, in the context of several different accelerator concepts, recently proposed for WDM studies.

Minimal information: an urgent need to assess the functional reliability of recombinant proteins used in biological experiments

Directory of Open Access Journals (Sweden)

de Marco Ario

2008-07-01

Full Text Available Abstract Structural characterization of proteins used in biological experiments is largely neglected. In most publications, the information available is totally insufficient to judge the functionality of the proteins used and, therefore, the significance of identified protein-protein interactions (was the interaction specific or due to unspecific binding of misfolded protein regions? or reliability of kinetic and thermodynamic data (how much protein was in its native form?. As a consequence, the results of single experiments might not only become questionable, but the whole reliability of systems biology, built on these fundaments, would be weakened. The introduction of Minimal Information concerning purified proteins to add as metadata to the main body of a manuscript would render straightforward the assessment of their functional and structural qualities and, consequently, of results obtained using these proteins. Furthermore, accepted standards for protein annotation would simplify data comparison and exchange. This article has been envisaged as a proposal for aggregating scientists who share the opinion that the scientific community needs a platform for Minimum Information for Protein Functionality Evaluation (MIPFE.

A continuous acceleration tube of ions under 200 KV

International Nuclear Information System (INIS)

Mongodin, G.

1954-01-01

The realization of an Van de Graaff accelerator required, for the preliminary studies, the construction of a small proton accelerator, functioning at 200 kV in order to resolve some parasitic effects inherent to the accelerators tubes. The aim of this report is to describe the different organs of the accelerator tube, to explain the operating system and to encode their characteristics. The report first presents the ion source and the beam buncher permitting to inject in the accelerator tube particles of about 9 kV and very batched in a thin beam of circular section. Then the study explain the tube characteristics considered like optic system. A method to obtain precise calculation of particle trajectories is exposed. Aberrations of the system were discussed and balance of the currents on all electrodes inside the tube for different regimes of working were provided. The influence of the residual pressure in the tube were explained. The report finally ends on a part of the fundamental problem of the straining occurring inside the tubes accelerators under high tension. (M.B.) [fr

Bacteriophage-based synthetic biology for the study of infectious diseases

Science.gov (United States)

Lu, Timothy K.

2014-01-01

Since their discovery, bacteriophages have contributed enormously to our understanding of molecular biology as model systems. Furthermore, bacteriophages have provided many tools that have advanced the fields of genetic engineering and synthetic biology. Here, we discuss bacteriophage-based technologies and their application to the study of infectious diseases. New strategies for engineering genomes have the potential to accelerate the design of novel phages as therapies, diagnostics, and tools. Though almost a century has elapsed since their discovery, bacteriophages continue to have a major impact on modern biological sciences, especially with the growth of multidrug-resistant bacteria and interest in the microbiome. PMID:24997401

Study on the limiting acceleration rate in the VLEPP linear accelerator

International Nuclear Information System (INIS)

Balakin, V.E.; Brezhnev, O.N.; Zakhvatkin, M.N.

1987-01-01

To realize the design of colliding linear electron-positron beams it is necessary to solve the radical problem of production of accelerating structure with acceleration rate of approximately 100 MeV/m which can accelerate 10 12 particles in a bunch. Results of experimental studies of the limiting acceleration rate in the VLEPP accelerating structure are presented. Accelerating sections of different length were tested. When testing sections 29 cm long the acceleration rate of 55 MeV/m was attained, and for 1 m section the value reached 40 MeV/m. The maximum rate of acceleration (90 MeV/m) was attained when electric field intensity on the structure surface constituted more than 150 MV/m

Particle-accelerator decommissioning

International Nuclear Information System (INIS)

Opelka, J.H.; Mundis, R.L.; Marmer, G.J.; Peterson, J.M.; Siskind, B.; Kikta, M.J.

1979-12-01

Generic considerations involved in decommissioning particle accelerators are examined. There are presently several hundred accelerators operating in the United States that can produce material containing nonnegligible residual radioactivity. Residual radioactivity after final shutdown is generally short-lived induced activity and is localized in hot spots around the beam line. The decommissioning options addressed are mothballing, entombment, dismantlement with interim storage, and dismantlement with disposal. The recycle of components or entire accelerators following dismantlement is a definite possibility and has occurred in the past. Accelerator components can be recycled either immediately at accelerator shutdown or following a period of storage, depending on the nature of induced activation. Considerations of cost, radioactive waste, and radiological health are presented for four prototypic accelerators. Prototypes considered range from small accelerators having minimal amounts of radioactive mmaterial to a very large accelerator having massive components containing nonnegligible amounts of induced activation. Archival information on past decommissionings is presented, and recommendations concerning regulations and accelerator design that will aid in the decommissioning of an accelerator are given

Synthetic Biology: Putting Synthesis into Biology

Science.gov (United States)

Liang, Jing; Luo, Yunzi; Zhao, Huimin

2010-01-01

The ability to manipulate living organisms is at the heart of a range of emerging technologies that serve to address important and current problems in environment, energy, and health. However, with all its complexity and interconnectivity, biology has for many years been recalcitrant to engineering manipulations. The recent advances in synthesis, analysis, and modeling methods have finally provided the tools necessary to manipulate living systems in meaningful ways, and have led to the coining of a field named synthetic biology. The scope of synthetic biology is as complicated as life itself – encompassing many branches of science, and across many scales of application. New DNA synthesis and assembly techniques have made routine the customization of very large DNA molecules. This in turn has allowed the incorporation of multiple genes and pathways. By coupling these with techniques that allow for the modeling and design of protein functions, scientists have now gained the tools to create completely novel biological machineries. Even the ultimate biological machinery – a self-replicating organism – is being pursued at this moment. It is the purpose of this review to dissect and organize these various components of synthetic biology into a coherent picture. PMID:21064036

