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Sample records for biological agent simulants

  1. A decontamination study of simulated chemical and biological agents

    NASA Astrophysics Data System (ADS)

    Uhm, Han S.; Lee, Han Y.; Hong, Yong C.; Shin, Dong H.; Park, Yun H.; Hong, Yi F.; Lee, Chong K.

    2007-07-01

    A comprehensive decontamination scheme of the chemical and biological agents, including airborne agents and surface contaminating agents, is presented. When a chemical and biological attack occurs, it is critical to decontaminate facilities or equipments to an acceptable level in a very short time. The plasma flame presented here may provide a rapid and effective elimination of toxic substances in the interior air in isolated spaces. As an example, a reaction chamber, with the dimensions of a 22cm diameter and 30cm length, purifies air with an airflow rate of 5000l/min contaminated with toluene, the simulated chemical agent, and soot from a diesel engine, the simulated aerosol for biological agents. Although the airborne agents in an isolated space are eliminated to an acceptable level by the plasma flame, the decontamination of the chemical and biological agents cannot be completed without cleaning surfaces of the facilities. A simulated sterilization study of micro-organisms was carried out using the electrolyzed ozone water. The electrolyzed ozone water very effectively kills endospores of Bacillus atrophaeus (ATCC 9372) within 3min. The electrolyzed ozone water also kills the vegetative micro-organisms, fungi, and virus. The electrolyzed ozone water, after the decontamination process, disintegrates into ordinary water and oxygen without any trace of harmful materials to the environment.

  2. A decontamination study of simulated chemical and biological agents

    SciTech Connect

    Uhm, Han S.; Lee, Han Y.; Hong, Yong C.; Shin, Dong H.; Park, Yun H.; Hong, Yi F.; Lee, Chong K.

    2007-07-01

    A comprehensive decontamination scheme of the chemical and biological agents, including airborne agents and surface contaminating agents, is presented. When a chemical and biological attack occurs, it is critical to decontaminate facilities or equipments to an acceptable level in a very short time. The plasma flame presented here may provide a rapid and effective elimination of toxic substances in the interior air in isolated spaces. As an example, a reaction chamber, with the dimensions of a 22 cm diameter and 30 cm length, purifies air with an airflow rate of 5000 l/min contaminated with toluene, the simulated chemical agent, and soot from a diesel engine, the simulated aerosol for biological agents. Although the airborne agents in an isolated space are eliminated to an acceptable level by the plasma flame, the decontamination of the chemical and biological agents cannot be completed without cleaning surfaces of the facilities. A simulated sterilization study of micro-organisms was carried out using the electrolyzed ozone water. The electrolyzed ozone water very effectively kills endospores of Bacillus atrophaeus (ATCC 9372) within 3 min. The electrolyzed ozone water also kills the vegetative micro-organisms, fungi, and virus. The electrolyzed ozone water, after the decontamination process, disintegrates into ordinary water and oxygen without any trace of harmful materials to the environment.

  3. Biological Agents

    MedlinePlus

    ... to Z Index Contact Us FAQs What's New Biological Agents This page requires that javascript be enabled ... and Health Topics A-Z Index What's New Biological agents include bacteria, viruses, fungi, other microorganisms and ...

  4. Fluorescence cross section measurements of biological agent simulants

    SciTech Connect

    Stephens, J.R.

    1996-11-01

    Fluorescence is a powerful technique that has potential uses in detection and characterization of biological aerosols both in the battlefield and in civilian environments. Fluorescence techniques can be used with ultraviolet (UV) light detection and ranging (LIDAR) equipment to detect biological aerosol clouds at a distance, to provide early warning of a biological attack, and to track an potentially noxious cloud. Fluorescence can also be used for detection in a point sensor to monitor biological materials and to distinguish agents from benign aerosols. This work is part of a continuing program by the Army`s Chemical and Biological Defense Command to characterized the optical properties of biological agents. Reported here are ultraviolet fluorescence measurements of Bacillus megaterium and Bacillus Globigii aerosols suspended in an electrodynamic particle trap. Fluorescence spectra of a common atmospheric aerosol, pine pollen, are also presented.

  5. Terahertz signatures of biological-warfare-agent simulants

    NASA Astrophysics Data System (ADS)

    Globus, Tatiana; Woolard, Dwight L.; Khromova, Tatyana; Partasarathy, Ramakrishnan; Majewski, Alexander; Abreu, Rene; Hesler, Jeffrey L.; Pan, Shing-Kuo; Ediss, Geoff

    2004-09-01

    This work presents spectroscopic characterization results for biological simulant materials measured in the terahertz gap. Signature data have been collected between 3 cm-1 and 10 cm-1 for toxin Ovalbumin, bacteria Erwinia herbicola, Bacillus Subtilis lyophilized cells and RNA MS2 phage, BioGene. Measurements were conducted on a modified Bruker FTIR spectrometer equipped with the noise source developed in the NRAL. The noise source provides two orders of magnitude higher power in comparison with a conventional mercury lamp. Photometric characterization of the instrument performance demonstrates that the expected error for sample characterization inside the interval from 3 to 9.5 cm-1 is less then 1%.

  6. Experimental Simulations for Elimination of Biological and/or Chemical Agents

    NASA Astrophysics Data System (ADS)

    Hong, Yong C.; Kim, Jeong H.; Uhm, Han S.

    2003-10-01

    The threat of biological and/or chemical agents in a domestic terrorist attack and in military conflict is increasing worldwide. The 2oo1 anthrax terror throughout the USA, 1995 sarin nerve gas attack on Tokyo subway, and the like are evident for this threat. Elimination and decontamination of biological and/or chemical agents are needed for such an attack. Experimental simulation for elimination of biological and/or chemical agents using an atmospheric-pressure microwave plasma torch is carried out. The elimination of biological and/or chemical agents through the vitrification or burnout of sewage sludge powders and the decomposition of toluene gas as a chemical agent stimulant is presented. A detailed characterization for the elimination of the simulant chemicals using Fourier Transform Infrared (FT-IR) and Gas Chromatography (GC) is also presented.

  7. Standoff lidar simulation for biological warfare agent detection, tracking, and classification

    NASA Astrophysics Data System (ADS)

    Jönsson, Erika; Steinvall, Ove; Gustafsson, Ove; Kullander, Fredrik; Jonsson, Per

    2010-04-01

    Lidar has been identified as a promising sensor for remote detection of biological warfare agents (BWA). Elastic IR lidar can be used for cloud detection at long ranges and UV laser induced fluorescence can be used for discrimination of BWA against naturally occurring aerosols. This paper will describe a simulation tool which enables the simulation of lidar for detection, tracking and classification of aerosol clouds. The cloud model was available from another project and has been integrated into the model. It takes into account the type of aerosol, type of release (plume or puff), amounts of BWA, winds, height above the ground and terrain roughness. The model input includes laser and receiver parameters for both the IR and UV channels as well as the optical parameters of the background, cloud and atmosphere. The wind and cloud conditions and terrain roughness are specified for the cloud simulation. The search area including the angular sampling resolution together with the IR laser pulse repetition frequency defines the search conditions. After cloud detection in the elastic mode, the cloud can be tracked using appropriate algorithms. In the tracking mode the classification using fluorescence spectral emission is simulated and tested using correlation against known spectra. Other methods for classification based on elastic backscatter are also discussed as well as the determination of particle concentration. The simulation estimates and displays the lidar response, cloud concentration as well as the goodness of fit for the classification using fluorescence.

  8. Optical recognition of biological agents

    NASA Astrophysics Data System (ADS)

    Baumgart, Chris W.; Linder, Kim Dalton; Trujillo, Josh J.

    2008-04-01

    Differentiation between particulate biological agents and non-biological agents is typically performed via a time-consuming "wet chemistry" process or through the use of fluorescent and spectroscopic analysis. However, while these methods can provide definitive recognition of biological agents, many of them have to be performed in a laboratory environment, or are difficult to implement in the field. Optical recognition techniques offer an additional recognition approach that can provide rapid analysis of a material in-situ to identify those materials that may be biological in nature. One possible application is to use these techniques to "screen" suspicious materials and to identify those that are potentially biological in nature. Suspicious materials identified by this screening process can then be analyzed in greater detail using the other, more definitive (but time consuming) analysis techniques. This presentation will describe the results of a feasibility study to determine whether optical pattern recognition techniques can be used to differentiate biological related materials from non-biological materials. As part of this study, feature extraction algorithms were developed utilizing multiple contrast and texture based features to characterize the macroscopic properties of different materials. In addition, several pattern recognition approaches using these features were tested including cluster analysis and neural networks. Test materials included biological agent simulants, biological agent related materials, and non-biological materials (suspicious white powders). Results of a series of feasibility tests will be presented along with a discussion of the potential field applications for these techniques.

  9. Biological warfare agents

    PubMed Central

    Thavaselvam, Duraipandian; Vijayaraghavan, Rajagopalan

    2010-01-01

    The recent bioterrorist attacks using anthrax spores have emphasized the need to detect and decontaminate critical facilities in the shortest possible time. There has been a remarkable progress in the detection, protection and decontamination of biological warfare agents as many instrumentation platforms and detection methodologies are developed and commissioned. Even then the threat of biological warfare agents and their use in bioterrorist attacks still remain a leading cause of global concern. Furthermore in the past decade there have been threats due to the emerging new diseases and also the re-emergence of old diseases and development of antimicrobial resistance and spread to new geographical regions. The preparedness against these agents need complete knowledge about the disease, better research and training facilities, diagnostic facilities and improved public health system. This review on the biological warfare agents will provide information on the biological warfare agents, their mode of transmission and spread and also the detection systems available to detect them. In addition the current information on the availability of commercially available and developing technologies against biological warfare agents has also been discussed. The risk that arise due to the use of these agents in warfare or bioterrorism related scenario can be mitigated with the availability of improved detection technologies. PMID:21829313

  10. Biophysically Realistic Filament Bending Dynamics in Agent-Based Biological Simulation

    PubMed Central

    Alberts, Jonathan B.

    2009-01-01

    An appealing tool for study of the complex biological behaviors that can emerge from networks of simple molecular interactions is an agent-based, computational simulation that explicitly tracks small-scale local interactions – following thousands to millions of states through time. For many critical cell processes (e.g. cytokinetic furrow specification, nuclear centration, cytokinesis), the flexible nature of cytoskeletal filaments is likely to be critical. Any computer model that hopes to explain the complex emergent behaviors in these processes therefore needs to encode filament flexibility in a realistic manner. Here I present a numerically convenient and biophysically realistic method for modeling cytoskeletal filament flexibility in silico. Each cytoskeletal filament is represented by a series of rigid segments linked end-to-end in series with a variable attachment point for the translational elastic element. This connection scheme allows an empirically tuning, for a wide range of segment sizes, viscosities, and time-steps, that endows any filament species with the experimentally observed (or theoretically expected) static force deflection, relaxation time-constant, and thermal writhing motions. I additionally employ a unique pair of elastic elements – one representing the axial and the other the bending rigidity– that formulate the restoring force in terms of single time-step constraint resolution. This method is highly local –adjacent rigid segments of a filament only interact with one another through constraint forces—and is thus well-suited to simulations in which arbitrary additional forces (e.g. those representing interactions of a filament with other bodies or cross-links / entanglements between filaments) may be present. Implementation in code is straightforward; Java source code is available at www.celldynamics.org. PMID:19283085

  11. Transport behavior of surrogate biological warfare agents in a simulated landfill: effect of leachate recirculation and water infiltration.

    PubMed

    Saikaly, Pascal E; Hicks, Kristin; Barlaz, Morton A; de Los Reyes, Francis L

    2010-11-15

    An understanding of the transport behavior of biological warfare (BW) agents in landfills is required to evaluate the suitability of landfills for the disposal of building decontamination residue (BDR) following a bioterrorist attack on a building. Surrogate BW agents, Bacillus atrophaeus spores and Serratia marcescens, were spiked into simulated landfill reactors that were filled with synthetic building debris (SBD) and operated for 4 months with leachate recirculation or water infiltration. Quantitative polymerase chain reaction (Q-PCR) was used to monitor surrogate transport. In the leachate recirculation reactors, <10% of spiked surrogates were eluted in leachate over 4 months. In contrast, 45% and 31% of spiked S. marcescens and B. atrophaeus spores were eluted in leachate in the water infiltration reactors. At the termination of the experiment, the number of retained cells and spores in SBD was measured over the depth of the reactor. Less than 3% of the total spiked S. marcescens cells and no B. atrophaeus spores were detected in SBD. These results suggest that significant fractions of the spiked surrogates were strongly attached to SBD. PMID:20973546

  12. Biologic agents in juvenile spondyloarthropathies.

    PubMed

    Katsicas, María Martha; Russo, Ricardo

    2016-01-01

    The juvenile spondyloarthropathies (JSpA) are a group of related rheumatic diseases characterized by involvement of peripheral large joints, axial joints, and entheses (enthesitis) that begin in the early years of life (prior to 16(th) birthday).The nomenclature and concept of spondyloarthropathies has changed during the last few decades. Although there is not any specific classification of JSpA, diseases under the spondyloarthropathy nomenclature umbrella in the younger patients include: the seronegative enthesitis and arthropathy (SEA) syndrome, juvenile ankylosing spondylitis, reactive arthritis, and inflammatory bowel disease-associated arthritis. Moreover, the ILAR criteria for Juvenile Idiopathic Arthritis includes two categories closely related to spondyloarthritis: Enthesitis-related arthritis and psoriatic arthritis.We review the pathophysiology and the use of biological agents in JSpA. JSpA are idiopathic inflammatory diseases driven by an altered balance in the proinflammatory cytokines. There is ample evidence on the role of tumor necrosis factor (TNF) and interleukin-17 in the physiopathology of these entities. Several non-biologic and biologic agents have been used with conflicting results in the treatment of these complex diseases. The efficacy and safety of anti-TNF agents, such as etanercept, infliximab and adalimumab, have been analysed in controlled and uncontrolled trials, usually showing satisfactory outcomes. Other biologic agents, such as abatacept, tocilizumab and rituximab, have been insufficiently studied and their role in the therapy of SpA is uncertain. Interleukin-17-blocking agents are promising alternatives for the treatment of JSpA patients in the near future. Recommendations for the treatment of patients with JSpA have recently been proposed and are discussed in the present review. PMID:26968522

  13. Real-Time Agent-Based Modeling Simulation with in-situ Visualization of Complex Biological Systems

    PubMed Central

    Seekhao, Nuttiiya; Shung, Caroline; JaJa, Joseph; Mongeau, Luc; Li-Jessen, Nicole Y. K.

    2016-01-01

    We present an efficient and scalable scheme for implementing agent-based modeling (ABM) simulation with In Situ visualization of large complex systems on heterogeneous computing platforms. The scheme is designed to make optimal use of the resources available on a heterogeneous platform consisting of a multicore CPU and a GPU, resulting in minimal to no resource idle time. Furthermore, the scheme was implemented under a client-server paradigm that enables remote users to visualize and analyze simulation data as it is being generated at each time step of the model. Performance of a simulation case study of vocal fold inflammation and wound healing with 3.8 million agents shows 35× and 7× speedup in execution time over single-core and multi-core CPU respectively. Each iteration of the model took less than 200 ms to simulate, visualize and send the results to the client. This enables users to monitor the simulation in real-time and modify its course as needed. PMID:27547508

  14. Babybot: a biologically inspired developing robotic agent

    NASA Astrophysics Data System (ADS)

    Metta, Giorgio; Panerai, Francesco M.; Sandini, Giulio

    2000-10-01

    The study of development, either artificial or biological, can highlight the mechanisms underlying learning and adaptive behavior. We shall argue whether developmental studies might provide a different and potentially interesting perspective either on how to build an artificial adaptive agent, or on understanding how the brain solves sensory, motor, and cognitive tasks. It is our opinion that the acquisition of the proper behavior might indeed be facilitated because within an ecological context, the agent, its adaptive structure and the environment dynamically interact thus constraining the otherwise difficult learning problem. In very general terms we shall describe the proposed approach and supporting biological related facts. In order to further analyze these aspects from the modeling point of view, we shall demonstrate how a twelve degrees of freedom baby humanoid robot acquires orienting and reaching behaviors, and what advantages the proposed framework might offer. In particular, the experimental setup consists of five degrees-of-freedom (dof) robot head, and an off-the-shelf six dof robot manipulator, both mounted on a rotating base: i.e. the torso. From the sensory point of view, the robot is equipped with two space-variant cameras, an inertial sensor simulating the vestibular system, and proprioceptive information through motor encoders. The biological parallel is exploited at many implementation levels. It is worth mentioning, for example, the space- variant eyes, exploiting foveal and peripheral vision in a single arrangement, the inertial sensor providing efficient image stabilization (vestibulo-ocular reflex).

  15. Software agents in molecular computational biology.

    PubMed

    Keele, John W; Wray, James E

    2005-12-01

    Progress made in applying agent systems to molecular computational biology is reviewed and strategies by which to exploit agent technology to greater advantage are investigated. Communities of software agents could play an important role in helping genome scientists design reagents for future research. The advent of genome sequencing in cattle and swine increases the complexity of data analysis required to conduct research in livestock genomics. Databases are always expanding and semantic differences among data are common. Agent platforms have been developed to deal with generic issues such as agent communication, life cycle management and advertisement of services (white and yellow pages). This frees computational biologists from the drudgery of having to re-invent the wheel on these common chores, giving them more time to focus on biology and bioinformatics. Agent platforms that comply with the Foundation for Intelligent Physical Agents (FIPA) standards are able to interoperate. In other words, agents developed on different platforms can communicate and cooperate with one another if domain-specific higher-level communication protocol details are agreed upon between different agent developers. Many software agent platforms are peer-to-peer, which means that even if some of the agents and data repositories are temporarily unavailable, a subset of the goals of the system can still be met. Past use of software agents in bioinformatics indicates that an agent approach should prove fruitful. Examination of current problems in bioinformatics indicates that existing agent platforms should be adaptable to novel situations. PMID:16420735

  16. Biological agents database in the armed forces.

    PubMed

    Niemcewicz, Marcin; Kocik, Janusz; Bielecka, Anna; Wierciński, Michał

    2014-10-01

    Rapid detection and identification of the biological agent during both, natural or deliberate outbreak is crucial for implementation of appropriate control measures and procedures in order to mitigate the spread of disease. Determination of pathogen etiology may not only support epidemiological investigation and safety of human beings, but also enhance forensic efforts in pathogen tracing, collection of evidences and correct inference. The article presents objectives of the Biological Agents Database, which was developed for the purpose of the Ministry of National Defense of the Republic of Poland under the European Defence Agency frame. The Biological Agents Database is an electronic catalogue of genetic markers of highly dangerous pathogens and biological agents of weapon of mass destruction concern, which provides full identification of biological threats emerging in Poland and in locations of activity of Polish troops. The Biological Agents Database is a supportive tool used for tracing biological agents' origin as well as rapid identification of agent causing the disease of unknown etiology. It also provides support in diagnosis, analysis, response and exchange of information between institutions that use information contained in it. Therefore, it can be used not only for military purposes, but also in a civilian environment. PMID:25033774

  17. Approaches to detection of airborne biological agents

    NASA Astrophysics Data System (ADS)

    Chang, An-Cheng; Tabacco, Mary Beth

    2009-05-01

    Three approaches to detection of biological agents based on biological processes will be presented. The first example demonstrates the use of dendrimers to deliver a membrane-impermeable fluorescent dye into live bacteria, similar to viral infection and delivery of DNA/RNA into a bacterial cell. The second example mimics collection and capture of airborne biological particles by the respiratory mucosa through the use of a hygroscopic sensing membrane. The third example is based on the use of multiple fluorescent probes with diverse functionalities to detect airborne biological agents in a manner similar to the olfactory receptors in the nasal tract.

  18. Simulating Biological and Non-Biological Motion

    ERIC Educational Resources Information Center

    Bruzzo, Angela; Gesierich, Benno; Wohlschlager, Andreas

    2008-01-01

    It is widely accepted that the brain processes biological and non-biological movements in distinct neural circuits. Biological motion, in contrast to non-biological motion, refers to active movements of living beings. Aim of our experiment was to investigate the mechanisms underlying mental simulation of these two movement types. Subjects had to…

  19. History of chemical and biological warfare agents.

    PubMed

    Szinicz, L

    2005-10-30

    Chemical and biological warfare agents constitute a low-probability, but high-impact risk both to the military and to the civilian population. The use of hazardous materials of chemical or biological origin as weapons and for homicide has been documented since ancient times. The first use of chemicals in terms of weapons of mass destruction goes back to World War I, when on April 22, 1915 large amounts of chlorine were released by German military forces at Ypres, Belgium. Until around the 1970s of the 20th century, the awareness of the threat by chemical and biological agents had been mainly confined to the military sector. In the following time, the development of increasing range delivery systems by chemical and biological agents possessors sensitised public attention to the threat emanating from these agents. Their proliferation to the terrorists field during the 1990s with the expanding scale and globalisation of terrorist attacks suggested that these agents are becoming an increasing threat to the whole world community. The following article gives a condensed overview on the history of use and development of the more prominent chemical and biological warfare agents. PMID:16111798

  20. Method For Detecting Biological Agents

    DOEpatents

    Chen, Liaohai; McBranch, Duncan W.; Wang, Hsing-Lin; Whitten, David G.

    2005-12-27

    A sensor is provided including a polymer capable of having an alterable measurable property from the group of luminescence and electrical conductivity, the polymer having an intermediate combination of a recognition element, a tethering element and a property-altering element bound thereto and capable of altering the measurable property, the intermediate combination adapted for subsequent separation from the polymer upon exposure to an agent having an affinity for binding to the recognition element whereupon the separation of the intermediate combination from the polymer results in a detectable change in the alterable measurable property, and, detecting said detectable change in the alterable measurable property.

  1. An Introduced Insect Biological Control Agent Preys on an Introduced Weed Biological Control Agent.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Biotic interference, especially by generalist predators, has been implicated in preventing establishment or limiting the impact of introduced weed biological control agents. Boreioglycaspis melaleucae Moore (Homoptera: Psyllidae) was released into Florida in 2002 as part of a classical biological c...

  2. Air monitoring and detection of chemical and biological agents

    SciTech Connect

    Leonelli, J.; Althouse, M.L.

    1999-06-01

    This volume contains the proceedings of SPIE`s remote sensing symposium which was held November 2--3, 1998 in Boston, Massachusetts. Topics of discussion include the following: system simulations, atmospheric modeling, and performance prediction studies of chemical warfare remote sensing technologies; ultraviolet laser-induced fluorescence and aerosol detection methods for remote sensing of biological warfare agents; passive detection methods for remote detection of chemical warfare agents; and lidar-based system performance assessments, demonstrations, and new concepts for chemical warfare/biological warfare detection.

  3. [Decontamination of chemical and biological warfare agents].

    PubMed

    Seto, Yasuo

    2009-01-01

    Chemical and biological warfare agents (CBWA's) are diverse in nature; volatile acute low-molecular-weight toxic compounds, chemical warfare agents (CWA's, gaseous choking and blood agents, volatile nerve gases and blister agents, nonvolatile vomit agents and lacrymators), biological toxins (nonvolatile low-molecular-weight toxins, proteinous toxins) and microbes (bacteria, viruses, rickettsiae). In the consequence management against chemical and biological terrorism, speedy decontamination of victims, facilities and equipment is required for the minimization of the damage. In the present situation, washing victims and contaminated materials with large volumes of water is the basic way, and additionally hypochlorite salt solution is used for decomposition of CWA's. However, it still remains unsolved how to dispose large volumes of waste water, and the decontamination reagents have serious limitation of high toxicity, despoiling nature against the environments, long finishing time and non-durability in effective decontamination. Namely, the existing decontamination system is not effective, nonspecifically affecting the surrounding non-target materials. Therefore, it is the urgent matter to build up the usable decontamination system surpassing the present technologies. The symposiast presents the on-going joint project of research and development of the novel decontamination system against CBWA's, in the purpose of realizing nontoxic, fast, specific, effective and economical terrorism on-site decontamination. The projects consists of (1) establishment of the decontamination evaluation methods and verification of the existing technologies and adaptation of bacterial organophosphorus hydrolase, (2) development of adsorptive elimination technologies using molecular recognition tools, and (4) development of deactivation technologies using photocatalysis. PMID:19122437

  4. Decontamination of biological warfare agents by a microwave plasma torch

    SciTech Connect

    Lai, Wilson; Lai, Henry; Kuo, Spencer P.; Tarasenko, Olga; Levon, Kalle

    2005-02-01

    A portable arc-seeded microwave plasma torch running stably with airflow is described and applied for the decontamination of biological warfare agents. Emission spectroscopy of the plasma torch indicated that this torch produced an abundance of reactive atomic oxygen that could effectively oxidize biological agents. Bacillus cereus was chosen as a simulant of Bacillus anthracis spores for biological agent in the decontamination experiments. Decontamination was performed with the airflow rate of 0.393 l/s, corresponding to a maximum concentration of atomic oxygen produced by the torch. The experimental results showed that all spores were killed in less than 8 s at 3 cm distance, 12 s at 4 cm distance, and 16 s at 5 cm distance away from the nozzle of the torch.

  5. Biologic agents in the treatment of glomerulonephritides.

    PubMed

    Yeo, See Cheng; Liew, Adrian

    2015-11-01

    Current immunosuppression strategies in the treatment of glomerulonephritides remain unsatisfactory, especially in glomerular diseases that are frequently relapsing or are resistant to treatment. Toxicities associated with the use of drugs with non-specific targets for the immune response result in treatment non-compliance, and increase morbidity and mortality in these patients. Advances in our understanding of the immunopathogenesis of glomerulonephritis and the availability of biologics have led to their successful use in the treatment of immune-mediated glomerular diseases. Biologics are usually very large complex molecules, often produced using recombinant DNA technology and manufactured in a living system such as a microorganism, or plant or animal cells. They are novel agents that can target specific immune cell types, cytokines or immune pathways involved in the pathogenesis of these disorders. It is attractive to consider that, given their specific mode of action, these agents can potentially offer a more directed and effective immunosuppression, with side-effect profiles that are much more desirable. However, there have been few randomized controlled trials comparing biologic agents to conventional immunosuppression, and in many of these studies the side-effect profiles have been disappointingly similar. In this review, we will examine the rationale, efficacy and safety of some commonly used biologics in the treatment of primary and secondary glomerulonephritides. We will also discuss some of the key challenges that may be encountered with the use of biologics in treating glomerulonephritis in the future. PMID:26040770

  6. Pathogenetic validation of the use of biological protective agents and early treatment in cases of radiation injury simulating radiation effects under space flight conditions

    NASA Technical Reports Server (NTRS)

    Rogozkin, V. D.; Varteres, V.; Sabo, L.; Groza, N.; Nikolov, I.

    1974-01-01

    In considering a radiation safety system for space flights, the various measures to protect man against radiation include drug prophylaxis. At the present time a great deal of experimental material has been accumulated on the prevention and treatment of radiation injuries. Antiradiation effectiveness has been established for sulfur- and nitrogen-containing substances, auxins, cyanides, polynucleotides, mucopolysaccharides, lipopolysaccharides, aminosaccharides, synthetic polymers, vitamins, hormones, amino acids and other compounds which can be divided into two basic groups - biological and chemical protective agents.

  7. Agent-based models in translational systems biology

    PubMed Central

    An, Gary; Mi, Qi; Dutta-Moscato, Joyeeta; Vodovotz, Yoram

    2013-01-01

    Effective translational methodologies for knowledge representation are needed in order to make strides against the constellation of diseases that affect the world today. These diseases are defined by their mechanistic complexity, redundancy, and nonlinearity. Translational systems biology aims to harness the power of computational simulation to streamline drug/device design, simulate clinical trials, and eventually to predict the effects of drugs on individuals. The ability of agent-based modeling to encompass multiple scales of biological process as well as spatial considerations, coupled with an intuitive modeling paradigm, suggests that this modeling framework is well suited for translational systems biology. This review describes agent-based modeling and gives examples of its translational applications in the context of acute inflammation and wound healing. PMID:20835989

  8. Biological agents as occupational hazards - selected issues.

    PubMed

    Dutkiewicz, Jacek; Cisak, Ewa; Sroka, Jacek; Wójcik-Fatla, Angelina; Zając, Violetta

    2011-01-01

    There are two main groups of biological agents regarded as occupational hazards: allergenic and/or toxic agents forming bioaerosols, and agents causing zoonoses and other infectious diseases. Bioaerosols occurring in the agricultural work environments comprise: bacteria, fungi, high molecular polymers produced by bacteria (endotoxin) or by fungi (β-glucans), low molecular secondary metabolites of fungi (mycotoxins, volatile organic compounds) and various particles of plant and animal origin. All these agents could be a cause of allergic and/or immunotoxic occupational diseases of respiratory organ (airways inflammation, rhinitis, toxic pneumonitis, hypersensitivity pneumonitis and asthma), conjunctivitis and dermatitis in exposed workers. Very important among zoonotic agents causing occupational diseases are those causing tick-borne diseases: Lyme borreliosis, anaplasmosis, babesiosis, bartonellosis. Agricultural workers in tropical zones are exposed to mosquito bites causing malaria, the most prevalent vector-borne disease in the world. The group of agents causing other, basically not vector-borne zoonoses, comprises those evoking emerging or re-emerging diseases of global concern, such as: hantaviral diseases, avian and swine influenza, Q fever, leptospiroses, staphylococcal diseases caused by the methicillin-resistant Staphylococcus aureus (MRSA) strains, and diseases caused by parasitic protozoa. Among other infectious, non-zoonotic agents, the greatest hazard for health care workers pose the blood-borne human hepatitis and immunodeficiency viruses (HBV, HCV, HIV). Of interest are also bacteria causing legionellosis in people occupationally exposed to droplet aerosols, mainly from warm water. PMID:22216801

  9. Investigation of statistics strategies for improving the discriminating power of laser-induced breakdown spectroscopy for chemical and biological warfare agent simulants

    NASA Astrophysics Data System (ADS)

    Munson, Chase A.; De Lucia, Frank C.; Piehler, Thuvan; McNesby, Kevin L.; Miziolek, Andrzej W.

