Science.gov

Sample records for cross-species platform optimizing

  1. Optimal platform strength in the presence of moving ice

    SciTech Connect

    Enns, E.G.; Smith, B.R.

    1984-01-01

    The design of a moveable platform which is to operate in an environment which includes moving ice depends on a number of ice dependent variables. The optimal strength based on minimum cost objectives is obtained and illustrated by an example.

  2. Cross-species transmission of CWD prions.

    PubMed

    Kurt, Timothy D; Sigurdson, Christina J

    2016-01-01

    Prions cause fatal neurodegenerative diseases in humans and animals and can be transmitted zoonotically. Chronic wasting disease (CWD) is a highly transmissible prion disease of wild deer and elk that affects cervids over extensive regions of the United States and Canada. The risk of cross-species CWD transmission has been experimentally evaluated in a wide array of mammals, including non-human primates and mouse models expressing human cellular prion protein. Here we review the determinants of cross-species CWD transmission, and propose a model that may explain a structural barrier for CWD transmission to humans.

  3. REopt: A Platform for Energy System Integration and Optimization: Preprint

    SciTech Connect

    Simpkins, T.; Cutler, D.; Anderson, K.; Olis, D.; Elgqvist, E.; Callahan, M.; Walker, A.

    2014-08-01

    REopt is NREL's energy planning platform offering concurrent, multi-technology integration and optimization capabilities to help clients meet their cost savings and energy performance goals. The REopt platform provides techno-economic decision-support analysis throughout the energy planning process, from agency-level screening and macro planning to project development to energy asset operation. REopt employs an integrated approach to optimizing a site?s energy costs by considering electricity and thermal consumption, resource availability, complex tariff structures including time-of-use, demand and sell-back rates, incentives, net-metering, and interconnection limits. Formulated as a mixed integer linear program, REopt recommends an optimally-sized mix of conventional and renewable energy, and energy storage technologies; estimates the net present value associated with implementing those technologies; and provides the cost-optimal dispatch strategy for operating them at maximum economic efficiency. The REopt platform can be customized to address a variety of energy optimization scenarios including policy, microgrid, and operational energy applications. This paper presents the REopt techno-economic model along with two examples of recently completed analysis projects.

  4. OPTIMED Platform: Curriculum Harmonisation System for Medical and Healthcare Education.

    PubMed

    Komenda, Martin; Schwarz, Daniel; Vaitsis, Christos; Zary, Nabil; Štěrba, Jaroslav; Dušek, Ladislav

    2015-01-01

    This contribution introduces a new web-based OPTIMED platform for an effective harmonisation of medical and healthcare curriculum. Behind the engineering background stays an original methodology covering planning model based on formal parameterisation of curriculum, which fully support the outcome-based approach to education. With the use of developed system curriculum, designers and senior guarantors can provide a clear and transparent composition of compulsory and optional courses, and easily identify potential duplicities and overlaps across a domain of medical and healthcare education. For students, it means an absolutely new way of how to understand what is really taught during a learning period, including all necessary meta information. All members across the academic community are able to search and consequently display in detail the most important domains related to the particular year, term, course, medical discipline or topic. The presented solution significantly enhances the transparency and continuity of the environment in which the authors of the teaching materials as well as their consumers work daily. Suggestions for future improvements of the OPTIMED platform are discussed.

  5. Optimization of image processing algorithms on mobile platforms

    NASA Astrophysics Data System (ADS)

    Poudel, Pramod; Shirvaikar, Mukul

    2011-03-01

    This work presents a technique to optimize popular image processing algorithms on mobile platforms such as cell phones, net-books and personal digital assistants (PDAs). The increasing demand for video applications like context-aware computing on mobile embedded systems requires the use of computationally intensive image processing algorithms. The system engineer has a mandate to optimize them so as to meet real-time deadlines. A methodology to take advantage of the asymmetric dual-core processor, which includes an ARM and a DSP core supported by shared memory, is presented with implementation details. The target platform chosen is the popular OMAP 3530 processor for embedded media systems. It has an asymmetric dual-core architecture with an ARM Cortex-A8 and a TMS320C64x Digital Signal Processor (DSP). The development platform was the BeagleBoard with 256 MB of NAND RAM and 256 MB SDRAM memory. The basic image correlation algorithm is chosen for benchmarking as it finds widespread application for various template matching tasks such as face-recognition. The basic algorithm prototypes conform to OpenCV, a popular computer vision library. OpenCV algorithms can be easily ported to the ARM core which runs a popular operating system such as Linux or Windows CE. However, the DSP is architecturally more efficient at handling DFT algorithms. The algorithms are tested on a variety of images and performance results are presented measuring the speedup obtained due to dual-core implementation. A major advantage of this approach is that it allows the ARM processor to perform important real-time tasks, while the DSP addresses performance-hungry algorithms.

  6. Natural frequency of uniform and optimized tetrahedral truss platforms

    NASA Technical Reports Server (NTRS)

    Wu, K. Chauncey; Lake, Mark S.

    1994-01-01

    Qualitative and quantitative estimates for the fundamental frequency of uniform and optimized tetrahedral truss platforms are determined. A semiempirical equation is developed for the frequency of free-free uniform trusses as a function of member material properties, truss dimensions, and parasitic (nonstructural) mass fraction Mp/Mt. Optimized trusses with frequencies approximately two times those of uniform trusses are determined by varying the cross-sectional areas of member groups. Trusses with 3 to 8 rings, no parasitic mass, and member areas up to 25 times the minimum area are optimized. Frequencies computed for ranges of both Mp/Mt and the ratio of maximum area to minimum area are normalized to the frequency of a uniform truss with no parasitic mass. The normalized frequency increases with the number of rings, and both frequency and the ratio of maximum area to minimum area decrease with increasing Mp/Mt. Frequency improvements that are achievable with a limited number of member areas are estimated for a 3-ring truss by using Taguchi methods. Joint stiffness knockdown effects are also considered. Comparison of optimized and baseline uniform truss frequencies indicates that tailoring can significantly increase structural frequency; maximum gains occur for trusses with low values of Mp/Mt. This study examines frequency trends for ranges of structural parameters and may be used as a preliminary design guide.

  7. Lattice Boltzmann Simulation Optimization on Leading Multicore Platforms

    SciTech Connect

    Williams, Samuel; Carter, Jonathan; Oliker, Leonid; Shalf, John; Yelick, Katherine

    2008-02-01

    We present an auto-tuning approach to optimize application performance on emerging multicore architectures. The methodology extends the idea of search-based performance optimizations, popular in linear algebra and FFT libraries, to application-specific computational kernels. Our work applies this strategy to a lattice Boltzmann application (LBMHD) that historically has made poor use of scalar microprocessors due to its complex data structures and memory access patterns. We explore one of the broadest sets of multicore architectures in the HPC literature, including the Intel Clovertown, AMD Opteron X2, Sun Niagara2, STI Cell, as well as the single core Intel Itanium2. Rather than hand-tuning LBMHD for each system, we develop a code generator that allows us identify a highly optimized version for each platform, while amortizing the human programming effort. Results show that our auto-tuned LBMHD application achieves up to a 14x improvement compared with the original code. Additionally, we present detailed analysis of each optimization, which reveal surprising hardware bottlenecks and software challenges for future multicore systems and applications.

  8. Cross- species communication in bacterial world.

    PubMed

    Majumdar, Sarangam; Pal, Sukla

    2017-02-20

    Biofilms are the compact association of micro organisms and the communication processes in these biofilms are always a wonder. Electrical and chemical signaling mechanism are the key to understand the bacterial communication network. Quorum sensing so far has been able to explain the coordinated motion of bacteria through its chemical signaling mechanism. Bacteria residing within biofilm communities are trivial to communicate. But the recent observation in 2017 by Humphries et al. has revealed that the ion channels enabled electrical signaling mechanism can be as powerful as to attract the distant cells i.e., this signaling mechanism are capable of holding a long range behavior. As a result long range cross species communication in the bacterial world have been possible. This substantial outcome has brought this field into a new paradigm to investigate the complex co-existence of biofilm communities and distant cells with a possible scope of application in synthetic biology. In this present article, we briefly describe this new signaling mechanism and how it gives rise to a long range communication ability in bacterial communities.

  9. Platform-dependent optimization considerations for mHealth applications

    NASA Astrophysics Data System (ADS)

    Kaghyan, Sahak; Akopian, David; Sarukhanyan, Hakob

    2015-03-01

    Modern mobile devices contain integrated sensors that enable multitude of applications in such fields as mobile health (mHealth), entertainment, sports, etc. Human physical activity monitoring is one of such the emerging applications. There exists a range of challenges that relate to activity monitoring tasks, and, particularly, exploiting optimal solutions and architectures for respective mobile software application development. This work addresses mobile computations related to integrated inertial sensors for activity monitoring, such as accelerometers, gyroscopes, integrated global positioning system (GPS) and WLAN-based positioning, that can be used for activity monitoring. Some of the aspects will be discussed in this paper. Each of the sensing data sources has its own characteristics such as specific data formats, data rates, signal acquisition durations etc., and these specifications affect energy consumption. Energy consumption significantly varies as sensor data acquisition is followed by data analysis including various transformations and signal processing algorithms. This paper will address several aspects of more optimal activity monitoring implementations exploiting state-of-the-art capabilities of modern platforms.

  10. Energy efficiency analysis and optimization for mobile platforms

    NASA Astrophysics Data System (ADS)

    Metri, Grace Camille

    The introduction of mobile devices changed the landscape of computing. Gradually, these devices are replacing traditional personal computer (PCs) to become the devices of choice for entertainment, connectivity, and productivity. There are currently at least 45.5 million people in the United States who own a mobile device, and that number is expected to increase to 1.5 billion by 2015. Users of mobile devices expect and mandate that their mobile devices have maximized performance while consuming minimal possible power. However, due to the battery size constraints, the amount of energy stored in these devices is limited and is only growing by 5% annually. As a result, we focused in this dissertation on energy efficiency analysis and optimization for mobile platforms. We specifically developed SoftPowerMon, a tool that can power profile Android platforms in order to expose the power consumption behavior of the CPU. We also performed an extensive set of case studies in order to determine energy inefficiencies of mobile applications. Through our case studies, we were able to propose optimization techniques in order to increase the energy efficiency of mobile devices and proposed guidelines for energy-efficient application development. In addition, we developed BatteryExtender, an adaptive user-guided tool for power management of mobile devices. The tool enables users to extend battery life on demand for a specific duration until a particular task is completed. Moreover, we examined the power consumption of System-on-Chips (SoCs) and observed the impact on the energy efficiency in the event of offloading tasks from the CPU to the specialized custom engines. Based on our case studies, we were able to demonstrate that current software-based power profiling techniques for SoCs can have an error rate close to 12%, which needs to be addressed in order to be able to optimize the energy consumption of the SoC. Finally, we summarize our contributions and outline possible

  11. "Clickable", polymerized liposomes as a versatile and stable platform for rapid optimization of their peripheral compositions.

    PubMed

    Kumar, Amit; Erasquin, Uriel J; Qin, Guoting; Li, King; Cai, Chengzhi

    2010-08-21

    A versatile and stable liposomal platform is developed for rapid optimization of its peripheral composition. The platform is based on polydiacetylene lipids terminated with alkynyl groups. Conditions for copper-catalyzed azide-alkyne cycloaddition (a "click" reaction) are optimized for rapid attachment of azides with controlled composition onto the liposomes.

  12. GENOMIC APPROACHES FOR CROSS-SPECIES EXTRAPOLATION IN TOXICOLOGY

    EPA Science Inventory

    The latest tools for investigating stress in organisms, genomic technologies provide great insight into how different organisms respond to environmental conditions. However, their usefulness needs testing, verification, and codification. Genomic Approaches for Cross-Species Extra...

  13. Optimizing Flight Control Software With an Application Platform

    NASA Technical Reports Server (NTRS)

    Smith, Irene Skupniewicz; Shi, Nija; Webster, Christopher

    2012-01-01

    Flight controllers in NASA s mission control centers work day and night to ensure that missions succeed and crews are safe. The IT goals of NASA mission control centers are similar to those of most businesses: to evolve IT infrastructure from basic to dynamic. This paper describes Mission Control Technologies (MCT), an application platform that is powering mission control today and is designed to meet the needs of future NASA control centers. MCT is an extensible platform that provides GUI components and a runtime environment. The platform enables NASA s IT goals through its use of lightweight interfaces and configurable components, which promote standardization and incorporate useful solution patterns. The MCT architecture positions mission control centers to reach the goal of dynamic IT, leading to lower cost of ownership, and treating software as a strategic investment.

  14. The Platform Switching Approach to Optimize Split Crest Technique

    PubMed Central

    Sammartino, G.; Cerone, V.; Gasparro, R.; Riccitiello, F.; Trosino, O.

    2014-01-01

    The split crest technique is a reliable procedure used simultaneously in the implant positioning. In the literature some authors describe a secondary bone resorption as postoperative complication. The authors show how platform switching can be able to avoid secondary resorption as complication of split crest technique. PMID:25165586

  15. Selecting Observation Platforms for Optimized Anomaly Detectability under Unreliable Partial Observations

    SciTech Connect

    Wen-Chiao Lin; Humberto E. Garcia; Tae-Sic Yoo

    2011-06-01

    Diagnosers for keeping track on the occurrences of special events in the framework of unreliable partially observed discrete-event dynamical systems were developed in previous work. This paper considers observation platforms consisting of sensors that provide partial and unreliable observations and of diagnosers that analyze them. Diagnosers in observation platforms typically perform better as sensors providing the observations become more costly or increase in number. This paper proposes a methodology for finding an observation platform that achieves an optimal balance between cost and performance, while satisfying given observability requirements and constraints. Since this problem is generally computational hard in the framework considered, an observation platform optimization algorithm is utilized that uses two greedy heuristics, one myopic and another based on projected performances. These heuristics are sequentially executed in order to find best observation platforms. The developed algorithm is then applied to an observation platform optimization problem for a multi-unit-operation system. Results show that improved observation platforms can be found that may significantly reduce the observation platform cost but still yield acceptable performance for correctly inferring the occurrences of special events.

  16. Traffic Patrol Service Platform Scheduling and Containment Optimization Strategy

    NASA Astrophysics Data System (ADS)

    Wang, Tiane; Niu, Taiyang; Wan, Baocheng; Li, Jian

    This article is based on the traffic and patrol police service platform settings and scheduling, in order to achieve the main purpose of rapid containment for the suspect in an emergency event. Proposing new boundary definition based on graph theory, using 0-1 programming, Dijkstra algorithm, the shortest path tree (SPT) and some of the related knowledge establish a containment model. Finally, making a combination with a city-specific data and using this model obtain the best containment plan.

  17. Towards bipedal behavior on a quadrupedal platform using optimal control

    NASA Astrophysics Data System (ADS)

    Topping, T. Turner; Vasilopoulos, Vasileios; De, Avik; Koditschek, Daniel E.

    2016-05-01

    This paper explores the applicability of a Linear Quadratic Regulator (LQR) controller design to the problem of bipedal stance on the Minitaur [1] quadrupedal robot. Restricted to the sagittal plane, this behavior exposes a three degree of freedom (DOF) double inverted pendulum with extensible length that can be projected onto the familiar underactuated revolute-revolute "Acrobot" model by assuming a locked prismatic DOF, and a pinned toe. While previous work has documented the successful use of local LQR control to stabilize a physical Acrobot, simulations reveal that a design very similar to those discussed in the past literature cannot achieve an empirically viable controller for our physical plant. Experiments with a series of increasingly close physical facsimiles leading to the actual Minitaur platform itself corroborate and underscore the physical Minitaur platform corroborate and underscore the implications of the simulation study. We conclude that local LQR-based linearized controller designs are too fragile to stabilize the physical Minitaur platform around its vertically erect equilibrium and end with a brief assessment of a variety of more sophisticated nonlinear control approaches whose pursuit is now in progress.

  18. Contingency Contractor Optimization Phase 3 Sustainment Platform Requirements - Contingency Contractor Optimization Tool - Prototype

    SciTech Connect

    Durfee, Justin David; Frazier, Christopher Rawls; Bandlow, Alisa; Gearhart, Jared Lee; Jones, Katherine A.

    2016-06-01

    Sandia National Laboratories (Sandia) is in Phase 3 Sustainment of development of a prototype tool, currently referred to as the Contingency Contractor Optimization Tool - Prototype (CCOTP), under the direction of OSD Program Support. CCOT-P is intended to help provide senior Department of Defense (DoD) leaders with comprehensive insight into the global availability, readiness and capabilities of the Total Force Mix. The CCOT-P will allow senior decision makers to quickly and accurately assess the impacts, risks and mitigating strategies for proposed changes to force/capabilities assignments, apportionments and allocations options, focusing specifically on contingency contractor planning. During Phase 2 of the program, conducted during fiscal year 2012, Sandia developed an electronic storyboard prototype of the Contingency Contractor Optimization Tool that can be used for communication with senior decision makers and other Operational Contract Support (OCS) stakeholders. Phase 3 used feedback from demonstrations of the electronic storyboard prototype to develop an engineering prototype for planners to evaluate. Sandia worked with the DoD and Joint Chiefs of Staff strategic planning community to get feedback and input to ensure that the engineering prototype was developed to closely align with future planning needs. The intended deployment environment was also a key consideration as this prototype was developed. Initial release of the engineering prototype was done on servers at Sandia in the middle of Phase 3. In 2013, the tool was installed on a production pilot server managed by the OUSD(AT&L) eBusiness Center. The purpose of this document is to specify the CCOT-P engineering prototype platform requirements as of May 2016. Sandia developed the CCOT-P engineering prototype using common technologies to minimize the likelihood of deployment issues. CCOT-P engineering prototype was architected and designed to be as independent as possible of the major deployment

  19. MULTIPLE SOLVENT EXPOSURE IN HUMANS: CROSS-SPECIES EXTRAPOLATIONS

    EPA Science Inventory

    Multiple Solvent Exposures in Humans:
    Cross-Species Extrapolations
    (Future Research Plan)

    Vernon A. Benignus1, Philip J. Bushnell2 and William K. Boyes2

    A few solvents can be safely studied in acute experiments in human subjects. Data exist in rats f...

  20. CROSS-SPECIES DOSE EXTRAPOLATION FOR DIESEL EMISSIONS

    EPA Science Inventory

    Models for cross-species (rat to human) dose extrapolation of diesel emission were evaluated for purposes of establishing guidelines for human exposure to diesel emissions (DE) based on DE toxicological data obtained in rats. Ideally, a model for this extrapolation would provide...

  1. Cross-Species PTM Mapping from Phosphoproteomic Data.

    PubMed

    Chaudhuri, Rima; Yang, Jean Yee Hwa

    2017-01-01

    Protein post-translational modifications (PTMs) are crucial for signal transduction in cells. In order to understand key cell signaling events, identification of functionally important PTMs, which are more likely to be evolutionarily conserved, is necessary. In recent times, high-throughput mass spectrometry (MS) has made quantitative datasets in diverse species readily available, which has led to a growing need for tools to facilitate cross-species comparison of PTM data. Cross-species comparison of PTM sites is difficult since they often lie in structurally disordered protein domains. Current tools that address this can only map known PTMs between species based on previously annotated orthologous phosphosites and do not enable cross-species mapping of newly identified modification sites. Here, we describe an automated web-based tool, PhosphOrtholog, that accurately maps annotated and novel orthologous PTM sites from high-throughput MS-based experimental data obtained from different species without relying on existing PTM databases. Identification of conserved PTMs across species from large-scale experimental data increases our knowledgebase of evolutionarily conserved and functional PTM sites that influence most biological processes. In this Chapter, we illustrate with examples how to use PhosphOrtholog to map novel PTM sites from cross-species MS-based phosphoproteomics data.

  2. A technique of optimization of microfiltration using a tunable platform

    NASA Astrophysics Data System (ADS)

    Alvankarian, Jafar; Yeop Majlis, Burhanuddin

    2015-08-01

    The optimum efficiency of size-based filtration in microfluidic devices is highly dependent on characteristics of design, deformability of microparticles/cells, and fluid flow. The effects of filter pores and flow rate, which are the two major determining and related factors of characterization in the separation of particles and cells are investigated in this work. An elastomeric microfluidic device consisting of parallel arrays of pillars with mechanically tunable spacings is employed as an adjustable microfiltration platform. The tunable filtration system is used for finding the best conditions of separation of solid microbeads or deformable blood cells in a crossflow pillar-based method. It is demonstrated that increasing flow rate in the range of 1.0-80.0 µl min-1 has an adverse effect on the device performance in terms of decreased separation efficiency of deformable blood cells. However, by tuning the gap size in the range of 2.5-7.5 µm, the selectivity of the separation is controlled from about 5.0 to 95.0% for white blood cells (WBCs) and 40.0 to 95.0% for red blood cells (RBCs). Finally, the best range of trapping and passing efficiencies of ~70-80.0% simultaneously for WBCs and RBCs in whole blood sample is achieved at optimum gap size of ~3.5-4.0 µm.

  3. Optimization of atmospheric transport models on HPC platforms

    NASA Astrophysics Data System (ADS)

    de la Cruz, Raúl; Folch, Arnau; Farré, Pau; Cabezas, Javier; Navarro, Nacho; Cela, José María

    2016-12-01

    The performance and scalability of atmospheric transport models on high performance computing environments is often far from optimal for multiple reasons including, for example, sequential input and output, synchronous communications, work unbalance, memory access latency or lack of task overlapping. We investigate how different software optimizations and porting to non general-purpose hardware architectures improve code scalability and execution times considering, as an example, the FALL3D volcanic ash transport model. To this purpose, we implement the FALL3D model equations in the WARIS framework, a software designed from scratch to solve in a parallel and efficient way different geoscience problems on a wide variety of architectures. In addition, we consider further improvements in WARIS such as hybrid MPI-OMP parallelization, spatial blocking, auto-tuning and thread affinity. Considering all these aspects together, the FALL3D execution times for a realistic test case running on general-purpose cluster architectures (Intel Sandy Bridge) decrease by a factor between 7 and 40 depending on the grid resolution. Finally, we port the application to Intel Xeon Phi (MIC) and NVIDIA GPUs (CUDA) accelerator-based architectures and compare performance, cost and power consumption on all the architectures. Implications on time-constrained operational model configurations are discussed.

  4. MIDAS intelligent platform for medical services, support for decision optimization in virtual medical communities.

    PubMed

    Arotăriţei, D; Toma, C M; Turnea, M; Toma, Vasilica

    2008-01-01

    The paper describes the implementation of a open multifunctional platform--MIDAS--for heterogeneous medical data management--support for optimization of clinical decision in virtual medical communities. The objectives of this intelligent environment are: diagnostic easier by access to heterogeneous medical data, a virtual support for medical personal in order to reduce medical errors, fast access to resources for education and improvement of medical education for physicians and students. The structure of the platform is based on a core module and a number of dedicated modules that give an important advantage as re-configurable platform depending on necessities. The core module tries to be as general is possible in order to be used in the future as core model in a platform focused on dentistry cases.

  5. Microsatellites Cross-Species Amplification across Some African Cichlids.

    PubMed

    Bezault, Etienne; Rognon, Xavier; Gharbi, Karim; Baroiller, Jean-Francois; Chevassus, Bernard

    2012-01-01

    The transfer of the genomic resources developed in the Nile tilapia, Oreochromis niloticus, to other Tilapiines sensu lato and African cichlid would provide new possibilities to study this amazing group from genetics, ecology, evolution, aquaculture, and conservation point of view. We tested the cross-species amplification of 32 O. niloticus microsatellite markers in a panel of 15 species from 5 different African cichlid tribes: Oreochromines (Oreochromis, Sarotherodon), Boreotilapiines (Tilapia), Chromidotilapines, Hemichromines, and Haplochromines. Amplification was successfully observed for 29 markers (91%), with a frequency of polymorphic (P(95)) loci per species around 70%. The mean number of alleles per locus and species was 3.2 but varied from 3.7 within Oreochromis species to 1.6 within the nontilapia species. The high level of cross-species amplification and polymorphism of the microsatellite markers tested in this study provides powerful tools for a wide range of molecular genetic studies within tilapia species as well as for other African cichlids.

  6. Receptor recognition and cross-species infections of SARS coronavirus.

    PubMed

    Li, Fang

    2013-10-01

    Receptor recognition is a major determinant of the host range, cross-species infections, and pathogenesis of the severe acute respiratory syndrome coronavirus (SARS-CoV). A defined receptor-binding domain (RBD) in the SARS-CoV spike protein specifically recognizes its host receptor, angiotensin-converting enzyme 2 (ACE2). This article reviews the latest knowledge about how RBDs from different SARS-CoV strains interact with ACE2 from several animal species. Detailed research on these RBD/ACE2 interactions has established important principles on host receptor adaptations, cross-species infections, and future evolution of SARS-CoV. These principles may apply to other emerging animal viruses, including the recently emerged Middle East respiratory syndrome coronavirus (MERS-CoV). This paper forms part of a series of invited articles in Antiviral Research on "From SARS to MERS: 10years of research on highly pathogenic human coronaviruses".

  7. A cross-species bi-clustering approach to identifying conserved co-regulated genes

    PubMed Central

    Sun, Jiangwen; Jiang, Zongliang; Tian, Xiuchun; Bi, Jinbo

    2016-01-01

    Motivation: A growing number of studies have explored the process of pre-implantation embryonic development of multiple mammalian species. However, the conservation and variation among different species in their developmental programming are poorly defined due to the lack of effective computational methods for detecting co-regularized genes that are conserved across species. The most sophisticated method to date for identifying conserved co-regulated genes is a two-step approach. This approach first identifies gene clusters for each species by a cluster analysis of gene expression data, and subsequently computes the overlaps of clusters identified from different species to reveal common subgroups. This approach is ineffective to deal with the noise in the expression data introduced by the complicated procedures in quantifying gene expression. Furthermore, due to the sequential nature of the approach, the gene clusters identified in the first step may have little overlap among different species in the second step, thus difficult to detect conserved co-regulated genes. Results: We propose a cross-species bi-clustering approach which first denoises the gene expression data of each species into a data matrix. The rows of the data matrices of different species represent the same set of genes that are characterized by their expression patterns over the developmental stages of each species as columns. A novel bi-clustering method is then developed to cluster genes into subgroups by a joint sparse rank-one factorization of all the data matrices. This method decomposes a data matrix into a product of a column vector and a row vector where the column vector is a consistent indicator across the matrices (species) to identify the same gene cluster and the row vector specifies for each species the developmental stages that the clustered genes co-regulate. Efficient optimization algorithm has been developed with convergence analysis. This approach was first validated on

  8. eIMRT: a web platform for the verification and optimization of radiation treatment plans.

    PubMed

    González-Castaño, Diego M; Pena, Javier; Gómez, Faustino; Gago-Arias, Araceli; González-Castaño, Francisco J; Rodríguez-Silva, Daniel A; Gómez, Andrés; Mouriño, Carlos; Pombar, Miguel; Sánchez, Manuel

    2009-07-21

    The eIMRT platform is a remote distributed computing tool that provides users with Internet access to three different services: Monte Carlo optimization of treatment plans, CRT & IMRT treatment optimization, and a database of relevant radiation treatments/clinical cases. These services are accessible through a user-friendly and platform independent web page. Its flexible and scalable design focuses on providing the final users with services rather than a collection of software pieces. All input and output data (CT, contours, treatment plans and dose distributions) are handled using the DICOM format. The design, implementation, and support of the verification and optimization algorithms are hidden to the user. This allows a unified, robust handling of the software and hardware that enables these computation-intensive services. The eIMRT platform is currently hosted by the Galician Supercomputing Center (CESGA) and may be accessible upon request (there is a demo version at http://eimrt.cesga.es:8080/eIMRT2/demo; request access in http://eimrt.cesga.es/signup.html). This paper describes all aspects of the eIMRT algorithms in depth, its user interface, and its services. Due to the flexible design of the platform, it has numerous applications including the intercenter comparison of treatment planning, the quality assurance of radiation treatments, the design and implementation of new approaches to certain types of treatments, and the sharing of information on radiation treatment techniques. In addition, the web platform and software tools developed for treatment verification and optimization have a modular design that allows the user to extend them with new algorithms. This software is not a commercial product. It is the result of the collaborative effort of different public research institutions and is planned to be distributed as an open source project. In this way, it will be available to any user; new releases will be generated with the new implemented codes or

  9. Structural optimization for heat detection of DNA thermosequencing platform using finite element analysis

    PubMed Central

    Esfandyarpour, Hesaam; Zheng, Bo; Pease, R. Fabian W.; Davis, Ronald W.

    2008-01-01

    For the past three decades, Sanger’s method has been the primary DNA sequencing technology; however, inherent limitations in cost and complexity have limited its usage in personalized medicine and ecological studies. A new technology called “thermosequencing” can potentially reduce both the cost and complexity of DNA sequencing by using a microfluidic platform [Esfandyarpour, Pease, and Davis, J. Vac. Sci. Technol. B26, 661 (2008)]. To optimize the efficiency of the technology, finite element analysis was used to model the thermosequencing system by simulating the DNA incorporation reaction series and the resulting product concentration and heat production. Different models of the thermosequencing platform were created to simulate the effects of the materials surrounding the system, to optimize the geometry of the system, and to concentrate reaction heat into specific regions for detection in the real system. The resulting concentrations of reaction products were used to calibrate the reaction speed and to design the heat sensors in the thermosequencing technology. We recommend a modified gated structure for the microfluidic detection platform by using control valves and show how this new platform could dramatically improve the detection efficiency. PMID:19693405

  10. Drug regimens identified and optimized by output-driven platform markedly reduce tuberculosis treatment time

    PubMed Central

    Lee, Bai-Yu; Clemens, Daniel L.; Silva, Aleidy; Dillon, Barbara Jane; Masleša-Galić, Saša; Nava, Susana; Ding, Xianting; Ho, Chih-Ming; Horwitz, Marcus A.

    2017-01-01

    The current drug regimens for treating tuberculosis are lengthy and onerous, and hence complicated by poor adherence leading to drug resistance and disease relapse. Previously, using an output-driven optimization platform and an in vitro macrophage model of Mycobacterium tuberculosis infection, we identified several experimental drug regimens among billions of possible drug-dose combinations that outperform the current standard regimen. Here we use this platform to optimize the in vivo drug doses of two of these regimens in a mouse model of pulmonary tuberculosis. The experimental regimens kill M. tuberculosis much more rapidly than the standard regimen and reduce treatment time to relapse-free cure by 75%. Thus, these regimens have the potential to provide a markedly shorter course of treatment for tuberculosis in humans. As these regimens omit isoniazid, rifampicin, fluoroquinolones and injectable aminoglycosides, they would be suitable for treating many cases of multidrug and extensively drug-resistant tuberculosis. PMID:28117835

  11. Drug regimens identified and optimized by output-driven platform markedly reduce tuberculosis treatment time.

    PubMed

    Lee, Bai-Yu; Clemens, Daniel L; Silva, Aleidy; Dillon, Barbara Jane; Masleša-Galić, Saša; Nava, Susana; Ding, Xianting; Ho, Chih-Ming; Horwitz, Marcus A

    2017-01-24

    The current drug regimens for treating tuberculosis are lengthy and onerous, and hence complicated by poor adherence leading to drug resistance and disease relapse. Previously, using an output-driven optimization platform and an in vitro macrophage model of Mycobacterium tuberculosis infection, we identified several experimental drug regimens among billions of possible drug-dose combinations that outperform the current standard regimen. Here we use this platform to optimize the in vivo drug doses of two of these regimens in a mouse model of pulmonary tuberculosis. The experimental regimens kill M. tuberculosis much more rapidly than the standard regimen and reduce treatment time to relapse-free cure by 75%. Thus, these regimens have the potential to provide a markedly shorter course of treatment for tuberculosis in humans. As these regimens omit isoniazid, rifampicin, fluoroquinolones and injectable aminoglycosides, they would be suitable for treating many cases of multidrug and extensively drug-resistant tuberculosis.

  12. Microsatellites Cross-Species Amplification across Some African Cichlids

    PubMed Central

    Bezault, Etienne; Rognon, Xavier; Gharbi, Karim; Baroiller, Jean-Francois; Chevassus, Bernard

    2012-01-01

    The transfer of the genomic resources developed in the Nile tilapia, Oreochromis niloticus, to other Tilapiines sensu lato and African cichlid would provide new possibilities to study this amazing group from genetics, ecology, evolution, aquaculture, and conservation point of view. We tested the cross-species amplification of 32 O. niloticus microsatellite markers in a panel of 15 species from 5 different African cichlid tribes: Oreochromines (Oreochromis, Sarotherodon), Boreotilapiines (Tilapia), Chromidotilapines, Hemichromines, and Haplochromines. Amplification was successfully observed for 29 markers (91%), with a frequency of polymorphic (P95) loci per species around 70%. The mean number of alleles per locus and species was 3.2 but varied from 3.7 within Oreochromis species to 1.6 within the nontilapia species. The high level of cross-species amplification and polymorphism of the microsatellite markers tested in this study provides powerful tools for a wide range of molecular genetic studies within tilapia species as well as for other African cichlids. PMID:22701809

  13. Synthesis and Optimization of Surface Functionalized Mesoporous Silica Nanoparticles for Bioconjugation Platforms

    NASA Astrophysics Data System (ADS)

    Gopalan, Anand Srinath

    A large amount of emphasis has been dedicated in recent years to introduce nanoparticles as a viable candidate for targeted therapies. In comparison to other candidates, mesoporous silica nanoparticles have the advantages of being biocompatible, easy to produce, and have the ability to prove to be a theranostic platform. To better study the specific targeting of diseased cells, adhesion studies of drug carrying bioconjugation constructs in fluid environments is required. The goal of this project was to develop a platform based on mesoporous silica nanoparticles that will be used for future multivalent adhesion studies. Specifically, mesoporous silica nanoparticles were synthesized with various sizes and aspect ratios, containing fluorescent dye to enable tracking studies, and with surface treatments that optimized stability and introduced primary-amine functional groups to facilitate attachment with targeted proteins and biomarkers. The effects of various parameters such as solvents, washing methods, secondary modifications and difference in concentrations of the starting materials for the synthesis mixture on the nanoparticles were studied in detail in this thesis. A portion of the study is also dedicated to optimizing a washing procedure to stabilize the particles in an aqueous medium in order to facilitate further modifications. The results of the work in this project can be utilized to provide a platform for further assays in flow chambers after bioconjugation with targeting proteins through orthogonal chemistries to study the adhesion properties in much greater detail.

  14. Toward a cross-species understanding of empathy

    PubMed Central

    Panksepp, Jaak; Panksepp, Jules B.

    2013-01-01

    Although signs of empathy have now been well documented in non-human primates, only during the past few years have systematic observations suggested that a primal form of empathy exists in rodents. Thus, the study of empathy in animals has started in earnest. Here we review recent studies indicating that rodents are able to share states of fear, and highlight how affective neuroscience approaches to the study of primary-process emotional systems can help to delineate how primal empathy is constituted in mammalian brains. Cross-species evolutionary approaches to understanding the neural circuitry of emotional ‘contagion’ or ‘resonance’ between nearby animals, together with the underlying neurochemistries, may help to clarify the origins of human empathy. PMID:23746460

  15. Cross-Species Rhesus Cytomegalovirus Infection of Cynomolgus Macaques

    PubMed Central

    Bimber, Benjamin N.; Reed, Jason S.; Uebelhoer, Luke S.; Bhusari, Amruta; Hammond, Katherine B.; Klug, Alex; Legasse, Alfred W.; Axthelm, Michael K.; Nelson, Jay A.; Streblow, Daniel N.; Picker, Louis J.; Früh, Klaus; Sacha, Jonah B.

    2016-01-01

    Cytomegaloviruses (CMV) are highly species-specific due to millennia of co-evolution and adaptation to their host, with no successful experimental cross-species infection in primates reported to date. Accordingly, full genome phylogenetic analysis of multiple new CMV field isolates derived from two closely related nonhuman primate species, Indian-origin rhesus macaques (RM) and Mauritian-origin cynomolgus macaques (MCM), revealed distinct and tight lineage clustering according to the species of origin, with MCM CMV isolates mirroring the limited genetic diversity of their primate host that underwent a population bottleneck 400 years ago. Despite the ability of Rhesus CMV (RhCMV) laboratory strain 68–1 to replicate efficiently in MCM fibroblasts and potently inhibit antigen presentation to MCM T cells in vitro, RhCMV 68–1 failed to productively infect MCM in vivo, even in the absence of host CD8+ T and NK cells. In contrast, RhCMV clone 68–1.2, genetically repaired to express the homologues of the HCMV anti-apoptosis gene UL36 and epithelial cell tropism genes UL128 and UL130 absent in 68–1, efficiently infected MCM as evidenced by the induction of transgene-specific T cells and virus shedding. Recombinant variants of RhCMV 68–1 and 68–1.2 revealed that expression of either UL36 or UL128 together with UL130 enabled productive MCM infection, indicating that multiple layers of cross-species restriction operate even between closely related hosts. Cumulatively, these results implicate cell tropism and evasion of apoptosis as critical determinants of CMV transmission across primate species barriers, and extend the macaque model of human CMV infection and immunology to MCM, a nonhuman primate species with uniquely simplified host immunogenetics. PMID:27829026

  16. Collective Framework and Performance Optimizations to Open MPI for Cray XT Platforms

    SciTech Connect

    Ladd, Joshua S; Gorentla Venkata, Manjunath; Shamis, Pavel; Graham, Richard L

    2011-01-01

    The performance and scalability of collective operations plays a key role in the performance and scalability of many scientific applications. Within the Open MPI code base we have developed a general purpose hierarchical collective operations framework called Cheetah, and applied it at large scale on the Oak Ridge Leadership Computing Facility's Jaguar (OLCF) platform, obtaining better performance and scalability than the native MPI implementation. This paper discuss Cheetah's design and implementation, and optimizations to the framework for Cray XT 5 platforms. Our results show that the Cheetah's Broadcast and Barrier perform better than the native MPI implementation. For medium data, the Cheetah's Broadcast outperforms the native MPI implementation by 93% for 49,152 processes problem size. For small and large data, it out performs the native MPI implementation by 10% and 9%, respectively, at 24,576 processes problem size. The Cheetah's Barrier performs 10% better than the native MPI implementation for 12,288 processes problem size.

  17. Optimization and automation of the semi-submersible platforms mooring design

    SciTech Connect

    Ferrari, J.A. Jr.; Morooka, C.K.

    1994-12-31

    There are a few calculation programs around the world used for determining the main aspects of the Mooring Design of Semi-Submersible Platforms . These programs bold a worldwide acknowledgement and their results are actually reliable. But they require many runs to get a solution that comply with the Classification Society requirements. This paper presents some procedures in order to optimize the semi-submersible mooring design as well as to make it automatic. Regarding the optimization philosophies, the following aspects are treated: (1) the optimization of the platform heading and the mooring pattern based on the spreading of the environmental forces; (2) the searching for the optimum mooring line composition in an automatic mode. Basically, the paper`s main goal is to introduce some methods to find the lowest cost solution for the mooring system in a short time. All of these methods were computationally implemented creating the intelligent system named PROANC, which deals with the semi-submersible mooring design in a quasi-static and deterministic approach. It should be noted that the proposed system exerts a strong appeal as a design tool for feasibility studies of a given oil field and its quasi-static results can be directly applied to a mooring program capable of performing dynamic analysis. Finally some simulations are executed for different water depths and its final results, including the expended time to run, are presented in order to prove the PROANC system wide potential as a design tool.

  18. Development of a Platform for Simulating and Optimizing Thermoelectric Energy Systems

    NASA Astrophysics Data System (ADS)

    Kreuder, John J.

    Thermoelectrics are solid state devices that can convert thermal energy directly into electrical energy. They have historically been used only in niche applications because of their relatively low efficiencies. With the advent of nanotechnology and improved manufacturing processes thermoelectric materials have become less costly and more efficient As next generation thermoelectric materials become available there is a need for industries to quickly and cost effectively seek out feasible applications for thermoelectric heat recovery platforms. Determining the technical and economic feasibility of such systems requires a model that predicts performance at the system level. Current models focus on specific system applications or neglect the rest of the system altogether, focusing on only module design and not an entire energy system. To assist in screening and optimizing entire energy systems using thermoelectrics, a novel software tool, Thermoelectric Power System Simulator (TEPSS), is developed for system level simulation and optimization of heat recovery systems. The platform is designed for use with a generic energy system so that most types of thermoelectric heat recovery applications can be modeled. TEPSS is based on object-oriented programming in MATLABRTM. A modular, shell based architecture is developed to carry out concept generation, system simulation and optimization. Systems are defined according to the components and interconnectivity specified by the user. An iterative solution process based on Newton's Method is employed to determine the system's steady state so that an objective function representing the cost of the system can be evaluated at the operating point. An optimization algorithm from MATLAB's Optimization Toolbox uses sequential quadratic programming to minimize this objective function with respect to a set of user specified design variables and constraints. During this iterative process many independent system simulations are executed and

  19. Optimal platform skewing for Space Shuttle inertial measurement unit redundancy management

    NASA Technical Reports Server (NTRS)

    Rasmussen, M. C.

    1980-01-01

    Constraints are applied to a general quaternion which describes the skewing between platforms of the Space Shuttle IMU. Once a skewing is derived, the use of the failure magnitude to threshold ratio makes possible predictions of the identification sensitivities for various failure modes. This in turn simplifies analyses and identifies portions of the flight envelope where second failure coverage is lacking. The square root of 6 and square root of 2 skewings have been baselined for use during nominal entry; the realignment software will be used on orbit to reskew the IMUs to the optimal configuration.

  20. Supercontinuum optimization for dual-soliton based light sources using genetic algorithms in a grid platform.

    PubMed

    Arteaga-Sierra, F R; Milián, C; Torres-Gómez, I; Torres-Cisneros, M; Moltó, G; Ferrando, A

    2014-09-22

    We present a numerical strategy to design fiber based dual pulse light sources exhibiting two predefined spectral peaks in the anomalous group velocity dispersion regime. The frequency conversion is based on the soliton fission and soliton self-frequency shift occurring during supercontinuum generation. The optimization process is carried out by a genetic algorithm that provides the optimum input pulse parameters: wavelength, temporal width and peak power. This algorithm is implemented in a Grid platform in order to take advantage of distributed computing. These results are useful for optical coherence tomography applications where bell-shaped pulses located in the second near-infrared window are needed.

  1. In search for significant cognitive features in Klinefelter syndrome through cross-species comparison of a supernumerary X chromosome.

    PubMed

    Bruining, H; Swaab, H; de Sonneville, L M J; van Rijn, S; van Engeland, H; Kas, M J H

    2011-08-01

    The behavioral characterization of animals that carry genetic disorder abnormalities in a controlled genetic and environmental background may be used to identify human deficits that are significant to understand underlying neurobiological mechanisms. Here, we studied whether previously reported object recognition impairments in mice with a supernumerary X chromosome relate to specific cognitive deficits in Klinefelter syndrome (47,XXY). We aimed to optimize face validity by studying temporal object recognition in human cognitive assays. Thirty-four boys with Klinefelter syndrome (mean age 12.01) were compared with 90 age-matched normal controls, on a broad range of visual object memory tasks, including tests for pattern and temporal order discrimination. The results indicate that subjects with Klinefelter syndrome have difficulty in the processing of visual object and pattern information. Visual object patterns seem difficult to discriminate especially when temporal information needs to be processed and reproduced. On the basis of cross-species comparison, we propose that impaired temporal processing of object pattern information is an important deficit in Klinefelter syndrome. The current study shows how cross-species behavioral characterization may be used as a starting point to understand the neurobiology of syndromal phenotypic expression. The features of this study may serve as markers for interventions in Klinefelter syndrome. Similar cross-species evaluations of standard mouse behavioral paradigms in different genetic contexts may be powerful tools to optimize genotype-phenotype relationships.

  2. Use of chemometrics to optimize a glucose assay on a paper microfluidic platform.

    PubMed

    Avoundjian, Ani; Jalali-Heravi, Mehdi; Gomez, Frank A

    2017-04-01

    We describe the use of a chemometrics-based computational platform to optimize a glucose assay on a microfluidic paper-based analytical device (μPAD). Glucose is colorimetrically detected in the presence of glucose oxidase (GOx), horseradish peroxidase (HRP), and potassium iodide (KI). Using a Y-shaped paper microfluidic chip, the concentration of glucose, volume of reagents, and the length and width of the microfluidic channel were examined. The responses of the microfluidic chips were analyzed at the halfway point of the channel length. Variables affecting the response were screened by using a 2(4) factorial design, and among them, volume and concentration of the glucose were optimized by applying a rotatable central composite design (CCD). The optimum and experimental responses are 151.58 and 149.80, respectively, with an absolute error of 1.2%.

  3. An automated workflow for enhancing microbial bioprocess optimization on a novel microbioreactor platform

    PubMed Central

    2012-01-01

    Background High-throughput methods are widely-used for strain screening effectively resulting in binary information regarding high or low productivity. Nevertheless achieving quantitative and scalable parameters for fast bioprocess development is much more challenging, especially for heterologous protein production. Here, the nature of the foreign protein makes it impossible to predict the, e.g. best expression construct, secretion signal peptide, inductor concentration, induction time, temperature and substrate feed rate in fed-batch operation to name only a few. Therefore, a high number of systematic experiments are necessary to elucidate the best conditions for heterologous expression of each new protein of interest. Results To increase the throughput in bioprocess development, we used a microtiter plate based cultivation system (Biolector) which was fully integrated into a liquid-handling platform enclosed in laminar airflow housing. This automated cultivation platform was used for optimization of the secretory production of a cutinase from Fusarium solani pisi with Corynebacterium glutamicum. The online monitoring of biomass, dissolved oxygen and pH in each of the microtiter plate wells enables to trigger sampling or dosing events with the pipetting robot used for a reliable selection of best performing cutinase producers. In addition to this, further automated methods like media optimization and induction profiling were developed and validated. All biological and bioprocess parameters were exclusively optimized at microtiter plate scale and showed perfect scalable results to 1 L and 20 L stirred tank bioreactor scale. Conclusions The optimization of heterologous protein expression in microbial systems currently requires extensive testing of biological and bioprocess engineering parameters. This can be efficiently boosted by using a microtiter plate cultivation setup embedded into a liquid-handling system, providing more throughput by parallelization and

  4. CAROTID - a web-based platform for optimal personalized management of atherosclerotic patients.

    PubMed

    Gastounioti, Aimilia; Kolias, Vasileios; Golemati, Spyretta; Tsiaparas, Nikolaos N; Matsakou, Aikaterini; Stoitsis, John S; Kadoglou, Nikolaos P E; Gkekas, Christos; Kakisis, John D; Liapis, Christos D; Karakitsos, Petros; Sarafis, Ioannis; Angelidis, Pantelis; Nikita, Konstantina S

    2014-04-01

    Carotid atherosclerosis is the main cause of fatal cerebral ischemic events, thereby posing a major burden for public health and state economies. We propose a web-based platform named CAROTID to address the need for optimal management of patients with carotid atherosclerosis in a twofold sense: (a) objective selection of patients who need carotid-revascularization (i.e., high-risk patients), using a multifaceted description of the disease consisting of ultrasound imaging, biochemical and clinical markers, and (b) effective storage and retrieval of patient data to facilitate frequent follow-ups and direct comparisons with related cases. These two services are achieved by two interconnected modules, namely the computer-aided diagnosis (CAD) tool and the intelligent archival system, in a unified, remotely accessible system. We present the design of the platform and we describe three main usage scenarios to demonstrate the CAROTID utilization in clinical practice. Additionally, the platform was evaluated in a real clinical environment in terms of CAD performance, end-user satisfaction and time spent on different functionalities. CAROTID classification of high- and low-risk cases was 87%; the corresponding stenosis-degree-based classification would have been 61%. Questionnaire-based user satisfaction showed encouraging results in terms of ease-of-use, clinical usefulness and patient data protection. Times for different CAROTID functionalities were generally short; as an example, the time spent for generating the diagnostic decision was 5min in case of 4-s ultrasound video. Large datasets and future evaluation sessions in multiple medical institutions are still necessary to reveal with confidence the full potential of the platform.

  5. Integrated platform for optimized solar PV system design and engineering plan set generation

    SciTech Connect

    Adeyemo, Samuel

    2015-12-30

    The Aurora team has developed software that allows users to quickly generate a three-dimensional model for a building, with a corresponding irradiance map, from any two-dimensional image with associated geo-coordinates. The purpose of this project is to build upon that technology by developing and distributing to solar installers a software platform that automatically retrieves engineering, financial and geographic data for a specific site, and quickly generates an optimal customer proposal and corresponding engineering plans for that site. At the end of the project, Aurora’s optimization platform would have been used to make at least one thousand proposals from at least ten unique solar installation companies, two of whom would sign economically viable contracts to use the software. Furthermore, Aurora’s algorithms would be tested to show that in at least seventy percent of cases, Aurora automatically generated a design equivalent to or better than what a human could have done manually. A ‘better’ design is one that generates more energy for the same cost, or that generates a higher return on investment, while complying with all site-specific aesthetic, electrical and spatial requirements.

  6. A Plea for Cross-species Social Neuroscience.

    PubMed

    Keysers, Christian; Gazzola, Valeria

    2017-01-01

    Over the past two decades, the question of how our brain makes us sensitive to the state of conspecifics and how that affects our behaviour has undergone a profound change. Twenty years ago what would now be called social neuroscience was focused on the visual processing of facial expressions and body movements in temporal lobe structures of primates (Puce and Perrett 2003). With the discovery of mirror neurons, this changed rapidly towards the modern field of social neuroscience, in which high-level vision is but one of many focuses of interest. In this essay, we will argue that for the further progress of the field, the integration of animal neuroscience and human neuroscience is paramount. We will do so, by focusing on the field of embodied social cognition. We will first show how the combination of animal and human neuroscience was critical in how the discovery of mirror neurons placed the motor system on the map of social cognition. We will then argue why an integrated cross-species approach will be pivotal to our understanding of the neural basis of emotional empathy and its link to prosocial behaviour.

  7. Optimization of a Lattice Boltzmann Computation on State-of-the-Art Multicore Platforms

    SciTech Connect

    Williams, Samuel; Carter, Jonathan; Oliker, Leonid; Shalf, John; Yelick, Katherine

    2009-04-10

    We present an auto-tuning approach to optimize application performance on emerging multicore architectures. The methodology extends the idea of search-based performance optimizations, popular in linear algebra and FFT libraries, to application-specific computational kernels. Our work applies this strategy to a lattice Boltzmann application (LBMHD) that historically has made poor use of scalar microprocessors due to its complex data structures and memory access patterns. We explore one of the broadest sets of multicore architectures in the HPC literature, including the Intel Xeon E5345 (Clovertown), AMD Opteron 2214 (Santa Rosa), AMD Opteron 2356 (Barcelona), Sun T5140 T2+ (Victoria Falls), as well as a QS20 IBM Cell Blade. Rather than hand-tuning LBMHD for each system, we develop a code generator that allows us to identify a highly optimized version for each platform, while amortizing the human programming effort. Results show that our auto-tuned LBMHD application achieves up to a 15x improvement compared with the original code at a given concurrency. Additionally, we present detailed analysis of each optimization, which reveal surprising hardware bottlenecks and software challenges for future multicore systems and applications.

  8. Across scanner platform optimization to enable EUV lithography at the 10-nm logic node

    NASA Astrophysics Data System (ADS)

    Mulkens, Jan; Karssenberg, Jaap; Wei, Hannah; Beckers, Marcel; Verstappen, Leon; Hsu, Stephen; Chen, Guangqin

    2014-04-01

    EUV lithography is expected to be introduced in volume manufacturing at the 10-nm and 7-nm node. Especially in these first EUV nodes, critical layer patterning will be balanced with the use of ArF immersion. As a consequence a good overlay and placement matching between both lithography methods becomes an enabling factor for EUV. In this paper we present an integral method to optimize critical layer patterning across the EUV and ArF scanner platform, such that good overlay and device pattern placement is achieved. It is discussed that besides classical overlay control methods, also the optimization of the ArF and EUV imaging steps is needed. Best matching is achieved by applying high-order field-to-field overlay corrections for both imaging and overlay. The lithography architecture we build for these higher order corrections connects the dynamic scanner actuators with the angle resolved scatterometer via a separate computational application server. Improvements of CD uniformity are based on source mask optimization for EUV combined with CD optimization using freeform intra-field dose actuator in the immersion scanner.

  9. A brief history of cross-species organ transplantation

    PubMed Central

    2012-01-01

    Cross-species transplantation (xenotransplantation) offers the prospect of an unlimited supply of organs and cells for clinical transplantation, thus resolving the critical shortage of human tissues that currently prohibits a majority of patients on the waiting list from receiving transplants. Between the 17th and 20th centuries, blood was transfused from various animal species into patients with a variety of pathological conditions. Skin grafts were carried out in the 19th century from a variety of animals, with frogs being the most popular. In the 1920s, Voronoff advocated the transplantation of slices of chimpanzee testis into aged men whose “zest for life” was deteriorating, believing that the hormones produced by the testis would rejuvenate his patients. Following the pioneering surgical work of Carrel, who developed the technique of blood vessel anastomosis, numerous attempts at nonhuman primate organ transplantation in patients were carried out in the 20th century. In 1963–1964, when human organs were not available and chronic dialysis was not yet in use, Reemtsma transplanted chimpanzee kidneys into 13 patients, one of whom returned to work for almost 9 months before suddenly dying from what was believed to be an electrolyte disturbance. The first heart transplant in a human ever performed was by Hardy in 1964, using a chimpanzee heart, but the patient died within 2 hours. Starzl carried out the first chimpanzee-to-human liver transplantation in 1966; in 1992, he obtained patient survival for 70 days following a baboon liver transplant. With the advent of genetic engineering and cloning technologies, pigs are currently available with a number of different manipulations that protect their tissues from the human immune response, resulting in increasing pig graft survival in nonhuman primate models. Genetically modified pigs offer hope of a limitless supply of organs and cells for those in need of a transplant. PMID:22275786

  10. Optimization of a nanotechnology based antimicrobial platform for food safety applications using Engineered Water Nanostructures (EWNS).