Beam-time for biology

CERN Multimedia

Jordan Juras

2010-01-01

There's no question that playing with mercury or handling radioactive cadmium with your bare hands is a risky business. But understanding how these and other toxic metals interact with biomolecules within the body is a challenging feat; one for which the ISOLDE IS488 collaboration hopes to provide valuable insight.   General view of the ISOLDE experimental area. Unlike most of the facilities at CERN's accelerator complex, ISOLDE is not targeted mainly at particle physics. Rather, it produces radioactive nuclei during proton bombardment to study, among other things, physical and biological chemistry. At ISOLDE, the 1.4 GeV proton beam of the PS Booster (an early stage in CERN's accelerator complex) produces nuclear reactions in a thick target, creating a large variety of radioactive nuclei, which are mass-separated for use in experiments. In the case of the IS488 collaboration, the ion beam is directed into ice. "We implant radioactive metal ions into ice", explains Monika Stac...

Variations in the Biological Functions of HIV-1 Clade C Envelope in a SHIV-Infected Rhesus Macaque during Disease Progression.

Directory of Open Access Journals (Sweden)

For Yue Tso

Full Text Available A better understanding of how the biological functions of the HIV-1 envelope (Env changes during disease progression may aid the design of an efficacious anti-HIV-1 vaccine. Although studies from patient had provided some insights on this issue, the differences in the study cohorts and methodology had make it difficult to reach a consensus of the variations in the HIV-1 Env functions during disease progression. To this end, an animal model that can be infected under controlled environment and reflect the disease course of HIV-1 infection in human will be beneficial. Such an animal model was previously demonstrated by the infection of macaque with SHIV, expressing HIV-1 clade C Env V1-V5 region. By using this model, we examined the changes in biological functions of Env in the infected animal over the entire disease course. Our data showed an increase in the neutralization resistance phenotype over time and coincided with the decrease in the net charges of the V1-V5 region. Infection of PBMC with provirus expressing various Env clones, isolated from the infected animal over time, showed a surprisingly better replicative fitness for viruses expressing the Env from early time point. Biotinylation and ELISA data also indicated a decrease of cell-surface-associated Env and virion-associated gp120 content with disease progression. This decrease did not affect the CD4-binding capability of Env, but were positively correlated with the decrease of Env fusion ability. Interestingly, some of these changes in biological functions reverted to the pre-AIDS level during advance AIDS. These data suggested a dynamic relationship between the Env V1-V5 region with the host immune pressure. The observed changes of biological functions in this setting might reflect and predict those occurring during natural disease progression in human.

Perturbation analysis of octupoles in circular accelerators

International Nuclear Information System (INIS)

Moohyun Yoon

1998-01-01

The octupole effects in a circular accelerator are analyzed using a first-order canonical perturbation theory. It is shown that, to the first order, the nonlinear amplitude-dependent tune shifts due to an octupole are composed of two types: terms of second order and terms of fourth order in betatron-oscillation amplitudes. The fourth-order part of tune shifts is expressed in terms of distortion functions. Distortion functions are also expanded in harmonics to express the higher-order tune shifts in harmonically expanded form. Finally, the results are applied to an accelerator and compared with the results of numerical tracking of particles. Laskar's algorithm for numerical analysis of the fundamental frequency is used to determine tunes from the tracking data, in which the error becomes inversely proportional to the cube of the number of data points. (author)

The development of peptide-based interfacial biomaterials for generating biological functionality on the surface of bioinert materials.

Science.gov (United States)

Meyers, Steven R; Khoo, Xiaojuan; Huang, Xin; Walsh, Elisabeth B; Grinstaff, Mark W; Kenan, Daniel J

2009-01-01

Biomaterials used in implants have traditionally been selected based on their mechanical properties, chemical stability, and biocompatibility. However, the durability and clinical efficacy of implantable biomedical devices remain limited in part due to the absence of appropriate biological interactions at the implant interface and the lack of integration into adjacent tissues. Herein, we describe a robust peptide-based coating technology capable of modifying the surface of existing biomaterials and medical devices through the non-covalent binding of modular biofunctional peptides. These peptides contain at least one material binding sequence and at least one biologically active sequence and thus are termed, "Interfacial Biomaterials" (IFBMs). IFBMs can simultaneously bind the biomaterial surface while endowing it with desired biological functionalities at the interface between the material and biological realms. We demonstrate the capabilities of model IFBMs to convert native polystyrene, a bioinert surface, into a bioactive surface that can support a range of cell activities. We further distinguish between simple cell attachment with insufficient integrin interactions, which in some cases can adversely impact downstream biology, versus biologically appropriate adhesion, cell spreading, and cell survival mediated by IFBMs. Moreover, we show that we can use the coating technology to create spatially resolved patterns of fluorophores and cells on substrates and that these patterns retain their borders in culture.

Electrostatic accelerators

CERN Document Server

Hinterberger, F

2006-01-01

The principle of electrostatic accelerators is presented. We consider Cockcroft– Walton, Van de Graaff and Tandem Van de Graaff accelerators. We resume high voltage generators such as cascade generators, Van de Graaff band generators, Pelletron generators, Laddertron generators and Dynamitron generators. The speci c features of accelerating tubes, ion optics and methods of voltage stabilization are described. We discuss the characteristic beam properties and the variety of possible beams. We sketch possible applications and the progress in the development of electrostatic accelerators.