    2005-08-01

    Laser-induced breakdown spectroscopy spectra of bacterial spores, molds, pollens and nerve agent simulants have been acquired. The performance of several statistical methodologies-linear correlation, principal components analysis, and soft independent model of class analogy-has been evaluated for their ability to differentiate between the various samples. The effect of data selection (total spectra, peak intensities, and intensity ratios) and pre-treatments (e.g., averaging) on the statistical models have also been studied. Results indicate the use of spectral averaging and weighting schemes may be used to significantly improve sample differentiation.

  10. Biological Simulations in Distance Learning.

    ERIC Educational Resources Information Center

    Murphy, P. J.

    1982-01-01

    The problems of introducing biological simulations into two Open University courses and the proposed solutions are discussed in relation to sound computer assisted learning practice. Eight references are included. (Author/CHC)

  11. Spectrally-resolved fluorescence cross sections of aerosolized biological live agents and simulants using five excitation wavelengths in a BSL-3 laboratory.

    PubMed

    Pan, Yong-Le; Hill, Steven C; Santarpia, Joshua L; Brinkley, Kelly; Sickler, Todd; Coleman, Mark; Williamson, Chatt; Gurton, Kris; Felton, Melvin; Pinnick, Ronald G; Baker, Neal; Eshbaugh, Jonathan; Hahn, Jerry; Smith, Emily; Alvarez, Ben; Prugh, Amber; Gardner, Warren

    2014-04-01

    A system for measuring spectrally-resolved fluorescence cross sections of single bioaerosol particles has been developed and employed in a biological safety level 3 (BSL-3) facility at Edgewood Chemical and Biological Center (ECBC). It is used to aerosolize the slurry or solution of live agents and surrogates into dried micron-size particles, and to measure the fluorescence spectra and sizes of the particles one at a time. Spectrally-resolved fluorescence cross sections were measured for (1) bacterial spores: Bacillus anthracis Ames (BaA), B. atrophaeus var. globigii (BG) (formerly known as Bacillus globigii), B. thuringiensis israelensis (Bti), B. thuringiensis kurstaki (Btk), B. anthracis Sterne (BaS); (2) vegetative bacteria: Escherichia coli (E. coli), Pantoea agglomerans (Eh) (formerly known as Erwinia herbicola), Yersinia rohdei (Yr), Yersinia pestis CO92 (Yp); and (3) virus preparations: Venezuelan equine encephalitis TC83 (VEE) and the bacteriophage MS2. The excitation wavelengths were 266 nm, 273 nm, 280 nm, 365 nm and 405 nm. PMID:24718194

  12. Laser-induced fluorescence-cued, laser-induced breakdown spectroscopy biological-agent detection

    SciTech Connect

    Hybl, John D.; Tysk, Shane M.; Berry, Shaun R.; Jordan, Michael P

    2006-12-01

    Methods for accurately characterizing aerosols are required for detecting biological warfare agents. Currently, fluorescence-based biological agent sensors provide adequate detection sensitivity but suffer from high false-alarm rates. Combining single-particle fluorescence analysis with laser-induced breakdown spectroscopy (LIBS) provides additional discrimination and potentially reduces false-alarm rates. A transportable UV laser-induced fluorescence-cued LIBS test bed has been developed and used to evaluate the utility of LIBS for biological-agent detection. Analysis of these data indicates that LIBS adds discrimination capability to fluorescence-based biological-agent detectors.However, the data also show that LIBS signatures of biological agent simulants are affected by washing. This may limit the specificity of LIBS and narrow the scope of its applicability in biological-agent detection.

  13. Biological agents in management of osteoporosis.

    PubMed

    Tella, Sri Harsha; Gallagher, J Christopher

    2014-11-01

    Osteoporosis is a skeletal disease associated with an imbalance between formation and resorption, leading to net loss of bone mass, loss of bone microarchitecture, and development of fractures. Bone resorption is primarily due to an activation of osteoclastogenesis and an increase in receptor activator of nuclear factor kappa-B ligand (RANKL) expression, a cytokine involved in the final pathway of the osteoclast cycle.Recent studies of genetic diseases led to the discovery of the wingless-type (Wnt) signaling pathway that plays a major role in bone formation. Further work showed that sclerostin produced by osteocytes and the Dickkopf (DKK1) protein secreted in bone were negative regulators of the Wnt signaling bone formation pathway that act directly by binding to the co-receptors LRP5 and LRP6 of WnT and thereby inhibiting the anabolic Wnt pathway. This understanding of the bone remodeling led to the discovery of new biological drugs that target these pathways and have been evaluated in clinical trials.The current article discusses the role of these newer "biological" agents in management of osteoporosis. Denosumab, a human monoclonal antibody that specifically binds RANKL, blocks the binding of RANK to its ligand markedly reducing bone resorption, increases bone density, and reduces fractures and is approved for osteoporosis. Parathyroid hormone PTH 1-34 (teriparatide) stimulates bone formation through inhibition of sclerostin, DKK1, and frizzled protein; increases BMD; improves microarchitecture; and decreases fractures and is approved for osteoporosis. The anti-sclerostin antibodies (romosozumab, blosozumab) increase bone mass by neutralizing the negative effects of sclerostin on the Wnt signaling pathway. These biologics are being evaluated now in a clinical trial and early data looks promising. Cathepsin K is a proteolytic enzyme that degrades bone matrix and inhibitors such as odanacatib show increasing bone density and perhaps decreased fractures. The

  14. Biomaterials for mediation of chemical and biological warfare agents.

    PubMed

    Russell, Alan J; Berberich, Jason A; Drevon, Geraldine F; Koepsel, Richard R

    2003-01-01

    Recent events have emphasized the threat from chemical and biological warfare agents. Within the efforts to counter this threat, the biocatalytic destruction and sensing of chemical and biological weapons has become an important area of focus. The specificity and high catalytic rates of biological catalysts make them appropriate for decommissioning nerve agent stockpiles, counteracting nerve agent attacks, and remediation of organophosphate spills. A number of materials have been prepared containing enzymes for the destruction of and protection against organophosphate nerve agents and biological warfare agents. This review discusses the major chemical and biological warfare agents, decontamination methods, and biomaterials that have potential for the preparation of decontamination wipes, gas filters, column packings, protective wear, and self-decontaminating paints and coatings. PMID:12704086

  15. Detection of biological warfare agents using ultra violet-laser induced fluorescence LIDAR.

    PubMed

    Joshi, Deepti; Kumar, Deepak; Maini, Anil K; Sharma, Ramesh C

    2013-08-01

    This review has been written to highlight the threat of biological warfare agents, their types and detection. Bacterial biological agent Bacillus anthracis (bacteria causing the disease anthrax) which is most likely to be employed in biological warfare is being discussed in detail. Standoff detection of biological warfare agents in aerosol form using Ultra violet-Laser Induced Fluorescence (UV-LIF) spectroscopy method has been studied. Range-resolved detection and identification of biological aerosols by both nano-second and non-linear femto-second LIDAR is also discussed. Calculated received fluorescence signal for a cloud of typical biological agent Bacillus globigii (Simulants of B. anthracis) at a location of ~5.0 km at different concentrations in presence of solar background radiation has been described. Overview of current research efforts in internationally available working UV-LIF LIDAR systems are also mentioned briefly. PMID:23719340

  16. Detection of biological warfare agents using ultra violet-laser induced fluorescence LIDAR

    NASA Astrophysics Data System (ADS)

    Joshi, Deepti; Kumar, Deepak; Maini, Anil K.; Sharma, Ramesh C.

    This review has been written to highlight the threat of biological warfare agents, their types and detection. Bacterial biological agent Bacillus anthracis (bacteria causing the disease anthrax) which is most likely to be employed in biological warfare is being discussed in detail. Standoff detection of biological warfare agents in aerosol form using Ultra violet-Laser Induced Fluorescence (UV-LIF) spectroscopy method has been studied. Range-resolved detection and identification of biological aerosols by both nano-second and non-linear femto-second LIDAR is also discussed. Calculated received fluorescence signal for a cloud of typical biological agent Bacillus globigii (Simulants of B. anthracis) at a location of ˜5.0 km at different concentrations in presence of solar background radiation has been described. Overview of current research efforts in internationally available working UV-LIF LIDAR systems are also mentioned briefly.

  17. Biologic agents-a panacea for inflammatory arthritis or not?

    PubMed

    Ninan, J; Smith, Malcolm D; Dugar, M; O'Brien, Karen; Ahern, Michael

    2009-01-01

    Aim. To describe the retention rates for biological therapies in patients with rheumatoid arthritis (RA), psoriatic arthritis (PsA), and ankylosing spondylitis (AS) in a clinical setting. Methods. All patients managed in a dedicated biological therapy clinic in a teaching hospital in Australia were assessed for continuation on biological treatments and reasons for switching to an alternative biological agent or cessation of treatment. Results. There was a lower retention rate for RA patients on biological therapies compared to PsA and AS patients and the retention rate for RA patients was lower than that reported in RCTs. Conclusions. The retention rate on biological therapies for RA patients was lower in the clinic setting than what is reported in RCTs. The reasons for the lower retention rate in the clinical setting are discussed but no clear determinants for nonresponse to biological agents were identifiable. These agents have very limited steroid sparing effects. PMID:20130798

  18. Stochastic simulation in systems biology

    PubMed Central

    Székely, Tamás; Burrage, Kevin

    2014-01-01

    Natural systems are, almost by definition, heterogeneous: this can be either a boon or an obstacle to be overcome, depending on the situation. Traditionally, when constructing mathematical models of these systems, heterogeneity has typically been ignored, despite its critical role. However, in recent years, stochastic computational methods have become commonplace in science. They are able to appropriately account for heterogeneity; indeed, they are based around the premise that systems inherently contain at least one source of heterogeneity (namely, intrinsic heterogeneity). In this mini-review, we give a brief introduction to theoretical modelling and simulation in systems biology and discuss the three different sources of heterogeneity in natural systems. Our main topic is an overview of stochastic simulation methods in systems biology. There are many different types of stochastic methods. We focus on one group that has become especially popular in systems biology, biochemistry, chemistry and physics. These discrete-state stochastic methods do not follow individuals over time; rather they track only total populations. They also assume that the volume of interest is spatially homogeneous. We give an overview of these methods, with a discussion of the advantages and disadvantages of each, and suggest when each is more appropriate to use. We also include references to software implementations of them, so that beginners can quickly start using stochastic methods for practical problems of interest. PMID:25505503

  19. Plasma flame for mass purification of contaminated air with chemical and biological warfare agents

    NASA Astrophysics Data System (ADS)

    Uhm, Han S.; Shin, Dong H.; Hong, Yong C.

    2006-09-01

    An elimination of airborne simulated chemical and biological warfare agents was carried out by making use of a plasma flame made of atmospheric plasma and a fuel-burning flame, which can purify the interior air of a large volume in isolated spaces such as buildings, public transportation systems, and military vehicles. The plasma flame generator consists of a microwave plasma torch connected in series to a fuel injector and a reaction chamber. For example, a reaction chamber, with the dimensions of a 22cm diameter and 30cm length, purifies an airflow rate of 5000lpm contaminated with toluene (the simulated chemical agent) and soot from a diesel engine (the simulated aerosol for biological agents). Large volumes of purification by the plasma flame will free mankind from the threat of airborne warfare agents. The plasma flame may also effectively purify air that is contaminated with volatile organic compounds, in addition to eliminating soot from diesel engines as an environmental application.

  20. Plasma flame for mass purification of contaminated air with chemical and biological warfare agents

    SciTech Connect

    Uhm, Han S.; Shin, Dong H.; Hong, Yong C.

    2006-09-18

    An elimination of airborne simulated chemical and biological warfare agents was carried out by making use of a plasma flame made of atmospheric plasma and a fuel-burning flame, which can purify the interior air of a large volume in isolated spaces such as buildings, public transportation systems, and military vehicles. The plasma flame generator consists of a microwave plasma torch connected in series to a fuel injector and a reaction chamber. For example, a reaction chamber, with the dimensions of a 22 cm diameter and 30 cm length, purifies an airflow rate of 5000 lpm contaminated with toluene (the simulated chemical agent) and soot from a diesel engine (the simulated aerosol for biological agents). Large volumes of purification by the plasma flame will free mankind from the threat of airborne warfare agents. The plasma flame may also effectively purify air that is contaminated with volatile organic compounds, in addition to eliminating soot from diesel engines as an environmental application.

  1. Biological control agents elevate hantavirus by subsidizing deer mouse populations.

    PubMed

    Pearson, Dean E; Callaway, Ragan M

    2006-04-01

    Biological control of exotic invasive plants using exotic insects is practiced under the assumption that biological control agents are safe if they do not directly attack non-target species. We tested this assumption by evaluating the potential for two host-specific biological control agents (Urophora spp.), widely established in North America for spotted knapweed (Centaurea maculosa) control, to indirectly elevate Sin Nombre hantavirus by providing food subsidies to populations of deer mice (Peromyscus maniculatus), the primary reservoir for the virus. We show that seropositive deer mice (mice testing positive for hantavirus) were over three times more abundant in the presence of the biocontrol food subsidy. Elevating densities of seropositive mice may increase risk of hantavirus infection in humans and significantly alter hantavirus ecology. Host specificity alone does not ensure safe biological control. To minimize indirect risks to non-target species, biological control agents must suppress pest populations enough to reduce their own numbers. PMID:16623730

  2. SURVIVABILITY OF BIOLOGICAL WARFARE AGENTS IN MUNICIPAL SOLID WASTE LANDFILLS

    EPA Science Inventory

    To tests and provide a comprehensive, integrated list of survival rates of biological warfare agents' survival of landfill conditions.
    Research into the permanence of the final disposal contaminated building debris of the inactivated or active agent of terrorism is being exam...

  3. Solid-water detoxifying reagents for chemical and biological agents

    DOEpatents

    Hoffman, Dennis M.; Chiu, Ing Lap

    2006-04-18

    Formation of solid-water detoxifying reagents for chemical and biological agents. Solutions of detoxifying reagent for chemical and biological agents are coated using small quantities of hydrophobic nanoparticles by vigorous agitation or by aerosolization of the solution in the presence of the hydrophobic nanoparticles to form a solid powder. For example, when hydrophobic fumed silica particles are shaken in the presence of IN oxone solution in approximately a 95:5-weight ratio, a dry powder results. The hydrophobic silica forms a porous coating of insoluble fine particles around the solution. Since the chemical or biological agent tends to be hydrophobic on contact with the weakly encapsulated detoxifying solution, the porous coating breaks down and the detoxifying reagent is delivered directly to the chemical or biological agent for maximum concentration at the point of need. The solid-water (coated) detoxifying solutions can be blown into contaminated ventilation ducting or other difficult to reach sites for detoxification of pools of chemical or biological agent. Once the agent has been detoxified, it can be removed by flushing the area with air or other techniques.

  4. Computational Spectrum of Agent Model Simulation

    SciTech Connect

    Perumalla, Kalyan S

    2010-01-01

    The study of human social behavioral systems is finding renewed interest in military, homeland security and other applications. Simulation is the most generally applied approach to studying complex scenarios in such systems. Here, we outline some of the important considerations that underlie the computational aspects of simulation-based study of human social systems. The fundamental imprecision underlying questions and answers in social science makes it necessary to carefully distinguish among different simulation problem classes and to identify the most pertinent set of computational dimensions associated with those classes. We identify a few such classes and present their computational implications. The focus is then shifted to the most challenging combinations in the computational spectrum, namely, large-scale entity counts at moderate to high levels of fidelity. Recent developments in furthering the state-of-the-art in these challenging cases are outlined. A case study of large-scale agent simulation is provided in simulating large numbers (millions) of social entities at real-time speeds on inexpensive hardware. Recent computational results are identified that highlight the potential of modern high-end computing platforms to push the envelope with respect to speed, scale and fidelity of social system simulations. Finally, the problem of shielding the modeler or domain expert from the complex computational aspects is discussed and a few potential solution approaches are identified.

  5. Biological agent detection and identification using pattern recognition

    NASA Astrophysics Data System (ADS)

    Braun, Jerome J.; Glina, Yan; Judson, Nicholas; Transue, Kevin D.

    2005-05-01

    This paper discusses a novel approach for the automatic identification of biological agents. The essence of the approach is a combination of gene expression, microarray-based sensing, information fusion, machine learning and pattern recognition. Integration of these elements is a distinguishing aspect of the approach, leading to a number of significant advantages. Amongst them are the applicability to various agent types including bacteria, viruses, toxins, and other, ability to operate without the knowledge of a pathogen's genome sequence and without the need for bioagent-speciific materials or reagents, and a high level of extensibility. Furthermore, the approach allows detection of uncatalogued agents, including emerging pathogens. The approach offers a promising avenue for automatic identification of biological agents for applications such as medical diagnostics, bioforensics, and biodefense.

  6. Oxidizer gels for detoxification of chemical and biological agents

    DOEpatents

    Hoffman, Dennis M.; McGuire, Raymond R.

    2002-01-01

    A gel composition containing oxidizing agents and thickening or gelling agents is used to detoxify chemical and biological agents by application directly to a contaminated area. The gelling agent is a colloidal material, such as silica, alumina, or alumino-silicate clays, which forms a viscous gel that does not flow when applied to tilted or contoured surfaces. Aqueous or organic solutions of oxidizing agents can be readily gelled with less than about 30% colloidal material. Gel preparation is simple and suitable for field implementation, as the gels can be prepared at the site of decontamination and applied quickly and uniformly over an area by a sprayer. After decontamination, the residue can be washed away or vacuumed up for disposal.

  7. Current laboratory methods for biological threat agent identification.

    PubMed

    Henchal, E A; Teska, J D; Ludwig, G V; Shoemaker, D R; Ezzell, J W

    2001-09-01

    The authors present an integrated approach for the identification of biological threat agents. The methods used have been used extensively in field exercises and during response to incidents of biological terrorism. A diagnostic system, which integrates the clinical diagnosis or medical intelligence with immunodiagnostic tests, rapid gene amplification assays, and standard culture, provides results of the highest quality and confidence. In the future, selected reagents and technologies will be distributed through a network of civilian and military laboratories. PMID:11572145

  8. DISCOVERY AND DEVELOMENT OF BIOLOGICAL AGENTS TO CONTROL CROP PESTS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    "Biological control" refers to the reduction of crop pests or their deleterious activities by one or more antagonistic organisms present in the environment. Thousands of potential microbial biocontrol agents have been isolated from agricultural fields and crops during research over the last 80 year...

  9. Surface-enhanced Raman scattering (SERS) detection for chemical and biological agents

    NASA Astrophysics Data System (ADS)

    Yan, Fei; Stokes, David L.; Wabuyele, Musundi B.; Griffin, Guy D.; Vass, Arpad A.; Vo-Dinh, Tuan

    2004-07-01

    Surface-enhanced Raman scattering (SERS) spectra of chemical agent simulants such as dimethyl methylphonate (DMMP), pinacolyl methylphosphonate (PMP), diethyl phosphoramidate (DEPA), and 2-chloroethyl ethylsulfide (CEES), and biological agent simulants such as bacillus globigii (BG), erwinia herbicola (EH), and bacillus thuringiensis (BT) were obtained from silver oxide film-deposited substrates. Thin AgO films ranging in thickness from 50 nm to 250 nm were produced by chemical bath deposition onto glass slides. Further Raman intensity enhancements were noticed in UV irradiated surfaces due to photo-induced Ag nanocluster formation, which may provide a possible route to producing highly useful plasmonic sensors for the detection of chemical and biological agents upon visible light illumination.

  10. A Bayesian Dose-finding Design for Oncology Clinical Trials of Combinational Biological Agents

    PubMed Central

    Cai, Chunyan; Yuan, Ying; Ji, Yuan

    2013-01-01

    Treating patients with novel biological agents is becoming a leading trend in oncology. Unlike cytotoxic agents, for which efficacy and toxicity monotonically increase with dose, biological agents may exhibit non-monotonic patterns in their dose-response relationships. Using a trial with two biological agents as an example, we propose a dose-finding design to identify the biologically optimal dose combination (BODC), which is defined as the dose combination of the two agents with the highest efficacy and tolerable toxicity. A change-point model is used to reflect the fact that the dose-toxicity surface of the combinational agents may plateau at higher dose levels, and a flexible logistic model is proposed to accommodate the possible non-monotonic pattern for the dose-efficacy relationship. During the trial, we continuously update the posterior estimates of toxicity and efficacy and assign patients to the most appropriate dose combination. We propose a novel dose-finding algorithm to encourage sufficient exploration of untried dose combinations in the two-dimensional space. Extensive simulation studies show that the proposed design has desirable operating characteristics in identifying the BODC under various patterns of dose-toxicity and dose-efficacy relationships. PMID:24511160

  11. A Bayesian Dose-finding Design for Oncology Clinical Trials of Combinational Biological Agents.

    PubMed

    Cai, Chunyan; Yuan, Ying; Ji, Yuan

    2014-01-01

    Treating patients with novel biological agents is becoming a leading trend in oncology. Unlike cytotoxic agents, for which efficacy and toxicity monotonically increase with dose, biological agents may exhibit non-monotonic patterns in their dose-response relationships. Using a trial with two biological agents as an example, we propose a dose-finding design to identify the biologically optimal dose combination (BODC), which is defined as the dose combination of the two agents with the highest efficacy and tolerable toxicity. A change-point model is used to reflect the fact that the dose-toxicity surface of the combinational agents may plateau at higher dose levels, and a flexible logistic model is proposed to accommodate the possible non-monotonic pattern for the dose-efficacy relationship. During the trial, we continuously update the posterior estimates of toxicity and efficacy and assign patients to the most appropriate dose combination. We propose a novel dose-finding algorithm to encourage sufficient exploration of untried dose combinations in the two-dimensional space. Extensive simulation studies show that the proposed design has desirable operating characteristics in identifying the BODC under various patterns of dose-toxicity and dose-efficacy relationships. PMID:24511160

  12. Functional Agents to Biologically Control Deoxynivalenol Contamination in Cereal Grains

    PubMed Central

    Tian, Ye; Tan, Yanglan; Liu, Na; Liao, Yucai; Sun, Changpo; Wang, Shuangxia; Wu, Aibo

    2016-01-01

    Mycotoxins, as microbial secondary metabolites, frequently contaminate cereal grains and pose a serious threat to human and animal health around the globe. Deoxynivalenol (DON), a commonly detected Fusarium mycotoxin, has drawn utmost attention due to high exposure levels and contamination frequency in the food chain. Biological control is emerging as a promising technology for the management of DON contamination. Functional biological control agents (BCAs), which include antagonistic microbes, natural fungicides derived from plants and detoxification enzymes, can be used to control DON contamination at different stages of grain production. In this review, studies regarding different biological agents for DON control in recent years are summarized for the first time. Furthermore, this article highlights the significance of BCAs for controlling DON contamination, as well as the need for more practical and efficient BCAs concerning food safety. PMID:27064760

  13. Biological warfare agents as threats to potable water.

    PubMed Central

    Burrows, W D; Renner, S E

    1999-01-01

    Nearly all known biological warfare agents are intended for aerosol application. Although less effective as potable water threats, many are potentially capable of inflicting heavy casualties when ingested. Significant loss of mission capability can be anticipated even when complete recovery is possible. Properly maintained field army water purification equipment can counter this threat, but personnel responsible for the operation and maintenance of the equipment may be most at risk of exposure. Municipal water treatment facilities would be measurably less effective. Some replicating (infectious) agents and a few biotoxins are inactivated by chlorine disinfection; for others chlorine is ineffective or of unknown efficacy. This report assesses the state of our knowledge of agents as potable water threats and contemplates the consequences of intentional or collateral contamination of potable water supplies by 18 replicating agents and 9 biotoxins known or likely to be weaponized or otherwise used as threats. PMID:10585901

  14. The Use of Biologic Agents in Athletes with Knee Injuries.

    PubMed

    Kopka, Michaela; Bradley, James P

    2016-07-01

    Biologic agents are gaining popularity in the management of bony and soft tissue conditions about the knee. They are becoming the mainstay of nonoperative therapy in the high-demand athletic population. The most well-studied agents include platelet-rich plasma (PRP) and stem cells-both of which have shown promise in the treatment of various conditions. Animal and clinical studies have demonstrated improved outcomes following PRP treatment in early osteoarthritis of the knee, as well as in chronic patellar tendinopathy. Early clinical evidence also lends support for PRP in the augmentation of anterior cruciate ligament (ACL) reconstruction. Research investigating the role of biologic agents in collateral ligament and meniscal injuries is ongoing. Studies assessing the utility of stem cells have shown encouraging results in the setting of osteoarthritis. Unfortunately, strict regulations by the FDA continue to restrict their application in clinical practice. A major limitation in the interpretation of current data is the significant variability in the harvesting and preparation of both PRP and stem cells. As the volume and quality of evidence continue to grow, biologic agents are poised to become an integral component of comprehensive patient care throughout all orthopedic specialties. PMID:27206071

  15. Biologic Agents for Periodontal Regeneration and Implant Site Development.

    PubMed

    Suárez-López Del Amo, Fernando; Monje, Alberto; Padial-Molina, Miguel; Tang, ZhiHui; Wang, Hom-Lay

    2015-01-01

    The advancement of molecular mediators or biologic agents has increased tremendously during the last decade in periodontology and dental implantology. Implant site development and reconstruction of the lost periodontium represent main fields in which these molecular mediators have been employed and investigated. Different growth factors trigger different reactions in the tissues of the periodontium at various cellular levels. Proliferation, migration, and differentiation constitute the main target areas of these molecular mediators. It was the purpose of this comprehensive review to describe the origin and rationale, evidence, and the most current understanding of the following biologic agents: Recombinant Human Platelet-Derived Growth Factor-BB (rhPDGF-BB), Enamel Matrix Derivate (EMD), Platelet-Rich Plasma (PRP) and Platelet-Rich Fibrin (PRF), Recombinant Human Fibroblast Growth Factor-2 (rhFGF-2), Bone Morphogenic Proteins (BMPs, BMP-2 and BMP-7), Teriparatide PTH, and Growth Differential Factor-5 (GDF-5). PMID:26509173

  16. Biologic Agents for Periodontal Regeneration and Implant Site Development

    PubMed Central

    Suárez-López del Amo, Fernando; Monje, Alberto; Padial-Molina, Miguel; Tang, ZhiHui; Wang, Hom-Lay

    2015-01-01

    The advancement of molecular mediators or biologic agents has increased tremendously during the last decade in periodontology and dental implantology. Implant site development and reconstruction of the lost periodontium represent main fields in which these molecular mediators have been employed and investigated. Different growth factors trigger different reactions in the tissues of the periodontium at various cellular levels. Proliferation, migration, and differentiation constitute the main target areas of these molecular mediators. It was the purpose of this comprehensive review to describe the origin and rationale, evidence, and the most current understanding of the following biologic agents: Recombinant Human Platelet-Derived Growth Factor-BB (rhPDGF-BB), Enamel Matrix Derivate (EMD), Platelet-Rich Plasma (PRP) and Platelet-Rich Fibrin (PRF), Recombinant Human Fibroblast Growth Factor-2 (rhFGF-2), Bone Morphogenic Proteins (BMPs, BMP-2 and BMP-7), Teriparatide PTH, and Growth Differential Factor-5 (GDF-5). PMID:26509173

  17. Spatial Aspects in Biological System Simulations

    SciTech Connect

    Resat, Haluk; Costa, Michelle N.; Shankaran, Harish

    2011-01-30

    Mathematical models of the dynamical properties of biological systems aim to improve our understanding of the studied system with the ultimate goal of being able to predict system responses in the absence of experimentation. Despite the enormous advances that have been made in biological modeling and simulation, the inherently multiscale character of biological systems and the stochasticity of biological processes continue to present significant computational and conceptual challenges. Biological systems often consist of well-organized structural hierarchies, which inevitably lead to multiscale problems. This chapter introduces and discusses the advantages and shortcomings of several simulation methods that are being used by the scientific community to investigate the spatio-temporal properties of model biological systems. We first describe the foundations of the methods and then describe their relevance and possible application areas with illustrative examples from our own research. Possible ways to address the encountered computational difficulties are also discussed.

  18. Biological in situ characterization of polymeric microbubble contrast agents.

    PubMed

    Wan, Sha; Egri, Gabriella; Oddo, Letizia; Cerroni, Barbara; Dähne, Lars; Paradossi, Gaio; Salvati, Anna; Lynch, Iseult; Dawson, Kenneth A; Monopoli, Marco P

    2016-06-01

    Polymeric microbubbles (MBs) are gas filled particles composed of a thin stabilized polymer shell that have been recently developed as valid contrast agents for the combined use of ultrasonography (US), magnetic resonance imaging (MRI) and single photon emission computer tomography (SPECT) imaging. Due to their buoyancy, the commonly available approaches to study their behaviour in complex media are not easily applicable and their use in modern medicine requires such behaviour to be fully elucidated. Here we have used for the first time flow cytometry as a new high throughput approach that allows characterisation of the MB dispersion, prior to and after exposure in different biological media and we have additionally developed a method that allows characterisation of the strongly bound proteins adsorbed on the MBs, to fully predict their biological behaviour in biological milieu. PMID:26993210

  19. Validation techniques of agent based modelling for geospatial simulations

    NASA Astrophysics Data System (ADS)

    Darvishi, M.; Ahmadi, G.

    2014-10-01

    One of the most interesting aspects of modelling and simulation study is to describe the real world phenomena that have specific properties; especially those that are in large scales and have dynamic and complex behaviours. Studying these phenomena in the laboratory is costly and in most cases it is impossible. Therefore, Miniaturization of world phenomena in the framework of a model in order to simulate the real phenomena is a reasonable and scientific approach to understand the world. Agent-based modelling and simulation (ABMS) is a new modelling method comprising of multiple interacting agent. They have been used in the different areas; for instance, geographic information system (GIS), biology, economics, social science and computer science. The emergence of ABM toolkits in GIS software libraries (e.g. ESRI's ArcGIS, OpenMap, GeoTools, etc) for geospatial modelling is an indication of the growing interest of users to use of special capabilities of ABMS. Since ABMS is inherently similar to human cognition, therefore it could be built easily and applicable to wide range applications than a traditional simulation. But a key challenge about ABMS is difficulty in their validation and verification. Because of frequent emergence patterns, strong dynamics in the system and the complex nature of ABMS, it is hard to validate and verify ABMS by conventional validation methods. Therefore, attempt to find appropriate validation techniques for ABM seems to be necessary. In this paper, after reviewing on Principles and Concepts of ABM for and its applications, the validation techniques and challenges of ABM validation are discussed.