    PubMed

    Pyrgiotakis, Georgios; Vedantam, Pallavi; Cirenza, Caroline; McDevitt, James; Eleftheriadou, Mary; Leonard, Stephen S; Demokritou, Philip

    2016-02-15

    A chemical free, nanotechnology-based, antimicrobial platform using Engineered Water Nanostructures (EWNS) was recently developed. EWNS have high surface charge, are loaded with reactive oxygen species (ROS), and can interact-with, and inactivate an array of microorganisms, including foodborne pathogens. Here, it was demonstrated that their properties during synthesis can be fine tuned and optimized to further enhance their antimicrobial potential. A lab based EWNS platform was developed to enable fine-tuning of EWNS properties by modifying synthesis parameters. Characterization of EWNS properties (charge, size and ROS content) was performed using state-of-the art analytical methods. Further their microbial inactivation potential was evaluated with food related microorganisms such as Escherichia coli, Salmonella enterica, Listeria innocua, Mycobacterium parafortuitum, and Saccharomyces cerevisiae inoculated onto the surface of organic grape tomatoes. The results presented here indicate that EWNS properties can be fine-tuned during synthesis resulting in a multifold increase of the inactivation efficacy. More specifically, the surface charge quadrupled and the ROS content increased. Microbial removal rates were microorganism dependent and ranged between 1.0 to 3.8 logs after 45 mins of exposure to an EWNS aerosol dose of 40,000 #/cm(3).

  11. An optimized microfabricated platform for the optical generation and detection of hyperpolarized 129Xe

    PubMed Central

    Kennedy, Daniel J.; Seltzer, Scott J.; Jiménez-Martínez, Ricardo; Ring, Hattie L.; Malecek, Nicolas S.; Knappe, Svenja; Donley, Elizabeth A.; Kitching, John; Bajaj, Vikram S.; Pines, Alexander

    2017-01-01

    Low thermal-equilibrium nuclear spin polarizations and the need for sophisticated instrumentation render conventional nuclear magnetic resonance (NMR) spectroscopy and imaging (MRI) incompatible with small-scale microfluidic devices. Hyperpolarized 129Xe gas has found use in the study of many materials but has required very large and expensive instrumentation. Recently a microfabricated device with modest instrumentation demonstrated all-optical hyperpolarization and detection of 129Xe gas. This device was limited by 129Xe polarizations less than 1%, 129Xe NMR signals smaller than 20 nT, and transport of hyperpolarized 129Xe over millimeter lengths. Higher polarizations, versatile detection schemes, and flow of 129Xe over larger distances are desirable for wider applications. Here we demonstrate an ultra-sensitive microfabricated platform that achieves 129Xe polarizations reaching 7%, NMR signals exceeding 1 μT, lifetimes up to 6 s, and simultaneous two-mode detection, consisting of a high-sensitivity in situ channel with signal-to-noise of 105 and a lower-sensitivity ex situ detection channel which may be useful in a wider variety of conditions. 129Xe is hyperpolarized and detected in locations more than 1 cm apart. Our versatile device is an optimal platform for microfluidic magnetic resonance in particular, but equally attractive for wider nuclear spin applications benefitting from ultra-sensitive detection, long coherences, and simple instrumentation. PMID:28266629

  12. An optimized microfabricated platform for the optical generation and detection of hyperpolarized 129Xe

    NASA Astrophysics Data System (ADS)

    Kennedy, Daniel J.; Seltzer, Scott J.; Jiménez-Martínez, Ricardo; Ring, Hattie L.; Malecek, Nicolas S.; Knappe, Svenja; Donley, Elizabeth A.; Kitching, John; Bajaj, Vikram S.; Pines, Alexander

    2017-03-01

    Low thermal-equilibrium nuclear spin polarizations and the need for sophisticated instrumentation render conventional nuclear magnetic resonance (NMR) spectroscopy and imaging (MRI) incompatible with small-scale microfluidic devices. Hyperpolarized 129Xe gas has found use in the study of many materials but has required very large and expensive instrumentation. Recently a microfabricated device with modest instrumentation demonstrated all-optical hyperpolarization and detection of 129Xe gas. This device was limited by 129Xe polarizations less than 1%, 129Xe NMR signals smaller than 20 nT, and transport of hyperpolarized 129Xe over millimeter lengths. Higher polarizations, versatile detection schemes, and flow of 129Xe over larger distances are desirable for wider applications. Here we demonstrate an ultra-sensitive microfabricated platform that achieves 129Xe polarizations reaching 7%, NMR signals exceeding 1 μT, lifetimes up to 6 s, and simultaneous two-mode detection, consisting of a high-sensitivity in situ channel with signal-to-noise of 105 and a lower-sensitivity ex situ detection channel which may be useful in a wider variety of conditions. 129Xe is hyperpolarized and detected in locations more than 1 cm apart. Our versatile device is an optimal platform for microfluidic magnetic resonance in particular, but equally attractive for wider nuclear spin applications benefitting from ultra-sensitive detection, long coherences, and simple instrumentation.

  13. Optimization of a nanotechnology based antimicrobial platform for food safety applications using Engineered Water Nanostructures (EWNS)

    NASA Astrophysics Data System (ADS)

    Pyrgiotakis, Georgios; Vedantam, Pallavi; Cirenza, Caroline; McDevitt, James; Eleftheriadou, Mary; Leonard, Stephen S.; Demokritou, Philip

    2016-02-01

    A chemical free, nanotechnology-based, antimicrobial platform using Engineered Water Nanostructures (EWNS) was recently developed. EWNS have high surface charge, are loaded with reactive oxygen species (ROS), and can interact-with, and inactivate an array of microorganisms, including foodborne pathogens. Here, it was demonstrated that their properties during synthesis can be fine tuned and optimized to further enhance their antimicrobial potential. A lab based EWNS platform was developed to enable fine-tuning of EWNS properties by modifying synthesis parameters. Characterization of EWNS properties (charge, size and ROS content) was performed using state-of-the art analytical methods. Further their microbial inactivation potential was evaluated with food related microorganisms such as Escherichia coli, Salmonella enterica, Listeria innocua, Mycobacterium parafortuitum, and Saccharomyces cerevisiae inoculated onto the surface of organic grape tomatoes. The results presented here indicate that EWNS properties can be fine-tuned during synthesis resulting in a multifold increase of the inactivation efficacy. More specifically, the surface charge quadrupled and the ROS content increased. Microbial removal rates were microorganism dependent and ranged between 1.0 to 3.8 logs after 45 mins of exposure to an EWNS aerosol dose of 40,000 #/cm3.

  14. Optimization of a nanotechnology based antimicrobial platform for food safety applications using Engineered Water Nanostructures (EWNS)

    PubMed Central

    Pyrgiotakis, Georgios; Vedantam, Pallavi; Cirenza, Caroline; McDevitt, James; Eleftheriadou, Mary; Leonard, Stephen S.; Demokritou, Philip

    2016-01-01

    A chemical free, nanotechnology-based, antimicrobial platform using Engineered Water Nanostructures (EWNS) was recently developed. EWNS have high surface charge, are loaded with reactive oxygen species (ROS), and can interact-with, and inactivate an array of microorganisms, including foodborne pathogens. Here, it was demonstrated that their properties during synthesis can be fine tuned and optimized to further enhance their antimicrobial potential. A lab based EWNS platform was developed to enable fine-tuning of EWNS properties by modifying synthesis parameters. Characterization of EWNS properties (charge, size and ROS content) was performed using state-of-the art analytical methods. Further their microbial inactivation potential was evaluated with food related microorganisms such as Escherichia coli, Salmonella enterica, Listeria innocua, Mycobacterium parafortuitum, and Saccharomyces cerevisiae inoculated onto the surface of organic grape tomatoes. The results presented here indicate that EWNS properties can be fine-tuned during synthesis resulting in a multifold increase of the inactivation efficacy. More specifically, the surface charge quadrupled and the ROS content increased. Microbial removal rates were microorganism dependent and ranged between 1.0 to 3.8 logs after 45 mins of exposure to an EWNS aerosol dose of 40,000 #/cm3. PMID:26875817

  15. Optimization of sparse matrix-vector multiplication on emerging multicore platforms

    SciTech Connect

    Williams, S; Oliker, L; Vuduc, R; Shalf, J; Yelick, K; Demmel, J

    2007-04-16

    We are witnessing a dramatic change in computer architecture due to the multicore paradigm shift, as every electronic device from cell phones to supercomputers confronts parallelism of unprecedented scale. To fully unleash the potential of these systems, the HPC community must develop multicore specific optimization methodologies for important scientific computations. In this work, we examine sparse matrix-vector multiply (SpMV)--one of the most heavily used kernels in scientific computing--across a broad spectrum of multicore designs. Our experimental platform includes the homogeneous AMD dual-core and Intel quad-core designs, as well as the highly multithreaded Sun Niagara and heterogeneous STI Cell. We present several optimization strategies especially effective for the multicore environment, and demonstrate significant performance improvements compared to existing state-of-the-art serial and parallel SpMV implementations. Additionally, we present key insights into the architectural tradeoffs of leading multicore design strategies, in the context of demanding memory-bound numerical algorithms.

  16. Optimization of Sparse Matrix-Vector Multiplication on Emerging Multicore Platforms

    SciTech Connect

    Williams, Samuel; Oliker, Leonid; Vuduc, Richard; Shalf, John; Yelick, Katherine; Demmel, James

    2008-10-16

    We are witnessing a dramatic change in computer architecture due to the multicore paradigm shift, as every electronic device from cell phones to supercomputers confronts parallelism of unprecedented scale. To fully unleash the potential of these systems, the HPC community must develop multicore specific-optimization methodologies for important scientific computations. In this work, we examine sparse matrix-vector multiply (SpMV) - one of the most heavily used kernels in scientific computing - across a broad spectrum of multicore designs. Our experimental platform includes the homogeneous AMD quad-core, AMD dual-core, and Intel quad-core designs, the heterogeneous STI Cell, as well as one of the first scientific studies of the highly multithreaded Sun Victoria Falls (a Niagara2 SMP). We present several optimization strategies especially effective for the multicore environment, and demonstrate significant performance improvements compared to existing state-of-the-art serial and parallel SpMV implementations. Additionally, we present key insights into the architectural trade-offs of leading multicore design strategies, in the context of demanding memory-bound numerical algorithms.

  17. Optimal prediction of human postural response under anterior-posterior platform tilting

    NASA Astrophysics Data System (ADS)

    Naderi, D.; Miripour Fard, B.; Sadeghi-Mehr, M.

    2013-01-01

    Previous studies have suggested that human beings movements can be related to the problem of cost function minimization. But at the present time it is not clear that which objective function(s) and constraints are used by central nervous system (CNS) to produce optimal reactions under perturbations. Present study has been done experimentally and by numerical simulations to explore the stability constraints which should be used in combination with energy based cost function (weighted minimum torque) to estimate the motor planning criterion is used by CNS for disturbance rejections. The influence of three stability criterions (ZMP, extrapolated center of mass and a vertical force criterion) in combination with minimum torque model on the optimal trajectory formation is investigated. First, the response of 10 male healthy persons to platform oscillation was recorded by motion analysis system and the hip, knee and ankle angular trajectories were derived from recorded data. Second, the dynamic simulation of a four-segment, three actuated degrees of freedom mechanical model of the human body was performed using predictive dynamic method which leads to an optimization problem. The simulated trajectories were then compared to the experimental data. With comparison between experimental results, the weighting coefficients of the objective function were found to achieve best estimation. It was seen that the minimum torque objective function with weighting coefficients gives trajectories that are mostly matched with experimental observation. Moreover, the results showed that between stability criterions, the ZMP predictions are near to experimental results. Although by using vertical force criterion some nearness to experimental results are lost (in comparison with ZMP criterion) but a secured flat-foot posture for the model is obtained which this posture is more applicable than others in humanoid implementations.

  18. Ultra-deep sequencing of intra-host rabies virus populations during cross-species transmission.

    PubMed

    Borucki, Monica K; Chen-Harris, Haiyin; Lao, Victoria; Vanier, Gilda; Wadford, Debra A; Messenger, Sharon; Allen, Jonathan E

    2013-11-01

    One of the hurdles to understanding the role of viral quasispecies in RNA virus cross-species transmission (CST) events is the need to analyze a densely sampled outbreak using deep sequencing in order to measure the amount of mutation occurring on a small time scale. In 2009, the California Department of Public Health reported a dramatic increase (350) in the number of gray foxes infected with a rabies virus variant for which striped skunks serve as a reservoir host in Humboldt County. To better understand the evolution of rabies, deep-sequencing was applied to 40 unpassaged rabies virus samples from the Humboldt outbreak. For each sample, approximately 11 kb of the 12 kb genome was amplified and sequenced using the Illumina platform. Average coverage was 17,448 and this allowed characterization of the rabies virus population present in each sample at unprecedented depths. Phylogenetic analysis of the consensus sequence data demonstrated that samples clustered according to date (1995 vs. 2009) and geographic location (northern vs. southern). A single amino acid change in the G protein distinguished a subset of northern foxes from a haplotype present in both foxes and skunks, suggesting this mutation may have played a role in the observed increased transmission among foxes in this region. Deep-sequencing data indicated that many genetic changes associated with the CST event occurred prior to 2009 since several nonsynonymous mutations that were present in the consensus sequences of skunk and fox rabies samples obtained from 20032010 were present at the sub-consensus level (as rare variants in the viral population) in skunk and fox samples from 1995. These results suggest that analysis of rare variants within a viral population may yield clues to ancestral genomes and identify rare variants that have the potential to be selected for if environment conditions change.

  19. Cross-species transcriptomic approach reveals genes in hamster implantation sites.

    PubMed

    Lei, Wei; Herington, Jennifer; Galindo, Cristi L; Ding, Tianbing; Brown, Naoko; Reese, Jeff; Paria, Bibhash C

    2014-12-01

    The mouse model has greatly contributed to understanding molecular mechanisms involved in the regulation of progesterone (P4) plus estrogen (E)-dependent blastocyst implantation process. However, little is known about contributory molecular mechanisms of the P4-only-dependent blastocyst implantation process that occurs in species such as hamsters, guineapigs, rabbits, pigs, rhesus monkeys, and perhaps humans. We used the hamster as a model of P4-only-dependent blastocyst implantation and carried out cross-species microarray (CSM) analyses to reveal differentially expressed genes at the blastocyst implantation site (BIS), in order to advance the understanding of molecular mechanisms of implantation. Upregulation of 112 genes and downregulation of 77 genes at the BIS were identified using a mouse microarray platform, while use of the human microarray revealed 62 up- and 38 down-regulated genes at the BIS. Excitingly, a sizable number of genes (30 up- and 11 down-regulated genes) were identified as a shared pool by both CSMs. Real-time RT-PCR and in situ hybridization validated the expression patterns of several up- and down-regulated genes identified by both CSMs at the hamster and mouse BIS to demonstrate the merit of CSM findings across species, in addition to revealing genes specific to hamsters. Functional annotation analysis found that genes involved in the spliceosome, proteasome, and ubiquination pathways are enriched at the hamster BIS, while genes associated with tight junction, SAPK/JNK signaling, and PPARα/RXRα signalings are repressed at the BIS. Overall, this study provides a pool of genes and evidence of their participation in up- and down-regulated cellular functions/pathways at the hamster BIS.

  20. Clinical optimization of antigen specific modulation of type 1 diabetes with the plasmid DNA platform.

    PubMed

    Gottlieb, Peter; Utz, Paul J; Robinson, William; Steinman, Lawrence

    2013-12-01

    Some clinical trials in humans have aimed at modulation of type 1 diabetes (T1D) via alteration of the immune response to putative islet cell antigens, particularly proinsulin and insulin, glutamic acid decarboxylase and the peptide, DiaPep 277, derived from heat shock protein 60. The focus here is on development of a specially engineered DNA plasmid encoding proinsulin to treat T1D. The plasmid is engineered to turn off adaptive immunity to proinsulin. This approach yielded exciting results in a randomized placebo controlled trial in 80 adult patients with T1D. The implications of this trial are explored in regards to the potential for sparing inflammation in islets and thus allowing the functioning beta cells to recover and produce more insulin. Strategies to further strengthen the effects seen thus far with the tolerizing DNA plasmid to proinsulin will be elucidated. The DNA platform affords an opportunity for easy modifications. In addition standard exploration of dose levels, route of administration and frequency of dose are practical. Optimization of the effects seen to date on C-peptide and on depletion of proinsulin specific CD8 T cells are feasible, with expected concomitant improvement in other parameters like hemoglobin A1c and reduction in insulin usage. T1D is one of the few autoimmune conditions where antigen specific therapy can be achieved, provided the approach is tested intelligently. Tolerizing DNA vaccines to proinsulin and other islet cell autoantigens is a worthy pursuit to potentially treat, prevent and to perhaps even 'cure' or 'prevent' type 1 diabetes.

  1. Simultaneously reconstructing viral cross-species transmission history and identifying the underlying constraints

    PubMed Central

    Faria, Nuno Rodrigues; Suchard, Marc A.; Rambaut, Andrew; Streicker, Daniel G.; Lemey, Philippe

    2013-01-01

    The factors that determine the origin and fate of cross-species transmission events remain unclear for the majority of human pathogens, despite being central for the development of predictive models and assessing the efficacy of prevention strategies. Here, we describe a flexible Bayesian statistical framework to reconstruct virus transmission between different host species based on viral gene sequences, while simultaneously testing and estimating the contribution of several potential predictors of cross-species transmission. Specifically, we use a generalized linear model extension of phylogenetic diffusion to perform Bayesian model averaging over candidate predictors. By further extending this model with branch partitioning, we allow for distinct host transition processes on external and internal branches, thus discriminating between recent cross-species transmissions, many of which are likely to result in dead-end infections, and host shifts that reflect successful onwards transmission in the new host species. Our approach corroborates genetic distance between hosts as a key determinant of both host shifts and cross-species transmissions of rabies virus in North American bats. Furthermore, our results indicate that geographical range overlap is a modest predictor for cross-species transmission, but not for host shifts. Although our evolutionary framework focused on the multi-host reservoir dynamics of bat rabies virus, it is applicable to other pathogens and to other discrete state transition processes. PMID:23382420

  2. Optimization of beam angles for intensity modulated radiation therapy treatment planning using genetic algorithm on a distributed computing platform.

    PubMed

    Nazareth, Daryl P; Brunner, Stephen; Jones, Matthew D; Malhotra, Harish K; Bakhtiari, Mohammad

    2009-07-01

    Planning intensity modulated radiation therapy (IMRT) treatment involves selection of several angle parameters as well as specification of structures and constraints employed in the optimization process. Including these parameters in the combinatorial search space vastly increases the computational burden, and therefore the parameter selection is normally performed manually by a clinician, based on clinical experience. We have investigated the use of a genetic algorithm (GA) and distributed-computing platform to optimize the gantry angle parameters and provide insight into additional structures, which may be necessary, in the dose optimization process to produce optimal IMRT treatment plans. For an IMRT prostate patient, we produced the first generation of 40 samples, each of five gantry angles, by selecting from a uniform random distribution, subject to certain adjacency and opposition constraints. Dose optimization was performed by distributing the 40-plan workload over several machines running a commercial treatment planning system. A score was assigned to each resulting plan, based on how well it satisfied clinically-relevant constraints. The second generation of 40 samples was produced by combining the highest-scoring samples using techniques of crossover and mutation. The process was repeated until the sixth generation, and the results compared with a clinical (equally-spaced) gantry angle configuration. In the sixth generation, 34 of the 40 GA samples achieved better scores than the clinical plan, with the best plan showing an improvement of 84%. Moreover, the resulting configuration of beam angles tended to cluster toward the patient's sides, indicating where the inclusion of additional structures in the dose optimization process may avoid dose hot spots. Additional parameter selection in IMRT leads to a large-scale computational problem. We have demonstrated that the GA combined with a distributed-computing platform can be applied to optimize gantry angle

  3. New roles for microRNAs in cross-species communication.

    PubMed

    Liang, Hongwei; Zen, Ke; Zhang, Junfeng; Zhang, Chen-Yu; Chen, Xi

    2013-03-01

    Communication between cells ensures coordinated behavior. In prokaryotes, this signaling is typically referred to as quorum sensing, whereas in eukaryotic cells, communication occurs through hormones. In recent years, reports have shown that small noncoding RNAs, called microRNAs (miRNAs), can be transmitted from one species to another, inducing signal interference in distant species, even in a cross-kingdom manner. This new mode of cross-species communication might mediate symbiotic and pathogenic relationships between various organisms (e.g., microorganisms and their hosts). Here, we discuss several recent studies concerning miRNA-mediated cross-species gene regulation.

  4. Arsenic removal from contaminated groundwater by membrane-integrated hybrid plant: optimization and control using Visual Basic platform.

    PubMed

    Chakrabortty, S; Sen, M; Pal, P

    2014-03-01

    A simulation software (ARRPA) has been developed in Microsoft Visual Basic platform for optimization and control of a novel membrane-integrated arsenic separation plant in the backdrop of absence of such software. The user-friendly, menu-driven software is based on a dynamic linearized mathematical model, developed for the hybrid treatment scheme. The model captures the chemical kinetics in the pre-treating chemical reactor and the separation and transport phenomena involved in nanofiltration. The software has been validated through extensive experimental investigations. The agreement between the outputs from computer simulation program and the experimental findings are excellent and consistent under varying operating conditions reflecting high degree of accuracy and reliability of the software. High values of the overall correlation coefficient (R (2) = 0.989) and Willmott d-index (0.989) are indicators of the capability of the software in analyzing performance of the plant. The software permits pre-analysis, manipulation of input data, helps in optimization and exhibits performance of an integrated plant visually on a graphical platform. Performance analysis of the whole system as well as the individual units is possible using the tool. The software first of its kind in its domain and in the well-known Microsoft Excel environment is likely to be very useful in successful design, optimization and operation of an advanced hybrid treatment plant for removal of arsenic from contaminated groundwater.

  5. High content analysis platform for optimization of lipid mediated CRISPR-Cas9 delivery strategies in human cells

    PubMed Central

    Steyer, Benjamin; Carlson-Stevermer, Jared; Angenent-Mari, Nicolas; Khalil, Andrew; Harkness, Ty; Saha, Krishanu

    2016-01-01

    Non-viral gene-editing of human cells using the CRISPR-Cas9 system requires optimized delivery of multiple components. Both the Cas9 endonuclease and a single guide RNA, that defines the genomic target, need to be present and co-localized within the nucleus for efficient gene-editing to occur. This work describes a new high-throughput screening platform for the optimization of CRISPR-Cas9 delivery strategies. By exploiting high content image analysis and microcontact printed plates, multi-parametric gene-editing outcome data from hundreds to thousands of isolated cell populations can be screened simultaneously. Employing this platform, we systematically screened four commercially available cationic lipid transfection materials with a range of RNAs encoding the CRISPR-Cas9 system. Analysis of Cas9 expression and editing of a fluorescent mCherry reporter transgene within human embryonic kidney cells was monitored over several days after transfection. Design of experiments analysis enabled rigorous evaluation of delivery materials and RNA concentration conditions. The results of this analysis indicated that the concentration and identity of transfection material have significantly greater effect on gene-editing than ratio or total amount of RNA. Cell subpopulation analysis on microcontact printed plates, further revealed that low cell number and high Cas9 expression, 24 hours after CRISPR-Cas9 delivery, were strong predictors of gene-editing outcomes. These results suggest design principles for the development of materials and transfection strategies with lipid-based materials. This platform could be applied to rapidly optimize materials for gene-editing in a variety of cell/tissue types in order to advance genomic medicine, regenerative biology and drug discovery. PMID:26747759

  6. Use of nonlinear design optimization techniques in the comparison of battery discharger topologies for the space platform

    NASA Technical Reports Server (NTRS)

    Sable, Dan M.; Cho, Bo H.; Lee, Fred C.

    1990-01-01

    A detailed comparison of a boost converter, a voltage-fed, autotransformer converter, and a multimodule boost converter, designed specifically for the space platform battery discharger, is performed. Computer-based nonlinear optimization techniques are used to facilitate an objective comparison. The multimodule boost converter is shown to be the optimum topology at all efficiencies. The margin is greatest at 97 percent efficiency. The multimodule, multiphase boost converter combines the advantages of high efficiency, light weight, and ample margin on the component stresses, thus ensuring high reliability.

  7. Ecological dynamics of influenza A viruses: cross-species transmission and global migration

    PubMed Central

    Ren, Hongguang; Jin, Yuan; Hu, Mingda; Zhou, Jing; Song, Ting; Huang, Zhisong; Li, Beiping; Li, Kaiwu; Zhou, Wei; Dai, Hongmei; Shi, Weifeng; Yue, Junjie; Liang, Long

    2016-01-01

    A comprehensive study of cross-species transmission and inter-regional migration would provide insights into the global ecology of influenza A viruses (IAVs). To this end, we assembled 17,241 non-redundant IAV whole-genome sequences with complete epidemiological information. We hierarchically divided the movements of IAVs into the cross-species transmission in each region and the inter-regional migration driven by each host species. We then systematically identified the potential cross-species transmission and inter-regional migration events. Cross-species transmission networks were obtained for each gene segment of the IAVs. Waterfowl, domestic birds and swine showed higher degrees of connection than did other species in all of the transmission networks. East Asia and Southeast Asia were hot regions for avian-mammal transmissions. Swine and migratory birds were the dominant species for global virus delivery. The importance of swine was reemphasized because it has not only provided an environment for adaptive evolution during the avian-human transmission of IAVs (as incubators) but also served as a key species for the global dissemination of the viruses (as carriers). Therefore, monitoring the global live trade of swine and survey of migratory birds along flyways would be beneficial for the prevention and control of IAVs. PMID:27827462

  8. EMERGING MOLECULAR AND COMPUTATIONAL APPROACHES FOR CROSS-SPECIES EXTRAPLATIONS: A WORKSHOP SUMMARY REPORT

    EPA Science Inventory

    Benson, W.H., R.T. Di Giulio, J.C. Cook, J. Freedman, R.L. Malek, C. Thompson and D. Versteeg. In press. Emerging Molecular and Computational Approaches for Cross-Species Extrapolations: A Workshop Summary Report (Abstract). To be presented at the SETAC Fourth World Congress, 14-...

  9. Cross-species gene-family fluctuations reveal the dynamics of horizontal transfers.

    PubMed

    Grilli, Jacopo; Romano, Mariacristina; Bassetti, Federico; Cosentino Lagomarsino, Marco

    2014-06-01

    Prokaryotes vary their protein repertoire mainly through horizontal transfer and gene loss. To elucidate the links between these processes and the cross-species gene-family statistics, we perform a large-scale data analysis of the cross-species variability of gene-family abundance (the number of members of the family found on a given genome). We find that abundance fluctuations are related to the rate of horizontal transfers. This is rationalized by a minimal theoretical model, which predicts this link. The families that are not captured by the model show abundance profiles that are markedly peaked around a mean value, possibly because of specific abundance selection. Based on these results, we define an abundance variability index that captures a family's evolutionary behavior (and thus some of its relevant functional properties) purely based on its cross-species abundance fluctuations. Analysis and model, combined, show a quantitative link between cross-species family abundance statistics and horizontal transfer dynamics, which can be used to analyze genome 'flux'. Groups of families with different values of the abundance variability index correspond to genome sub-parts having different plasticity in terms of the level of horizontal exchange allowed by natural selection.

  10. Discovery and bio-optimization of human antibody therapeutics using the XenoMouse® transgenic mouse platform.

    PubMed

    Foltz, Ian N; Gunasekaran, Kannan; King, Chadwick T

    2016-03-01

    Since the late 1990s, the use of transgenic animal platforms has transformed the discovery of fully human therapeutic monoclonal antibodies. The first approved therapy derived from a transgenic platform--the epidermal growth factor receptor antagonist panitumumab to treat advanced colorectal cancer--was developed using XenoMouse(®) technology. Since its approval in 2006, the science of discovering and developing therapeutic monoclonal antibodies derived from the XenoMouse(®) platform has advanced considerably. The emerging array of antibody therapeutics developed using transgenic technologies is expected to include antibodies and antibody fragments with novel mechanisms of action and extreme potencies. In addition to these impressive functional properties, these antibodies will be designed to have superior biophysical properties that enable highly efficient large-scale manufacturing methods. Achieving these new heights in antibody drug discovery will ultimately bring better medicines to patients. Here, we review best practices for the discovery and bio-optimization of monoclonal antibodies that fit functional design goals and meet high manufacturing standards.

  11. Optimal control/structure integrated design of a flexible space platform with articulated appendages

    NASA Technical Reports Server (NTRS)

    Kelkar, Atul G.; Alberts, Thomas E.

    1991-01-01

    A complete set of closed form symbolic equations are developed for a 2-D model of a system comprised of a flexible platform with articulated appendages. The system considered has a flexible two link manipulator, with joint compliance, at one end of the flexible platform and an articulated antenna on the other end. The model is formulated using a Lagrangian approach which incorporates homogeneous transformation matrices, similar to those typically seen in the robotics literature, for the kinematic representation. The integrated control/structure design strategy considered emphasizes rapid system response and minimal structural weight. Constraints are included to keep antenna pointing error to a minimum, and at the same time achieve accurate end point positioning of the manipulator with minimal oscillations.

  12. Cross-species amplification and optimization of microsatellite markers for use in six Neotropical parrots.

    PubMed

    Gebhardt, Kara J; Waits, Lisette P

    2008-07-01

    Short amplicon primers were redesigned for 17 microsatellite loci developed in St. Vincent's Amazon and six loci developed in blue-and-yellow macaw and tested using six species of Neotropical parrot. Polymorphism was observed at 12 loci in blue-and-yellow macaw, 10 in red-and-green macaw, 11 in scarlet macaw, 10 in chestnut-fronted macaw, 11 in red-bellied macaw and 16 in mealy parrot. Number of alleles per locus ranged from two to 23 and expected heterozygosity ranged from 0.05 to 0.95. The resulting multiplexed loci will be useful in evaluating genetic diversity, genetic structure and mating system in Neotropical parrots.

  13. Comparison and optimization of two MALDI-TOF MS platforms for the identification of medically relevant yeast species.

    PubMed

    Pence, M A; McElvania TeKippe, E; Wallace, M A; Burnham, C-A D

    2014-10-01

    The rapid identification of yeast is essential for the optimization of antifungal therapy. The objective of our study was to evaluate two matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) platforms, the bioMérieux VITEK MS (IVD Knowledgebase v.2.0) and Bruker Biotyper (software version 3.1), for the rapid identification of medically relevant yeast. One hundred and seventeen isolates, representing six genera and 18 species, were analyzed using multiple direct smear methods to optimize identification. Sequence analysis was the gold standard for comparison. Isolates were analyzed with VITEK MS using the direct smear method +/- a 25 % formic acid on-plate extraction. For Biotyper, isolates were analyzed using direct smear without formic acid, and with 25 % and 100 % formic acid on-plate extractions. When all methods were included, VITEK MS correctly identified 113 (96.6 %) isolates after 24 h with one misidentification, and Biotyper correctly identified 77 (65.8 %) isolates using a threshold of ≥2.0 with no misidentifications. Using a revised threshold of ≥1.7, Biotyper correctly identified 103 (88.0 %) isolates, with 3 (2.6 %) misidentifications. For both platforms, the number of identifications was significantly increased using a formic acid overlay (VITEK MS, p < 0.01; Biotyper, p < 0.001), and reducing the Biotyper threshold from ≥2.0 to ≥1.7 significantly increased the rate of identification (p < 0.001). The data in this study demonstrate that the direct smear method with on-plate formic acid extraction can be used for yeast identification on both MS platforms, and more isolates are identified using the VITEK MS system (p < 0.01).

  14. Feline immunodeficiency virus cross-species transmission: Implications for emergence of new lentiviral infections

    USGS Publications Warehouse

    Lee, Justin; Malmberg, Jennifer L.; Wood, Britta A.; Hladky, Sahaja; Troyer, Ryan; Roelke, Melody; Cunningham, Mark W.; McBride, Roy; Vickers, Winston; Boyce, Walter; Boydston, Erin E.; Serieys, Laurel E.K.; Riley, Seth P D; Crooks, Kevin R.; VandeWoude, Sue

    2016-01-01

    Owing to a complex history of host-parasite coevolution, lentiviruses exhibit a high degree of species specificity. Given the well-documented viral archeology of HIV emergence following human exposures to SIV, understanding processes that promote successful cross-species lentiviral transmissions is highly relevant. We have previously reported natural cross-species transmission of a subtype of feline immunodeficiency virus, puma lentivirus A (PLVA), between bobcats (Lynx rufus) and mountain lions (Puma concolor) in a small number of animals in California and Florida. In this study we investigate host-specific selection pressures, within-host viral fitness, and inter- vs. intra-species transmission patterns among a larger collection of PLV isolates from free-ranging bobcats and mountain lions. Analysis of proviral and viral RNA levels demonstrates that PLVA fitness is severely restricted in mountain lions compared to bobcats. We document evidence of diversifying selection in three of six PLVA genomes from mountain lions, but did not detect selection among twenty PLVA isolates from bobcats. These findings support that PLVA is a bobcat-adapted virus, which is less fit in mountain lions and under intense selection pressure in the novel host. Ancestral reconstruction of transmission events reveals intraspecific PLVA transmission has occurred among panthers (Puma concolor coryi) in Florida following initial cross-species infection from bobcats. In contrast, interspecific transmission from bobcats to mountain lions predominates in California. These findings document outcomes of cross-species lentiviral transmission events among felids that compare to emergence of HIV from nonhuman primates.IMPORTANCE Cross-species transmission episodes can be singular, dead-end events or can result in viral replication and spread in the new species. The factors that determine which outcome will occur are complex, and the risk of new virus emergence is therefore difficult to predict. Here

  15. Feline Immunodeficiency Virus Cross-Species Transmission: Implications for Emergence of New Lentiviral Infections.

    PubMed

    Lee, Justin; Malmberg, Jennifer L; Wood, Britta A; Hladky, Sahaja; Troyer, Ryan; Roelke, Melody; Cunningham, Mark; McBride, Roy; Vickers, Winston; Boyce, Walter; Boydston, Erin; Serieys, Laurel; Riley, Seth; Crooks, Kevin; VandeWoude, Sue

    2017-03-01

    Owing to a complex history of host-parasite coevolution, lentiviruses exhibit a high degree of species specificity. Given the well-documented viral archeology of human immunodeficiency virus (HIV) emergence following human exposures to simian immunodeficiency virus (SIV), an understanding of processes that promote successful cross-species lentiviral transmissions is highly relevant. We previously reported natural cross-species transmission of a subtype of feline immunodeficiency virus, puma lentivirus A (PLVA), between bobcats (Lynx rufus) and mountain lions (Puma concolor) for a small number of animals in California and Florida. In this study, we investigate host-specific selection pressures, within-host viral fitness, and inter- versus intraspecies transmission patterns among a larger collection of PLV isolates from free-ranging bobcats and mountain lions. Analyses of proviral and viral RNA levels demonstrate that PLVA fitness is severely restricted in mountain lions compared to that in bobcats. We document evidence of diversifying selection in three of six PLVA genomes from mountain lions, but we did not detect selection among 20 PLVA isolates from bobcats. These findings support the hypothesis that PLVA is a bobcat-adapted virus which is less fit in mountain lions and under intense selection pressure in the novel host. Ancestral reconstruction of transmission events reveals that intraspecific PLVA transmission has occurred among panthers (Puma concolor coryi) in Florida following the initial cross-species infection from bobcats. In contrast, interspecific transmission from bobcats to mountain lions predominates in California. These findings document outcomes of cross-species lentiviral transmission events among felids that compare to the emergence of HIV from nonhuman primates.IMPORTANCE Cross-species transmission episodes can be singular, dead-end events or can result in viral replication and spread in the new species. The factors that determine which outcome

  16. A Neuron-Based Screening Platform for Optimizing Genetically-Encoded Calcium Indicators

    PubMed Central

    Schreiter, Eric R.; Hasseman, Jeremy P.; Tsegaye, Getahun; Fosque, Benjamin F.; Behnam, Reza; Shields, Brenda C.; Ramirez, Melissa; Kimmel, Bruce E.; Kerr, Rex A.; Jayaraman, Vivek; Looger, Loren L.; Svoboda, Karel; Kim, Douglas S.

    2013-01-01

    Fluorescent protein-based sensors for detecting neuronal activity have been developed largely based on non-neuronal screening systems. However, the dynamics of neuronal state variables (e.g., voltage, calcium, etc.) are typically very rapid compared to those of non-excitable cells. We developed an electrical stimulation and fluorescence imaging platform based on dissociated rat primary neuronal cultures. We describe its use in testing genetically-encoded calcium indicators (GECIs). Efficient neuronal GECI expression was achieved using lentiviruses containing a neuronal-selective gene promoter. Action potentials (APs) and thus neuronal calcium levels were quantitatively controlled by electrical field stimulation, and fluorescence images were recorded. Images were segmented to extract fluorescence signals corresponding to individual GECI-expressing neurons, which improved sensitivity over full-field measurements. We demonstrate the superiority of screening GECIs in neurons compared with solution measurements. Neuronal screening was useful for efficient identification of variants with both improved response kinetics and high signal amplitudes. This platform can be used to screen many types of sensors with cellular resolution under realistic conditions where neuronal state variables are in relevant ranges with respect to timing and amplitude. PMID:24155972

  17. A neuron-based screening platform for optimizing genetically-encoded calcium indicators.

    PubMed

    Wardill, Trevor J; Chen, Tsai-Wen; Schreiter, Eric R; Hasseman, Jeremy P; Tsegaye, Getahun; Fosque, Benjamin F; Behnam, Reza; Shields, Brenda C; Ramirez, Melissa; Kimmel, Bruce E; Kerr, Rex A; Jayaraman, Vivek; Looger, Loren L; Svoboda, Karel; Kim, Douglas S

    2013-01-01

    Fluorescent protein-based sensors for detecting neuronal activity have been developed largely based on non-neuronal screening systems. However, the dynamics of neuronal state variables (e.g., voltage, calcium, etc.) are typically very rapid compared to those of non-excitable cells. We developed an electrical stimulation and fluorescence imaging platform based on dissociated rat primary neuronal cultures. We describe its use in testing genetically-encoded calcium indicators (GECIs). Efficient neuronal GECI expression was achieved using lentiviruses containing a neuronal-selective gene promoter. Action potentials (APs) and thus neuronal calcium levels were quantitatively controlled by electrical field stimulation, and fluorescence images were recorded. Images were segmented to extract fluorescence signals corresponding to individual GECI-expressing neurons, which improved sensitivity over full-field measurements. We demonstrate the superiority of screening GECIs in neurons compared with solution measurements. Neuronal screening was useful for efficient identification of variants with both improved response kinetics and high signal amplitudes. This platform can be used to screen many types of sensors with cellular resolution under realistic conditions where neuronal state variables are in relevant ranges with respect to timing and amplitude.

  18. "Controlled, cross-species dataset for exploring biases in genome annotation and modification profiles".

    PubMed

    McAfee, Alison; Michaud, Sarah; Foster, Leonard J

    2015-12-01

    Since the sequencing of the honey bee genome, proteomics by mass spectrometry has become increasingly popular for biological analyses of this insect; but we have observed that the number of honey bee protein identifications is consistently low compared to other organisms [1]. In this dataset, we use nanoelectrospray ionization-coupled liquid chromatography-tandem mass spectrometry (nLC-MS/MS) to systematically investigate the root cause of low honey bee proteome coverage. To this end, we present here data from three key experiments: a controlled, cross-species analyses of samples from Apis mellifera, Drosophila melanogaster, Caenorhabditis elegans, Saccharomyces cerevisiae, Mus musculus and Homo sapiens; a proteomic analysis of an individual honey bee whose genome was also sequenced; and a cross-tissue honey bee proteome comparison. The cross-species dataset was interrogated to determine relative proteome coverages between species, and the other two datasets were used to search for polymorphic sequences and to compare protein cleavage profiles, respectively.

  19. Optimal Defaults in the Prevention of Pediatric Obesity: From Platform to Practice

    PubMed Central

    Radnitz, Cynthia; Loeb, Katharine L; DiMatteo, Julie; Keller, Kathleen L.; Zucker, Nancy; Schwartz, Marlene B.

    2014-01-01

    The term “optimal defaults” refers to imparting pre-selected choices which are designed to produce a desired behavior change. The concept is attractive to policymakers because it steers people toward desirable behaviors while preserving free choice through the ability to opt out. It has been found to be a powerful behavioral determinant in areas such as pension plan enrollment, organ donation, and green energy utilization. We discuss how optimal defaults can be applied to pediatric obesity prevention in several domains including public policy, institutional, private sector, and home environment. Although there are obstacles to overcome in implementing optimal defaults, it is a promising component to incorporate in a multi-level strategy for preventing pediatric obesity. PMID:25328903

  20. Vocal learning in Grey parrots: A brief review of perception, production, and cross-species comparisons.

    PubMed

    Pepperberg, Irene M

    2010-10-01

    This chapter briefly reviews what is known-and what remains to be understood-about Grey parrot vocal learning. I review Greys' physical capacities-issues of auditory perception and production-then discuss how these capacities are used in vocal learning and can be recruited for referential communication with humans. I discuss cross-species comparisons where applicable and conclude with a description of recent research that integrates issues of reference, production and perception.

  1. Identification of cross-species shared transcriptional networks of diabetic nephropathy in human and mouse glomeruli.

    PubMed

    Hodgin, Jeffrey B; Nair, Viji; Zhang, Hongyu; Randolph, Ann; Harris, Raymond C; Nelson, Robert G; Weil, E Jennifer; Cavalcoli, James D; Patel, Jignesh M; Brosius, Frank C; Kretzler, Matthias

    2013-01-01

    Murine models are valuable instruments in defining the pathogenesis of diabetic nephropathy (DN), but they only partially recapitulate disease manifestations of human DN, limiting their utility. To define the molecular similarities and differences between human and murine DN, we performed a cross-species comparison of glomerular transcriptional networks. Glomerular gene expression was profiled in patients with early type 2 DN and in three mouse models (streptozotocin DBA/2, C57BLKS db/db, and eNOS-deficient C57BLKS db/db mice). Species-specific transcriptional networks were generated and compared with a novel network-matching algorithm. Three shared human-mouse cross-species glomerular transcriptional networks containing 143 (Human-DBA STZ), 97 (Human-BKS db/db), and 162 (Human-BKS eNOS(-/-) db/db) gene nodes were generated. Shared nodes across all networks reflected established pathogenic mechanisms of diabetes complications, such as elements of Janus kinase (JAK)/signal transducer and activator of transcription (STAT) and vascular endothelial growth factor receptor (VEGFR) signaling pathways. In addition, novel pathways not previously associated with DN and cross-species gene nodes and pathways unique to each of the human-mouse networks were discovered. The human-mouse shared glomerular transcriptional networks will assist DN researchers in selecting mouse models most relevant to the human disease process of interest. Moreover, they will allow identification of new pathways shared between mice and humans.

  2. Cross-Species Network Analysis Uncovers Conserved Nitrogen-Regulated Network Modules in Rice1[OPEN

    PubMed Central

    Obertello, Mariana; Shrivastava, Stuti; Katari, Manpreet S.; Coruzzi, Gloria M.

    2015-01-01

    In this study, we used a cross-species network approach to uncover nitrogen (N)-regulated network modules conserved across a model and a crop species. By translating gene network knowledge from the data-rich model Arabidopsis (Arabidopsis thaliana) to a crop, rice (Oryza sativa), we identified evolutionarily conserved N-regulatory modules as targets for translational studies to improve N use efficiency in transgenic plants. To uncover such conserved N-regulatory network modules, we first generated an N-regulatory network based solely on rice transcriptome and gene interaction data. Next, we enhanced the network knowledge in the rice N-regulatory network using transcriptome and gene interaction data from Arabidopsis and new data from Arabidopsis and rice plants exposed to the same N treatment conditions. This cross-species network analysis uncovered a set of N-regulated transcription factors (TFs) predicted to target the same genes and network modules in both species. Supernode analysis of the TFs and their targets in these conserved network modules uncovered genes directly related to N use (e.g. N assimilation) and to other shared biological processes indirectly related to N. This cross-species network approach was validated with members of two TF families in the supernode network, BASIC-LEUCINE ZIPPER TRANSCRIPTION FACTOR1-TGA and HYPERSENSITIVITY TO LOW PI-ELICITED PRIMARY ROOT SHORTENING1 (HRS1)/HRS1 Homolog family, which have recently been experimentally validated to mediate the N response in Arabidopsis. PMID:26045464

  3. A portable expression resource for engineering cross-species genetic circuits and pathways

    PubMed Central

    Kushwaha, Manish; Salis, Howard M.

    2015-01-01

    Genetic circuits and metabolic pathways can be reengineered to allow organisms to process signals and manufacture useful chemicals. However, their functions currently rely on organism-specific regulatory parts, fragmenting synthetic biology and metabolic engineering into host-specific domains. To unify efforts, here we have engineered a cross-species expression resource that enables circuits and pathways to reuse the same genetic parts, while functioning similarly across diverse organisms. Our engineered system combines mixed feedback control loops and cross-species translation signals to autonomously self-regulate expression of an orthogonal polymerase without host-specific promoters, achieving nontoxic and tuneable gene expression in diverse Gram-positive and Gram-negative bacteria. Combining 50 characterized system variants with mechanistic modelling, we show how the cross-species expression resource's dynamics, capacity and toxicity are controlled by the control loops' architecture and feedback strengths. We also demonstrate one application of the resource by reusing the same genetic parts to express a biosynthesis pathway in both model and non-model hosts. PMID:26184393

  4. Enzyme sequence similarity improves the reaction alignment method for cross-species pathway comparison

    SciTech Connect

    Ovacik, Meric A.; Androulakis, Ioannis P.

    2013-09-15

    Pathway-based information has become an important source of information for both establishing evolutionary relationships and understanding the mode of action of a chemical or pharmaceutical among species. Cross-species comparison of pathways can address two broad questions: comparison in order to inform evolutionary relationships and to extrapolate species differences used in a number of different applications including drug and toxicity testing. Cross-species comparison of metabolic pathways is complex as there are multiple features of a pathway that can be modeled and compared. Among the various methods that have been proposed, reaction alignment has emerged as the most successful at predicting phylogenetic relationships based on NCBI taxonomy. We propose an improvement of the reaction alignment method by accounting for sequence similarity in addition to reaction alignment method. Using nine species, including human and some model organisms and test species, we evaluate the standard and improved comparison methods by analyzing glycolysis and citrate cycle pathways conservation. In addition, we demonstrate how organism comparison can be conducted by accounting for the cumulative information retrieved from nine pathways in central metabolism as well as a more complete study involving 36 pathways common in all nine species. Our results indicate that reaction alignment with enzyme sequence similarity results in a more accurate representation of pathway specific cross-species similarities and differences based on NCBI taxonomy.

  5. Approaching the Functional Annotation of Fungal Virulence Factors Using Cross-Species Genetic Interaction Profiling

    PubMed Central

    Brown, Jessica C. S.; Madhani, Hiten D.

    2012-01-01

    In many human fungal pathogens, genes required for disease remain largely unannotated, limiting the impact of virulence gene discovery efforts. We tested the utility of a cross-species genetic interaction profiling approach to obtain clues to the molecular function of unannotated pathogenicity factors in the human pathogen Cryptococcus neoformans. This approach involves expression of C. neoformans genes of interest in each member of the Saccharomyces cerevisiae gene deletion library, quantification of their impact on growth, and calculation of the cross-species genetic interaction profiles. To develop functional predictions, we computed and analyzed the correlations of these profiles with existing genetic interaction profiles of S. cerevisiae deletion mutants. For C. neoformans LIV7, which has no S. cerevisiae ortholog, this profiling approach predicted an unanticipated role in the Golgi apparatus. Validation studies in C. neoformans demonstrated that Liv7 is a functional Golgi factor where it promotes the suppression of the exposure of a specific immunostimulatory molecule, mannose, on the cell surface, thereby inhibiting phagocytosis. The genetic interaction profile of another pathogenicity gene that lacks an S. cerevisiae ortholog, LIV6, strongly predicted a role in endosome function. This prediction was also supported by studies of the corresponding C. neoformans null mutant. Our results demonstrate the utility of quantitative cross-species genetic interaction profiling for the functional annotation of fungal pathogenicity proteins of unknown function including, surprisingly, those that are not conserved in sequence across fungi. PMID:23300468

  6. Approaching the functional annotation of fungal virulence factors using cross-species genetic interaction profiling.

    PubMed

    Brown, Jessica C S; Madhani, Hiten D

    2012-01-01

    In many human fungal pathogens, genes required for disease remain largely unannotated, limiting the impact of virulence gene discovery efforts. We tested the utility of a cross-species genetic interaction profiling approach to obtain clues to the molecular function of unannotated pathogenicity factors in the human pathogen Cryptococcus neoformans. This approach involves expression of C. neoformans genes of interest in each member of the Saccharomyces cerevisiae gene deletion library, quantification of their impact on growth, and calculation of the cross-species genetic interaction profiles. To develop functional predictions, we computed and analyzed the correlations of these profiles with existing genetic interaction profiles of S. cerevisiae deletion mutants. For C. neoformans LIV7, which has no S. cerevisiae ortholog, this profiling approach predicted an unanticipated role in the Golgi apparatus. Validation studies in C. neoformans demonstrated that Liv7 is a functional Golgi factor where it promotes the suppression of the exposure of a specific immunostimulatory molecule, mannose, on the cell surface, thereby inhibiting phagocytosis. The genetic interaction profile of another pathogenicity gene that lacks an S. cerevisiae ortholog, LIV6, strongly predicted a role in endosome function. This prediction was also supported by studies of the corresponding C. neoformans null mutant. Our results demonstrate the utility of quantitative cross-species genetic interaction profiling for the functional annotation of fungal pathogenicity proteins of unknown function including, surprisingly, those that are not conserved in sequence across fungi.

  7. Optimization of flow assisted entrapment of pollen grains in a microfluidic platform for tip growth analysis.

    PubMed

    Sanati Nezhad, Amir; Ghanbari, Mahmood; Agudelo, Carlos G; Naghavi, Mahsa; Packirisamy, Muthukumaran; Bhat, Rama B; Geitmann, Anja

    2014-02-01

    A biocompatible polydimethylsiloxane (PDMS) biomicrofluidic platform is designed, fabricated and tested to study protuberance growth of single plant cells in a micro-vitro environment. The design consists of an inlet to introduce the cell suspension into the chip, three outlets to conduct the medium or cells out of the chip, a main distribution chamber and eight microchannels connected to the main chamber to guide the growth of tip growing plant cells. The test cells used here were pollen grains which produce cylindrical protrusions called pollen tubes. The goal was to adjust the design of the microfluidic network with the aim to enhance the uniformly distributed positioning of pollen grains at the entrances of the microchannels and to provide identical fluid flow conditions for growing pollen tubes along each microchannel. Computational fluid analysis and experimental testing were carried out to estimate the trapping efficiencies of the different designs.

  8. Computational and experimental platform for understanding and optimizing water flux and salt rejection in nanoporous membranes.

    SciTech Connect

    Rempe, Susan B.

    2010-09-01

    Affordable clean water is both a global and a national security issue as lack of it can cause death, disease, and international tension. Furthermore, efficient water filtration reduces the demand for energy, another national issue. The best current solution to clean water lies in reverse osmosis (RO) membranes that remove salts from water with applied pressure, but widely used polymeric membrane technology is energy intensive and produces water depleted in useful electrolytes. Furthermore incremental improvements, based on engineering solutions rather than new materials, have yielded only modest gains in performance over the last 25 years. We have pursued a creative and innovative new approach to membrane design and development for cheap desalination membranes by approaching the problem at the molecular level of pore design. Our inspiration comes from natural biological channels, which permit faster water transport than current reverse osmosis membranes and selectively pass healthy ions. Aiming for an order-of-magnitude improvement over mature polymer technology carries significant inherent risks. The success of our fundamental research effort lies in our exploiting, extending, and integrating recent advances by our team in theory, modeling, nano-fabrication and platform development. A combined theoretical and experimental platform has been developed to understand the interplay between water flux and ion rejection in precisely-defined nano-channels. Our innovative functionalization of solid state nanoporous membranes with organic protein-mimetic polymers achieves 3-fold improvement in water flux over commercial RO membranes and has yielded a pending patent and industrial interest. Our success has generated useful contributions to energy storage, nanoscience, and membrane technology research and development important for national health and prosperity.