On the limitations of standard statistical modeling in biological systems: a full Bayesian approach for biology.

Science.gov (United States)

Gomez-Ramirez, Jaime; Sanz, Ricardo

2013-09-01

One of the most important scientific challenges today is the quantitative and predictive understanding of biological function. Classical mathematical and computational approaches have been enormously successful in modeling inert matter, but they may be inadequate to address inherent features of biological systems. We address the conceptual and methodological obstacles that lie in the inverse problem in biological systems modeling. We introduce a full Bayesian approach (FBA), a theoretical framework to study biological function, in which probability distributions are conditional on biophysical information that physically resides in the biological system that is studied by the scientist. Copyright © 2013 Elsevier Ltd. All rights reserved.

Pulsed Light Accelerated Crosslinking versus Continuous Light Accelerated Crosslinking: One-Year Results

Directory of Open Access Journals (Sweden)

Cosimo Mazzotta

2014-01-01

Full Text Available Purpose. To compare functional results in two cohorts of patients undergoing epithelium-off pulsed (pl-ACXL and continuous light accelerated corneal collagen crosslinking (cl-ACXL with dextran-free riboflavin solution and high-fluence ultraviolet A irradiation. Design. It is a prospective, comparative, and interventional clinical study. Methods. 20 patients affected by progressive keratoconus were enrolled in the study. 10 eyes of 10 patients underwent an epithelium-off pl-ACXL by the KXL UV-A source (Avedro Inc., Waltham, MS, USA with 8 minutes (1 sec. on/1 sec. off of UV-A exposure at 30 mW/cm2 and energy dose of 7.2 J/cm2; 10 eyes of 10 patients underwent an epithelium-off cl-ACXL at 30 mW/cm2 for 4 minutes. Riboflavin 0.1% dextran-free solution was used for a 10-minutes corneal soaking. Patients underwent clinical examination of uncorrected distance visual acuity and corrected distance visual acuity (UDVA and CDVA, corneal topography and aberrometry (CSO EyeTop, Florence, Italy, corneal OCT optical pachymetry (Cirrus OCT, Zeiss Meditec, Jena, Germany, endothelial cells count (I-Conan Non Co Robot, and in vivo scanning laser confocal microscopy (Heidelberg, Germany at 1, 3, 6, and 12 months of follow-up. Results. Functional results one year after cl-ACXL and pl-ACXL demonstrated keratoconus stability in both groups. Functional outcomes were found to be better in epithelium-off pulsed light accelerated treatment together with showing a deeper stromal penetration. No endothelial damage was recorded during the follow-up in both groups. Conclusions. The study confirmed that oxygen represents the main driver of collagen crosslinking reaction. Pulsed light treatment optimized intraoperative oxygen availability improving postoperative functional outcomes compared with continuous light treatment.

Synthetic biology projects in vitro.

Science.gov (United States)

Forster, Anthony C; Church, George M

2007-01-01

Advances in the in vitro synthesis and evolution of DNA, RNA, and polypeptides are accelerating the construction of biopolymers, pathways, and organisms with novel functions. Known functions are being integrated and debugged with the aim of synthesizing life-like systems. The goals are knowledge, tools, smart materials, and therapies.

Library Support for Resource Constrained Accelerators

DEFF Research Database (Denmark)

Brock-Nannestad, Laust; Karlsson, Sven

2014-01-01

. In this paper, we present a lightweight system where an accelerator can remotely execute library functions on a host processor. The implementation takes up 750 bytes but can replace arbitrary library calls leading to significant savings in memory foot print. We evaluate with a set of SPLASH-2 applications...

Acceleration of 14C beams in electrostatic accelerators

International Nuclear Information System (INIS)

Rowton, L.J.; Tesmer, J.R.

1981-01-01

Operational problems in the production and acceleration of 14 C beams for nuclear structure research in Los Alamos National Laboratory's Van de Graaff accelerators are discussed. Methods for the control of contamination in ion sources, accelerators and personnel are described. Sputter source target fabrication techniques and the relative beam production efficiencies of various types of bound particulate carbon sputter source targets are presented

Multiperiodic accelerator structures for linear particle accelerators

International Nuclear Information System (INIS)

Tran, D.T.

1975-01-01

High efficiency linear accelerator structures, comprised of a succession of cylindrical resonant cavities for acceleration, are described. Coupling annular cavities are located at the periphery, each being coupled to two adjacent cylindrical cavities. (auth)

Accelerated decline in lung function in smoking women with airway obstruction: SAPALDIA 2 cohort study

Directory of Open Access Journals (Sweden)

Zemp Elisabeth

2005-05-01

Full Text Available Abstract Background The aim was to determine if effects from smoking on lung function measured over 11 years differ between men and women. Methods In a prospective population based cohort study (Swiss Study on Air Pollution and Lung Diseases in Adults current smokers in 1991 (18 – 60 yrs were reassessed in 2002 (n = 1792. Multiple linear regression was used to estimate effects from pack-years of cigarettes smoked to 1991 and mean packs of cigarettes smoked per day between 1991 and 2002 on change in lung volume and flows over the 11 years. Results In both sexes, packs smoked between assessments were related to lung function decline but pack-years smoked before 1991 were not. Mean annual decline in FEV1 was -10.4 mL(95%CI -15.3, -5.5 per pack per day between assessments in men and -13.8 mL(95%CI-19.5,-8.1 in women. Decline per pack per day between 1991 and 2002 was lower in women who smoked in 1991 but quit before 2002 compared to persistent smokers (-6.4 vs -11.6 mL, p = 0.05 but this was not seen in men (-14.3 vs -8.8 mL p = 0.49. Smoking related decline was accelerated in men and women with airway obstruction, particularly in women where decline in FEV1 was three fold higher in participants with FEV1/FVC Conclusion There are differences in effects from smoking on lung function between men and women. Lung function recovers faster in women quitters than in men. Women current smokers with airway obstruction experience a greater smoking related decline in lung function than men.