  20. HISTOCHEMICAL EFFECTS OF SOME BIOLOGICAL AGENTS ON CULEX PIPIENS LARVAE.

    PubMed

    El Sobky, Mona M; Ismail, Howaida I H; Assar, Abada A

    2016-04-01

    The histochemical effects of the lethal concentration that kills 50% of larvae (LC50) of three biological agents, abamectin, Bacillus thuringiensis and spinosad on the carbohydrates (polysaccharides), proteins, nucleic acids and lipids content of the midgut and fat bodies of Culex pipiens 2nd instar larvae were studied. The results showed that the three tested compounds reduced the carbohydrates (polysaccharides), proteins, RNA synthesis and lipids content after 72 hours of treatment where abamectin was the most effective followed by Bacillus thuringiensis then spinosad. PMID:27363043

  1. Towards the implementation of a spectral database for the detection of biological warfare agents

    NASA Astrophysics Data System (ADS)

    Carestia, M.; Pizzoferrato, R.; Gelfusa, M.; Cenciarelli, O.; D'Amico, F.; Malizia, A.; Scarpellini, D.; Murari, A.; Vega, J.; Gaudio, P.

    2014-10-01

    The deliberate use of biological warfare agents (BWA) and other pathogens can jeopardize the safety of population, fauna and flora, and represents a concrete concern from the military and civil perspective. At present, the only commercially available tools for fast warning of a biological attack can perform point detection and require active or passive sampling collection. The development of a stand-off detection system would be extremely valuable to minimize the risk and the possible consequences of the release of biological aerosols in the atmosphere. Biological samples can be analyzed by means of several optical techniques, covering a broad region of the electromagnetic spectrum. Strong evidence proved that the informative content of fluorescence spectra could provide good preliminary discrimination among those agents and it can also be obtained through stand-off measurements. Such a system necessitates a database and a mathematical method for the discrimination of the spectral signatures. In this work, we collected fluorescence emission spectra of the main BWA simulants, to implement a spectral signature database and apply the Universal Multi Event Locator (UMEL) statistical method. Our preliminary analysis, conducted in laboratory conditions with a standard UV lamp source, considers the main experimental setups influencing the fluorescence signature of some of the most commonly used BWA simulants. Our work represents a first step towards the implementation of a spectral database and a laser-based biological stand-off detection and identification technique.

  2. Multispectral analysis of biological agents to implement a quick tool for stand-off biological detection

    NASA Astrophysics Data System (ADS)

    Carestia, M.; Pizzoferrato, R.; Lungaroni, M.; Gabriele, J.; Ludovici, G. M.; Cenciarelli, O.; Gelfusa, M.; Murari, A.; Malizia, A.; Gaudio, P.

    2015-10-01

    With the aim of identifying an approach to exploit the differences in the fluorescence signatures of biological agents BAs, we have investigated the response of some BAs simulants to a set of different excitation wavelengths in the UV spectral range (i.e. 266, 273, 280, 300, 340, 355 nm). Our preliminary results on bacterial spores and vegetative forms, dispersed in water, showed that the differences in the fluorescence spectra can be enhanced, and more easily revealed, by using different excitation wavelengths. Specifically, the photo luminescence (PL) spectra coming from different species of Bacillus, in the form of spores (used as simulants of Bacillus anthracis), show significant differences under excitation at all the wavelengths, with slightly larger differences at 300, 340, 355 nm. On the other hand, the vegetative forms of two Bacillus species, did not show any appreciable difference, i.e. the PL spectra are virtually identical, for the excitation wavelengths of 266, 273, 280 nm. Conversely, small yet appreciable difference appear at 300, 340, 355 nm. Finally, large difference appear between the spore and the vegetative form of each species at all the wavelengths, with slightly larger variations at 300, 340, 355 nm. Together, these preliminary results support the hypothesis that a multi-wavelength approach could be used to improve the sensitivity and specificity of UV-LIF based BAs detection systems. The second step of this work concerns the application of a Support Vector Regression (SVR) method, as evaluated in our previous work to define a methodology for the setup of a multispectral database for the stand-off detection of BAs.

  3. Virtual agents in a simulated virtual training environment

    NASA Technical Reports Server (NTRS)

    Achorn, Brett; Badler, Norman L.

    1993-01-01

    A drawback to live-action training simulations is the need to gather a large group of participants in order to train a few individuals. One solution to this difficulty is the use of computer-controlled agents in a virtual training environment. This allows a human participant to be replaced by a virtual, or simulated, agent when only limited responses are needed. Each agent possesses a specified set of behaviors and is capable of limited autonomous action in response to its environment or the direction of a human trainee. The paper describes these agents in the context of a simulated hostage rescue training session, involving two human rescuers assisted by three virtual (computer-controlled) agents and opposed by three other virtual agents.

  4. Biocellion: accelerating computer simulation of multicellular biological system models

    PubMed Central

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

    2014-01-01

    Motivation: 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. Results: 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. Availability and implementation: 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. Contact: seunghwa.kang@pnnl.gov PMID:25064572

  5. Micro-radiography of biological samples with medical contrast agents

    NASA Astrophysics Data System (ADS)

    Dammer, J.; Weyda, F.; Benes, J.; Sopko, V.; Gelbic, I.

    2013-12-01

    Micro-radiography is an imaging technique that uses X-rays to study the internal structures of objects. This fast and easy imaging tool is based on differential X-ray attenuation by various tissues and structures within biological samples. The experimental setup described is based on the semiconductor pixel X-ray detector Medipix2 and X-ray micro-focus tube. Our micro-radiographic system has been recently used not only for the examination of internal structures of various arthropods and other biological objects but also for tracing some processes in selected model species (we used living larvae of mosquito Culex quinquefasciatus). Low concentrations of iodine, lanthanum or gold particles were used as a tracer (contrast agent). Such contrast agents increase the absorption of X-rays and allow a better visibility of internal structures of model organisms (especially the various cavities, pores, etc.). In addition, the movement of tracers in selected timing experiments demonstrates some physiological functions of digestive and excretory system.

  6. Development of a persistent chemical agent simulation system

    NASA Technical Reports Server (NTRS)

    1983-01-01

    A Persistent Chemical Agent Simulation System was developed (PCASS) to simulate, for force-on-force training exercises, the field environment produced by the presence of persistent chemical agents. Such a simulant system must satisfy several requirements to be of value as a training aid. Specifically, it must provide for realistic training which will generate competency in at least the following areas: (1) detection of the persistent agent presence; (2) proper use of protective equipment and procedures; (3) determination of the extent of contamination; and (4) decontamination of equipment and personnel.

  7. A simulation-based tutor that reasons about multiple agents

    SciTech Connect

    Rhodes Eliot, C. III; Park Woolf, B.

    1996-12-31

    This paper examines the problem of modeling multiple agents within an intelligent simulation-based tutor. Multiple agent and planning technology were used to enable the system to critique a human agent`s reasoning about multiple agents. This perspective arises naturally whenever a student must learn to lead and coordinate a team of people. The system dynamically selected teaching goals, instantiated plans and modeled the student and the domain as it monitored the student`s progress. The tutor provides one of the first complete integrations of a real-time simulation with knowledge-based reasoning. Other novel techniques of the system are reported, such as common-sense reasoning about plans, reasoning about protocol mechanisms, and using a real-time simulation for training.

  8. Detection of nerve agents and biological molecules using embedded piezoresistive microcantilever sensors.

    NASA Astrophysics Data System (ADS)

    Porter, Timothy; Vail, Tim; Wooley, Amanda

    2008-03-01

    Embedded piezoresistive microcantilever (EPM) sensors have been used in the detection of a variety of analyte species. EPM sensors utilize a tiny piezoresistive microcantilever partially embedded into a sensing material to produce a sensing element that is compact, simple, resistant to movement and shock, and suitable for remote sensing applications. In the current project, we have used sensing materials comprised of an immobilizing polymer functionalized with either target enzymes or antibodies to detect two biological agents, bacillus globigi (BG) and Diisopropyl fluorophosphate (DFP). DFP is an organophosphate used as a simulant for organophosphate nerve agents, while BG is a large bacterial spore used as a simulant for other bacterial spores such as bacillus anthracis. Sensing results are presented for both types of EPM sensors.

  9. Engineered plant biomass particles coated with biological agents

    DOEpatents

    Dooley, James H.; Lanning, David N.

    2014-06-24

    Plant biomass particles coated with a biological agent such as a bacterium or seed, characterized by a length dimension (L) aligned substantially parallel to a grain direction and defining a substantially uniform distance along the grain, a width dimension (W) normal to L and aligned cross grain, and a height dimension (H) normal to W and L. In particular, the L.times.H dimensions define a pair of substantially parallel side surfaces characterized by substantially intact longitudinally arrayed fibers, the W.times.H dimensions define a pair of substantially parallel end surfaces characterized by crosscut fibers and end checking between fibers, and the L.times.W dimensions define a pair of substantially parallel top and bottom surfaces.

  10. Evolution of cooperative behavior in simulation agents

    SciTech Connect

    Stroud, P.D.

    1998-04-01

    A simulated automobile factory paint shop is used as a testbed for exploring the emulation of human decision making behavior. A discrete events simulation of the paint shop as a collection of interacting Java actors is described. An evolutionary cognitive architecture is under development for building software actors to emulate humans in simulations of human dominated complex systems. In this paper, the cognitive architecture is extended by implementing a persistent population of trial behaviors with an incremental fitness valuation update strategy, and by allowing a group of cognitive actors to share information. A proof of principle demonstration is presented.

  11. System integration and development for biological warfare agent surveillance

    NASA Astrophysics Data System (ADS)

    Mark, Jacob A.; Green, Lance D.; Deshpande, Alina; White, P. Scott

    2007-04-01

    A wide variety of technical needs exist for surveillance, monitoring, identifying, or detecting pathogens with potential use as biological terrorism or warfare agents. Because the needs vary greatly among diverse applications, tailored systems are needed that meet performance, information, and cost requirements. A systems perspective allows developers to identify chokepoints for each application, and focus R&D investments on the limiting factors. Surveillance and detection systems are comprised of three primary components: information (markers), chemistries (assays), and instrumentation for "readout". Careful consideration of these components within the context of each application will allow for increases in efficiency and performance not generally realized when researchers focus on a single component in isolation. In fact, many application requirements can be met with simple novel combinations of existing technologies, without the need for huge investments in basic research. Here we discuss some of the key parameters for surveillance, detection, and identification of biothreat agents, and provide examples of focused development that addresses key bottlenecks, and greatly improve system performance.

  12. Brahms An Agent-Oriented Language for Work Practice Simulation and Multi-Agent Systems Development

    NASA Astrophysics Data System (ADS)

    Sierhuis, Maarten; Clancey, William J.; van Hoof, Ron J. J.

    Brahms is a multi-agent modeling language for simulating human work practice that emerges from work processes in organizations. The same Brahms language can be used to implement and execute distributed multi-agent systems, based on models of work practice that were first simulated. Brahms demonstrates how a multi-agent belief-desire-intention language, symbolic cognitive modeling, traditional business process modeling, activity-and situated cognition theories are brought together in a coherent approach for analysis and design of organizations and human-centered systems.

  13. Evanescent planar waveguide detection of biological warfare simulants

    NASA Astrophysics Data System (ADS)

    Sipe, David M.; Schoonmaker, Kenneth P.; Herron, James N.; Mostert, Michael J.

    2000-04-01

    An evanescent planar waveguide Mark 1.5 instrument was used to detect simulants of biological warfare agents; ovalbumin (OV), MS2 bacteriophage, BG, and Erwinia herbicola (EH). Polyclonal tracer antibodies were labeled with the fluorescent dye, Cy5. Discrete bands of polyclonal capture antibodies were immobilized to a polystyrene planar waveguide with molded integral lenses. An ST-6 CCD camera was used for detection. OV. MS2 and BG were detected in a simultaneous 3 by 3 array; with a total of nine measurements within 6 minutes. EH was analyzed in a separate array. Results were evaluate dat the US Army Joint Field Trials V, at the Dugway Proving Grounds. Over a 10 day period, 32 unknown samples were analyzed daily for each simulant. Detection limits: OV 10 ng/ml, MS2 107 pfu/ml, BG 105 cfu/ml. EH was detectable at 5 X 105 cfu/ml. Overall false positives were 3.0 percent. Therefore, the Mark 1.5 instrument, with a parallel array of detectors, evanescent flourescent excitation, and CCD imaging provides for rapid, sensitive, and specific detection of biological warfare agent simulants.

  14. Comparative sporicidal effects of disinfectants after release of a biological agent.

    PubMed

    Kenar, Levent; Ortatatli, Mesut; Yaren, Hakan; Karayilanoglu, Turan; Aydogan, Hakan

    2007-06-01

    Because of spore formation, Bacillus anthracis is considered the most resistant biological warfare agent known. The present study aimed to assess and compare well-known decontamination routes to inactivate the spores on daily-use environmental tools contaminated previously. To simulate the agent, Bacillus atrophaeus was used. Various environmental samples (such as tile, fabric clothing, wood, protective suit, glass, paper, soil, water, plastic, and metal) that may be contaminated after a biological incident were used as test carriers and inoculated with B. atrophaeus. Sodium hypochlorite, free chlorine, autoclaving, ethylene oxide, hydrogen peroxide, ultraviolet irradiation, and boiling decontaminated the samples. Glutaraldehyde (2%) and free chlorine solution (10,000 mg/L) were also found to be effective in decontaminating the samples and are recommended as alternatives to the use of sodium hypochlorite solution. Soil, tile, paper, and metal were determined to be the most difficult materials to decontaminate. It was concluded that 5% hypochlorite adjusted with acetic acid might also be used for decontamination. Decontamination strategies to reduce contamination of the environment by biological warfare agents need to be applied to mitigate the number of victims, in terms of prominent characteristics like cost-effectiveness and user-friendliness. PMID:17615843

  15. Advanced nanoelectronic architectures for THz-based biological agent detection

    NASA Astrophysics Data System (ADS)

    Woolard, Dwight L.; Jensen, James O.

    2009-02-01

    The U.S. Army Research Office (ARO) and the U.S. Army Edgewood Chemical Biological Center (ECBC) jointly lead and support novel research programs that are advancing the state-of-the-art in nanoelectronic engineering in application areas that have relevance to national defense and security. One fundamental research area that is presently being emphasized by ARO and ECBC is the exploratory investigation of new bio-molecular architectural concepts that can be used to achieve rapid, reagent-less detection and discrimination of biological warfare (BW) agents, through the control of multi-photon and multi-wavelength processes at the nanoscale. This paper will overview an ARO/ECBC led multidisciplinary research program presently under the support of the U.S. Defense Threat Reduction Agency (DTRA) that seeks to develop new devices and nanoelectronic architectures that are effective for extracting THz signatures from target bio-molecules. Here, emphasis will be placed on the new nanosensor concepts and THz/Optical measurement methodologies for spectral-based sequencing/identification of genetic molecules.

  16. Biological agent detection based on principal component analysis

    NASA Astrophysics Data System (ADS)

    Mudigonda, Naga R.; Kacelenga, Ray

    2006-05-01

    This paper presents an algorithm, based on principal component analysis for the detection of biological threats using General Dynamics Canada's 4WARN Sentry 3000 biodetection system. The proposed method employs a statistical method for estimating background biological activity so as to make the algorithm adaptive to varying background situations. The method attempts to characterize the pattern of change that occurs in the fluorescent particle counts distribution and uses the information to suppress false-alarms. The performance of the method was evaluated using a total of 68 tests including 51 releases of Bacillus Globigii (BG), six releases of BG in the presence of obscurants, six releases of obscurants only, and five releases of ovalbumin at the Ambient Breeze Tunnel Test facility, Battelle, OH. The peak one-minute average concentration of BG used in the tests ranged from 10 - 65 Agent Containing Particles per Liter of Air (ACPLA). The obscurants used in the tests included diesel smoke, white grenade smoke, and salt solution. The method successfully detected BG at a sensitivity of 10 ACPLA and resulted in an overall probability of detection of 94% for BG without generating any false-alarms for obscurants at a detection threshold of 0.6 on a scale of 0 to 1. Also, the method successfully detected BG in the presence of diesel smoke and salt water fumes. The system successfully responded to all the five ovalbumin releases with noticeable trends in algorithm output and alarmed for two releases at the selected detection threshold.

  17. Chemiluminescence assay for the detection of biological warfare agents

    SciTech Connect

    Langry, K; Horn, J

    1999-11-05

    A chemiluminescent homogeneous immunoassay and a hand-size multiassay reader are described that could be used for detecting biological materials. The special feature of the assay is that it employs two different antibodies that each bind to a unique epitope on the same antigen. Each group of epitope-specific antibodies has linked to it an enzyme of a proximal-enzyme pair. One enzyme of the pair utilizes a substrate in high concentration to produce a second substrate required by the second enzyme. This new substrate enables the second enzyme to function. The reaction of the second enzyme is configured to produce light. This chemiluminescence is detected with a charge-coupled device (CCD) camera. The proximal pair enzymes must be in close proximity to one another to allow the second enzyme to react with the product of the first enzyme. This only occurs when the enzyme-linked antibodies are attached to the antigen, whether antigen is a single protein with multiple epitopes or the surface of a cell with a variety of different antigens. As a result of their juxtaposition, the enzymes produce light only in the presence of the biological material. A brief description is given as to how this assay could be utilized in a personal bio-agent detector system.

  18. 75 FR 64984 - Availability of an Environmental Assessment for a Biological Control Agent for Hawkweeds

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-10-21

    ... Assessment for a Biological Control Agent for Hawkweeds AGENCY: Animal and Plant Health Inspection Service... States as a biological control agent to reduce the severity of infestations of hawkweeds. We are making... subterminalis, into the continental United States for the biological control of hawkweeds (Hieracium...

  19. 77 FR 46373 - Availability of an Environmental Assessment for a Biological Control Agent for Hemlock Woolly...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-08-03

    ... Animal and Plant Health Inspection Service Availability of an Environmental Assessment for a Biological... of Symnus coniferarum into the eastern United States for use as a biological control agent to reduce... as a biological control agent to reduce the severity of hemlock woolly adelgid (Adelges...

  20. An abundant biological control agent does not provide a significant predator subsidy

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Classical weed biological control agents, regardless of their effectiveness, may provide subsidies to predators and parasites. The chemically defended weevil Oxyops vitiosa Pascoe is a successful agent that was introduced to control the invasive tree Melaleuca quinquenervia. Two consecutive small ...

  1. High-throughput assay for optimising microbial biological control agent production and delivery

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Lack of technologies to produce and deliver effective biological control agents (BCAs) is a major barrier to their commercialization. A myriad of variables associated with BCA cultivation, formulation, drying, storage, and reconstitution processes complicates agent quality maximization. An efficie...

  2. Love-Wave Sensors Combined with Microfluidics for Fast Detection of Biological Warfare Agents

    PubMed Central

    Matatagui, Daniel; Fontecha, José Luis; Fernández, María Jesús; Gràcia, Isabel; Cané, Carles; Santos, José Pedro; Horrillo, María Carmen

    2014-01-01

    The following paper examines a time-efficient method for detecting biological warfare agents (BWAs). The method is based on a system of a Love-wave immunosensor combined with a microfluidic chip which detects BWA samples in a dynamic mode. In this way a continuous flow-through of the sample is created, promoting the reaction between antigen and antibody and allowing a fast detection of the BWAs. In order to prove this method, static and dynamic modes have been simulated and different concentrations of BWA simulants have been tested with two immunoreactions: phage M13 has been detected using the mouse monoclonal antibody anti-M13 (AM13), and the rabbit immunoglobulin (Rabbit IgG) has been detected using the polyclonal antibody goat anti-rabbit (GAR). Finally, different concentrations of each BWA simulants have been detected with a fast response time and a desirable level of discrimination among them has been achieved. PMID:25029282

  3. Love-wave sensors combined with microfluidics for fast detection of biological warfare agents.

    PubMed

    Matatagui, Daniel; Fontecha, José Luis; Fernández, María Jesús; Gràcia, Isabel; Cané, Carles; Santos, José Pedro; Horrillo, María Carmen

    2014-01-01

    The following paper examines a time-efficient method for detecting biological warfare agents (BWAs). The method is based on a system of a Love-wave immunosensor combined with a microfluidic chip which detects BWA samples in a dynamic mode. In this way a continuous flow-through of the sample is created, promoting the reaction between antigen and antibody and allowing a fast detection of the BWAs. In order to prove this method, static and dynamic modes have been simulated and different concentrations of BWA simulants have been tested with two immunoreactions: phage M13 has been detected using the mouse monoclonal antibody anti-M13 (AM13), and the rabbit immunoglobulin (Rabbit IgG) has been detected using the polyclonal antibody goat anti-rabbit (GAR). Finally, different concentrations of each BWA simulants have been detected with a fast response time and a desirable level of discrimination among them has been achieved. PMID:25029282

  4. The systems biology simulation core algorithm

    PubMed Central

    2013-01-01

    Background With the increasing availability of high dimensional time course data for metabolites, genes, and fluxes, the mathematical description of dynamical systems has become an essential aspect of research in systems biology. Models are often encoded in formats such as SBML, whose structure is very complex and difficult to evaluate due to many special cases. Results This article describes an efficient algorithm to solve SBML models that are interpreted in terms of ordinary differential equations. We begin our consideration with a formal representation of the mathematical form of the models and explain all parts of the algorithm in detail, including several preprocessing steps. We provide a flexible reference implementation as part of the Systems Biology Simulation Core Library, a community-driven project providing a large collection of numerical solvers and a sophisticated interface hierarchy for the definition of custom differential equation systems. To demonstrate the capabilities of the new algorithm, it has been tested with the entire SBML Test Suite and all models of BioModels Database. Conclusions The formal description of the mathematics behind the SBML format facilitates the implementation of the algorithm within specifically tailored programs. The reference implementation can be used as a simulation backend for Java™-based programs. Source code, binaries, and documentation can be freely obtained under the terms of the LGPL version 3 from http://simulation-core.sourceforge.net. Feature requests, bug reports, contributions, or any further discussion can be directed to the mailing list simulation-core-development@lists.sourceforge.net. PMID:23826941

  5. Image simulation for biological microscopy: microlith

    PubMed Central

    Mehta, Shalin B.; Oldenbourg, Rudolf

    2014-01-01

    Image simulation remains under-exploited for the most widely used biological phase microscopy methods, because of difficulties in simulating partially coherent illumination. We describe an open-source toolbox, microlith (https://code.google.com/p/microlith), which accurately predicts three-dimensional images of a thin specimen observed with any partially coherent imaging system, as well as images of coherently illuminated and self-luminous incoherent specimens. Its accuracy is demonstrated by comparing simulated and experimental bright-field and dark-field images of well-characterized amplitude and phase targets, respectively. The comparison provides new insights about the sensitivity of the dark-field microscope to mass distributions in isolated or periodic specimens at the length-scale of 10nm. Based on predictions using microlith, we propose a novel approach for detecting nanoscale structural changes in a beating axoneme using a dark-field microscope. PMID:24940543

  6. Cognitive Modeling for Agent-Based Simulation of Child Maltreatment

    NASA Astrophysics Data System (ADS)

    Hu, Xiaolin; Puddy, Richard

    This paper extends previous work to develop cognitive modeling for agent-based simulation of child maltreatment (CM). The developed model is inspired from parental efficacy, parenting stress, and the theory of planned behavior. It provides an explanatory, process-oriented model of CM and incorporates causality relationship and feedback loops from different factors in the social ecology in order for simulating the dynamics of CM. We describe the model and present simulation results to demonstrate the features of this model.

  7. Agent-Based Simulations for Project Management

    NASA Technical Reports Server (NTRS)

    White, J. Chris; Sholtes, Robert M.

    2011-01-01

    Currently, the most common approach used in project planning tools is the Critical Path Method (CPM). While this method was a great improvement over the basic Gantt chart technique being used at the time, it now suffers from three primary flaws: (1) task duration is an input, (2) productivity impacts are not considered , and (3) management corrective actions are not included. Today, computers have exceptional computational power to handle complex simulations of task e)(eculion and project management activities (e.g ., dynamically changing the number of resources assigned to a task when it is behind schedule). Through research under a Department of Defense contract, the author and the ViaSim team have developed a project simulation tool that enables more realistic cost and schedule estimates by using a resource-based model that literally turns the current duration-based CPM approach "on its head." The approach represents a fundamental paradigm shift in estimating projects, managing schedules, and reducing risk through innovative predictive techniques.

  8. Potential of Biological Agents in Decontamination of Agricultural Soil.

    PubMed

    Javaid, Muhammad Kashif; Ashiq, Mehrban; Tahir, Muhammad

    2016-01-01

    Pesticides are widely used for the control of weeds, diseases, and pests of cultivated plants all over the world, mainly since the period after the Second World War. The use of pesticides is very extensive to control harm of pests all over the globe. Persistent nature of most of the synthetic pesticides causes serious environmental concerns. Decontamination of these hazardous chemicals is very essential. This review paper elaborates the potential of various biological agents in decontamination of agricultural soils. The agricultural crop fields are contaminated by the periodic applications of pesticides. Biodegradation is an ecofriendly, cost-effective, highly efficient approach compared to the physical and chemical methods which are expensive as well as unfriendly towards environment. Biodegradation is sensitive to the concentration levels of hydrogen peroxide and nitrogen along with microbial community, temperature, and pH changes. Experimental work for optimum conditions at lab scale can provide very fruitful results about specific bacterial, fungal strains. This study revealed an upper hand of bioremediation over physicochemical approaches. Further studies should be carried out to understand mechanisms of biotransformation. PMID:27293964

  9. Potential of Biological Agents in Decontamination of Agricultural Soil

    PubMed Central

    Javaid, Muhammad Kashif; Ashiq, Mehrban; Tahir, Muhammad

    2016-01-01

    Pesticides are widely used for the control of weeds, diseases, and pests of cultivated plants all over the world, mainly since the period after the Second World War. The use of pesticides is very extensive to control harm of pests all over the globe. Persistent nature of most of the synthetic pesticides causes serious environmental concerns. Decontamination of these hazardous chemicals is very essential. This review paper elaborates the potential of various biological agents in decontamination of agricultural soils. The agricultural crop fields are contaminated by the periodic applications of pesticides. Biodegradation is an ecofriendly, cost-effective, highly efficient approach compared to the physical and chemical methods which are expensive as well as unfriendly towards environment. Biodegradation is sensitive to the concentration levels of hydrogen peroxide and nitrogen along with microbial community, temperature, and pH changes. Experimental work for optimum conditions at lab scale can provide very fruitful results about specific bacterial, fungal strains. This study revealed an upper hand of bioremediation over physicochemical approaches. Further studies should be carried out to understand mechanisms of biotransformation. PMID:27293964

  10. Arthritis in pregnancy: the role and safety of biological agents

    PubMed Central

    Youssef, Peter; Kennedy, Debra

    2009-01-01

    As the average age of mothers is increasing there is a greater likelihood that they will have intercurrent medical problems at the time of their pregnancy. As a group, autoimmune diseases are relatively common with an estimated population prevalence of 5–8%. At least 75% of autoimmune diseases occur in women, most frequently during the child-bearing years. Rheumatoid arthritis (RA) is the most common chronic inflammatory disease of joints and occurs in approximately 1% of the population with women being affected two or three times more than men and many of the women being of child-bearing age. The pathogenesis of RA is multifactorial with a role for T-lymphocytes, B-lymphocytes, macrophages and other pro-inflammatory cells producing a plethora of cytokines including interleukin-1 and tumour necrosis factor-α in the synovial cavity resulting in irreversible damage to cartilage, soft tissues and bone.1 The drug treatment of RA involves the use of disease-modifying agents to reduce or prevent permanent tissue damage. There is a new class of drugs that can be used to target specific cells and cytokines that have been called ‘biological agents’. These drugs have been shown to significantly reduce inflammation and to retard the progression of joint damage in RA thereby reducing symptoms and improving function.2

  11. Bioforensics: Characterization of biological weapons agents by NanoSIMS

    SciTech Connect

    Weber, P K; Ghosal, S; Leighton, T J; Wheeler, K E; Hutcheon, I D

    2007-02-26

    The anthrax attacks of Fall 2001 highlight the need to develop forensic methods based on multiple identifiers to determine the origin of biological weapons agents. Genetic typing methods (i.e., DNA and RNA-based) provide one attribution technology, but genetic information alone is not usually sufficient to determine the provenance of the material. Non-genetic identifiers, including elemental and isotopic signatures, provide complementary information that can be used to identify the means, geographic location and date of production. Under LDRD funding, we have successfully developed the techniques necessary to perform bioforensic characterization with the NanoSIMS at the individual spore level. We have developed methods for elemental and isotopic characterization at the single spore scale. We have developed methods for analyzing spore sections to map elemental abundance within spores. We have developed rapid focused ion beam (FIB) sectioning techniques for spores to preserve elemental and structural integrity. And we have developed a high-resolution depth profiling method to characterize the elemental distribution in individual spores without sectioning. We used these newly developed methods to study the controls on elemental abundances in spores, characterize the elemental distribution of in spores, and to study elemental uptake by spores. Our work under this LDRD project attracted FBI and DHS funding for applied purposes.

  12. Teaching Basic Biological Simulation Techniques With the Programmable Calculator.

    ERIC Educational Resources Information Center

    Spain, J. D.

    1972-01-01

    The programable calculator has great potential for the development of simulations which provide new dimensions to instruction in the biological sciences. Basic principles of both biology and simulation itself can be presented. An introductory course on digital computer simulation in biology is now taught at Michigan Technological University; the…

  13. Agent-Based Modeling and Simulation on Emergency Evacuation

    NASA Astrophysics Data System (ADS)

    Ren, Chuanjun; Yang, Chenghui; Jin, Shiyao

    Crowd stampedes and evacuation induced by panic caused by emergences often lead to fatalities as people are crushed, injured, trampled or even dead. Such phenomena may be triggered in life-threatening situations such as fires, explosions in crowded buildings. Emergency evacuation simulation has recently attracted the interest of a rapidly increasing number of scientists. This paper presents an Agent-Based Modeling and Simulation using Repast software to construct crowd evacuations for emergency response from an area under a fire. Various types of agents and different attributes of agents are designed in contrast to traditional modeling. The attributes that govern the characteristics of the people are studied and tested by iterative simulations. Simulations are also conducted to demonstrate the effect of various parameters of agents. Some interesting results were observed such as "faster is slower" and the ignorance of available exits. At last, simulation results suggest practical ways of minimizing the harmful consequences of such events and the existence of an optimal escape strategy.