  9. Implementation of a genetically tuned neural platform in optimizing fluorescence from receptor-ligand binding interactions on microchips.

    PubMed

    Alvarado, Judith; Hanrahan, Grady; Nguyen, Huong T H; Gomez, Frank A

    2012-09-01

    This paper describes the use of a genetically tuned neural network platform to optimize the fluorescence realized upon binding 5-carboxyfluorescein-D-Ala-D-Ala-D-Ala (5-FAM-(D-Ala)(3) ) (1) to the antibiotic teicoplanin from Actinoplanes teichomyceticus electrostatically attached to a microfluidic channel originally modified with 3-aminopropyltriethoxysilane. Here, three parameters: (i) the length of time teicoplanin was in the microchannel; (ii) the length of time 1 was in the microchannel, thereby, in equilibrium with teicoplanin, and; (iii) the amount of time buffer was flushed through the microchannel to wash out any unbound 1 remaining in the channel, are examined at a constant concentration of 1, with neural network methodology applied to optimize fluorescence. Optimal neural structure provided a best fit model, both for the training set (r(2) = 0.985) and testing set (r(2) = 0.967) data. Simulated results were experimentally validated demonstrating efficiency of the neural network approach and proved superior to the use of multiple linear regression and neural networks using standard back propagation.

  10. Lipid nanoparticles as an emerging platform for cannabinoid delivery: physicochemical optimization and biocompatibility.

    PubMed

    Durán-Lobato, M; Martín-Banderas, L; Lopes, R; Gonçalves, L M D; Fernández-Arévalo, M; Almeida, A J

    2016-01-01

    This work aims at developing and optimizing a valuable oral delivery carrier for the cannabinoid derivative CB13, which presents a high therapeutic potential in chronic pain states that respond poorly to conventional analgesics, but also shows highly unfavorable physicochemical properties. CB13-loaded lipid nanoparticles (LNP) formulations were developed through solvent-emulsion evaporation and optimized in terms of physicochemical properties, long-term stability, integrity under gastric simulated conditions and in vitro interaction with NIH 3T3, HEK 293T and Caco-2 cells. An optimized formulation of LNP containing CB13 was obtained from a wide range of conditions assayed and analyzed. The selection of the lipid core, production conditions and the inclusion of lecithin proved to be key factors for the final properties of encapsulation, integrity and performance of the carriers. The LNP formulation proposed proved to be a promising carrier for the oral delivery of CB13, a cannabinoid with high therapeutic potential in chronic pain states that currently lack a valid oral treatment.

  11. Drug Target Optimization in Chronic Myeloid Leukemia Using Innovative Computational Platform

    NASA Astrophysics Data System (ADS)

    Chuang, Ryan; Hall, Benjamin A.; Benque, David; Cook, Byron; Ishtiaq, Samin; Piterman, Nir; Taylor, Alex; Vardi, Moshe; Koschmieder, Steffen; Gottgens, Berthold; Fisher, Jasmin

    2015-02-01

    Chronic Myeloid Leukemia (CML) represents a paradigm for the wider cancer field. Despite the fact that tyrosine kinase inhibitors have established targeted molecular therapy in CML, patients often face the risk of developing drug resistance, caused by mutations and/or activation of alternative cellular pathways. To optimize drug development, one needs to systematically test all possible combinations of drug targets within the genetic network that regulates the disease. The BioModelAnalyzer (BMA) is a user-friendly computational tool that allows us to do exactly that. We used BMA to build a CML network-model composed of 54 nodes linked by 104 interactions that encapsulates experimental data collected from 160 publications. While previous studies were limited by their focus on a single pathway or cellular process, our executable model allowed us to probe dynamic interactions between multiple pathways and cellular outcomes, suggest new combinatorial therapeutic targets, and highlight previously unexplored sensitivities to Interleukin-3.

  12. Lyophilized phytosomal nanocarriers as platforms for enhanced diosmin delivery: optimization and ex vivo permeation

    PubMed Central

    Freag, May S; Elnaggar, Yosra SR; Abdallah, Ossama Y

    2013-01-01

    Diosmin (DSN) is an outstanding phlebotonic flavonoid with a tolerable potential for the treatment of colon and hepatocellular carcinoma. Being highly insoluble, DSN bioavailability suffers from high inter-subject variation due to variable degrees of permeation. This work endeavored to develop novel DSN loaded phytosomes in order to improve drug dissolution and intestinal permeability. Three preparation methods (solvent evaporation, salting out, and lyophilization) were compared. Nanocarrier optimization encompassed different soybean phospholipid (SPC) types, different solvents, and different DSN:SPC molar ratios (1:1, 1:2, and 1:4). In vitro appraisal encompassed differential scanning calorimetry, infrared spectroscopy, particle size, zeta potential, polydispersity index, transmission electron microscopy, drug content, and in vitro stability. Comparative dissolution studies were performed under sink versus non-sink conditions. Ex vivo intestinal permeation studies were performed on rats utilizing noneverted sac technique and high-performance liquid chromatography analysis. The results revealed lyophilization as the optimum preparation technique using SPC and solvent mixture (Dimethyl sulphoxide:t-butylalchol) in a 1:2 ratio. Complex formation was contended by differential scanning calorimetry and infrared data. Optimal lyophilized phytosomal nanocarriers (LPNs) exhibited the lowest particle size (316 nm), adequate zeta-potential (−27 mV), and good in vitro stability. Well formed, discrete vesicles were revealed by transmission electron microscopy, drug content, and in vitro stability. Comparative dissolution studies were performed. LPNs demonstrated significant enhancement in DSN dissolution compared to crude drug, physical mixture, and generic and brand DSN products. Permeation studies revealed 80% DSN permeated from LPNs via oxygenated rat intestine compared to non-detectable amounts from suspension. In this study, LPNs (99% drug loading) could be successfully

  13. Experimental Cross-Species Infection of Common Marmosets by Titi Monkey Adenovirus

    PubMed Central

    Chen, Eunice C.; Liu, Maria; Brasky, Kathleen M.; Lanford, Robert E.; Kelly, Kristi R.; Bales, Karen L.; Schnurr, David P.; Canfield, Don R.; Patterson, Jean L.; Chiu, Charles Y.

    2013-01-01

    Adenoviruses are DNA viruses that infect a number of vertebrate hosts and are associated with both sporadic and epidemic disease in humans. We previously identified a novel adenovirus, titi monkey adenovirus (TMAdV), as the cause of a fulminant pneumonia outbreak in a colony of titi monkeys (Callicebus cupreus) at a national primate center in 2009. Serological evidence of infection by TMAdV was also found in a human researcher at the facility and household family member, raising concerns for potential cross-species transmission of the virus. Here we present experimental evidence of cross-species TMAdV infection in common marmosets (Callithrix jacchus). Nasal inoculation of a cell cultured-adapted TMAdV strain into three marmosets produced an acute, mild respiratory illness characterized by low-grade fever, reduced activity, anorexia, and sneezing. An increase in virus-specific neutralization antibody titers accompanied the development of clinical signs. Although serially collected nasal swabs were positive for TMAdV for at least 8 days, all 3 infected marmosets spontaneously recovered by day 12 post-inoculation, and persistence of the virus in tissues could not be established. Thus, the pathogenesis of experimental inoculation of TMAdV in common marmosets resembled the mild, self-limiting respiratory infection typically seen in immunocompetent human hosts rather than the rapidly progressive, fatal pneumonia observed in 19 of 23 titi monkeys during the prior 2009 outbreak. These findings further establish the potential for adenovirus cross-species transmission and provide the basis for development of a monkey model useful for assessing the zoonotic potential of adenoviruses. PMID:23894316

  14. Dissection of a Ciona regulatory element reveals complexity of cross-species enhancer activity

    PubMed Central

    Chen, Wei-Chung; Pauls, Stefan; Bacha, Jamil; Elgar, Greg; Loose, Matthew; Shimeld, Sebastian M.

    2014-01-01

    Vertebrate genomes share numerous conserved non-coding elements, many of which function as enhancer elements and are hypothesised to be under evolutionary constraint due to a need to be bound by combinations of sequence-specific transcription factors. In contrast, few such conserved elements can be detected between vertebrates and their closest invertebrate relatives. Despite this lack of sequence identity, cross-species transgenesis has identified some cases where non-coding DNA from invertebrates drives reporter gene expression in transgenic vertebrates in patterns reminiscent of the expression of vertebrate orthologues. Such instances are presumed to reflect the presence of conserved suites of binding sites in the regulatory regions of invertebrate and vertebrate orthologues, such that both regulatory elements can correctly interpret the trans-activating environment. Shuffling of binding sites has been suggested to lie behind loss of sequence conservation; however this has not been experimentally tested. Here we examine the underlying basis of enhancer activity for the Ciona intestinalis βγ-crystallin gene, which drives expression in the lens of transgenic vertebrates despite the Ciona lineage predating the evolution of the lens. We construct an interactive gene regulatory network (GRN) for vertebrate lens development, allowing network interactions to be robustly catalogued and conserved network components and features to be identified. We show that a small number of binding motifs are necessary for Ciona βγ-crystallin expression, and narrow down the likely factors that bind to these motifs. Several of these overlap with the conserved core of the vertebrate lens GRN, implicating these sites in cross species function. However when we test these motifs in a transgenic vertebrate they prove to be dispensable for reporter expression in the lens. These results show that current models depicting cross species enhancer function as dependent on conserved binding

  15. Frequent cross-species transmission of parvoviruses among diverse carnivore hosts

    USGS Publications Warehouse

    Allison, Andrew B.; Kohler, Dennis J.; Fox, Karen A.; Brown, Justin D.; Gerhold, Richard W.; Shearn-Bochsler, Valerie I.; Dubovi, Edward J.; Parrish, Colin R.; Holmes, Edward C.

    2013-01-01

    Although parvoviruses are commonly described in domestic carnivores, little is known about their biodiversity in nondomestic species. A phylogenetic analysis of VP2 gene sequences from puma, coyote, gray wolf, bobcat, raccoon, and striped skunk revealed two major groups related to either feline panleukopenia virus (“FPV-like”) or canine parvovirus (“CPV-like”). Cross-species transmission was commonplace, with multiple introductions into each host species but, with the exception of raccoons, relatively little evidence for onward transmission in nondomestic species.

  16. A modular and adaptive mass spectrometry-based platform for support of bioprocess development toward optimal host cell protein clearance.

    PubMed

    Walker, Donald E; Yang, Feng; Carver, Joseph; Joe, Koman; Michels, David A; Yu, X Christopher

    2017-03-27

    A modular and adaptive mass spectrometry (MS)-based platform was developed to provide fast, robust and sensitive host cell protein (HCP) analytics to support process development. This platform relies on one-dimensional ultra-high performance liquid chromatography (1D UHPLC) combined with several different MS data acquisition strategies to meet the needs of purification process development. The workflow was designed to allow HCP composition and quantitation for up to 20 samples per day, a throughput considered essential for real time bioprocess development support. With data-dependent acquisition (DDA), the 1D UHPLC-MS/MS method had excellent speed and demonstrated robustness in detecting unknown HCPs at ≥ 50 ng/mg (ppm) level. Combining 1D UHPLC with sequential window acquisition of all theoretical spectra (SWATH) MS enabled simultaneous detection and quantitation of all HCPs in single-digit ng/mg range within 1 hour, demonstrating for the first time the benefit of SWATH MS as a technique for HCP analysis. As another alternative, a targeted MS approach can be used to track the clearance of specific known HCP under various process conditions. This study highlights the importance of designing a robust LC-MS/MS workflow that not only allows HCP discovery, but also affords greatly improved process knowledge and capability in HCP removal. As an orthogonal and complementary detection approach to traditional HCP analysis by enzyme-linked immunosorbent assay, the reported LC-MS/MS workflow supports the development of bioprocesses with optimal HCP clearance and the production of safe and high quality therapeutic biopharmaceuticals.

  17. Cross-Species Protection Mediated by a Bordetella bronchiseptica Strain Lacking Antigenic Homologs Present in Acellular Pertussis Vaccines▿

    PubMed Central

    Sukumar, Neelima; Sloan, Gina Parise; Conover, Matt S.; Love, Cheraton F.; Mattoo, Seema; Kock, Nancy D.; Deora, Rajendar

    2010-01-01

    The Bordetella species are Gram-negative bacterial pathogens that are characterized by long-term colonization of the mammalian respiratory tract and are causative agents of respiratory diseases in humans and animals. Despite widespread and efficient vaccination, there has been a world-wide resurgence of pertussis, which remains the leading cause of vaccine-preventable death in developed countries. It has been proposed that current acellular vaccines (Pa) composed of only a few bacterial proteins may be less efficacious because of vaccine-induced antigenic shifts and adaptations. To gain insight into the development of a newer generation of vaccines, we constructed a Bordetella bronchiseptica strain (LPaV) that does not express the antigenic homologs included in any of the Pa vaccines currently in use. This strain also lacks adenylate cyclase toxin, an essential virulence factor, and BipA, a surface protein. While LPaV colonized the mouse nose as efficiently as the wild-type strain, it was highly deficient in colonization of the lower respiratory tract and was attenuated in induction of inflammation and injury to the lungs. Strikingly, to our surprise, we found that in an intranasal murine challenge model, LPaV elicited cross-species protection against both B. bronchiseptica and Bordetella pertussis. Our data suggest the presence of immunogenic protective components other than those included in the pertussis vaccine. Combined with the whole-genome sequences of many Bordetella spp. that are available, the results of this study should serve as a platform for strategic development of the next generation of acellular pertussis vaccines. PMID:20176797

  18. A cross-species socio-emotional behaviour development revealed by a multivariate analysis.

    PubMed

    Koshiba, Mamiko; Senoo, Aya; Mimura, Koki; Shirakawa, Yuka; Karino, Genta; Obara, Saya; Ozawa, Shinpei; Sekihara, Hitomi; Fukushima, Yuta; Ueda, Toyotoshi; Kishino, Hirohisa; Tanaka, Toshihisa; Ishibashi, Hidetoshi; Yamanouchi, Hideo; Yui, Kunio; Nakamura, Shun

    2013-01-01

    Recent progress in affective neuroscience and social neurobiology has been propelled by neuro-imaging technology and epigenetic approach in neurobiology of animal behaviour. However, quantitative measurements of socio-emotional development remains lacking, though sensory-motor development has been extensively studied in terms of digitised imaging analysis. Here, we developed a method for socio-emotional behaviour measurement that is based on the video recordings under well-defined social context using animal models with variously social sensory interaction during development. The behaviour features digitized from the video recordings were visualised in a multivariate statistic space using principal component analysis. The clustering of the behaviour parameters suggested the existence of species- and stage-specific as well as cross-species behaviour modules. These modules were used to characterise the behaviour of children with or without autism spectrum disorders (ASDs). We found that socio-emotional behaviour is highly dependent on social context and the cross-species behaviour modules may predict neurobiological basis of ASDs.

  19. Cross-species identification of genomic drivers of squamous cell carcinoma development across preneoplastic intermediates

    PubMed Central

    Chitsazzadeh, Vida; Coarfa, Cristian; Drummond, Jennifer A.; Nguyen, Tri; Joseph, Aaron; Chilukuri, Suneel; Charpiot, Elizabeth; Adelmann, Charles H.; Ching, Grace; Nguyen, Tran N.; Nicholas, Courtney; Thomas, Valencia D.; Migden, Michael; MacFarlane, Deborah; Thompson, Erika; Shen, Jianjun; Takata, Yoko; McNiece, Kayla; Polansky, Maxim A.; Abbas, Hussein A.; Rajapakshe, Kimal; Gower, Adam; Spira, Avrum; Covington, Kyle R.; Xiao, Weimin; Gunaratne, Preethi; Pickering, Curtis; Frederick, Mitchell; Myers, Jeffrey N.; Shen, Li; Yao, Hui; Su, Xiaoping; Rapini, Ronald P.; Wheeler, David A.; Hawk, Ernest T.; Flores, Elsa R.; Tsai, Kenneth Y.

    2016-01-01

    Cutaneous squamous cell carcinoma (cuSCC) comprises 15–20% of all skin cancers, accounting for over 700,000 cases in USA annually. Most cuSCC arise in association with a distinct precancerous lesion, the actinic keratosis (AK). To identify potential targets for molecularly targeted chemoprevention, here we perform integrated cross-species genomic analysis of cuSCC development through the preneoplastic AK stage using matched human samples and a solar ultraviolet radiation-driven Hairless mouse model. We identify the major transcriptional drivers of this progression sequence, showing that the key genomic changes in cuSCC development occur in the normal skin to AK transition. Our data validate the use of this ultraviolet radiation-driven mouse cuSCC model for cross-species analysis and demonstrate that cuSCC bears deep molecular similarities to multiple carcinogen-driven SCCs from diverse sites, suggesting that cuSCC may serve as an effective, accessible model for multiple SCC types and that common treatment and prevention strategies may be feasible. PMID:27574101

  20. Restrictions to cross species transmission of lentiviral infection gleaned from studies of FIV

    PubMed Central

    Troyer, Jennifer; Poss, Mary

    2009-01-01

    More than 40 species of primates and over 20 species of cats harbor antibodies that sero-react to lentiviral antigens. In nearly all cases where viral genetic analysis has been conducted, each host species is infected with a unique lentivirus. Though lentivirus clades within a species can be substantially divergent, they are typically monophyletic within that species. A notable significant departure from this observation is apparent cross-species transmission of FIV between bobcats (Lynx rufus) and pumas (Puma concolor) in southern California that has occurred at least three times; evidence from one bobcat sequence suggests this cross-over may have also occurred in Florida between bobcats and the endangered Florida panther. Several other isolated reports demonstrate cross-species transmission of FIV isolates among captive animals housed in close proximity, and it is well established that HIV-1 and HIV-2 arose from human contact with SIV-infected nonhuman primates. Using an experimental model, we have determined that domestic cats (Felis catus) are susceptible to FIVs originating from pumas or lions. While infections are initially replicative, and animals seroconvert, within a relatively short period of time circulating virus is reduced to nearly undetectable levels in a majority of animals. This diminution of viral load is proportional to initial viral peak. Although viral reservoirs can be identified in gastrointestinal tissues, most viral genomes recovered peripherally are highly mutated, suggesting that the non-adapted host successfully inhibits normal viral replication, leading to replication incompetent viral progeny. Mechanisms possible for such restriction of cross-species infections in natural settings include: 1. Lack of contact conducive to lentiviral transmission between infected and shedding animals of different species; 2. Lack of suitable receptor repertoire to allow viral entry to susceptible cells of a new species; 3. Cellular machinery in the new

  1. Restrictions to cross-species transmission of lentiviral infection gleaned from studies of FIV.

    PubMed

    VandeWoude, Sue; Troyer, Jennifer; Poss, Mary

    2010-03-15

    More than 40 species of primates and over 20 species of cats harbor antibodies that sero-react to lentiviral antigens. In nearly all cases where viral genetic analysis has been conducted, each host species is infected with a unique lentivirus. Though lentivirus clades within a species can be substantially divergent, they are typically monophyletic within that species. A notable significant departure from this observation is apparent cross-species transmission of FIV between bobcats (Lynx rufus) and pumas (Puma concolor) in Southern California that has occurred at least three times; evidence from one bobcat sequence suggests this cross-over may have also occurred in Florida between bobcats and the endangered Florida panther. Several other isolated reports demonstrate cross-species transmission of FIV isolates among captive animals housed in close proximity, and it is well established that HIV-1 and HIV-2 arose from human contact with SIV-infected non-human primates. Using an experimental model, we have determined that domestic cats (Felis catus) are susceptible to FIVs originating from pumas or lions. While infections are initially replicative, and animals seroconvert, within a relatively short period of time circulating virus is reduced to nearly undetectable levels in a majority of animals. This diminution of viral load is proportional to initial viral peak. Although viral reservoirs can be identified in gastrointestinal tissues, most viral genomes recovered peripherally are highly mutated, suggesting that the non-adapted host successfully inhibits normal viral replication, leading to replication incompetent viral progeny. Mechanisms possible for such restriction of cross-species infections in natural settings include: (1) Lack of contact conducive to lentiviral transmission between infected and shedding animals of different species; (2) Lack of suitable receptor repertoire to allow viral entry to susceptible cells of a new species; (3) Cellular machinery in the

  2. HEK293 cell culture media study towards bioprocess optimization: Animal derived component free and animal derived component containing platforms.

    PubMed

    Liste-Calleja, Leticia; Lecina, Martí; Cairó, Jordi Joan

    2014-04-01

    The increasing demand for biopharmaceuticals produced in mammalian cells has lead industries to enhance bioprocess volumetric productivity through different strategies. Among those strategies, cell culture media development is of major interest. In the present work, several commercially available culture media for Human Embryonic Kidney cells (HEK293) were evaluated in terms of maximal specific growth rate and maximal viable cell concentration supported. The main objective was to provide different cell culture platforms which are suitable for a wide range of applications depending on the type and the final use of the product obtained. Performing simple media supplementations with and without animal derived components, an enhancement of cell concentration from 2 × 10(6) cell/mL to 17 × 10(6) cell/mL was achieved in batch mode operation. Additionally, the media were evaluated for adenovirus production as a specific application case of HEK293 cells. None of the supplements interfered significantly with the adenovirus infection although some differences were encountered in viral productivity. To the best of our knowledge, the high cell density achieved in the work presented has never been reported before in HEK293 batch cell cultures and thus, our results are greatly promising to further study cell culture strategies in bioreactor towards bioprocess optimization.

  3. Flavones as Quorum Sensing Inhibitors Identified by a Newly Optimized Screening Platform Using Chromobacterium violaceum as Reporter Bacteria.

    PubMed

    Skogman, Malena E; Kanerva, Sonja; Manner, Suvi; Vuorela, Pia M; Fallarero, Adyary

    2016-09-10

    Quorum sensing (QS) is the process by which bacteria produce and detect signal molecules to coordinate their collective behavior. This intercellular communication is a relevant target for anti-biofilm therapies. Here we have optimized a screening-applicable assay to search for new quorum sensing inhibitors from natural compound libraries. In this system, QS is correlated with the production of violacein, which is directly controlled by the LuxI/LuxR system in Chromobacterium violaceum ATCC 31532. The parallel use of C. violaceum Tn5-mutant CV026, which depends on auto-inducer addition, allows simultaneous discrimination of compounds that act as quenchers of the AHL signal (quorum quenchers). The incorporation of a redox stain into the platform allowed further distinction between QS inhibitors, quorum quenchers and antibacterial compounds. A pilot screening was performed with 465 natural and synthetic flavonoids. All the most active compounds were flavones and they displayed potencies (IC50) in the range of 3.69 to 23.35 μM. These leads were particularly promising as they inhibited the transition from microcolonies into mature biofilms from Escherichia coli and Pseudomonas aeruginosa strains. This approach can be very effective in identifying new antimicrobials posing lesser risks of resistance.

  4. Using the Eclipse Parallel Tools Platform to Assist Earth Science Model Development and Optimization on High Performance Computers

    NASA Astrophysics Data System (ADS)

    Alameda, J. C.

    2011-12-01

    Development and optimization of computational science models, particularly on high performance computers, and with the advent of ubiquitous multicore processor systems, practically on every system, has been accomplished with basic software tools, typically, command-line based compilers, debuggers, performance tools that have not changed substantially from the days of serial and early vector computers. However, model complexity, including the complexity added by modern message passing libraries such as MPI, and the need for hybrid code models (such as openMP and MPI) to be able to take full advantage of high performance computers with an increasing core count per shared memory node, has made development and optimization of such codes an increasingly arduous task. Additional architectural developments, such as many-core processors, only complicate the situation further. In this paper, we describe how our NSF-funded project, "SI2-SSI: A Productive and Accessible Development Workbench for HPC Applications Using the Eclipse Parallel Tools Platform" (WHPC) seeks to improve the Eclipse Parallel Tools Platform, an environment designed to support scientific code development targeted at a diverse set of high performance computing systems. Our WHPC project to improve Eclipse PTP takes an application-centric view to improve PTP. We are using a set of scientific applications, each with a variety of challenges, and using PTP to drive further improvements to both the scientific application, as well as to understand shortcomings in Eclipse PTP from an application developer perspective, to drive our list of improvements we seek to make. We are also partnering with performance tool providers, to drive higher quality performance tool integration. We have partnered with the Cactus group at Louisiana State University to improve Eclipse's ability to work with computational frameworks and extremely complex build systems, as well as to develop educational materials to incorporate into

  5. Characterization of highly informative cross-species microsatellite panels for the Australian dugong (Dugong dugon) and Florida manatee (Trichechus manatus latirostris) including five novel primers.

    PubMed

    Hunter, Margaret Kellogg; Broderick, Damien; Ovenden, Jennifer R; Tucker, Kimberly Pause; Bonde, Robert K; McGuire, Peter M; Lanyon, Janet M

    2010-03-01

    The Australian dugong (Dugong dugon) and Florida manatee (Trichechus manatus latirostris) are threatened species of aquatic mammals in the order Sirenia. Sirenian conservation and management actions would benefit from a more complete understanding of genetic diversity and population structure. Generally, species-specific microsatellite markers are employed in conservation genetic studies; however, robust markers can be difficult and costly to isolate. To increase the number of available markers, dugong and manatee microsatellite primers were evaluated for cross-species amplification. Furthermore, one manatee and four dugong novel primers are reported. After polymerase chain reaction optimization, 23 (92%) manatee primers successfully amplified dugong DNA, of which 11 (48%) were polymorphic. Of the 32 dugong primers tested, 27 (84%) yielded product in the manatee, of which 17 (63%) were polymorphic. Dugong and manatee primers were compared and the most informative markers were selected to create robust and informative marker-panels for each species. These cross-species microsatellite marker-panels can be employed to assess other sirenian populations and can provide beneficial information for the protection and management of these unique mammals.

  6. Cross-species transmission and emergence of novel viruses from birds.

    PubMed

    Chan, Jasper Fuk-Woo; To, Kelvin Kai-Wang; Chen, Honglin; Yuen, Kwok-Yung

    2015-02-01

    Birds, the only living member of the Dinosauria clade, are flying warm-blooded vertebrates displaying high species biodiversity, roosting and migratory behavior, and a unique adaptive immune system. Birds provide the natural reservoir for numerous viral species and therefore gene source for evolution, emergence and dissemination of novel viruses. The intrusions of human into natural habitats of wild birds, the domestication of wild birds as pets or racing birds, and the increasing poultry consumption by human have facilitated avian viruses to cross species barriers to cause zoonosis. Recently, a novel adenovirus was exclusively found in birds causing an outbreak of Chlamydophila psittaci infection among birds and humans. Instead of being the primary cause of an outbreak by jumping directly from bird to human, a novel avian virus can be an augmenter of another zoonotic agent causing the outbreak. A comprehensive avian virome will improve our understanding of birds' evolutionary dynamics.

  7. Cross Species Genomic Analysis Identifies a Mouse Model as Undifferentiated Pleomorphic Sarcoma/Malignant Fibrous Histiocytoma

    PubMed Central

    Mito, Jeffrey K.; Riedel, Richard F.; Dodd, Leslie; Lahat, Guy; Lazar, Alexander J.; Dodd, Rebecca D.; Stangenberg, Lars; Eward, William C.; Hornicek, Francis J.; Yoon, Sam S.; Brigman, Brian E.; Jacks, Tyler; Lev, Dina; Mukherjee, Sayan; Kirsch, David G.

    2009-01-01

    Undifferentiated pleomorphic sarcoma/Malignant Fibrous Histiocytoma (MFH) is one of the most common subtypes of human soft tissue sarcoma. Using cross species genomic analysis, we define a geneset from the LSL-KrasG12D; Trp53Flox/Flox mouse model of soft tissue sarcoma that is highly enriched in human MFH. With this mouse geneset as a filter, we identify expression of the RAS target FOXM1 in human MFH. Expression of Foxm1 is elevated in mouse sarcomas that metastasize to the lung and tissue microarray analysis of human MFH correlates overexpression of FOXM1 with metastasis. These results suggest that genomic alterations present in human MFH are conserved in the LSL-KrasG12D; p53Flox/Flox mouse model of soft tissue sarcoma and demonstrate the utility of this pre-clinical model. PMID:19956606

  8. Hepatitis B virus lineages in mammalian hosts: Potential for bidirectional cross-species transmission

    PubMed Central

    Bonvicino, Cibele R; Moreira, Miguel A; Soares, Marcelo A

    2014-01-01

    The hepatitis B virus (HBV) is a cosmopolitan infectious agent currently affecting over 350 million people worldwide, presently accounting for more than two billion infections. In addition to man, other hepatitis virus strains infect species of several mammalian families of the Primates, Rodentia and Chiroptera orders, in addition to birds. The mounting evidence of HBV infection in African, Asian and neotropical primates draws attention to the potential cross-species, zoonotic transmission of these viruses to man. Moreover, recent evidence also suggests the humans may also function as a source of viral infection to other mammals, particularly to domestic animals like poultry and swine. In this review, we list all evidence of HBV and HBV-like infection of nonhuman mammals and discuss their potential roles as donors or recipients of these viruses to humans and to other closely-related species. PMID:24976704

  9. Serologic survey for cross-species pathogens in urban coyotes (Canis latrans), Colorado, USA.

    PubMed

    Malmlov, Ashley; Breck, Stewart; Fry, Tricia; Duncan, Colleen

    2014-10-01

    Abstract As coyotes (Canis latrans) adapt to living in urban environments, the opportunity for cross-species transmission of pathogens may increase. We investigated the prevalence of antibodies to pathogens that are either zoonotic or affect multiple animal species in urban coyotes in the Denver metropolitan area, Colorado, USA, in 2012. We assayed for antibodies to canine parvovirus-2, canine distemper virus, rabies virus, Toxoplasma gondii, Yersinia pestis, and serotypes of Leptospira interrogans. Overall, 84% of the animals had antibodies to canine parvovirus-2, 44% for canine distemper virus, 20% for T. gondii (IgG), 28% for Y. pestis, and 4% for L. interrogans serotype Grippotyphosa. No neutralizing antibodies were detected to rabies virus, T. gondii (IgM), or L. interrogans serotypes other than Grippotyphosa. With 88% of animals exposed to at least one pathogen, our results suggest that coyotes may serve as important reservoirs and sentinels for etiologic agents.

  10. COLOMBOS v3.0: leveraging gene expression compendia for cross-species analyses

    PubMed Central

    Moretto, Marco; Sonego, Paolo; Dierckxsens, Nicolas; Brilli, Matteo; Bianco, Luca; Ledezma-Tejeida, Daniela; Gama-Castro, Socorro; Galardini, Marco; Romualdi, Chiara; Laukens, Kris; Collado-Vides, Julio; Meysman, Pieter; Engelen, Kristof

    2016-01-01

    COLOMBOS is a database that integrates publicly available transcriptomics data for several prokaryotic model organisms. Compared to the previous version it has more than doubled in size, both in terms of species and data available. The manually curated condition annotation has been overhauled as well, giving more complete information about samples’ experimental conditions and their differences. Functionality-wise cross-species analyses now enable users to analyse expression data for all species simultaneously, and identify candidate genes with evolutionary conserved expression behaviour. All the expression-based query tools have undergone a substantial improvement, overcoming the limit of enforced co-expression data retrieval and instead enabling the return of more complex patterns of expression behaviour. COLOMBOS is freely available through a web application at http://colombos.net/. The complete database is also accessible via REST API or downloadable as tab-delimited text files. PMID:26586805

  11. Cross-species infection of hepatitis E virus in a zoo-like location, including birds.

    PubMed

    Zhang, W; Shen, Q; Mou, J; Yang, Z B; Yuan, C L; Cui, L; Zhu, J G; Hua, X G; Xu, C M; Hu, J

    2008-08-01

    Hepatitis E virus (HEV) is a zoonotic pathogen of which several species of animals are considered to be reservoirs. Thirty-eight faecal samples, obtained from 22 species of animals including birds in a wildlife first-aid centre in Eastern China, were tested for HEV RNA. Our survey revealed that in total 28.9% (95% confidence interval 14.5-43.4) of the faecal samples from various mammals and birds were HEV RNA positive. Sequence and phylogenetic analyses of the 11 isolates demonstrated that all sequences clustered in genotype 4 with 96-100% identity to each other. In addition, serum samples from seven animal handlers have shown that five (71.4%) were seropositive. The findings imply that cross-species infection of HEV had probably occurred in this zoo-like location, and moreover, birds can be infected naturally with mammalian HEV.

  12. Microsatellite loci in the tiger shark and cross-species amplification using pyrosequencing technology

    PubMed Central

    Mendes, Natália J.; Cruz, Vanessa P.; Ashikaga, Fernando Y.; Camargo, Sâmia M.; Oliveira, Claudio; Piercy, Andrew N.; Burgess, George H.; Coelho, Rui; Santos, Miguel N.; Foresti, Fausto

    2016-01-01

    The tiger shark (Galeocerdo cuvier) has a global distribution in tropical and warm temperate seas, and it is caught in numerous fisheries worldwide, mainly as bycatch. It is currently assessed as near threatened by the International Union for Conservation of Nature (IUCN) Red List. In this study, we identified nine microsatellite loci through next generation sequencing (454 pyrosequencing) using 29 samples from the western Atlantic. The genetic diversity of these loci were assessed and revealed a total of 48 alleles ranging from 3 to 7 alleles per locus (average of 5.3 alleles). Cross-species amplification was successful at most loci for other species such as Carcharhinus longimanus, C. acronotus and Alopias superciliosus. Given the potential applicability of genetic markers for biological conservation, these data may contribute to the population assessment of this and other species of sharks worldwide. PMID:27635306

  13. Cross-species transferability of microsatellite markers in the genus Lippia.

    PubMed

    Santos, C P; Rocha, D S; Bajay, M M; Santos, F R C; Campos, J B; Pinheiro, J B; Zucchi, M I; Silva-Mann, R; Arrigoni-Blank, M F; Blank, A F

    2014-11-27

    The cross-species transferability of 20 microsatellite markers was tested in the genus Lippia. Eleven markers were polymorphic after screening 19 accessions of Lippia sidoides and Lippia gracilis maintained in the Active Germplasm Bank (AGB) from Universidade Federal de Sergipe. Additionally, 40 accessions of Lippia spp were collected in Sergipe to increase the germplasm bank. A total of 23, 22, and 36 alleles were identified, with an average of 2.3, 2.2, and 3.27 alleles per locus, respectively, for each group. The markers that were used were efficient tools to access genetic diversity in the germplasm bank and will be useful for further research aiming at the conservation and management of these important aromatic species.

  14. Evolutionary factors affecting the cross-species utility of newly developed microsatellite markers in seabirds.

    PubMed

    Moodley, Yoshan; Masello, Juan F; Cole, Theresa L; Calderon, Luciano; Munimanda, Gopi K; Thali, Marco R; Alderman, Rachael; Cuthbert, Richard J; Marin, Manuel; Massaro, Melanie; Navarro, Joan; Phillips, Richard A; Ryan, Peter G; Suazo, Cristián G; Cherel, Yves; Weimerskirch, Henri; Quillfeldt, Petra

    2015-09-01

    Microsatellite loci are ideal for testing hypotheses relating to genetic segregation at fine spatio-temporal scales. They are also conserved among closely related species, making them potentially useful for clarifying interspecific relationships between recently diverged taxa. However, mutations at primer binding sites may lead to increased nonamplification, or disruptions that may result in decreased polymorphism in nontarget species. Furthermore, high mutation rates and constraints on allele size may also with evolutionary time, promote an increase in convergently evolved allele size classes, biasing measures of interspecific genetic differentiation. Here, we used next-generation sequencing to develop microsatellite markers from a shotgun genome sequence of the sub-Antarctic seabird, the thin-billed prion (Pachyptila belcheri), that we tested for cross-species amplification in other Pachyptila and related sub-Antarctic species. We found that heterozygosity decreased and the proportion of nonamplifying loci increased with phylogenetic distance from the target species. Surprisingly, we found that species trees estimated from interspecific FST provided better approximations of mtDNA relationships among the studied species than those estimated using DC , even though FST was more affected by null alleles. We observed a significantly nonlinear second order polynomial relationship between microsatellite and mtDNA distances. We propose that the loss of linearity with increasing mtDNA distance stems from an increasing proportion of homoplastic allele size classes that are identical in state, but not identical by descent. Therefore, despite high cross-species amplification success and high polymorphism among the closely related Pachyptila species, we caution against the use of microsatellites in phylogenetic inference among distantly related taxa.

  15. Alternative splicing in teleost fish genomes: same-species and cross-species analysis and comparisons.

    PubMed

    Lu, Jianguo; Peatman, Eric; Wang, Wenqi; Yang, Qing; Abernathy, Jason; Wang, Shaolin; Kucuktas, Huseyin; Liu, Zhanjiang

    2010-06-01

    Alternative splicing (AS) is a mechanism by which the coding diversity of the genome can be greatly increased. Rates of AS are known to vary according to the complexity of eukaryotic species potentially explaining the tremendous phenotypic diversity among species with similar numbers of coding genes. Little is known, however, about the nature or rate of AS in teleost fish. Here, we report the characteristics of AS in teleost fish and classification and frequency of five canonical AS types. We conducted both same-species and cross-species analysis utilizing the Genome Mapping and Alignment Program (GMAP) and an AS pipeline (ASpipe) to study AS in four genome-enabled species (Danio rerio, Oryzias latipes, Gasterosteus aculeatus, and Takifugu rubripes) and one species lacking a complete genome sequence, Ictalurus punctatus. AS frequency was lowest in the highly duplicated genome of zebrafish (17% of mapped genes). The compact genome of the pufferfish showed the highest occurrence of AS (approximately 43% of mapped genes). An inverse correlation between AS frequency and genome size was consistent across all analyzed species. Cross-species comparisons utilizing zebrafish as the reference genome allowed the identification of additional putative AS genes not revealed by zebrafish transcripts. Approximately, 50% of AS genes identified by same-species comparisons were shared among two or more species. A searchable website, the Teleost Alternative Splicing Database, was created to allow easy identification and visualization of AS transcripts in the studied teleost genomes. Our results and associated database should further our understanding of alternative splicing as an important functional and evolutionary mechanism in the genomes of teleost fish.

  16. Ketamine Suppresses the Ventral Striatal Response to Reward Anticipation: A Cross-Species Translational Neuroimaging Study

    PubMed Central

    Francois, Jennifer; Grimm, Oliver; Schwarz, Adam J; Schweiger, Janina; Haller, Leila; Risterucci, Celine; Böhringer, Andreas; Zang, Zhenxiang; Tost, Heike; Gilmour, Gary; Meyer-Lindenberg, Andreas

    2016-01-01

    Convergent evidence implicates regional neural responses to reward anticipation in the pathogenesis of several psychiatric disorders, such as schizophrenia, where blunted ventral striatal responses to positive reward are observed in patients and at-risk populations. In vivo oxygen amperometry measurements in the ventral striatum in awake, behaving rats reveal reward-related tissue oxygen changes that closely parallel blood oxygen level dependent (BOLD) signal changes observed in human functional magnetic resonance imaging (fMRI), suggesting that a cross-species approach targeting this mechanism might be feasible in psychopharmacology. The present study explored modulatory effects of acute, subanaesthetic doses of ketamine—a pharmacological model widely used in psychopharmacological research, both preclinically and clinically—on ventral striatum activity during performance of a reward anticipation task in both species, using fMRI in humans and in vivo oxygen amperometry in rats. In a region-of-interest analysis conducted following a cross-over placebo and ketamine study in human subjects, an attenuated ventral striatal response during reward anticipation was observed following ketamine relative to placebo during performance of a monetary incentive delay task. In rats, a comparable attenuation of ventral striatal signal was found after ketamine challenge, relative to vehicle, in response to a conditioned stimulus that predicted delivery of reward. This study provides the first data in both species demonstrating an attenuating effect of acute ketamine on reward-related ventral striatal (O2) and fMRI signals. These findings may help elucidate a deeper mechanistic understanding of the potential role of ketamine as a model for psychosis, show that cross-species pharmacological experiments targeting reward signaling are feasible, and suggest this phenotype as a promising translational biomarker for the development of novel compounds, assessment of disease status, and

  17. Cross-Species Gene Expression Analysis of Species Specific Differences in the Preclinical Assessment of Pharmaceutical Compounds

    PubMed Central

    Okyere, John; Oppon, Ekow; Dzidzienyo, Daniel; Sharma, Lav; Ball, Graham

    2014-01-01

    Animals are frequently used as model systems for determination of safety and efficacy in pharmaceutical research and development. However, significant quantitative and qualitative differences exist between humans and the animal models used in research. This is as a result of genetic variation between human and the laboratory animal. Therefore the development of a system that would allow the assessment of all molecular differences between species after drug exposure would have a significant impact on drug evaluation for toxicity and efficacy. Here we describe a cross-species microarray methodology that identifies and selects orthologous probes after cross-species sequence comparison to develop an orthologous cross-species gene expression analysis tool. The assumptions made by the use of this orthologous gene expression strategy for cross-species extrapolation is that; conserved changes in gene expression equate to conserved pharmacodynamic endpoints. This assumption is supported by the fact that evolution and selection have maintained the structure and function of many biochemical pathways over time, resulting in the conservation of many important processes. We demonstrate this cross-species methodology by investigating species specific differences of the peroxisome proliferator-activator receptor (PPAR) α response in rat and human. PMID:24823806

  18. Ion Channel Function and Cross-Species Determinants in Viral Assembly of Nonprimate Hepacivirus p7

    PubMed Central

    Walter, Stephanie; Bollenbach, Alexander; Doerrbecker, Juliane; Pfaender, Stephanie; Brown, Richard J. P.; Vieyres, Gabrielle; Scott, Claire; Foster, Richard; Kumar, Abhinav; Zitzmann, Nicole; Griffin, Stephen; Penin, François; Pietschmann, Thomas

    2016-01-01

    ABSTRACT Nonprimate hepacivirus (NPHV), the closest homolog of hepatitis C virus (HCV) described to date, has recently been discovered in horses. Even though the two viruses share a similar genomic organization, conservation of the encoded hepaciviral proteins remains undetermined. The HCV p7 protein is localized within endoplasmic reticulum (ER) membranes and is important for the production of infectious particles. In this study, we analyzed the structural and functional features of NPHV p7 in addition to its role during virus assembly. Three-dimensional homology models for NPHV p7 using various nuclear magnetic resonance spectroscopy (NMR) structures were generated, highlighting the conserved residues important for ion channel function. By applying a liposome permeability assay, we observed that NPHV p7 exhibited liposome permeability features similar to those of HCV p7, indicative of similar ion channel activity. Next, we characterized the viral protein using a p7-based trans-complementation approach. A similar subcellular localization pattern at the ER membrane was observed, although production of infectious particles was likely hindered by genetic incompatibilities with HCV proteins. To further characterize these cross-species constraints, chimeric viruses were constructed by substituting different regions of HCV p7 with NPHV p7. The N terminus and transmembrane domains were nonexchangeable and therefore constitute a cross-species barrier in hepaciviral assembly. In contrast, the basic loop and the C terminus of NPHV p7 were readily exchangeable, allowing production of infectious trans-complemented viral particles. In conclusion, comparison of NPHV and HCV p7 revealed structural and functional homology of these proteins, including liposome permeability, and broadly acting determinants that modulate hepaciviral virion assembly and contribute to the host-species barrier were identified. IMPORTANCE The recent discovery of new relatives of hepatitis C virus (HCV

  19. Molecular Epidemiology of Cross-Species Giardia duodenalis Transmission in Western Uganda

    PubMed Central

    Johnston, Amanda R.; Gillespie, Thomas R.; Rwego, Innocent B.; Tranby McLachlan, Traci L.; Kent, Angela D.; Goldberg, Tony L.

    2010-01-01

    Background Giardia duodenalis is prevalent in tropical settings where diverse opportunities exist for transmission between people and animals. We conducted a cross-sectional study of G. duodenalis in people, livestock, and wild primates near Kibale National Park, Uganda, where human-livestock-wildlife interaction is high due to habitat disturbance. Our goal was to infer the cross-species transmission potential of G. duodenalis using molecular methods and to investigate clinical consequences of infection. Methodology/Principal Findings Real-time PCR on DNA extracted from fecal samples revealed a combined prevalence of G. duodenalis in people from three villages of 44/108 (40.7%), with prevalence reaching 67.5% in one village. Prevalence rates in livestock and primates were 12.4% and 11.1%, respectively. Age was associated with G. duodenalis infection in people (higher prevalence in individuals ≤15 years) and livestock (higher prevalence in subadult versus adult animals), but other potential risk factors in people (gender, contact with domestic animals, working in fields, working in forests, source of drinking water, and medication use) were not. G. duodenalis infection was not associated with gastrointestinal symptoms in people, nor was clinical disease noted in livestock or primates. Sequence analysis of four G. duodenalis genes identified assemblage AII in humans, assemblage BIV in humans and endangered red colobus monkeys, and assemblage E in livestock and red colobus, representing the first documentation of assemblage E in a non-human primate. In addition, genetic relationships within the BIV assemblage revealed sub-clades of identical G. duodenalis sequences from humans and red colobus. Conclusions/Significance Our finding of G. duodenalis in people and primates (assemblage BIV) and livestock and primates (assemblage E) underscores that cross-species transmission of multiple G. duodenalis assemblages may occur in locations such as western Uganda where people

  20. Evolution of genome organizations of squirrels (Sciuridae) revealed by cross-species chromosome painting.

    PubMed

    Li, Tangliang; O'Brien, Patricia C M; Biltueva, Larisa; Fu, Beiyuan; Wang, Jinhuan; Nie, Wenhui; Ferguson-Smith, Malcolm A; Graphodatsky, Alexander S; Yang, Fengtang

    2004-01-01

    With complete sets of chromosome-specific painting probes derived from flow-sorted chromosomes of human and grey squirrel (Sciurus carolinensis), the whole genome homologies between human and representatives of tree squirrels (Sciurus carolinensis, Callosciurus erythraeus), flying squirrels (Petaurista albiventer) and chipmunks (Tamias sibiricus) have been defined by cross-species chromosome painting. The results show that, unlike the highly rearranged karyotypes of mouse and rat, the karyotypes of squirrels are highly conserved. Two methods have been used to reconstruct the genome phylogeny of squirrels with the laboratory rabbit (Oryctolagus cuniculus) as the out-group: (1) phylogenetic analysis by parsimony using chromosomal characters identified by comparative cytogenetic approaches; (2) mapping the genome rearrangements onto recently published sequence-based molecular trees. Our chromosome painting results, in combination with molecular data, show that flying squirrels are phylogenetically close to New World tree squirrels. Chromosome painting and G-banding comparisons place chipmunks (Tamias sibiricus ), with a derived karyotype, outside the clade comprising tree and flying squirrels. The superorder Glires (orde Rodentia + order Lagomorpha) is firmly supported by two conserved syntenic associations between human chromosomes 1 and 10p homologues, and between 9 and 11 homologues.

  1. Development of polymorphic SSR markers in the razor clam (Sinonovacula constricta) and cross-species amplification.

    PubMed

    Dong, Y H; Yao, H H; Sun, C S; Lv, D M; Li, M Q; Lin, Z H

    2016-01-26

    Next-generation sequencing provides large-scale sequencing data with relative ease and at a reasonable cost, making it possible to identify a large amount of SSR markers in a timely and cost-effective manner. On the basis of the transcriptome database of Sinonovacula constricta obtained by Illumina/Solexa pyrosequencing, 60 polymorphic SSR markers were developed and characterized in 30 individuals. The number of alleles per polymorphic locus ranged from 2 to 7 with an average of 3.75 alleles. The observed and expected heterozygosities varied from 0.050 to 1.000 and from 0.050 to 0.836, respectively. Nineteen loci significantly deviated from Hardy-Weinberg equilibrium (P < 0.01) after Bonferroni's correction for multiple tests. In addition, interspecific transferability revealed that 20 polymorphic loci in Solen linearis were first characterized in this study. To the best of our knowledge, this is the highest number of SSRs in S. constricta and the first report of cross-species amplification. These novel polymorphic SSR markers will be particularly useful for conservation genetics, evolutionary studies, genetic trait mapping, and marker assisted selection in the species.

  2. Role of multiple hosts in the cross-species transmission and emergence of a pandemic parvovirus.

    PubMed

    Allison, Andrew B; Harbison, Carole E; Pagan, Israel; Stucker, Karla M; Kaelber, Jason T; Brown, Justin D; Ruder, Mark G; Keel, M Kevin; Dubovi, Edward J; Holmes, Edward C; Parrish, Colin R

    2012-01-01

    Understanding the mechanisms of cross-species virus transmission is critical to anticipating emerging infectious diseases. Canine parvovirus type 2 (CPV-2) emerged as a variant of a feline parvovirus when it acquired mutations that allowed binding to the canine transferrin receptor type 1 (TfR). However, CPV-2 was soon replaced by a variant virus (CPV-2a) that differed in antigenicity and receptor binding. Here we show that the emergence of CPV involved an additional host range variant virus that has circulated undetected in raccoons for at least 24 years, with transfers to and from dogs. Raccoon virus capsids showed little binding to the canine TfR, showed little infection of canine cells, and had altered antigenic structures. Remarkably, in capsid protein (VP2) phylogenies, most raccoon viruses fell as evolutionary intermediates between the CPV-2 and CPV-2a strains, suggesting that passage through raccoons assisted in the evolution of CPV-2a. This highlights the potential role of alternative hosts in viral emergence.

  3. Multidirectional cross-species painting illuminates the history of karyotypic evolution in Perissodactyla.

    PubMed

    Trifonov, Vladimir A; Stanyon, Roscoe; Nesterenko, Anastasia I; Fu, Beiyuan; Perelman, Polina L; O'Brien, Patricia C M; Stone, Gary; Rubtsova, Nadezhda V; Houck, Marlys L; Robinson, Terence J; Ferguson-Smith, Malcolm A; Dobigny, Gauthier; Graphodatsky, Alexander S; Yang, Fengtang

    2008-01-01

    The order Perissodactyla, the group of odd-toed ungulates, includes three extant families: Equidae, Tapiridae, and Rhinocerotidae. The extremely rapid karyotypic diversification in perissodactyls has so far prevented the establishment of genome-wide homology maps between these three families by traditional cytogenetic approaches. Here we report the first genome-wide comparative chromosome maps of African rhinoceroses, four tapir species, four equine species, and humans. These maps were established by multidirectional chromosome painting, with paint probes derived from flow-sorted chromosomes of Equus grevyi, Tapirus indicus, and Ceratotherium simum as well as painting probes from horse and human. The Malayan tapir (Tapirus indicus), Baird's tapir (T. bairdii), mountain tapir (T. pinchaque), lowland tapir (T. terrestris), and onager (E. hemionus onager), were studied by cross-species chromosome painting for the first time. Our results, when integrated with previously published comparative chromosome maps of the other perissodactyl species, have enabled the reconstruction of perissodactyl, ceratomorph, and equid ancestral karyotypes, and the identification of the defining evolutionary chromosomal rearrangements along each lineage. Our results allow a more reliable estimate of the mode and tempo of evolutionary chromosomal rearrangements, revealing a striking switch between the slowly evolving ceratomorphs and extremely rapidly evolving equids.

  4. Aleutian mink disease virus in striped skunks (Mephitis mephitis): evidence for cross-species spillover.

    PubMed

    Nituch, Larissa A; Bowman, Jeff; Wilson, Paul J; Schulte-Hostedde, Albrecht I

    2015-04-01

    Aleutian mink disease virus (AMDV) causes a parvovirus infection, initially characterized in American mink (Neovison vison), that may have harmful effects on wild populations of susceptible animals. In North America, where American mink are native, the origin, host range, and prevalence of AMDV in wild species is not clear. We studied striped skunks (Mephitis mephitis) and raccoons (Procyon lotor) to determine whether species sympatric with mink are potential reservoirs in the transmission of AMDV to wild mink and mink farms. Antibodies to AMDV were detected in 41% of skunk serum samples (143/347) and AMDV nucleic acids were detected in 32% (14/40) of skunk spleen samples by PCR, indicating that AMDV exposure and infection were frequent in skunks. We detected no AMDV antibodies in 144 raccoon blood samples. Phylogenetic analysis revealed a newly identified AMDV haplogroup consisting of isolates from Ontario skunks and a free-ranging domestic mink from Ontario. Our findings of frequent AMDV infection in skunks, close genetic similarity between skunk and mink AMDV isolates, and evidence of AMDV transmission from skunks to mink support the hypothesis that skunks may be acting as alternative hosts and reservoirs of AMDV to wild mink through cross-species virus spillover.

  5. Cross species selection scans identify components of C4 photosynthesis in the grasses.

    PubMed

    Huang, Pu; Studer, Anthony J; Schnable, James C; Kellogg, Elizabeth A; Brutnell, Thomas P

    2017-01-01

    C4 photosynthesis is perhaps one of the best examples of convergent adaptive evolution with over 25 independent origins in the grasses (Poaceae) alone. The availability of high quality grass genome sequences presents new opportunities to explore the mechanisms underlying this complex trait using evolutionary biology-based approaches. In this study, we performed genome-wide cross-species selection scans in C4 lineages to facilitate discovery of C4 genes. The study was enabled by the well conserved collinearity of grass genomes and the recently sequenced genome of a C3 panicoid grass, Dichanthelium oligosanthes This method, in contrast to previous studies, does not rely on any a priori knowledge of the genes that contribute to biochemical or anatomical innovations associated with C4 photosynthesis. We identified a list of 88 candidate genes that include both known and potentially novel components of the C4 pathway. This set includes the carbon shuttle enzymes pyruvate, phosphate dikinase, phosphoenolpyruvate carboxylase and NADP malic enzyme as well as several predicted transporter proteins that likely play an essential role in promoting the flux of metabolites between the bundle sheath and mesophyll cells. Importantly, this approach demonstrates the application of fundamental molecular evolution principles to dissect the genetic basis of a complex photosynthetic adaptation in plants. Furthermore, we demonstrate how the output of the selection scans can be combined with expression data to provide additional power to prioritize candidate gene lists and suggest novel opportunities for pathway engineering.