Synthetic biological networks

International Nuclear Information System (INIS)

Archer, Eric; Süel, Gürol M

2013-01-01

Despite their obvious relationship and overlap, the field of physics is blessed with many insightful laws, while such laws are sadly absent in biology. Here we aim to discuss how the rise of a more recent field known as synthetic biology may allow us to more directly test hypotheses regarding the possible design principles of natural biological networks and systems. In particular, this review focuses on synthetic gene regulatory networks engineered to perform specific functions or exhibit particular dynamic behaviors. Advances in synthetic biology may set the stage to uncover the relationship of potential biological principles to those developed in physics. (review article)

Accelerated differentiation of osteoblast cells on polycaprolactone scaffolds driven by a combined effect of protein coating and plasma modification

Energy Technology Data Exchange (ETDEWEB)

Yildirim, Eda D; Gueceri, Selcuk; Sun, Wei [Department of Mechanical Engineering and Mechanics, Drexel University, 3141 Chestnut Street, Philadelphia, PA 19104 (United States); Besunder, Robyn; Allen, Fred [Drexel University, School of Biomedical Engineering Science and Health System, 3141 Chestnut Street, Philadelphia, PA 19104 (United States); Pappas, Daphne, E-mail: edy22@drexel.ed [Army Research Laboratory, Aberdeen Proving Ground, MD 21005 (United States)

2010-03-15

A combined effect of protein coating and plasma modification on the quality of the osteoblast-scaffold interaction was investigated. Three-dimensional polycaprolactone (PCL) scaffolds were manufactured by the precision extrusion deposition (PED) system. The structural, physical, chemical and biological cues were introduced to the surface through providing 3D structure, coating with adhesive protein fibronectin and modifying the surface with oxygen-based plasma. The changes in the surface properties of PCL after those modifications were examined by contact angle goniometry, surface energy calculation, surface chemistry analysis (XPS) and surface topography measurements (AFM). The effects of modification techniques on osteoblast short-term and long-term functions were examined by cell adhesion, proliferation assays and differentiation markers, namely alkaline phosphatase activity (ALP) and osteocalcin secretion. The results suggested that the physical and chemical cues introduced by plasma modification might be sufficient for improved cell adhesion, but for accelerated osteoblast differentiation the synergetic effects of structural, physical, chemical and biological cues should be introduced to the PCL surface.

Research and development achievement report for fiscal 1998 on accelerated type biological function construction technologies. Development of new-type advanced-function enzyme creating technologies; 1998 nendo kasokugata seibutsu kino kochiku gijutsu no kenkyu kaihatsu seika hokokusho. Shingata kokino koso sosei gijutsu kaihatsu

Energy Technology Data Exchange (ETDEWEB)

NONE

1999-03-01

An artificial mutation/selection system was constructed in a laboratory based on molecular-level findings collected about the biological evolution mechanism, and biotechnology was studied for creating excellent biological functions. In the study of novel mutation generating technologies, selection is performed after the formation of numerous chimera enzymes by a family shuffling process using resistance to heat as the index. Then, a hybrid enzyme with its resistance to heat more than 10 times higher than that of the parent enzyme was obtained. In the study of establishing coordination between genotype and phenotype, a highly sensitive bacterial coordination technology was developed, and a highly sensitive detection method was constructed using a flow cytometer. As for technologies of highly efficient selection, a research was conducted about the selection of catalytic antibodies equipped with protease and esterase activity. In the study of technologies for enhancing adaptive walk in an evolution experimenting system, the usefulness is studied of a terrain survey based on the adaptive walk theory and a high-efficiency adaptive walk method using the mutation scrambling method. (NEDO)

PREFACE: Nanobiology: from physics and engineering to biology

Science.gov (United States)

Nussinov, Ruth; Alemán, Carlos

2006-03-01

shapes and materials. Inspection of the protein structure databank illustrates the breadth of scaffolds, shapes and properties that protein molecules and their building blocks can provide. Via a shape-guided self-assembly strategy, these can be put together toward a specific function. Further, by inserting synthetic non-natural residues at judiciously selected positions, or synthetic peptide linkers, we may selectively rigidify the construct, or obtain a totally new world of shapes and scaffolds. Such broadening of the chemical space may lead to an almost unlimited range of nanosystems and architectures. Merging computation with experiment will accelerate nanodesign. Computational modeling will enhance the application of nanotechnology to key areas such as drug delivery and biomaterial design. Nanobiology is a field where interdisciplinary collaborations are essential and disciplines converge. Discipline convergence should enable the quantitation, leading to a better understanding of the regulatory networks within cells and between cells of an organism. These networks dictate how a cell responds to external stimuli, which in turn activate signaling cascades. It should allow the addressing of a broad range of questions on the structure and function of the cytoskeleton; the nuclear envelope; signal transduction by membrane embedded receptors; the nanomechanical properties of the extracellular matrix; nuclear transport; and voltage induced channel gating. For successful nanostructure design, we need to figure out and be able to control the intermolecular associations. For a stable functional construct, there are two key elements: first, the conformations of the building blocks in the designed structure should follow their natural tendencies; and second, the associations should be favorable. Molecules interact through their surfaces. Thus, favorable associations derive from shape complementarity and contributions of the various physical components. Nanobiology is in its