  14. 75 FR 39437 - Optimizing the Security of Biological Select Agents and Toxins in the United States

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-07-08

    ..., 2010. [FR Doc. 2010-16864 Filed 7-7-10; 11:15 am] Billing code 3195-W0-P ... Executive Order 13546--Optimizing the Security of Biological Select Agents and Toxins in the United States... July 2, 2010 Optimizing the Security of Biological Select Agents and Toxins in the United States By...

  15. Modeling Dispersion of Chemical-Biological Agents in Three Dimensional Living Space

    SciTech Connect

    William S. Winters

    2002-02-01

    This report documents a series of calculations designed to demonstrate Sandia's capability in modeling the dispersal of chemical and biological agents in complex three-dimensional spaces. The transport of particles representing biological agents is modeled in a single room and in several connected rooms. The influence of particle size, particle weight and injection method are studied.

  16. Insect pathogens as biological control agents: Back to the future.

    PubMed

    Lacey, L A; Grzywacz, D; Shapiro-Ilan, D I; Frutos, R; Brownbridge, M; Goettel, M S

    2015-11-01

    The development and use of entomopathogens as classical, conservation and augmentative biological control agents have included a number of successes and some setbacks in the past 1years. In this forum paper we present current information on development, use and future directions of insect-specific viruses, bacteria, fungi and nematodes as components of integrated pest management strategies for control of arthropod pests of crops, forests, urban habitats, and insects of medical and veterinary importance. Insect pathogenic viruses are a fruitful source of microbial control agents (MCAs), particularly for the control of lepidopteran pests. Most research is focused on the baculoviruses, important pathogens of some globally important pests for which control has become difficult due to either pesticide resistance or pressure to reduce pesticide residues. Baculoviruses are accepted as safe, readily mass produced, highly pathogenic and easily formulated and applied control agents. New baculovirus products are appearing in many countries and gaining an increased market share. However, the absence of a practical in vitro mass production system, generally higher production costs, limited post application persistence, slow rate of kill and high host specificity currently contribute to restricted use in pest control. Overcoming these limitations are key research areas for which progress could open up use of insect viruses to much larger markets. A small number of entomopathogenic bacteria have been commercially developed for control of insect pests. These include several Bacillus thuringiensis sub-species, Lysinibacillus (Bacillus) sphaericus, Paenibacillus spp. and Serratia entomophila. B. thuringiensis sub-species kurstaki is the most widely used for control of pest insects of crops and forests, and B. thuringiensis sub-species israelensis and L. sphaericus are the primary pathogens used for control of medically important pests including dipteran vectors. These pathogens

  17. Modeling and simulating human teamwork behaviors using intelligent agents

    NASA Astrophysics Data System (ADS)

    Fan, Xiaocong; Yen, John

    2004-12-01

    Among researchers in multi-agent systems there has been growing interest in using intelligent agents to model and simulate human teamwork behaviors. Teamwork modeling is important for training humans in gaining collaborative skills, for supporting humans in making critical decisions by proactively gathering, fusing, and sharing information, and for building coherent teams with both humans and agents working effectively on intelligence-intensive problems. Teamwork modeling is also challenging because the research has spanned diverse disciplines from business management to cognitive science, human discourse, and distributed artificial intelligence. This article presents an extensive, but not exhaustive, list of work in the field, where the taxonomy is organized along two main dimensions: team social structure and social behaviors. Along the dimension of social structure, we consider agent-only teams and mixed human-agent teams. Along the dimension of social behaviors, we consider collaborative behaviors, communicative behaviors, helping behaviors, and the underpinning of effective teamwork-shared mental models. The contribution of this article is that it presents an organizational framework for analyzing a variety of teamwork simulation systems and for further studying simulated teamwork behaviors.

  18. Deciphering endophyte behaviour: the link between endophyte biology and efficacious biological control agents.

    PubMed

    Card, Stuart; Johnson, Linda; Teasdale, Suliana; Caradus, John

    2016-08-01

    Endophytes associate with the majority of plant species found in natural and managed ecosystems. They are regarded as extremely important plant partners that provide improved stress tolerance to the host compared with plants that lack this symbiosis. Fossil records of endophytes date back more than 400 million years, implicating these microorganisms in host plant adaptation to habitat transitions. However, it is only recently that endophytes, and their bioactive products, have received meaningful attention from the scientific community. The benefits some endophytes can confer on their hosts include plant growth promotion and survival through the inhibition of pathogenic microorganisms and invertebrate pests, the removal of soil contaminants, improved tolerance of low fertility soils, and increased tolerance of extreme temperatures and low water availability. Endophytes are extremely diverse and can exhibit many different biological behaviours. Not all endophyte technologies have been successfully commercialised. Of interest in the development of the next generation of plant protection products is how much of this is due to the biology of the particular endophytic microorganism. In this review, we highlight selected case studies of endophytes and discuss their lifestyles and behavioural traits, and discuss how these factors contribute towards their effectiveness as biological control agents. PMID:27222223

  19. Agent 2003 Conference on Challenges in Social Simulation

    SciTech Connect

    Margaret Clemmons, ed.

    2003-01-01

    Welcome to the Proceedings of the fourth in a series of agent simulation conferences cosponsored by Argonne National Laboratory and The University of Chicago. Agent 2003 is the second conference in which three Special Interest Groups from the North American Association for Computational Social and Organizational Science (NAACSOS) have been involved in planning the program--Computational Social Theory; Simulation Applications; and Methods, Toolkits and Techniques. The theme of Agent 2003, Challenges in Social Simulation, is especially relevant, as there seems to be no shortage of such challenges. Agent simulation has been applied with increasing frequency to social domains for several decades, and its promise is clear and increasingly visible. Like any nascent scientific methodology, however, it faces a number of problems or issues that must be addressed in order to progress. These challenges include: (1) Validating models relative to the social settings they are designed to represent; (2) Developing agents and interactions simple enough to understand but sufficiently complex to do justice to the social processes of interest; (3) Bridging the gap between empirically spare artificial societies and naturally occurring social phenomena; (4) Building multi-level models that span processes across domains; (5) Promoting a dialog among theoretical, qualitative, and empirical social scientists and area experts, on the one hand, and mathematical and computational modelers and engineers, on the other; (6) Using that dialog to facilitate substantive progress in the social sciences; and (7) Fulfilling the aspirations of users in business, government, and other application areas, while recognizing and addressing the preceding challenges. Although this list hardly exhausts the challenges the field faces, it does identify topics addressed throughout the presentations of Agent 2003. Agent 2003 is part of a much larger process in which new methods and techniques are applied to

  20. Tutorial on agent-based modeling and simulation. Part 2 : how to model with agents.

    SciTech Connect

    Macal, C. M.; North, M. J.; Decision and Information Sciences

    2006-01-01

    Agent-based modeling and simulation (ABMS) is a new approach to modeling systems comprised of interacting autonomous agents. ABMS promises to have far-reaching effects on the way that businesses use computers to support decision-making and researchers use electronic laboratories to do research. Some have gone so far as to contend that ABMS is a new way of doing science. Computational advances make possible a growing number of agent-based applications across many fields. Applications range from modeling agent behavior in the stock market and supply chains, to predicting the spread of epidemics and the threat of bio-warfare, from modeling the growth and decline of ancient civilizations to modeling the complexities of the human immune system, and many more. This tutorial describes the foundations of ABMS, identifies ABMS toolkits and development methods illustrated through a supply chain example, and provides thoughts on the appropriate contexts for ABMS versus conventional modeling techniques.

  1. Agent-based simulation of a financial market

    NASA Astrophysics Data System (ADS)

    Raberto, Marco; Cincotti, Silvano; Focardi, Sergio M.; Marchesi, Michele

    2001-10-01

    This paper introduces an agent-based artificial financial market in which heterogeneous agents trade one single asset through a realistic trading mechanism for price formation. Agents are initially endowed with a finite amount of cash and a given finite portfolio of assets. There is no money-creation process; the total available cash is conserved in time. In each period, agents make random buy and sell decisions that are constrained by available resources, subject to clustering, and dependent on the volatility of previous periods. The model proposed herein is able to reproduce the leptokurtic shape of the probability density of log price returns and the clustering of volatility. Implemented using extreme programming and object-oriented technology, the simulator is a flexible computational experimental facility that can find applications in both academic and industrial research projects.

  2. Tutorial on agent-based modeling and simulation.

    SciTech Connect

    Macal, C. M.; North, M. J.; Decision and Information Sciences

    2005-01-01

    Agent-based modeling and simulation (ABMS) is a new approach to modeling systems comprised of autonomous, interacting agents. ABMS promises to have far-reaching effects on the way that businesses use computers to support decision-making and researchers use electronic laboratories to support their research. Some have gone so far as to contend that ABMS is a third way of doing science besides deductive and inductive reasoning. Computational advances have made possible a growing number of agent-based applications in a variety of fields. Applications range from modeling agent behavior in the stock market and supply chains, to predicting the spread of epidemics and the threat of bio-warfare, from modeling consumer behavior to understanding the fall of ancient civilizations, to name a few. This tutorial describes the theoretical and practical foundations of ABMS, identifies toolkits and methods for developing ABMS models, and provides some thoughts on the relationship between ABMS and traditional modeling techniques.

  3. Simulation of convoy of unmanned vehicles using agent based modeling

    NASA Astrophysics Data System (ADS)

    Sharma, Sharad; Singh, Harpreet; Gerhart, G. R.

    2007-10-01

    There has been an increasing interest of unmanned vehicles keeping the importance of defense and security. A few models for a convoy of unmanned vehicle exist in literature. The objective of this paper is to exploit agent based modeling technique for a convoy of unmanned vehicles where each vehicle is an agent. Using this approach, the convoy of vehicles reaches a specified goal from a starting point. Each agent is associated with number of sensors. The agents make intelligent decisions based on sensor inputs and at the same time maintaining their group capability and behavior. The simulation is done for a battlefield environment from a single starting point to a single goal. This approach can be extended for multiple starting points to reach multiple goals. The simulation gives the time taken by the convoy to reach a goal from its initial position. In the battlefield environment, commanders make various tactical decisions depending upon the location of an enemy outpost, minefields, number of soldiers in platoons, and barriers. The simulation can help the commander to make effective decisions depending on battlefield, convoy and obstacles to reach a particular goal. The paper describes the proposed approach and gives the simulation results. The paper also gives problems for future research in this area.

  4. Detection of Chemical/Biological Agents and Stimulants using Quadrupole Ion Trap Mass Spectrometry

    SciTech Connect

    Harmon, S.H.; Hart, K.J.; Vass, A.A.; Wise, M.B.; Wolf, D.A.

    1999-06-14

    Detection of Chemical/Biological Agents and Simulants A new detector for chemical and biological agents is being developed for the U. S. Army under the Chemical and Biological Mass Spectrometer Block II program. The CBMS Block II is designed to optimize detection of both chemical and biological agents through the use of direct sampling inlets [I], a multi- ported sampling valve and a turbo- based vacuum system to support chemical ionization. Unit mass resolution using air as the buffer gas [2] has been obtained using this design. Software to control the instrument and to analyze the data generated from the instrument has also been newly developed. Detection of chemical agents can be accomplished. using the CBMS Block II design via one of two inlets - a l/ I 6'' stainless steel sample line -Chemical Warfare Air (CW Air) or a ground probe with enclosed capillary currently in use by the US Army - CW Ground. The Block II design is capable of both electron ionization and chemical ionization. Ethanol is being used as the Cl reagent based on a study indicating best performance for the Biological Warfare (BW) detection task (31). Data showing good signal to noise for 500 pg of methyl salicylate injected into the CW Air inlet, 50 ng of dimethylmethylphosphonate exposed to the CW Ground probe and 5 ng of methyl stearate analyzed using the pyrolyzer inlet were presented. Biological agents are sampled using a ''bio-concentrator'' unit that is designed to concentrate particles in the low micron range. Particles are collected in the bottom of a quartz pyrolyzer tube. An automated injector is being developed to deliver approximately 2 pL of a methylating reagent, tetramethylamonium- hydroxide to 'the collected particles. Pyrolysis occurs by rapid heating to ca. 55OOC. Biological agents are then characterized by their fatty acid methyl ester profiles and by other biomarkers. A library of ETOH- Cl/ pyrolysis MS data of microorganisms used for a recently published study [3] has been

  5. Development of a rapid method for the automatic classification of biological agents' fluorescence spectral signatures

    NASA Astrophysics Data System (ADS)

    Carestia, Mariachiara; Pizzoferrato, Roberto; Gelfusa, Michela; Cenciarelli, Orlando; Ludovici, Gian Marco; Gabriele, Jessica; Malizia, Andrea; Murari, Andrea; Vega, Jesus; Gaudio, Pasquale

    2015-11-01

    Biosecurity and biosafety are key concerns of modern society. Although nanomaterials are improving the capacities of point detectors, standoff detection still appears to be an open issue. Laser-induced fluorescence of biological agents (BAs) has proved to be one of the most promising optical techniques to achieve early standoff detection, but its strengths and weaknesses are still to be fully investigated. In particular, different BAs tend to have similar fluorescence spectra due to the ubiquity of biological endogenous fluorophores producing a signal in the UV range, making data analysis extremely challenging. The Universal Multi Event Locator (UMEL), a general method based on support vector regression, is commonly used to identify characteristic structures in arrays of data. In the first part of this work, we investigate fluorescence emission spectra of different simulants of BAs and apply UMEL for their automatic classification. In the second part of this work, we elaborate a strategy for the application of UMEL to the discrimination of different BAs' simulants spectra. Through this strategy, it has been possible to discriminate between these BAs' simulants despite the high similarity of their fluorescence spectra. These preliminary results support the use of SVR methods to classify BAs' spectral signatures.

  6. Biological soil crusts: a fundamental organizing agent in global drylands

    NASA Astrophysics Data System (ADS)

    Belnap, J.; Zhang, Y.

    2013-12-01

    Ecosystem function is profoundly affected by plant community composition, which is ultimately determined by factors that govern seed retention. Dryland ecosystems constitute ~35% of terrestrial surfaces, with most soils in these regions covered by biological soil crusts (biocrusts), a community whose autotrophs are dominated by cyanobacteria, lichens, and mosses. Studies at 550 sites revealed that plant community composition was controlled by the interaction among biocrust type, disturbance regime, and external morphology of seeds. In bare soils (due to disturbance), all seed types were present in the seedbank and plant community. As biocrusts became better developed (i.e., the cover of lichens and mosses increased), they more strongly filtered out seeds with appendages. Thus, soils under late successional biocrusts contained seedbanks dominated by smooth seeds and vascular plants growing in late successional biocrusts were dominated by those with smooth seeds. Therefore, the tension between the removal of biocrusts by soil surface disturbance and their recovery creates a shifting mosaic of plant patch types in both space and time. Because changes in vascular plant communities reverberate throughout both below ground and above ground food webs and thus affect multiple trophic levels, we propose that biocrusts are a fundamental organizing agent in drylands worldwide. Future increased demand for resources will intensify land use both temporally and spatially, resulting in an increased rate of biocrust loss across larger areas. As a result, we can expect shifts in the composition and distribution of plant communities, accompanied by concomitant changes in many aspects of dryland ecosystems. Conceptual model of shifting dryland plant mosaics through space and time. Within the large circles, soil surface type changes with time in the same space, going from bare uncrusted soil (B) to cyanobacterial biocrust (C) to lichen/moss (L/M) biocrust. Disturbance (D) drives the

  7. MATING BIOLOGY OF AUSTROMUSOTIMA CAMPTOZONALE (LEPIDOPTERA: CRAMBIDAE) - A POTENTIAL BIOLOGICAL CONTROL AGENT OF OLD WORLD CLIMBING FERN, LYGODIUM MICROPHYLLUM (SCHIZAEACEAE)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Austromusotima camptozonale (Hampson) is under investigation as a potential biological control agent of Old World Climbing fern, Lygodium microphyllum (Cav.) R. Br., which is a serious invasive weed in southern Florida. Studies were conducted to investigate aspects of the mating biology of A. campto...

  8. Agent-based modeling and simulation Part 3 : desktop ABMS.

    SciTech Connect

    Macal, C. M.; North, M. J.; Decision and Information Sciences

    2007-01-01

    Agent-based modeling and simulation (ABMS) is a new approach to modeling systems comprised of autonomous, interacting agents. ABMS promises to have far-reaching effects on the way that businesses use computers to support decision-making and researchers use electronic laboratories to support their research. Some have gone so far as to contend that ABMS 'is a third way of doing science,' in addition to traditional deductive and inductive reasoning (Axelrod 1997b). Computational advances have made possible a growing number of agent-based models across a variety of application domains. Applications range from modeling agent behavior in the stock market, supply chains, and consumer markets, to predicting the spread of epidemics, the threat of bio-warfare, and the factors responsible for the fall of ancient civilizations. This tutorial describes the theoretical and practical foundations of ABMS, identifies toolkits and methods for developing agent models, and illustrates the development of a simple agent-based model of shopper behavior using spreadsheets.

  9. Technological advancements for the detection of and protection against biological and chemical warfare agents.

    PubMed

    Eubanks, Lisa M; Dickerson, Tobin J; Janda, Kim D

    2007-03-01

    There is a growing need for technological advancements to combat agents of chemical and biological warfare, particularly in the context of the deliberate use of a chemical and/or biological warfare agent by a terrorist organization. In this tutorial review, we describe methods that have been developed both for the specific detection of biological and chemical warfare agents in a field setting, as well as potential therapeutic approaches for treating exposure to these toxic species. In particular, nerve agents are described as a typical chemical warfare agent, and the two potent biothreat agents, anthrax and botulinum neurotoxin, are used as illustrative examples of potent weapons for which countermeasures are urgently needed. PMID:17325785

  10. Comparison and analysis of biological agent category lists based on biosafety and biodefense.

    PubMed

    Tian, Deqiao; Zheng, Tao

    2014-01-01

    Biological agents pose a serious threat to human health, economic development, social stability and even national security. The classification of biological agents is a basic requirement for both biosafety and biodefense. We compared and analyzed the Biological Agent Laboratory Biosafety Category list and the defining criteria according to the World Health Organization (WHO), the National Institutes of Health (NIH), the European Union (EU) and China. We also compared and analyzed the Biological Agent Biodefense Category list and the defining criteria according to the Centers for Disease Control and Prevention (CDC) of the United States, the EU and Russia. The results show some inconsistencies among or between the two types of category lists and criteria. We suggest that the classification of biological agents based on laboratory biosafety should reduce the number of inconsistencies and contradictions. Developing countries should also produce lists of biological agents to direct their development of biodefense capabilities.To develop a suitable biological agent list should also strengthen international collaboration and cooperation. PMID:24979754

  11. Comparison and Analysis of Biological Agent Category Lists Based On Biosafety and Biodefense

    PubMed Central

    Tian, Deqiao; Zheng, Tao

    2014-01-01

    Biological agents pose a serious threat to human health, economic development, social stability and even national security. The classification of biological agents is a basic requirement for both biosafety and biodefense. We compared and analyzed the Biological Agent Laboratory Biosafety Category list and the defining criteria according to the World Health Organization (WHO), the National Institutes of Health (NIH), the European Union (EU) and China. We also compared and analyzed the Biological Agent Biodefense Category list and the defining criteria according to the Centers for Disease Control and Prevention (CDC) of the United States, the EU and Russia. The results show some inconsistencies among or between the two types of category lists and criteria. We suggest that the classification of biological agents based on laboratory biosafety should reduce the number of inconsistencies and contradictions. Developing countries should also produce lists of biological agents to direct their development of biodefense capabilities.To develop a suitable biological agent list should also strengthen international collaboration and cooperation. PMID:24979754

  12. Use of agent-based simulations to design and interpret HIV clinical trials.

    PubMed

    Cuadros, Diego F; Abu-Raddad, Laith J; Awad, Susanne F; García-Ramos, Gisela

    2014-07-01

    In this study, we illustrate the utility of an agent-based simulation to inform a trial design and how this supports outcome interpretation of randomized controlled trials (RCTs). We developed agent-based Monte Carlo models to simulate existing landmark HIV RCTs, such as the Partners in Prevention HSV/HIV Transmission Study. We simulated a variation of this study using valacyclovir therapy as the intervention, and we used a male circumcision RCT based on the Rakai Male Circumcision Trial. Our results indicate that a small fraction (20%) of the simulated Partners in Prevention HSV/HIV Transmission Study realizations rejected the null hypothesis, which was no effect from the intervention. Our results also suggest that an RCT designed to evaluate the effectiveness of a more potent drug regimen for HSV-2 suppression (valacyclovir therapy) is more likely to identify the efficacy of the intervention. For the male circumcision RCT simulation, the greater biological effect of the male circumcision yielded a major fraction (81%) of RCT realizations' that rejects the null hypothesis, which was no effect from the intervention. Our study highlights how agent-based simulations synthesize individual variation in the epidemiological context of the RCT. This methodology will be particularly useful for designing RCTs aimed at evaluating combination prevention interventions in community-based RCTs, wherein an intervention׳s effectiveness is challenging to predict. PMID:24792492

  13. Multi-Agent Flight Simulation with Robust Situation Generation

    NASA Technical Reports Server (NTRS)

    Johnson, Eric N.; Hansman, R. John, Jr.

    1994-01-01

    A robust situation generation architecture has been developed that generates multi-agent situations for human subjects. An implementation of this architecture was developed to support flight simulation tests of air transport cockpit systems. This system maneuvers pseudo-aircraft relative to the human subject's aircraft, generating specific situations for the subject to respond to. These pseudo-aircraft maneuver within reasonable performance constraints, interact in a realistic manner, and make pre-recorded voice radio communications. Use of this system minimizes the need for human experimenters to control the pseudo-agents and provides consistent interactions between the subject and the pseudo-agents. The achieved robustness of this system to typical variations in the subject's flight path was explored. It was found to successfully generate specific situations within the performance limitations of the subject-aircraft, pseudo-aircraft, and the script used.

  14. Insect pathogens as biological control agents: back to the future

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In the past 15 years a number of successes and setbacks have taken place regarding development and use of microbial control agents. In this Forum paper we present current information on development, use and future directions of entomopathogenic virus, bacteria, fungi and nematodes as components of i...

  15. Agent-based model of angiogenesis simulates capillary sprout initiation in multicellular networks.

    PubMed

    Walpole, J; Chappell, J C; Cluceru, J G; Mac Gabhann, F; Bautch, V L; Peirce, S M

    2015-09-01

    Many biological processes are controlled by both deterministic and stochastic influences. However, efforts to model these systems often rely on either purely stochastic or purely rule-based methods. To better understand the balance between stochasticity and determinism in biological processes a computational approach that incorporates both influences may afford additional insight into underlying biological mechanisms that give rise to emergent system properties. We apply a combined approach to the simulation and study of angiogenesis, the growth of new blood vessels from existing networks. This complex multicellular process begins with selection of an initiating endothelial cell, or tip cell, which sprouts from the parent vessels in response to stimulation by exogenous cues. We have constructed an agent-based model of sprouting angiogenesis to evaluate endothelial cell sprout initiation frequency and location, and we have experimentally validated it using high-resolution time-lapse confocal microscopy. ABM simulations were then compared to a Monte Carlo model, revealing that purely stochastic simulations could not generate sprout locations as accurately as the rule-informed agent-based model. These findings support the use of rule-based approaches for modeling the complex mechanisms underlying sprouting angiogenesis over purely stochastic methods. PMID:26158406

  16. At the Biological Modeling and Simulation Frontier

    PubMed Central

    Ropella, Glen E. P.; Lam, Tai Ning; Tang, Jonathan; Kim, Sean H. J.; Engelberg, Jesse A.; Sheikh-Bahaei, Shahab

    2009-01-01

    We provide a rationale for and describe examples of synthetic modeling and simulation (M&S) of biological systems. We explain how synthetic methods are distinct from familiar inductive methods. Synthetic M&S is a means to better understand the mechanisms that generate normal and disease-related phenomena observed in research, and how compounds of interest interact with them to alter phenomena. An objective is to build better, working hypotheses of plausible mechanisms. A synthetic model is an extant hypothesis: execution produces an observable mechanism and phenomena. Mobile objects representing compounds carry information enabling components to distinguish between them and react accordingly when different compounds are studied simultaneously. We argue that the familiar inductive approaches contribute to the general inefficiencies being experienced by pharmaceutical R&D, and that use of synthetic approaches accelerates and improves R&D decision-making and thus the drug development process. A reason is that synthetic models encourage and facilitate abductive scientific reasoning, a primary means of knowledge creation and creative cognition. When synthetic models are executed, we observe different aspects of knowledge in action from different perspectives. These models can be tuned to reflect differences in experimental conditions and individuals, making translational research more concrete while moving us closer to personalized medicine. Electronic supplementary material The online version of this article (doi:10.1007/s11095-009-9958-3) contains supplementary material, which is available to authorized users. PMID:19756975

  17. Biological agents with potential for misuse: a historical perspective and defensive measures.

    PubMed

    Bhalla, Deepak K; Warheit, David B

    2004-08-15

    Biological and chemical agents capable of producing serious illness or mortality have been used in biowarfare from ancient times. Use of these agents has progressed from crude forms in early and middle ages, when snakes and infected cadavers were used as weapons in battles, to sophisticated preparations for use during and after the second World War. Cults and terrorist organizations have attempted the use of biological agents with an aim to immobilize populations or cause serious harm. The reasons for interest in these agents by individuals and organizations include relative ease of acquisition, potential for causing mass casualty or panic, modest financing requirement, availability of technology, and relative ease of delivery. The Centers for Disease Control and Prevention has classified Critical Biological Agents into three major categories. This classification was based on several criteria, which include severity of impact on human health, potential for delivery in a weapon, capacity to cause panic and special needs for development, and stockpiling of medication. Agents that could cause the greatest harm following deliberate use were placed in category A. Category B included agents capable of producing serious harm and significant mortality but of lower magnitude than category A agents. Category C included emerging pathogens that could be developed for mass dispersion in future and their potential as a major health threat. A brief description of the category A bioagents is included and the pathophysiology of two particularly prominent agents, namely anthrax and smallpox, is discussed in detail. The potential danger from biological agents and their ever increasing threat to human populations have created a need for developing technologies for their early detection, for developing treatment strategies, and for refinement of procedures to ensure survival of affected individuals so as to attain the ultimate goal of eliminating the threat from intentional use of

  18. Anti-tick biological control agents: assessment and future perspectives

    USGS Publications Warehouse

    Samish, M., H.; Ginsberg, H.S.; Glazer, I.

    2008-01-01

    Widespread and increasing resistance to most available acaracides threatens both global livestock industries and public health. This necessitates better understanding of ticks and the diseases they transmit in the development of new control strategies. Ticks: Biology, Disease and Control is written by an international collection of experts and covers in-depth information on aspects of the biology of the ticks themselves, various veterinary and medical tick-borne pathogens, and aspects of traditional and potential new control methods. A valuable resource for graduate students, academic researchers and professionals, the book covers the whole gamut of ticks and tick-borne diseases from microsatellites to satellite imagery and from exploiting tick saliva for therapeutic drugs to developing drugs to control tick populations. It encompasses the variety of interconnected fields impinging on the economically important and biologically fascinating phenomenon of ticks, the diseases they transmit and methods of their control.

  19. Development of a Persistent Chemical Agent Simulator System (PCASS)

    NASA Technical Reports Server (NTRS)

    Mcginness, W. G.

    1983-01-01

    The development of a persistent chemical agent simulation system (PCASS) is described. This PCASS is to be used for the military training of troops to simulate actual chemical warfare. The purpose of this system is to facilitate in the determination of chemical contamination and effectiveness of decontamination for training purposes. The fluorescent tracer employed has no daylight activation, but yet is easily removed with a decontaminate solution or water and surfactants. Also employed is a time delayed color developing system. When an individual is subjected to the PCASS and does not decontaminate adequately, red blotches or red coloration will develop as a function of time and temperature. The intent of this is to simulate the delayed chemical reaction of mustard contaminates.

  20. Task-level object grasping for simulated agents.

    PubMed

    Douville, B; Levison, L; Badler, N I

    1996-01-01

    Simulating a human figure performing a manual task requires that the agent interact with objects in the environment in a realistic manner. Graphic or programming interfaces to control human figure animation, however, do not allow the animator to instruct the system with concise "high-level" commands. Instructions coming from a high-level planner cannot be directly given to a synthetic agent because they do not specify such details as which end-effector to use or where on the object to grasp. Because current animation systems require joint angle displacement descriptions of motion--even for motions that incorporate upwards of 15 joints--an efficient connection between high-level specifications and low-level hand joint motion is required. In this paper we describe a system that directs task-level, general-purpose, object grasping for a simulated human agent. The Object-Specific Reasoner (OSR) is a reasoning module that uses knowledge of the object of the underspecified action to generate values for missing parameters. The Grasp Behavior manages simultaneous motions of the joints in the hand, wrist, and arm, and provides a programmer with a high-level description of the desired action. When composed hierarchically, the OSR and the Grasp behavior interpret task-level commands and direct specific motions to the animation system. These modules are implemented as part of the Jack system at the University of Pennsylvania. PMID:11539378

  1. Biological agents and biosimilars: Essential information for the internist.

    PubMed

    Pasina, Luca; Casadei, Gianluigi; Nobili, Alessandro

    2016-09-01

    Biologics embrace a wide range of substances synthesized by cells or living organisms by means of different biological processes, including recombinant DNA technology, controlled gene expression, or antibody technologies. A biosimilar establishes similarity to the reference medicinal product in terms of quality characteristics, biological activity, safety, and efficacy based on a comprehensive comparability exercise. Minimizing development costs and accelerating their market access create a convergence of interests between health services, worried about sustainability, and generic manufacturers. While the demonstration of bioequivalence is sufficient for small synthetic molecules, this approach is not scientifically applicable to a copy of biological drug constituted by large and complex molecules, which are similar but not identical to the originator and are also subject to different post-translational processes. Internists should be confident that the development process of biosimilars ensures a comparable risk-to-benefit balance with the originators. On the basis of available evidence and pharmacovigilance network, there are no grounds to believe that the use of a biosimilar carries more risks for the patient than the use of an originator. Since the first biosimilar was authorized in Europe in 2006, no clinical alerts have raised red flags about the established EMA biosimilar pathway. In this article, we discuss some of the most frequent concerns raised by clinicians about biosimilars and try to explains the scientific principles underlying the biosimilar concept established in the EU in order to license biosimilar drugs. PMID:27342030

  2. Integrating the Agents of Bioterrorism into the General Biology Curriculum: II. Mode of Action of the Biological Agents.