  6. Cross-Species Functional Genomic Analysis Identifies Resistance Genes of the Histone Deacetylase Inhibitor Valproic Acid

    PubMed Central

    Forthun, Rakel Brendsdal; SenGupta, Tanima; Skjeldam, Hanne Kim; Lindvall, Jessica Margareta; McCormack, Emmet; Gjertsen, Bjørn Tore; Nilsen, Hilde

    2012-01-01

    The mechanisms of successful epigenetic reprogramming in cancer are not well characterized as they involve coordinated removal of repressive marks and deposition of activating marks by a large number of histone and DNA modification enzymes. Here, we have used a cross-species functional genomic approach to identify conserved genetic interactions to improve therapeutic effect of the histone deacetylase inhibitor (HDACi) valproic acid, which increases survival in more than 20% of patients with advanced acute myeloid leukemia (AML). Using a bidirectional synthetic lethality screen revealing genes that increased or decreased VPA sensitivity in C. elegans, we identified novel conserved sensitizers and synthetic lethal interactors of VPA. One sensitizer identified as a conserved determinant of therapeutic success of HDACi was UTX (KDM6A), which demonstrates a functional relationship between protein acetylation and lysine-specific methylation. The synthetic lethal screen identified resistance programs that compensated for the HDACi-induced global hyper-acetylation, and confirmed MAPKAPK2, HSP90AA1, HSP90AB1 and ACTB as conserved hubs in a resistance program for HDACi that are drugable in human AML cell lines. Hence, these resistance hubs represent promising novel targets for refinement of combinatorial epigenetic anti-cancer therapy. PMID:23155442

  7. Cross-Species Extrapolation of Models for Predicting Lead Transfer from Soil to Wheat Grain

    PubMed Central

    Liu, Ke; Lv, Jialong; Dai, Yunchao; Zhang, Hong; Cao, Yingfei

    2016-01-01

    The transfer of Pb from the soil to crops is a serious food hygiene security problem in China because of industrial, agricultural, and historical contamination. In this study, the characteristics of exogenous Pb transfer from 17 Chinese soils to a popular wheat variety (Xiaoyan 22) were investigated. In addition, bioaccumulation prediction models of Pb in grain were obtained based on soil properties. The results of the analysis showed that pH and OC were the most important factors contributing to Pb uptake by wheat grain. Using a cross-species extrapolation approach, the Pb uptake prediction models for cultivar Xiaoyan 22 in different soil Pb levels were satisfactorily applied to six additional non-modeled wheat varieties to develop a prediction model for each variety. Normalization of the bioaccumulation factor (BAF) to specific soil physico-chemistry is essential, because doing so could significantly reduce the intra-species variation of different wheat cultivars in predicted Pb transfer and eliminate the influence of soil properties on ecotoxicity parameters for organisms of interest. Finally, the prediction models were successfully verified against published data (including other wheat varieties and crops) and used to evaluate the ecological risk of Pb for wheat in contaminated agricultural soils. PMID:27518712

  8. Cross-species assessments of motor and exploratory behavior related to bipolar disorder.

    PubMed

    Henry, Brook L; Minassian, Arpi; Young, Jared W; Paulus, Martin P; Geyer, Mark A; Perry, William

    2010-07-01

    Alterations in exploratory behavior are a fundamental feature of bipolar mania, typically characterized as motor hyperactivity and increased goal-directed behavior in response to environmental cues. In contrast, abnormal exploration associated with schizophrenia and depression can manifest as prominent withdrawal, limited motor activity, and inattention to the environment. While motor abnormalities are cited frequently as clinical manifestations of these disorders, relatively few empirical studies have quantified human exploratory behavior. This article reviews the literature characterizing motor and exploratory behavior associated with bipolar disorder and genetic and pharmacological animal models of the illness. Despite sophisticated assessment of exploratory behavior in rodents, objective quantification of human motor activity has been limited primarily to actigraphy studies with poor cross-species translational value. Furthermore, symptoms that reflect the cardinal features of bipolar disorder have proven difficult to establish in putative animal models of this illness. Recently, however, novel tools such as the human behavioral pattern monitor provide multivariate translational measures of motor and exploratory activity, enabling improved understanding of the neurobiology underlying psychiatric disorders.

  9. Cross-species Transcriptomic Comparison of In Vitro and In Vivo Mammalian Neural Cells

    PubMed Central

    LoVerso, Peter R.; Wachter, Christopher M.; Cui, Feng

    2015-01-01

    The mammalian brain is characterized by distinct classes of cells that differ in morphology, structure, signaling, and function. Dysregulation of gene expression in these cell populations leads to various neurological disorders. Neural cells often need to be acutely purified from animal brains for research, which requires complicated procedure and specific expertise. Primary culture of these cells in vitro is a viable alternative, but the differences in gene expression of cells grown in vitro and in vivo remain unclear. Here, we cultured three major neural cell classes of rat brain (ie, neurons, astrocytes, and oligodendrocyte precursor cells [OPCs]) obtained from commercial sources. We measured transcript abundance of these cell types by RNA sequencing (RNA-seq) and compared with their counterparts acutely purified from mouse brains. Cross-species RNA-seq data analysis revealed hundreds of genes that are differentially expressed between the cultured and acutely purified cells. Astrocytes have more such genes compared to neurons and OPCs, indicating that signaling pathways are greatly perturbed in cultured astrocytes. This dataset provides a powerful resource to demonstrate the similarities and differences of biological processes in mammalian neural cells grown in vitro and in vivo at the molecular level. PMID:26640375

  10. Novel and highly informative Capsicum SSR markers and their cross-species transferability.

    PubMed

    Buso, G S C; Reis, A M M; Amaral, Z P S; Ferreira, M E

    2016-09-23

    This study was undertaken primarily to develop new simple sequence repeat (SSR) markers for Capsicum. As part of this project aimed at broadening the use of molecular tools in Capsicum breeding, two genomic libraries enriched for AG/TC repeat sequences were constructed for Capsicum annuum. A total of 475 DNA clones were sequenced from both libraries and 144 SSR markers were tested on cultivated and wild species of Capsicum. Forty-five SSR markers were randomly selected to genotype a panel of 48 accessions of the Capsicum germplasm bank. The number of alleles per locus ranged from 2 to 11, with an average of 6 alleles. The polymorphism information content was on average 0.60, ranging from 0.20 to 0.83. The cross-species transferability to seven cultivated and wild Capsicum species was tested with a set of 91 SSR markers. We found that a high proportion of the loci produced amplicons in all species tested. C. frutescens had the highest number of transferable markers, whereas the wild species had the lowest. Our results indicate that the new markers can be readily used in genetic analyses of Capsicum.

  11. CO2 exposure as translational cross-species experimental model for panic

    PubMed Central

    Leibold, N K; van den Hove, D L A; Viechtbauer, W; Buchanan, G F; Goossens, L; Lange, I; Knuts, I; Lesch, K P; Steinbusch, H W M; Schruers, K R J

    2016-01-01

    The current diagnostic criteria of the Diagnostic and Statistical Manual of Mental Disorders are being challenged by the heterogeneity and the symptom overlap of psychiatric disorders. Therefore, a framework toward a more etiology-based classification has been initiated by the US National Institute of Mental Health, the research domain criteria project. The basic neurobiology of human psychiatric disorders is often studied in rodent models. However, the differences in outcome measurements hamper the translation of knowledge. Here, we aimed to present a translational panic model by using the same stimulus and by quantitatively comparing the same outcome measurements in rodents, healthy human subjects and panic disorder patients within one large project. We measured the behavioral–emotional and bodily response to CO2 exposure in all three samples, allowing for a reliable cross-species comparison. We show that CO2 exposure causes a robust fear response in terms of behavior in mice and panic symptom ratings in healthy volunteers and panic disorder patients. To improve comparability, we next assessed the respiratory and cardiovascular response to CO2, demonstrating corresponding respiratory and cardiovascular effects across both species. This project bridges the gap between basic and human research to improve the translation of knowledge between these disciplines. This will allow significant progress in unraveling the etiological basis of panic disorder and will be highly beneficial for refining the diagnostic categories as well as treatment strategies. PMID:27598969

  12. Measurement of lentiviral vector titre and copy number by cross-species duplex quantitative PCR.

    PubMed

    Christodoulou, I; Patsali, P; Stephanou, C; Antoniou, M; Kleanthous, M; Lederer, C W

    2016-01-01

    Lentiviruses are the vectors of choice for many preclinical studies and clinical applications of gene therapy. Accurate measurement of biological vector titre before treatment is a prerequisite for vector dosing, and the calculation of vector integration sites per cell after treatment is as critical to the characterisation of modified cell products as it is to long-term follow-up and the assessment of risk and therapeutic efficiency in patients. These analyses are typically based on quantitative real-time PCR (qPCR), but as yet compromise accuracy and comparability between laboratories and experimental systems, the former by using separate simplex reactions for the detection of endogene and lentiviral sequences and the latter by designing different PCR assays for analyses in human cells and animal disease models. In this study, we validate in human and murine cells a qPCR system for the single-tube assessment of lentiviral vector copy numbers that is suitable for analyses in at least 33 different mammalian species, including human and other primates, mouse, pig, cat and domestic ruminants. The established assay combines the accuracy of single-tube quantitation by duplex qPCR with the convenience of one-off assay optimisation for cross-species analyses and with the direct comparability of lentiviral transduction efficiencies in different species.

  13. Polymorphic microsatellite loci identified through development and cross-species amplification within shorebirds

    USGS Publications Warehouse

    Williams, I.; Guzzetti, B.M.; Gust, Judy R.; Sage, G.K.; Gill, R.E.; Tibbitts, T.L.; Sonsthagen, S.A.; Talbot, S.L.

    2012-01-01

    We developed microsatellite loci for demographic assessments of shorebirds, a group with limited markers. First, we isolated five dinucleotide repeat microsatellite loci from the Black Oystercatcher (Haematopodidae: Haematopus bachmani), and three from the Bristle-thighed Curlew (Scolopacidae: Numenius tahitiensis); both species are of conservation concern. All eight loci were polymorphic in their respective target species. Hbaμ loci were characterized by two to three alleles with observed heterozygosity ranging from 0.07 to 0.33, and two to nine alleles were detected for Nut loci with observed heterozygosity ranging from 0.08 to 0.72. No linkage disequilibrium or departures from Hardy–Weinberg equilibrium were observed. The eight loci were also tested for cross-species amplification in 12 other species within Charadriidae and Scolopacidae, and the results demonstrated transferability across several genera. We further tested all 14 species at 12 additional microsatellite markers developed for other shorebirds: Dunlin (Calidris alpina; four loci) and Ruff (Philomachus pugnax; eight loci). Two markers (Hbaμ4 and Ruff6) were polymorphic in 13 species, while two (Calp6 and Ruff9) were monomorphic. The remaining eight markers revealed polymorphism in one to nine species each. Our results provide further evidence that locus Ruff10 is sex-linked, contrary to the initial description. These markers can be used to enhance our understanding of shorebird biology by, for example, helping to determine migratory connectivity among breeding and wintering populations and detecting relatedness among individuals.

  14. Cross-species transcriptional network analysis defines shared inflammatory responses in murine and human lupus nephritis.

    PubMed

    Berthier, Celine C; Bethunaickan, Ramalingam; Gonzalez-Rivera, Tania; Nair, Viji; Ramanujam, Meera; Zhang, Weijia; Bottinger, Erwin P; Segerer, Stephan; Lindenmeyer, Maja; Cohen, Clemens D; Davidson, Anne; Kretzler, Matthias

    2012-07-15

    Lupus nephritis (LN) is a serious manifestation of systemic lupus erythematosus. Therapeutic studies in mouse LN models do not always predict outcomes of human therapeutic trials, raising concerns about the human relevance of these preclinical models. In this study, we used an unbiased transcriptional network approach to define, in molecular terms, similarities and differences among three lupus models and human LN. Genome-wide gene-expression networks were generated using natural language processing and automated promoter analysis and compared across species via suboptimal graph matching. The three murine models and human LN share both common and unique features. The 20 commonly shared network nodes reflect the key pathologic processes of immune cell infiltration/activation, endothelial cell activation/injury, and tissue remodeling/fibrosis, with macrophage/dendritic cell activation as a dominant cross-species shared transcriptional pathway. The unique nodes reflect differences in numbers and types of infiltrating cells and degree of remodeling among the three mouse strains. To define mononuclear phagocyte-derived pathways in human LN, gene sets activated in isolated NZB/W renal mononuclear cells were compared with human LN kidney profiles. A tissue compartment-specific macrophage-activation pattern was seen, with NF-κB1 and PPARγ as major regulatory nodes in the tubulointerstitial and glomerular networks, respectively. Our study defines which pathologic processes in murine models of LN recapitulate the key transcriptional processes active in human LN and suggests that there are functional differences between mononuclear phagocytes infiltrating different renal microenvironments.

  15. Cross-Species Transmission and Differential Fate of an Endogenous Retrovirus in Three Mammal Lineages

    PubMed Central

    Zhuo, Xiaoyu; Feschotte, Cédric

    2015-01-01

    Endogenous retroviruses (ERVs) arise from retroviruses chromosomally integrated in the host germline. ERVs are common in vertebrate genomes and provide a valuable fossil record of past retroviral infections to investigate the biology and evolution of retroviruses over a deep time scale, including cross-species transmission events. Here we took advantage of a catalog of ERVs we recently produced for the bat Myotis lucifugus to seek evidence for infiltration of these retroviruses in other mammalian species (>100) currently represented in the genome sequence database. We provide multiple lines of evidence for the cross-ordinal transmission of a gammaretrovirus endogenized independently in the lineages of vespertilionid bats, felid cats and pangolin ~13–25 million years ago. Following its initial introduction, the ERV amplified extensively in parallel in both bat and cat lineages, generating hundreds of species-specific insertions throughout evolution. However, despite being derived from the same viral species, phylogenetic and selection analyses suggest that the ERV experienced different amplification dynamics in the two mammalian lineages. In the cat lineage, the ERV appears to have expanded primarily by retrotransposition of a single proviral progenitor that lost infectious capacity shortly after endogenization. In the bat lineage, the ERV followed a more complex path of germline invasion characterized by both retrotransposition and multiple infection events. The results also suggest that some of the bat ERVs have maintained infectious capacity for extended period of time and may be still infectious today. This study provides one of the most rigorously documented cases of cross-ordinal transmission of a mammalian retrovirus. It also illustrates how the same retrovirus species has transitioned multiple times from an infectious pathogen to a genomic parasite (i.e. retrotransposon), yet experiencing different invasion dynamics in different mammalian hosts. PMID

  16. A cross-species genetic analysis identifies candidate genes for mouse anxiety and human bipolar disorder

    PubMed Central

    Ashbrook, David G.; Williams, Robert W.; Lu, Lu; Hager, Reinmar

    2015-01-01

    Bipolar disorder (BD) is a significant neuropsychiatric disorder with a lifetime prevalence of ~1%. To identify genetic variants underlying BD genome-wide association studies (GWAS) have been carried out. While many variants of small effect associated with BD have been identified few have yet been confirmed, partly because of the low power of GWAS due to multiple comparisons being made. Complementary mapping studies using murine models have identified genetic variants for behavioral traits linked to BD, often with high power, but these identified regions often contain too many genes for clear identification of candidate genes. In the current study we have aligned human BD GWAS results and mouse linkage studies to help define and evaluate candidate genes linked to BD, seeking to use the power of the mouse mapping with the precision of GWAS. We use quantitative trait mapping for open field test and elevated zero maze data in the largest mammalian model system, the BXD recombinant inbred mouse population, to identify genomic regions associated with these BD-like phenotypes. We then investigate these regions in whole genome data from the Psychiatric Genomics Consortium's bipolar disorder GWAS to identify candidate genes associated with BD. Finally we establish the biological relevance and pathways of these genes in a comprehensive systems genetics analysis. We identify four genes associated with both mouse anxiety and human BD. While TNR is a novel candidate for BD, we can confirm previously suggested associations with CMYA5, MCTP1, and RXRG. A cross-species, systems genetics analysis shows that MCTP1, RXRG, and TNR coexpress with genes linked to psychiatric disorders and identify the striatum as a potential site of action. CMYA5, MCTP1, RXRG, and TNR are associated with mouse anxiety and human BD. We hypothesize that MCTP1, RXRG, and TNR influence intercellular signaling in the striatum. PMID:26190982

  17. Cross-Species Extrapolation of Prediction Models for Cadmium Transfer from Soil to Corn Grain

    PubMed Central

    Yang, Hua; Li, Zhaojun; Lu, Lu; Long, Jian; Liang, Yongchao

    2013-01-01

    Cadmium (Cd) is a highly toxic heavy metal for both plants and animals. The presence of Cd in agricultural soils is of great concern regarding its transfer in the soil-plant system. This study investigated the transfer of Cd (exogenous salts) from a wide range of Chinese soils to corn grain (Zhengdan 958). Through multiple stepwise regressions, prediction models were developed, with the combination of Cd bioconcentration factor (BCF) of Zhengdan 958 and soil pH, organic matter (OM) content, and cation exchange capacity (CEC). Moreover, these prediction models from Zhengdan 958 were applied to other non-model corn species through cross-species extrapolation approach. The results showed that the pH of the soil was the most important factor that controlled Cd uptake and lower pH was more favorable for Cd bioaccumulation in corn grain. There was no significant difference among three prediction models in the different Cd levels. When the prediction models were applied to other non-model corn species, the ratio ranges between the predicted BCF values and the measured BCF values were within an interval of 2 folds and close to the solid line of 1∶1 relationship. Furthermore, these prediction models also reduced the measured BCF intra-species variability for all non-model corn species. Therefore, the prediction models established in this study can be applied to other non-model corn species and be useful for predicting the Cd bioconcentration in corn grain and assessing the ecological risk of Cd in different soils. PMID:24324636

  18. Population genetics of Cryptosporidium meleagridis in humans and birds: evidence for cross-species transmission.

    PubMed

    Wang, Yuanfei; Yang, Wenli; Cama, Vitaliano; Wang, Lin; Cabrera, Lilia; Ortega, Ynes; Bern, Caryn; Feng, Yaoyu; Gilman, Robert; Xiao, Lihua

    2014-07-01

    Population genetic studies have been used to understand the transmission of pathogens in humans and animals, especially the role of zoonotic infections and evolution and dispersal of virulent subtypes. In this study, we analysed the genetic diversity and population structure of Cryptosporidium meleagridis, the only known Cryptosporidium species that infects both avian and mammalian hosts and is responsible for approximately 10% of human cryptosporidiosis in some areas. A total of 62 C. meleagridis specimens from children, AIDS patients, and birds in Lima, Peru were characterised by sequence analysis of the ssrRNA gene and five minisatellite, microsatellite and polymorphic markers in chromosome 6, including the 60 kDa glycoprotein (gp60), 47 kDa glycoprotein (CP47), a serine repeat antigen (MSC6-5), retinitis pigmentosa GTPase regulator (RPGR) and thrombospondin protein 8 (TSP8). The multilocus sequence analysis identified concurrent infections with Cryptosporidium hominis in four AIDS patients and three children. Unique subtypes of C. meleagridis ranged from eight at the gp60 locus (gene diversity -Hd=0.651), three at the RPGR (Hd=0.556), three at the MSC6-5 locus (Hd=0.242), two at TSP8 (Hd=0.198), to one at CP47 (monomorphic), much lower than that of C. hominis in the same area. Intragenic linkage disequilibrium was strong and complete at all gene loci. Intergenic linkage disequilibrium was highly significant (P<0.001) for all pairs of polymorphic loci. Two major groups of subtypes were seen, with most subtypes belonging to group 1. Within group 1, there was no clear population segregation, and two of the 14 multilocus subtypes of C. meleagridis were found in both AIDS patients and birds. We believe that these results provide the first evidence of a clonal population structure of C. meleagridis and the likely occurrence of cross-species transmission of C. meleagridis between birds and humans.

  19. Identifying candidate oocyte reprogramming factors using cross-species global transcriptional analysis.

    PubMed

    Awe, Jason P; Byrne, James A

    2013-04-01

    There is mounting evidence to suggest that the epigenetic reprogramming capacity of the oocyte is superior to that of the current factor-based reprogramming approaches and that some factor-reprogrammed induced pluripotent stem cells (iPSCs) retain a degree of epigenetic memory that can influence differentiation capacity and may be linked to the observed expression of immunogenicity genes in iPSC derivatives. One hypothesis for this differential reprogramming capacity is the "chromatin loosening/enhanced reprogramming" concept, as previously described by John Gurdon and Ian Wilmut, as well as others, which postulates that the oocyte possesses factors that loosen the somatic cell chromatin structure, providing the epigenetic and transcriptional regulatory factors more ready access to repressed genes and thereby significantly increasing epigenetic reprogramming. However, to empirically test this hypothesis a list of candidate oocyte reprogramming factors (CORFs) must be ascertained that are significantly expressed in metaphase II oocytes. Previous studies have focused on intraspecies or cross-species transcriptional analysis of up to two different species of oocytes. In this study, we have identified eight CORFs (ARID2, ASF1A, ASF1B, DPPA3, ING3, MSL3, H1FOO, and KDM6B) based on unbiased global transcriptional analysis of oocytes from three different species (human, rhesus monkey, and mouse) that both demonstrate significant (p<0.05, FC>3) expression in oocytes of all three species and have well-established roles in loosening/opening up chromatin structure. We also identified an additional 15 CORFs that fit within our proposed "chromatin opening/fate transformative" (COFT) model. These CORFs may be able to augment Shinya Yamanaka's previously identified reprogramming factors (OCT4, SOX2, KLF4, and cMYC) and potentially facilitate the removal of epigenetic memory in iPSCs and/or reduce the expression of immunogenicity genes in iPSC derivatives, and may have

  20. Cross-Species Transmission and Differential Fate of an Endogenous Retrovirus in Three Mammal Lineages.

    PubMed

    Zhuo, Xiaoyu; Feschotte, Cédric

    2015-01-01

    Endogenous retroviruses (ERVs) arise from retroviruses chromosomally integrated in the host germline. ERVs are common in vertebrate genomes and provide a valuable fossil record of past retroviral infections to investigate the biology and evolution of retroviruses over a deep time scale, including cross-species transmission events. Here we took advantage of a catalog of ERVs we recently produced for the bat Myotis lucifugus to seek evidence for infiltration of these retroviruses in other mammalian species (>100) currently represented in the genome sequence database. We provide multiple lines of evidence for the cross-ordinal transmission of a gammaretrovirus endogenized independently in the lineages of vespertilionid bats, felid cats and pangolin ~13-25 million years ago. Following its initial introduction, the ERV amplified extensively in parallel in both bat and cat lineages, generating hundreds of species-specific insertions throughout evolution. However, despite being derived from the same viral species, phylogenetic and selection analyses suggest that the ERV experienced different amplification dynamics in the two mammalian lineages. In the cat lineage, the ERV appears to have expanded primarily by retrotransposition of a single proviral progenitor that lost infectious capacity shortly after endogenization. In the bat lineage, the ERV followed a more complex path of germline invasion characterized by both retrotransposition and multiple infection events. The results also suggest that some of the bat ERVs have maintained infectious capacity for extended period of time and may be still infectious today. This study provides one of the most rigorously documented cases of cross-ordinal transmission of a mammalian retrovirus. It also illustrates how the same retrovirus species has transitioned multiple times from an infectious pathogen to a genomic parasite (i.e. retrotransposon), yet experiencing different invasion dynamics in different mammalian hosts.

  1. Cross-species genomics matches driver mutations and cell compartments to model ependymoma.

    PubMed

    Johnson, Robert A; Wright, Karen D; Poppleton, Helen; Mohankumar, Kumarasamypet M; Finkelstein, David; Pounds, Stanley B; Rand, Vikki; Leary, Sarah E S; White, Elsie; Eden, Christopher; Hogg, Twala; Northcott, Paul; Mack, Stephen; Neale, Geoffrey; Wang, Yong-Dong; Coyle, Beth; Atkinson, Jennifer; DeWire, Mariko; Kranenburg, Tanya A; Gillespie, Yancey; Allen, Jeffrey C; Merchant, Thomas; Boop, Fredrick A; Sanford, Robert A; Gajjar, Amar; Ellison, David W; Taylor, Michael D; Grundy, Richard G; Gilbertson, Richard J

    2010-07-29

    Understanding the biology that underlies histologically similar but molecularly distinct subgroups of cancer has proven difficult because their defining genetic alterations are often numerous, and the cellular origins of most cancers remain unknown. We sought to decipher this heterogeneity by integrating matched genetic alterations and candidate cells of origin to generate accurate disease models. First, we identified subgroups of human ependymoma, a form of neural tumour that arises throughout the central nervous system (CNS). Subgroup-specific alterations included amplifications and homozygous deletions of genes not yet implicated in ependymoma. To select cellular compartments most likely to give rise to subgroups of ependymoma, we matched the transcriptomes of human tumours to those of mouse neural stem cells (NSCs), isolated from different regions of the CNS at different developmental stages, with an intact or deleted Ink4a/Arf locus (that encodes Cdkn2a and b). The transcriptome of human supratentorial ependymomas with amplified EPHB2 and deleted INK4A/ARF matched only that of embryonic cerebral Ink4a/Arf(-/-) NSCs. Notably, activation of Ephb2 signalling in these, but not other, NSCs generated the first mouse model of ependymoma, which is highly penetrant and accurately models the histology and transcriptome of one subgroup of human supratentorial tumour. Further, comparative analysis of matched mouse and human tumours revealed selective deregulation in the expression and copy number of genes that control synaptogenesis, pinpointing disruption of this pathway as a critical event in the production of this ependymoma subgroup. Our data demonstrate the power of cross-species genomics to meticulously match subgroup-specific driver mutations with cellular compartments to model and interrogate cancer subgroups.

  2. Oxalic acid and diacylglycerol 36:3 are cross-species markers of sleep debt.

    PubMed

    Weljie, Aalim M; Meerlo, Peter; Goel, Namni; Sengupta, Arjun; Kayser, Matthew S; Abel, Ted; Birnbaum, Morris J; Dinges, David F; Sehgal, Amita

    2015-02-24

    Sleep is an essential biological process that is thought to have a critical role in metabolic regulation. In humans, reduced sleep duration has been associated with risk for metabolic disorders, including weight gain, diabetes, obesity, and cardiovascular disease. However, our understanding of the molecular mechanisms underlying effects of sleep loss is only in its nascent stages. In this study we used rat and human models to simulate modern-day conditions of restricted sleep and addressed cross-species consequences via comprehensive metabolite profiling. Serum from sleep-restricted rats was analyzed using polar and nonpolar methods in two independent datasets (n = 10 per study, 3,380 measured features, 407 identified). A total of 38 features were changed across independent experiments, with the majority classified as lipids (18 from 28 identified). In a parallel human study, 92 metabolites were identified as potentially significant, with the majority also classified as lipids (32 of 37 identified). Intriguingly, two metabolites, oxalic acid and diacylglycerol 36:3, were robustly and quantitatively reduced in both species following sleep restriction, and recovered to near baseline levels after sleep restriction (P < 0.05, false-discovery rate < 0.2). Elevated phospholipids were also noted after sleep restriction in both species, as well as metabolites associated with an oxidizing environment. In addition, polar metabolites reflective of neurotransmitters, vitamin B3, and gut metabolism were elevated in sleep-restricted humans. These results are consistent with induction of peroxisome proliferator-activated receptors and disruptions of the circadian clock. The findings provide a potential link between known pathologies of reduced sleep duration and metabolic dysfunction, and potential biomarkers for sleep loss.

  3. Preclinical optimization of a broad-spectrum anti-bladder cancer tri-drug regimen via the Feedback System Control (FSC) platform

    NASA Astrophysics Data System (ADS)

    Liu, Qi; Zhang, Cheng; Ding, Xianting; Deng, Hui; Zhang, Daming; Cui, Wei; Xu, Hongwei; Wang, Yingwei; Xu, Wanhai; Lv, Lei; Zhang, Hongyu; He, Yinghua; Wu, Qiong; Szyf, Moshe; Ho, Chih-Ming; Zhu, Jingde

    2015-06-01

    Therapeutic outcomes of combination chemotherapy have not significantly advanced during the past decades. This has been attributed to the formidable challenges of optimizing drug combinations. Testing a matrix of all possible combinations of doses and agents in a single cell line is unfeasible due to the virtually infinite number of possibilities. We utilized the Feedback System Control (FSC) platform, a phenotype oriented approach to test 100 options among 15,625 possible combinations in four rounds of assaying to identify an optimal tri-drug combination in eight distinct chemoresistant bladder cancer cell lines. This combination killed between 82.86% and 99.52% of BCa cells, but only 47.47% of the immortalized benign bladder epithelial cells. Preclinical in vivo verification revealed its markedly enhanced anti-tumor efficacy as compared to its bi- or mono-drug components in cell line-derived tumor xenografts. The collective response of these pathways to component drugs was both cell type- and drug type specific. However, the entire spectrum of pathways triggered by the tri-drug regimen was similar in all four cancer cell lines, explaining its broad spectrum killing of BCa lines, which did not occur with its component drugs. Our findings here suggest that the FSC platform holdspromise for optimization of anti-cancer combination chemotherapy.

  4. Microsatellite cross-species amplification and utility in southern African elasmobranchs: A valuable resource for fisheries management and conservation

    PubMed Central

    2014-01-01

    Background Similarly to the rest of the world, southern Africa’s diverse chondrichthyan fauna is currently experiencing high fishing pressures from direct and non-direct fisheries to satisfy market demands for shark products such as fins and meat. In this study, the development of microsatellite markers through cross-species amplification of primer sets previously developed for closely related species is reported as an alternative approach to de novo marker development. This included the design of four microsatellite multiplex assays and their cross-species utility in genetic diversity analysis of southern African elasmobranchs. As this study forms part of a larger project on the development of genetic resources for commercially important and endemic southern African species, Mustelus mustelus was used as a candidate species for testing these multiplex assays in down-stream applications. Results Thirty five microsatellite primer sets previously developed for five elasmobranch species were selected from literature for testing cross-species amplification in 16 elasmobranch species occurring in southern Africa. Cross-species amplification success rates ranged from 28.6%-71.4%. From the successfully amplified microsatellites, 22 loci were selected and evaluated for levels of polymorphism, and four multiplex assays comprising of the 22 microsatellites were successfully constructed, optimised and characterised in a panel of 87 Mustelus mustelus individuals. A total of 125 alleles were observed across all loci, with the number of alleles ranging from 3–12 alleles. Cross-species amplification of the four optimised multiplex assays was further tested on 11 commercially important and endemic southern African elasmobranch species. Percentage of polymorphism ranged from 31.8%-95.5% in these species with polymorphic information content decreasing exponentially with evolutionary distance from the source species. Conclusions Cross-species amplification of the 35

  5. Wildlife-livestock interactions and risk areas for cross-species spread of bovine tuberculosis.

    PubMed

    Meunier, Natascha V; Sebulime, Peregrine; White, Richard G; Kock, Richard

    2017-01-23

    The transmission of diseases between livestock and wildlife can be a hindrance to effective disease control. Maintenance hosts and contact rates should be explored to further understand the transmission dynamics at the wildlife-livestock interface. Bovine tuberculosis (BTB) has been shown to have wildlife maintenance hosts and has been confirmed as present in the African buffalo (Syncerus caffer) in the Queen Elizabeth National Park (QENP) in Uganda since the 1960s. The first aim of this study was to explore the spatio-temporal spread of cattle illegally grazing within the QENP recorded by the Uganda Wildlife Authority (UWA) rangers in a wildlife crime database. Secondly, we aimed to quantify wildlife-livestock interactions and cattle movements, on the border of QENP, using a longitudinal questionnaire completed by 30 livestock owners. From this database, 426 cattle sightings were recorded within QENP in 8 years. Thirteen (3.1%) of these came within a 300 m-4 week space-time window of a buffalo herd, using the recorded GPS data. Livestock owners reported an average of 1.04 (95% CI 0.97-1.11) sightings of Uganda kob, waterbuck, buffalo or warthog per day over a 3-month period, with a rate of 0.22 (95% CI 0.20-0.25) sightings of buffalo per farmer per day. Reports placed 85.3% of the ungulate sightings and 88.0% of the buffalo sightings as further than 50 m away. Ungulate sightings were more likely to be closer to cattle at the homestead (OR 2.0, 95% CI 1.1-3.6) compared with the grazing area. Each cattle herd mixed with an average of five other cattle herds at both the communal grazing and watering points on a daily basis. Although wildlife and cattle regularly shared grazing and watering areas, they seldom came into contact close enough for aerosol transmission. Between species infection transmission is therefore likely to be by indirect or non-respiratory routes, which is suspected to be an infrequent mechanism of transmission of BTB. Occasional cross-species

  6. Optimizing the Army’s Aerial Reconnaissance and Surveillance Asset Mix via the Joint Platform Allocation Tool (JPAT)

    DTIC Science & Technology

    2013-08-01

    OF FIGURES Figure 1. Three example systems composed of platforms P1, P2, and P3, and sensors SN1, SN2 , SN3, and SN4...sensors SN1, SN2 , SN3, and SN4. 4 Figure 2. An example configuration consisting of equipment derived from multiple systems. At times, it may be...of assets considered by JPAT will expand to include assets other than those with a program of record, or those that are quick reaction capabilities

  7. Single Particle and PET-based Platform for Identifying Optimal Plasmonic Nano-Heaters for Photothermal Cancer Therapy

    NASA Astrophysics Data System (ADS)

    Jørgensen, Jesper Tranekjær; Norregaard, Kamilla; Tian, Pengfei; Bendix, Poul Martin; Kjaer, Andreas; Oddershede, Lene B.

    2016-08-01

    Plasmonic nanoparticle-based photothermal cancer therapy is a promising new tool to inflict localized and irreversible damage to tumor tissue by hyperthermia, without harming surrounding healthy tissue. We developed a single particle and positron emission tomography (PET)-based platform to quantitatively correlate the heat generation of plasmonic nanoparticles with their potential as cancer killing agents. In vitro, the heat generation and absorption cross-section of single irradiated nanoparticles were quantified using a temperature sensitive lipid-based assay and compared to their theoretically predicted photo-absorption. In vivo, the heat generation of irradiated nanoparticles was evaluated in human tumor xenografts in mice using 2-deoxy-2-[F-18]fluoro-D-glucose (18F-FDG) PET imaging. To validate the use of this platform, we quantified the photothermal efficiency of near infrared resonant silica-gold nanoshells (AuNSs) and benchmarked this against the heating of colloidal spherical, solid gold nanoparticles (AuNPs). As expected, both in vitro and in vivo the heat generation of the resonant AuNSs performed superior compared to the non-resonant AuNPs. Furthermore, the results showed that PET imaging could be reliably used to monitor early treatment response of photothermal treatment. This multidisciplinary approach provides a much needed platform to benchmark the emerging plethora of novel plasmonic nanoparticles for their potential for photothermal cancer therapy.

  8. Bioelectronic platforms for optimal bio-anode of bio-electrochemical systems: From nano- to macro scopes.

    PubMed

    Kim, Bongkyu; An, Junyeong; Fapyane, Deby; Chang, In Seop

    2015-11-01

    The current trend of bio-electrochemical systems is to improve strategies related to their applicability and potential for scaling-up. To date, literature has suggested strategies, but the proposal of correlations between each research field remains insufficient. This review paper provides a correlation based on platform techniques, referred to as bio-electronics platforms (BEPs). These BEPs consist of three platforms divided by scope scale: nano-, micro-, and macro-BEPs. In the nano-BEP, several types of electron transfer mechanisms used by electrochemically active bacteria are discussed. In the micro-BEP, factors affecting the formation of conductive biofilms and transport of electrons in the conductive biofilm are investigated. In the macro-BEP, electrodes and separators in bio-anode are debated in terms of real applications, and a scale-up strategy is discussed. Overall, the challenges of each BEP are highlighted, and potential solutions are suggested. In addition, future research directions are provided and research ideas proposed to develop research interest.

  9. Single Particle and PET-based Platform for Identifying Optimal Plasmonic Nano-Heaters for Photothermal Cancer Therapy

    PubMed Central

    Jørgensen, Jesper Tranekjær; Norregaard, Kamilla; Tian, Pengfei; Bendix, Poul Martin; Kjaer, Andreas; Oddershede, Lene B.

    2016-01-01

    Plasmonic nanoparticle-based photothermal cancer therapy is a promising new tool to inflict localized and irreversible damage to tumor tissue by hyperthermia, without harming surrounding healthy tissue. We developed a single particle and positron emission tomography (PET)-based platform to quantitatively correlate the heat generation of plasmonic nanoparticles with their potential as cancer killing agents. In vitro, the heat generation and absorption cross-section of single irradiated nanoparticles were quantified using a temperature sensitive lipid-based assay and compared to their theoretically predicted photo-absorption. In vivo, the heat generation of irradiated nanoparticles was evaluated in human tumor xenografts in mice using 2-deoxy-2-[F-18]fluoro-D-glucose (18F-FDG) PET imaging. To validate the use of this platform, we quantified the photothermal efficiency of near infrared resonant silica-gold nanoshells (AuNSs) and benchmarked this against the heating of colloidal spherical, solid gold nanoparticles (AuNPs). As expected, both in vitro and in vivo the heat generation of the resonant AuNSs performed superior compared to the non-resonant AuNPs. Furthermore, the results showed that PET imaging could be reliably used to monitor early treatment response of photothermal treatment. This multidisciplinary approach provides a much needed platform to benchmark the emerging plethora of novel plasmonic nanoparticles for their potential for photothermal cancer therapy. PMID:27481537

  10. Comparative analysis estimates the relative frequencies of co-divergence and cross-species transmission within viral families

    PubMed Central

    Geoghegan, Jemma L.

    2017-01-01

    The cross-species transmission of viruses from one host species to another is responsible for the majority of emerging infections. However, it is unclear whether some virus families have a greater propensity to jump host species than others. If related viruses have an evolutionary history of co-divergence with their hosts there should be evidence of topological similarities between the virus and host phylogenetic trees, whereas host jumping generates incongruent tree topologies. By analyzing co-phylogenetic processes in 19 virus families and their eukaryotic hosts we provide a quantitative and comparative estimate of the relative frequency of virus-host co-divergence versus cross-species transmission among virus families. Notably, our analysis reveals that cross-species transmission is a near universal feature of the viruses analyzed here, with virus-host co-divergence occurring less frequently and always on a subset of viruses. Despite the overall high topological incongruence among virus and host phylogenies, the Hepadnaviridae, Polyomaviridae, Poxviridae, Papillomaviridae and Adenoviridae, all of which possess double-stranded DNA genomes, exhibited more frequent co-divergence than the other virus families studied here. At the other extreme, the virus and host trees for all the RNA viruses studied here, particularly the Rhabdoviridae and the Picornaviridae, displayed high levels of topological incongruence, indicative of frequent host switching. Overall, we show that cross-species transmission plays a major role in virus evolution, with all the virus families studied here having the potential to jump host species, and that increased sampling will likely reveal more instances of host jumping. PMID:28178344

  11. Short Communication Microsatellite loci in the tetraploid spined loach, Cobitis biwae, and cross-species amplification in four related species.

    PubMed

    Jablonska, O; Marín, A; Kowalewska, K; Fujimoto, T; Arai, K

    2016-09-23

    Fifteen microsatellite loci were identified in the tetraploid spined loach, Cobitis biwae (Teleostei: Cobitidae). Among these, 14 were polymorphic (5-31 alleles) and showed moderate to high cross-species amplification transferability in four related species, Cobitis matsubarai, Cobitis taenia, Misgurnus anguillicaudatus, and Misgurnus fossilis. The loci, described herein, will be useful for population genetics, phylogeny, parentage analysis, and detection of hybridization among Cobitis species.

  12. When humans are the exception: cross-species databases at the interface of biological and clinical research.

    PubMed

    Leonelli, Sabina

    2012-04-01

    Cross-species comparison has long been regarded as a stepping-stone for medical research, enabling the discovery and testing of prospective treatments before they undergo clinical trial on humans. Post-genomic medicine has made cross-species comparison crucial in another respect: the 'community databases' developed to collect and disseminate data on model organisms are now often used as a template for the dissemination of data on humans and as a tool for comparing results of medical significance across the human-animal boundary. This paper identifies and discusses four key problems encountered by database curators when integrating human and non-human data within the same database: (1) picking criteria for what counts as reliable evidence, (2) selecting metadata, (3) standardising and describing research materials and (4) choosing nomenclature to classify data. An analysis of these hurdles reveals epistemic disagreement and controversies underlying cross-species comparisons, which in turn highlight important differences in the experimental cultures of biologists and clinicians trying to make sense of these data. By considering database development through the eyes of curators, this study casts new light on the complex conjunctions of biological and clinical practice, model organisms and human subjects, and material and virtual sources of evidence--thus emphasizing the fragmented, localized and inherently translational nature of biomedicine.

  13. Control Parameters Optimization Based on Co-Simulation of a Mechatronic System for an UA-Based Two-Axis Inertially Stabilized Platform.

    PubMed

    Zhou, Xiangyang; Zhao, Beilei; Gong, Guohao

    2015-08-14

    This paper presents a method based on co-simulation of a mechatronic system to optimize the control parameters of a two-axis inertially stabilized platform system (ISP) applied in an unmanned airship (UA), by which high control performance and reliability of the ISP system are achieved. First, a three-dimensional structural model of the ISP is built by using the three-dimensional parametric CAD software SOLIDWORKS(®); then, to analyze the system's kinematic and dynamic characteristics under operating conditions, dynamics modeling is conducted by using the multi-body dynamics software ADAMS™, thus the main dynamic parameters such as displacement, velocity, acceleration and reaction curve are obtained, respectively, through simulation analysis. Then, those dynamic parameters were input into the established MATLAB(®) SIMULINK(®) controller to simulate and test the performance of the control system. By these means, the ISP control parameters are optimized. To verify the methods, experiments were carried out by applying the optimized parameters to the control system of a two-axis ISP. The results show that the co-simulation by using virtual prototyping (VP) is effective to obtain optimized ISP control parameters, eventually leading to high ISP control performance.

  14. Control Parameters Optimization Based on Co-Simulation of a Mechatronic System for an UA-Based Two-Axis Inertially Stabilized Platform

    PubMed Central

    Zhou, Xiangyang; Zhao, Beilei; Gong, Guohao

    2015-01-01

    This paper presents a method based on co-simulation of a mechatronic system to optimize the control parameters of a two-axis inertially stabilized platform system (ISP) applied in an unmanned airship (UA), by which high control performance and reliability of the ISP system are achieved. First, a three-dimensional structural model of the ISP is built by using the three-dimensional parametric CAD software SOLIDWORKS®; then, to analyze the system’s kinematic and dynamic characteristics under operating conditions, dynamics modeling is conducted by using the multi-body dynamics software ADAMS™, thus the main dynamic parameters such as displacement, velocity, acceleration and reaction curve are obtained, respectively, through simulation analysis. Then, those dynamic parameters were input into the established MATLAB® SIMULINK® controller to simulate and test the performance of the control system. By these means, the ISP control parameters are optimized. To verify the methods, experiments were carried out by applying the optimized parameters to the control system of a two-axis ISP. The results show that the co-simulation by using virtual prototyping (VP) is effective to obtain optimized ISP control parameters, eventually leading to high ISP control performance. PMID:26287210

  15. Noninvasive individual and species identification of jaguars (Panthera onca), pumas (Puma concolor) and ocelots (Leopardus pardalis) in Belize, Central America using cross-species microsatellites and faecal DNA.

    PubMed

    Wultsch, Claudia; Waits, Lisette P; Kelly, Marcella J

    2014-11-01

    There is a great need to develop efficient, noninvasive genetic sampling methods to study wild populations of multiple, co-occurring, threatened felids. This is especially important for molecular scatology studies occurring in challenging tropical environments where DNA degrades quickly and the quality of faecal samples varies greatly. We optimized 14 polymorphic microsatellite loci for jaguars (Panthera onca), pumas (Puma concolor) and ocelots (Leopardus pardalis) and assessed their utility for cross-species amplification. Additionally, we tested their reliability for species and individual identification using DNA from faeces of wild felids detected by a scat detector dog across Belize in Central America. All microsatellite loci were successfully amplified in the three target species, were polymorphic with average expected heterozygosities of HE = 0.60 ± 0.18 (SD) for jaguars, HE = 0.65 ± 0.21 (SD) for pumas and HE = 0.70 ± 0.13 (SD) for ocelots and had an overall PCR amplification success of 61%. We used this nuclear DNA primer set to successfully identify species and individuals from 49% of 1053 field-collected scat samples. This set of optimized microsatellite multiplexes represents a powerful tool for future efforts to conduct noninvasive studies on multiple, wild Neotropical felids.

  16. SU-E-T-256: Optimizing the Combination of Targeted Radionuclide Therapy Agents Using a Multi-Scale Patient-Specific Monte Carlo Dosimetry Platform

    SciTech Connect

    Besemer, A; Bednarz, B; Titz, B; Grudzinski, J; Weichert, J; Hall, L

    2014-06-01

    Purpose: Combination targeted radionuclide therapy (TRT) is appealing because it can potentially exploit different mechanisms of action from multiple radionuclides as well as the variable dose rates due to the different radionuclide half-lives. The work describes the development of a multiobjective optimization algorithm to calculate the optimal ratio of radionuclide injection activities for delivery of combination TRT. Methods: The ‘diapeutic’ (diagnostic and therapeutic) agent, CLR1404, was used as a proof-of-principle compound in this work. Isosteric iodine substitution in CLR1404 creates a molecular imaging agent when labeled with I-124 or a targeted radiotherapeutic agent when labeled with I-125 or I-131. PET/CT images of high grade glioma patients were acquired at 4.5, 24, and 48 hours post injection of 124I-CLR1404. The therapeutic 131I-CLR1404 and 125ICLR1404 absorbed dose (AD) and biological effective dose (BED) were calculated for each patient using a patient-specific Monte Carlo dosimetry platform. The optimal ratio of injection activities for each radionuclide was calculated with a multi-objective optimization algorithm using the weighted sum method. Objective functions such as the tumor dose heterogeneity and the ratio of the normal tissue to tumor doses were minimized and the relative importance weights of each optimization function were varied. Results: For each optimization function, the program outputs a Pareto surface map representing all possible combinations of radionuclide injection activities so that values that minimize the objective function can be visualized. A Pareto surface map of the weighted sum given a set of user-specified importance weights is also displayed. Additionally, the ratio of optimal injection activities as a function of the all possible importance weights is generated so that the user can select the optimal ratio based on the desired weights. Conclusion: Multi-objective optimization of radionuclide injection activities

  17. Mapping complementary features of cross-species structural connectivity to construct realistic "Virtual Brains".

    PubMed

    Bezgin, Gleb; Solodkin, Ana; Bakker, Rembrandt; Ritter, Petra; McIntosh, Anthony R

    2017-04-01

    Modern systems neuroscience increasingly leans on large-scale multi-lab neuroinformatics initiatives to provide necessary capacity for biologically realistic modeling of primate whole-brain activity. Here, we present a framework to assemble primate brain's biologically plausible anatomical backbone for such modeling initiatives. In this framework, structural connectivity is determined by adding complementary information from invasive macaque axonal tract tracing and non-invasive human diffusion tensor imaging. Both modalities are combined by means of available interspecies registration tools and a newly developed Bayesian probabilistic modeling approach to extract common connectivity evidence. We demonstrate how this novel framework is embedded in the whole-brain simulation platform called The Virtual Brain (TVB). Hum Brain Mapp 38:2080-2093, 2017. © 2017 Wiley Periodicals, Inc.

  18. Detection of Genotype 4 Swine Hepatitis E Virus in Systemic Tissues in Cross-Species Infected Rabbits

    PubMed Central

    Wu, Qiaoxing; An, Junqing; She, Ruiping; Shi, Ruihan; Hao, Wenzhuo; Soomro, MajidHussain; Yuan, Xuerui; Yang, Jinling; Wang, Jingyuan

    2017-01-01

    Increasing evidence demonstrates that hepatitis E virus (HEV) can be transmitted across species. According to previous reports, swine HEV has two genotypes, genotype 3 and 4, and both can infect humans by the fecal-oral route. Thus, it is crucial for the control of HEV zoonotic transmission to evaluate the dynamics of viral shedding and distribution in different tissues during cross-species infection by HEV. In this study, rabbits were infected with genotype 4 swine HEV by the intraperitoneal route. The results showed that HEV RNA not only shed in the feces but also in the saliva of some rabbits during infection with swine HEV. Viremia appeared late after infection, and anti-HEV IgG was not obvious until the appearance of high viremia levels. After the rabbits were euthanized, a histopathological examination showed that the livers developed overt hepatitis accompanied by an elevation of alanine aminotransferase (ALT) and aspartate transaminase (AST). Furthermore, HEV RNA was detected in various tissues, especially in the salivary glands and tonsils. Subsequently, negative-stranded HEV RNA was practiced in tissues with positive HEV RNA, which demonstrated that HEV replicated in the tissues. Next, we harvested additional tissues from the liver, salivary gland, tonsil, spleen, thymus gland, lymph node and intestine, which are known as replication sites of swine HEV. Additionally, we also observed the HEV antigen distributed in the organs above through immunohistochemical staining. These results demonstrate that rabbits could be used as an animal model for researching cross-species infection of genotype 4 HEV. It is also noteworthy that HEV can shed in the saliva and presents the risk of droplet transmission. These new data provide valuable information for understanding cross-species infection by HEV. PMID:28129390

  19. Detection of RHDV strains in the Iberian hare (Lepus granatensis): earliest evidence of rabbit lagovirus cross-species infection.

    PubMed

    Lopes, Ana M; Marques, Sara; Silva, Eliane; Magalhães, Maria J; Pinheiro, Ana; Alves, Paulo C; Le Pendu, Jacques; Esteves, Pedro J; Thompson, Gertrude; Abrantes, Joana

    2014-09-24

    Rabbit hemorrhagic disease virus (RHDV) is a highly lethal Lagovirus, family Caliciviridae, that threatens European rabbits (Oryctolagus cuniculus). Although a related virus severely affects hares, cross-species infection was only recently described for new variant RHDV in Cape hares (Lepus capensis mediterraneus). We sequenced two strains from dead Iberian hares (Lepus granatensis) collected in the 1990s in Portugal. Clinical signs were compatible with a Lagovirus infection. Phylogenetic analysis of the complete capsid gene positioned them in the RHDV genogroup that circulated on the Iberian Peninsula at that time. This is the earliest evidence of RHDV affecting a species other than European rabbits.

  20. Overview of the commercial OPAL LiDAR optimized for rotorcraft platforms operating in degraded visual environments

    NASA Astrophysics Data System (ADS)

    Church, Philip; Borribanbunpotkat, Kiatchai; Trickey, Evan; Iles, Peter; Sekerka, Mike

    2014-06-01

    Neptec has developed a family of obscurant-penetrating 3D laser scanners called OPAL 2.0 that are being adapted for rotorcraft platforms. Neptec and Boeing have been working on an integrated system utilizing the OPAL LiDAR to support operations in degraded visual environments. OPAL scanners incorporate Neptec's patented obscurantpenetrating LiDAR technology which was extensively tested in controlled dust environments and helicopters for brownout mitigation. The OPAL uses a scanning mechanism based on the Risley prism pair. Data acquisition rates can go as high as 200kHz for ranges within 200m and 25kHz for ranges exceeding 200m. The scan patterns are created by the rotation of two prisms under independent motor control. The geometry and material properties of the prisms will define the conical field-of-view of the sensor, which can be set up to 120 degrees. Through detailed simulations and analysis of mission profiles, the system can be tailored for applications to rotorcrafts. Examples of scan patterns and control schemes based on these simulations will be provided along with data density predictions versus acquisition time for applicable DVE scenarios. Preliminary 3D data acquired in clear and obscurant conditions will be presented.

  1. Characterization of highly informative cross-species microsatellite panels for the Australian dugong (Dugong dugon) and Florida manatee (Trichechus manatus latirostris) including five novel primers

    USGS Publications Warehouse

    Hunter, Margaret Kellogg; Broderick, Damien; Ovenden, Jennifer R.; Tucker, Kimberly Pause; Bonde, Robert K.; McGuire, Peter M.; Lanyon, Janet M.