An Accelerator Control Middle Layer Using MATLAB

International Nuclear Information System (INIS)

Portmann, Gregory J.; Corbett, Jeff; Terebilo, Andrei

2005-01-01

Matlab is an interpretive programming language originally developed for convenient use with the LINPACK and EISPACK libraries. Matlab is appealing for accelerator physics because it is matrix-oriented, provides an active workspace for system variables, powerful graphics capabilities, built-in math libraries, and platform independence. A number of accelerator software toolboxes have been written in Matlab -- the Accelerator Toolbox (AT) for model-based machine simulations, LOCO for on-line model calibration, and Matlab Channel Access (MCA) to connect with EPICS. The function of the MATLAB ''MiddleLayer'' is to provide a scripting language for machine simulations and on-line control, including non-EPICS based control systems. The MiddleLayer has simplified and streamlined development of high-level applications including configuration control, energy ramp, orbit correction, photon beam steering, ID compensation, beam-based alignment, tune correction and response matrix measurement. The database-driven Middle Layer software is largely machine-independent and easy to port. Six accelerators presently use the software package with more scheduled to come on line soon

From laser-plasma accelerators to femtosecond X-ray sources: study, development and applications

International Nuclear Information System (INIS)

Corde, S.

2012-01-01

During the relativistic interaction between a short and intense laser pulse and an underdense plasma, electrons can be injected and accelerated up to hundreds of MeV in an accelerating structure formed in the wake of the pulse: this is the so-called laser-plasma accelerator. One of the major perspectives for laser-plasma accelerators resides in the realization of compact sources of femtosecond x-ray beams. In this thesis, two x-ray sources was studied and developed. The betatron radiation, intrinsic to laser-plasma accelerators, comes from the transverse oscillations of electrons during their acceleration. Its characterization by photon counting revealed an x-ray beam containing 10"9 photons, with energies extending above 10 keV. We also developed an all-optical Compton source producing photons with energies up to hundreds of keV, based on the collision between a photon beam and an electron beam. The potential of these x-ray sources was highlighted by the realization of single shot phase contrast imaging of a biological sample. Then, we showed that the betatron x-ray radiation can be a powerful tool to study the physics of laser-plasma acceleration. We demonstrated the possibility to map the x-ray emission region, which gives a unique insight into the interaction, permitting us for example to locate the region where electrons are injected. The x-ray angular and spectral properties allow us to gain information on the transverse dynamics of electrons during their acceleration. (author)

Beam transport through electrostatic accelerators and matching into post accelerators

International Nuclear Information System (INIS)

Larson, J.D.

1986-01-01

Ion beam transport through electrostatic acceleration is briefly reviewed. Topics discussed include injection, matching into the low-energy acceleration stage, matching from the terminal stripper into the high-energy stage, transport to a post accelerator, space charge, bunching isochronism, dispersion and charge selection. Beam transport plans for the proposed Vivitron accelerator are described. (orig.)

Rapidly restoring biological soil crusts and ecosystem functions in a severely disturbed desert ecosystem.

Science.gov (United States)

Chiquoine, Lindsay P; Abella, Scott R; Bowker, Matthew A

2016-06-01

Restoring biological soil crusts (biocrusts) in degraded drylands can contribute to recovery of ecosystem functions that have global implications, including erosion resistance and nutrient cycling. To examine techniques for restoring biocrusts, we conducted a replicated, factorial experiment on recently abandoned road surfaces by applying biocrust inoculation (salvaged and stored dry for two years), salvaged topsoil, an abiotic soil amendment (wood shavings), and planting of a dominant perennial shrub (Ambrosia dumosa). Eighteen months after treatments, we measured biocrust abundance and species composition, soil chlorophyll a content and fertility, and soil resistance to erosion. Biocrust addition significantly accelerated biocrust recovery on disturbed soils, including increasing lichen and moss cover and cyanobacteria colonization. Compared to undisturbed controls, inoculated plots had similar lichen and moss composition, recovered 43% of total cyanobacteria density, had similar soil chlorophyll content, and exhibited recovery of soil fertility and soil stability. Inoculation was the only treatment that generated lichen and moss cover. Topsoil application resulted in partial recovery of the cyanobacteria community and soil properties. Compared to untreated disturbed plots, topsoil application without inoculum increased cyanobacteria density by 186% and moderately improved soil chlorophyll and ammonium content and soil stability. Topsoil application produced 22% and 51% of the cyanobacteria density g⁻¹ soil compared to undisturbed and inoculated plots, respectively. Plots not treated with either topsoil or inoculum had significantly lower cyanobacteria density, soil chlorophyll and ammonium concentrations, and significantly higher soil nitrate concentration. Wood shavings and Ambrosia had no influence on biocrust lichen and moss species recovery but did affect cyanobacteria composition and soil fertility. Inoculation of severely disturbed soil with native

Mammalian Synthetic Biology: Engineering Biological Systems.