    ERIC Educational Resources Information Center

    Pommerville, Jeffrey C.

    2003-01-01

    Integrates bioterrorism into the science curriculum and explains actions against serious agents such as anthrax, plague, smallpox, botulinum toxin, and ricin toxin. Uses the learning cycle as the instructional tool which is student-centered and has three phases that include exploring, explaining, and extending. (Contains 24 references.) (YDS)

  3. Indirect ecological effects in invaded landscapes: Spillover and spillback from biological control agents to native analogues

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Biological control remains an effective option for managing large-scale weed problems in natural areas. The predation or parasitism of biological control agents by other species present in the introduced range (biotic resistance) is well studied and is often cited as the cause for a lack of establis...

  4. Plant-mediated interactions: considerations for agent selection in weed biological control programs

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Plant-mediated indirect interactions among herbivores (arthropods and pathogens) are common and extensively reported in the ecological literature. However, they are not well-documented with respect to weed biological control. Such interactions between biological control agents can have net positive...

  5. PERMANENCE OF BIOLOGICAL AND CHEMICAL WARFARE AGENTS IN MUNICIPAL SOLID WASTE LANDFILL LEACHATES

    EPA Science Inventory

    The objective of this work is to permit EPA/ORD's National Homeland Security Research Center (NHSRC) and Edgewood Chemical Biological Center to collaborate together to test the permanence of biological and chemical warfare agents in municipal solid waste landfills. Research into ...

  6. Water-driven micromotors for rapid photocatalytic degradation of biological and chemical warfare agents.

    PubMed

    Li, Jinxing; Singh, Virendra V; Sattayasamitsathit, Sirilak; Orozco, Jahir; Kaufmann, Kevin; Dong, Renfeng; Gao, Wei; Jurado-Sanchez, Beatriz; Fedorak, Yuri; Wang, Joseph

    2014-11-25

    Threats of chemical and biological warfare agents (CBWA) represent a serious global concern and require rapid and efficient neutralization methods. We present a highly effective micromotor strategy for photocatalytic degradation of CBWA based on light-activated TiO2/Au/Mg microspheres that propel autonomously in natural water and obviate the need for external fuel, decontaminating reagent, or mechanical agitation. The activated TiO2/Au/Mg micromotors generate highly reactive oxygen species responsible for the efficient destruction of the cell membranes of the anthrax simulant Bacillus globigii spore, as well as rapid and complete in situ mineralization of the highly persistent organophosphate nerve agents into nonharmful products. The water-driven propulsion of the TiO2/Au/Mg micromotors facilitates efficient fluid transport and dispersion of the photogenerated reactive oxidative species and their interaction with the CBWA. Coupling of the photocatalytic surface of the micromotors and their autonomous water-driven propulsion thus leads to a reagent-free operation which holds a considerable promise for diverse "green" defense and environmental applications. PMID:25289459

  7. Flexible carbon nanotube sensors for nerve agent simulants

    NASA Astrophysics Data System (ADS)

    Cattanach, Kyle; Kulkarni, Rashmi D.; Kozlov, Mikhail; Manohar, Sanjeev K.

    2006-08-01

    Chemiresistor-based vapour sensors made from network films of single-walled carbon nanotube (SWNT) bundles on flexible plastic substrates (polyethylene terephthalate, PET) can be used to detect chemical warfare agent simulants for the nerve agents Sarin (diisopropyl methylphosphonate, DIMP) and Soman (dimethyl methylphosphonate, DMMP). Large, reproducible resistance changes (75-150%), are observed upon exposure to DIMP or DMMP vapours, and concentrations as low as 25 ppm can be detected. Robust sensor response to simulant vapours is observed even in the presence of large equilibrium concentrations of interferent vapours commonly found in battle-space environments, such as hexane, xylene and water (10 000 ppm each), suggesting that both DIMP and DMMP vapours are capable of selectively displacing other vapours from the walls of the SWNTs. Response to these interferent vapours can be effectively filtered out by using a 2 µm thick barrier film of the chemoselective polymer polyisobutylene (PIB) on the SWNT surface. These network films are composed of a 1-2 µm thick non-woven mesh of SWNT bundles (15-30 nm diameter), whose sensor response is qualitatively and quantitatively different from previous studies on individual SWNTs, or a network of individual SWNTs, suggesting that vapour sorption at interbundle sites could be playing an important role. This study also shows that the line patterning method used in device fabrication to obtain any desired pattern of films of SWNTs on flexible substrates can be used to rapidly screen simulants at high concentrations before developing more complicated sensor systems.

  8. Biologically hazardous agents at work and efforts to protect workers' health: a review of recent reports.

    PubMed

    Rim, Kyung-Taek; Lim, Cheol-Hong

    2014-06-01

    Because information on biological agents in the workplace is lacking, biological hazard analyses at the workplace to securely recognize the harmful factors with biological basis are desperately needed. This review concentrates on literatures published after 2010 that attempted to detect biological hazards to humans, especially workers, and the efforts to protect them against these factors. It is important to improve the current understanding of the health hazards caused by biological factors at the workplace. In addition, this review briefly describes these factors and provides some examples of their adverse health effects. It also reviews risk assessments, protection with personal protective equipment, prevention with training of workers, regulations, as well as vaccinations. PMID:25180133

  9. Biologically Hazardous Agents at Work and Efforts to Protect Workers' Health: A Review of Recent Reports

    PubMed Central

    Rim, Kyung-Taek; Lim, Cheol-Hong

    2014-01-01

    Because information on biological agents in the workplace is lacking, biological hazard analyses at the workplace to securely recognize the harmful factors with biological basis are desperately needed. This review concentrates on literatures published after 2010 that attempted to detect biological hazards to humans, especially workers, and the efforts to protect them against these factors. It is important to improve the current understanding of the health hazards caused by biological factors at the workplace. In addition, this review briefly describes these factors and provides some examples of their adverse health effects. It also reviews risk assessments, protection with personal protective equipment, prevention with training of workers, regulations, as well as vaccinations. PMID:25180133

  10. Episodic positive selection at mitochondrial genome in an introduced biological control agent.

    PubMed

    Li, Hao-Sen; Liang, Xin-Yu; Zou, Shang-Jun; Liu, Yang; De Clercq, Patrick; Ślipiński, Adam; Pang, Hong

    2016-05-01

    Artificial introduction in classical biological control provides a unique opportunity to understand mitochondrial evolution driving adaptation to novel environments. We studied mitochondrial genomes of a world-wide introduced agent, Cryptolaemus montrouzieri. We detected positive selection in complex I genes (ND5 and ND4) against a background of widespread negative selection. We further detected significant signals in neutrality tests within 11 populations at ND5 gene, indicating a recent selective sweep/positive selection. Our results imply that these candidate mutations may contribute local adaptation of exotic biological control agents and these provide new insights into the improvement of classical biological control programs. PMID:26994640

  11. Use of hyperspectral remote sensing for detection and monitoring of chemical and biological agents: a survey

    NASA Astrophysics Data System (ADS)

    Gomez, Richard B.; Dasgupta, Swarvanu

    2004-12-01

    This paper surveys the potential use of hyperspectral imaging technology for standoff detection of chemical and biological agents in terrorism defense applications. In particular it focuses on the uses of hyperspectral imaging technology to detect and monitor chemical and biological attacks. In so doing it examines current technologies, their advantages and disadvantages, and investigates the possible role of hyperspectral imaging for homeland security applications. The study also addresses and provides applicable solutions for several of the potential challenges that currently create barriers to the full use of hyperspectral technology in the standoff detection of likely available chemical and biological agents.

  12. A convenient first aid kit for chemical and biological agents and for radiation exposure.

    PubMed

    Vijayaraghavan, R; Bhaskar, A S B; Gautam, Anshoo; Gopalan, N; Singh, A K; Singh, Beer; Flora, S J S

    2012-05-01

    The chemical and biological warfare agents are extremely toxic in nature. They act rapidly even in very small quantities and death may occur in minutes. Hence, physical and medical protection must be provided immediately to save life or avoid serious injury. A first aid kit has thus been developed for providing immediate relief from chemical and biological warfare agents (FAKCBW) with the objective of easy detection, personal decontamination, antidote for chemical warfare agents (like nerve agents, sulphur mustard, phosgene, cyanide, radiation exposure and bacterial agents), along with basic medication aid for pain, fever and inflammation. The kit box also includes a user friendly handbook with a simple standard operating procedure. In addition, the kit is rugged to withstand normal jerks, vibration and is water-proof. PMID:23029921

  13. Synthesis and biological evaluation of hydrazone derivatives as antifungal agents.

    PubMed

    Casanova, Bruna B; Muniz, Mauro N; de Oliveira, Thayse; de Oliveira, Luís Flavio; Machado, Michel M; Fuentefria, Alexandre M; Gosmann, Grace; Gnoatto, Simone C B

    2015-01-01

    Emerging yeasts are among the most prevalent causes of systemic infections with high mortality rates and there is an urgent need to develop specific, effective and non-toxic antifungal agents to respond to this issue. In this study 35 aldehydes, hydrazones and hydrazines were obtained and their antifungal activity was evaluated against Candida species (C. parapsilosis, C. tropicalis, C. krusei, C. albicans, C. glabrata and C. lusitaneae) and Trichosporon asahii, in an in vitro screening. The minimum inhibitory concentrations (MICs) of the active compounds in the screening was determined against 10 clinical isolates of C. parapsilosis and 10 of T. asahii. The compounds 4-pyridin-2-ylbenzaldehyde] (13a) and tert-butyl-(2Z)-2-(3,4,5-trihydroxybenzylidine)hydrazine carboxylate (7b) showed the most promising MIC values in the range of 16-32 μg/mL and 8-16 μg/mL, respectively. The compounds' action on the stability of the cell membrane and cell wall was evaluated, which suggested the action of the compounds on the fungal cell membrane. Cell viability of leukocytes and an alkaline comet assay were performed to evaluate the cytotoxicity. Compound 13a was not cytotoxic at the active concentrations. These results support the discovery of promising candidates for the development of new antifungal agents. PMID:26007181

  14. A medicoeconomic review of early intervention with biologic agents in the treatment of inflammatory bowel diseases.

    PubMed

    Odes, Shmuel; Greenberg, Dan

    2014-01-01

    The treatment of inflammatory bowel disease with standard therapy fails to control the disease in many patients. Biologic therapy has an increasing role in altering the natural history of Crohn's disease and ulcerative colitis, and is improving patient prognosis. However, indications for treatment and issues with drug costs and value for money remain unclear. Also, when to perform early intervention with biologic agents is at present unclear. We performed an extensive literature search and review to address these issues. The biologics provide better care for many patients. The choice of biologic agent, the indications for its use, the switch between agents, and the considerations of cost are outlined, with a view to guiding the treating physician in managing these cases. Outstanding issues and anticipated future developments are defined. PMID:25336980

  15. Supercritical fluid extraction of chemical warfare agent simulants from soil.

    PubMed

    Griest, W H; Ramsey, R S; Ho, C H; Caldwell, W M

    1992-05-29

    Chemical warfare agent simulants are efficiently recovered from 2-ppm spikes in 1 g of Rocky Mountain Arsenal Standard Soil using methanol-carbon dioxide (5:95) at 300 atm for 2 min at 60 degrees C. Recoveries (n = 3) were 79 +/- 23% for dimethylmethylphosphonate, 93 +/- 14% for 2-chloroethylethyl sulfide, 92 +/- 13% for diisopropylfluorophosphate and 95 +/- 17% for diisopropylmethylphosphonate. Recoveries are higher than, but less precise than those achieved from a 5-min ultrasonic micro-scale extraction using methanol. Much less laboratory waste is generated than the current standard organic solvent extraction method (33 g of soil shaken with 100 ml of chloroform). PMID:1400849

  16. BSim: an agent-based tool for modeling bacterial populations in systems and synthetic biology.

    PubMed

    Gorochowski, Thomas E; Matyjaszkiewicz, Antoni; Todd, Thomas; Oak, Neeraj; Kowalska, Kira; Reid, Stephen; Tsaneva-Atanasova, Krasimira T; Savery, Nigel J; Grierson, Claire S; di Bernardo, Mario

    2012-01-01

    Large-scale collective behaviors such as synchronization and coordination spontaneously arise in many bacterial populations. With systems biology attempting to understand these phenomena, and synthetic biology opening up the possibility of engineering them for our own benefit, there is growing interest in how bacterial populations are best modeled. Here we introduce BSim, a highly flexible agent-based computational tool for analyzing the relationships between single-cell dynamics and population level features. BSim includes reference implementations of many bacterial traits to enable the quick development of new models partially built from existing ones. Unlike existing modeling tools, BSim fully considers spatial aspects of a model allowing for the description of intricate micro-scale structures, enabling the modeling of bacterial behavior in more realistic three-dimensional, complex environments. The new opportunities that BSim opens are illustrated through several diverse examples covering: spatial multicellular computing, modeling complex environments, population dynamics of the lac operon, and the synchronization of genetic oscillators. BSim is open source software that is freely available from http://bsim-bccs.sf.net and distributed under the Open Source Initiative (OSI) recognized MIT license. Developer documentation and a wide range of example simulations are also available from the website. BSim requires Java version 1.6 or higher. PMID:22936991

  17. Naphthoflavones as Antiproliferative Agents: Design, Synthesis and Biological Evaluation.

    PubMed

    Kumar, Dinesh; Singh, Onkar; Nepali, Kunal; Bedi, Pms; Qayum, Arem; Singh, Shashank; Jain, Subheet K

    2016-01-01

    The present study involves the design and synthesis of naphthoflavones as antiproliferative agents. The strategy presents naphthoflavones as hybrids of naphthyl based chalcones and flavones. A panel of human cancer cell lines were employed for the cytotoxicity studies. DK-13 exhibited significant cytoxicity against MiaPaCa-2 cell lines with IC50 value of 1.93 μM and 5.63 μM against MCF-7 cell lines. The compound DK-13 was found to induce apoptosis evidenced through phase contrast microscopy, DAPI staining, and mitochondrial membrane potential loss. The cell phase distribution studies indicated an increase from 11.26 % (control sample) to 55.19 % (sample treated with 20 μM compound DK-13) in the apoptotic population. PMID:26845133

  18. Mass spectrometry in identification of ecotoxicants including chemical and biological warfare agents.

    PubMed

    Lebedev, Albert T

    2005-09-01

    Mass spectrometry is a unique tool to detect and identify trace levels of organic and bioorganic compounds as well as microorganisms in the environment. The range of potential chemical warfare (CW) and biological warfare (BW) agents is very broad. An important advantage of mass spectrometry over other techniques involves potential for full spectrum detection of chemical and biological agents including mid-spectrum materials (i.e. bioactive peptides, toxins, etc.) for which biological approaches are inadequate. Being very fast (seconds and minutes), extremely sensitive (zeptomoles 10(-21)), and informative (detailed qualitative and quantitative composition of mixtures containing hundreds of chemicals), mass spectrometry is a principal analytical tool at the sites of destruction of CW. Due to its unique features, mass spectrometry is applied not only for the detection of CW agents, but for the analysis of products of metabolism and degradation of these agents in organisms or environment as well. The present paper deals with some examples of successful application of mass spectrometry for the analyses of ecotoxicants, chemical warfare agents, explosives, and microorganisms including biology warfare agents. PMID:16024060

  19. Mass spectrometry in identification of ecotoxicants including chemical and biological warfare agents

    SciTech Connect

    Lebedev, Albert T. . E-mail: lebedev@org.chem.msu.ru

    2005-09-01

    Mass spectrometry is a unique tool to detect and identify trace levels of organic and bioorganic compounds as well as microorganisms in the environment. The range of potential chemical warfare (CW) and biological warfare (BW) agents is very broad. An important advantage of mass spectrometry over other techniques involves potential for full spectrum detection of chemical and biological agents including mid-spectrum materials (i.e. bioactive peptides, toxins, etc.) for which biological approaches are inadequate. Being very fast (seconds and minutes), extremely sensitive (zeptomoles 10{sup -21}), and informative (detailed qualitative and quantitative composition of mixtures containing hundreds of chemicals), mass spectrometry is a principal analytical tool at the sites of destruction of CW. Due to its unique features, mass spectrometry is applied not only for the detection of CW agents, but for the analysis of products of metabolism and degradation of these agents in organisms or environment as well. The present paper deals with some examples of successful application of mass spectrometry for the analyses of ecotoxicants, chemical warfare agents, explosives, and microorganisms including biology warfare agents.

  20. Airborne exposure limits for chemical and biological warfare agents: is everything set and clear?

    PubMed

    Sabelnikov, Alex; Zhukov, Vladimir; Kempf, C Ruth

    2006-08-01

    Emergency response strategies (guidelines) for biological, chemical, nuclear, or radiological terrorist events should be based on scientifically established exposure limits for all the agents or materials involved. In the case of a radiological terrorist event, emergency response guidelines (ERG) have been worked out. In the case of a terrorist event with the use of chemical warfare (CW) agents the situation is not that clear, though the new guidelines and clean-up values are being generated based on re-evaluation of toxicological and risk data. For biological warfare (BW) agents, such guidelines do not yet exist. In this paper the current status of airborne exposure limits (AELs) for chemical and biological warfare (CBW) agents are reviewed. Particular emphasis is put on BW agents that lack such data. An efficient, temporary solution to bridge the gap in experimental infectious data and to set provisional AELs for BW agents is suggested. It is based on mathematically generated risks of infection for BW agents grouped by their alleged ID50 values in three categories: with low, intermediate and high ID50 values. PMID:16854669

  1. Comparing stochastic differential equations and agent-based modelling and simulation for early-stage cancer.

    PubMed

    Figueredo, Grazziela P; Siebers, Peer-Olaf; Owen, Markus R; Reps, Jenna; Aickelin, Uwe

    2014-01-01

    There is great potential to be explored regarding the use of agent-based modelling and simulation as an alternative paradigm to investigate early-stage cancer interactions with the immune system. It does not suffer from some limitations of ordinary differential equation models, such as the lack of stochasticity, representation of individual behaviours rather than aggregates and individual memory. In this paper we investigate the potential contribution of agent-based modelling and simulation when contrasted with stochastic versions of ODE models using early-stage cancer examples. We seek answers to the following questions: (1) Does this new stochastic formulation produce similar results to the agent-based version? (2) Can these methods be used interchangeably? (3) Do agent-based models outcomes reveal any benefit when compared to the Gillespie results? To answer these research questions we investigate three well-established mathematical models describing interactions between tumour cells and immune elements. These case studies were re-conceptualised under an agent-based perspective and also converted to the Gillespie algorithm formulation. Our interest in this work, therefore, is to establish a methodological discussion regarding the usability of different simulation approaches, rather than provide further biological insights into the investigated case studies. Our results show that it is possible to obtain equivalent models that implement the same mechanisms; however, the incapacity of the Gillespie algorithm to retain individual memory of past events affects the similarity of some results. Furthermore, the emergent behaviour of ABMS produces extra patters of behaviour in the system, which was not obtained by the Gillespie algorithm. PMID:24752131

  2. Probiotic Bacteria as Biological Control Agents in Aquaculture

    PubMed Central

    Verschuere, Laurent; Rombaut, Geert; Sorgeloos, Patrick; Verstraete, Willy

    2000-01-01

    There is an urgent need in aquaculture to develop microbial control strategies, since disease outbreaks are recognized as important constraints to aquaculture production and trade and since the development of antibiotic resistance has become a matter of growing concern. One of the alternatives to antimicrobials in disease control could be the use of probiotic bacteria as microbial control agents. This review describes the state of the art of probiotic research in the culture of fish, crustaceans, mollusks, and live food, with an evaluation of the results obtained so far. A new definition of probiotics, also applicable to aquatic environments, is proposed, and a detailed description is given of their possible modes of action, i.e., production of compounds that are inhibitory toward pathogens, competition with harmful microorganisms for nutrients and energy, competition with deleterious species for adhesion sites, enhancement of the immune response of the animal, improvement of water quality, and interaction with phytoplankton. A rationale is proposed for the multistep and multidisciplinary process required for the development of effective and safe probiotics for commercial application in aquaculture. Finally, directions for further research are discussed. PMID:11104813

  3. Synthesis and biological evaluation of aryloxyacetamide derivatives as neuroprotective agents.

    PubMed

    Zhong, Yan; Xu, Yi; Zhang, Ai-Xia; Li, Xiao-Feng; Xu, Zhao-Ying; Li, Ping; Wu, Bin

    2016-05-15

    A series of new aryloxyacetamide derivatives 10a-s and 14a-m are designed and synthesized. Their protective activities against the glutamate-induced cell death were investigated in differentiated rat pheochromocytoma cells (PC12 cells). Most compounds exhibited neuroprotective effects, especially for 10m, 10r, 14b and 14c, which showed potential protection of PC12 cells at three doses (0.1, 1.0, 10μM). MTT assay, Hoechst 33342/PI double staining, and high content screening (HCS) revealed that pretreatment of the cells with 10m, 10r, 14b and 14c has significantly decreased the extent of cell apoptosis in a dose-dependent manner. The results of western blot analysis demonstrated these compounds suppressed apoptosis of glutamate-induced PC12 cells via caspase-3 pathway. These compounds can be lead compounds for further discovery of neuroprotective agents for treating cerebral ischemic stroke. Basic structure-activity relationships are also presented. PMID:27038495

  4. Probiotic bacteria as biological control agents in aquaculture.

    PubMed

    Verschuere, L; Rombaut, G; Sorgeloos, P; Verstraete, W

    2000-12-01

    There is an urgent need in aquaculture to develop microbial control strategies, since disease outbreaks are recognized as important constraints to aquaculture production and trade and since the development of antibiotic resistance has become a matter of growing concern. One of the alternatives to antimicrobials in disease control could be the use of probiotic bacteria as microbial control agents. This review describes the state of the art of probiotic research in the culture of fish, crustaceans, mollusks, and live food, with an evaluation of the results obtained so far. A new definition of probiotics, also applicable to aquatic environments, is proposed, and a detailed description is given of their possible modes of action, i.e., production of compounds that are inhibitory toward pathogens, competition with harmful microorganisms for nutrients and energy, competition with deleterious species for adhesion sites, enhancement of the immune response of the animal, improvement of water quality, and interaction with phytoplankton. A rationale is proposed for the multistep and multidisciplinary process required for the development of effective and safe probiotics for commercial application in aquaculture. Finally, directions for further research are discussed. PMID:11104813

  5. A unified biological modeling and simulation system for analyzing biological reaction networks

    NASA Astrophysics Data System (ADS)

    Yu, Seok Jong; Tung, Thai Quang; Park, Junho; Lim, Jongtae; Yoo, Jaesoo

    2013-12-01

    In order to understand the biological response in a cell, a researcher has to create a biological network and design an experiment to prove it. Although biological knowledge has been accumulated, we still don't have enough biological models to explain complex biological phenomena. If a new biological network is to be created, integrated modeling software supporting various biological models is required. In this research, we design and implement a unified biological modeling and simulation system, called ezBioNet, for analyzing biological reaction networks. ezBioNet designs kinetic and Boolean network models and simulates the biological networks using a server-side simulation system with Object Oriented Parallel Accelerator Library framework. The main advantage of ezBioNet is that a user can create a biological network by using unified modeling canvas of kinetic and Boolean models and perform massive simulations, including Ordinary Differential Equation analyses, sensitivity analyses, parameter estimates and Boolean network analysis. ezBioNet integrates useful biological databases, including the BioModels database, by connecting European Bioinformatics Institute servers through Web services Application Programming Interfaces. In addition, we employ Eclipse Rich Client Platform, which is a powerful modularity framework to allow various functional expansions. ezBioNet is intended to be an easy-to-use modeling tool and a simulation system for understanding the control mechanism by monitoring the change of each component in a biological network. The simulation result can be managed and visualized on ezBioNet, which is available free of charge at http://ezbionet.sourceforge.net or http://ezbionet.cbnu.ac.kr.

  6. Flexible carbon nanotube sensors for nerve agent simulants.

    PubMed

    Cattanach, Kyle; Kulkarni, Rashmi D; Kozlov, Mikhail; Manohar, Sanjeev K

    2006-08-28

    Chemiresistor-based vapour sensors made from network films of single-walled carbon nanotube (SWNT) bundles on flexible plastic substrates (polyethylene terephthalate, PET) can be used to detect chemical warfare agent simulants for the nerve agents Sarin (diisopropyl methylphosphonate, DIMP) and Soman (dimethyl methylphosphonate, DMMP). Large, reproducible resistance changes (75-150%), are observed upon exposure to DIMP or DMMP vapours, and concentrations as low as 25 ppm can be detected. Robust sensor response to simulant vapours is observed even in the presence of large equilibrium concentrations of interferent vapours commonly found in battle-space environments, such as hexane, xylene and water (10 000 ppm each), suggesting that both DIMP and DMMP vapours are capable of selectively displacing other vapours from the walls of the SWNTs. Response to these interferent vapours can be effectively filtered out by using a 2 µm thick barrier film of the chemoselective polymer polyisobutylene (PIB) on the SWNT surface. These network films are composed of a 1-2 µm thick non-woven mesh of SWNT bundles (15-30 nm diameter), whose sensor response is qualitatively and quantitatively different from previous studies on individual SWNTs, or a network of individual SWNTs, suggesting that vapour sorption at interbundle sites could be playing an important role. This study also shows that the line patterning method used in device fabrication to obtain any desired pattern of films of SWNTs on flexible substrates can be used to rapidly screen simulants at high concentrations before developing more complicated sensor systems. PMID:21727548

  7. Polysaccharide Immunomodulators as Therapeutic Agents: Structural Aspects and Biologic Function

    PubMed Central

    Tzianabos, Arthur O.

    2000-01-01

    Polysaccharide immunomodulators were first discovered over 40 years ago. Although very few have been rigorously studied, recent reports have revealed the mechanism of action and structure-function attributes of some of these molecules. Certain polysaccharide immunomodulators have been identified that have profound effects in the regulation of immune responses during the progression of infectious diseases, and studies have begun to define structural aspects of these molecules that govern their function and interaction with cells of the host immune system. These polymers can influence innate and cell-mediated immunity through interactions with T cells, monocytes, macrophages, and polymorphonuclear lymphocytes. The ability to modulate the immune response in an appropriate way can enhance the host's immune response to certain infections. In addition, this strategy can be utilized to augment current treatment regimens such as antimicrobial therapy that are becoming less efficacious with the advent of antibiotic resistance. This review focuses on recent studies that illustrate the structural and biologic activities of specific polysaccharide immunomodulators and outlines their potential for clinical use. PMID:11023954

  8. 42 CFR 71.54 - Import regulations for infectious biological agents, infectious substances, and vectors.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... threat to public health and safety as listed in 42 CFR 73.3 and 73.4. Vector. Any animals (vertebrate or... issued under this part is not required for an item if: (1) It is a biological agent listed in 42 CFR Part 73 as a select agent and its importation has been authorized in accordance with 42 CFR 73.16 or 9...

  9. 42 CFR 71.54 - Import regulations for infectious biological agents, infectious substances, and vectors.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... threat to public health and safety as listed in 42 CFR 73.3 and 73.4. Vector. Any animals (vertebrate or... issued under this part is not required for an item if: (1) It is a biological agent listed in 42 CFR Part 73 as a select agent and its importation has been authorized in accordance with 42 CFR 73.16 or 9...

  10. Current, new and future biological agents on the horizon for the treatment of inflammatory bowel diseases

    PubMed Central

    Peyrin-Biroulet, Laurent

    2015-01-01

    Biological agents for inflammatory bowel diseases (IBD) targeting tumor necrosis factor (TNF) have changed the way to treat IBD refractory to standard medications and allowed us to reach new therapeutic goals such as mucosal healing and deep remission. A better understanding of the components of the pathological processes that are a hallmark of IBD has led to the development of a new family of biological agents in Crohn’s disease and ulcerative colitis. Biosimilars, which are copy versions of currently licensed biological agents, will be soon available. The biosimilar of infliximab is as effective and as safe as its originator in rheumatologic conditions, while a new anti-TNF agent, namely golimumab, has been recently approved for refractory ulcerative colitis. Beyond TNF blockers, anti-adhesion molecules appear to be a potent drug class for IBD. Vedolizumab was recently approved for both Crohn’s disease and ulcerative colitis. Numerous other compounds are in the pipeline. Ustekinumab looks very promising for Crohn’s disease. Smad7 antisense oligonucleotide might enrich our armamentarium if preliminary data are confirmed in upcoming clinical trials. Herein, we review the efficacy and safety of new and emerging biological agents that are currently investigated in IBD clinical trials. PMID:25729432

  11. Agent-based modeling to simulate the dengue spread

    NASA Astrophysics Data System (ADS)

    Deng, Chengbin; Tao, Haiyan; Ye, Zhiwei

    2008-10-01

    In this paper, we introduce a novel method ABM in simulating the unique process for the dengue spread. Dengue is an acute infectious disease with a long history of over 200 years. Unlike the diseases that can be transmitted directly from person to person, dengue spreads through a must vector of mosquitoes. There is still no any special effective medicine and vaccine for dengue up till now. The best way to prevent dengue spread is to take precautions beforehand. Thus, it is crucial to detect and study the dynamic process of dengue spread that closely relates to human-environment interactions where Agent-Based Modeling (ABM) effectively works. The model attempts to simulate the dengue spread in a more realistic way in the bottom-up way, and to overcome the limitation of ABM, namely overlooking the influence of geographic and environmental factors. Considering the influence of environment, Aedes aegypti ecology and other epidemiological characteristics of dengue spread, ABM can be regarded as a useful way to simulate the whole process so as to disclose the essence of the evolution of dengue spread.