    2010-01-01

    The Australian dugong (Dugong dugon) and Florida manatee (Trichechus manatus latirostris) are threatened species of aquatic mammals in the order Sirenia. Sirenian conservation and management actions would benefit from a more complete understanding of genetic diversity and population structure. Generally, species-specific microsatellite markers are employed in conservation genetic studies; however, robust markers can be difficult and costly to isolate. To increase the number of available markers, dugong and manatee microsatellite primers were evaluated for cross-species amplification. Furthermore, one manatee and four dugong novel primers are reported. After polymerase chain reaction optimization, 23 (92%) manatee primers successfully amplified dugong DNA, of which 11 (48%) were polymorphic. Of the 32 dugong primers tested, 27 (84%) yielded product in the manatee, of which 17 (63%) were polymorphic. Dugong and manatee primers were compared and the most informative markers were selected to create robust and informative marker-panels for each species. These crossspecies microsatellite marker-panels can be employed to assess other sirenian populations and can provide beneficial information for the protection and management of these unique mammals.

  2. CROSS-SPECIES COMPARISON OF CONAZOLE FUNGICIDE METABOLITES USING RAT AND RAINBOW TROUT (ONCHLORHYNCHUS MYKISS) HEPATIC MICROSOMES AND PURIFIED HUMAN CYP 3A4

    EPA Science Inventory

    Ecological risk assessment frequently relies on cross-species extrapolation to predict acute toxicity from chemical exposures. A major concern for environmental risk characterization is the degree of uncertainty in assessing xenobiotic biotansformation processes. Although inheren...

  3. Cross-Species Integrative Functional Genomics in GeneWeaver Reveals a Role for Pafah1b1 in Altered Response to Alcohol

    PubMed Central

    Bubier, Jason A.; Wilcox, Troy D.; Jay, Jeremy J.; Langston, Michael A.; Baker, Erich J.; Chesler, Elissa J.

    2016-01-01

    Identifying the biological substrates of complex neurobehavioral traits such as alcohol dependency pose a tremendous challenge given the diverse model systems and phenotypic assessments used. To address this problem we have developed a platform for integrated analysis of high-throughput or genome-wide functional genomics studies. A wealth of such data exists, but it is often found in disparate, non-computable forms. Our interactive web-based software system, Gene Weaver (http://www.geneweaver.org), couples curated results from genomic studies to graph-theoretical tools for combinatorial analysis. Using this system we identified a gene underlying multiple alcohol-related phenotypes in four species. A search of over 60,000 gene sets in GeneWeaver's database revealed alcohol-related experimental results including genes identified in mouse genetic mapping studies, alcohol selected Drosophila lines, Rattus differential expression, and human alcoholic brains. We identified highly connected genes and compared these to genes currently annotated to alcohol-related behaviors and processes. The most highly connected gene not annotated to alcohol was Pafah1b1. Experimental validation using a Pafah1b1 conditional knock-out mouse confirmed that this gene is associated with an increased preference for alcohol and an altered thermoregulatory response to alcohol. Although this gene has not been previously implicated in alcohol-related behaviors, its function in various neural mechanisms makes a role in alcohol-related phenomena plausible. By making diverse cross-species functional genomics data readily computable, we were able to identify and confirm a novel alcohol-related gene that may have implications for alcohol use disorders and other effects of alcohol. PMID:26834590

  4. Parallelizing ATLAS Reconstruction and Simulation: Issues and Optimization Solutions for Scaling on Multi- and Many-CPU Platforms

    NASA Astrophysics Data System (ADS)

    Leggett, C.; Binet, S.; Jackson, K.; Levinthal, D.; Tatarkhanov, M.; Yao, Y.

    2011-12-01

    Thermal limitations have forced CPU manufacturers to shift from simply increasing clock speeds to improve processor performance, to producing chip designs with multi- and many-core architectures. Further the cores themselves can run multiple threads as a zero overhead context switch allowing low level resource sharing (Intel Hyperthreading). To maximize bandwidth and minimize memory latency, memory access has become non uniform (NUMA). As manufacturers add more cores to each chip, a careful understanding of the underlying architecture is required in order to fully utilize the available resources. We present AthenaMP and the Atlas event loop manager, the driver of the simulation and reconstruction engines, which have been rewritten to make use of multiple cores, by means of event based parallelism, and final stage I/O synchronization. However, initial studies on 8 andl6 core Intel architectures have shown marked non-linearities as parallel process counts increase, with as much as 30% reductions in event throughput in some scenarios. Since the Intel Nehalem architecture (both Gainestown and Westmere) will be the most common choice for the next round of hardware procurements, an understanding of these scaling issues is essential. Using hardware based event counters and Intel's Performance Tuning Utility, we have studied the performance bottlenecks at the hardware level, and discovered optimization schemes to maximize processor throughput. We have also produced optimization mechanisms, common to all large experiments, that address the extreme nature of today's HEP code, which due to it's size, places huge burdens on the memory infrastructure of today's processors.

  5. Design of an enzyme cocktail consisting of different fungal platforms for efficient hydrolysis of sugarcane bagasse: Optimization and synergism studies.

    PubMed

    Méndez Arias, Johanna; Modesto, Luiz Felipe Amarante; Polikarpov, Igor; Pereira, Nei

    2016-09-01

    Lignocellulosic materials represent a very important and promising source of renewable biomass. In order to turn them into fermentable sugars, synergism among the different enzymes that carry out bioconversion of these materials is one of the main factors that should be considered. Experimental mixture design was performed to optimize the proportion of enzymes produced by native strains of Trichoderma harzianum IOC 3844, Penicillium funiculosum ATCC 11797, and Aspergillus niger ATCC 1004, resulting in a proportion of 15, 50, and 35%, respectively. This mixture was able to hydrolyze 25 g/L of pretreated sugarcane bagasse with 91% of yield after 48 h of enzymatic reaction. Synergism along the hydrolysis process, besides the influence of lignin, hemicellulose, and solids loading, were also studied. Response surface methodology (RSM) based on Central Composite Rotatable Design was used to optimize solids and protein loadings to increase glucose release and enzymatic hydrolysis yield. The optimum solid and protein loadings established with RSM were 196 g/L and 24 mg/g cellulose, respectively, and under these conditions (94.1 ± 8) g/L of glucose were obtained, corresponding to a hydrolysis yield of 64%. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 32:1222-1229, 2016.

  6. Development of a mobile device optimized cross platform-compatible oral pathology and radiology spaced repetition system for dental education.

    PubMed

    Al-Rawi, Wisam; Easterling, Lauren; Edwards, Paul C

    2015-04-01

    Combining active recall testing with spaced repetition increases memory retention. The aim of this study was to evaluate and compare students' perception and utilization of an electronic spaced repetition oral pathology-radiology system in dental hygiene education and predoctoral dental education. The study employed an open-source suite of applications to create electronic "flashcards" that can be individually adjusted for frequency of repetition, depending on a user's assessment of difficulty. Accessible across multiple platforms (iOS, Android, Linux, OSX, Windows) as well as via any web-based browser, this framework was used to develop an oral radiology-oral pathology database of case-based questions. This system was introduced in two courses: sophomore oral pathology for dental students and sophomore radiology for dental hygiene students. Students were provided free software and/or mobile tablet devices as well as a database of 300 electronic question cards. Study participants were surveyed on frequency and extent of use. Perception-based surveys were used to evaluate their attitudes towards this technology. Of the eligible students, 12 of 22 (54.5%) dental hygiene and 49 of 107 (45.8%) dental students responded to the surveys. Adoption rates and student feedback were compared between the two groups. Among the respondents, acceptance of this technology with respect to educational usefulness was similar for the dental and dental hygiene students (median=5 on a five-point scale; dental hygiene interquartile range (IQR)=0; dental IQR=1). Only a minority of the survey respondents (25% dental, 33% dental hygiene) took advantage of one of the main benefits of this technology: automated spaced repetition.

  7. HTLV-3/4 and simian foamy retroviruses in humans: discovery, epidemiology, cross-species transmission and molecular virology.

    PubMed

    Gessain, Antoine; Rua, Réjane; Betsem, Edouard; Turpin, Jocelyn; Mahieux, Renaud

    2013-01-05

    Non-human primates are considered to be likely sources of viruses that can infect humans and thus pose a significant threat to human population. This is well illustrated by some retroviruses, as the simian immunodeficiency viruses and the simian T lymphotropic viruses, which have the ability to cross-species, adapt to a new host and sometimes spread. This leads to a pandemic situation for HIV-1 or an endemic one for HTLV-1. Here, we present the available data on the discovery, epidemiology, cross-species transmission and molecular virology of the recently discovered HTLV-3 and HTLV-4 deltaretroviruses, as well as the simian foamy retroviruses present in different human populations at risk, especially in central African hunters. We discuss also the natural history in humans of these retroviruses of zoonotic origin (magnitude and geographical distribution, possible inter-human transmission). In Central Africa, the increase of the bushmeat trade during the last decades has opened new possibilities for retroviral emergence in humans, especially in immuno-compromised persons.

  8. Distribution of baboon endogenous virus among species of African monkeys suggests multiple ancient cross-species transmissions in shared habitats.

    PubMed Central

    van der Kuyl, A C; Dekker, J T; Goudsmit, J

    1995-01-01

    PCR amplification of baboon endogenous virus (BaEV) long terminal repeat, reverse transcriptase gene, and env fragments from 24 different species of African monkeys indicates that BaEV is less widespread than was formerly thought. Instead of being present in every species of African primates, BaEV can be found only in baboons, geladas, and mangabeys (all belonging to the Papionini tribe) and in African green monkey (Cercopithecus aethiops)subspecies. BaEV, which can be activated from baboon and gelada tissues, was most likely introduced in the germ line only recently (less than a few million years ago) and has not been inherited from a common ancestor of all extant African monkeys. Neighbor-joining and maximum-likelihood analyses of the sequences obtained showed that two distinct virus clusters can be distinguished: the first containing baboon, gelada, and African green monkey BaEV sequences and the second consisting of mandrill and mangabey BaEV sequences. This viral evolutionary tree does not follow host phylogeny, indicating the cross-species transmissions and multiple germ line fixations of the virus must have occurred in the past. BaEV sequences are found in monkeys inhabiting savannas (baboons, geladas, and African green monkeys) as well as forests (managabeys and mandrills) and cluster according to the habitats of their hosts, providing evidence for cross-species transmission in shared habitats. PMID:7494300

  9. Cross-species amplification of microsatellite markers in Mycteria leucocephala Pennant 1769: molted feathers as successful DNA source.

    PubMed

    Sharma, Bharat Bhushan; Mustafa, Mohd; Sharma, Tusha; Banerjee, Basu Dev; Urfi, Abdul Jamil

    2014-10-01

    DNA from molted feathers is being increasingly used for genetic studies on birds. However, the DNA obtained from such non-invasive sources is often not of enough quantity and quality for isolation of new microsatellite markers. The present study examined the potential of shed feathers of near threatened Painted Stork as a source of its DNA for cross-species amplification of microsatellites. Thirty-one shed feathers of varying conditions ('good' and 'deteriorated') and sizes ('large', 'intermediate' and 'small') collected in a north Indian population were used to isolate DNA by a standard isopropanol method and 11 microsatellite markers already developed in the Wood Stork were screened for amplification. Nine plucked feathers from two dead Painted Storks were also used to compare the DNA yield and amplification success. The DNA yield of feathers varied significantly in relation to the calamus size and condition. Among molted feathers, 'good' and 'large' samples provided more DNA than 'deteriorated' and 'small' ones, respectively. 'Large' plucked feathers yielded more DNA than 'large' molted feathers. DNA was almost degraded in all the samples and ratio of absorbance at 260/280 nm varied from 1.0 to 1.8, indicating impurity in many samples. Independent of DNA yields, all microsatellites were cross-amplified in all kinds of feathers, with > 80% success in different feather categories. It is concluded that the shed feathers can be successfully used to isolate DNA in the Painted Stork and for cross-species amplification of microsatellites.

  10. A unified optimization platform comparison of three radiosurgery techniques: Gamma Knife, BrainLAB micro-MLC, and NOMOS MIMiC

    NASA Astrophysics Data System (ADS)

    Cheek, Dennis Allen

    The objective of this research is to build a unified optimization treatment planning system in order to accurately compare the three modalities unburdened by underlying assumptions that could alter the outcome of the comparison. The hypothesis for the dissertation is: Three photon radiosurgery delivery mechanisms are utilized for the delivery of necrotic radiation doses to a cranial lesion: the Gamma Knife, micro-MLC intensity modulated radiosurgery, and MIMiC based intensity modulated radiosurgery. Each modality has its own strength and weaknesses in their ability to deliver radiosurgery treatments. We hypothesize the MIMiC based intensity modulated radiosurgery will allow improvements to radiosurgery treatments compared to the conventional Gamma Knife and micro-MLC, as quantified by the following metrics: isodose line display, dose volume histograms, Ian Paddick conformality index, homogeneity index, and objective function score. The specific aims for the dissertation are: (1) Develop a radiosurgery treatment planning software platform to import image and structure data and to offer evaluation tools. The evaluation tools will include isodose line display, dose volume histogram, Ian Paddick conformality index, homogeneity index, and objective function score. (2) Develop a simulated annealing optimization routine, with an associated objective function, that will determine the optimal treatment plan for the defined solution space. The objective, or cost function will be based on Ian Paddick conformality index. (3) Perform multiple repeat optimizations of each modality for a given lesion in order to gather statistical information about the minimum solution found. This test will quantify the ability of the optimization routine to arrive at a similar local minimum and therefore quantify the reliability of the comparison performed in specific aim five. (4) Investigate the affect of the Gamma Knife's shot limitation on the resulting dose distribution for a given lesion

  11. An Eddy Current Testing Platform System for Pipe Defect Inspection Based on an Optimized Eddy Current Technique Probe Design

    PubMed Central

    Rifai, Damhuji; Abdalla, Ahmed N.; Razali, Ramdan; Ali, Kharudin; Faraj, Moneer A.

    2017-01-01

    The use of the eddy current technique (ECT) for the non-destructive testing of conducting materials has become increasingly important in the past few years. The use of the non-destructive ECT plays a key role in the ensuring the safety and integrity of the large industrial structures such as oil and gas pipelines. This paper introduce a novel ECT probe design integrated with the distributed ECT inspection system (DSECT) use for crack inspection on inner ferromagnetic pipes. The system consists of an array of giant magneto-resistive (GMR) sensors, a pneumatic system, a rotating magnetic field excitation source and a host PC acting as the data analysis center. Probe design parameters, namely probe diameter, an excitation coil and the number of GMR sensors in the array sensor is optimized using numerical optimization based on the desirability approach. The main benefits of DSECT can be seen in terms of its modularity and flexibility for the use of different types of magnetic transducers/sensors, and signals of a different nature with either digital or analog outputs, making it suited for the ECT probe design using an array of GMR magnetic sensors. A real-time application of the DSECT distributed system for ECT inspection can be exploited for the inspection of 70 mm carbon steel pipe. In order to predict the axial and circumference defect detection, a mathematical model is developed based on the technique known as response surface methodology (RSM). The inspection results of a carbon steel pipe sample with artificial defects indicate that the system design is highly efficient. PMID:28335399

  12. An Eddy Current Testing Platform System for Pipe Defect Inspection Based on an Optimized Eddy Current Technique Probe Design.

    PubMed

    Rifai, Damhuji; Abdalla, Ahmed N; Razali, Ramdan; Ali, Kharudin; Faraj, Moneer A

    2017-03-13

    The use of the eddy current technique (ECT) for the non-destructive testing of conducting materials has become increasingly important in the past few years. The use of the non-destructive ECT plays a key role in the ensuring the safety and integrity of the large industrial structures such as oil and gas pipelines. This paper introduce a novel ECT probe design integrated with the distributed ECT inspection system (DSECT) use for crack inspection on inner ferromagnetic pipes. The system consists of an array of giant magneto-resistive (GMR) sensors, a pneumatic system, a rotating magnetic field excitation source and a host PC acting as the data analysis center. Probe design parameters, namely probe diameter, an excitation coil and the number of GMR sensors in the array sensor is optimized using numerical optimization based on the desirability approach. The main benefits of DSECT can be seen in terms of its modularity and flexibility for the use of different types of magnetic transducers/sensors, and signals of a different nature with either digital or analog outputs, making it suited for the ECT probe design using an array of GMR magnetic sensors. A real-time application of the DSECT distributed system for ECT inspection can be exploited for the inspection of 70 mm carbon steel pipe. In order to predict the axial and circumference defect detection, a mathematical model is developed based on the technique known as response surface methodology (RSM). The inspection results of a carbon steel pipe sample with artificial defects indicate that the system design is highly efficient.

  13. Development, characterization and cross species amplification of polymorphic microsatellite markers from expressed sequence tags of turmeric (Curcuma longa L.).

    PubMed

    Siju, S; Dhanya, K; Syamkumar, S; Sasikumar, B; Sheeja, T E; Bhat, A I; Parthasarathy, V A

    2010-02-01

    Expressed sequence tags (ESTs) from turmeric (Curcuma longa L.) were used for the screening of type and frequency of Class I (hypervariable) simple sequence repeats (SSRs). A total of 231 microsatellite repeats were detected from 12,593 EST sequences of turmeric after redundancy elimination. The average density of Class I SSRs accounts to one SSR per 17.96 kb of EST. Mononucleotides were the most abundant class of microsatellite repeat in turmeric ESTs followed by trinucleotides. A robust set of 17 polymorphic EST-SSRs were developed and used for evaluating 20 turmeric accessions. The number of alleles detected ranged from 3 to 8 per loci. The developed markers were also evaluated in 13 related species of C. longa confirming high rate (100%) of cross species transferability. The polymorphic microsatellite markers generated from this study could be used for genetic diversity analysis and resolving the taxonomic confusion prevailing in the genus.

  14. Cross-species transmission of gibbon and orangutan hepatitis B virus to uPA/SCID mice with human hepatocytes.

    PubMed

    Sa-Nguanmoo, Pattaratida; Tanaka, Yasuhito; Ratanakorn, Parntep; Sugiyama, Masaya; Murakami, Shuko; Payungporn, Sunchai; Sommanustweechai, Angkana; Mizokami, Masashi; Poovorawan, Yong

    2011-06-01

    To investigate the potential of cross-species transmission of non-human primate HBV to humans, severe combined immunodeficiency mice transgenic for urokinase-type plasminogen activator, in which the mouse liver has been engrafted with human hepatocytes, were inoculated with non-human primate HBV. HBV-DNA positive serum samples from a gibbon or orangutan were inoculated into 6 chimeric mice. HBV-DNA, hepatitis B surface antigen (HBsAg), and HB core-related antigen in sera and HBV cccDNA in liver were detectable in 2 of 3 mice each from the gibbon and orangutan. Likewise, applying immunofluorescence HBV core protein was only found in human hepatocytes expressing human albumin. The HBV sequences from mouse sera were identical to those from orangutan and gibbon sera determined prior to inoculation. In conclusion, human hepatocytes have been infected with gibbon/orangutan HBV.

  15. Cross-species transferability of eastern white pine (Pinus strobus) nuclear microsatellite markers to five Mexican white pines.

    PubMed

    Villalobos-Arámbula, A R; Pérez de la Rosa, J A; Arias, A; Rajora, O P

    2014-09-12

    We examined cross-species transferability and usefulness of six nuclear microsatellite markers developed in consubgeneric eastern white pine (Pinus strobus) with regard to ecologically and commercially important Mexican white pine species of conservation genetics concern: Pinus chiapensis (Mart.) Andresen, P. flexilis James, P. strobiformis Engelm., P. ayacahuite Ehrenb. Ex Schltdl, and P. ayacahuite var. veitchii (Roezl) G.R. Shaw. Four to six microsatellite loci were found to be polymorphic in different species, with moderate to high informativeness in a relatively small number of samples (PIC/HE=0.25-0.93). This successful transfer sidesteps the time- and resource-consuming development of species-specific microsatellite markers, and will facilitate population and conservation genetic studies and genetic resource management of the less studied Mexican white pines.

  16. Quantitative Cross-Species Extrapolation between Humans and Fish: The Case of the Anti-Depressant Fluoxetine

    PubMed Central

    Margiotta-Casaluci, Luigi; Owen, Stewart F.; Cumming, Rob I.; de Polo, Anna; Winter, Matthew J.; Panter, Grace H.; Rand-Weaver, Mariann; Sumpter, John P.

    2014-01-01

    Fish are an important model for the pharmacological and toxicological characterization of human pharmaceuticals in drug discovery, drug safety assessment and environmental toxicology. However, do fish respond to pharmaceuticals as humans do? To address this question, we provide a novel quantitative cross-species extrapolation approach (qCSE) based on the hypothesis that similar plasma concentrations of pharmaceuticals cause comparable target-mediated effects in both humans and fish at similar level of biological organization (Read-Across Hypothesis). To validate this hypothesis, the behavioural effects of the anti-depressant drug fluoxetine on the fish model fathead minnow (Pimephales promelas) were used as test case. Fish were exposed for 28 days to a range of measured water concentrations of fluoxetine (0.1, 1.0, 8.0, 16, 32, 64 µg/L) to produce plasma concentrations below, equal and above the range of Human Therapeutic Plasma Concentrations (HTPCs). Fluoxetine and its metabolite, norfluoxetine, were quantified in the plasma of individual fish and linked to behavioural anxiety-related endpoints. The minimum drug plasma concentrations that elicited anxiolytic responses in fish were above the upper value of the HTPC range, whereas no effects were observed at plasma concentrations below the HTPCs. In vivo metabolism of fluoxetine in humans and fish was similar, and displayed bi-phasic concentration-dependent kinetics driven by the auto-inhibitory dynamics and saturation of the enzymes that convert fluoxetine into norfluoxetine. The sensitivity of fish to fluoxetine was not so dissimilar from that of patients affected by general anxiety disorders. These results represent the first direct evidence of measured internal dose response effect of a pharmaceutical in fish, hence validating the Read-Across hypothesis applied to fluoxetine. Overall, this study demonstrates that the qCSE approach, anchored to internal drug concentrations, is a powerful tool to guide the

  17. Systematic engineering of TCA cycle for optimal production of a four-carbon platform chemical 4-hydroxybutyric acid in Escherichia coli.

    PubMed

    Choi, Sol; Kim, Hyun Uk; Kim, Tae Yong; Lee, Sang Yup

    2016-11-01

    To address climate change and environmental problems, it is becoming increasingly important to establish biorefineries for the production of chemicals from renewable non-food biomass. Here we report the development of Escherichia coli strains capable of overproducing a four-carbon platform chemical 4-hybroxybutyric acid (4-HB). Because 4-HB production is significantly affected by aeration level, genome-scale metabolic model-based engineering strategies were designed under aerobic and microaerobic conditions with emphasis on oxidative/reductive TCA branches and glyoxylate shunt. Several different metabolic engineering strategies were employed to develop strains suitable for fermentation both under aerobic and microaerobic conditions. It was found that microaerobic condition was more efficient than aerobic condition in achieving higher titer and productivity of 4-HB. The final engineered strain produced 103.4g/L of 4-HB by microaerobic fed-batch fermentation using glycerol. The aeration-dependent optimization strategy of TCA cycle will be useful for developing microbial strains producing other reduced derivative chemicals of TCA cycle intermediates.

  18. Optimized inducible shRNA and CRISPR/Cas9 platforms for in vitro studies of human development using hPSCs

    PubMed Central

    Bertero, Alessandro; Pawlowski, Matthias; Ortmann, Daniel; Snijders, Kirsten; Yiangou, Loukia; Cardoso de Brito, Miguel; Brown, Stephanie; Bernard, William G.; Cooper, James D.; Giacomelli, Elisa; Gambardella, Laure; Hannan, Nicholas R. F.; Iyer, Dharini; Sampaziotis, Fotios; Serrano, Felipe; Zonneveld, Mariëlle C. F.; Sinha, Sanjay; Kotter, Mark

    2016-01-01

    Inducible loss of gene function experiments are necessary to uncover mechanisms underlying development, physiology and disease. However, current methods are complex, lack robustness and do not work in multiple cell types. Here we address these limitations by developing single-step optimized inducible gene knockdown or knockout (sOPTiKD or sOPTiKO) platforms. These are based on genetic engineering of human genomic safe harbors combined with an improved tetracycline-inducible system and CRISPR/Cas9 technology. We exemplify the efficacy of these methods in human pluripotent stem cells (hPSCs), and show that generation of sOPTiKD/KO hPSCs is simple, rapid and allows tightly controlled individual or multiplexed gene knockdown or knockout in hPSCs and in a wide variety of differentiated cells. Finally, we illustrate the general applicability of this approach by investigating the function of transcription factors (OCT4 and T), cell cycle regulators (cyclin D family members) and epigenetic modifiers (DPY30). Overall, sOPTiKD and sOPTiKO provide a unique opportunity for functional analyses in multiple cell types relevant for the study of human development. PMID:27899508

  19. Mining online genomic resources in Anolis carolinensis facilitates rapid and inexpensive development of cross-species microsatellite markers for the Anolis lizard genus.

    PubMed

    Wordley, Claire; Slate, Jon; Stapley, Jessica

    2011-01-01

    Online sequence databases can provide valuable resources for the development of cross-species genetic markers. In particular, mining expressed tag sequences (EST) for microsatellites and developing conserved cross-species microsatellite markers can provide a rapid and relatively inexpensive method to develop new markers for a range of species. Here, we adopt this approach to develop cross-species microsatellite markers in Anolis lizards, which is a model genus in evolutionary biology and ecology. Using EST sequences from Anolis carolinensis, we identified 127 microsatellites that satisfied our criteria, and tested 49 of these in five species of Anolis (carolinensis, distichus, apletophallus, porcatus and sagrei). We identified between 8 and 25 new variable genetic markers for five Anolis species. These markers will be a valuable resource for studies of population genetics, comparative mapping, mating systems, behavioural ecology and adaptive radiations in this diverse lineage.

  20. Electronic Attack Platform Placement Optimization

    DTIC Science & Technology

    2014-09-01

    SECURITY CLASSIFICATION OF REPORT Unclassified 18. SECURITY CLASSIFICATION OF THIS PAGE Unclassified 19. SECURITY CLASSIFICATION OF...GB DDR3) Display 10.1” (IPS, 1366 X 768) Multi-touch HD display Operating System Windows 8 Storage 256 GB SSD (SATA-III) Network Intel WLAN ...programming the GPU: 1) security and 2) determining when the GPU is advantageous. Security is a problem applicable to all software development. With the

  1. Cross-species protein sequence and gene structure prediction with fine-tuned Webscipio 2.0 and Scipio

    PubMed Central

    2011-01-01

    Background Obtaining transcripts of homologs of closely related organisms and retrieving the reconstructed exon-intron patterns of the genes is a very important process during the analysis of the evolution of a protein family and the comparative analysis of the exon-intron structure of a certain gene from different species. Due to the ever-increasing speed of genome sequencing, the gap to genome annotation is growing. Thus, tools for the correct prediction and reconstruction of genes in related organisms become more and more important. The tool Scipio, which can also be used via the graphical interface WebScipio, performs significant hit processing of the output of the Blat program to account for sequencing errors, missing sequence, and fragmented genome assemblies. However, Scipio has so far been limited to high sequence similarity and unable to reconstruct short exons. Results Scipio and WebScipio have fundamentally been extended to better reconstruct very short exons and intron splice sites and to be better suited for cross-species gene structure predictions. The Needleman-Wunsch algorithm has been implemented for the search for short parts of the query sequence that were not recognized by Blat. Those regions might either be short exons, divergent sequence at intron splice sites, or very divergent exons. We have shown the benefit and use of new parameters with several protein examples from completely different protein families in searches against species from several kingdoms of the eukaryotes. The performance of the new Scipio version has been tested in comparison with several similar tools. Conclusions With the new version of Scipio very short exons, terminal and internal, of even just one amino acid can correctly be reconstructed. Scipio is also able to correctly predict almost all genes in cross-species searches even if the ancestors of the species separated more than 100 Myr ago and if the protein sequence identity is below 80%. For our test cases Scipio

  2. Optimism

    PubMed Central

    Carver, Charles S.; Scheier, Michael F.; Segerstrom, Suzanne C.

    2010-01-01

    Optimism is an individual difference variable that reflects the extent to which people hold generalized favorable expectancies for their future. Higher levels of optimism have been related prospectively to better subjective well-being in times of adversity or difficulty (i.e., controlling for previous well-being). Consistent with such findings, optimism has been linked to higher levels of engagement coping and lower levels of avoidance, or disengagement, coping. There is evidence that optimism is associated with taking proactive steps to protect one's health, whereas pessimism is associated with health-damaging behaviors. Consistent with such findings, optimism is also related to indicators of better physical health. The energetic, task-focused approach that optimists take to goals also relates to benefits in the socioeconomic world. Some evidence suggests that optimism relates to more persistence in educational efforts and to higher later income. Optimists also appear to fare better than pessimists in relationships. Although there are instances in which optimism fails to convey an advantage, and instances in which it may convey a disadvantage, those instances are relatively rare. In sum, the behavioral patterns of optimists appear to provide models of living for others to learn from. PMID:20170998

  3. Optimization of transplastomic production of hemicellulases in tobacco: effects of expression cassette configuration and tobacco cultivar used as production platform on recombinant protein yields

    PubMed Central

    2013-01-01

    Background Chloroplast transformation in tobacco has been used extensively to produce recombinant proteins and enzymes. Chloroplast expression cassettes can be designed with different configurations of the cis-acting elements that govern foreign gene expression. With the aim to optimize production of recombinant hemicellulases in transplastomic tobacco, we developed a set of cassettes that incorporate elements known to facilitate protein expression in chloroplasts and examined expression and accumulation of a bacterial xylanase XynA. Biomass production is another important factor in achieving sustainable and high-volume production of cellulolytic enzymes. Therefore, we compared productivity of two tobacco cultivars – a low-alkaloid and a high-biomass - as transplastomic expression platforms. Results Four different cassettes expressing XynA produced various mutant phenotypes of the transplastomic plants, affected their growth rate and resulted in different accumulation levels of the XynA enzyme. The most productive cassette was identified and used further to express XynA and two additional fungal xylanases, Xyn10A and Xyn11B, in a high-biomass tobacco cultivar. The high biomass cultivar allowed for a 60% increase in XynA production per plant. Accumulation of the fungal enzymes reached more than 10-fold higher levels than the bacterial enzyme, constituting up to 6% of the total soluble protein in the leaf tissue. Use of a well-characterized translational enhancer with the selected expression cassette revealed inconsistent effects on accumulation of the recombinant xylanases. Additionally, differences in the enzymatic activity of crude plant extracts measured in leaves of different age suggest presence of a specific xylanase inhibitor in the green leaf tissue. Conclusion Our results demonstrate the pivotal importance of the expression cassette design and appropriate tobacco cultivar for high-level transplastomic production of recombinant proteins. PMID:23642171

  4. Lysimeter Platform

    NASA Astrophysics Data System (ADS)

    Klammler, Gernot; Murer, Erwin; Plieschnegger, Markus

    2014-05-01

    The existing European Lysimeter Platform (www.lysimeter.at/HP_EuLP) provides an overview of lysimeter types used in Europe and show details on equipment, research results and future perspectives of lysimeter facilities. However, this platform is not user-editable and has not been updated since 2008. Thus, the Lysimeter Research Group (www.lysimeter.at) intends to serve a new database based website called Lysimeter Platform, where existing information of the former European Lysimeter Platform will be transferred to the new Lysimeter Platform and, furthermore, registered users are able to create and edit sites where lysimeters, soil water samplers and soil hydrologic measuring profiles are operated. The Lysimeter Research Group is a scientific association and, therefore, the membership is free of charge. The new Lysimeter Platform contains general information of lysimeter sites worldwide (e.g., what is measured at which site) in a standardized form to get a quick but informative overview of the sites and can be linked to more detailed, already existing information provided by the site operators. Due to the standardized information in the database the Lysimeter Platform serves also as search-engine for soil water measurements and helps to find sites of interest and corresponding contact information worldwide. The Session "Estimation of soil-atmosphere and vadose zone water fluxes by use of precision lysimeter measurements" at the EGU General Assembly 2014 would be an excellent chance to present the idea and the concept of this new Lysimeter Platform to international site operators and scientists.

  5. Network Modules of the Cross-Species Genotype-Phenotype Map Reflect the Clinical Severity of Human Diseases

    PubMed Central

    Han, Seong Kyu; Kim, Inhae; Hwang, Jihye; Kim, Sanguk

    2015-01-01

    Recent advances in genome sequencing techniques have improved our understanding of the genotype-phenotype relationship between genetic variants and human diseases. However, genetic variations uncovered from patient populations do not provide enough information to understand the mechanisms underlying the progression and clinical severity of human diseases. Moreover, building a high-resolution genotype-phenotype map is difficult due to the diverse genetic backgrounds of the human population. We built a cross-species genotype-phenotype map to explain the clinical severity of human genetic diseases. We developed a data-integrative framework to investigate network modules composed of human diseases mapped with gene essentiality measured from a model organism. Essential and nonessential genes connect diseases of different types which form clusters in the human disease network. In a large patient population study, we found that disease classes enriched with essential genes tended to show a higher mortality rate than disease classes enriched with nonessential genes. Moreover, high disease mortality rates are explained by the multiple comorbid relationships and the high pleiotropy of disease genes found in the essential gene-enriched diseases. Our results reveal that the genotype-phenotype map of a model organism can facilitate the identification of human disease-gene associations and predict human disease progression. PMID:26301634

  6. Using cross-species comparisons and a neurobiological framework to understand early social deprivation effects on behavioral development

    PubMed Central

    BRETT, ZOË H.; HUMPHREYS, KATHRYN L.; FLEMING, ALISON S.; KRAEMER, GARY W.; DRURY, STACY S.

    2017-01-01

    Building upon the transactional model of brain development, we explore the impact of early maternal deprivation on neural development and plasticity in three neural systems: hyperactivity/impulsivity, executive function, and hypothalamic–pituitary–adrenal axis functioning across rodent, nonhuman primate, and human studies. Recognizing the complexity of early maternal–infant interactions, we limit our cross-species comparisons to data from rodent models of artificial rearing, nonhuman primate studies of peer rearing, and the relations between these two experimental approaches and human studies of children exposed to the early severe psychosocial deprivation associated with institutional care. In addition to discussing the strengths and limitations of these paradigms, we present the current state of research on the neurobiological impact of early maternal deprivation and the evidence of sensitive periods, noting methodological challenges. Integrating data across preclinical animal models and human studies, we speculate about the underlying biological mechanisms; the differential impact of deprivation due to temporal factors including onset, offset, and duration of the exposure; and the possibility and consequences of reopening of sensitive periods during adolescence. PMID:25997759

  7. Development of novel microsatellite markers for the Northern Goshawk (Accipiter gentilis) and their utility in cross-species amplification

    USGS Publications Warehouse

    Haughey, Christy; Sage, George K.; Degange, Gabriel; Sonsthagen, Sarah A.; Talbot, Sandra

    2016-01-01

    The Northern Goshawk (Accipiter gentilis) is a large forest raptor with a Holarctic distribution and, in some portions of its range, a species of conservation concern. To augment previously reported genetic markers, 13 novel polymorphic microsatellite markers were developed to establish individual identification and familial relationships, to assess levels of genetic diversity, and to identify diagnostic markers. Of the 22 loci tested, 13 were polymorphic, seven were monomorphic, and two failed to amplify. This suite of microsatellite loci yielded a combined probability of parental exclusion of 98%; a single individual sampled from a North American population can be reliably identified using a combination of seven of the 13 polymorphic loci. Cross-species screening in Cooper's Hawks (A. cooperii) and Sharp-shinned Hawks (A. striatus) of the 20 loci that successfully amplified in Northern Goshawks identified 13 loci as polymorphic in each species. Six of these loci (Age1303, Age1308, Age1309, Age1312, and Age1314) appeared to be useful in distinguishing between Accipiter species. These markers will be useful to researchers investigating populations of North American accipiters.

  8. Isolation and characterization of 45 Polymorphie microsatellite loci of turbot ( Scophthalmus maximus) and cross-species amplification

    NASA Astrophysics Data System (ADS)

    Hou, Shiying; Ma, Aijun; Wang, Xin'an; Huang, Zhihui; Xue, Baogui; Yang, Zhi; Qu, Jiangbo

    2011-03-01

    Turbot ( Scophthalmus maximus) is a flatfish species commercially important for aquaculture. In this study, we generated a microsatellite-enriched genomic DNA library for Scophthalmus maximus, and then isolated and characterized 45 microsatellite loci by genotyping 30 individuals. The observed number of alleles ranged from 2 to 19 with an average of 6.24, while the effective number of alleles ranged from 1.30 to 11.11 with an average of 3.66. The expected heterozygosities varied from 0.235 to 0.925 4 and Polymorphie information content ranged from 0.2044 to 0.903 3, with an average of 0.622. Twelve loci deviated significantly from Hardy-Weinberg equilibrium, and no significant linkage disequilibrium was observed between any pair of loci after Bonferroni correction. In cross-species amplification, five flatfish species ( Paralichthys lethostigma, Verasper moseri, platichthys stellatus, Hippoglossoides dubius and Cynoglossus semilaevis) showed at least one Polymorphie locus. These Polymorphie microsatellite loci should prove useful for Population analysis of turbot and other related species.

  9. Identification of novel and diverse rotaviruses in rodents and insectivores, and evidence of cross-species transmission into humans.

    PubMed

    Li, Kun; Lin, Xian-Dan; Huang, Kai-Yu; Zhang, Bing; Shi, Mang; Guo, Wen-Ping; Wang, Miao-Ruo; Wang, Wen; Xing, Jian-Guang; Li, Ming-Hui; Hong, Wang-Sheng; Holmes, Edward C; Zhang, Yong-Zhen

    2016-07-01

    Rotaviruses are an important cause of severe diarrheal illness in children globally. We characterized rotaviruses sampled in humans, insectivores (shrews) and rodents from urban and rural regions of Zhejiang province, China. Phylogenetic analyses revealed seven genotypic constellations of human rotaviruses with six different combinations of G and P genotypes - G3P[8] (50.06%), G9P[8] (36.16%), G1P[8] (8.92%), G2P[4] (4.63%), G3P[3] (0.12%), and G3P[9] (0.12%). In rodents and shrews sampled from the same locality we identified a novel genotype constellation (G32-P[46]-I24-R18-C17-M17-A28-N17-T19-E24-H19), a novel P genotype (P[45]), and two different AU-1-like rotaviruses associated with a G3P[3] genotype combination. Of particular note was a novel rotavirus from a human patient that was closely related to viruses sampled from rodents in the same region, indicative of a local species jump. In sum, these data are suggestive of the cross-species transmission of rodent rotaviruses into humans and for reassortment among human and animal rotaviruses.

  10. Exposure to early adversity: Points of cross-species translation that can lead to improved understanding of depression

    PubMed Central

    ANDERSEN, SUSAN L.

    2017-01-01

    The relationship between developmental exposure to adversity and affective disorders is reviewed. Adversity discussed herein includes physical and sexual abuse, neglect, or loss of a caregiver in humans. While these stressors can occur at any point during development, the unique temporal relationship to specific depressive symptoms was the focus of discussion. Further influences of stress exposure during sensitive periods can vary by gender and duration of abuse as well. Data from animal studies are presented to provide greater translational and causal understanding of how sensitive periods, different types of psychosocial stressors, and sex interact to produce depressive-like behaviors. Findings from maternal separation, isolation rearing, chronic variable stress, and peer–peer rearing paradigms clarify interpretation about how various depressive behaviors are influenced by age of exposure. Depressive behaviors are broken down into the following categories: mood and affect, anhedonia, energy, working memory, sleep–wake, appetite changes, suicide, and general malaise. Cross-species evidence from humans, nonhuman primates, rats, and mice within each of these categories is discussed. In conclusion, sensitive periods for affective-related behaviors (anxiety, mood, and controllability) occur earlier in life, while other aspects of depression are associated with adversity later during adolescence. PMID:25997766

  11. Identifying a Network of Brain Regions Involved in Aversion-Related Processing: A Cross-Species Translational Investigation

    PubMed Central

    Hayes, Dave J.; Northoff, Georg

    2011-01-01

    The ability to detect and respond appropriately to aversive stimuli is essential for all organisms, from fruit flies to humans. This suggests the existence of a core neural network which mediates aversion-related processing. Human imaging studies on aversion have highlighted the involvement of various cortical regions, such as the prefrontal cortex, while animal studies have focused largely on subcortical regions like the periaqueductal gray and hypothalamus. However, whether and how these regions form a core neural network of aversion remains unclear. To help determine this, a translational cross-species investigation in humans (i.e., meta-analysis) and other animals (i.e., systematic review of functional neuroanatomy) was performed. Our results highlighted the recruitment of the anterior cingulate cortex, the anterior insula, and the amygdala as well as other subcortical (e.g., thalamus, midbrain) and cortical (e.g., orbitofrontal) regions in both animals and humans. Importantly, involvement of these regions remained independent of sensory modality. This study provides evidence for a core neural network mediating aversion in both animals and humans. This not only contributes to our understanding of the trans-species neural correlates of aversion but may also carry important implications for psychiatric disorders where abnormal aversive behavior can often be observed. PMID:22102836

  12. Cross-species amplification from crop soybean Glycine max provides informative microsatellite markers for the study of inbreeding wild relatives.

    PubMed

    Hempel, K; Peakall, R

    2003-06-01

    The development of microsatellite markers through transfer of primers from related species (cross-species amplification) remains a little-explored alternative to the de novo method in plants. In this study of 100 microsatellite loci from Glycine max, we examined two aspects of primer transfer. First, we tested if source locus properties can predict primer transfer and polymorphism in Glycine cyrtoloba and Glycine clandestina. We transferred 23 primers to G. cyrtoloba and 42 to G. clandestina, with 19 loci polymorphic within G. clandestina. However, we could not predict transfer or polymorphism from the source locus properties. Second, we evaluated the subset of 11 polymorphic loci for study in G. clandestina populations representing two local morphotypes. All loci were informative within populations (population mean He +/- SE = 0.58 +/- 0.04). We directly sequenced 28 alleles at 4 representative loci. The allelic patterns and sequencing results established that 8 of 11 loci were typical microsatellites, confirming the utility of primer transfer as an alternative to de novo development. Additionally, we found that morphotypic differentiation between populations was paralleled by changes in polymorphism level at six loci and size homoplasy at one locus. We interpret these patterns as being a product of selfing in G. clandestina. Our results demonstrate the value of allele sequence knowledge for the most effective use of microsatellites.

  13. Cross-species comparison of orthologous gene expression in human bladder cancer and carcinogen-induced rodent models

    PubMed Central

    Lu, Yan; Liu, Pengyuan; Wen, Weidong; Grubbs, Clinton J; Townsend, Reid R; Malone, James P; Lubet, Ronald A; You, Ming

    2011-01-01

    Genes differentially expressed by tumor cells represent promising drug targets for anti-cancer therapy. Such candidate genes need to be validated in appropriate animal models. This study examined the suitability of rodent models of bladder cancer in B6D2F1 mice and Fischer-344 rats to model clinical bladder cancer specimens in humans. Using a global gene expression approach cross-species analysis showed that 13-34% of total genes in the genome were differentially expressed between tumor and normal tissues in each of five datasets from humans, rats, and mice. About 20% of these differentially expressed genes overlapped among species, corresponding to 2.6 to 4.8% of total genes in the genome. Several genes were consistently dysregulated in bladder tumors in both humans and rodents. Notably, CNN1, MYL9, PDLIM3, ITIH5, MYH11, PCP4 and FM05 were found to commonly down-regulated; while T0P2A, CCNB2, KIF20A and RRM2 were up-regulated. These genes are likely to have conserved functions contributing to bladder carcinogenesis. Gene set enrichment analysis detected a number of molecular pathways commonly activated in both humans and rodent bladder cancer. These pathways affect the cell cycle, HIF-1 and MYC expression, and regulation of apoptosis. We also compared expression changes at mRNA and protein levels in the rat model and identified several genes/proteins exhibiting concordant changes in bladder tumors, including ANXA1, ANXA2, CA2, KRT14, LDHA, LGALS4, SERPINA1, KRT18 and LDHB. In general, rodent models of bladder cancer represent the clinical disease to an extent that will allow successful mining of target genes and permit studies on the molecular mechanisms of bladder carcinogenesis. PMID:21139803

  14. Cross-species chromosome painting unveils cytogenetic signatures for the Eulipotyphla and evidence for the polyphyly of Insectivora.

    PubMed

    Ye, Jianping; Biltueva, Larisa; Huang, Ling; Nie, Wenhui; Wang, Jinhuan; Jing, Meidong; Su, Weiting; Vorobieva, Nadezhda V; Jiang, Xuelong; Graphodatsky, Alexander S; Yang, Fengtang

    2006-01-01

    Insectivore-like animals are traditionally believed among the first eutherian mammals that have appeared on the earth. The modern insectivores are thus crucial for understanding the systematics and phylogeny of eutherian mammals as a whole. Here cross-species chromosome painting, with probes derived from flow-sorted chromosomes of human, was used to delimit the homologous chromosomal segments in two Soricidae species, the common shrew (Sorex araneus, 2n = 20/21), and Asiatic short-tailed shrew (Blarinella griselda, 2n = 44), and one Erinaceidae species, the shrew-hedgehog (Neotetracus sinensis, 2n = 32), and human. We report herewith the first comparative maps for the Asiatic short-tailed shrew and the shrew-hedgehog, in addition to a refined comparative map for the common shrew. In total, the 22 human autosomal paints detected 40, 51 and 58 evolutionarily conserved segments in the genomes of common shrew, Asiatic short-tailed shrew, and shrew-hedgehog, respectively, demonstrating that the common shrew has retained a conserved genome organization while the Asiatic short-tailed shrew and shrew-hedgehog have relatively rearranged genomes. In addition to confirming the existence of such ancestral human segmental combinations as HSA 3/21, 12/22, 14/15 and 7/16 that are shared by most eutherian mammals, our study reveals a shared human segmental combination, HSA 4/20, that could phylogenetically unite the Eulipotyphlan (i.e., the core insectivores) species. Our results provide cytogenetic evidence for the polyphyly of the order Insectivora and additional data for the eventual reconstruction of the ancestral eutherian karyotype.

  15. Tamoxifen-elicited uterotrophy: cross-species and cross-ligand analysis of the gene expression program

    PubMed Central

    Kwekel, Joshua C; Forgacs, Agnes L; Burgoon, Lyle D; Williams, Kurt J; Zacharewski, Timothy R

    2009-01-01

    Background Tamoxifen (TAM) is a well characterized breast cancer drug and selective estrogen receptor modulator (SERM) which also has been associated with a small increase in risk for uterine cancers. TAM's partial agonist activation of estrogen receptor has been characterized for specific gene promoters but not at the genomic level in vivo.Furthermore, reducing uncertainties associated with cross-species extrapolations of pharmaco- and toxicogenomic data remains a formidable challenge. Results A comparative ligand and species analysis approach was conducted to systematically assess the physiological, morphological and uterine gene expression alterations elicited across time by TAM and ethynylestradiol (EE) in immature ovariectomized Sprague-Dawley rats and C57BL/6 mice. Differential gene expression was evaluated using custom cDNA microarrays, and the data was compared to identify conserved and divergent responses. 902 genes were differentially regulated in all four studies, 398 of which exhibit identical temporal expression patterns. Conclusion Comparative analysis of EE and TAM differentially expressed gene lists suggest TAM regulates no unique uterine genes that are conserved in the rat and mouse. This demonstrates that the partial agonist activities of TAM extend to molecular targets in regulating only a subset of EE-responsive genes. Ligand-conserved, species-divergent expression of carbonic anhydrase 2 was observed in the microarray data and confirmed by real time PCR. The identification of comparable temporal phenotypic responses linked to related gene expression profiles demonstrates that systematic comparative genomic assessments can elucidate important conserved and divergent mechanisms in rodent estrogen signalling during uterine proliferation. PMID:19400957

  16. Efficient cross-species capture hybridization and next-generation sequencing of mitochondrial genomes from noninvasively sampled museum specimens

    PubMed Central

    Mason, Victor C.; Li, Gang; Helgen, Kristofer M.; Murphy, William J.

    2011-01-01

    The ability to uncover the phylogenetic history of recently extinct species and other species known only from archived museum material has rapidly improved due to the reduced cost and increased sequence capacity of next-generation sequencing technologies. One limitation of these approaches is the difficulty of isolating and sequencing large, orthologous DNA regions across multiple divergent species, which is exacerbated for museum specimens, where DNA quality varies greatly between samples and contamination levels are often high. Here we describe the use of cross-species DNA capture hybridization techniques and next-generation sequencing to selectively isolate and sequence partial to full-length mitochondrial DNA genomes from the degraded DNA of museum specimens, using probes generated from the DNA of a single extant species. We demonstrate our approach on specimens from an enigmatic gliding mammal, the Sunda colugo, which is widely distributed throughout Southeast Asia. We isolated DNA from 13 colugo specimens collected 47–170 years ago, and successfully captured and sequenced mitochondrial DNA from every specimen, frequently recovering fragments with 10%–13% sequence divergence from the capture probe sequence. Phylogenetic results reveal deep genetic divergence among colugos, both within and between the islands of Borneo and Java, as well as between the Malay Peninsula and different Sundaic islands. Our method is based on noninvasive sampling of minute amounts of soft tissue material from museum specimens, leaving the original specimen essentially undamaged. This approach represents a paradigm shift away from standard PCR-based approaches for accessing population genetic and phylogenomic information from poorly known and difficult-to-study species. PMID:21880778

  17. Cross-species chromosome painting in bats from Madagascar: the contribution of Myzopodidae to revealing ancestral syntenies in Chiroptera.

    PubMed

    Richards, Leigh R; Rambau, Ramugondo V; Lamb, Jennifer M; Taylor, Peter J; Yang, Fengtang; Schoeman, M Corrie; Goodman, Steven M

    2010-09-01

    The chiropteran fauna of Madagascar comprises eight of the 19 recognized families of bats, including the endemic Myzopodidae. While recent systematic studies of Malagasy bats have contributed to our understanding of the morphological and genetic diversity of the island's fauna, little is known about their cytosystematics. Here we investigate karyotypic relationships among four species, representing four families of Chiroptera endemic to the Malagasy region using cross-species chromosome painting with painting probes of Myotis myotis: Myzopodidae (Myzopoda aurita, 2n = 26), Molossidae (Mormopterus jugularis, 2n = 48), Miniopteridae (Miniopterus griveaudi, 2n = 46), and Vespertilionidae (Myotis goudoti, 2n = 44). This study represents the first time a member of the family Myzopodidae has been investigated using chromosome painting. Painting probes of M. myotis were used to delimit 29, 24, 23, and 22 homologous chromosomal segments in the genomes of M. aurita, M. jugularis, M. griveaudi, and M. goudoti, respectively. Comparison of GTG-banded homologous chromosomes/chromosomal segments among the four species revealed the genome of M. aurita has been structured through 14 fusions of chromosomes and chromosomal segments of M. myotis chromosomes leading to a karyotype consisting solely of bi-armed chromosomes. In addition, chromosome painting revealed a novel X-autosome translocation in M. aurita. Comparison of our results with published chromosome maps provided further evidence for karyotypic conservatism within the genera Mormopterus, Miniopterus, and Myotis. Mapping of chromosomal rearrangements onto a molecular consensus phylogeny revealed ancestral syntenies shared between Myzopoda and other bat species of the infraorders Pteropodiformes and Vespertilioniformes. Our study provides further evidence for the involvement of Robertsonian (Rb) translocations and fusions/fissions in chromosomal evolution within Chiroptera.

  18. [Lens platform].

    PubMed

    Łukaszewska-Smyk, Agnieszka; Kałuzny, Józef

    2010-01-01

    The lens platform defines lens structure and lens material. Evolution of lens comprises change in their shape, angulation of haptens and transition of three-piece lens into one-piece lens. The lens fall into two categories: rigid (PMMA) and soft (siliconic, acrylic, colameric). The main lens maaterials are polymers (hydrophilic and hydrophobic). The lens platform has an effect on biocompatibility, bioadhesion, stability of lens in capsule, degree of PCO evolution and sensitiveness to laser damages.

  19. Development of Genomic Microsatellite Markers in Carthamus tinctorius L. (Safflower) Using Next Generation Sequencing and Assessment of Their Cross-Species Transferability and Utility for Diversity Analysis

    PubMed Central

    Variath, Murali Tottekkad; Joshi, Gopal; Bali, Sapinder; Agarwal, Manu; Kumar, Amar; Jagannath, Arun; Goel, Shailendra

    2015-01-01

    Background Safflower (Carthamus tinctorius L.), an Asteraceae member, yields high quality edible oil rich in unsaturated fatty acids and is resilient to dry conditions. The crop holds tremendous potential for improvement through concerted molecular breeding programs due to the availability of significant genetic and phenotypic diversity. Genomic resources that could facilitate such breeding programs remain largely underdeveloped in the crop. The present study was initiated to develop a large set of novel microsatellite markers for safflower using next generation sequencing. Principal Findings Low throughput genome sequencing of safflower was performed using Illumina paired end technology providing ~3.5X coverage of the genome. Analysis of sequencing data allowed identification of 23,067 regions harboring perfect microsatellite loci. The safflower genome was found to be rich in dinucleotide repeats followed by tri-, tetra-, penta- and hexa-nucleotides. Primer pairs were designed for 5,716 novel microsatellite sequences with repeat length ≥ 20 bases and optimal flanking regions. A subset of 325 microsatellite loci was tested for amplification, of which 294 loci produced robust amplification. The validated primers were used for assessment of 23 safflower accessions belonging to diverse agro-climatic zones of the world leading to identification of 93 polymorphic primers (31.6%). The numbers of observed alleles at each locus ranged from two to four and mean polymorphism information content was found to be 0.3075. The polymorphic primers were tested for cross-species transferability on nine wild relatives of cultivated safflower. All primers except one showed amplification in at least two wild species while 25 primers amplified across all the nine species. The UPGMA dendrogram clustered C. tinctorius accessions and wild species separately into two major groups. The proposed progenitor species of safflower, C. oxyacantha and C. palaestinus were genetically closer to

  20. Functional interaction of nuclear domain 10 and its components with cytomegalovirus after infections: cross-species host cells versus native cells.