Science.gov (United States)

Black, Joshua B; Perez-Pinera, Pablo; Gersbach, Charles A

2017-06-21

The programming of new functions into mammalian cells has tremendous application in research and medicine. Continued improvements in the capacity to sequence and synthesize DNA have rapidly increased our understanding of mechanisms of gene function and regulation on a genome-wide scale and have expanded the set of genetic components available for programming cell biology. The invention of new research tools, including targetable DNA-binding systems such as CRISPR/Cas9 and sensor-actuator devices that can recognize and respond to diverse chemical, mechanical, and optical inputs, has enabled precise control of complex cellular behaviors at unprecedented spatial and temporal resolution. These tools have been critical for the expansion of synthetic biology techniques from prokaryotic and lower eukaryotic hosts to mammalian systems. Recent progress in the development of genome and epigenome editing tools and in the engineering of designer cells with programmable genetic circuits is expanding approaches to prevent, diagnose, and treat disease and to establish personalized theranostic strategies for next-generation medicines. This review summarizes the development of these enabling technologies and their application to transforming mammalian synthetic biology into a distinct field in research and medicine.

Ferrite measurements for SNS accelerating cavities

International Nuclear Information System (INIS)

Bendall, R.G.; Church, R.A.

1979-03-01

The RF system for the SNS has six double accelerating cavities each containing seventy ferrite toroids. Difficulties experienced in obtaining toroids to the required specifications are discussed and the two toroid test cavity built to test those supplied is described. Ferrite measurements are reported which were undertaken to measure; (a) μQf as a function of frequency and RF field level and (b) bias current as a function of frequency for different ranges of ferrite permeability μ. (U.K.)

Permeating disciplines: Overcoming barriers between molecular simulations and classical structure-function approaches in biological ion transport.

Science.gov (United States)

Howard, Rebecca J; Carnevale, Vincenzo; Delemotte, Lucie; Hellmich, Ute A; Rothberg, Brad S

2018-04-01

Ion translocation across biological barriers is a fundamental requirement for life. In many cases, controlling this process-for example with neuroactive drugs-demands an understanding of rapid and reversible structural changes in membrane-embedded proteins, including ion channels and transporters. Classical approaches to electrophysiology and structural biology have provided valuable insights into several such proteins over macroscopic, often discontinuous scales of space and time. Integrating these observations into meaningful mechanistic models now relies increasingly on computational methods, particularly molecular dynamics simulations, while surfacing important challenges in data management and conceptual alignment. Here, we seek to provide contemporary context, concrete examples, and a look to the future for bridging disciplinary gaps in biological ion transport. This article is part of a Special Issue entitled: Beyond the Structure-Function Horizon of Membrane Proteins edited by Ute Hellmich, Rupak Doshi and Benjamin McIlwain. Copyright © 2017 Elsevier B.V. All rights reserved.

Accelerated Testing with Multiple Failure Modes under Several Temperature Conditions

Directory of Open Access Journals (Sweden)

Zongyue Yu

2014-01-01

Full Text Available A complicated device may have multiple failure modes, and some of the failure modes are sensitive to low temperatures. To assess the reliability of a product with multiple failure modes, this paper presents an accelerated testing in which both of the high temperatures and the low temperatures are applied. Firstly, an acceleration model based on the Arrhenius model but accounting for the influence of both the high temperatures and low temperatures is proposed. Accordingly, an accelerated testing plan including both the high temperatures and low temperatures is designed, and a statistical analysis method is developed. The reliability function of the product with multiple failure modes under variable working conditions is given by the proposed statistical analysis method. Finally, a numerical example is studied to illustrate the proposed accelerated testing. The results show that the proposed accelerated testing is rather efficient.

Shielding Calculations for Industrial 5/7.5MeV Electron Accelerators Using the MCNP Monte Carlo Code

International Nuclear Information System (INIS)

Peri, E.; Orion, I.

2014-01-01

High energy X-rays from accelerators are used to irradiate food ingredients to prevent growth and development of unwanted biological organisms in food, in order to extend the shelf life of products. High energy photons can cause food activation due to (D 3 ,n) reactions. Until 2004, to eliminate the possibility of food activation, the electron energy was limited to 5 MeV X-rays for food irradiation. In 2004, the FDA approved the usage of up to 7.5 MeV, but only with tantalum and gold targets (1). Higher X-ray energy results an increased flux of X-rays in the forward direction, increased penetration, and higher photon dose rate due to better electron-to-photon conversion. These improvements could decrease the irradiation time and allow irradiation of larger packages, thereby providing higher production rates with lower treatment cost. Medical accelerators usually work with 6-18 MV electron energy with tungsten target to convert the electron beam to X-rays. In order to protect the patients, the accelerator head is protected with a heavy lead shielding; therefore, the bremsstrahlung is emitted only in the forward direction. There are many publications and standards that guide how to design optimal shielding for medical accelerator rooms. The shielding data for medical accelerators is not applicable for industrial accelerators, since the data is for different conversion targets, different X-Ray energies, and only for the forward direction. Collimators are not always in use in industrial accelerators, and therefore bremsstrahlung photons can be emitted in all directions. The bremsstrahlung spectrum and dose rate change as a function of the emission angle. The dose rate decreases from maximum in the forward direction (0°) to minimum at 180° by 1-2 orders of magnitude. In order to design and calculate optimal shielding for food accelerator rooms, there is a need to have the bremsstrahlung spectrum data, dose rates and concrete attenuation data in all emission directions

Plant biology research and training for the 21st century

Energy Technology Data Exchange (ETDEWEB)

Kelly, K. [ed.