  12. Method and apparatus for the gas phase decontamination of chemical and biological agents

    DOEpatents

    O'Neill, Hugh J.; Brubaker, Kenneth L.

    2003-10-07

    An apparatus and method for decontaminating chemical and biological agents using the reactive properties of both the single atomic oxygen and the hydroxyl radical for the decontamination of chemical and biological agents. The apparatus is self contained and portable and allows for the application of gas reactants directly at the required decontamination point. The system provides for the use of ultraviolet light of a specific spectral range to photolytically break down ozone into molecular oxygen and hydroxyl radicals where some of the molecular oxygen is in the first excited state. The excited molecular oxygen will combine with water vapor to produce two hydroxyl radicals.

  13. Detection of biological warfare agents using the polymerase chain reaction. Final report, June-August 1991

    SciTech Connect

    Mann, B.J.

    1992-09-01

    The detection of biological warfare agents is an important mission for the U.S. Army. This report explores the feasibility of using the polymerase chain reaction as a means of rapid detection of biological warfare agents. Two levels of detection are proposed. The first level is group specific detection, using primers derived from 16S rDNA sequences, to detect various groups of pathogenic bacteria. The second level is species-specific detection using primers derived from DNA sequences, unique to each pathogenic organism targeted for detection. Specific examples of Vibrio cholerae, Francisella tularensis, Yersinia pestis, Staphylococcus aureus, and Bacillus anthracis are described.

  14. Biology of the galling wasp, Tetramesa romana, a biological control agent of giant reed

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The biology of the gall-forming wasp, Tetramesa romana Walker (Hymenoptera: Eurytomidae), from southern France and Spain was studied for biological control of giant reed (Arundo donax L.), an exotic and invasive riparian weed in the U.S. Females developed eggs parthenogenetically and deposited them...

  15. Using Agent Based Modeling (ABM) to Develop Cultural Interaction Simulations

    NASA Technical Reports Server (NTRS)

    Drucker, Nick; Jones, Phillip N.

    2012-01-01

    Today, most cultural training is based on or built around "cultural engagements" or discrete interactions between the individual learner and one or more cultural "others". Often, success in the engagement is the end or the objective. In reality, these interactions usually involve secondary and tertiary effects with potentially wide ranging consequences. The concern is that learning culture within a strict engagement context might lead to "checklist" cultural thinking that will not empower learners to understand the full consequence of their actions. We propose the use of agent based modeling (ABM) to collect, store, and, simulating the effects of social networks, promulgate engagement effects over time, distance, and consequence. The ABM development allows for rapid modification to re-create any number of population types, extending the applicability of the model to any requirement for social modeling.

  16. Agent-based modeling: Methods and techniques for simulating human systems

    PubMed Central

    Bonabeau, Eric

    2002-01-01

    Agent-based modeling is a powerful simulation modeling technique that has seen a number of applications in the last few years, including applications to real-world business problems. After the basic principles of agent-based simulation are briefly introduced, its four areas of application are discussed by using real-world applications: flow simulation, organizational simulation, market simulation, and diffusion simulation. For each category, one or several business applications are described and analyzed. PMID:12011407

  17. Pedestrian simulation and distribution in urban space based on visibility analysis and agent simulation

    NASA Astrophysics Data System (ADS)

    Ying, Shen; Li, Lin; Gao, Yurong

    2009-10-01

    Spatial visibility analysis is the important direction of pedestrian behaviors because our visual conception in space is the straight method to get environment information and navigate your actions. Based on the agent modeling and up-tobottom method, the paper develop the framework about the analysis of the pedestrian flow depended on visibility. We use viewshed in visibility analysis and impose the parameters on agent simulation to direct their motion in urban space. We analyze the pedestrian behaviors in micro-scale and macro-scale of urban open space. The individual agent use visual affordance to determine his direction of motion in micro-scale urban street on district. And we compare the distribution of pedestrian flow with configuration in macro-scale urban environment, and mine the relationship between the pedestrian flow and distribution of urban facilities and urban function. The paper first computes the visibility situations at the vantage point in urban open space, such as street network, quantify the visibility parameters. The multiple agents use visibility parameters to decide their direction of motion, and finally pedestrian flow reach to a stable state in urban environment through the simulation of multiple agent system. The paper compare the morphology of visibility parameters and pedestrian distribution with urban function and facilities layout to confirm the consistence between them, which can be used to make decision support in urban design.

  18. Detection of biological warfare agents with fiber-optic microsphere-based DNA arrays

    NASA Astrophysics Data System (ADS)

    Song, Linan; Walt, David R.

    2005-11-01

    Biological warfare agents (BWAs) pose significant threats to both military forces and civilian populations. The increased concern about bioterrorism has promoted the development of rapid, sensitive, and reliable detection systems to provide an early warning for detecting the release of BWAs. We have developed a high-density DNA array to detect BWAs in real environmental samples with fast response times and high sensitivity. An optical fiber bundle containing approximately 50,000 individual 3.1 μm diameter fibers was chemically etched to yield an array of microwells and used as the substrate for the array. 50-mer single-stranded DNA probes designed to be specific for target BWAs were covalently attached to 3.1-μm microspheres, and the microspheres were distributed into the microwells to form a randomized high-density DNA array. We demonstrated the applicability of this DNA array for the identification of Bacillus thuringiensis kurstaki, a BWA simulant, in real samples. PCR was used to amplify the sequences, introduce fluorescent labels into the target molecules, and provide a second level of specificity. After hybridization of test solutions to the array, analysis was performed by evaluating the specific responses of individual probes on the array.

  19. Patient-centered appointment scheduling using agent-based simulation.

    PubMed

    Turkcan, Ayten; Toscos, Tammy; Doebbeling, Brad N

    2014-01-01

    Enhanced access and continuity are key components of patient-centered care. Existing studies show that several interventions such as providing same day appointments, walk-in services, after-hours care, and group appointments, have been used to redesign the healthcare systems for improved access to primary care. However, an intervention focusing on a single component of care delivery (i.e. improving access to acute care) might have a negative impact other components of the system (i.e. reduced continuity of care for chronic patients). Therefore, primary care clinics should consider implementing multiple interventions tailored for their patient population needs. We collected rapid ethnography and observations to better understand clinic workflow and key constraints. We then developed an agent-based simulation model that includes all access modalities (appointments, walk-ins, and after-hours access), incorporate resources and key constraints and determine the best appointment scheduling method that improves access and continuity of care. This paper demonstrates the value of simulation models to test a variety of alternative strategies to improve access to care through scheduling. PMID:25954423

  20. Enhancement of biological control agents for use against forest insect pests and diseases through biotechnology

    NASA Technical Reports Server (NTRS)

    Slavicek, James M.

    1991-01-01

    Research and development efforts in our research group are focused on the generation of more efficacious biological control agents through the techniques of biotechnology for use against forest insect pests and diseases. Effective biological controls for the gypsy moth and for tree fungal wilt pathogens are under development. The successful use of Gypchek, a formulation of the Lymantria dispar nuclear polyhedrosis virus (LdNPV), in gypsy moth control programs has generated considerable interest in that agent. As a consequence of its specificity, LdPNV has negligible adverse ecological impacts compared to most gypsy moth control agents. However, LdNPV is not competitive with other control agents in terms of cost and efficacy. We are investigating several parameters of LdNPV replication and polyhedra production in order to enhance viral potency and efficacy thus mitigating the current disadvantages of LdNPV for gypsy moth control, and have identified LdNPV variants that will facilitate these efforts. Tree endophytic bacteria that synthesize antifungal compounds were identified and an antibiotic compound from one of these bacteria was characterized. The feasibility of developing tree endophytes as biological control agents for tree vascular fungal pathogens is being investigated.

  1. From Here to Autonomicity: Self-Managing Agents and the Biological Metaphors that Inspire Them

    NASA Technical Reports Server (NTRS)

    Sterritt, Roy; Hinchey, Mike

    2005-01-01

    We seek inspiration for self-managing systems from (obviously, pre-existing) biological mechanisms. Autonomic Computing (AC), a self-managing systems initiative based on the biological metaphor of the autonomic nervous system, is increasingly gaining momentum as the way forward for integrating and designing reliable systems, while agent technologies have been identified as a key enabler for engineering autonomicity in systems. This paper looks at other biological metaphors such as reflex and healing, heart- beat monitors, pulse monitors and apoptosis for assisting in the realization of autonomicity.

  2. 75 FR 69396 - Availability of an Environmental Assessment for a Biological Control Agent for Arundo donax

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-11-12

    ...; ] DEPARTMENT OF AGRICULTURE Animal and Plant Health Inspection Service Availability of an Environmental Assessment for a Biological Control Agent for Arundo donax AGENCY: Animal and Plant Health Inspection Service... the Animal and Plant Health Inspection Service has prepared an environmental assessment relative...

  3. Risk assessment and stakeholder perceptions in novel biological control agent release: YST as a case study

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The objectives of risk assessment are to learn about whether a candidate agent would be safe to use in the environment where release is planned, and to present such information in a clear, understandable format to regulators, stakeholders, and the public. Plant pathogens evaluated for biological co...

  4. Acquired natural enemies of the weed biological control agent Oxyops vitiosa (Coleoptera: Curculionidae)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The Australian curculionid Oxyops vitiosa Pascoe was introduced into Florida during 1997 as a biological control agent of the invasive tree Melaleuca quinquenervia (Cav.) S.T. Blake. Populations of the weevil increased rapidly and became widely distributed throughout much of the invasive tree’s adve...

  5. Larval dispersal of the weed biological control agent Oxyops vitiosa (Coleoptera: Curculionidae)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The Australian weevil Oxyops vitiosa is a biological control agent of the exotic tree Melaleuca quinquenervia in Florida, USA. Evidence suggests that the last instar drops from the canopy to the forest floor to pupate in the soil or leaf litter. This dispersal method preempts weevil population persi...

  6. POTENTIAL OF ENTOMOPATHOGENIC FUNGI AS BIOLOGICAL CONTROL AGENTS AGAINST THE FORMOSAN SUBTERRANEAN TERMITE

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Tolerance, pathogenicity and transmission studies of the fungi Metarhizium and Beauveria, show that biological control agents can enhance termite treatment flexibility. Subterranean termites cause significant damage to wood structures and trees, especially in the Gulf of Mexico region of the United ...

  7. Microarray Analysis and Mutagenesis of the Biological Control Agent Pseudomonas fluorescens Pf-5

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The biological control agent Pseudomonas fluorescens Pf-5 suppresses seedling emergence diseases caused by soilborne fungi and Oomycetes. Pf-5 produces at least ten secondary metabolites. These include hydrogen cyanide, pyrrolnitrin, pyoluteorin and 2,4-diacetylphloroglucinol, which have known funct...

  8. Establishment of the armored scale, Rhizaspidiotus donacis, a biological control agent of Arundo donax

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The armored scale biological control agent, Rhizaspidiotus donacis (Leonardi) (Hemiptera; Diaspididae) has established populations on the invasive weed, Arundo donax L. (Poaceae; Arundinoideae) in Del Rio (Val Verde, Co.) and in field plots at the USDA-APHIS-PPQ-Moore Airbase, Edinburg (Hidalgo Co.)...

  9. Trichogramma spp. as biological control agents in the Philippines: history and current practice

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Trichogramma parasitoids have long been recognized as important and viable biological control agents against lepidopteran pests of rice, corn and sugarcane in the Philippines. We describe the history of research and use of Trichogramma spp. in the Philippines in three main areas: 1) field surveys – ...

  10. Trichogramma spp. (Hymenoptera: Trichogrammatidae) as biological control agents in the Philippines: history and current practice

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Trichogramma parasitoids have long been recognized as important and viable biological control agents against lepidopteran pests of rice, corn and sugarcane in the Philippines. We describe the history of research and use of Trichogramma spp. in the Philippines in three main areas: 1) field surveys – ...

  11. Compatability of a Biological Control Agent with Herbicides for Control of Invasive Plant Species

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Kudzu, Pueraria montana var lobata, is an exotic invasive weed that is difficult to control with available products and management practices. The fungal pathogen, Myrothecium verrucaria, is being developed as a bioherbicide for kudzu and other invasive vines. This biological control agent might be...

  12. A fully integrated microdevice for biobarcode assay based biological agent detection.

    PubMed

    Cho, Minkyung; Chung, Soyi; Kim, Yong Tae; Jung, Jae Hwan; Kim, Do Hyun; Seo, Tae Seok

    2015-07-01

    An integrated microdevice, consisting of a micropump, a passive mixer, a magnetic separation chamber, and a microcapillary electrophoretic channel, was constructed for biobarcode assay based multiplex biological agent detection in a sample-to-answer-out manner within 30 min with high sensitivity. PMID:26032690

  13. Performance of Traditional and Molecular Methods for Detecting Biological Agents in Drinking Water

    EPA Science Inventory

    USGS Report - To reduce the impact from a possible bioterrorist attack on drinking-water supplies, analytical methods are needed to rapidly detect the presence of biological agents in water. To this end, 13 drinking-water samples were collected at 9 water-treatment plants in Ohio...

  14. Effects of a biological control agent on the use of saltcedar habitat by passerine birds

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Invasion of native riparian habitats by saltcedar (Tamarix spp.) in the southwestern United States, has caused declines in population density of birds. The saltcedar leaf beetle (Diorhabda elongata) has been released at several sites as a biological control agent. At two northern Nevada locations,...

  15. Use of pupal parasitoids as biological control agents of filth flies on equine facilities

    Technology Transfer Automated Retrieval System (TEKTRAN)

    House flies, Musca domestica L., and stable flies, Stomoxys calcitrans (L.), (Diptera: Muscidae), are common pests on horse farms. The use of pupal parasitoids as biological control agents for filth flies is becoming more popular on equine facilities; however, there is a lack of information on the e...

  16. Evaluation of Serangium parcesetosum (Coleoptera: Coccinellidae) as a biological control agent of the silverleaf whitefly

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The coccinellid predator from India, Serangium parcesetosum Sicard, was studied as a potential biological control agent of the silverleaf whitefly, Bemisia argentifolii Bellows & Perring [also known as the sweetpotato whitefly, B. tahaci (Gennadius) Biotype B]. Studies were performed on prey prefere...

  17. Physiological host range of Ceratapion basicorne, a prospective biological control agent of Centaurea solstitialis (Asteraceae)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Ceratapion basicorne (Coleoptera: Apionidae) is a weevil native to Europe and western Asia has been proposed as a prospective classical biological control agent of yellow starthistle (Centaurea solstitialis), which is an important invasive alien weed in the western United States. Host plant specifi...

  18. Search for fungi as potential biological control agents of Echinochloa crus-galli

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Cockspur dace, Echinochloa crus-galli (family Poaceae), is the most widespread and harmful weed in Russian rice production. Heavy infestations of the weed cause rice-crop losses up to 50 percent. With the purpose of discovering pathogenic fungi as potential agents for biological control of E. crus-g...

  19. Pheromone and host odor attractants for managing Diorhabda spp.: Biological control agents of saltcedar

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The recent identification of the aggregation pheromone (Cossé et al., 2005, Journal of Chemical Ecology 26:1735-1748), and host odor attractant (Cossé et al., 2005, Journal of Chemical Ecology, in press) for the leaf beetle Diorhabda elongata, a biological control agent of saltcedar, allowed for a m...

  20. Modeling and simulation of biological systems from image data

    PubMed Central

    Sbalzarini, Ivo F

    2013-01-01

    This essay provides an introduction to the terminology, concepts, methods, and challenges of image-based modeling in biology. Image-based modeling and simulation aims at using systematic, quantitative image data to build predictive models of biological systems that can be simulated with a computer. This allows one to disentangle molecular mechanisms from effects of shape and geometry. Questions like “what is the functional role of shape” or “how are biological shapes generated and regulated” can be addressed in the framework of image-based systems biology. The combination of image quantification, model building, and computer simulation is illustrated here using the example of diffusion in the endoplasmic reticulum. PMID:23533152

  1. BioNSi: A Discrete Biological Network Simulator Tool.

    PubMed

    Rubinstein, Amir; Bracha, Noga; Rudner, Liat; Zucker, Noga; Sloin, Hadas E; Chor, Benny

    2016-08-01

    Modeling and simulation of biological networks is an effective and widely used research methodology. The Biological Network Simulator (BioNSi) is a tool for modeling biological networks and simulating their discrete-time dynamics, implemented as a Cytoscape App. BioNSi includes a visual representation of the network that enables researchers to construct, set the parameters, and observe network behavior under various conditions. To construct a network instance in BioNSi, only partial, qualitative biological data suffices. The tool is aimed for use by experimental biologists and requires no prior computational or mathematical expertise. BioNSi is freely available at http://bionsi.wix.com/bionsi , where a complete user guide and a step-by-step manual can also be found. PMID:27354160

  2. Unit testing, model validation, and biological simulation

    PubMed Central

    Watts, Mark D.; Ghayoomie, S. Vahid; Larson, Stephen D.; Gerkin, Richard C.

    2016-01-01

    The growth of the software industry has gone hand in hand with the development of tools and cultural practices for ensuring the reliability of complex pieces of software. These tools and practices are now acknowledged to be essential to the management of modern software. As computational models and methods have become increasingly common in the biological sciences, it is important to examine how these practices can accelerate biological software development and improve research quality. In this article, we give a focused case study of our experience with the practices of unit testing and test-driven development in OpenWorm, an open-science project aimed at modeling Caenorhabditis elegans. We identify and discuss the challenges of incorporating test-driven development into a heterogeneous, data-driven project, as well as the role of model validation tests, a category of tests unique to software which expresses scientific models.

  3. When Do We Simulate Non-Human Agents? Dissociating Communicative and Non-Communicative Actions

    ERIC Educational Resources Information Center

    Liepelt, Roman; Prinz, Wolfgang; Brass, Marcel

    2010-01-01

    There is strong evidence that we automatically simulate observed behavior in our motor system. Previous research suggests that this simulation process depends on whether we observe a human or a non-human agent. Measuring a motor priming effect, this study investigated the question of whether agent-sensitivity of motor simulation depends on the…

  4. Novel fluorescence-based integrated sensor for chemical and biological agent detection

    NASA Astrophysics Data System (ADS)

    Frye-Mason, Greg; Leuschen, Martin; Wald, Lara; Paul, Kateri; Hancock, Lawrence F.; Fagan, Steve; Krouse, Justin; Hutchinson, Kira D.

    2004-12-01

    There is a renewed interest in the development of chemical and biological agent sensors due to the increased threat of weapons deployment by terrorist organizations and rogue states. Optically based sensors address the needs of military and homeland security forces in that they are reliable, rapidly deployed, and can provide continuous monitoring with little to no operator involvement. Nomadics has developed optically based chemical weapons sensors that utilize reactive fluorescent chromophores initially developed by Professor Tim Swager at MIT. The chromophores provide unprecedented sensitivity and selectivity toward toxic industrial chemicals and certain chemical weapon agents. The selectivity is based upon the reactivity of the G-class nerve agents (phosphorylation of acetylcholinesterase enzyme) that makes them toxic. Because the sensor recognizes the reactivity of strong electrophiles and not molecular weight, chemical affinity or ionizability, our system detects a specific class of reactive agents and will be able to detect newly developed or modified agents that are not currently known. We have recently extended this work to pursue a combined chemical/biological agent sensor system incorporating technologies based upon novel deep ultraviolet (UV) light emitting diodes (LEDs) developed out of the DARPA Semiconductor UV Optical Sources (SUVOS) program.

  5. Agent-Based Crowd Simulation Considering Emotion Contagion for Emergency Evacuation Problem

    NASA Astrophysics Data System (ADS)

    Faroqi, H.; Mesgari, M.-S.

    2015-12-01

    During emergencies, emotions greatly affect human behaviour. For more realistic multi-agent systems in simulations of emergency evacuations, it is important to incorporate emotions and their effects on the agents. In few words, emotional contagion is a process in which a person or group influences the emotions or behavior of another person or group through the conscious or unconscious induction of emotion states and behavioral attitudes. In this study, we simulate an emergency situation in an open square area with three exits considering Adults and Children agents with different behavior. Also, Security agents are considered in order to guide Adults and Children for finding the exits and be calm. Six levels of emotion levels are considered for each agent in different scenarios and situations. The agent-based simulated model initialize with the random scattering of agent populations and then when an alarm occurs, each agent react to the situation based on its and neighbors current circumstances. The main goal of each agent is firstly to find the exit, and then help other agents to find their ways. Numbers of exited agents along with their emotion levels and damaged agents are compared in different scenarios with different initialization in order to evaluate the achieved results of the simulated model. NetLogo 5.2 is used as the multi-agent simulation framework with R language as the developing language.

  6. Update on the use of systemic biologic agents in the treatment of noninfectious uveitis

    PubMed Central

    Pasadhika, Sirichai; Rosenbaum, James T

    2014-01-01

    Uveitis is one of the leading causes of blindness worldwide. Noninfectious uveitis may be associated with other systemic conditions, such as human leukocyte antigen B27-related spondyloarthropathies, inflammatory bowel disease, juvenile idiopathic arthritis, Behçet’s disease, and sarcoidosis. Conventional therapy with corticosteroids and immunosuppressive agents (such as methotrexate, azathioprine, mycophenolate mofetil, and cyclosporine) may not be sufficient to control ocular inflammation or prevent non-ophthalmic complications in refractory patients. Off-label use of biologic response modifiers has been studied as primary and secondary therapeutic agents. They are very useful when conventional immunosuppressive therapy has failed or has been poorly tolerated, or to treat concomitant ophthalmic and systemic inflammation that might benefit from these medications. Biologic therapy, primarily infliximab, and adalimumab, have been shown to be rapidly effective for the treatment of various subtypes of refractory uveitis and retinal vasculitis, especially Behçet’s disease-related eye conditions and the uveitis associated with juvenile idiopathic arthritis. Other agents such as golimumab, abatacept, canakinumab, gevokizumab, tocilizumab, and alemtuzumab may have great future promise for the treatment of uveitis. It has been shown that with proper monitoring, biologic therapy can significantly improve quality of life in patients with uveitis, particularly those with concurrent systemic symptoms. However, given high cost as well as the limited long-term safety data, we do not routinely recommend biologics as first-line therapy for noninfectious uveitis in most patients. These agents should be used with caution by experienced clinicians. The present work aims to provide a broad and updated review of the current and in-development systemic biologic agents for the treatment of noninfectious uveitis. PMID:24600203

  7. Chamber LIDAR measurements of aerosolized biological simulants

    NASA Astrophysics Data System (ADS)

    Brown, David M.; Thrush, Evan P.; Thomas, Michael E.; Siegrist, Karen M.; Baldwin, Kevin; Quizon, Jason; Carter, Christopher C.

    2009-05-01

    A chamber aerosol LIDAR is being developed to perform well-controlled tests of optical scattering characteristics of biological aerosols, including Bacillus atrophaeus (BG) and Bacillus thuringiensis (BT), for validation of optical scattering models. The 1.064 μm, sub-nanosecond pulse LIDAR allows sub-meter measurement resolution of particle depolarization ratio or backscattering cross-section at a 1 kHz repetition rate. Automated data acquisition provides the capability for real-time analysis or recording. Tests administered within the refereed 1 cubic meter chamber can provide high quality near-field backscatter measurements devoid of interference from entrance and exit window reflections. Initial chamber measurements of BG depolarization ratio are presented.

  8. Portable Raman device for detection of chemical and biological warfare agents

    NASA Astrophysics Data System (ADS)

    Wabuyele, Musundi B.; Martin, Matthew E.; Yan, Fei; Stokes, David L.; Mobley, Joel; Cullum, Brian M.; Wintenberg, Alan; Lenarduzzi, Roberto; Vo-Dinh, Tuan

    2005-04-01

    This paper describes a compact, self-contained, cost effective, and portable Raman Integrated Tunable Sensor (RAMiTs) for screening a wide variety of chemical and biological agents for homeland defense applications. The instrument is a fully-integrated, tunable, "point-and-shoot" Raman monitor based on solid-state acousto-optic tunable filter (AOTF) technology. It can provide direct identification and quantitative analysis of chemical and biological samples in a few seconds under field conditions. It also consists of a 830-nm diode laser for excitation, and an avalanche photodiode for detection. Evaluation of this instrument has been performed by analyzing several standard samples and comparing the results those obtained using a conventional Raman system. In addition to system evaluation, this paper will also discuss potential applications of the RAMiTs for detection of chemical and biological warfare agents.

  9. Development of biosensors for the detection of biological warfare agents: its issues and challenges.

    PubMed

    Kumar, Harish; Rani, Renu

    2013-01-01

    This review discusses current development in biosensors for the detection of biological warfare agents (BWAs). BWAs include bacteria, virus and toxins that are added deliberately into air water and food to spread terrorism and cause disease or death. The rapid and unambiguous detection and identification of BWAs with early warning signals for detecting possible biological attack is a major challenge for government agencies particularly military and health. The detection devices--biosensors--can be classified (according to their physicochemical transducers) into four types: electrochemical, nucleic acid, optical and piezoelectric. Advantages and limitations of biosensors are discussed in this review followed by an assessment of the current state of development of different types of biosensors. The research and development in biosensors for biological warfare agent detection is of great interest for the public as well as for governments. PMID:24244972

  10. Agent-Based Spatiotemporal Simulation of Biomolecular Systems within the Open Source MASON Framework

    PubMed Central

    Pérez-Rodríguez, Gael; Pérez-Pérez, Martín; Glez-Peña, Daniel; Azevedo, Nuno F.; Lourenço, Anália

    2015-01-01

    Agent-based modelling is being used to represent biological systems with increasing frequency and success. This paper presents the implementation of a new tool for biomolecular reaction modelling in the open source Multiagent Simulator of Neighborhoods framework. The rationale behind this new tool is the necessity to describe interactions at the molecular level to be able to grasp emergent and meaningful biological behaviour. We are particularly interested in characterising and quantifying the various effects that facilitate biocatalysis. Enzymes may display high specificity for their substrates and this information is crucial to the engineering and optimisation of bioprocesses. Simulation results demonstrate that molecule distributions, reaction rate parameters, and structural parameters can be adjusted separately in the simulation allowing a comprehensive study of individual effects in the context of realistic cell environments. While higher percentage of collisions with occurrence of reaction increases the affinity of the enzyme to the substrate, a faster reaction (i.e., turnover number) leads to a smaller number of time steps. Slower diffusion rates and molecular crowding (physical hurdles) decrease the collision rate of reactants, hence reducing the reaction rate, as expected. Also, the random distribution of molecules affects the results significantly. PMID:25874228

  11. Simulations in Medicine and Biology: Insights and perspectives

    NASA Astrophysics Data System (ADS)

    Spyrou, George M.

    2015-01-01

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

  12. How psoriasis patients perceive, obtain, and use biologic agents: Survey from an academic medical center.

    PubMed

    Kamangar, Faranak; Isip, Leah; Bhutani, Tina; Dennis, Madison; Heller, Misha M; Lee, Eric S; Nie, Hong; Liao, Wilson

    2013-02-01

    The availability of new biologic agents for the treatment of psoriasis provides hope for improved quality of life outcomes. However, the way patients come to use biologics, the potential barriers they encounter, and their attitudes towards using these medications are still not well studied. Here, we conducted a survey of 106 psoriasis patients at an academic medical center to discern patient attitudes towards biologics. We found that most patients learn of biologics through their physician and perform follow-up research using the Internet. Most patients did not find it difficult to make the decision to start a biologic. Difficulty in obtaining biologics was associated with age less than 55 (p = 0.01), lower income level (p = 0.007), and lack of insurance (p = 0.04). Patients were found to have high satisfaction and compliance rates on biologics. Of patients who missed a dose of their biologic, this was mainly due to logistical reasons such as not having the medication or forgetting to take it, rather than being depressed or overwhelmed. Patients with lower income levels had increased cut backs in personal expenses due to co-payments (p = 0.001). Among respondents, the mean annual out-of-pocket expense for a biologic was $557.12 per year, with a range of $0-7000. PMID:22007699

  13. CRITTERS! A Realistic Simulation for Teaching Evolutionary Biology

    ERIC Educational Resources Information Center

    Latham, Luke G., II; Scully, Erik P.

    2008-01-01

    Evolutionary processes can be studied in nature and in the laboratory, but time and financial constraints result in few opportunities for undergraduate and high school students to explore the agents of genetic change in populations. One alternative to time consuming and expensive teaching laboratories is the use of computer simulations. We…

  14. Nucleic acid approaches for detection and identification of biological warfare and infectious disease agents.

    PubMed

    Ivnitski, Dmitri; O'Neil, Daniel J; Gattuso, Anthony; Schlicht, Roger; Calidonna, Michael; Fisher, Rodney

    2003-10-01

    Biological warfare agents are the most problematic of the weapons of mass destruction and terror. Both civilian and military sources predict that over the next decade the threat from proliferation of these agents will increase significantly. In this review we summarize the state of the art in detection and identification of biological threat agents based on PCR technology with emphasis on the new technology of microarrays. The advantages and limitations of real-time PCR technology and a review of the literature as it applies to pathogen and virus detection are presented. The paper covers a number of issues related to the challenges facing biological threat agent detection technologies and identifies critical components that must be overcome for the emergence of reliable PCR-based DNA technologies as bioterrorism countermeasures and for environmental applications. The review evaluates various system components developed for an integrated DNA microchip and the potential applications of the next generation of fully automated DNA analyzers with integrated sample preparation and biosensing elements. The article also reviews promising devices and technologies that are near to being, or have been, commercialized. PMID:14579752

  15. nab-Paclitaxel in combination with biologically targeted agents for early and metastatic breast cancer.