    PubMed

    Cosme, Ruth Cruz; Martínez, Francisco Puerta; Tang, Qiyi

    2011-04-28

    Species-specificity is one of the major characteristics of cytomegaloviruses (CMVs) and is the primary reason for the lack of a mouse model for the direct infection of human CMV (HCMV). It has been determined that CMV cross-species infections are blocked at the post-entry level by intrinsic cellular defense mechanisms, but few details are known. It is important to explore how CMVs interact with the subnuclear structure of the cross-species host cell. In our present study, we discovered that nuclear domain 10 (ND10) of human cells was not disrupted by murine CMV (MCMV) and that the ND10 of mouse cells was not disrupted by HCMV, although the ND10-disrupting protein, immediate-early protein 1 (IE1), also colocalized with ND10 in cross-species infections. In addition, we found that the UL131-repaired HCMV strain AD169 (vDW215-BADrUL131) can infect mouse cells to produce immediate-early (IE) and early (E) proteins but that neither DNA replication nor viral particles were detectable in mouse cells. Unrepaired AD169 can express IE1 only in mouse cells. In both HCMV-infected mouse cells and MCMV-infected human cells, the knocking-down of ND10 components (PML, Daxx, and SP100) resulted in significantly increased viral-protein production. Our observations provide evidence to support our hypothesis that ND10 and ND10 components might be important defensive factors against the CMV cross-species infection.

  1. A novel endogenous betaretrovirus in the common vampire bat (Desmodus rotundus) suggests multiple independent infection and cross-species transmission events.

    PubMed

    Escalera-Zamudio, Marina; Mendoza, M Lisandra Zepeda; Heeger, Felix; Loza-Rubio, Elizabeth; Rojas-Anaya, Edith; Méndez-Ojeda, Maria L; Taboada, Blanca; Mazzoni, Camila J; Arias, Carlos F; Greenwood, Alex D

    2015-05-01

    The Desmodus rotundus endogenous betaretrovirus (DrERV) is fixed in the vampire bat D. rotundus population and in other phyllostomid bats but is not present in all species from this family. DrERV is not phylogenetically related to Old World bat betaretroviruses but to betaretroviruses from rodents and New World primates, suggesting recent cross-species transmission. A recent integration age estimation of the provirus in some taxa indicates that an exogenous counterpart might have been in recent circulation.

  2. Analysis of the long control region of bovine papillomavirus type 1 associated with sarcoids in equine hosts indicates multiple cross-species transmission events and phylogeographical structure.

    PubMed

    Trewby, Hannah; Ayele, Gizachew; Borzacchiello, Giuseppe; Brandt, Sabine; Campo, M Saveria; Del Fava, Claudia; Marais, Johan; Leonardi, Leonardo; Vanselow, Barbara; Biek, Roman; Nasir, Lubna

    2014-12-01

    Papillomaviruses are a family of slowly evolving DNA viruses and their evolution is commonly linked to that of their host species. However, whilst bovine papillomavirus-1 (BPV-1) primarily causes warts in its natural host, the cow, it can also cause locally aggressive and invasive skin tumours in equids, known as sarcoids, and thus provides a rare contemporary example of cross-species transmission of a papillomavirus. Here, we describe the first phylogenetic analysis of BPV-1 in equine sarcoids to our knowledge, allowing us to explore the evolutionary history of BPV-1 and investigate its cross-species association with equids. A phylogenetic analysis of the BPV-1 transcriptional promoter region (the long control region or LCR) was conducted on 15 bovine and 116 equine samples from four continents. Incorporating previous estimates for evolutionary rates in papillomavirus implied that the genetic diversity in the LCR variants was ancient and predated domestication of both equids and cattle. The phylogeny demonstrated geographical segregation into an ancestral group (African, South American and Australian samples), and a more recently derived, largely European clade. Whilst our data are consistent with BPV-1 originating in cattle, we found evidence of multiple, probably relatively recent, cross-species transmission events into horses. We also demonstrated the high prevalence of one particular sequence variant (variant 20), and suggest this may indicate that this variant shows a fitness advantage in equids. Although strong host specificity remains the norm in papillomaviruses, our results demonstrate that exceptions to this rule exist and can become epidemiologically relevant.

  3. Optimized design of a nanostructured SPCE-based multipurpose biosensing platform formed by ferrocene-tethered electrochemically-deposited cauliflower-shaped gold nanoparticles

    PubMed Central

    Argoubi, Wicem; Saadaoui, Maroua

    2015-01-01

    Summary The demand for on-site nanodevices is constantly increasing. The technology development for the design of such devices is highly regarded. In this work, we report the design of a disposable platform that is structured with cauliflower-shaped gold nanoparticles (cfAuNPs) and we show its applications in immunosensing and enzyme-based detection. The electrochemical reduction of Au(III) allows for the electrodeposition of highly dispersed cauliflower-shaped gold nanoparticles on the surface of screen-printed carbon electrodes (SPCEs). The nanostructures were functionalized using ferrocenylmethyl lipoic acid ester which allowed for the tethering of the ferrocene group to gold, which serves as an electrochemical transducer/mediator. The bioconjugation of the surface with anti-human IgG antibody (α-hIgG) or horseradish peroxidase (HRP) enzyme yields biosensors, which have been applied for the selective electrochemical detection of human IgG (hIgG) or H2O2 as model analytes, respectively. Parameters such as the number of sweeps, amount of charge generated from the oxidation of the electrodeposited gold, time of incubation and concentration of the ferrocene derivatives have been studied using cyclic voltammetry (CV), electrochemical impedance spectroscopy (EIS) and scanning electron microscopy (SEM). Selectivity and specificity tests have been also performed in the presence of potentially interfering substances to either hIgG or H2O2. Results showed that the devised immunosensor is endowed with good selectivity and specificity in the presence of several folds of competitive analytes. The enzyme-based platform showed a good catalytic activity towards H2O2 oxidation which predestined it to potential applications pertaining to enzymatic kinetics studies. The levels of hIgG in human serum and H2O2 in honey were successfully determined and served as assessment tools of the applicability of the platforms for real samples analysis. PMID:26425435

  4. APOBEC3G polymorphism as a selective barrier to cross-species transmission and emergence of pathogenic SIV and AIDS in a primate host.

    PubMed

    Krupp, Annabel; McCarthy, Kevin R; Ooms, Marcel; Letko, Michael; Morgan, Jennifer S; Simon, Viviana; Johnson, Welkin E

    2013-01-01

    Cellular restriction factors, which render cells intrinsically resistant to viruses, potentially impose genetic barriers to cross-species transmission and emergence of viral pathogens in nature. One such factor is APOBEC3G. To overcome APOBEC3G-mediated restriction, many lentiviruses encode Vif, a protein that targets APOBEC3G for degradation. As with many restriction factor genes, primate APOBEC3G displays strong signatures of positive selection. This is interpreted as evidence that the primate APOBEC3G locus reflects a long-term evolutionary "arms-race" between retroviruses and their primate hosts. Here, we provide direct evidence that APOBEC3G has functioned as a barrier to cross-species transmission, selecting for viral resistance during emergence of the AIDS-causing pathogen SIVmac in captive colonies of Asian macaques in the 1970s. Specifically, we found that rhesus macaques have multiple, functionally distinct APOBEC3G alleles, and that emergence of SIVmac and simian AIDS required adaptation of the virus to evade APOBEC3G-mediated restriction. Our evidence includes the first comparative analysis of APOBEC3G polymorphism and function in both a reservoir and recipient host species (sooty mangabeys and rhesus macaques, respectively), and identification of adaptations unique to Vif proteins of the SIVmac lineage that specifically antagonize rhesus APOBEC3G alleles. By demonstrating that interspecies variation in a known restriction factor selected for viral counter-adaptations in the context of a documented case of cross-species transmission, our results lend strong support to the evolutionary "arms-race" hypothesis. Importantly, our study confirms that APOBEC3G divergence can be a critical determinant of interspecies transmission and emergence of primate lentiviruses, including viruses with the potential to infect and spread in human populations.

  5. Cross-species transfer of viruses: implications for the use of viral vectors in biomedical research, gene therapy and as live-virus vaccines.

    PubMed

    Louz, Derrick; Bergmans, Hans E; Loos, Birgit P; Hoeben, Rob C

    2005-10-01

    All living organisms are continuously exposed to a plethora of viruses. In general, viruses tend to be restricted to the natural host species which they infect. From time to time viruses cross the host-range barrier expanding their host range. However, in very rare cases cross-species transfer is followed by the establishment and persistence of a virus in the new host species, which may result in disease. Recent examples of viruses that have crossed the species barrier from animal reservoirs to humans are hantavirus, haemorrhagic fever viruses, arboviruses, Nipah and Hendra viruses, avian influenza virus (AI), monkeypox virus, and the SARS-associated coronavirus (SARS-CoV). The opportunities for cross-species transfer of mammalian viruses have increased in recent years due to increased contact between humans and animal reservoirs. However, it is difficult to predict when such events will take place since the viral adaptation that is needed to accomplish this is multifactorial and stochastic. Against this background the intensified use of viruses and their genetically modified variants as viral gene transfer vectors for biomedical research, experimental gene therapy and for live-vector vaccines is a cause for concern. This review addresses a number of potential risk factors and their implications for activities with viral vectors from the perspective of cross-species transfer of viruses in nature, with emphasis on the occurrence of host-range mutants resulting from either cell culture or tropism engineering. The issues are raised with the intention to assist in risk assessments for activities with vector viruses.

  6. Development of nine new microsatellite loci for the American beaver, Castor canadensis (Rodentia: Castoridae), and cross-species amplification in the European beaver, Castor fiber.

    PubMed

    Pelz-Serrano, Karla; Munguia-Vega, Adrian; Piaggio, Antoinette J; Neubaum, Melissa; Munclinger, Pavel; Pártl, Adam; VAN Riper Iii, Charles; Culver, Melanie

    2009-03-01

    We developed nine new nuclear dinucleotide microsatellite loci for Castor canadensis. All loci were polymorphic, except for one. The number of alleles ranged from two to four and from five to 12 in populations from Arizona and Wisconsin, respectively. Average heterozygosity ranged from 0.13 to 0.86 per locus. Since cross-species amplification in Castor fiber was successful only in four loci, we tested also nine recently published C. canadensis loci in the Eurasian species. Eight of the published loci amplified; however, three were monomorphic. The number of alleles was lower in C. fiber than in C. canadensis at all loci tested.

  7. Development of nine new microsatellite loci for the American beaver, Castor canadensis (Rodentia: Castoridae), and cross-species amplification in the European beaver, Castor fiber

    USGS Publications Warehouse

    Pelz-Serrano, K.; Munguia-Vega, A.; Piaggio, A.J.; Neubaum, M.; Munclinger, P.; PArtl, A.; van Riper, Charles; Culver, M.

    2009-01-01

    We developed nine new nuclear dinucleotide microsatellite loci for Castor canadensis. All loci were polymorphic, except for one. The number of alleles ranged from two to four and from five to 12 in populations from Arizona and Wisconsin, respectively. Average heterozygosity ranged from 0.13 to 0.86 per locus. Since cross-species amplification in Castor fiber was successful only in four loci, we tested also nine recently published C. canadensis loci in the Eurasian species. Eight of the published loci amplified; however, three were monomorphic. The number of alleles was lower in C. fiber than in C. canadensis at all loci tested. ?? 2009 Blackwell Publishing Ltd.

  8. Genetic differences accounting for evolution and pathogenicity of simian immunodeficiency virus from a sooty mangabey monkey after cross-species transmission to a pig-tailed macaque.

    PubMed Central

    Courgnaud, V; Lauré, F; Fultz, P N; Montagnier, L; Bréchot, C; Sonigo, P

    1992-01-01

    We determined the nucleotide sequences of two related isolates of simian immunodeficiency virus from the sooty mangabey monkey (SIVsmm) that exhibit dramatic differences in virulence. These isolates are separated by one experimental cross-species transmission, from sooty mangabey to pig-tailed macaque. The parental virus (SIVsmm9), nonpathogenic in the original host (sooty mangabeys), causes a chronic AIDS-like disease in macaques. In contrast, the variant virus (SIVsmmPBj14) induces an acute lethal disease in various macaque species and is also pathogenic for sooty mangabeys. The combination of necessary and sufficient mutations that determined the acutely lethal phenotype on the SIVsmm9 genetic background is included within a maximal set of 57 point mutations, plus two insertions located in the long terminal repeat (22 bp spanning an NF-kappa B-like enhancer element) and in the surface envelope glycoprotein (5 amino acids). Comparisons of synonymous and nonsynonymous nucleotide substitutions in the genome of SIVsmm indicated that selective pressures, probably due to the host immune response, favored amino acid changes in the envelope. This immunoevolutionary mechanism could explain the increase in diversity and the apparition of new virulent phenotypes after cross-species transmission. PMID:1727495

  9. Cross-Species Extrapolation of Uptake and Disposition of Neutral Organic Chemicals in Fish Using a Multispecies Physiologically-Based Toxicokinetic Model Framework.

    PubMed

    Brinkmann, Markus; Schlechtriem, Christian; Reininghaus, Mathias; Eichbaum, Kathrin; Buchinger, Sebastian; Reifferscheid, Georg; Hollert, Henner; Preuss, Thomas G

    2016-02-16

    The potential to bioconcentrate is generally considered to be an unwanted property of a substance. Consequently, chemical legislation, including the European REACH regulations, requires the chemical industry to provide bioconcentration data for chemicals that are produced or imported at volumes exceeding 100 tons per annum or if there is a concern that a substance is persistent, bioaccumulative, and toxic. For the filling of the existing data gap for chemicals produced or imported at levels that are below this stipulated volume, without the need for additional animal experiments, physiologically-based toxicokinetic (PBTK) models can be used to predict whole-body and tissue concentrations of neutral organic chemicals in fish. PBTK models have been developed for many different fish species with promising results. In this study, we developed PBTK models for zebrafish (Danio rerio) and roach (Rutilus rutilus) and combined them with existing models for rainbow trout (Onchorhynchus mykiss), lake trout (Salvelinus namaycush), and fathead minnow (Pimephales promelas). The resulting multispecies model framework allows for cross-species extrapolation of the bioaccumulative potential of neutral organic compounds. Predictions were compared with experimental data and were accurate for most substances. Our model can be used for probabilistic risk assessment of chemical bioaccumulation, with particular emphasis on cross-species evaluations.

  10. Feline lentivirus evolution in cross-species infection reveals extensive G-to-A mutation and selection on key residues in the viral polymerase.

    PubMed

    Poss, Mary; Ross, Howard A; Painter, Sally L; Holley, David C; Terwee, Julie A; Vandewoude, Sue; Rodrigo, Allen

    2006-03-01

    Factors that restrict a virus from establishing productive infection in a new host species are important to understand because cross-species transmission events are often associated with emergent viral diseases. To determine the evolutionary pressures on viruses in new host species, we evaluated the molecular evolution of a feline immunodeficiency virus derived from a wild cougar, Puma concolor, during infection of domestic cats. Analyses were based on the coding portion of genome sequences recovered at intervals over 37 weeks of infection of six cats inoculated by either intravenous or oral-nasal routes. All cats inoculated intravenously, but only one inoculated orally-nasally, became persistently viremic. There were notable accumulations of lethal errors and predominance of G-to-A alterations throughout the genome, which were marked in the viral polymerase gene, pol. Viral structural (env and gag) and accessory (vif and orfA) genes evolved neutrally or were under purifying selection. However, sites under positive selection were identified in reverse transcriptase that involved residues in the nucleotide binding pocket or those contacting the RNA-DNA duplex. The findings of extensive G-to-A alterations in this cross-species infection are consistent with the recently described editing of host cytidine deaminase on lentivirus genomes. Additionally, we demonstrate that the primary site of hypermutation is the viral pol gene and the dominant selective force acting on this feline immunodeficiency virus as it replicates in a new host species is on key residues of the virus polymerase.

  11. Cross-species coherence in effects and modes of action in support of causality determinations in the U.S. Environmental Protection Agency's Integrated Science Assessment for Lead.

    PubMed

    Lassiter, Meredith Gooding; Owens, Elizabeth Oesterling; Patel, Molini M; Kirrane, Ellen; Madden, Meagan; Richmond-Bryant, Jennifer; Hines, Erin Pias; Davis, J Allen; Vinikoor-Imler, Lisa; Dubois, Jean-Jacques

    2015-04-01

    The peer-reviewed literature on the health and ecological effects of lead (Pb) indicates common effects and underlying modes of action across multiple organisms for several endpoints. Based on such observations, the United States (U.S.) Environmental Protection Agency (EPA) applied a cross-species approach in the 2013 Integrated Science Assessment (ISA) for Lead for evaluating the causality of relationships between Pb exposure and specific endpoints that are shared by humans, laboratory animals, and ecological receptors (i.e., hematological effects, reproductive and developmental effects, and nervous system effects). Other effects of Pb (i.e., cardiovascular, renal, and inflammatory responses) are less commonly assessed in aquatic and terrestrial wildlife limiting the application of cross-species comparisons. Determinations of causality in ISAs are guided by a framework for classifying the weight of evidence across scientific disciplines and across related effects by considering aspects such as biological plausibility and coherence. As illustrated for effects of Pb where evidence across species exists, the integration of coherent effects and common underlying modes of action can serve as a means to substantiate conclusions regarding the causal nature of the health and ecological effects of environmental toxicants.

  12. Ortho2ExpressMatrix—a web server that interprets cross-species gene expression data by gene family information

    PubMed Central

    2011-01-01

    Background The study of gene families is pivotal for the understanding of gene evolution across different organisms and such phylogenetic background is often used to infer biochemical functions of genes. Modern high-throughput experiments offer the possibility to analyze the entire transcriptome of an organism; however, it is often difficult to deduct functional information from that data. Results To improve functional interpretation of gene expression we introduce Ortho2ExpressMatrix, a novel tool that integrates complex gene family information, computed from sequence similarity, with comparative gene expression profiles of two pre-selected biological objects: gene families are displayed with two-dimensional matrices. Parameters of the tool are object type (two organisms, two individuals, two tissues, etc.), type of computational gene family inference, experimental meta-data, microarray platform, gene annotation level and genome build. Family information in Ortho2ExpressMatrix bases on computationally different protein family approaches such as EnsemblCompara, InParanoid, SYSTERS and Ensembl Family. Currently, respective all-against-all associations are available for five species: human, mouse, worm, fruit fly and yeast. Additionally, microRNA expression can be examined with respect to miRBase or TargetScan families. The visualization, which is typical for Ortho2ExpressMatrix, is performed as matrix view that displays functional traits of genes (differential expression) as well as sequence similarity of protein family members (BLAST e-values) in colour codes. Such translations are intended to facilitate the user's perception of the research object. Conclusions Ortho2ExpressMatrix integrates gene family information with genome-wide expression data in order to enhance functional interpretation of high-throughput analyses on diseases, environmental factors, or genetic modification or compound treatment experiments. The tool explores differential gene expression in

  13. Optimizing the Presentation of Mental Health Information in Social Media: The Effects of Health Testimonials and Platform on Source Perceptions, Message Processing, and Health Outcomes.

    PubMed

    Quintero Johnson, Jessie M; Yilmaz, Gamze; Najarian, Kristy

    2016-08-30

    Using social media for the purpose of disseminating mental health information is a critical area of scientific inquiry for health communication professionals. The purpose of this study was to investigate whether the presence of a first-person testimonial in educational mental health information placed in Facebook and Twitter messages influenced college students' (N = 257) source perceptions, information processing, cognitive elaboration, health information recall, beliefs, and behavioral intentions. Results show that exposure to social media messages that featured mental health information embedded with a testimonial predicted less source homophily and more critical thoughts about the social media source, less systematic message processing, and less cognitive elaboration. Health information recall was significantly impacted by both the social media platform and message content such that participants in the testimonial condition on Facebook were more likely to recall the health facts in those messages whereas participants who viewed the testimonial in Twitter were less likely to recall the facts in those tweets. Compared to those who read Facebook messages, participants who read Twitter messages reported higher levels of systematic message processing. These findings suggest that the integration of health testimonials into social media messages might inadvertently provoke psychological resistance to mental health information, thereby reducing the persuasive impact of those messages.

  14. Age-Specific Gene Expression Signatures for Breast Tumors and Cross-Species Conserved Potential Cancer Progression Markers in Young Women

    PubMed Central

    Colak, Dilek; Nofal, Asmaa; AlBakheet, AlBandary; Nirmal, Maimoona; Jeprel, Hatim; Eldali, Abdelmoneim; AL-Tweigeri, Taher; Tulbah, Asma; Ajarim, Dahish; Malik, Osama Al; Kaya, Namik; Park, Ben H.; Bin Amer, Suad M.

    2013-01-01

    Breast cancer in young women is more aggressive with a poorer prognosis and overall survival compared to older women diagnosed with the disease. Despite recent research, the underlying biology and molecular alterations that drive the aggressive nature of breast tumors associated with breast cancer in young women have yet to be elucidated. In this study, we performed transcriptomic profile and network analyses of breast tumors arising in Middle Eastern women to identify age-specific gene signatures. Moreover, we studied molecular alterations associated with cancer progression in young women using cross-species comparative genomics approach coupled with copy number alterations (CNA) associated with breast cancers from independent studies. We identified 63 genes specific to tumors in young women that showed alterations distinct from two age cohorts of older women. The network analyses revealed potential critical regulatory roles for Myc, PI3K/Akt, NF-κB, and IL-1 in disease characteristics of breast tumors arising in young women. Cross-species comparative genomics analysis of progression from pre-invasive ductal carcinoma in situ (DCIS) to invasive ductal carcinoma (IDC) revealed 16 genes with concomitant genomic alterations, CCNB2, UBE2C, TOP2A, CEP55, TPX2, BIRC5, KIAA0101, SHCBP1, UBE2T, PTTG1, NUSAP1, DEPDC1, HELLS, CCNB1, KIF4A, and RRM2, that may be involved in tumorigenesis and in the processes of invasion and progression of disease. Array findings were validated using qRT-PCR, immunohistochemistry, and extensive in silico analyses of independently performed microarray datasets. To our knowledge, this study provides the first comprehensive genomic analysis of breast cancer in Middle Eastern women in age-specific cohorts and potential markers for cancer progression in young women. Our data demonstrate that cancer appearing in young women contain distinct biological characteristics and deregulated signaling pathways. Moreover, our integrative genomic and cross-species

  15. Detection of superficial zone protein in human and animal body fluids by cross-species monoclonal antibodies specific to superficial zone protein.

    PubMed

    Su, J L; Schumacher, B L; Lindley, K M; Soloveychik, V; Burkhart, W; Triantafillou, J A; Kuettner, K; Schmid, T

    2001-06-01

    In this report we describe the purification of human superficial zone protein (SZP), the generation of cross-species monoclonal antibodies (MAbs) and the detection of this protein in human and animal body fluids. Human SZPs, used as immunizing antigens, were purified either from culture media of human cartilage organ cultures or from human synovial fluids. The immunizing antigens were mixed with RIBI adjuvant in one of three forms: nonmodified SZP, superficial zone protein-keyhole limpet hemocyanin conjugate (SZP-KLH), or a mixture of superficial zone protein and hyaluronic acid (SZP-HA). A panel of MAbs including GW4.23, S6.79, S13.52, S13.233, and S17.109 were generated and characterized. Monoclonal antibody (MAb) S6.79, an IgG2b with K(D) 3.14 x 10(-9) M from SZP-KLH immunization, is of particular interest. It reacts strongly to a large molecular weight form of SZP in both enzyme-linked immunosorbent assay (ELISA) and Western blotting. It stains the most superficial layer of articular cartilage in immunohistochemistry, whereas the middle and deep zones of cartilage are not stained. When MAb S6.79 was applied to Western blots of human body fluids, a strong 345-kDa band was detected in samples of synovial fluid and weaker bands of similar size were detected in samples of plasma and serum. MAb S6.79 also showed cross-species immunoreactivity with SZP in samples of synovial fluids harvested from bovine, dog, guinea pig, and rabbit, as demonstrated by Western blotting and antibody absorption experiments. This cross-species MAb will be a useful tool in human and animal model studies for monitoring SZP levels and tissue distribution. It may help define the roles of SZP in normal articular joints and may be of diagnostic or prognostic value for the measurement of SZP in pathological conditions such as osteoarthritis, rheumatoid arthritis, and camptodactyly-arthropathy-coxa vara-pericarditis.

  16. ConBind: motif-aware cross-species alignment for the identification of functional transcription factor binding sites

    PubMed Central

    Lelieveld, Stefan H.; Schütte, Judith; Dijkstra, Maurits J.J.; Bawono, Punto; Kinston, Sarah J.; Göttgens, Berthold; Heringa, Jaap; Bonzanni, Nicola

    2016-01-01

    Eukaryotic gene expression is regulated by transcription factors (TFs) binding to promoter as well as distal enhancers. TFs recognize short, but specific binding sites (TFBSs) that are located within the promoter and enhancer regions. Functionally relevant TFBSs are often highly conserved during evolution leaving a strong phylogenetic signal. While multiple sequence alignment (MSA) is a potent tool to detect the phylogenetic signal, the current MSA implementations are optimized to align the maximum number of identical nucleotides. This approach might result in the omission of conserved motifs that contain interchangeable nucleotides such as the ETS motif (IUPAC code: GGAW). Here, we introduce ConBind, a novel method to enhance alignment of short motifs, even if their mutual sequence similarity is only partial. ConBind improves the identification of conserved TFBSs by improving the alignment accuracy of TFBS families within orthologous DNA sequences. Functional validation of the Gfi1b + 13 enhancer reveals that ConBind identifies additional functionally important ETS binding sites that were missed by all other tested alignment tools. In addition to the analysis of known regulatory regions, our web tool is useful for the analysis of TFBSs on so far unknown DNA regions identified through ChIP-sequencing. PMID:26721389

  17. The Center for Optimized Structural Studies (COSS) platform for automation in cloning, expression, and purification of single proteins and protein-protein complexes.

    PubMed

    Mlynek, Georg; Lehner, Anita; Neuhold, Jana; Leeb, Sarah; Kostan, Julius; Charnagalov, Alexej; Stolt-Bergner, Peggy; Djinović-Carugo, Kristina; Pinotsis, Nikos

    2014-06-01

    Expression in Escherichia coli represents the simplest and most cost effective means for the production of recombinant proteins. This is a routine task in structural biology and biochemistry where milligrams of the target protein are required in high purity and monodispersity. To achieve these criteria, the user often needs to screen several constructs in different expression and purification conditions in parallel. We describe a pipeline, implemented in the Center for Optimized Structural Studies, that enables the systematic screening of expression and purification conditions for recombinant proteins and relies on a series of logical decisions. We first use bioinformatics tools to design a series of protein fragments, which we clone in parallel, and subsequently screen in small scale for optimal expression and purification conditions. Based on a scoring system that assesses soluble expression, we then select the top ranking targets for large-scale purification. In the establishment of our pipeline, emphasis was put on streamlining the processes such that it can be easily but not necessarily automatized. In a typical run of about 2 weeks, we are able to prepare and perform small-scale expression screens for 20-100 different constructs followed by large-scale purification of at least 4-6 proteins. The major advantage of our approach is its flexibility, which allows for easy adoption, either partially or entirely, by any average hypothesis driven laboratory in a manual or robot-assisted manner.

  18. Cross-Species, Amplifiable Microsatellite Markers for Neoverrucid Barnacles from Deep-Sea Hydrothermal Vents Developed Using Next-Generation Sequencing

    PubMed Central

    Nakajima, Yuichi; Shinzato, Chuya; Khalturina, Mariia; Watanabe, Hiromi; Inagaki, Fumio; Satoh, Nori; Mitarai, Satoshi

    2014-01-01

    Barnacles of the genus Neoverruca are abundant near deep-sea hydrothermal vents of the northwestern Pacific Ocean, and are useful for understanding processes of population formation and maintenance of deep-sea vent faunas. Using next-generation sequencing, we isolated 12 polymorphic microsatellite loci from Neoverruca sp., collected in the Okinawa Trough. These microsatellite loci revealed 2–19 alleles per locus. The expected and observed heterozygosities ranged from 0.286 to 1.000 and 0.349 to 0.935, respectively. Cross-species amplification showed that 9 of the 12 loci were successfully amplified for Neoverruca brachylepadoformis in the Mariana Trough. A pairwise FST value calculated using nine loci showed significant genetic differentiation between the two species. Consequently, the microsatellite markers we developed will be useful for further population genetic studies to elucidate genetic diversity, differentiation, classification, and evolutionary processes in the genus Neoverruca. PMID:25196437

  19. Cross-species, amplifiable microsatellite markers for neoverrucid barnacles from deep-sea hydrothermal vents developed using next-generation sequencing.

    PubMed

    Nakajima, Yuichi; Shinzato, Chuya; Khalturina, Mariia; Watanabe, Hiromi; Inagaki, Fumio; Satoh, Nori; Mitarai, Satoshi

    2014-08-18

    Barnacles of the genus Neoverruca are abundant near deep-sea hydrothermal vents of the northwestern Pacific Ocean, and are useful for understanding processes of population formation and maintenance of deep-sea vent faunas. Using next-generation sequencing, we isolated 12 polymorphic microsatellite loci from Neoverruca sp., collected in the Okinawa Trough. These microsatellite loci revealed 2-19 alleles per locus. The expected and observed heterozygosities ranged from 0.286 to 1.000 and 0.349 to 0.935, respectively. Cross-species amplification showed that 9 of the 12 loci were successfully amplified for Neoverruca brachylepadoformis in the Mariana Trough. A pairwise FST value calculated using nine loci showed significant genetic differentiation between the two species. Consequently, the microsatellite markers we developed will be useful for further population genetic studies to elucidate genetic diversity, differentiation, classification, and evolutionary processes in the genus Neoverruca.

  20. Rabbit hepatitis E virus is an opportunistic pathogen in specific-pathogen-free rabbits with the capability of cross-species transmission.

    PubMed

    Liu, Baoyuan; Sun, Yani; Du, Taofeng; Chen, Yiyang; Wang, Xinjie; Huang, Baicheng; Li, Huixia; Nan, Yuchen; Xiao, Shuqi; Zhang, Gaiping; Hiscox, Julian A; Zhou, En-Min; Zhao, Qin

    2017-03-01

    Hepatitis E virus (HEV) has been detected in rabbits, a recently identified natural reservoir. In this study, anti-HEV antibodies and viral RNA were detected in rabbits sourced from a specific-pathogen-free (SPF) rabbit vendor in Shaanxi Province, China. BLAST results of partial HEV ORF2 genes cloned here indicated that two viral strains circulated in the rabbits. Sequence determination of the complete genome (7302bp) of one strain and a partial ORF1 gene (1537bp) of the other strain showed that they shared 90% identity with one another and 78%-94% identity with other known rabbit HEVs. In addition, inoculation with rabbit HEV from SPF rabbits studied here resulted in infection of SPF pigs; this cross-species transmission was evidenced by seroconversion, viremia and faecal virus shedding. These results suggest that to prevent spread of this zoonotic pathogen, rabbits should be tested routinely for HEV RNA in SPF vendor facilities.

  1. Microsatellite DNA primers for the candy darter, Etheostoma osburni and variegate darter, Etheostoma variatum, and cross-species amplification in other darters (Percidae)

    USGS Publications Warehouse

    Switzer, J.F.; Welsh, S.A.; King, T.L.

    2008-01-01

    In order to investigate a potential hybrid zone between the candy darter, Etheostoma osburni, and variegate darter, Etheostoma variatum, and examine population variation within E. osburni, a suite of primers for 15 polymorphic microsatellite loci were developed. The average number of alleles per locus was 5.5 in E. osburni and 7.6 in E. variatum, and the average observed heterozygosities were 62.5% and 71.4%, respectively. There were no deviations from Hardy-Weinberg equilibrium and no observed linkage disequilibrium after Bonferroni correction. The utility of these primers was also tested in 11 species of darters representing all four genera of darters. Success of cross-species amplification was largely consistent with phylogenetic relationships of darters. ?? 2007 The Authors.

  2. Development of a biodegradable nanoparticle platform for sildenafil: formulation optimization by factorial design analysis combined with application of charge-modified branched polyesters.

    PubMed

    Beck-Broichsitter, Moritz; Schmehl, Thomas; Gessler, Tobias; Seeger, Werner; Kissel, Thomas

    2012-02-10

    Biodegradable nanoparticles have gained tremendous attraction as carriers for controlled drug delivery to the lung. Despite numerous advances in the field, e.g. development of suitable methods for pulmonary administration of polymeric nanoparticles, a sufficient association of the therapeutic agent with the carrier system as well as drug release in a controlled fashion remain considerable challenges. Hence, this study examines the optimization of biodegradable sildenafil-loaded nanoparticle formulations intended for aerosol treatment of pulmonary hypertension. A factorial design analysis was employed to identify the important experimental factors involved in the preparation of nanoparticles by the solvent evaporation technique. The effect of tailored charge-modified branched polyesters on drug loading and in vitro drug release from nanoparticles was also evaluated. Moreover, colloidal stability of obtained nanoparticles was assessed, and stabilization of nanoparticles by lyophilization was accomplished without additional excipients. Essential experimental factors were identified and optimized to allow the preparation of nanoparticles composed of linear polyesters with a sildenafil content of ~5 wt.%. The in vitro drug release profile from these nanoparticles demonstrated a sustained release of sildenafil over ~90 min. Application of charge-modified branched polyesters enhanced the drug content in nanoparticles and drug release profile, according to the charge-density present in the employed polymer. Accordingly an increase in drug loading by a factor of ~1.4, a prolonged drug release profile from nanoparticles over ~240 min was achieved. Sildenafil release from nanoparticles made of linear and charge-modified branched polyesters was governed by a diffusion process. The obtained drug diffusion coefficients were decreased as the charge-density present in the applied polymer was increased, which promotes the strategy to improve drug loading and release rates by

  3. INVESTIGATING THE IMPORTANCE OF ANATOMICAL HOMOLOGY FOR CROSS-SPECIES PHENOTYPE COMPARISONS USING SEMANTIC SIMILARITY. Accepted at Pacific Symposium on Biocomputing, 2016.

    PubMed

    Manda, Prashanti; Mungall, Christopher J; Balhoff, James P; Lapp, Hilmar; Vision, Todd J

    2016-01-01

    There is growing use of ontologies for the measurement of cross-species phenotype similarity. Such similarity measurements contribute to diverse applications, such as identifying genetic models for human diseases, transferring knowledge among model organisms, and studying the genetic basis of evolutionary innovations. Two organismal features, whether genes, anatomical parts, or any other inherited feature, are considered to be homologous when they are evolutionarily derived from a single feature in a common ancestor. A classic example is the homology between the paired fins of fishes and vertebrate limbs. Anatomical ontologies that model the structural relations among parts may fail to include some known anatomical homologies unless they are deliberately added as separate axioms. The consequences of neglecting known homologies for applications that rely on such ontologies has not been well studied. Here, we examine how semantic similarity is affected when external homology knowledge is included. We measure phenotypic similarity between orthologous and non-orthologous gene pairs between humans and either mouse or zebrafish, and compare the inclusion of real with faux homology axioms. Semantic similarity was preferentially increased for orthologs when using real homology axioms, but only in the more divergent of the two species comparisons (human to zebrafish, not human to mouse), and the relative increase was less than 1% to non-orthologs. By contrast, inclusion of both real and faux random homology axioms preferentially increased similarities between genes that were initially more dissimilar in the other comparisons. Biologically meaningful increases in semantic similarity were seen for a select subset of gene pairs. Overall, the effect of including homology axioms on cross-species semantic similarity was modest at the levels of divergence examined here, but our results hint that it may be greater for more distant species comparisons.

  4. Genetic diversity and differentiation in reef-building Millepora species, as revealed by cross-species amplification of fifteen novel microsatellite loci.

    PubMed

    Dubé, Caroline E; Planes, Serge; Zhou, Yuxiang; Berteaux-Lecellier, Véronique; Boissin, Emilie

    2017-01-01

    Quantifying the genetic diversity in natural populations is crucial to address ecological and evolutionary questions. Despite recent advances in whole-genome sequencing, microsatellite markers have remained one of the most powerful tools for a myriad of population genetic approaches. Here, we used the 454 sequencing technique to develop microsatellite loci in the fire coral Millepora platyphylla, an important reef-builder of Indo-Pacific reefs. We tested the cross-species amplification of these loci in five other species of the genus Millepora and analysed its success in correlation with the genetic distances between species using mitochondrial 16S sequences. We succeeded in discovering fifteen microsatellite loci in our target species M. platyphylla, among which twelve were polymorphic with 2-13 alleles and a mean observed heterozygosity of 0.411. Cross-species amplification in the five other Millepora species revealed a high probability of amplification success (71%) and polymorphism (59%) of the loci. Our results show no evidence of decreased heterozygosity with increasing genetic distance. However, only one locus enabled measures of genetic diversity in the Caribbean species M. complanata due to high proportions of null alleles for most of the microsatellites. This result indicates that our novel markers may only be useful for the Indo-Pacific species of Millepora. Measures of genetic diversity revealed significant linkage disequilibrium, moderate levels of observed heterozygosity (0.323-0.496) and heterozygote deficiencies for the Indo-Pacific species. The accessibility to new polymorphic microsatellite markers for hydrozoan Millepora species creates new opportunities for future research on processes driving the complexity of their colonisation success on many Indo-Pacific reefs.

  5. Insights into gene expression changes impacting B-cell transformation: cross-species microarray analysis of bovine leukemia virus tax-responsive genes in ovine B cells.

    PubMed

    Klener, Pavel; Szynal, Maud; Cleuter, Yvette; Merimi, Makram; Duvillier, Hugues; Lallemand, Françoise; Bagnis, Claude; Griebel, Philip; Sotiriou, Christos; Burny, Arsène; Martiat, Philippe; Van den Broeke, Anne

    2006-02-01

    Large-animal models for leukemia have the potential to aid in the understanding of networks that contribute to oncogenesis. Infection of cattle and sheep with bovine leukemia virus (BLV), a complex retrovirus related to human T-cell leukemia virus type 1 (HTLV-1), is associated with the development of B-cell leukemia. Whereas the natural disease in cattle is characterized by a low tumor incidence, experimental infection of sheep leads to overt leukemia in the majority of infected animals, providing a model for studying the pathogenesis associated with BLV and HTLV-1. Tax(BLV), the major oncoprotein, initiates a cascade of events leading toward malignancy, although the basis of transformation is not fully understood. We have taken a cross-species ovine-to-human microarray approach to identify Tax(BLV)-responsive transcriptional changes in two sets of cultured ovine B cells following retroviral vector-mediated delivery of Tax(BLV). Using cDNA-spotted microarrays comprising 10,336 human genes/expressed sequence tags, we identified a cohort of differentially expressed genes, including genes related to apoptosis, DNA transcription, and repair; proto-oncogenes; cell cycle regulators; transcription factors; small Rho GTPases/GTPase-binding proteins; and previously reported Tax(HTLV-1)-responsive genes. Interestingly, genes known to be associated with human neoplasia, especially B-cell malignancies, were extensively represented. Others were novel or unexpected. The results suggest that Tax(BLV) deregulates a broad network of interrelated pathways rather than a single B-lineage-specific regulatory process. Although cross-species approaches do not permit a comprehensive analysis of gene expression patterns, they can provide initial clues for the functional roles of genes that participate in B-cell transformation and pinpoint molecular targets not identified using other methods in animal models.

  6. Multi-linear regression analysis, preliminary biotic ligand modeling, and cross species comparison of the effects of water chemistry on chronic lead toxicity in invertebrates.

    PubMed

    Esbaugh, A J; Brix, K V; Mager, E M; De Schamphelaere, K; Grosell, M

    2012-03-01

    The current study examined the chronic toxicity of lead (Pb) to three invertebrate species: the cladoceran Ceriodaphnia dubia, the snail Lymnaea stagnalis and the rotifer Philodina rapida. The test media consisted of natural waters from across North America, varying in pertinent water chemistry parameters including dissolved organic carbon (DOC), calcium, pH and total CO(2). Chronic toxicity was assessed using reproductive endpoints for C. dubia and P. rapida while growth was assessed for L. stagnalis, with chronic toxicity varying markedly according to water chemistry. A multi-linear regression (MLR) approach was used to identify the relative importance of individual water chemistry components in predicting chronic Pb toxicity for each species. DOC was an integral component of MLR models for C. dubia and L. stagnalis, but surprisingly had no predictive impact on chronic Pb toxicity for P. rapida. Furthermore, sodium and total CO(2) were also identified as important factors affecting C. dubia toxicity; no other factors were predictive for L. stagnalis. The Pb toxicity of P. rapida was predicted by calcium and pH. The predictive power of the C. dubia and L. stagnalis MLR models was generally similar to that of the current C. dubia BLM, with R(2) values of 0.55 and 0.82 for the respective MLR models, compared to 0.45 and 0.79 for the respective BLMs. In contrast the BLM poorly predicted P. rapida toxicity (R(2)=0.19), as compared to the MLR (R(2)=0.92). The cross species variability in the effects of water chemistry, especially with respect to rotifers, suggests that cross species modeling of invertebrate chronic Pb toxicity using a C. dubia model may not always be appropriate.

  7. Genetic diversity and differentiation in reef-building Millepora species, as revealed by cross-species amplification of fifteen novel microsatellite loci

    PubMed Central

    Planes, Serge; Zhou, Yuxiang; Berteaux-Lecellier, Véronique; Boissin, Emilie

    2017-01-01

    Quantifying the genetic diversity in natural populations is crucial to address ecological and evolutionary questions. Despite recent advances in whole-genome sequencing, microsatellite markers have remained one of the most powerful tools for a myriad of population genetic approaches. Here, we used the 454 sequencing technique to develop microsatellite loci in the fire coral Millepora platyphylla, an important reef-builder of Indo-Pacific reefs. We tested the cross-species amplification of these loci in five other species of the genus Millepora and analysed its success in correlation with the genetic distances between species using mitochondrial 16S sequences. We succeeded in discovering fifteen microsatellite loci in our target species M. platyphylla, among which twelve were polymorphic with 2–13 alleles and a mean observed heterozygosity of 0.411. Cross-species amplification in the five other Millepora species revealed a high probability of amplification success (71%) and polymorphism (59%) of the loci. Our results show no evidence of decreased heterozygosity with increasing genetic distance. However, only one locus enabled measures of genetic diversity in the Caribbean species M. complanata due to high proportions of null alleles for most of the microsatellites. This result indicates that our novel markers may only be useful for the Indo-Pacific species of Millepora. Measures of genetic diversity revealed significant linkage disequilibrium, moderate levels of observed heterozygosity (0.323–0.496) and heterozygote deficiencies for the Indo-Pacific species. The accessibility to new polymorphic microsatellite markers for hydrozoan Millepora species creates new opportunities for future research on processes driving the complexity of their colonisation success on many Indo-Pacific reefs. PMID:28243525

  8. Patient-derived xenograft platform of OSCC: a renewable human bio-bank for preclinical cancer research and a new co-clinical model for treatment optimization.

    PubMed

    Sun, Shuyang; Zhang, Zhiyuan

    2016-03-01

    Advances in next-generation sequencing and bioinformatics have begun to reveal the complex genetic landscape in human cancer genomes, including oral squamous cell carcinoma (OSCC). Sophisticated preclinical models that fully represent intra- and inter-tumoral heterogeneity are required to understand the molecular diversity of cancer and achieve the goal of personalized therapies. Over the last decade, patient-derived xenograft (PDX) models generated from human tumor samples that can retain the histological and genetic features of their donor tumors have been shown to be the preferred preclinical tool in translational cancer research compared with other conventional preclinical models. Specifically, genetically well-defined PDX models can be applied to accelerate targeted antitumor drug development and biomarker discovery. Recently, we have successfully established and characterized an OSCC PDX panel as part of our tumor bio-bank for translational cancer research. In this paper, we discuss the establishment, characterization, and preclinical applications of the PDX models. In particular, we focus on the classification and applications of the PDX models based on validated annotations, including clinicopathological features, genomic profiles, and pharmacological testing information. We also explore the translational value of this well-annotated PDX panel in the development of co-clinical trials for patient stratification and treatment optimization in the near future. Although various limitations still exist, this preclinical approach should be further tested and improved.

  9. Ufasomes nano-vesicles-based lyophilized platforms for intranasal delivery of cinnarizine: preparation, optimization, ex-vivo histopathological safety assessment and mucosal confocal imaging.

    PubMed

    Salama, Alaa Hamed; Aburahma, Mona Hassan

    2016-09-01

    To circumvent the low and erratic absorption of orally administrated cinnarizine (CN), intranasal lyophilized gels containing unsaturated fatty acid liposomes (ufasomes) and encapsulating CN were prepared from oleic acid using a simple assembling strategy. The effects of varying drug concentration and cholesterol percentage on ufasomes size, polydispersity index and entrapment efficiency were investigated using 3(1)4(1) full factorial design. The optimized ufasomes that contained 14% cholesterol relative to oleic acid displayed spherical morphology with average size of 788 nm and entrapment efficiency of 80.49%. To overcome the colloidal instability of CN-loaded ufasomes dispersions and their short residence time in the nasal cavity, the ufasomes were incorporated into mucoadhesive hydrogels that were lyophilized into unit dosage forms for accurate dosing. Scanning electron micrographs of the lyophilized gel revealed that the included ufasomes were intact, non-aggregating and maintained their spherical morphology. Rheological characterization of reconstituted ufasomal lyophilized gel ensured ease of application. Furthermore, the gel induced minor histopathological alterations in sheeps' nasal mucosa. Ex-vivo confocal laser imaging confirmed the ability of ufasomes to penetrate deep through nasal mucosa layers. The results highlighted in the current work confirm the feasibility of using CN-loaded ufasomal gels for intranasal drug delivery.

  10. Validation of a rapid DNA process with the RapidHIT(®) ID system using GlobalFiler(®) Express chemistry, a platform optimized for decentralized testing environments.

    PubMed

    Salceda, Susana; Barican, Arnaldo; Buscaino, Jacklyn; Goldman, Bruce; Klevenberg, Jim; Kuhn, Melissa; Lehto, Dennis; Lin, Frank; Nguyen, Phong; Park, Charles; Pearson, Francesca; Pittaro, Rick; Salodkar, Sayali; Schueren, Robert; Smith, Corey; Troup, Charles; Tsou, Dean; Vangbo, Mattias; Wunderle, Justus; King, David

    2017-05-01

    The RapidHIT(®) ID is a fully automated sample-to-answer system for short tandem repeat (STR)-based human identification. The RapidHIT ID has been optimized for use in decentralized environments and processes presumed single source DNA samples, generating Combined DNA Index System (CODIS)-compatible DNA profiles in less than 90min. The system is easy to use, requiring less than one minute of hands-on time. Profiles are reviewed using centralized linking software, RapidLINK™ (IntegenX, Pleasanton, CA), a software tool designed to collate DNA profiles from single or multiple RapidHIT ID systems at different geographic locations. The RapidHIT ID has been designed to employ GlobalFiler(®) Express and AmpFLSTR(®) NGMSElect™, Thermo Fisher Scientific (Waltham, MA) STR chemistries. The Developmental Validation studies were performed using GlobalFiler(®) Express with single source reference samples according to Scientific Working Group for DNA Analysis Methods guidelines. These results show that multiple RapidHIT ID systems networked with RapidLINK software form a highly reliable system for wide-scale deployment in locations such as police booking stations and border crossings enabling real-time testing of arrestees, potential human trafficking victims, and other instances where rapid turnaround is essential.

  11. Diversity of the G3 genes of human rotaviruses in isolates from Spain from 2004 to 2006: cross-species transmission and inter-genotype recombination generates alleles.

    PubMed

    Martínez-Laso, Jorge; Román, Angela; Rodriguez, Miriam; Cervera, Isabel; Head, Jacqueline; Rodríguez-Avial, Iciar; Picazo, Juan J

    2009-04-01

    Rotavirus evolves by using multiple genetic mechanisms which are an accumulation of spontaneous point mutations and reassortment events. Other mechanisms, such as cross-species transmission and inter-genotype recombination, may be also involved. One of the most interesting genotypes in the accumulation of these events is the G3 genotype. In this work, six new Spanish G3 sequences belonging to 0-2-year-old patients from Madrid were analysed and compared with 160 others of the same genotype obtained from humans and other host species to establish the evolutionary pathways of the G3 genotype. The following results were obtained: (i) there are four different lineages of the G3 genotype which have evolved in different species; (ii) Spanish G3 rotavirus sequences are most similar to the described sequences that belong to lineage I; (iii) several G3 genotype alleles were reassigned as other G genotypes; and (iv) inter-genotype recombination events in G3 viruses involving G1 and G2 were described. These findings strongly suggest multiple inter-species transmission events between different non-human mammalian species and humans.

  12. Eimeria tenella and E. acervulina: differences in ability to elicit cross-species protection as compared with the turkey coccidium, E. adenoeides.

    PubMed

    Augustine, P C; Danforth, H D

    1995-01-01

    Repeated oral inoculation of turkey poults with large doses (1 x 10(6) oocysts) of the chicken coccidia, Eimeria tenella or E. acervulina, failed to prevent weight loss, poor feed conversion, and intestinal pathology in turkeys challenged with the turkey coccidium, E. adenoeides. Invasion by E. tenella in turkeys was significantly greater than invasion by E. adenoeides in chickens; by 24 hr postinoculation (PI), the numbers of E. tenella and E. adenoeides sporozoites in the ceca had decreased markedly as compared with the numbers that initially invaded, and they did not differ significantly from each other. At 24 hr PI, however, transfer of cecal scrapings from chickens or turkeys inoculated with E. adenoeides produced infection in 53% of the recipient turkeys, but transfer of scrapings from either chickens or turkeys inoculated with E. tenella failed to produce infection in 20 attempts with recipient chickens. Cultured chicken peripheral blood monocytes (PBMs) that were inoculated with E. adenoeides sporozoites contained numerous vesicles that were recognized by the refractile body-specific monoclonal antibody 1209; the number of vesicles was markedly decreased in PBM cultures inoculated with gamma-irradiated E. adenoeides sporozoites. Very few vesicles were detected in the cytoplasm of turkey PBMs that contained E. tenella sporozoites, and none were detected in turkey PBMs containing E. adenoeides sporozoites. The survival of infective sporozoites, along with the secretion of refractile body antigen, may be more critical to the development of cross-species immunity than the number of sporozoites that initially invade the foreign host.

  13. Increased prevalence of carbapenem resistant Enterobacteriaceae in hospital setting due to cross-species transmission of the bla NDM-1 element and clonal spread of progenitor resistant strains.

    PubMed

    Wang, Xuan; Chen, Gongxiang; Wu, Xiaoyan; Wang, Liangping; Cai, Jiachang; Chan, Edward W; Chen, Sheng; Zhang, Rong

    2015-01-01

    This study investigated the transmission characteristics of carbapenem-resistant Enterobacteriaceae (CRE) strains collected from a hospital setting in China, in which consistent emergence of CRE strains were observable during the period of May 2013 to February 2014. Among the 45 CRE isolates tested, 21 (47%) strains were found to harbor the bla NDM-1 element, and the rest of 24 CRE strains were all positive for bla KPC-2. The 21 bla NDM-1-borne strains were found to comprise multiple Enterobacteriaceae species including nine Enterobacter cloacae, three Escherichia coli, three Citrobacter freundii, two Klebsiella pneumoniae, two Klebsiella oxytoca, and two Morganella morganii strains, indicating that cross-species transmission of bla NDM-1 is a common event. Genetic analyses by PFGE and MLST showed that, with the exception of E. coli and E. cloacae, strains belonging to the same species were often genetically unrelated. In addition to bla NDM-1, several CRE strains were also found to harbor the bla KPC-2, bla VIM-1, and bla IMP-4 elements. Conjugations experiments confirmed that the majority of carbapenem resistance determinants were transferable. Taken together, our findings suggest that transmission of mobile resistance elements among members of Enterobacteriaceae and clonal spread of CRE strains may contribute synergistically to a rapid increase in the population of CRE in clinical settings, prompting a need to implement more rigorous infection control measures to arrest such vicious transmission cycle in CRE-prevalent areas.

  14. Simian foamy virus in non-human primates and cross-species transmission to humans in Gabon: an emerging zoonotic disease in central Africa?