1992-12-31

The committee was assembled in response to a request from the National Science Foundation (NSF), the US Department of Agriculture (USDA), and the US Department of Energy (DoE). The leadership of these agencies asked the National Academy of Sciences through the National Research Council (NRC) to assess the status of plant-science research in the United States in light of the opportunities arising from advances inother areas of biology. NRC was asked to suggest ways of accelerating the application of these new biologic concepts and tools to research in plant science with the aim of enhancing the acquisition of new knowledge about plants. The charge to the committee was to examine the following: Organizations, departments, and institutions conducting plant biology research; human resources involved in plant biology research; graduate training programs in plant biology; federal, state, and private sources of support for plant-biology research; the role of industry in conducting and supporting plant-biology research; the international status of US plant-biology research; and the relationship of plant biology to leading-edge research in biology.

Plant biology research and training for the 21st century

Energy Technology Data Exchange (ETDEWEB)

Kelly, K. (ed.)

1992-01-01

The committee was assembled in response to a request from the National Science Foundation (NSF), the US Department of Agriculture (USDA), and the US Department of Energy (DoE). The leadership of these agencies asked the National Academy of Sciences through the National Research Council (NRC) to assess the status of plant-science research in the United States in light of the opportunities arising from advances inother areas of biology. NRC was asked to suggest ways of accelerating the application of these new biologic concepts and tools to research in plant science with the aim of enhancing the acquisition of new knowledge about plants. The charge to the committee was to examine the following: Organizations, departments, and institutions conducting plant biology research; human resources involved in plant biology research; graduate training programs in plant biology; federal, state, and private sources of support for plant-biology research; the role of industry in conducting and supporting plant-biology research; the international status of US plant-biology research; and the relationship of plant biology to leading-edge research in biology.

Can Accelerators Accelerate Learning?

International Nuclear Information System (INIS)

Santos, A. C. F.; Fonseca, P.; Coelho, L. F. S.

2009-01-01

The 'Young Talented' education program developed by the Brazilian State Funding Agency (FAPERJ)[1] makes it possible for high-schools students from public high schools to perform activities in scientific laboratories. In the Atomic and Molecular Physics Laboratory at Federal University of Rio de Janeiro (UFRJ), the students are confronted with modern research tools like the 1.7 MV ion accelerator. Being a user-friendly machine, the accelerator is easily manageable by the students, who can perform simple hands-on activities, stimulating interest in physics, and getting the students close to modern laboratory techniques.

Can Accelerators Accelerate Learning?

Science.gov (United States)

Santos, A. C. F.; Fonseca, P.; Coelho, L. F. S.

2009-03-01

The 'Young Talented' education program developed by the Brazilian State Funding Agency (FAPERJ) [1] makes it possible for high-schools students from public high schools to perform activities in scientific laboratories. In the Atomic and Molecular Physics Laboratory at Federal University of Rio de Janeiro (UFRJ), the students are confronted with modern research tools like the 1.7 MV ion accelerator. Being a user-friendly machine, the accelerator is easily manageable by the students, who can perform simple hands-on activities, stimulating interest in physics, and getting the students close to modern laboratory techniques.

Electromagnetic forming - a potentially viable technique for accelerator technology

International Nuclear Information System (INIS)

Rajawat, R.K.; Desai, S.V.; Kulkarni, M.R.; Dolly Rani; Nagesh, K.V.; Sethi, R.C.

2003-01-01

Modern day accelerator development encompasses a myriad technologies required for their diverse needs. Whereas RF, high voltage, vacuum, cryogenics etc., technologies meet their functional requirements, high finish lapping processes, ceramic-metal joining, oven brazing, spark erosion or wire cutting etc., are a must to meet their fabrication requirements. Electromagnetic (EM) forming technique falls in the latter category and is developed as a special technology. It is currently catering to the development as a nuclear reactor technology, but has the potential to meet accelerator requirements too. This paper highlights the general principle of its working, simple design guidelines, advantages, and suggests some specific areas where this could benefit accelerator technologies

Surface functionalization of bioactive glasses with natural molecules of biological significance, Part I: Gallic acid as model molecule

Science.gov (United States)

Zhang, Xin; Ferraris, Sara; Prenesti, Enrico; Verné, Enrica

2013-12-01

Gallic acid (3,4,5-trihydroxybenzoic acid, GA) and its derivatives are a group of biomolecules (polyphenols) obtained from plants. They have effects which are potentially beneficial to heath, for example they are antioxidant, anticarcinogenic and antibacterial, as recently investigated in many fields such as medicine, food and plant sciences. The main drawbacks of these molecules are both low stability and bioavailability. In this research work the opportunity to graft GA to bioactive glasses is investigated, in order to deliver the undamaged biological molecule into the body, using the biomaterial surfaces as a localized carrier. GA was considered for functionalization since it is a good model molecule for polyphenols and presents several interesting biological activities, like antibacterial, antioxidant and anticarcinogenic properties. Two different silica based bioactive glasses (SCNA and CEL2), with different reactivity, were employed as substrates. UV photometry combined with the Folin&Ciocalteu reagent was adopted to test the concentration of GA in uptake solution after functionalization. This test verified how much GA consumption occurred with surface modification and it was also used on solid samples to test the presence of GA on functionalized glasses. XPS and SEM-EDS techniques were employed to characterize the modification of material surface properties and functional group composition before and after functionalization.