    PubMed

    Megerdichian, Christine; Olimpiadi, Yuliya; Hurvitz, Sara A

    2014-06-01

    Taxanes are highly active chemotherapeutic agents used in the treatment of early-stage and metastatic breast cancer. Novel formulations have been developed to improve efficacy and decrease toxicity associated with these cytotoxic agents. nab-Paclitaxel is a biologically interactive, solvent-free, 130-nm-sized albumin-bound paclitaxel, developed to avoid the Cremophor vehicle used in solvent-based paclitaxel. Based on a pivotal phase 3 study, nab-paclitaxel was shown to be safely infused at a significantly higher dose of paclitaxel than the doses used with standard paclitaxel therapy, and had a shorter infusion time, no premedication, and higher response rates. It is now approved in the United States for treatment of breast cancer after failure of combination chemotherapy for metastatic disease or relapse within 6 months of adjuvant therapy, and has demonstrated promising efficacy and favorable tolerability. Recently, several phase 2 and 3 studies have suggested a role for nab-paclitaxel in combination with biologically targeted agents for the treatment of early- and late-stage breast cancer. This review will discuss the findings of clinical trials evaluating nab-paclitaxel in combination with biologically targeted therapeutic agents for breast cancer in the neoadjuvant, adjuvant, and metastatic settings. PMID:24560997

  16. Insect-gene-activity detection system for chemical and biological warfare agents and toxic industrial chemicals

    NASA Astrophysics Data System (ADS)

    Mackie, Ryan S.; Schilling, Amanda S.; Lopez, Arturo M.; Rayms-Keller, Alfredo

    2002-02-01

    Detection of multiple chemical and biological weapons (CBW) agents and/or complex mixtures of toxic industrial chemicals (TIC) is imperative for both the commercial and military sectors. In a military scenario, a multi-CBW attack would create confusion, thereby delaying decontamination and therapeutic efforts. In the commercial sector, polluted sites invariably contain a mixture of TIC. Novel detection systems capable of detecting CBW and TIC are sorely needed. While it may be impossible to build a detector capable of discriminating all the possible combinations of CBW, a detection system capable of statistically predicting the most likely composition of a given mixture is within the reach of current emerging technologies. Aquatic insect-gene activity may prove to be a sensitive, discriminating, and elegant paradigm for the detection of CBW and TIC. We propose to systematically establish the expression patterns of selected protein markers in insects exposed to specific mixtures of chemical and biological warfare agents to generate a library of biosignatures of exposure. The predicting capabilities of an operational library of biosignatures of exposures will allow the detection of emerging novel or genetically engineered agents, as well as complex mixtures of chemical and biological weapons agents. CBW and TIC are discussed in the context of war, terrorism, and pollution.

  17. Real-time biological agent detection using particle size, shape, and fluorescence characterisation

    NASA Astrophysics Data System (ADS)

    Shelton, Matthew J.; Evans, Steve P.; Smith, Paul D.; Simpson, Innes A.; Kaye, Paul H.; Clark, James M.

    2004-12-01

    Developments in real time optical biological agent detection and sensing are presented which describe start of the art advances in the detection and warning of these pathogens. The following paper describes the basic operating principles of the current BIRAL ASAS (Aerosol Size and Shape) system which measures the optically determined particle properties, on a particle by particle basis, and uses the information to describe the size and shape characteristics of the aerosol. Furthermore, recent development of the existing technology to also encompass fluorescence detection is described, which significantly increases the detection ability of the ASAS aerosol suite. This operational improvement is a major advancement in the field of airborne biological agent detection and allows for near generic detection and warning. Applications of this device include all aspects of bio-aerosol monitoring, including the use as a biological agent detector and generic identifier, use as a general bio-agent monitor and also for use as a hazardous environment monitor. Such a device would be particularly useful in the fields of Armed Forces protection and National Defence either as a point detector or as a "plug and play" biosensor detector in a network.

  18. Numerical simulations and modeling for stochastic biological systems with jumps

    NASA Astrophysics Data System (ADS)

    Zou, Xiaoling; Wang, Ke

    2014-05-01

    This paper gives a numerical method to simulate sample paths for stochastic differential equations (SDEs) driven by Poisson random measures. It provides us a new approach to simulate systems with jumps from a different angle. The driving Poisson random measures are assumed to be generated by stationary Poisson point processes instead of Lévy processes. Methods provided in this paper can be used to simulate SDEs with Lévy noise approximately. The simulation is divided into two parts: the part of jumping integration is based on definition without approximation while the continuous part is based on some classical approaches. Biological explanations for stochastic integrations with jumps are motivated by several numerical simulations. How to model biological systems with jumps is showed in this paper. Moreover, method of choosing integrands and stationary Poisson point processes in jumping integrations for biological models are obtained. In addition, results are illustrated through some examples and numerical simulations. For some examples, earthquake is chose as a jumping source which causes jumps on the size of biological population.

  19. Agent-Based Knowledge Discovery for Modeling and Simulation

    SciTech Connect

    Haack, Jereme N.; Cowell, Andrew J.; Marshall, Eric J.; Fligg, Alan K.; Gregory, Michelle L.; McGrath, Liam R.

    2009-09-15

    This paper describes an approach to using agent technology to extend the automated discovery mechanism of the Knowledge Encapsulation Framework (KEF). KEF is a suite of tools to enable the linking of knowledge inputs (relevant, domain-specific evidence) to modeling and simulation projects, as well as other domains that require an effective collaborative workspace for knowledge-based tasks. This framework can be used to capture evidence (e.g., trusted material such as journal articles and government reports), discover new evidence (covering both trusted and social media), enable discussions surrounding domain-specific topics and provide automatically generated semantic annotations for improved corpus investigation. The current KEF implementation is presented within a semantic wiki environment, providing a simple but powerful collaborative space for team members to review, annotate, discuss and align evidence with their modeling frameworks. The novelty in this approach lies in the combination of automatically tagged and user-vetted resources, which increases user trust in the environment, leading to ease of adoption for the collaborative environment.

  20. Pre-release efficacy test of the prospective biological control agent Arytinnis hakani on the invasive weed Genista monspessulana

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In weed biological control, conducting a pre-release efficacy test can help ascertain if prospective biological control agents will be capable of controlling the target plant. Currently, the phloem-feeding psyllid, Arytinnis hakani, is being evaluated as a prospective agent for the exotic invasive w...

  1. Principles of risk assessment for illness caused by foodborne biological agents. National Advisory Committee on Microbiological Criteria for Foods.

    PubMed

    Buchanan, R

    1998-08-01

    The Risk Assessment Subcommittee of the National Advisory Committee on Microbiological Criteria in Foods has prepared a generic document on the principles of risk assessment as applied to biological agents that can cause human foodborne disease. Typical biological agents include bacteria, viruses, fungi, helminths, protozoa, algae, parasites, and the toxic products that these agents may produce. Basic principles elaborated to characterize food pathogen risks include the four broadly accepted components of risk assessment. The role of surveillance and investigational activities to link biological agents and their food sources to consumer illness is described as is the role of predictive modeling for food pathogens. PMID:9713775

  2. Coarse-grained models for biological simulations

    NASA Astrophysics Data System (ADS)

    Wu, Zhe; Cui, Qiang; Yethiraj, Arun

    2011-03-01

    The large timescales and length-scales of interest in biophysics preclude atomistic study of many systems and processes. One appealing approach is to use coarse-grained (CG) models where several atoms are grouped into a single CG site. In this work we describe a new CG force field for lipids, surfactants, and amino acids. The topology of CG sites is the same as in the MARTINI force field, but the new model is compatible with a recently developed CG electrostatic water (Big Multiple Water, BMW) model. The model not only gives correct structural, elastic properties and phase behavior for lipid and surfactants, but also reproduces electrostatic properties at water-membrane interface that agree with experiment and atomistic simulations, including the potential of mean force for charged amino acid residuals at membrane. Consequently, the model predicts stable attachment of cationic peptides (i.e., poly-Arg) on lipid bilayer surface, which is not shown in previous models with non-electrostatic water.

  3. DNA capture elements for rapid detection and identification of biological agents

    NASA Astrophysics Data System (ADS)

    Kiel, Johnathan L.; Parker, Jill E.; Holwitt, Eric A.; Vivekananda, Jeeva

    2004-08-01

    DNA capture elements (DCEs; aptamers) are artificial DNA sequences, from a random pool of sequences, selected for their specific binding to potential biological warfare agents. These sequences were selected by an affinity method using filters to which the target agent was attached and the DNA isolated and amplified by polymerase chain reaction (PCR) in an iterative, increasingly stringent, process. Reporter molecules were attached to the finished sequences. To date, we have made DCEs to Bacillus anthracis spores, Shiga toxin, Venezuelan Equine Encephalitis (VEE) virus, and Francisella tularensis. These DCEs have demonstrated specificity and sensitivity equal to or better than antibody.

  4. Medical applications of nanoparticles in biological imaging, cell labeling, antimicrobial agents, and anticancer nanodrugs.

    PubMed

    Singh, Ravina; Nalwa, Hari Singh

    2011-08-01

    This article reviews the applications of nanotechnology in the fields of medical and life sciences. Nanoparticles have shown promising applications from diagnosis to treatment of various types of diseases including cancer. In this review, we discuss the applications of nanostructured materials such as nanoparticles, quantum dots, nanorods, nanowires, and carbon nanotubes in diagnostics, biomarkers, cell labeling, contrast agents for biological imaging, antimicrobial agents, drug delivery systems, and anticancer nanodrugs for treatment of cancer and other infectious diseases. The adverse affects of nanoparticles on human skin from daily use in cosmetics and general toxicology of nanoscale materials are also reviewed. PMID:21870454

  5. Simulation of transmission electron microscope images of biological specimens.

    PubMed

    Rullgård, H; Ofverstedt, L-G; Masich, S; Daneholt, B; Oktem, O

    2011-09-01

    We present a new approach to simulate electron cryo-microscope images of biological specimens. The framework for simulation consists of two parts; the first is a phantom generator that generates a model of a specimen suitable for simulation, the second is a transmission electron microscope simulator. The phantom generator calculates the scattering potential of an atomic structure in aqueous buffer and allows the user to define the distribution of molecules in the simulated image. The simulator includes a well defined electron-specimen interaction model based on the scalar Schrödinger equation, the contrast transfer function for optics, and a noise model that includes shot noise as well as detector noise including detector blurring. To enable optimal performance, the simulation framework also includes a calibration protocol for setting simulation parameters. To test the accuracy of the new framework for simulation, we compare simulated images to experimental images recorded of the Tobacco Mosaic Virus (TMV) in vitreous ice. The simulated and experimental images show good agreement with respect to contrast variations depending on dose and defocus. Furthermore, random fluctuations present in experimental and simulated images exhibit similar statistical properties. The simulator has been designed to provide a platform for development of new instrumentation and image processing procedures in single particle electron microscopy, two-dimensional crystallography and electron tomography with well documented protocols and an open source code into which new improvements and extensions are easily incorporated. PMID:21631500

  6. A Systematic Review of Agent-Based Modelling and Simulation Applications in the Higher Education Domain

    ERIC Educational Resources Information Center

    Gu, X.; Blackmore, K. L.

    2015-01-01

    This paper presents the results of a systematic review of agent-based modelling and simulation (ABMS) applications in the higher education (HE) domain. Agent-based modelling is a "bottom-up" modelling paradigm in which system-level behaviour (macro) is modelled through the behaviour of individual local-level agent interactions (micro).…

  7. Serious games experiment toward agent-based simulation

    USGS Publications Warehouse

    Wein, Anne; Labiosa, William

    2013-01-01

    We evaluate the potential for serious games to be used as a scientifically based decision-support product that supports the United States Geological Survey’s (USGS) mission--to provide integrated, unbiased scientific information that can make a substantial contribution to societal well-being for a wide variety of complex environmental challenges. Serious or pedagogical games are an engaging way to educate decisionmakers and stakeholders about environmental challenges that are usefully informed by natural and social scientific information and knowledge and can be designed to promote interactive learning and exploration in the face of large uncertainties, divergent values, and complex situations. We developed two serious games that use challenging environmental-planning issues to demonstrate and investigate the potential contributions of serious games to inform regional-planning decisions. Delta Skelta is a game emulating long-term integrated environmental planning in the Sacramento-San Joaquin Delta, California, that incorporates natural hazards (flooding and earthquakes) and consequences for California water supplies amidst conflicting water interests. Age of Ecology is a game that simulates interactions between economic and ecologic processes, as well as natural hazards while implementing agent-based modeling. The content of these games spans the USGS science mission areas related to water, ecosystems, natural hazards, land use, and climate change. We describe the games, reflect on design and informational aspects, and comment on their potential usefulness. During the process of developing these games, we identified various design trade-offs involving factual information, strategic thinking, game-winning criteria, elements of fun, number and type of players, time horizon, and uncertainty. We evaluate the two games in terms of accomplishments and limitations. Overall, we demonstrated the potential for these games to usefully represent scientific information

  8. Portuguese guidelines for the use of biological agents in rheumatoid arthritis - March 2010 update.

    PubMed

    Fonseca, João Eurico; Canhão, Helena; Reis, Paulo; Santos, Maria José; Branco, Jaime; Quintal, Alberto; Malcata, Armando; Araújo, Domingos; Ventura, Francisco; Figueiredo, Guilherme; da Silva, José Canas; Patto, José Vaz; de Queiroz, Mário Viana; Santos, Rui André; Neto, Adriano José; de Matos, Alves de; Rodrigues, Ana; Mourão, Ana Filipa; Ribeiro, Ana Sofia; Cravo, Ana Rita; Barcelos, Anabela; Cardoso, Anabela; Vilar, António; Braña, Arecili; Faustino, Augusto; Silva, Candida; Godinho, Fátima; Cunha, Inês; Costa, José António; Gomes, José António Melo; Pinto, José António Araújo; da Silva, J A Pereira; Miranda, Luís Cunha; Inês, Luís; Santos, Luís Maurício; Cruz, Margarida; Salvador, Maria João; Ferreira, Maria Júlia; Rial, Maria; Bernardes, Miguel; Bogas, Mónica; Araújo, Paula; Machado, Pedro; Pinto, Patrícia; de Melo, Rui Gomes; Cortes, Sara; Alcino, Sérgio; Capela, Susana

    2010-01-01

    The authors present the revised version of the Portuguese Society of Rheumatology (SPR) guidelines for the treatment of rheumatoid arthritis (RA) with biological therapies. In these guidelines the criteria for introduction and maintenance of biological agents are discussed as well as the contraindications and procedures in the case of non-responders. Biological treatment should be considered in RA patients with a disease activity score 28 (DAS 28) superior to 3.2 despite treatment with 20mg/week of methotrexate (MTX) for at least 3 months or, if such treatment is not possible, after 6 months of other conventional disease modifying drug or combination therapy. A DAS 28 score between 2.6 and 3.2 with a significant functional or radiological deterioration under treatment with conventional regimens could also constitute an indication for biological treatment. The treatment goal should be remission or, if that is not achievable, at least a low disease activity, characterized by a DAS28 lower than 3.2, without significative functional or radiological worsening. The response criteria, at the end of the first 3 months of treatment, are a decrease of 0.6 in the DAS28 score. After 6 months of treatment response criteria is defined as a decrease of more than 1.2 in the DAS28 score. Non-responders, in accordance to the Rheumatologist's clinical opinion, should try a switch to another biological agent (tumour necrosis factor antagonist, abatacept, rituximab or tocilizumab). PMID:20505635

  9. Persistence with biologic agents for the treatment of rheumatoid arthritis in Japan

    PubMed Central

    Mahlich, Jörg; Sruamsiri, Rosarin

    2016-01-01

    Background To assess persistence rates of biologic agents for the treatment of rheumatoid arthritis in Japan. Methods Based on Japanese claims data of 16,214 patients between 2012 and 2014, 6-, 12-, and 18-month persistence rates of different biologic agents were calculated. Determinants of persistence were assessed by means of a multivariate Cox proportional hazard model controlling for age, sex, and comorbidities. A sensitivity analysis was performed with different definitions of persistence and parametric survival analysis. Results Overall persistence rates in Japan are high and reach 86% after 1 year in the entire sample. The persistence rate for the biologic-naïve subpopulation is above 95%. Persistence is higher for older patients (hazard ratio 0.60 [95% confidence interval 0.40–0.91] for >75 years compared to ≤60 years) and lower for patients with a high comorbidity score (hazard ratio 1.33; 95% confidence interval 1.03–1.70 for Charlson Comorbidity Index score 3–5 compared to ≤2). We found a high variation of persistence between different drugs. Conclusion Japanese rheumatoid arthritis patients have a high persistence rate of biologic treatments. However, multiple factors affect the persistence rate of Japanese patients, including age, comorbidities, and patient type. Naïve patients tend to have a higher persistence rate than continuing biologic patients. PMID:27540283

  10. Biologically-inspired hexapod robot design and simulation

    NASA Technical Reports Server (NTRS)

    Espenschied, Kenneth S.; Quinn, Roger D.

    1994-01-01

    The design and construction of a biologically-inspired hexapod robot is presented. A previously developed simulation is modified to include models of the DC drive motors, the motor driver circuits and their transmissions. The application of this simulation to the design and development of the robot is discussed. The mechanisms thought to be responsible for the leg coordination of the walking stick insect were previously applied to control the straight-line locomotion of a robot. We generalized these rules for a robot walking on a plane. This biologically-inspired control strategy is used to control the robot in simulation. Numerical results show that the general body motion and performance of the simulated robot is similar to that of the robot based on our preliminary experimental results.

  11. Manipulating biological agents and cells in micro-scale volumes for applications in medicine

    PubMed Central

    Tasoglu, Savas; Gurkan, Umut Atakan; Wang, ShuQi

    2013-01-01

    Recent technological advances provide new tools to manipulate cells and biological agents in micro/nano-liter volumes. With precise control over small volumes, the cell microenvironment and other biological agents can be bioengineered; interactions between cells and external stimuli can be monitored; and the fundamental mechanisms such as cancer metastasis and stem cell differentiation can be elucidated. Technological advances based on the principles of electrical, magnetic, chemical, optical, acoustic, and mechanical forces lead to novel applications in point-of-care diagnostics, regenerative medicine, in vitro drug testing, cryopreservation, and cell isolation/purification. In this review, we first focus on the underlying mechanisms of emerging examples for cell manipulation in small volumes targeting applications such as tissue engineering. Then, we illustrate how these mechanisms impact the aforementioned biomedical applications, discuss the associated challenges, and provide perspectives for further development. PMID:23575660

  12. Novel reversible and selective nerve agent simulant detection in conjunction with superoxide "turn-on" probing.

    PubMed

    Jang, Yoon Jeong; Murale, Dhiraj P; Churchill, David G

    2014-04-01

    Herein, we present fluorescein as a reversible fluorescent sensor for nerve agent simulants diethylchlorophosphate (DCP), diethyl methylphosphonate (DEMP), and diethyl cyanophosphonate (DECP). The superoxide allows for an "off-on" mechanism to regenerate fluorescein. The order of decrease in fluorescence intensity for nerve agent simulants is DCP > DEMP ≫ DECP. PMID:24558644

  13. Identifying Evacuees' Demand of Tsunami Shelters using Agent Based Simulation

    NASA Astrophysics Data System (ADS)

    Mas, E.; Adriano, B.; Koshimura, S.; Imamura, F.; Kuroiwa, J.; Yamazaki, F.; Zavala, C.; Estrada, M.

    2012-12-01

    Amongst the lessons learned in tsunami events such as the 2004 Indian Ocean and 2011 Great Tohoku Japan earthquake is that sometimes nature exceeds structural countermeasures like seawalls, breakwaters or tsunami gates. In such situations it is a challenging task for people in plain areas to find sheltering places. The vertical evacuation to multistory buildings is one alternative to provide areas for sheltering in a complex environment of evacuation. However, if the spatial distribution and the available capacity of these structures are not well displayed, conditions of evacuee over-demand or under-demand might be observed in several structures. In this study, we present the integration of the tsunami numerical modeling and the agent based simulation of evacuation as the method to estimate the sheltering demand of evacuees in an emergent behavior approach. The case study is set in La Punta district in Peru. Here, we used in the tsunami simulation a seismic source of slip distribution model (Pulido et.al. ,2011; Chlieh et.al, 2011) for a possible future tsunami scenario in the central Andes. We modeled three alternatives of evacuation. First, the horizontal evacuation scenario was analyzed to support the necessity of the sheltering-in-place option for the district. Second, the vertical evacuation scenario and third, the combination of vertical and horizontal evacuation scenarios of pedestrians and vehicles were conducted. In the last two alternatives, the demand of evacuees were measured at each official tsunami evacuation building and compared to the sheltering capacity of the structure. Results showed that out of twenty tsunami evacuation buildings, thirteen resulted with over-demands and seven were still with available space. Also it is confirmed that in this case the horizontal evacuation might lead to a high number of casualties due to the traffic congestion at the neck of the district. Finally the vertical evacuation would be a suitable solution for this area

  14. Chemistry and biology of chromatin remodeling agents: state of art and future perspectives of HDAC inhibitors.

    PubMed

    Rodriquez, Manuela; Aquino, Maurizio; Bruno, Ines; De Martino, Giovanni; Taddei, Maurizio; Gomez-Paloma, Luigi

    2006-01-01

    Chromatin remodeling is a fundamental phenomenon in the life of eukaryotic cells, bearing implications to numerous physiological and pathological phenomena. This review outlines the chemistry of natural and synthetic agents endowed with the ability to interfere with such biological function, with a particular emphasis on histone deacetylase (HDAC) inhibitors. Other aspects covered in this article comprise structure activity relationships (SAR) and modes of action at molecular level, including the description of crystal structures of enzyme-inhibitor complexes. PMID:16719774

  15. The Next Wave of Biological Agents for the Treatment of IBD: Evidence from Cochrane Reviews.

    PubMed

    Khanna, Reena; Chande, Nilesh; Vermeire, Séverine; Sandborn, William J; Parker, Claire E; Feagan, Brian G

    2016-07-01

    Multiple new biological treatments for Crohn's disease and ulcerative colitis are becoming available. Specifically, vedolizumab and ustekinumab are monoclonal antibodies that target molecular pathways relevant to disease pathogenesis. What can Cochrane reviews tell us about the efficacy, safety, and immunogenicity of these new agents? A Cochrane inflammatory bowel disease group symposium held at the 2015 Digestive Diseases Week annual meeting addressed these questions. This article reviews the data presented at that session. PMID:27306074

  16. Molecular modeling toward selective inhibitors of dihydrofolate reductase from the biological warfare agent Bacillus anthracis.

    PubMed

    Giacoppo, Juliana O S; Mancini, Daiana T; Guimarães, Ana P; Gonçalves, Arlan S; da Cunha, Elaine F F; França, Tanos C C; Ramalho, Teodorico C

    2015-02-16

    In the present work, we applied docking and molecular dynamics techniques to study 11 compounds inside the enzymes dihydrofolate reductase (DHFR) from the biological warfare agent Bacillus anthracis (BaDHFR) and Homo sapiens sapiens (HssDHFR). Six of these compounds were selected for a study with the mutant BaF96IDHFR. Our results corroborated with experimental data and allowed the proposition of a new molecule with potential activity and better selectivity for BaDHFR. PMID:24985033

  17. Canada thistle biological control agents on two South Dakota wildlife refuges

    USGS Publications Warehouse

    Reed, C.C.; Larson, D.L.; Larson, J.L.

    2006-01-01

    We monitored populations of Canada thistle biocontrol agents Cassida rubiginosa, Ceutorhynchus litura, Larinus (= Hadroplantus) planus, Urophora cardui, Orellia (= Terellia) ruficauda, and Rhinocyllus conicus on Canada thistle (Cirsium arvense) at two national wildlife refuges in South Dakota from 1999 through 2003. C. litura, U. cardui, O. ruficauda, and R. conicus were present on both refuges. Agent populations were low except for C. litura, which was present in up to 90% of stems in some plots. C. litura infestation did not reduce thistle flowering, stem length, or over-winter survival. There was no change in thistle stem numbers over the study period and no difference in stem numbers in areas of high C. litura populations compared to areas of low C. litura populations. Our results suggest that insect biological control agents are inadequate for reduction of Canada thistle in southern South Dakota.

  18. Differential orientation effect in the neural response to interacting biological motion of two agents

    PubMed Central

    Hirai, Masahiro; Kakigi, Ryusuke

    2009-01-01

    Background A recent behavioral study demonstrated that the meaningful interaction of two agents enhances the detection sensitivity of biological motion (BM), however, it remains unclear when and how the 'interaction' information of two agents is represented in our neural system. To clarify this point, we used magnetoencephalography and introduced a novel experimental technique to extract a neuromagnetic response relating to two-agent BM perception. We then investigated how this response was modulated by the interaction of two agents. In the present experiment, we presented two kinds of visual stimuli (interacting and non-interacting BM) with two orientations (upright and inverted). Results We found a neuromagnetic response in the bilateral occipitotemporal region, on average 300 – 400 ms after the onset of a two-agent BM stimulus. This result showed that interhemispheric differences were apparent for the peak amplitudes. For the left hemisphere, the orientation effect was manifest when the two agents were made to interact, and the interaction effect was manifest when the stimulus was inverted. In the right hemisphere, the main effects of both orientation and interaction were significant, suggesting that the peak amplitude was attenuated when the visual stimulus was inverted or made to interact. Conclusion These results demonstrate that the 'interaction' information of two agents can affect the neural activities in the bilateral occipitotemporal region, on average 300 – 400 ms after the onset of a two-agent BM stimulus, however, the modulation was different between hemispheres: the left hemisphere is more concerned with dynamics, whereas the right hemisphere is more concerned with form information. PMID:19397815

  19. Strategies for efficient numerical implementation of hybrid multi-scale agent-based models to describe biological systems

    PubMed Central

    Cilfone, Nicholas A.; Kirschner, Denise E.; Linderman, Jennifer J.

    2015-01-01

    Biologically related processes operate across multiple spatiotemporal scales. For computational modeling methodologies to mimic this biological complexity, individual scale models must be linked in ways that allow for dynamic exchange of information across scales. A powerful methodology is to combine a discrete modeling approach, agent-based models (ABMs), with continuum models to form hybrid models. Hybrid multi-scale ABMs have been used to simulate emergent responses of biological systems. Here, we review two aspects of hybrid multi-scale ABMs: linking individual scale models and efficiently solving the resulting model. We discuss the computational choices associated with aspects of linking individual scale models while simultaneously maintaining model tractability. We demonstrate implementations of existing numerical methods in the context of hybrid multi-scale ABMs. Using an example model describing Mycobacterium tuberculosis infection, we show relative computational speeds of various combinations of numerical methods. Efficient linking and solution of hybrid multi-scale ABMs is key to model portability, modularity, and their use in understanding biological phenomena at a systems level. PMID:26366228

  20. A Perspective on Vascular Disrupting Agents that Interact with Tubulin: Preclinical Tumor Imaging and Biological Assessment#

    PubMed Central

    Mason, Ralph P.; Zhao, Dawen; Liu, Li; Trawick, Mary Lynn; Pinney, Kevin G.

    2011-01-01

    The tumor microenvironment provides a rich source of potential targets for selective therapeutic intervention with properly designed anticancer agents. Significant physiological differences exist between the microvessels that nourish tumors and those that supply healthy tissue. Selective drug-mediated damage of these tortuous and chaotic microvessels starves a tumor of necessary nutrients and oxygen and eventually leads to massive tumor necrosis. Vascular targeting strategies in oncology are divided into two separate groups: angiogenesis inhibiting agents (AIAs) and vascular disrupting agents (VDAs). The mechanisms of action between these two classes of compounds are profoundly distinct. The AIAs inhibit the actual formation of new vessels, while the VDAs damage and/or destroy existing tumor vasculature. One subset of small-molecule VDAs functions by inhibiting the assembly of tubulin into microtubules, thus causing morphology changes to the endothelial cells lining the tumor vasculature, triggered by a cascade of cell signaling events. Ultimately this results in catastrophic damage to the vessels feeding the tumor. The rapid emergence and subsequent development of the VDA field over the past decade has led to the establishment of a synergistic combination of preclinical state-of-the-art tumor imaging and biological evaluation strategies that are often indicative of future clinical efficacy for a given VDA. This review focuses on an integration of the appropriate biochemical and biological tools necessary to assess (preclinically) new small-molecule, tubulin active VDAs for their potential to be clinically effective anticancer agents. PMID:21321746

  1. Development of an integrated system for rapid detection of biological agents

    NASA Astrophysics Data System (ADS)

    Terazono, Hideyuki; Takei, Hiroyuki; Hayashi, Masahito; Hattori, Akihiro; Yasuda, Kenji

    2010-04-01

    Weaponized biological agents are as great a threat as nuclear or chemical weapons. They must be detected at the earliest stage to prevent diffusion because once these agents are dispersed into the air, the rapidly decreasing concentration makes detection more of a challenge. Polymerase chain reaction (PCR) is a common method to create copies of a specific target region of a DNA sequence and to produce large quantities of DNA molecules. A few DNA molecules are rapidly amplified by PCR into billions of copies. While PCR is a powerful technique and is capable of countering new threats relatively easily, it is plagued by the number of processes necessary. Therefore, we have developed an integrated PCR system for rapid detection of biological agents captured from the air. Each processing function is performed by a dedicated module, and reduction in the process time has been made the top priority, without loss in the signal/noise ratio of the total system. Agents can be identified within 15 min from capture. A fully automated operation protects operators from exposure to potentially highly lethal samples.