    PubMed

    Mouinga-Ondémé, Augustin; Kazanji, Mirdad

    2013-06-19

    It is now known that all human retroviruses have a non-human primate counterpart. It has been reported that the presence of these retroviruses in humans is the result of interspecies transmission. Several authors have described the passage of a simian retrovirus, simian foamy virus (SFV), from primates to humans. To better understand this retroviral "zoonosis" in natural settings, we evaluated the presence of SFV in both captive and wild non-human primates and in humans at high risk, such as hunters and people bitten by a non-human primate, in Gabon, central Africa. A high prevalence of SFV was found in blood samples from non-human primates and in bush meat collected across the country. Mandrills were found to be highly infected with two distinct strains of SFV, depending on their geographical location. Furthermore, samples collected from hunters and non-human primate laboratory workers showed clear, extensive cross-species transmission of SFV. People who had been bitten by mandrills, gorillas and chimpanzees had persistent SFV infection with low genetic drift. Thus, SFV is presumed to be transmitted from non-human primates mainly through severe bites, involving contact between infected saliva and blood. In this review, we summarize and discuss our five-year observations on the prevalence and dissemination of SFV in humans and non-human primates in Gabon.

  15. Identification of Putative Ortholog Gene Blocks Involved in Gestant and Lactating Mammary Gland Development: A Rodent Cross-Species Microarray Transcriptomics Approach

    PubMed Central

    Rodríguez-Cruz, Maricela; Coral-Vázquez, Ramón M.; Hernández-Stengele, Gabriel; Sánchez, Raúl; Salazar, Emmanuel; Sanchez-Muñoz, Fausto; Encarnación-Guevara, Sergio; Ramírez-Salcedo, Jorge

    2013-01-01

    The mammary gland (MG) undergoes functional and metabolic changes during the transition from pregnancy to lactation, possibly by regulation of conserved genes. The objective was to elucidate orthologous genes, chromosome clusters and putative conserved transcriptional modules during MG development. We analyzed expression of 22,000 transcripts using murine microarrays and RNA samples of MG from virgin, pregnant, and lactating rats by cross-species hybridization. We identified 521 transcripts differentially expressed; upregulated in early (78%) and midpregnancy (89%) and early lactation (64%), but downregulated in mid-lactation (61%). Putative orthologous genes were identified. We mapped the altered genes to orthologous chromosomal locations in human and mouse. Eighteen sets of conserved genes associated with key cellular functions were revealed and conserved transcription factor binding site search entailed possible coregulation among all eight block sets of genes. This study demonstrates that the use of heterologous array hybridization for screening of orthologous gene expression from rat revealed sets of conserved genes arranged in chromosomal order implicated in signaling pathways and functional ontology. Results demonstrate the utilization power of comparative genomics and prove the feasibility of using rodent microarrays to identification of putative coexpressed orthologous genes involved in the control of human mammary gland development. PMID:24288657

  16. The Challenge of Cancer Genomics in Rare Nervous System Neoplasms: Malignant Peripheral Nerve Sheath Tumors as a Paradigm for Cross-Species Comparative Oncogenomics.

    PubMed

    Carroll, Steven L

    2016-03-01

    Comprehensive genomic analyses of common nervous system cancers provide new insights into their pathogenesis, diagnosis, and treatment. Although analogous studies of rare nervous system tumors are needed, there are major barriers to performing such studies. Cross-species comparative oncogenomics, identifying driver mutations in mouse cancer models and validating them in human tumors, is a promising alternative. Although still in its infancy, this approach is being applied to malignant peripheral nerve sheath tumors (MPNSTs), rare Schwann cell-derived malignancies that occur sporadically, after radiotherapy, and in neurofibromatosis type 1. Studies of human neurofibromatosis type 1-associated tumors suggest that NF1 tumor suppressor loss in Schwann cells triggers cell-autonomous and intercellular changes, resulting in development of benign neurofibromas; subsequent neurofibroma-MPNST progression is caused by aberrant growth factor signaling and mutations affecting the p16(INK4A)-cyclin D1-CDK4-Rb and p19(ARF)-Mdm2-p53 cell cycle pathways. Mice with Nf1, Trp53, and/or Cdkn2a mutations that overexpress the Schwann cell mitogen neuregulin-1 or overexpress the epidermal growth factor receptor validate observations in human tumors and, to various degrees, model human tumorigenesis. Genomic analyses of MPNSTs arising in neuregulin-1 and epidermal growth factor receptor-overexpressing mice and forward genetic screens with Sleeping Beauty transposons implicate additional signaling cascades in MPNST pathogenesis. These studies confirm the utility of mouse models for MPNST driver gene discovery and provide new insights into the complexity of MPNST pathogenesis.

  17. Development and cross-species transferability of unigene-derived microsatellite markers in an edible oil woody plant, Camellia oleifera (Theaceae).

    PubMed

    Jia, B G; Lin, Q; Feng, Y Z; Hu, X Y; Tan, X F; Shao, F G; Zhang, L

    2015-06-18

    Camellia oleifera is an important edible oil woody plant in China. Lack of useful molecular markers hinders current genetic research on this tree species. Transcriptome sequencing of developing C. oleifera seeds generated 69,798 unigenes. A total of 6949 putative microsatellites were discovered among 6042 SSR-containing unigenes. Then, 150 simple sequence repeats (SSRs) were evaluated in 20 varieties of C. oleifera. Of these, 52 SSRs revealed polymorphism, with the number of alleles per locus ranging from 2 to 15 and expected heterozygosity values from 0.269 to 0.888. The polymorphic information content varied from 0.32 to 0.897. Cross-species transferability rates in Camellia chekangoleosa and Camellia japonica were 90.4 and 78.8%, respectively. The 52 polymorphic unigene-derived SSR markers serve to enrich existing microsatellite marker resources for C. oleifera and offer potential for applications in genetic diversity evaluation, molecular fingerprinting, and genetic mapping in C. oleifera, C. chekangoleosa, and C. japonica.

  18. Stabilized floating platforms

    DOEpatents

    Thomas, David G.

    1976-01-01

    The subject invention is directed to a floating platform for supporting nuclear reactors and the like at selected offshore sites. The platform is provided with a stabilizer mechanism which significantly reduces the effects of wave action upon the platform and which comprises a pair of relatively small floats attached by rigid booms to the platform at locations spaced therefrom for reducing wave pitch, acceleration, and the resonance period of the wave.

  19. The International Society for Developmental Psychobiology Sackler Symposium: Early adversity and the maturation of emotion circuits - a cross-species analysis

    PubMed Central

    Callaghan, Bridget L.; Sullivan, Regina M; Howell, Brittany; Tottenham, Nim

    2016-01-01

    Early-life caregiving shapes the architecture and function of the developing brain. The fact that the infant-caregiver relationship is critically important for infant functioning across all altricial species, and that the anatomical circuits supporting emotional functioning are highly preserved across different species, suggests that the results of studies examining the role of early adversity and emotional functioning should be translatable across species. Here we present findings from 4 different research laboratories, using 3 different species, which have converged on a similar finding: adversity accelerates the developmental trajectory of amygdala-prefrontal cortex (PFC) development and modifies emotional behaviors. First, a rodent model of attachment learning associated with adversity is presented showing precocial disruption of attachment learning and emergence of heightened fear learning and emotionality. Second, a model of infant-mother separation is presented in which early adversity is shown to accelerate the developmental emergence of adult-like fear retention and extinction. Third, a model of early life adversity in Rhesus monkeys is presented in which a naturally occurring variation in maternal-care (abuse) is shown to alter the functioning of emotion circuits. Finally, a human model of maternal deprivation is presented in which children born into orphanages and then adopted abroad exhibit aberrant development of emotion circuits. The convergence of these cross-species studies on early life adversity suggests that adversity targets the amygdala and PFC and has immediate impact on infant behaviour with the caregiver, and emotional reactions to the world. These results provide insight into mechanisms responsible for caregiver induced mental health trajectory alterations. PMID:25290865

  20. Cross-species transmission of Giardia spp.: inoculation of beavers and muskrats with cysts of human, beaver, mouse, and muskrat origin.

    PubMed Central

    Erlandsen, S L; Sherlock, L A; Januschka, M; Schupp, D G; Schaefer, F W; Jakubowski, W; Bemrick, W J

    1988-01-01

    Giardia cysts isolated from humans, beavers, mice, and muskrats were tested in cross-species transmission experiments for their ability to infect either beavers or muskrats. Giardia cysts, derived from multiple symptomatic human donors and used for inoculation of beavers or muskrats, were shown to be viable by incorporation of fluorogenic dyes, excystation, and their ability to produce infections in the Mongolian gerbil model. Inoculation of beavers with 5 x 10(5) Giardia lamblia cysts resulted in the infection of 75% of the animals (n = 8), as judged by the presence of fecal cysts or intestinal trophozoites at necropsy. The mean prepatent period was 13.1 days. An infective dose experiment, using 5 x 10(1) to 5 x 10(5) viable G. lamblia cysts collected by fluorescence-activated cell sorting, demonstrated that doses of between, less than 50, and less than 500 viable cysts were required to produce infection in beavers. Scanning electron microscopy of beaver small intestine revealed that attachment of G. lamblia trophozoites produced lesions in the microvillous border. Inoculation of muskrats with G. lamblia cysts produced infections when the dose of cysts was equal to or greater than 1.25 x 10(5). The inoculation of beavers with Giardia ondatrae or Giardia muris cysts did not produce any infection; however, the administration to muskrats of Giardia cysts of beaver origin resulted in the infection of 62% of the animals (n = 8), with a prepatent period of 5 days. Our results demonstrated that beavers and muskrats could be infected with Giardia cysts derived from humans, but only by using large numbers of cysts.(ABSTRACT TRUNCATED AT 250 WORDS) Images PMID:3063208

  1. A Cross-Species Study of PI3K Protein-Protein Interactions Reveals the Direct Interaction of P85 and SHP2

    NASA Astrophysics Data System (ADS)

    Breitkopf, Susanne B.; Yang, Xuemei; Begley, Michael J.; Kulkarni, Meghana; Chiu, Yu-Hsin; Turke, Alexa B.; Lauriol, Jessica; Yuan, Min; Qi, Jie; Engelman, Jeffrey A.; Hong, Pengyu; Kontaridis, Maria I.; Cantley, Lewis C.; Perrimon, Norbert; Asara, John M.

    2016-02-01

    Using a series of immunoprecipitation (IP) – tandem mass spectrometry (LC-MS/MS) experiments and reciprocal BLAST, we conducted a fly-human cross-species comparison of the phosphoinositide-3-kinase (PI3K) interactome in a drosophila S2R+ cell line and several NSCLC and human multiple myeloma cell lines to identify conserved interacting proteins to PI3K, a critical signaling regulator of the AKT pathway. Using H929 human cancer cells and drosophila S2R+ cells, our data revealed an unexpected direct binding of Corkscrew, the drosophila ortholog of the non-receptor protein tyrosine phosphatase type II (SHP2) to the Pi3k21B (p60) regulatory subunit of PI3K (p50/p85 human ortholog) but no association with Pi3k92e, the human ortholog of the p110 catalytic subunit. The p85-SHP2 association was validated in human cell lines, and formed a ternary regulatory complex with GRB2-associated-binding protein 2 (GAB2). Validation experiments with knockdown of GAB2 and Far-Western blots proved the direct interaction of SHP2 with p85, independent of adaptor proteins and transfected FLAG-p85 provided evidence that SHP2 binding on p85 occurred on the SH2 domains. A disruption of the SHP2-p85 complex took place after insulin/IGF1 stimulation or imatinib treatment, suggesting that the direct SHP2-p85 interaction was both independent of AKT activation and positively regulates the ERK signaling pathway.

  2. New methods to identify conserved microsatellite loci and develop primer sets of high cross-species utility - as demonstrated for birds.

    PubMed

    Dawson, Deborah A; Horsburgh, Gavin J; Küpper, Clemens; Stewart, Ian R K; Ball, Alexander D; Durrant, Kate L; Hansson, Bengt; Bacon, Ida; Bird, Susannah; Klein, Akos; Krupa, Andrew P; Lee, Jin-Won; Martín-Gálvez, David; Simeoni, Michelle; Smith, Gemma; Spurgin, Lewis G; Burke, Terry

    2010-05-01

    We have developed a new approach to create microsatellite primer sets that have high utility across a wide range of species. The success of this method was demonstrated using birds. We selected 35 avian EST microsatellite loci that had a high degree of sequence homology between the zebra finch Taeniopygia guttata and the chicken Gallus gallus and designed primer sets in which the primer bind sites were identical in both species. For 33 conserved primer sets, on average, 100% of loci amplified in each of 17 passerine species and 99% of loci in five non-passerine species. The genotyping of four individuals per species revealed that 24-76% (mean 48%) of loci were polymorphic in the passerines and 18-26% (mean 21%) in the non-passerines. When at least 17 individuals were genotyped per species for four Fringillidae finch species, 71-85% of loci were polymorphic, observed heterozygosity was above 0.50 for most loci and no locus deviated significantly from Hardy-Weinberg proportions. This new set of microsatellite markers is of higher cross-species utility than any set previously designed. The loci described are suitable for a range of applications that require polymorphic avian markers, including paternity and population studies. They will facilitate comparisons of bird genome organization, including genome mapping and studies of recombination, and allow comparisons of genetic variability between species whilst avoiding ascertainment bias. The costs and time to develop new loci can now be avoided for many applications in numerous species. Furthermore, our method can be readily used to develop microsatellite markers of high utility across other taxa.

  3. Cross-species amplification and polymorphism of microsatellite loci in Helicoverpa armigera and Helicoverpa zea (Lepidoptera: Noctuidae) in Brazilian cropping systems.

    PubMed

    Leite, N A; Corrêa, A S; Alves-Pereira, A; Campos, J B; Zucchi, M I; Omoto, C

    2016-04-04

    The Old World bollworm Helicoverpa armigera (Hübner) was recently discovered in Brazil. This species is closely related to the New World bollworm H. zea (Boddie), and mating between these species has already been reported under laboratory conditions. Here, we tested the cross-species amplification of 20 microsatellite (SSR) loci in field populations of H. armigera and H. zea collected from Brazilian cropping systems. Seven SSR loci were successfully amplified and polymorphic in both species except for the locus HaC14, which was monomorphic for H. zea. All SSR loci were in linkage equilibrium, and deviations from Hardy- Weinberg equilibrium were only observed for the locus HarSSR1 in the HaRS-2 population, where null alleles were present. A moderate level of polymorphism was detected in H. armigera and H. zea populations with a mean allele number of 4.14, and 2.24, respectively. Interestingly, most of the populations of the recent invader H. armigera showed higher genetic diversity and inbreeding coefficients than H. zea populations. The genetic identity of each species was recovered using a STRUCTURE analysis, where the populations formed two clusters (K = 2) according to their species. STRUCTURE also suggested the occurrence of potential hybrid offspring between H. armigera and H. zea individuals in natural conditions. These SSR loci will be valuable in characterizing population differentiation, invasion routes, adaptation, reproductive behavior, and intra- and interspecific gene flow in H. armigera and H. zea populations in Brazil, the USA, and other areas where these two pests occur.

  4. MORC1 exhibits cross-species differential methylation in association with early life stress as well as genome-wide association with MDD

    PubMed Central

    Nieratschker, V; Massart, R; Gilles, M; Luoni, A; Suderman, M J; Krumm, B; Meier, S; Witt, S H; Nöthen, M M; Suomi, S J; Peus, V; Scharnholz, B; Dukal, H; Hohmeyer, C; Wolf, I A-C; Cirulli, F; Gass, P; Sütterlin, M W; Filsinger, B; Laucht, M; Riva, M A; Rietschel, M; Deuschle, M; Szyf, M

    2014-01-01

    Early life stress (ELS) is associated with increased vulnerability for diseases in later life, including psychiatric disorders. Animal models and human studies suggest that this effect is mediated by epigenetic mechanisms. In humans, epigenetic studies to investigate the influence of ELS on psychiatric phenotypes are limited by the inaccessibility of living brain tissue. Due to the tissue-specific nature of epigenetic signatures, it is impossible to determine whether ELS induced epigenetic changes in accessible peripheral cells, for example, blood lymphocytes, reflect epigenetic changes in the brain. To overcome these limitations, we applied a cross-species approach involving: (i) the analysis of CD34+ cells from human cord blood; (ii) the examination of blood-derived CD3+ T cells of newborn and adolescent nonhuman primates (Macaca mulatta); and (iii) the investigation of the prefrontal cortex of adult rats. Several regions in MORC1 (MORC family CW-type zinc finger 1; previously known as: microrchidia (mouse) homolog) were differentially methylated in response to ELS in CD34+ cells and CD3+ T cells derived from the blood of human and monkey neonates, as well as in CD3+ T cells derived from the blood of adolescent monkeys and in the prefrontal cortex of adult rats. MORC1 is thus the first identified epigenetic marker of ELS to be present in blood cell progenitors at birth and in the brain in adulthood. Interestingly, a gene-set-based analysis of data from a genome-wide association study of major depressive disorder (MDD) revealed an association of MORC1 with MDD. PMID:25158004

  5. Floor Plans Engine Removal Platform, Hold Down Arm Platform, ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    Floor Plans - Engine Removal Platform, Hold Down Arm Platform, Hydraulic Equipment Platforms, Isometric Cutaway of Engine Removal Platform, Isometric Cutaway of Hold Down Arm Platform, Isometric Cutaway of Hydraulic Platforms and Engine Support System Access - Marshall Space Flight Center, Saturn V S-IC Static Test Facility, West Test Area, Huntsville, Madison County, AL

  6. Isolation and characterization of microsatellite markers from the olive fly, Bactrocera oleae, and their cross-species amplification in the Tephritidae family

    PubMed Central

    Augustinos, Antonios A; Stratikopoulos, Elias E; Drosopoulou, Eleni; Kakani, Evdoxia G; Mavragani-Tsipidou, Penelope; Zacharopoulou, Antigone; Mathiopoulos, Kostas D

    2008-01-01

    Background The Tephritidae family of insects includes the most important agricultural pests of fruits and vegetables, belonging mainly to four genera (Bactrocera, Ceratitis, Anastrepha and Rhagoletis). The olive fruit fly, Bactrocera oleae, is the major pest of the olive fruit. Currently, its control is based on chemical insecticides. Environmentally friendlier methods have been attempted in the past (Sterile Insect Technique), albeit with limited success. This was mainly attributed to the lack of knowledge on the insect's behaviour, ecology and genetic structure of natural populations. The development of molecular markers could facilitate the access in the genome and contribute to the solution of the aforementioned problems. We chose to focus on microsatellite markers due to their abundance in the genome, high degree of polymorphism and easiness of isolation. Results Fifty-eight microsatellite-containing clones were isolated from the olive fly, Bactrocera oleae, bearing a total of sixty-two discrete microsatellite motifs. Forty-two primer pairs were designed on the unique sequences flanking the microsatellite motif and thirty-one of them amplified a PCR product of the expected size. The level of polymorphism was evaluated against wild and laboratory flies and the majority of the markers (93.5%) proved highly polymorphic. Thirteen of them presented a unique position on the olive fly polytene chromosomes by in situ hybridization, which can serve as anchors to correlate future genetic and cytological maps of the species, as well as entry points to the genome. Cross-species amplification of these markers to eleven Tephritidae species and sequencing of thirty-one of the amplified products revealed a varying degree of conservation that declines outside the Bactrocera genus. Conclusion Microsatellite markers are very powerful tools for genetic and population analyses, particularly in species deprived of any other means of genetic analysis. The presented set of

  7. Generation and infectivity titration of an infectious stock of avian hepatitis E virus (HEV) in chickens and cross-species infection of turkeys with avian HEV.

    PubMed

    Sun, Z F; Larsen, C T; Huang, F F; Billam, P; Pierson, F W; Toth, T E; Meng, X J

    2004-06-01

    together with the inoculated ones also became infected through direct contact. This is the first demonstration of cross-species infection by avian HEV.

  8. Platform switching and bone platform switching.

    PubMed

    Carinci, Francesco; Brunelli, Giorgio; Danza, Matteo

    2009-01-01

    Bone platform switching involves an inward bone ring in the coronal part of the implant that is in continuity with the alveolar bone crest. Bone platform switching is obtained by using a dental fixture with a reverse conical neck. A retrospective study was performed to evaluate the effectiveness of conventional vs reverse conical neck implants. In the period between May 2004 and November 2007, 86 patients (55 females and 31 males; median age, 53 years) were operated and 234 implants were inserted: 40 and 194 were conventional vs reverse conical neck implants, respectively. Kaplan-Meier algorithm and Cox regression were used to detect those variables associated with the clinical outcome. No differences in survival and success rates were detected between conventional vs reverse conical neck implants alone or in combination with any of the studied variables. Although bone platform switching leads to several advantages, no statistical difference in alveolar crest resorption is detected in comparison with reverse conical neck implants. We suppose that the proximity of the implant abutment junction to the alveolar crestal bone gives no protection against the microflora contained in the micrograph. Additional studies on larger series and a combination of platform switching and bone platform switching could lead to improved clinical outcomes.

  9. High-Performance Reaction Wheel Optimization for Fine-Pointing Space Platforms: Minimizing Induced Vibration Effects on Jitter Performance plus Lessons Learned from Hubble Space Telescope for Current and Future Spacecraft Applications

    NASA Technical Reports Server (NTRS)

    Hasha, Martin D.

    2016-01-01

    The Hubble Space Telescope (HST) applies large-diameter optics (2.5-m primary mirror) for diffraction-limited resolution spanning an extended wavelength range (approx. 100-2500 nm). Its Pointing Control System (PCS) Reaction Wheel Assemblies (RWAs), in the Support Systems Module (SSM), acquired an unprecedented set of high-sensitivity Induced Vibration (IV) data for 5 flight-certified RWAs: dwelling at set rotation rates. Focused on 4 key ratios, force and moment harmonic values (in 3 local principal directions) are extracted in the RWA operating range (0-3000 RPM). The IV test data, obtained under ambient lab conditions, are investigated in detail, evaluated, compiled, and curve-fitted; variational trends, core causes, and unforeseen anomalies are addressed. In aggregate, these values constitute a statistically-valid basis to quantify ground test-to-test variations and facilitate extrapolations to on-orbit conditions. Accumulated knowledge of bearing-rotor vibrational sources, corresponding harmonic contributions, and salient elements of IV key variability factors are discussed. An evolved methodology is presented for absolute assessments and relative comparisons of macro-level IV signal magnitude due to micro-level construction-assembly geometric details/imperfections stemming from both electrical drive and primary bearing design parameters. Based upon studies of same-size/similar-design momentum wheels' IV changes, upper estimates due to transitions from ground tests to orbital conditions are derived. Recommended HST RWA choices are discussed relative to system optimization/tradeoffs of Line-Of-Sight (LOS) vector-pointing focal-plane error driven by higher IV transmissibilities through low-damped structural dynamics that stimulate optical elements. Unique analytical disturbance results for orbital HST accelerations are described applicable to microgravity efforts. Conclusions, lessons learned, historical context/insights, and perspectives on future applications

  10. Omnidirectional holonomic platforms

    SciTech Connect

    Pin, F.G.; Killough, S.M.

    1994-06-01

    This paper presents the concepts for a new family of wheeled platforms which feature full omnidirectionality with simultaneous and independently controlled rotational and translational motion capabilities. The authors first present the orthogonal-wheels concept and the two major wheel assemblies on which these platforms are based. They then describe how a combination of these assemblies with appropriate control can be used to generate an omnidirectional capability for mobile robot platforms. The design and control of two prototype platforms are then presented and their respective characteristics with respect to rotational and translational motion control are discussed.

  11. View from second floor platform looking up at subsequent platforms. ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    View from second floor platform looking up at subsequent platforms. Note the Shuttle assembly outlined by the platform edges. - Marshall Space Flight Center, Saturn V Dynamic Test Facility, East Test Area, Huntsville, Madison County, AL

  12. Floor Plans Rolling Platform, Tech Systems Platform, and Load ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    Floor Plans - Rolling Platform, Tech Systems Platform, and Load Platform Plans - Marshall Space Flight Center, F-1 Engine Static Test Stand, On Route 565 between Huntsville and Decatur, Huntsville, Madison County, AL

  13. Ladder attachment platform

    DOEpatents

    Swygert,; Richard, W [Springfield, SC

    2012-08-28

    A ladder attachment platform is provided that includes a base for attachment to a ladder that has first and second side rails and a plurality of rungs that extend between in a lateral direction. Also included is a user platform for having a user stand thereon that is carried by the base. The user platform may be positioned with respect to the ladder so that it is not located between a first plane that extends through the first side rail and is perpendicular to the lateral direction and a second plane that extends through the second side rail and is perpendicular to the lateral direction.

  14. Assessing the Party Platforms.

    ERIC Educational Resources Information Center

    Farrell, Patrick J.

    1980-01-01

    From the perspective of a Catholic educator, the author examines the education planks of the 1980 Democratic and Republican Party platforms, particularly those planks relating to private education and tuition tax credits. (SJL)

  15. Feasibility of Floating Platform Systems for Wind Turbines: Preprint

    SciTech Connect

    Musial, W.; Butterfield, S.; Boone, A.

    2003-11-01

    This paper provides a general technical description of several types of floating platforms for wind turbines. Platform topologies are classified into multiple- or single-turbine floaters and by mooring method. Platforms using catenary mooring systems are contrasted to vertical mooring systems and the advantages and disadvantages are discussed. Specific anchor types are described in detail. A rough cost comparison is performed for two different platform architectures using a generic 5-MW wind turbine. One platform is a Dutch study of a tri-floater platform using a catenary mooring system, and the other is a mono-column tension-leg platform developed at the National Renewable Energy Laboratory. Cost estimates showed that single unit production cost is $7.1 M for the Dutch tri-floater, and $6.5 M for the NREL TLP concept. However, value engineering, multiple unit series production, and platform/turbine system optimization can lower the unit platform costs to $4.26 M and $2.88 M, respectively, with significant potential to reduce cost further with system optimization. These foundation costs are within the range necessary to bring the cost of energy down to the DOE target range of $0.05/kWh for large-scale deployment of offshore floating wind turbines.

  16. ARM for Platform Application

    NASA Astrophysics Data System (ADS)

    Patte, Mathieu; Poupat, Jean-Luc; Le Meur, Patrick

    2015-09-01

    The activities described in this paper are part of the CNES R&T “Study of a Cortex-R ARM based architecture” performed by Airbus DS Space System & Electronics in 2014. With the support of CNES, Airbus DS has performed the porting of a representative space application software on an ARM based demonstration platform. This paper presents the platform itself, the activities performed at software level and the first results on this evaluation study.

  17. Building Community Web Platform

    NASA Astrophysics Data System (ADS)

    Ohmukai, Ikki; Matsuo, Yutaka; Matsumura, Naohiro; Takeda, Hideaki

    In this paper we propose Web-based communication environment called ``Community Web Platform''. Our platform provides an easy way to exchange personal knowledge among people with lightweight metadata such like RSS and FOAF. We investigate the nature of ``personal trustness'' on the environment since it is one and only measure for evaluating subjective information and knowledge. We also discuss how to develop and maintain Community Web applications from our exrerience.

  18. National Community Solar Platform

    SciTech Connect

    Rupert, Bart

    2016-06-30

    This project was created to provide a National Community Solar Platform (NCSP) portal known as Community Solar Hub, that is available to any entity or individual who wants to develop community solar. This has been done by providing a comprehensive portal to make CEC’s solutions, and other proven community solar solutions, externally available for everyone to access – making the process easy through proven platforms to protect subscribers, developers and utilities. The successful completion of this project provides these tools via a web platform and integration APIs, a wide spectrum of community solar projects included in the platform, multiple groups of customers (utilities, EPCs, and advocates) using the platform to develop community solar, and open access to anyone interested in community solar. CEC’s Incubator project includes web-based informational resources, integrated systems for project information and billing systems, and engagement with customers and users by community solar experts. The combined effort externalizes much of Clean Energy Collective’s industry-leading expertise, allowing third parties to develop community solar without duplicating expensive start-up efforts. The availability of this platform creates community solar projects that are cheaper to build and cheaper to participate in, furthering the goals of DOE’s SunShot Initiative. Final SF 425 Final SF 428 Final DOE F 2050.11 Final Report Narrative

  19. Particle-Based Platforms for Malaria Vaccines

    PubMed Central

    Wu, Yimin; Narum, David L.; Fleury, Sylvain; Jennings, Gary; Yadava, Anjali

    2015-01-01

    Recombinant subunit vaccines in general are poor immunogens likely due to the small size of peptides and proteins, combined with the lack or reduced presentation of repetitive motifs and missing complementary signal(s) for optimal triggering of the immune response. Therefore, recombinant subunit vaccines require enhancement by vaccine delivery vehicles in order to attain adequate protective immunity. Particle-based delivery platforms, including particulate antigens and particulate adjuvants, are promising delivery vehicles for modifying the way in which immunogens are presented to both the innate and adaptive immune systems. These particle delivery platforms can also co-deliver non-specific immunostimodulators as additional adjuvants. This paper reviews efforts and advances of the Particle-based delivery platforms in development of vaccines against malaria, a disease that claims over 600,000 lives per year, most of them are children under 5 years of age in sub-Sahara Africa. PMID:26458803

  20. Comparison of small molecule inhibitors of the bacterial cell division protein FtsZ and identification of a reliable cross-species inhibitor.

    PubMed

    Anderson, David E; Kim, Michelle B; Moore, Jared T; O'Brien, Terrence E; Sorto, Nohemy A; Grove, Charles I; Lackner, Laura L; Ames, James B; Shaw, Jared T

    2012-11-16

    FtsZ is a guanosine triphosphatase (GTPase) that mediates cytokinesis in bacteria. FtsZ is homologous in structure to eukaryotic tubulin and polymerizes in a similar head-to-tail fashion. The study of tubulin's function in eukaryotic cells has benefited greatly from specific and potent small molecule inhibitors, including colchicine and taxol. Although many small molecule inhibitors of FtsZ have been reported, none has emerged as a generally useful probe for modulating bacterial cell division. With the goal of establishing a useful and reliable small molecule inhibitor of FtsZ, a broad biochemical cross-comparison of reported FtsZ inhibitors was undertaken. Several of these molecules, including phenolic natural products, are unselective inhibitors that seem to derive their activity from the formation of microscopic colloids or aggregates. Other compounds, including the natural product viriditoxin and the drug development candidate PC190723, exhibit no inhibition of GTPase activity using protocols in this work or under published conditions. Of the compounds studied, only zantrin Z3 exhibits good levels of inhibition, maintains activity under conditions that disrupt small molecule aggregates, and provides a platform for exploration of structure-activity relationships (SAR). Preliminary SAR studies have identified slight modifications to the two side chains of this structure that modulate the inhibitory activity of zantrin Z3. Collectively, these studies will help focus future investigations toward the establishment of probes for FtsZ that fill the roles of colchicine and taxol in studies of tubulin.

  1. Transactional Network Platform: Applications

    SciTech Connect

    Katipamula, Srinivas; Lutes, Robert G.; Ngo, Hung; Underhill, Ronald M.

    2013-10-31

    In FY13, Pacific Northwest National Laboratory (PNNL) with funding from the Department of Energy’s (DOE’s) Building Technologies Office (BTO) designed, prototyped and tested a transactional network platform to support energy, operational and financial transactions between any networked entities (equipment, organizations, buildings, grid, etc.). Initially, in FY13, the concept demonstrated transactions between packaged rooftop air conditioners and heat pump units (RTUs) and the electric grid using applications or "agents" that reside on the platform, on the equipment, on a local building controller or in the Cloud. The transactional network project is a multi-lab effort with Oakridge National Laboratory (ORNL) and Lawrence Berkeley National Laboratory (LBNL) also contributing to the effort. PNNL coordinated the project and also was responsible for the development of the transactional network (TN) platform and three different applications associated with RTUs. This document describes two applications or "agents" in details, and also summarizes the platform. The TN platform details are described in another companion document.

  2. Platforms for antibiotic discovery.

    PubMed

    Lewis, Kim

    2013-05-01

    The spread of resistant bacteria, leading to untreatable infections, is a major public health threat but the pace of antibiotic discovery to combat these pathogens has slowed down. Most antibiotics were originally isolated by screening soil-derived actinomycetes during the golden era of antibiotic discovery in the 1940s to 1960s. However, diminishing returns from this discovery platform led to its collapse, and efforts to create a new platform based on target-focused screening of large libraries of synthetic compounds failed, in part owing to the lack of penetration of such compounds through the bacterial envelope. This article considers strategies to re-establish viable platforms for antibiotic discovery. These include investigating untapped natural product sources such as uncultured bacteria, establishing rules of compound penetration to enable the development of synthetic antibiotics, developing species-specific antibiotics and identifying prodrugs that have the potential to eradicate dormant persisters, which are often responsible for hard-to-treat infections.

  3. The Personal Motion Platform

    NASA Technical Reports Server (NTRS)

    Park, Brian Vandellyn

    1993-01-01

    The Neutral Body Posture experienced in microgravity creates a biomechanical equilibrium by enabling the internal forces within the body to find their own balance. A patented reclining chair based on this posture provides a minimal stress environment for interfacing with computer systems for extended periods. When the chair is mounted on a 3 or 6 axis motion platform, a generic motion simulator for simulated digital environments is created. The Personal Motion Platform provides motional feedback to the occupant in synchronization with their movements inside the digital world which enhances the simulation experience. Existing HMD based simulation systems can be integrated to the turnkey system. Future developments are discussed.

  4. Manipulator mounted transfer platform

    DOEpatents

    Dobbins, James C.; Hoover, Mark A.; May, Kay W.; Ross, Maurice J.

    1990-01-01

    A transfer platform for the conveyance of objects by a manipulator includes a bed frame and saddle clamp secured along an edge of the bed frame and adapted so as to secure the bed frame to a horizontal crosspiece of the manipulator. The platform may thus move with the manipulator in a reciprocal linear path defined by a guide rail. A bed insert may be provided for the support of conveyed objects and a lifting bail may be provided to permit the manipulator arm to install the bed frame upon the crosspiece under remote control.

  5. Floating Ocean Platform

    DTIC Science & Technology

    2003-08-15

    water from the Bacia de Campos oil field offshore platforms, ENVIRONMENTAL FORENSICS , 115-123 Environ. Forensics , 2002 Bybee, K, Intelligent well...PORTILLO, H, JUVENILE TURTLES FOR MOSQUITO-CONTROL IN WATER STORAGE TANKS, JOURNAL OF MEDICAL ENTOMOLOGY , 943-946 J. Med. Entomol., 1993 LI, YS KAREEM

  6. Japan's builders study platforms

    SciTech Connect

    Burke, R.G.

    1984-07-05

    This paper discusses the developing role of Japan as a major supplier of offshore drilling and production equipment. Different firms are discussed along with their capacity. The marketing areas, work experience, and plans for designs are also included. There is special attention payed on the potential for developing Arctic platforms.

  7. Education Platforms for America

    ERIC Educational Resources Information Center

    District Administration, 2012

    2012-01-01

    What is at stake for K12 education in next month's presidential election? Both President Barack Obama (Democratic Party) and Gov. Mitt Romney (Republican Party) say improving education will be a top priority in their administrations, but their policies and initiatives would likely be quite different. While political platforms rarely offer detailed…

  8. PR-PR: Cross-Platform Laboratory Automation System

    SciTech Connect

    Linshiz, G; Stawski, N; Goyal, G; Bi, CH; Poust, S; Sharma, M; Mutalik, V; Keasling, JD; Hillson, NJ

    2014-08-01

    To enable protocol standardization, sharing, and efficient implementation across laboratory automation platforms, we have further developed the PR-PR open-source high-level biology-friendly robot programming language as a cross-platform laboratory automation system. Beyond liquid-handling robotics, PR-PR now supports microfluidic and microscopy platforms, as well as protocol translation into human languages, such as English. While the same set of basic PR-PR commands and features are available for each supported platform, the underlying optimization and translation modules vary from platform to platform. Here, we describe these further developments to PR-PR, and demonstrate the experimental implementation and validation of PR-PR protocols for combinatorial modified Golden Gate DNA assembly across liquid-handling robotic, microfluidic, and manual platforms. To further test PR-PR cross-platform performance, we then implement and assess PR-PR protocols for Kunkel DNA mutagenesis and hierarchical Gibson DNA assembly for microfluidic and manual platforms.

  9. An integrated platform for biomolecule interaction analysis

    NASA Astrophysics Data System (ADS)

    Jan, Chia-Ming; Tsai, Pei-I.; Chou, Shin-Ting; Lee, Shu-Sheng; Lee, Chih-Kung

    2013-02-01

    We developed a new metrology platform which can detect real-time changes in both a phase-interrogation mode and intensity mode of a SPR (surface plasmon resonance). We integrated a SPR and ellipsometer to a biosensor chip platform to create a new biomolecular interaction measurement mechanism. We adopted a conductive ITO (indium-tinoxide) film to the bio-sensor platform chip to expand the dynamic range and improve measurement accuracy. The thickness of the conductive film and the suitable voltage constants were found to enhance performance. A circularly polarized ellipsometry configuration was incorporated into the newly developed platform to measure the label-free interactions of recombinant human C-reactive protein (CRP) with immobilized biomolecule target monoclonal human CRP antibody at various concentrations. CRP was chosen as it is a cardiovascular risk biomarker and is an acute phase reactant as well as a specific prognostic indicator for inflammation. We found that the sensitivity of a phaseinterrogation SPR is predominantly dependent on the optimization of the sample incidence angle. The effect of the ITO layer effective index under DC and AC effects as well as an optimal modulation were experimentally performed and discussed. Our experimental results showed that the modulated dynamic range for phase detection was 10E-2 RIU based on a current effect and 10E-4 RIU based on a potential effect of which a 0.55 (°/RIU) measurement was found by angular-interrogation. The performance of our newly developed metrology platform was characterized to have a higher sensitivity and less dynamic range when compared to a traditional full-field measurement system.

  10. Mobile Platform for Large Structures

    NASA Technical Reports Server (NTRS)

    Wesselski, C. J.; Schneider, W. C.

    1987-01-01

    Proposed platform moves forward and in reverse, turns left and right, and changes planes. Mobile-platform concept proposed to move remote manipulators, workers, or other loads over truss panels on large structures. Platform moves at constant speed so does not cause swinging motion in hanging loads and overstress remote-manipulator arms. Transferred around corners to adjacent panels. Platform rides on sprocketed guide pins extending from structure at truss joints. Set of orthogonal tracks under platform slides on pins, which have enlarged heads to interlock with tracks. At least three tracks engage at least three pins at any position on panel so platform adequately and stably supported.

  11. Mobility platform coupling device and method for coupling mobility platforms

    DOEpatents

    Shirey, David L.; Hayward, David R.; Buttz, James H.

    2002-01-01

    A coupling device for connecting a first mobility platform to a second mobility platform in tandem. An example mobility platform is a robot. The coupling device has a loose link mode for normal steering conditions and a locking position, tight link mode for navigation across difficult terrain and across obstacles, for traversing chasms, and for navigating with a reduced footprint in tight steering conditions.

  12. Improvement in the amine glass platform by bubbling method for a DNA microarray.

    PubMed

    Jee, Seung Hyun; Kim, Jong Won; Lee, Ji Hyeong; Yoon, Young Soo

    2015-01-01

    A glass platform with high sensitivity for sexually transmitted diseases microarray is described here. An amino-silane-based self-assembled monolayer was coated on the surface of a glass platform using a novel bubbling method. The optimized surface of the glass platform had highly uniform surface modifications using this method, as well as improved hybridization properties with capture probes in the DNA microarray. On the basis of these results, the improved glass platform serves as a highly reliable and optimal material for the DNA microarray. Moreover, in this study, we demonstrated that our glass platform, manufactured by utilizing the bubbling method, had higher uniformity, shorter processing time, lower background signal, and higher spot signal than the platforms manufactured by the general dipping method. The DNA microarray manufactured with a glass platform prepared using bubbling method can be used as a clinical diagnostic tool.

  13. OGC Collaborative Platform undercover

    NASA Astrophysics Data System (ADS)

    Buehler, G.; Arctur, D. K.; Bermudez, L. E.

    2012-12-01

    The mission of the Open Geospatial Consortium (OGC) is to serve as a global forum for the collaboration of developers and users of spatial data products and services, and to advance the development of international standards for geospatial interoperability. The OGC coordinates with over 400 institutions in the development of geospatial standards. OGC has a dedicated staff supported by a Collaborative Web Platform to enable sophisticated and successful coordination among its members. Since its origins in the early 1990s, the OGC Collaborative Web Platform has evolved organically to be the collaboration hub for standards development in the exchange of geospatial and related types of information, among a global network of thousands of technical, scientific and management professionals spanning numerous disparate application domains. This presentation describes the structure of this collaboration hub, the relationships enabled (both among and beyond OGC members), and how this network fits in a broader ecosystem of technology development and information standards organizations.

  14. Common tester platform concept.

    SciTech Connect

    Hurst, Michael James

    2008-05-01

    This report summarizes the results of a case study on the doctrine of a common tester platform, a concept of a standardized platform that can be applicable across the broad spectrum of testing requirements throughout the various stages of a weapons program, as well as across the various weapons programs. The common tester concept strives to define an affordable, next-generation design that will meet testing requirements with the flexibility to grow and expand; supporting the initial development stages of a weapons program through to the final production and surveillance stages. This report discusses a concept investing key leveraging technologies and operational concepts combined with prototype tester-development experiences and practical lessons learned gleaned from past weapons programs.

  15. Secure Sensor Platform

    SciTech Connect

    Troy Ross, Barry Schoeneman

    2010-08-25

    The Secure Sensor Platform (SSP) software provides a framework of functionality to support the development of low-power autonomous sensors for nuclear safeguards. This framework provides four primary functional blocks of capabilities required to implement autonomous sensors. The capabilities are: communications, security, power management, and cryptography. Utilizing this framework establishes a common set of functional capabilities for seamless interoperability of any sensor based upon the SSP concept.

  16. HPC - Platforms Penta Chart

    SciTech Connect

    Trujillo, Angelina Michelle

    2015-10-08

    Strategy, Planning, Acquiring- very large scale computing platforms come and go and planning for immensely scalable machines often precedes actual procurement by 3 years. Procurement can be another year or more. Integration- After Acquisition, machines must be integrated into the computing environments at LANL. Connection to scalable storage via large scale storage networking, assuring correct and secure operations. Management and Utilization – Ongoing operations, maintenance, and trouble shooting of the hardware and systems software at massive scale is required.

  17. "Platform switching": serendipity.

    PubMed

    Kalavathy, N; Sridevi, J; Gehlot, Roshni; Kumar, Santosh

    2014-01-01

    Implant dentistry is the latest developing field in terms of clinical techniques, research, material science and oral rehabilitation. Extensive work is being done to improve the designing of implants in order to achieve better esthetics and function. The main drawback with respect to implant restoration is achieving good osseointegration along with satisfactory stress distribution, which in turn will improve the prognosis of implant prosthesis by reducing the crestal bone loss. Many concepts have been developed with reference to surface coating of implants, surgical techniques for implant placement, immediate and delayed loading, platform switching concept, etc. This article has made an attempt to review the concept of platform switching was in fact revealed accidentally due to the nonavailability of the abutment appropriate to the size of the implant placed. A few aspect of platform switching, an upcoming idea to reduce crestal bone loss have been covered. The various methods used for locating and preparing the data were done through textbooks, Google search and related articles.

  18. The Prodiguer Messaging Platform

    NASA Astrophysics Data System (ADS)

    Greenslade, Mark; Denvil, Sebastien; Raciazek, Jerome; Carenton, Nicolas; Levavasseur, Guillame

    2014-05-01

    CONVERGENCE is a French multi-partner national project designed to gather HPC and informatics expertise to innovate in the context of running French climate models with differing grids and at differing resolutions. Efficient and reliable execution of these models and the management and dissemination of model output (data and meta-data) are just some of the complexities that CONVERGENCE aims to resolve. The Institut Pierre Simon Laplace (IPSL) is responsible for running climate simulations upon a set of heterogenous HPC environments within France. With heterogeneity comes added complexity in terms of simulation instrumentation and control. Obtaining a global perspective upon the state of all simulations running upon all HPC environments has hitherto been problematic. In this presentation we detail how, within the context of CONVERGENCE, the implementation of the Prodiguer messaging platform resolves complexity and permits the development of real-time applications such as: 1. a simulation monitoring dashboard; 2. a simulation metrics visualizer; 3. an automated simulation runtime notifier; 4. an automated output data & meta-data publishing pipeline; The Prodiguer messaging platform leverages a widely used open source message broker software called RabbitMQ. RabbitMQ itself implements the Advanced Message Queue Protocol (AMPQ). Hence it will be demonstrated that the Prodiguer messaging platform is built upon both open source and open standards.

  19. North Sea platforms revamped

    SciTech Connect

    O'Hare, J.

    1999-12-01

    Many of the early North Sea platforms are reaching their end-of-field life. Most are still equipped with their original drilling package. In a few cases the package has either been removed or decommissioned. The early installations were designed for much simpler and less demanding wells than the horizontal, extended-reach or designer wells common today. Extended-reach wells now can be drilled realistically from ageing platforms, without incurring massive capital expenditure. This can be achieved using the existing drilling package to the limit of its capabilities and supplementing where necessary with relatively minor upgrades or the use of temporary equipment. Drilling even a few more wells from existing platforms not only prolongs field life, it enables any surplus processing capacity to be made available to develop near-field potential with extended-reach drilling (ERD) or by tying back subsea satellite wells, or for processing third-party fluids. The paper describes well design, surface equipment, mud pumps, shakers and solids control equipment, drill cuttings disposal systems, derrick and hoisting system, top drive and drillstring, downhole equipment, well planning, casing wear, logistics, rig preparations, and ERD vs. subsea tie-backs.

  20. The Prodiguer Messaging Platform

    NASA Astrophysics Data System (ADS)

    Denvil, S.; Greenslade, M. A.; Carenton, N.; Levavasseur, G.; Raciazek, J.

    2015-12-01

    CONVERGENCE is a French multi-partner national project designed to gather HPC and informatics expertise to innovate in the context of running French global climate models with differing grids and at differing resolutions. Efficient and reliable execution of these models and the management and dissemination of model output are some of the complexities that CONVERGENCE aims to resolve.At any one moment in time, researchers affiliated with the Institut Pierre Simon Laplace (IPSL) climate modeling group, are running hundreds of global climate simulations. These simulations execute upon a heterogeneous set of French High Performance Computing (HPC) environments. The IPSL's simulation execution runtime libIGCM (library for IPSL Global Climate Modeling group) has recently been enhanced so as to support hitherto impossible realtime use cases such as simulation monitoring, data publication, metrics collection, simulation control, visualizations … etc. At the core of this enhancement is Prodiguer: an AMQP (Advanced Message Queue Protocol) based event driven asynchronous distributed messaging platform. libIGCM now dispatches copious amounts of information, in the form of messages, to the platform for remote processing by Prodiguer software agents at IPSL servers in Paris. Such processing takes several forms: Persisting message content to database(s); Launching rollback jobs upon simulation failure; Notifying downstream applications; Automation of visualization pipelines; We will describe and/or demonstrate the platform's: Technical implementation; Inherent ease of scalability; Inherent adaptiveness in respect to supervising simulations; Web portal receiving simulation notifications in realtime.

  1. Novel biochip platform for nucleic acid analysis.

    PubMed

    Pernagallo, Salvatore; Ventimiglia, Giorgio; Cavalluzzo, Claudia; Alessi, Enrico; Ilyine, Hugh; Bradley, Mark; Diaz-Mochon, Juan J

    2012-01-01

    This manuscript describes the use of a novel biochip platform for the rapid analysis/identification of nucleic acids, including DNA and microRNAs, with very high specificity. This approach combines a unique dynamic chemistry approach for nucleic acid testing and analysis developed by DestiNA Genomics with the STMicroelectronics In-Check platform, which comprises two microfluidic optimized and independent PCR reaction chambers, and a sequential microarray area for nucleic acid capture and identification by fluorescence. With its compact bench-top "footprint" requiring only a single technician to operate, the biochip system promises to transform and expand routine clinical diagnostic testing and screening for genetic diseases, cancers, drug toxicology and heart disease, as well as employment in the emerging companion diagnostics market.

  2. The Geohazards Exploitation Platform

    NASA Astrophysics Data System (ADS)

    Laur, Henri; Casu, Francesco; Bally, Philippe; Caumont, Hervé; Pinto, Salvatore

    2016-04-01

    The Geohazards Exploitation Platform, or Geohazards TEP (GEP), is an ESA originated R&D activity of the EO ground segment to demonstrate the benefit of new technologies for large scale processing of EO data. This encompasses on-demand processing for specific user needs, systematic processing to address common information needs of the geohazards community, and integration of newly developed processors for scientists and other expert users. The platform supports the geohazards community's objectives as defined in the context of the International Forum on Satellite EO and Geohazards organised by ESA and GEO in Santorini in 2012. The GEP is a follow on to the Supersites Exploitation Platform (SSEP) an ESA initiative to support the Geohazards Supersites & Natural Laboratories initiative (GSNL). Today the GEP allows to exploit 70+ Terabyte of ERS and ENVISAT archive and the Copernicus Sentinel-1 data available on line. The platform has already engaged 22 European early adopters in a validation activity initiated in March 2015. Since September, this validation has reached 29 single user projects. Each project is concerned with either integrating an application, running on demand processing or systematically generating a product collection using an application available in the platform. The users primarily include 15 geoscience centres and universities based in Europe: British Geological Survey (UK), University of Leeds (UK), University College London (UK), ETH University of Zurich (CH), INGV (IT), CNR-IREA and CNR-IRPI (IT), University of L'Aquila (IT), NOA (GR), Univ. Blaise Pascal & CNRS (FR), Ecole Normale Supérieure (FR), ISTERRE / University of Grenoble-Alpes (FR). In addition, there are users from Africa and North America with the University of Rabat (MA) and the University of Miami (US). Furthermore two space agencies and four private companies are involved: the German Space Research Centre DLR (DE), the European Space Agency (ESA), Altamira Information (ES

  3. The EOS polar platform

    NASA Technical Reports Server (NTRS)

    Soffen, Gerald; Hobish, Mitchell K.

    1990-01-01

    An overview of NASA's Earth Observing System (EOS) is presented. The EOS will be part of the Mission to Planet Earth that will include a series of flight and scientific experiments. The initial polar-orbiting platform, EOS-A, will carry a suite of instruments designed to examine earth system processes at and near the planet's surface, and the interactions between various subsystems. Some of the instruments that will provide specialized data for geologists, meteorologists, biochemists, biologists, and physicists are described. Thus, EOS will provide an opportunity for technologists and scientists to examine the earth to a level of detail not previously attainable.

  4. Cots Correlator Platform

    NASA Astrophysics Data System (ADS)

    Schaaf, Kjeld; Overeem, Ruud

    2004-06-01

    Moore’s law is best exploited by using consumer market hardware. In particular, the gaming industry pushes the limit of processor performance thus reducing the cost per raw flop even faster than Moore’s law predicts. Next to the cost benefits of Common-Of-The-Shelf (COTS) processing resources, there is a rapidly growing experience pool in cluster based processing. The typical Beowulf cluster of PC’s supercomputers are well known. Multiple examples exists of specialised cluster computers based on more advanced server nodes or even gaming stations. All these cluster machines build upon the same knowledge about cluster software management, scheduling, middleware libraries and mathematical libraries. In this study, we have integrated COTS processing resources and cluster nodes into a very high performance processing platform suitable for streaming data applications, in particular to implement a correlator. The required processing power for the correlator in modern radio telescopes is in the range of the larger supercomputers, which motivates the usage of supercomputer technology. Raw processing power is provided by graphical processors and is combined with an Infiniband host bus adapter with integrated data stream handling logic. With this processing platform a scalable correlator can be built with continuously growing processing power at consumer market prices.

  5. Platform for Action: update.

    PubMed

    1995-01-01

    The Center for Women's Global Leadership (CWGL) has collaborated in the preparation of amendments and strategies designed to withstand the challenges being posed to the Platform for Action of the Fourth World Conference on Women. Specific challenges include the inappropriate use of the word "universal" to modify "human rights." This implies that some human rights are less than universal. The strategy proposed is to accept the use of the word "universal" in this context only when it affirms principles of universality contained in the Vienna Programme of Action and not where its use would restrict the rights to which women are entitled. A second concern is over the use of the word "equity" rather than "equality" when referring to gender relations. The use of these terms will be carefully monitored to insure that "equity" not be used to undermine the principle of gender equality. The third concern is the efforts of some governments to hinder the integration of women's human rights throughout the UN system. Such efforts will be opposed. Fourth, the CWGL will seek the inclusion of language which recognizes the barriers that different groups of women face when trying to secure their rights. Finally, the CWGL will propose inclusion of language recognizing and protecting sexual orientation rights. The CWGL is also going to work to translate the abstract language of the Platform for Action into political organizing potential to insure that governments will follow through on their agreements.

  6. Open systems storage platforms

    NASA Technical Reports Server (NTRS)

    Collins, Kirby

    1992-01-01

    The building blocks for an open storage system includes a system platform, a selection of storage devices and interfaces, system software, and storage applications CONVEX storage systems are based on the DS Series Data Server systems. These systems are a variant of the C3200 supercomputer with expanded I/O capabilities. These systems support a variety of medium and high speed interfaces to networks and peripherals. System software is provided in the form of ConvexOS, a POSIX compliant derivative of 4.3BSD UNIX. Storage applications include products such as UNITREE and EMASS. With the DS Series of storage systems, Convex has developed a set of products which provide open system solutions for storage management applications. The systems are highly modular, assembled from off the shelf components with industry standard interfaces. The C Series system architecture provides a stable base, with the performance and reliability of a general purpose platform. This combination of a proven system architecture with a variety of choices in peripherals and application software allows wide flexibility in configurations, and delivers the benefits of open systems to the mass storage world.