A comparison of quantitative reconstruction techniques for PIXE-tomography analysis applied to biological samples

Energy Technology Data Exchange (ETDEWEB)

Beasley, D.G., E-mail: dgbeasley@ctn.ist.utl.pt [IST/C2TN, Universidade de Lisboa, Campus Tecnológico e Nuclear, E.N.10, 2686-953 Sacavém (Portugal); Alves, L.C. [IST/C2TN, Universidade de Lisboa, Campus Tecnológico e Nuclear, E.N.10, 2686-953 Sacavém (Portugal); Barberet, Ph.; Bourret, S.; Devès, G.; Gordillo, N.; Michelet, C. [Univ. Bordeaux, CENBG, UMR 5797, F-33170 Gradignan (France); CNRS, IN2P3, CENBG, UMR 5797, F-33170 Gradignan (France); Le Trequesser, Q. [Univ. Bordeaux, CENBG, UMR 5797, F-33170 Gradignan (France); CNRS, IN2P3, CENBG, UMR 5797, F-33170 Gradignan (France); Institut de Chimie de la Matière Condensée de Bordeaux (ICMCB, UPR9048) CNRS, Université de Bordeaux, 87 avenue du Dr. A. Schweitzer, Pessac F-33608 (France); Marques, A.C. [IST/IPFN, Universidade de Lisboa, Campus Tecnológico e Nuclear, E.N.10, 2686-953 Sacavém (Portugal); Seznec, H. [Univ. Bordeaux, CENBG, UMR 5797, F-33170 Gradignan (France); CNRS, IN2P3, CENBG, UMR 5797, F-33170 Gradignan (France); Silva, R.C. da [IST/IPFN, Universidade de Lisboa, Campus Tecnológico e Nuclear, E.N.10, 2686-953 Sacavém (Portugal)

2014-07-15

The tomographic reconstruction of biological specimens requires robust algorithms, able to deal with low density contrast and low element concentrations. At the IST/ITN microprobe facility new GPU-accelerated reconstruction software, JPIXET, has been developed, which can significantly increase the speed of quantitative reconstruction of Proton Induced X-ray Emission Tomography (PIXE-T) data. It has a user-friendly graphical user interface for pre-processing, data analysis and reconstruction of PIXE-T and Scanning Transmission Ion Microscopy Tomography (STIM-T). The reconstruction of PIXE-T data is performed using either an algorithm based on a GPU-accelerated version of the Maximum Likelihood Expectation Maximisation (MLEM) method or a GPU-accelerated version of the Discrete Image Space Reconstruction Algorithm (DISRA) (Sakellariou (2001) [2]). The original DISRA, its accelerated version, and the MLEM algorithm, were compared for the reconstruction of a biological sample of Caenorhabditis elegans – a small worm. This sample was analysed at the microbeam line of the AIFIRA facility of CENBG, Bordeaux. A qualitative PIXE-T reconstruction was obtained using the CENBG software package TomoRebuild (Habchi et al. (2013) [6]). The effects of pre-processing and experimental conditions on the elemental concentrations are discussed.

Synthetic Biology and the Translational Imperative.

Science.gov (United States)

Heidari Feidt, Raheleh; Ienca, Marcello; Elger, Bernice Simone; Folcher, Marc

2017-12-18

Advances at the interface between the biological sciences and engineering are giving rise to emerging research fields such as synthetic biology. Harnessing the potential of synthetic biology requires timely and adequate translation into clinical practice. However, the translational research enterprise is currently facing fundamental obstacles that slow down the transition of scientific discoveries from the laboratory to the patient bedside. These obstacles including scarce financial resources and deficiency of organizational and logistic settings are widely discussed as primary impediments to translational research. In addition, a number of socio-ethical considerations inherent in translational research need to be addressed. As the translational capacity of synthetic biology is tightly linked to its social acceptance and ethical approval, ethical limitations may-together with financial and organizational problems-be co-determinants of suboptimal translation. Therefore, an early assessment of such limitations will contribute to proactively favor successful translation and prevent the promising potential of synthetic biology from remaining under-expressed. Through the discussion of two case-specific inventions in synthetic biology and their associated ethical implications, we illustrate the socio-ethical challenges ahead in the process of implementing synthetic biology into clinical practice. Since reducing the translational lag is essential for delivering the benefits of basic biomedical research to society at large and promoting global health, we advocate a moral obligation to accelerating translational research: the "translational imperative."

FUSE: a profit maximization approach for functional summarization of biological networks.

Science.gov (United States)

Seah, Boon-Siew; Bhowmick, Sourav S; Dewey, C Forbes; Yu, Hanry

2012-03-21

The availability of large-scale curated protein interaction datasets has given rise to the opportunity to investigate higher level organization and modularity within the protein interaction network (PPI) using graph theoretic analysis. Despite the recent progress, systems level analysis of PPIS remains a daunting task as it is challenging to make sense out of the deluge of high-dimensional interaction data. Specifically, techniques that automatically abstract and summarize PPIS at multiple resolutions to provide high level views of its functional landscape are still lacking. We present a novel data-driven and generic algorithm called FUSE (Functional Summary Generator) that generates functional maps of a PPI at different levels of organization, from broad process-process level interactions to in-depth complex-complex level interactions, through a pro t maximization approach that exploits Minimum Description Length (MDL) principle to maximize information gain of the summary graph while satisfying the level of detail constraint. We evaluate the performance of FUSE on several real-world PPIS. We also compare FUSE to state-of-the-art graph clustering methods with GO term enrichment by constructing the biological process landscape of the PPIS. Using AD network as our case study, we further demonstrate the ability of FUSE to quickly summarize the network and identify many different processes and complexes that regulate it. Finally, we study the higher-order connectivity of the human PPI. By simultaneously evaluating interaction and annotation data, FUSE abstracts higher-order interaction maps by reducing the details of the underlying PPI to form a functional summary graph of interconnected functional clusters. Our results demonstrate its effectiveness and superiority over state-of-the-art graph clustering methods with GO term enrichment.