  2. Detoxification of nerve agents by a substituted beta-cyclodextrin: application of a modified biological assay.

    PubMed

    Wille, T; Tenberken, O; Reiter, G; Müller, S; Le Provost, R; Lafont, O; Estour, F; Thiermann, H; Worek, F

    2009-11-30

    Chemical warfare agents (nerve agents) are still available and present a real threat to the population. Numerous in vitro and in vivo studies showed that various nerve agents, e.g. tabun and cyclosarin, are resistant towards standard therapy with atropine and oxime. Based on these facts we applied a modified biological assay for the easy, semi-quantitative testing of the detoxifying properties of the beta-cyclodextrin derivative CD-IBA. Cyclosarin, sarin, tabun and VX were incubated with CD-IBA for 1-50 min at 37 degrees C, then an aliquot was added to erythrocyte acetylcholinesterase (AChE) and the percentage of AChE inhibition was determined. The validity of the assay was confirmed by concomitant quantification of tabun by GC-MS. Different concentrations of cyclosarin were detoxified by CD-IBA in a concentration-dependent velocity. The ability to detoxify various nerve agents decreased in the order cyclosarin>sarin>tabun>VX. Hereby, no detoxification of VX could be detected. Sarin was detoxified in a biphasic reaction with a fast reduction of inhibitory potential in the first phase and a slower detoxification in the second phase. CD-IBA detoxified tabun in a one phase decay and, compared to cyclosarin and sarin, a longer half-life was determined with tabun. The modified biological assay is appropriate for the initial semi-quantitative screening of candidate compounds for the detoxification of nerve agents. The beta-cyclodextrin derivative CD-IBA demonstrated its ability to detoxify different nerve agents. PMID:19800384

  3. Reactively and Anticipatory Behaving Agents for Artificial Life Simulations

    NASA Astrophysics Data System (ADS)

    Kohout, Karel; Nahodil, Pavel

    2010-11-01

    Reactive behavior is still considered and the exact opposite for the anticipatory one. Despite the advances on the field of anticipation there are little thoughts on relation with the reactive behavior, the similarities and where the boundary is. In this article we will present our viewpoint and we will try to show that reactive and anticipatory behavior can be combined. This is the basic ground of our unified theory for anticipatory behavior architecture. We still miss such compact theory, which would integrate multiple aspects of anticipation. My multi-level anticipatory behavior approach is based on the current understanding of anticipation from both the artificial intelligence and biology point of view. As part of the explanation we will also elaborate on the topic of weak and strong artificial life. Anticipation is not matter of a single mechanism in a living organism. It was noted already that it happens on many different levels even in the very simple creatures. What we consider to be important for our work and what is our original though is that it happens even without voluntary control. We believe that this is novelty though for the anticipation theory. Naturally research of anticipation was in the beginning of this decade focused on the anticipatory principles bringing advances on the field itself. This allowed us to build on those, look at them from higher perspective, and use not one but multiple levels of anticipation in a creature design. This presents second original though and that is composition of the agent architecture that has anticipation built in almost every function. In this article we will focus only on first two levels within the 8-factor anticipation framework. We will introduce them as defined categories of anticipation and describe them from theory and implementation algorithm point of view. We will also present an experiment conducted, however this experiment serves more as explanatory example. These first two levels may seem trivial

  4. FETI Methods for the Simulation of Biological Tissues

    PubMed Central

    Augustin, Christoph; Steinbach, Olaf

    2016-01-01

    Summary In this paper we describe the application of finite element tearing and interconnecting methods for the simulation of biological tissues, as a particular application we consider the myocardium. As most other tissues, this material is characterized by anisotropic and nonlinear behavior. PMID:26925469

  5. Biology Students Building Computer Simulations Using StarLogo TNG

    ERIC Educational Resources Information Center

    Smith, V. Anne; Duncan, Ishbel

    2011-01-01

    Confidence is an important issue for biology students in handling computational concepts. This paper describes a practical in which honours-level bioscience students simulate complex animal behaviour using StarLogo TNG, a freely-available graphical programming environment. The practical consists of two sessions, the first of which guides students…

  6. The Introduction of Biological Mensuration Techniques Through Simulation.

    ERIC Educational Resources Information Center

    Spain, James D.

    New simulations for teaching quantitative biological techniques are now used at Michigan Technological University. Traditionally, such techniques work within a particular system and have the student assume certain initial conditions and employ appropriate constants. The computer generates time dependent data which are plotted. The student then…

  7. Environmental distribution and population biology of Candidatus Accumulibacter, a primary agent of biological phosphorus removal.

    PubMed

    Peterson, S Brook; Warnecke, Falk; Madejska, Julita; McMahon, Katherine D; Hugenholtz, Philip

    2008-10-01

    Members of the uncultured bacterial genus Candidatus Accumulibacter are capable of intracellular accumulation of inorganic phosphate in activated sludge wastewater treatment plants (WWTPs) performing enhanced biological phosphorus removal, but were also recently shown to inhabit freshwater and estuarine sediments. Additionally, metagenomic sequencing of two bioreactor cultures enriched in Candidatus Accumulibacter, but housed on separate continents, revealed the potential for global dispersal of particular Candidatus Accumulibacter strains, which we hypothesize is facilitated by the ability of Candidatus Accumulibacter to persist in environmental habitats. In the current study, we used sequencing of a phylogenetic marker, the ppk1 gene, to characterize Candidatus Accumulibacter populations in diverse environments, at varying distances from WWTPs. We discovered several new lineages of Candidatus Accumulibacter which had not previously been detected in WWTPs, and also uncovered new diversity and structure within previously detected lineages. Habitat characteristics were found to be a key determinant of Candidatus Accumulibacter lineage distribution while, as predicted, geographic distance played little role in limiting dispersal on a regional scale. However, on a local scale, enrichment of particular Candidatus Accumulibacter lineages in WWTP appeared to impact local environmental populations. These results provide evidence of ecological differences among Candidatus Accumulibacter lineages. PMID:18643843

  8. Biology, host specificity tests, and risk assessment of the sawfly Heteroperreyia hubrichi, a potential biological control agent of Schinus terebinthifolius in Hawaii

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Abstract. Heteroperreyia hubrichi Malaise (Hymenoptera: Pergidae), a foliage feeding sawfly of Schinus terebinthifolius Raddi (Sapindales: Anacardiaceae), was studied to assess its suitability as a classical biological control agent of this invasive weed in Hawaii. Nochoice host-specificity tests we...

  9. Advanced Algorithms for Rapidly Reconstructing Clandestine Releases of Biological Agents in Urban Areas

    SciTech Connect

    Shinn, J.H.; Hall, C.H.; Neher, L.A.; Wilder, F.J.; Gouveia, D.W.; Layton, D.W.; Daniels, J.I.

    2000-02-25

    As the United States plays a greater role in the 21st Century as global peacekeeper and international defender of human rights and democratic principles, there is an increasing likelihood that it will become the focus of acts of terrorism. Such acts of terrorism--sometimes described as ''asymmetric''--could involve the threat or use of weapons of mass destruction (WMD), particularly those considered unconventional, which include ones designed to release chemical or biological agents. In fact, biological agents are of great concern because, as noted by D.A. Henderson of the Center for Civilian Biodefense Studies at Johns Hopkins University in Baltimore, MD, ''... with shortages of hospital space, vaccines, antibiotics, there would be chaos.'' (Williams, 2000). Unfortunately, potential aggressor nations, terrorist groups, and even individuals, can, for a modest cost and effort, develop covert capabilities for manufacturing, transporting, and offensively using biological weapons of mass destruction. Furthermore, there is evidence to indicate that terrorist increasingly are targeting civilian populations--in order to inflict indiscriminate casualties--as well as other more traditional targets such as symbolic buildings or organizations (see Tucker, 1999), which suggest that introducing rapid treatment after a biological event may be more practical than concentrating on prevention (see Siegrist, 1999), especially because sensors are unlikely to be placed in all major urban areas to detect even an atmospheric biological release. For these reasons, and because symptoms for the majority of those effected may not occur or be directly identified for several days, early identification of a covert undetected biological event (CUBE) will contribute to timely medical intervention, which can save many lives.

  10. Modeling the transport of chemical warfare agents and simulants in polymeric substrates for reactive decontamination

    NASA Astrophysics Data System (ADS)

    Pearl, Thomas; Mantooth, Brent; Varady, Mark; Willis, Matthew

    2014-03-01

    Chemical warfare agent simulants are often used for environmental testing in place of highly toxic agents. This work sets the foundation for modeling decontamination of absorbing polymeric materials with the focus on determining relationships between agents and simulants. The correlations of agents to simulants must consider the three way interactions in the chemical-material-decontaminant system where transport and reaction occur in polymer materials. To this end, diffusion modeling of the subsurface transport of simulants and live chemical warfare agents was conducted for various polymer systems (e.g., paint coatings) with and without reaction pathways with applied decontamination. The models utilized 1D and 2D finite difference diffusion and reaction models to simulate absorption and reaction in the polymers, and subsequent flux of the chemicals out of the polymers. Experimental data including vapor flux measurements and dynamic contact angle measurements were used to determine model input parameters. Through modeling, an understanding of the relationship of simulant to live chemical warfare agent was established, focusing on vapor emission of agents and simulants from materials.

  11. Enhanced Sampling Techniques in Molecular Dynamics Simulations of Biological Systems

    PubMed Central

    Bernardi, Rafael C.; Melo, Marcelo C. R.; Schulten, Klaus

    2014-01-01

    Background Molecular Dynamics has emerged as an important research methodology covering systems to the level of millions of atoms. However, insufficient sampling often limits its application. The limitation is due to rough energy landscapes, with many local minima separated by high-energy barriers, which govern the biomolecular motion. Scope of review In the past few decades methods have been developed that address the sampling problem, such as replica-exchange molecular dynamics, metadynamics and simulated annealing. Here we present an overview over theses sampling methods in an attempt to shed light on which should be selected depending on the type of system property studied. Major Conclusions Enhanced sampling methods have been employed for a broad range of biological systems and the choice of a suitable method is connected to biological and physical characteristics of the system, in particular system size. While metadynamics and replica-exchange molecular dynamics are the most adopted sampling methods to study biomolecular dynamics, simulated annealing is well suited to characterize very flexible systems. The use of annealing methods for a long time was restricted to simulation of small proteins; however, a variant of the method, generalized simulated annealing, can be employed at a relatively low computational cost to large macromolecular complexes. General Significance Molecular dynamics trajectories frequently do not reach all relevant conformational substates, for example those connected with biological function, a problem that can be addressed by employing enhanced sampling algorithms. PMID:25450171

  12. An agent-based simulation of extirpation of Ceratitis capitata applied to invasions in California.

    PubMed

    Manoukis, Nicholas C; Hoffman, Kevin

    2014-01-01

    We present an agent-based simulation (ABS) of Ceratitis capitata ("Medfly") developed for estimating the time to extirpation of this pest in areas where quarantines and eradication treatments were immediately imposed. We use the ABS, implemented in the program MED-FOES, to study seven different outbreaks that occurred in Southern California from 2008 to 2010. Results are compared with the length of intervention and quarantine imposed by the State, based on a linear developmental model (thermal unit accumulation, or "degree-day"). MED-FOES is a useful tool for invasive species managers as it incorporates more information from the known biology of the Medfly, and includes the important feature of being demographically explicit, providing significant improvements over simple degree-day calculations. While there was general agreement between the length of quarantine by degree-day and the time to extirpation indicated by MED-FOES, the ABS suggests that the margin of safety varies among cases and that in two cases the quarantine may have been excessively long. We also examined changes in the number of individuals over time in MED-FOES and conducted a sensitivity analysis for one of the outbreaks to explore the role of various input parameters on simulation outcomes. While our implementation of the ABS in this work is motivated by C. capitata and takes extirpation as a postulate, the simulation is very flexible and can be used to study a variety of questions on the invasion biology of pest insects and methods proposed to manage or eradicate such species. PMID:24563646

  13. Assessment of disinfectants in explosive destruction system for biological agent destruction : LDRD final report FY04.

    SciTech Connect

    Simmons, Blake Alexander; Didlake, John E. Jr.; Bradshaw, Robert W.; Crooker, Paul J.; Buffleben, George M.

    2005-01-01

    Treatment systems that can neutralize biological agents are needed to mitigate risks from novel and legacy biohazards. Tests with Bacillus thuringiensis and Bacillus steurothemophilus spores were performed in a 190-liter, 1-112 lb TNT equivalent rated Explosive Destruction System (EDS) system to evaluate its capability to treat and destroy biological agents. Five tests were conducted using three different agents to kill the spores. The EDS was operated in steam autoclave, gas fumigation and liquid decontamination modes. The first three tests used EDS as an autoclave, which uses pressurized steam to kill the spores. Autoclaving was performed at 130-140 deg C for up to 2-hours. Tests with chlorine dioxide at 750 ppm concentration for 1 hour and 10% (vol) aqueous chlorine bleach solution for 1 hour were also performed. All tests resulted in complete neutralization of the bacterial spores based on no bacterial growth in post-treatment incubations. Explosively opening a glass container to expose the bacterial spores for treatment with steam was demonstrated and could easily be done for chlorine dioxide gas or liquid bleach.

  14. Fingerprinting malathion vapor: a simulant for VX nerve agent

    NASA Astrophysics Data System (ADS)

    Song, Renbo; Ding, Yujie J.; Zotova, Ioulia B.

    2008-04-01

    Being motivated by the possibility of fingerprinting and detecting VX nerve agent, we have investigated its stimulant, i.e. malathion vapor, which is less toxic and commercially available, in the far-infrared/THz transition region and THz frequency range. Such a spectroscopic study was carried out by using Fourier transform infrared spectroscopy (FTIR). Our intention is to obtain a specific spectroscopic signature of VX nerve agent as a chemical warfare agent. Following our experimental result, we have successfully observed eleven new absorption peaks from malathion vapor in the spectral ranges from 15 cm -1 to 68 cm -1 and from 75 cm -1 to 640 cm -1. Specifically, in the far-infrared/THz transition region, we have observed eight peaks and whereas in the THz region we have identified three relatively weak transition peaks. In addition, we have investigated the dependence of the absorption spectra on temperature in the range from room temperature to 60°C. In both of the frequency ranges, we have found that absorption coefficients significantly increase with increasing temperature. By comparing the transition peaks in the two frequency ranges, we have concluded that the frequency range of 400-640cm -1 is an optimal range for fingerprinting this chemical specie. We have designated two peaks for effectively and accurately identifying the VX nerve agents and one peak for differentiating between malathion and VX nerve agent.

  15. Differential detection of a surrogate biological threat agent (Bacillus globigii) with a portable surface plasmon resonance biosensor.

    PubMed

    Adducci, Benjamin A; Gruszewski, Hope A; Khatibi, Piyum A; Schmale, David G

    2016-04-15

    New methods and technology are needed to quickly and accurately detect potential biological warfare agents, such as Bacillus anthracis, causal agent of anthrax in humans and animals. Here, we report the detection of a simulant of B. anthracis (B. globigii) alone and in a mixture with a different species of Bacillus to test non-specific interference using a portable surface plasmon resonance (SPR) biosensor (SPIRIT 4.0, Seattle Sensor Systems). Both direct capture and antibody amplification were used to determine the limit of detection for spores of B. globigii, and to detect spores of B. globigii in a mixed sample containing another Bacillus spp. Spores of B. globigii were detected by anti-B. globigii (anti-Bg) coated sensors by direct capture at a concentration of 10(7)spores/mL, and with a secondary antibody amplification at a concentration of 10(5)spores/mL. Spores of B. globigii were differentially detected in a 1:1 mixture with B. pumilus spores from equal concentrations (10(7)spores/mL) with a secondary antibody amplification. To our knowledge, this is the first report of the differential detection of B. globigii with SPR in a mixed sample containing at least one additional Bacillus spp., highlighting the potential for SPR to detect any target bacterium in a mixed sample of closely related species. With the availability of portable instrumentation to accurately detect biological warfare agents such as B. anthracis, emergency responders can implement protocols in a timely fashion, limiting the amount of exposed individuals. PMID:26606307

  16. Biologic agents for rheumatoid arthritis--negotiating the NICE technology appraisals.

    PubMed

    Kiely, Patrick D W; Deighton, Chris; Dixey, Josh; Ostör, Andrew J K

    2012-01-01

    In England and Wales, the National Institute for Health and Clinical Excellence (NICE) has provided guidance [technology appraisals (TAs) 130, 186, 195, 198 and 225] on the use of biologic drugs for the treatment of RA. This is based on an analysis of efficacy, safety and cost-effectiveness, and has resulted in a complex management pathway that restricts freedom to prescribe biologics according to their licensed indications. Specifically, TNF antagonists are the only class of biologics that can be used first line in DMARD-inadequate responders, and only in patients with a persistent 28-joint DAS score of ≥5.1. Alternative biologic agents are denied to those with contraindications to anti-TNF drugs and are also not supported following intolerance to TNF antagonists. Rituximab is the only class of biologic permitted after TNF antagonist inefficacy, in the absence of a contraindication to its use, whereas abatacept and tocilizumab are licensed and may be a more efficacious choice at this stage in some patient groups. Furthermore, for patients who demonstrate sequential inadequate responses, treatment is restricted to one TNF antagonist, rituximab and tocilizumab, whereas abatacept is only a permitted choice when rituximab is contraindicated or has been withdrawn because of an adverse event. In this review, we discuss the treatment algorithm published by NICE, and suggest alternatives where perceived deficiencies exist. PMID:22039226

  17. A Participatory Agent-Based Simulation for Indoor Evacuation Supported by Google Glass.

    PubMed

    Sánchez, Jesús M; Carrera, Álvaro; Iglesias, Carlos Á; Serrano, Emilio

    2016-01-01

    Indoor evacuation systems are needed for rescue and safety management. One of the challenges is to provide users with personalized evacuation routes in real time. To this end, this project aims at exploring the possibilities of Google Glass technology for participatory multiagent indoor evacuation simulations. Participatory multiagent simulation combines scenario-guided agents and humans equipped with Google Glass that coexist in a shared virtual space and jointly perform simulations. The paper proposes an architecture for participatory multiagent simulation in order to combine devices (Google Glass and/or smartphones) with an agent-based social simulator and indoor tracking services. PMID:27563911

  18. Decontamination of biological agents from drinking water infrastructure: a literature review and summary.

    PubMed

    Szabo, Jeff; Minamyer, Scott

    2014-11-01

    This report summarizes the current state of knowledge on the persistence of biological agents on drinking water infrastructure (such as pipes) along with information on decontamination should persistence occur. Decontamination options for drinking water infrastructure have been explored for some biological agents, but data gaps remain. Data on bacterial spore persistence on common water infrastructure materials such as iron and cement-mortar lined iron show that spores can be persistent for weeks after contamination. Decontamination data show that common disinfectants such as free chlorine have limited effectiveness. Decontamination results with germinant and alternate disinfectants such as chlorine dioxide are more promising. Persistence and decontamination data were collected on vegetative bacteria, such as coliforms, Legionella and Salmonella. Vegetative bacteria are less persistent than spores and more susceptible to disinfection, but the surfaces and water quality conditions in many studies were only marginally related to drinking water systems. However, results of real-world case studies on accidental contamination of water systems with E. coli and Salmonella contamination show that flushing and chlorination can help return a water system to service. Some viral persistence data were found, but decontamination data were lacking. Future research suggestions focus on expanding the available biological persistence data to other common infrastructure materials. Further exploration of non-traditional drinking water disinfectants is recommended for future studies. PMID:24548733

  19. Prospects for the use of biological control agents against Anoplophora in Europe.

    PubMed

    Brabbs, Thomas; Collins, Debbie; Hérard, Franck; Maspero, Matteo; Eyre, Dominic

    2015-01-01

    This review summarises the literature on the biological control of Anoplophora spp. (Coleoptera: Cerambycidae) and discusses its potential for use in Europe. Entomopathogenic fungi: Beauveria brongniartii Petch (Hypocreales: Cordycipitaceae) has already been developed into a commercial product in Japan, and fungal infection results in high mortality rates. Parasitic nematodes: Steinernema feltiae Filipjev (Rhabditida: Steinernematidae) and Steinernema carpocapsae Weiser have potential for use as biopesticides as an alternative to chemical treatments. Parasitoids: a parasitoid of Anoplophora chinensis Forster, Aprostocetus anoplophorae Delvare (Hymenoptera: Eulophidae), was discovered in Italy in 2002 and has been shown to be capable of parasitising up to 72% of A. chinensis eggs; some native European parasitoid species (e.g. Spathius erythrocephalus) also have potential to be used as biological control agents. Predators: two woodpecker (Piciformis: Picidae) species that are native to Europe, Dendrocopos major Beicki and Picus canus Gmelin, have been shown to be effective at controlling Anoplophora glabripennis Motschulsky in Chinese forests. The removal and destruction of infested and potentially infested trees is the main eradication strategy for Anoplophora spp. in Europe, but biological control agents could be used in the future to complement other management strategies, especially in locations where eradication is no longer possible. PMID:25216358

  20. Applying GIS and high performance agent-based simulation for managing an Old World Screwworm fly invasion of Australia.

    PubMed

    Welch, M C; Kwan, P W; Sajeev, A S M

    2014-10-01

    Agent-based modelling has proven to be a promising approach for developing rich simulations for complex phenomena that provide decision support functions across a broad range of areas including biological, social and agricultural sciences. This paper demonstrates how high performance computing technologies, namely General-Purpose Computing on Graphics Processing Units (GPGPU), and commercial Geographic Information Systems (GIS) can be applied to develop a national scale, agent-based simulation of an incursion of Old World Screwworm fly (OWS fly) into the Australian mainland. The development of this simulation model leverages the combination of massively data-parallel processing capabilities supported by NVidia's Compute Unified Device Architecture (CUDA) and the advanced spatial visualisation capabilities of GIS. These technologies have enabled the implementation of an individual-based, stochastic lifecycle and dispersal algorithm for the OWS fly invasion. The simulation model draws upon a wide range of biological data as input to stochastically determine the reproduction and survival of the OWS fly through the different stages of its lifecycle and dispersal of gravid females. Through this model, a highly efficient computational platform has been developed for studying the effectiveness of control and mitigation strategies and their associated economic impact on livestock industries can be materialised. PMID:24705073

  1. Responses of fish chromatophore-based cytosensor to a broad range of biological agents.

    PubMed

    Dierksen, Karen P; Mojovic, Ljiljana; Caldwell, Bruce A; Preston, R Ryan; Upson, Rosalyn; Lawrence, Jeannine; McFadden, Philip N; Trempy, Janine E

    2004-01-01

    A cytosensor based on living chromatophores from Betta splendens Siamese fighting fish was used to test several classes of biologically active agents. Tested agents include neurotransmitters, adenyl cyclase activators, cytoskeleton effectors, cell membrane effectors and protein synthesis inhibitors. Characteristic cell responses were analyzed, and potential cytosensor applications were considered. Streptococcus pyogenes toxins streptolysin S and streptolysin O, Clostridium tetani tetanolysin, Staphylococcus aureus alpha-toxin and Vibrio parahemolyticus hemolysin, all bacterial toxins that act on cell membranes, elicited a strong response from chromatophores. A comparison of purified toxin to actual bacterial culture from Vibrio parahemolyticus demonstrated a nearly identical chromatophore cell response pattern. This suggests that the cytosensor response is reflective of bacterial toxin production. PMID:15478182

  2. Design, synthesis, and biological evaluation of anti-EV71 agents.

    PubMed

    Li, Peng; Yang, Bailing; Hao, Fei; Wang, Ping; He, Haiying; Huang, Lei; Zhang, Xuan; Zhang, Shengbin; Peng, Xuanjia; Yin, Ke; Hu, Jiao; Chen, Xinsheng; Gu, Zhengxian; Wang, Li; Shen, Liang; Hu, Guoping; Li, Ning; Li, Jian; Chen, Shuhui; Xiao, Wei; Wang, Zhenzhong; Guo, Qingming; Chang, Xiujuan; Zhang, Lanjun; Cai, Qixu; Lin, Tianwei

    2016-07-15

    Enterovirus 71 (EV71) is a major causative agent of hand, foot and mouth disease (HFMD), which can spread its infections to the central nervous and other systems with severe consequences. In this article, design, chemical synthesis, and biological evaluation of various anti-EV71 agents which incorporate Michael acceptors are described. Further SAR study demonstrated that lactone type of Michael acceptor provided a new lead of anti-EV71 drug candidates with high anti-EV71 activity in cell-based assay and enhanced mouse plasma stability. One of the most potent compounds (2K, cell-based anti-EV71 EC50=0.028μM), showed acceptable stability profile towards mouse plasma, which resulted into promising pharmacokinetics in mouse via IP administration. PMID:27234148

  3. Opportunities for improving risk communication during the permitting process for entomophagous biological control agents: A review of current systems

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Concerns about potentially irreversible non-target impacts from the importation and release of entomophagous biological control agents (BCAs) have resulted in increasingly stringent import requirements by National Plant Protection Organizations. Despite numerous scientific publications on the poten...

  4. Host plant oviposition preference of Ceratapion basicorne (Coleoptera:Apionidae), a potential biological control agent of yellow starthistle

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Ceratapion basicorne (Coleoptera: Apionidae) is a weevil native to Europe and western Asia that is being evaluated as a prospective classical biological control agent of Centaurea solstitialis (yellow starthistle) in the United States. Choice oviposition experiments were conducted under laboratory ...

  5. Natural history studies for the preliminary evaluation of a prospective biological control agent of yellow starthistle, Larinus filiformis (Coleoptera: Curculionidae).

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We conducted studies on the life history, behavior and ecology of Larinus filiformis (Coleoptera: Curculionidae) to determine if it is worthy of further evaluation as a classical biological control agent of yellow starthistle, Centaurea solstitialis (Asteraceae: Cardueae). Larinus filiformis occurs ...

  6. Viability and stability of biological control agents on cotton and snap bean seeds.

    PubMed

    Elliott, M L; Des Jardin, E A; Batson, W E; Caceres, J; Brannen, P M; Howell, C R; Benson, D M; Conway, K E; Rothrock, C S; Schneider, R W; Ownley, B H; Canaday, C H; Keinath, A P; Huber, D M; Sumner, D R; Motsenbocker, C E; Thaxton, P M; Cubeta, M A; Adams, P D; Backman, P A; Fajardo, J; Newman, M A; Pereira, R M

    2001-08-01

    Cotton and snap bean were selected for a multi-year, multi-state regional (south-eastern USA) research project to evaluate the efficacy of both commercial and experimental bacterial and fungal biological control agents for the management of damping-off diseases. The goal for this portion of the project was to determine the viability and stability of biological agents after application to seed. The biological seed treatments used included: (1) Bacillaceae bacteria, (2) non-Bacillaceae bacteria, (3) the fungus Trichoderma and (4) the fungus Beauveria bassiana. Seed assays were conducted to evaluate the following application factors: short-term (< or = 3 months) stability after seed treatment; quality (i.e. isolate purity); compatibility with chemical pesticides and other biocontrol agents; application uniformity between years and plant species. For the bacterial treatments, the Bacillaceae genera (Bacillus and Paenibacillus) maintained the greatest population of bacteria per seed, the best viability over time and the best application uniformity across years and seed type. The non-Bacillaceae genera Burkholderia and Pseudomonas had the least viability and uniformity. Although Beauveria bassiana was only evaluated one year, the seed fungal populations were high and uniform. The seed fungal populations and uniformity for the Trichoderma isolates were more variable, except for the commercial product T-22. However, this product was contaminated with a Streptomyces isolate in both the years that it was evaluated. The study demonstrated that Bacillaceae can be mixed with Trichoderma isolates or with numerous pesticides to provide an integrated pest control/growth enhancement package. PMID:11517723

  7. Biological agents: investigation into leprosy and other infectious diseases before indication*

    PubMed Central

    Antônio, João Roberto; Soubhia, Rosa Maria Cordeiro; Paschoal, Vania Del Arco; Amarante, Carolina Forte; Travolo, Ana Regina Franchi

    2013-01-01

    Biological agents are widely used for various immune-mediated diseases, with remarkable effectiveness in the treatment of rheumatoid arthritis (RA), psoriasis, psoriatic arthritis, ankylosing spondylitis and Crohn's disease. However, attention needs to be drawn to the adverse effects of these therapies and the risk of reactivating underlying granulomatous infectious diseases such as tuberculosis, leprosy, syphilis, leishmaniasis, among others. The objective of this paper is to describe a case of leprosy in a patient with RA using anti-TNF alfa, demonstrating the need for systematic investigation of skin lesions suggestive of leprosy in patients who require rheumatoid arthritis therapeutic treatment, especially in endemic regions like Brazil. PMID:24346871

  8. Biological agents: investigation into leprosy and other infectious diseases before indication.

    PubMed

    Antônio, João Roberto; Soubhia, Rosa Maria Cordeiro; Paschoal, Vania Del Arco; Amarante, Carolina Forte; Travolo, Ana Regina Franchi

    2013-01-01

    Biological agents are widely used for various immune-mediated diseases, with remarkable effectiveness in the treatment of rheumatoid arthritis (RA), psoriasis, psoriatic arthritis, ankylosing spondylitis and Crohn's disease. However, attention needs to be drawn to the adverse effects of these therapies and the risk of reactivating underlying granulomatous infectious diseases such as tuberculosis, leprosy, syphilis, leishmaniasis, among others. The objective of this paper is to describe a case of leprosy in a patient with RA using anti-TNF alfa, demonstrating the need for systematic investigation of skin lesions suggestive of leprosy in patients who require rheumatoid arthritis therapeutic treatment, especially in endemic regions like Brazil. PMID:24346871

  9. LANL organic analysis detection capabilities for chemical and biological warfare agents

    SciTech Connect

    Ansell, G.B.; Cournoyer, M.E.; Hollis, K.W.; Monagle, M.

    1996-12-31

    Organic analysis is the analytical arm for several Los Alamos National Laboratory (LANL) research programs and nuclear materials processes, including characterization and certification of nuclear and nonnuclear materials used in weapons, radioactive waste treatment and waste certification programs. Organic Analysis has an extensive repertoire of analytical technique within the group including headspace gas, PCBs/pesticides, volatile organics and semivolatile organic analysis. In addition organic analysis has mobile labs with analytic capabilities that include volatile organics, total petroleum hydrocarbon, PCBs, pesticides, polyaromatic hydrocarbons and high explosive screening. A natural extension of these capabilities can be applied to the detection of chemical and biological agents,

  10. Synthesis, analysis and biological evaluation of novel indolquinonecryptolepine analogues as potential anti-tumour agents.

    PubMed

    Le Gresley, A; Gudivaka, V; Carrington, S; Sinclair, A; Brown, J E

    2016-03-21

    A small library of cryptolepine analogues were synthesised incorporating halogens and/or nitrogen containing side chains to optimise their interaction with the sugar-phosphate backbone of DNA to give improved binding, interfering with topoisomerase II hence enhancing cytotoxicity. Cell viability, DNA binding and Topoisomerase II inhibition is discussed for these compounds. Fluorescence microscopy was used to investigate the uptake of the synthesised cryptolepines into the nucleus. We report the synthesis and anti-cancer biological evaluation of nine novel cryptolepine analogues, which have greater cytotoxicity than the parent compound and are important lead compounds in the development of novel potent and selective indoloquinone anti-neoplastic agents. PMID:26893255