  7. Long Read Alignment with Parallel MapReduce Cloud Platform.

    PubMed

    Al-Absi, Ahmed Abdulhakim; Kang, Dae-Ki

    2015-01-01

    Genomic sequence alignment is an important technique to decode genome sequences in bioinformatics. Next-Generation Sequencing technologies produce genomic data of longer reads. Cloud platforms are adopted to address the problems arising from storage and analysis of large genomic data. Existing genes sequencing tools for cloud platforms predominantly consider short read gene sequences and adopt the Hadoop MapReduce framework for computation. However, serial execution of map and reduce phases is a problem in such systems. Therefore, in this paper, we introduce Burrows-Wheeler Aligner's Smith-Waterman Alignment on Parallel MapReduce (BWASW-PMR) cloud platform for long sequence alignment. The proposed cloud platform adopts a widely accepted and accurate BWA-SW algorithm for long sequence alignment. A custom MapReduce platform is developed to overcome the drawbacks of the Hadoop framework. A parallel execution strategy of the MapReduce phases and optimization of Smith-Waterman algorithm are considered. Performance evaluation results exhibit an average speed-up of 6.7 considering BWASW-PMR compared with the state-of-the-art Bwasw-Cloud. An average reduction of 30% in the map phase makespan is reported across all experiments comparing BWASW-PMR with Bwasw-Cloud. Optimization of Smith-Waterman results in reducing the execution time by 91.8%. The experimental study proves the efficiency of BWASW-PMR for aligning long genomic sequences on cloud platforms.

  8. Long Read Alignment with Parallel MapReduce Cloud Platform

    PubMed Central

    Al-Absi, Ahmed Abdulhakim; Kang, Dae-Ki

    2015-01-01

    Genomic sequence alignment is an important technique to decode genome sequences in bioinformatics. Next-Generation Sequencing technologies produce genomic data of longer reads. Cloud platforms are adopted to address the problems arising from storage and analysis of large genomic data. Existing genes sequencing tools for cloud platforms predominantly consider short read gene sequences and adopt the Hadoop MapReduce framework for computation. However, serial execution of map and reduce phases is a problem in such systems. Therefore, in this paper, we introduce Burrows-Wheeler Aligner's Smith-Waterman Alignment on Parallel MapReduce (BWASW-PMR) cloud platform for long sequence alignment. The proposed cloud platform adopts a widely accepted and accurate BWA-SW algorithm for long sequence alignment. A custom MapReduce platform is developed to overcome the drawbacks of the Hadoop framework. A parallel execution strategy of the MapReduce phases and optimization of Smith-Waterman algorithm are considered. Performance evaluation results exhibit an average speed-up of 6.7 considering BWASW-PMR compared with the state-of-the-art Bwasw-Cloud. An average reduction of 30% in the map phase makespan is reported across all experiments comparing BWASW-PMR with Bwasw-Cloud. Optimization of Smith-Waterman results in reducing the execution time by 91.8%. The experimental study proves the efficiency of BWASW-PMR for aligning long genomic sequences on cloud platforms. PMID:26839887

  9. Geosynchronous platform definition study. Volume 5: Geosynchronous platform synthesis

    NASA Technical Reports Server (NTRS)

    1973-01-01

    The development is described of the platform configurations, support subsystems, mission equipment, and servicing concepts. A common support module is developed; subsystem concepts are traded off; data relay, TDRS, earth observational, astro-physics, and advanced navigation and traffic control mission equipment concepts are postulated; and ancillary equipment required for delivery and on-orbit servicing interfaces with geosynchronous platforms is grossly defined. The general approach was to develop a platform concept capable of evolving through three on-orbit servicing modes: remote, EVA, and shirtsleeve. The definition of the equipment is to the assembly level. Weight, power, and volumetric data are compiled for all the platforms.

  10. A novel probe density controllable electrochemiluminescence biosensor for ultra-sensitive detection of Hg2+ based on DNA hybridization optimization with gold nanoparticles array patterned self-assembly platform.

    PubMed

    Gao, Wenhua; Zhang, An; Chen, Yunsheng; Chen, Zixuan; Chen, Yaowen; Lu, Fushen; Chen, Zhanguang

    2013-11-15

    Biosensor based on DNA hybridization holds great potential to get higher sensitivity as the optimal DNA hybridization efficiency can be achieved by controlling the distribution and orientation of probe strands on the transducer surface. In this work, an innovative strategy is reported to tap the sensitivity potential of current electrochemiluminescence (ECL) biosensing system by dispersedly anchoring the DNA beacons on the gold nanoparticles (GNPs) array which was electrodeposited on the glassy carbon electrode surface, rather than simply sprawling the coil-like strands onto planar gold surface. The strategy was developed by designing a "signal-on" ECL biosensing switch fabricated on the GNPs nanopatterned electrode surface for enhanced ultra-sensitivity detection of Hg(2+). A 57-mer hairpin-DNA labeled with ferrocene as ECL quencher and a 13-mer DNA labeled with Ru(bpy)3(2+) as reporter were hybridized to construct the signal generator in off-state. A 31-mer thymine (T)-rich capture-DNA was introduced to form T-T mismatches with the loop sequence of the hairpin-DNA in the presence of Hg(2+) and induce the stem-loop open, meanwhile the ECL "signal-on" was triggered. The peak sensitivity with the lowest detection limit of 0.1 nM was achieved with the optimal GNPs number density while exorbitant GNPs deposition resulted in sensitivity deterioration for the biosensor. We expect the present strategy could lead the renovation of the existing probe-immobilized ECL genosensor design to get an even higher sensitivity in ultralow level of target detection such as the identification of genetic diseases and disorders in basic research and clinical application.

  11. An Application Development Platform for Neuromorphic Computing

    SciTech Connect

    Dean, Mark; Chan, Jason; Daffron, Christopher; Disney, Adam; Reynolds, John; Rose, Garrett; Plank, James; Birdwell, John Douglas; Schuman, Catherine D

    2016-01-01

    Dynamic Adaptive Neural Network Arrays (DANNAs) are neuromorphic computing systems developed as a hardware based approach to the implementation of neural networks. They feature highly adaptive and programmable structural elements, which model arti cial neural networks with spiking behavior. We design them to solve problems using evolutionary optimization. In this paper, we highlight the current hardware and software implementations of DANNA, including their features, functionalities and performance. We then describe the development of an Application Development Platform (ADP) to support efficient application implementation and testing of DANNA based solutions. We conclude with future directions.

  12. Chosen aspects of modeling and control of quadrotor platform

    NASA Astrophysics Data System (ADS)

    Zawiski, Radosław; Błachuta, Marian

    2012-11-01

    This article is presenting the extended model of quadrotor platform together with a bespoken control system based on optimal approach. It highlights particular aspects of the derived model, such as inclusion of rotor gyroscopic effects and thrust generation based on momentum theory. The controller's behavior is tested by simulations. Comparisons with literature-available solutions to the problem of full quadrotor optimal control are made and important differences exposed. Conclusions are drawn and future work proposed.

  13. A Scientific Cloud Computing Platform for Condensed Matter Physics

    NASA Astrophysics Data System (ADS)

    Jorissen, K.; Johnson, W.; Vila, F. D.; Rehr, J. J.

    2013-03-01

    Scientific Cloud Computing (SCC) makes possible calculations with high performance computational tools, without the need to purchase or maintain sophisticated hardware and software. We have recently developed an interface dubbed SC2IT that controls on-demand virtual Linux clusters within the Amazon EC2 cloud platform. Using this interface we have developed a more advanced, user-friendly SCC Platform configured especially for condensed matter calculations. This platform contains a GUI, based on a new Java version of SC2IT, that permits calculations of various materials properties. The cloud platform includes Virtual Machines preconfigured for parallel calculations and several precompiled and optimized materials science codes for electronic structure and x-ray and electron spectroscopy. Consequently this SCC makes state-of-the-art condensed matter calculations easy to access for general users. Proof-of-principle performance benchmarks show excellent parallelization and communication performance. Supported by NSF grant OCI-1048052

  14. Communications payloads for geostationary platforms

    NASA Technical Reports Server (NTRS)

    Fordyce, S. W.

    1978-01-01

    Trends in communication satellites show increasing reuse of the frequency spectrum through multiple spot beams and orthogonal polarization, as well as consortia operation. Current reliance on orbital arc separation for frequency reuse may be inadequate for the projected traffic growth and the orbital slotting proposals before the ITU. This paper notes that cost advantages can accrue through common use of spacecraft subsystems and multiple users' platforms aboard a common geostationary platform. The rationale for such platforms is described and potential payloads are suggested.

  15. An Autonomous Platform Simulator (APS)

    DTIC Science & Technology

    1989-06-01

    communications between vehicle sim- ulators, sufficient data is needed to display the platform on a remote simulator as well as model its movement. Information ...window manager interface, FOGM modeling , and the overall program structure. 2. The Firing Platform Simulator The Firing Platform Simulator was a class...brakes, and steering. 3. Vehicle Motion Modeling Realistically simulating the response of vehicles to controls, such as throttle and steering, and to

  16. Web Platform Application

    SciTech Connect

    Paulsworth, Ashley; Kurtz, Jim; Brun de Pontet, Stephanie

    2016-06-15

    Sunvestment Energy Group (previously called Sunvestment Group) was established to create a web application that brings together site hosts, those who will obtain the energy from the solar array, with project developers and funders, including affinity investors. Sunvestment Energy Group (SEG) uses a community-based model that engages with investors who have some affinity with the site host organization. In addition to a financial return, these investors receive non-financial value from their investments and are therefore willing to offer lower cost capital. This enables the site host to enjoy more savings from solar through these less expensive Community Power Purchase Agreements (CPPAs). The purpose of this award was to develop an online platform to bring site hosts and investors together virtually.

  17. VERCE Seismologie Platform

    NASA Astrophysics Data System (ADS)

    Schwichtenberg, Horst; moguilny, genevieve; gemuend, andre

    2014-05-01

    The VERCE Seismology platform is a Science Gateway and infrastructure solution that supports seismology users to access private as well as compute and data resources of European e-infrastructures. We will present an overview of how this infrastructure is structured on top of the existing e-infrastructures and what the challenges and obstacles consist of. In addition to providing consistently well-behaving applications on different hardware and software environments, the project, for example, has to deal with different authentication and authorization methods, policies (security etc.), data transfers between administrative domains with different policies (e.g. from data centres to compute centres) and missing out-of-the-box support for complex workflows from the e-infrastructure providers. We will show which problems can already be solved today and which requirements for providers and code developers exist.

  18. Energy Tracking Software Platform

    SciTech Connect

    Ryan Davis; Nathan Bird; Rebecca Birx; Hal Knowles

    2011-04-04

    Acceleration has created an interactive energy tracking and visualization platform that supports decreasing electric, water, and gas usage. Homeowners have access to tools that allow them to gauge their use and track progress toward a smaller energy footprint. Real estate agents have access to consumption data, allowing for sharing a comparison with potential home buyers. Home builders have the opportunity to compare their neighborhood's energy efficiency with competitors. Home energy raters have a tool for gauging the progress of their clients after efficiency changes. And, social groups are able to help encourage members to reduce their energy bills and help their environment. EnergyIT.com is the business umbrella for all energy tracking solutions and is designed to provide information about our energy tracking software and promote sales. CompareAndConserve.com (Gainesville-Green.com) helps homeowners conserve energy through education and competition. ToolsForTenants.com helps renters factor energy usage into their housing decisions.

  19. Turbine blade platform seal

    SciTech Connect

    Zagar, Thomas W.; Schiavo, Anthony L.

    2001-01-01

    A rotating blade group 90 for a turbo-machine having an improved device for sealing the gap 110 between the edges 112,114 of adjacent blade platforms 96,104. The gap 110 between adjacent blades 92,100 is sealed by a seal pin 20 its central portion 110 and by a seal plate 58,60 at each of the front 54 and rear 56 portions. The seal plates 58,60 are inserted into corresponding grooves 62,64 formed in the adjacent edges 112,114 of adjoining blades 92,100 and held in place by end plates 40,42. The end of the seal plates 58,60 may be chamfered 78,80 to improve the seal against the end plate 40,42. The seal pin 20 provides the required damping between the blades 92,100 and the seal plates 58,60 provide improved sealing effectiveness.

  20. An Extensible Sensing and Control Platform for Building Energy Management

    SciTech Connect

    Rowe, Anthony; Berges, Mario; Martin, Christopher

    2016-04-03

    The goal of this project is to develop Mortar.io, an open-source BAS platform designed to simplify data collection, archiving, event scheduling and coordination of cross-system interactions. Mortar.io is optimized for (1) robustness to network outages, (2) ease of installation using plug-and-play and (3) scalable support for small to large buildings and campuses.

  1. Multidisciplinary Optimization for Aerospace Using Genetic Optimization

    NASA Technical Reports Server (NTRS)

    Pak, Chan-gi; Hahn, Edward E.; Herrera, Claudia Y.

    2007-01-01

    In support of the ARMD guidelines NASA's Dryden Flight Research Center is developing a multidisciplinary design and optimization tool This tool will leverage existing tools and practices, and allow the easy integration and adoption of new state-of-the-art software. Optimization has made its way into many mainstream applications. For example NASTRAN(TradeMark) has its solution sequence 200 for Design Optimization, and MATLAB(TradeMark) has an Optimization Tool box. Other packages, such as ZAERO(TradeMark) aeroelastic panel code and the CFL3D(TradeMark) Navier-Stokes solver have no built in optimizer. The goal of the tool development is to generate a central executive capable of using disparate software packages ina cross platform network environment so as to quickly perform optimization and design tasks in a cohesive streamlined manner. A provided figure (Figure 1) shows a typical set of tools and their relation to the central executive. Optimization can take place within each individual too, or in a loop between the executive and the tool, or both.

  2. Precise control of miR-125b levels is required to create a regeneration-permissive environment after spinal cord injury: a cross-species comparison between salamander and rat.

    PubMed

    Diaz Quiroz, Juan Felipe; Tsai, Eve; Coyle, Matthew; Sehm, Tina; Echeverri, Karen

    2014-06-01

    Most spinal cord injuries lead to permanent paralysis in mammals. By contrast, the remarkable regenerative abilities of salamanders enable full functional recovery even from complete spinal cord transections. The molecular differences underlying this evolutionary divergence between mammals and amphibians are poorly understood. We focused on upstream regulators of gene expression as primary entry points into this question. We identified a group of microRNAs (miRNAs) that are conserved between the Mexican axolotl salamander (Ambystoma mexicanum) and mammals but show marked cross-species differences in regulation patterns following spinal cord injury. We found that precise post-injury levels of one of these miRNAs (miR-125b) is essential for functional recovery, and guides correct regeneration of axons through the lesion site in a process involving the direct downstream target Sema4D in axolotls. Translating these results to a mammalian model, we increased miR-125b levels in the rat through mimic treatments following spinal cord transection. These treatments downregulated Sema4D and other glial-scar-related genes, and enhanced the animal's functional recovery. Our study identifies a key regulatory molecule conserved between salamander and mammal, and shows that the expression of miR-125b and Sema4D must be carefully controlled in the right cells at the correct level to promote regeneration. We also show that these molecular components of the salamander's regeneration-permissive environment can be experimentally harnessed to improve treatment outcomes for mammalian spinal cord injuries.

  3. Optimally Stopped Optimization

    NASA Astrophysics Data System (ADS)

    Vinci, Walter; Lidar, Daniel A.

    2016-11-01

    We combine the fields of heuristic optimization and optimal stopping. We propose a strategy for benchmarking randomized optimization algorithms that minimizes the expected total cost for obtaining a good solution with an optimal number of calls to the solver. To do so, rather than letting the objective function alone define a cost to be minimized, we introduce a further cost-per-call of the algorithm. We show that this problem can be formulated using optimal stopping theory. The expected cost is a flexible figure of merit for benchmarking probabilistic solvers that can be computed when the optimal solution is not known and that avoids the biases and arbitrariness that affect other measures. The optimal stopping formulation of benchmarking directly leads to a real-time optimal-utilization strategy for probabilistic optimizers with practical impact. We apply our formulation to benchmark simulated annealing on a class of maximum-2-satisfiability (MAX2SAT) problems. We also compare the performance of a D-Wave 2X quantum annealer to the Hamze-Freitas-Selby (HFS) solver, a specialized classical heuristic algorithm designed for low-tree-width graphs. On a set of frustrated-loop instances with planted solutions defined on up to N =1098 variables, the D-Wave device is 2 orders of magnitude faster than the HFS solver, and, modulo known caveats related to suboptimal annealing times, exhibits identical scaling with problem size.

  4. A novel platform device for rodent echocardiography.

    PubMed

    Kutschka, Ingo; Sheikh, Ahmad Y; Sista, Ramachandra; Hendry, Stephen L; Chun, Hyung J; Hoyt, Grant; Kutschka, Werner; Pelletier, Marc P; Quertermous, Tom; Wu, Joseph C; Robbins, Robert C

    2007-06-06

    Acquisition of echocardiographic data from rodents is subject to wide variability due to variations in technique. We hypothesize that a dedicated imaging platform can aid in standardization of technique and improve the quality of images obtained. We constructed a device consisting of a boom-mounted steel platform frame (25 x 35 x 3 cm) on which a transparent polyethylene membrane is mounted. The animal is placed onto the membrane and receives continual inhaled anesthesia via an integrated port. The membrane allows for probe positioning from beneath the animal to obtain standard echo-views in left lateral decubitus or prone positions. The frame can be set at any desired angle ranging from 0 to 360 degrees along either the long or short axis. Adult male Sprague-Dawley rats (n = 5) underwent echocardiography (General Electric, Vivid 7, 14 MHz) using the platform. The device allowed for optimal positioning of animals for a variety of standard echocardiographic measurements. Evaluations among all animals showed minimal variability between two different operators and time points. We tested the feasibility of the device for supporting the assessment of cardiac function in a disease model by evaluating a separate cohort of adult male spontaneously hypertensive rats (n = 5) that underwent left anterior descending coronary artery ligation. Serial echocardiography demonstrated statistically significant decreases of fractional shortening and ejection fraction (p < 0.01) 240 days after surgery. Our novel imaging platform allowed for consistent collection of high-quality echocardiographic data from rats. Future studies will focus on improving this technology to allow for standardized high-throughput echocardiographic analysis in small animal models of disease.

  5. Offshore platform cathodic protection retrofits

    SciTech Connect

    Turnipseed, S.P.

    1996-10-01

    Cathodic protection (CP) is the primary technique used for underwater corrosion control on the majority of offshore steel structures. Offshore platforms are often kept in service far beyond their original design life. Refurbishment of the CP system is required when adequate protection can no longer be maintained. Various offshore platform CP retrofit designs are discussed.

  6. Plant Gene and Alternatively Spliced Variant Annotator. A plant genome annotation pipeline for rice gene and alternatively spliced variant identification with cross-species expressed sequence tag conservation from seven plant species.

    PubMed

    Chen, Feng-Chi; Wang, Sheng-Shun; Chaw, Shu-Miaw; Huang, Yao-Ting; Chuang, Trees-Juen

    2007-03-01

    The completion of the rice (Oryza sativa) genome draft has brought unprecedented opportunities for genomic studies of the world's most important food crop. Previous rice gene annotations have relied mainly on ab initio methods, which usually yield a high rate of false-positive predictions and give only limited information regarding alternative splicing in rice genes. Comparative approaches based on expressed sequence tags (ESTs) can compensate for the drawbacks of ab initio methods because they can simultaneously identify experimental data-supported genes and alternatively spliced transcripts. Furthermore, cross-species EST information can be used to not only offset the insufficiency of same-species ESTs but also derive evolutionary implications. In this study, we used ESTs from seven plant species, rice, wheat (Triticum aestivum), maize (Zea mays), barley (Hordeum vulgare), sorghum (Sorghum bicolor), soybean (Glycine max), and Arabidopsis (Arabidopsis thaliana), to annotate the rice genome. We developed a plant genome annotation pipeline, Plant Gene and Alternatively Spliced Variant Annotator (PGAA). Using this approach, we identified 852 genes (931 isoforms) not annotated in other widely used databases (i.e. the Institute for Genomic Research, National Center for Biotechnology Information, and Rice Annotation Project) and found 87% of them supported by both rice and nonrice EST evidence. PGAA also identified more than 44,000 alternatively spliced events, of which approximately 20% are not observed in the other three annotations. These novel annotations represent rich opportunities for rice genome research, because the functions of most of our annotated genes are currently unknown. Also, in the PGAA annotation, the isoforms with non-rice-EST-supported exons are significantly enriched in transporter activity but significantly underrepresented in transcription regulator activity. We have also identified potential lineage-specific and conserved isoforms, which are

  7. Identification of key genes in hepatocellular carcinoma and validation of the candidate gene, cdc25a, using gene set enrichment analysis, meta-analysis and cross-species comparison.

    PubMed

    Lu, Xiaoxu; Sun, Wen; Tang, Yanping; Zhu, Lingqun; Li, Yuan; Ou, Chao; Yang, Chun; Su, Jianjia; Luo, Chengpiao; Hu, Yanling; Cao, Ji

    2016-02-01

    The aim of the present study was to determine key pathways and genes involved in the pathogenesis of hepatocellular carcinoma (HCC) through bioinformatic analyses of HCC microarray data based on cross-species comparison. Microarray data of gene expression in HCC in different species were analyzed using gene set enrichment analysis (GSEA) and meta-analysis. Reverse transcription-quantitative polymerase chain reaction and western blotting were performed to determine the mRNA and protein expression levels of cdc25a, one of the identified candidate genes, in human, rat and tree shrew samples. The cell cycle pathway had the largest overlap between the GSEA and meta-analysis. Meta-analyses showed that 25 genes, including cdc25a, in the cell cycle pathway were differentially expressed. Cdc25a mRNA levels in HCC tissues were higher than those in normal liver tissues in humans, rats and tree shrews, and the expression level of cdc25a in HCC tissues was higher than in corresponding paraneoplastic tissues in humans and rats. In human HCC tissues, the cdc25a mRNA level was significantly correlated with clinical stage, portal vein tumor thrombosis and extrahepatic metastasis. Western blotting showed that, cdc25a protein levels were significantly upregulated in HCC tissues in humans, rats and tree shrews. In conclusion, GSEA and meta-analysis can be combined to identify key molecules and pathways involved in HCC. This study demonstrated that the cell cycle pathway and the cdc25a gene may be crucial in the pathogenesis and progression of HCC.

  8. Creating new growth platforms.

    PubMed

    Laurie, Donald L; Doz, Yves L; Sheer, Claude P

    2006-05-01

    Sooner or later, most companies can't attain the growth rates expected by their boards and CEOs and demanded by investors. To some extent, such businesses are victims of their own successes. Many were able to sustain high growth rates for a long time because they were in high-growth industries. But once those industries slowed down, the businesses could no longer deliver the performance that investors had come to take for granted. Often, companies have resorted to acquisition, though this strategy has a discouraging track record. Over time, 65% of acquisitions destroy more value than they create. So where does real growth come from? For the past 12 years, the authors have been researching and advising companies on this issue. With the support of researchers at Harvard Business School and Insead, they instituted a project titled "The CEO Agenda and Growth". They identified and approached 24 companies that had achieved significant organic growth and interviewed their CEOs, chief strategists, heads of R&D, CFOs, and top-line managers. They asked, "Where does your growth come from?" and found a consistent pattern in the answers. All the businesses grew by creating new growth platforms (NGPs) on which they could build families of products and services and extend their capabilities into multiple new domains. Identifying NGP opportunities calls for executives to challenge conventional wisdom. In all the companies studied, top management believed that NGP innovation differed significantly from traditional product or service innovation. They had independent, senior-level units with a standing responsibility to create NGPs, and their CEOs spent as much as 50% of their time working with these units. The payoff has been spectacular and lasting. For example, from 1985 to 2004, the medical devices company Medtronic grew revenues at 18% per year, earnings at 20%, and market capitalization at 30%.

  9. Establish a Data Transmission Platform of the Rig Based on the Distributed Network

    NASA Astrophysics Data System (ADS)

    Bao, Zefu; Li, Tao

    In order to control in real-time ,closed-loop feedback the information, saving the money and labor,we distribute a platform of network data. It through the establishment of the platform in the oil drilling to achieve the easiest route of each device of the rig that conveying timely. The design proposed the platform to transfer networking data by PA which allows the rig control for optimal use. Against the idea,achieving first through on-site cabling and the establishment of data transmission module in the rig monitoring system. The results of standard field application show that the platform solve the problem of rig control.

  10. HOPSPACK: Hybrid Optimization Parallel Search Package.

    SciTech Connect

    Gray, Genetha Anne.; Kolda, Tamara G.; Griffin, Joshua; Taddy, Matt; Martinez-Canales, Monica L.

    2008-12-01

    In this paper, we describe the technical details of HOPSPACK (Hybrid Optimization Parallel SearchPackage), a new software platform which facilitates combining multiple optimization routines into asingle, tightly-coupled, hybrid algorithm that supports parallel function evaluations. The frameworkis designed such that existing optimization source code can be easily incorporated with minimalcode modification. By maintaining the integrity of each individual solver, the strengths and codesophistication of the original optimization package are retained and exploited.4

  11. Space platform advanced technology study

    NASA Technical Reports Server (NTRS)

    Burns, G.

    1981-01-01

    Current and past space platform and power module studies were utilized to point the way to areas of development for mechanical devices that will be required for the ultimate implementation of a platform erected and serviced by the Shuttle/Orbiter. The study was performed in accordance with a study plan which included: a review of space platform technology; orbiter berthing system requirements; berthing latch interface requirements, design, and model fabrication; berthing umbilical interface requirements and design; adaptive end effector design and model fabrication; and adaptive end effector requirements.

  12. Establishment of a Long-Term Chick Forebrain Neuronal Culture on a Microelectrode Array Platform.

    PubMed

    Kuang, Serena Y; Huang, Ting; Wang, Zhonghai; Lin, Yongliang; Kindy, Mark; Xi, Tingfei; Gao, Bruce Z

    2015-01-01

    The biosensor system formed by culturing primary animal neurons on a microelectrode array (MEA) platform is drawing an increasing research interest for its power as a rapid, sensitive, functional neurotoxicity assessment, as well as for many other electrophysiological related research purposes. In this paper, we established a long-term chick forebrain neuron culture (C-FBN-C) on MEAs with a more than 5 month long lifespan and up to 5 month long stability in morphology and physiological function; characterized the C-FBN-C morphologically, functionally, and developmentally; partially compared its functional features with rodent counterpart; and discussed its pros and cons as a novel biosensor system in comparison to rodent counterpart and human induced pluripotent stem cells (hiPSCs). Our results show that C-FBN-C on MEA platform 1) can be used as a biosensor of its own type in a wide spectrum of basic biomedical research; 2) is of value in comparative physiology in cross-species studies; and 3) may have potential to be used as an alternative, cost-effective approach to rodent counterpart within shared common functional domains (such as specific types of ligand-gated ion channel receptors and subtypes expressed in the cortical tissues of both species) in large-scale environmental neurotoxicant screening that would otherwise require millions of animals.

  13. Programmable data collection platform study

    NASA Technical Reports Server (NTRS)

    1976-01-01

    The results of a feasibility study incorporating microprocessors in data collection platforms in described. An introduction to microcomputer hardware and software concepts is provided. The influence of microprocessor technology on the design of programmable data collection platform hardware is discussed. A standard modular PDCP design capable of meeting the design goals is proposed, and the process of developing PDCP programs is examined. A description of design and construction of the UT PDCP development system is given.

  14. The COMET Sleep Research Platform

    PubMed Central

    Nichols, Deborah A.; DeSalvo, Steven; Miller, Richard A.; Jónsson, Darrell; Griffin, Kara S.; Hyde, Pamela R.; Walsh, James K.; Kushida, Clete A.

    2014-01-01

    Introduction: The Comparative Outcomes Management with Electronic Data Technology (COMET) platform is extensible and designed for facilitating multicenter electronic clinical research. Background: Our research goals were the following: (1) to conduct a comparative effectiveness trial (CET) for two obstructive sleep apnea treatments—positive airway pressure versus oral appliance therapy; and (2) to establish a new electronic network infrastructure that would support this study and other clinical research studies. Discussion: The COMET platform was created to satisfy the needs of CET with a focus on creating a platform that provides comprehensive toolsets, multisite collaboration, and end-to-end data management. The platform also provides medical researchers the ability to visualize and interpret data using business intelligence (BI) tools. Conclusion: COMET is a research platform that is scalable and extensible, and which, in a future version, can accommodate big data sets and enable efficient and effective research across multiple studies and medical specialties. The COMET platform components were designed for an eventual move to a cloud computing infrastructure that enhances sustainability, overall cost effectiveness, and return on investment. PMID:25848590

  15. Building Spatiotemporal Cloud Platform for Supporting GIS Application

    NASA Astrophysics Data System (ADS)

    Song, W. W.; Jin, B. X.; Li, S. H.; Wei, X. Y.; Li, D.; Hu, F.

    2015-07-01

    Traditional geospatial information platforms are built, managed and maintained by the geoinformation agencies. They integrate various geospatial data (such as DLG, DOM, DEM, gazetteers, and thematic data) to provide data analysis services for supporting government decision making. In the era of big data, it is challenging to address the data- and computing- intensive issues by traditional platforms. In this research, we propose to build a spatiotemporal cloud platform, which uses HDFS for managing image data, and MapReduce-based computing service and workflow for high performance geospatial analysis, as well as optimizing auto-scaling algorithms for Web client users' quick access and visualization. Finally, we demonstrate the feasibility by several GIS application cases.

  16. OnCampus: a mobile platform towards a smart campus.

    PubMed

    Dong, Xin; Kong, Xiangjie; Zhang, Fulin; Chen, Zhen; Kang, Jialiang

    2016-01-01

    An increasing number of researchers and practitioners are working to develop smart cities. Considerable attention has been paid to the college campus as it is an important component of smart cities. Consequently, the question of how to construct a smart campus has become a topical one. Here, we propose a scheme that can facilitate the construction of a smart and friendly campus. We primarily focus on three aspects of smart campuses. These are: the formation of social circles based on interests mining, the provision of educational guidance based on emotion analysis of information posted on a platform, and development of a secondary trading platform aimed at optimizing the allocation of campus resources. Based on these objectives, we designed and implemented a mobile platform called OnCampus as the first step towards the development of a smart campus that has been introduced in some colleges. We found that OnCampus could successfully accomplish the three above mentioned functions of a smart campus.

  17. Imaging enabled platforms for development of therapeutics

    NASA Astrophysics Data System (ADS)

    Celli, Jonathan; Rizvi, Imran; Blanden, Adam R.; Evans, Conor L.; Abu-Yousif, Adnan O.; Spring, Bryan Q.; Muzikansky, Alona; Pogue, Brian W.; Finkelstein, Dianne M.; Hasan, Tayyaba

    2011-03-01

    Advances in imaging and spectroscopic technologies have enabled the optimization of many therapeutic modalities in cancer and noncancer pathologies either by earlier disease detection or by allowing therapy monitoring. Amongst the therapeutic options benefiting from developments in imaging technologies, photodynamic therapy (PDT) is exceptional. PDT is a photochemistry-based therapeutic approach where a light-sensitive molecule (photosensitizer) is activated with light of appropriate energy (wavelength) to produce reactive molecular species such as free radicals and singlet oxygen. These molecular entities then react with biological targets such as DNA, membranes and other cellular components to impair their function and lead to eventual cell and tissue death. Development of PDT-based imaging also provides a platform for rapid screening of new therapeutics in novel in vitro models prior to expensive and labor-intensive animal studies. In this study we demonstrate how an imaging platform can be used for strategizing a novel combination treatment strategy for multifocal ovarian cancer. Using an in vitro 3D model for micrometastatic ovarian cancer in conjunction with quantitative imaging we examine dose and scheduling strategies for PDT in combination with carboplatin, a chemotherapeutic agent presently in clinical use for management of this deadly form of cancer.

  18. Membrane technology works on North Sea platform

    SciTech Connect

    O`Donnell, K.

    1996-12-02

    The world`s first sulfate removal facility (SRF) on the Brae A production platform in the central North Sea demonstrates the effectiveness of membrane technology with only a few minor problems caused by the retrofit nature of the installation. This is the second in a three-part series that details experiences with membrane technology on the Brae A platform that future users of this membrane technology can use for optimizing their SRF installations. Formation water in the south and central Brae reservoirs contains very high levels of barium ions. Consequently, there is a high potential for forming barium sulfate scale when Brae formation water is mixed with seawater. Because of high levels of barium, conventional methods for preventing barium sulfate scale with chemical scale inhibitors proved difficult and expensive, and are of limited value for protecting the reservoir matrix. Therefore, the Brae field required a process that could selectively remove sulfate ions from seawater yet retain most other salt components. Reverse osmosis appeared to be one option, and subsequent collaboration with FilmTec identified a membrane that would only pass particles of 1 x 10{sup {minus}9} m (nanofiltration) and smaller. This membrane permitted passage of most sodium and chloride ions but let only a small percentage of sulfate ions through.

  19. Carousel for vertically moored platform

    SciTech Connect

    Beynet, P.A.; Hall, J.E.

    1984-04-24

    This invention involves a modification of the prior art subsea drilling system. A carousel is positioned on a central post surrounded by a coaxial circular array of well slots and is adapted to be rotated by drill pipe through conventional means, from the floating platform. The carousel utilizes a fixed support platform spaced from the axis of rotation a distance equal to the radius of the array of well slots. The platform has its own well slot and a bearing concentric with the well slot. A well slot platform, or support post platform, is journaled in this bearing and supports a plurality of guide posts on a circle centered at the axis of the well slot. The support posts support cables hanging from the drilling vessel, which are used to guide the drill bit down from the surface to the carousel well slot. The carousel is adapted to revolve while supported by circular rails concentric with the central guide post. Means are provided, such as two gears of equal diameter, one fixed to the template concentric with the turning post, the other fixed to the well slot platform, with an intervening pinion so that as the carousel revolves in one direction by a selected angle, the well slot platform and support rods will rotate through an equal angle with respect to the carousel, in the reverse direction. Thus the guide posts and guide cables will always remain with the same azimuth as that of the drill ship. In this way the twisting and tangling of the support cables is avoided.

  20. Design of a Parachute Canopy Instrumentation Platform

    NASA Technical Reports Server (NTRS)

    Alshahin, Wahab M.; Daum, Jared S.; Holley, James J.; Litteken, Douglas A.; Vandewalle, Michael T.

    2015-01-01

    This paper discusses the current technology available to design and develop a reliable and compact instrumentation platform for parachute system data collection and command actuation. Wireless communication with a parachute canopy will be an advancement to the state of the art of parachute design, development, and testing. Embedded instrumentation of the parachute canopy will provide reefing line tension, skirt position data, parachute health monitoring, and other telemetry, further validating computer models and giving engineering insight into parachute dynamics for both Earth and Mars entry that is currently unavailable. This will allow for more robust designs which are more optimally designed in terms of structural loading, less susceptible to adverse dynamics, and may eventually pave the way to currently unattainable advanced concepts of operations. The development of this technology has dual use potential for a variety of other applications including inflatable habitats, aerodynamic decelerators, heat shields, and other high stress environments.

  1. Parallel microwave chemistry in silicon carbide microtiter platforms: a review.

    PubMed

    Kappe, C Oliver; Damm, Markus

    2012-02-01

    In this review, applications of silicon carbide-based microtiter platforms designed for use in combination with dedicated multimode microwave reactors are described. These platforms are employed not only for the efficient parallel synthesis of compound libraries, but also in the context of high-throughput reaction screening/optimization and a number of other (bio)analytical and biomedical applications. Since the semiconducting plate material (silicon carbide) is strongly microwave absorbing and possesses high thermal conductivity, no temperature gradients across the microtiter plate exist. Therefore, many of the disadvantages experienced in attempting to perform microtiter plate chemistry under conventional microwave conditions can be eliminated. In general, the silicon carbide-based microtiter platforms allow sealed vessel processing (either directly in the well or in glass vials placed into the wells) of volumes ranging from 0.02-3.0 mL at a maximum temperature/pressure limit of 200°C/20 bar. Depending on the specific plate and rotor configuration, a maximum of 80-192 transformations can be carried out in parallel in a single microwave irradiation experiment under strict temperature control. A platform type utilizing HPLC/GC vials as reaction vessels allows analysis directly from the reaction vessel eliminating the need for a transfer step from the reaction to the analysis vial. The latter system is particularly useful for analytical applications as well as reaction optimization/screening.

  2. Centrifuge-Based Fluidic Platforms

    NASA Astrophysics Data System (ADS)

    Zoval, Jim; Jia, Guangyao; Kido, Horacio; Kim, Jitae; Kim, Nahui; Madou, Marc

    In this chapter centrifuge-based microfluidic platforms are reviewed and compared with other popular microfluidic propulsion methods. The underlying physical principles of centrifugal pumping in microfluidic systems are presented and the various centrifuge fluidic functions such as valving, decanting, calibration, mixing, metering, heating, sample splitting, and separation are introduced. Those fluidic functions have been combined with analytical measurements techniques such as optical imaging, absorbance and fluorescence spectroscopy and mass spectrometry to make the centrifugal platform a powerful solution for medical and clinical diagnostics and high-throughput screening (HTS) in drug discovery. Applications of a compact disc (CD)-based centrifuge platform analyzed in this review include: two-point calibration of an optode-based ion sensor, an automated immunoassay platform, multiple parallel screening assays and cellular-based assays. The use of modified commercial CD drives for high-resolution optical imaging is discussed as well. From a broader perspective, we compare the technical barriers involved in applying microfluidics for sensing and diagnostic as opposed to applying such techniques to HTS. The latter poses less challenges and explains why HTS products based on a CD fluidic platform are already commercially available, while we might have to wait longer to see commercial CD-based diagnostics.

  3. INL Subsurface Wireless Sensor Platform

    SciTech Connect

    Dennis C. Kunerth; John M. Svoboda; James T. Johnson

    2005-10-01

    The Idaho National Laboratory is developing a versatile micro-power sensor interface platform for periodic subsurface sensing of environmental variables important to waste disposal sites such as volumetric moisture, water potential, and temperature. The key characteristics of the platform architecture are that the platform is passive until externally energized --no internal power source is required -- and that it communicates with a "reader" via short-range telemetry - no wires penetrate the subsurface. Other significant attributes include the potential for a long service life and a compact size that makes it well suited for retrofitting existing landfill structures. Functionally, the sensor package is "read" by a short-range induction coil that activates and powers the sensor platform as well as detects the sensor output via a radio frequency signal generated by the onboard programmable interface controller microchip. As a result, the platform has a functional subsurface communication range of approximately 10 to 12 ft. and can only accept sensors that require low power to operate.

  4. Leasecraft - A commercial space platform

    NASA Astrophysics Data System (ADS)

    Burrowbridge, D. R.

    The Multimission Modular Spacecraft (MMS) is the result of a NASA program concerned with the identification of new approaches to spacecraft design. A mandatory requirement regarding the MMS was flexibility to accommodatae a wide variety of payloads. MMS derived subsystems will provide a platform in low orbit for scientific, commercial, and government users on a leased or service contract basis. The payload may consist of scientific instruments, materials processing equipment, or remote sensors. Secondary payloads may be mounted in standard MMS module boxes. The platform forms a part of the 'Leasecraft' system, which was developed by an American aerospace company. Attention is given to the Leasecraft vehicle, details regarding the Leasecraft platform, and payload accommodations and Leasecraft missions.

  5. Temporal Partitioning on Multicore Platform

    NASA Astrophysics Data System (ADS)

    Mahmud Pathan, Ristat; Hashi, Feysal; Stenstrom, Per; Green, Lars-Goran; Hult, Torbjorn; Sandin, Patrik

    2014-08-01

    This paper addresses the problem of ensuring temporal partitioning according to the ARINC-653 standard for integrating multiple applications on the same multicore platform. To employ temporal partitioning, we propose the design and analysis of a hierarchical scheduling framework (HSF) for multicore platform. In HSF, each application has a server task, which is mapped to one of the physical cores of the multicore platform. The HSF framework is based on scheduling at two-levels: (i) a system-level scheduler for each core schedules the server tasks that are mapped to that core, and (ii) a task- level scheduler for each application schedules the tasks of the application. This paper presents the design and analysis of this two-level HSF that can be used to ensure temporal partitioning and meeting all the deadlines of each application tasks. The effectiveness of our technique is demonstrated using real-world space applications provided by RUAG Space Sweden AB.

  6. Cerveza platforms offer economic options

    SciTech Connect

    Leblanc, L.A.

    1982-08-01

    Two single-piece platforms, Cerveze and Cerveza Ligera, were installed by Union Oil Co. in 925-935 ft of water. The technology and equipment used for the two platforms can be used for units to a depth of 1,400 ft in mild climates and to 1,000 ft in more critical weather areas such as the North Sea. The significant improvements in design and procedures in the construction and installation of the Cerveza Ligera platform are: (1) four leg structure, as opposed to eight, requiring less steel; (2) simplified fabrication; and (3) quicker installation. The most significant area of improvement in the Ligera project compared with Cerveza was in communications. Communications between naval architects and onshore launch foremen during loadout, and between surveyors and tug captains during positioning, are cited as examples.

  7. Persistent Monitoring Platforms Final Report

    SciTech Connect

    Bennett, C L

    2007-02-22

    This project was inspired and motivated by the need to provide better platforms for persistent surveillance. In the years since the inception of this work, the need for persistence of surveillance platforms has become even more widely appreciated, both within the defense community and the intelligence community. One of the most demanding technical requirements for such a platform involves the power plant and energy storage system, and this project concentrated almost exclusively on the technology associated with this system for a solar powered, high altitude, unmanned aircraft. An important realization for the feasibility of such solar powered aircraft, made at the outset of this project, was that thermal energy may be stored with higher specific energy density than for any other known practical form of rechargeable energy storage. This approach has proved to be extraordinarily fruitful, and a large number of spin-off applications of this technology were developed in the course of this project.

  8. Wearable FPGA based wireless sensor platform.

    PubMed

    Ahola, Tom; Korpinen, Pekka; Rakkola, Juha; Rämö, Teemu; Salminen, Jukka; Savolainen, Jari

    2007-01-01

    A new wearable sensor platform has been developed. It is based on a Field Programmable Gate Array (FPGA) device. Because of this the hardware is very flexible and gives the platform unique opportunities for research of a wide range of architectures, applications and signal processing algorithms. The platform has been named NWSP, for Nokia Wrist- Attached Sensor Platform. This document describes the hardware, the firmware and applications of the platform.

  9. Space platform utilities distribution study

    NASA Technical Reports Server (NTRS)

    Lefever, A. E.

    1980-01-01

    Generic concepts for the installation of power data and thermal fluid distribution lines on large space platforms were discussed. Connections with central utility subsystem modules and pallet interfaces were also considered. Three system concept study platforms were used as basepoints for the detail development. The tradeoff of high voltage low voltage power distribution and the impact of fiber optics as a data distribution mechanism were analyzed. Thermal expansion and temperature control of utility lines and ducts were considered. Technology developments required for implementation of the generic distribution concepts were identified.

  10. Multi-Criterion Preliminary Design of a Tetrahedral Truss Platform

    NASA Technical Reports Server (NTRS)

    Wu, K. Chauncey

    1995-01-01

    An efficient method is presented for multi-criterion preliminary design and demonstrated for a tetrahedral truss platform. The present method requires minimal analysis effort and permits rapid estimation of optimized truss behavior for preliminary design. A 14-m-diameter, 3-ring truss platform represents a candidate reflector support structure for space-based science spacecraft. The truss members are divided into 9 groups by truss ring and position. Design variables are the cross-sectional area of all members in a group, and are either 1, 3 or 5 times the minimum member area. Non-structural mass represents the node and joint hardware used to assemble the truss structure. Taguchi methods are used to efficiently identify key points in the set of Pareto-optimal truss designs. Key points identified using Taguchi methods are the maximum frequency, minimum mass, and maximum frequency-to-mass ratio truss designs. Low-order polynomial curve fits through these points are used to approximate the behavior of the full set of Pareto-optimal designs. The resulting Pareto-optimal design curve is used to predict frequency and mass for optimized trusses. Performance improvements are plotted in frequency-mass (criterion) space and compared to results for uniform trusses. Application of constraints to frequency and mass and sensitivity to constraint variation are demonstrated.

  11. Leadership Platforms: Perspectives and Prospects.

    ERIC Educational Resources Information Center

    Norris, Cynthia J.; And Others

    What leaders encourage others to do must be congruent with the values they espouse and demonstrate through action. The educational leadership platform has recently been used as a tool to assist aspiring leaders in clarifying their personal values. This paper presents findings of a study that explored the effect of the educational leadership…

  12. 2009 Analysis Platform Review Report

    SciTech Connect

    Ferrell, John

    2009-12-01

    This document summarizes the recommendations and evaluations provided by an independent external panel of experts at the U.S. Department of Energy Biomass Program’s Analysis platform review meeting, held on February 18, 2009, at the Marriott Residence Inn, National Harbor, Maryland.

  13. NAESP 2009-2010 Platform

    ERIC Educational Resources Information Center

    National Association of Elementary School Principals (NAESP), 2010

    2010-01-01

    The NAESP (National Association of Elementary School Principals) Platform consists of a summary of all resolutions adopted by business meetings and, since 1974, by Delegate Assemblies. Each resolution presented for action by the Delegate Assembly carries with it a rationale for its adoption as well as the specific area and section of the Platform…

  14. Earth Science Geostationary Platform Technology

    NASA Technical Reports Server (NTRS)

    Wright, Robert L. (Editor); Campbell, Thomas G. (Editor)

    1989-01-01

    The objective of the workshop was to address problems in science and in four technology areas (large space antenna technology, microwave sensor technology, electromagnetics-phased array adaptive systems technology, and optical metrology technology) related to Earth Science Geostationary Platform missions.

  15. 2009 Feedstocks Platform Review Report

    SciTech Connect

    Ferrell, John

    2009-12-01

    This document summarizes the recommendations and evaluations provided by an independent external panel of experts at the U.S. Department of Energy Biomass Program‘s Feedstock platform review meeting, held on April 8–10, 2009, at the Grand Hyatt Washington, Washington, D.C.

  16. Long range hopping mobility platform.

    SciTech Connect

    Spletzer, Barry Louis; Fischer, Gary John

    2003-03-01

    Sandia National Laboratories has developed a mesoscale hopping mobility platform (Hopper) to overcome the longstanding problems of mobility and power in small scale unmanned vehicles. The system provides mobility in situations such as negotiating tall obstacles and rough terrain that are prohibitive for other small ground base vehicles. The Defense Advanced Research Projects Administration (DARPA) provided the funding for the hopper project.

  17. 2009 Infrastructure Platform Review Report

    SciTech Connect

    Ferrell, John

    2009-12-01

    This document summarizes the recommendations and evaluations provided by an independent external panel of experts at the U.S. Department of Energy Biomass program‘s Infrastructure platform review meeting, held on February 19, 2009, at the Marriott Residence Inn, National Harbor, Maryland.

  18. The Platform Design of Space-based Optical Observations of Space Debris

    NASA Astrophysics Data System (ADS)

    Chen, B. R.; Xiong, J. N.

    2016-03-01

    The basic design method of the platform for the space-based optical observations of space debris is introduced. The observation schemes of GEO (geosynchronous equatorial orbit) and LEO (low Earth orbit) debris are given respectively, including orbital parameters of platforms and pointing of telescopes, etc. Debris studied here is all from foreign catalog. According to the real orbit of space debris, the observational results of different schemes are simulated. By studying single platform, the optimal observing altitude for GEO debris and the optimal telescope's deflection angles at different altitudes for LEO debris are given. According to these, multi-platforms observation networks are designed. By analyzing the advantages and disadvantages of each scheme, it can provide reference for the application of space-based optical debris observation.

  19. The Platform Design of Space-based Optical Observations of Space Debris

    NASA Astrophysics Data System (ADS)

    Bing-er, Chen; Jian-ning, Xiong

    2017-01-01

    The basic method to design a platform for the space-based optical observations of space debris is introduced. The observation schemes of GEO (geosynchronous equatorial orbit) and LEO (low Earth orbit) debris are given respectively, including the orbital parameters of platforms and the pointing of telescopes, etc. The debris studied here are all taken from the foreign catalog. According to the real orbits of space debris, the observational results of different schemes are simulated. By studying the single platform, the optimal observing altitude for the GEO debris and the optimal telescope's deflection angles at different altitudes for the LEO debris are given. According to these, the multi-platform observation networks are designed. By analyzing the advantages and disadvantages of different schemes, it can provide a reference for the application of space-based optical observations of space debris

  20. Optimal exploration systems

    NASA Astrophysics Data System (ADS)

    Klesh, Andrew T.

    This dissertation studies optimal exploration, defined as the collection of information about given objects of interest by a mobile agent (the explorer) using imperfect sensors. The key aspects of exploration are kinematics (which determine how the explorer moves in response to steering commands), energetics (which determine how much energy is consumed by motion and maneuvers), informatics (which determine the rate at which information is collected) and estimation (which determines the states of the objects). These aspects are coupled by the steering decisions of the explorer. We seek to improve exploration by finding trade-offs amongst these couplings and the components of exploration: the Mission, the Path and the Agent. A comprehensive model of exploration is presented that, on one hand, accounts for these couplings and on the other hand is simple enough to allow analysis. This model is utilized to pose and solve several exploration problems where an objective function is to be minimized. Specific functions to be considered are the mission duration and the total energy. These exploration problems are formulated as optimal control problems and necessary conditions for optimality are obtained in the form of two-point boundary value problems. An analysis of these problems reveals characteristics of optimal exploration paths. Several regimes are identified for the optimal paths including the Watchtower, Solar and Drag regime, and several non-dimensional parameters are derived that determine the appropriate regime of travel. The so-called Power Ratio is shown to predict the qualitative features of the optimal paths, provide a metric to evaluate an aircrafts design and determine an aircrafts capability for flying perpetually. Optimal exploration system drivers are identified that provide perspective as to the importance of these various regimes of flight. A bank-to-turn solar-powered aircraft flying at constant altitude on Mars is used as a specific platform for

  1. Auger tension leg platform cathodic protection system

    SciTech Connect

    Goolsby, A.D.; Smith, J.D.

    1995-11-01

    In 1986, Shell began investigating corrosion control systems for a generic 3,000 ft. water depth Tension Leg Platform (TLP) type structure to be located in the north-central Gulf of Mexico. In 1987, the 2,850 ft. deep Garden Banks block 426 ``Auger`` location was chosen for the first TLP, and the detailed design process began in earnest. During late 1993 and early 1994, the Auger hull was mated with the other components at its permanent site, and first oil and gas production began April 15, 1994. This paper describes the corrosion control design for the exterior submerged and buried steel surfaces of the 2,850 ft. (869 m) water depth Auger Tension Leg Platform structure. Each major type of component (hull, subsea marine wellhead/guidebase, tendon foundation template, tendon, and production riser) has its own combination of coating system and cathodic protection system designed for a thirty five year lifetime. Cathodic protection (CP) is achieved using a variety of sacrificial anode alloys and geometries (e.g. bracelet, flush-mount, and standoff anodes). Anode and cathode CP design parameters for each component depend upon water depth, and were developed using field test data, laboratory studies, field measurements on existing structures, and available literature information. CP design was performed using design spreadsheets constructed for each component, which optimized anode geometries. Extensive quality assurance efforts were part of the anode procurement process, to ensure performance for the intended life of the corrosion-control systems. Results of early in-service CP surveys of the tendons and guidebases are presented, showing the successful achievement of cathodic protection against seawater corrosion. Corrosion control of one additional system, the eight point lateral mooring system, is not addressed here.

  2. Multi-platform laser communication networking optical antenna system design

    NASA Astrophysics Data System (ADS)

    Zhang, Tao

    2016-10-01

    In this paper, a new conclusion based on rotating parabolic model and a different scheme of laser communication networking antenna system has been put forward in the paper. Based on rotating parabolic antenna, a new theory of the optical properties have been deduced, which can realize larger dynamic, duplex, networking communications among multiple platforms in 360° azimuth and pitch range. Meanwhile, depending on the operation mode of the system, multiple mathematical optimization models have been established. Tracking communication range, emission energy efficiency and receiving energy efficiency have been analyzed and optimized. Relationship among opening up and low apertures, the lens unit aperture, focal length of lens unit as well as rotating parabolic focal length have been analyzed. Tracking pitching range and emission energy utilization has carried on the theoretical derivation and optimization and networking platform link between energy receiver and transmitter has been analyzed. Taking some parameters of this new system into calculation, optimized results can be utilized with MATLAB software for its application and system of communication engineering. The rotating parabolic internal can form a hollow structure, which is utilized for miniaturization, light-weighted design and realize duplex communication in a wide range and distance. Circular orbit guidance is the modern way used in dynamic tracking system. The new theory and optical antenna system has widespread applications value as well.

  3. COMPASS: an efficient, scalable and versatile numerical platform for the development of ELT AO systems

    NASA Astrophysics Data System (ADS)

    Gratadour, D.; Puech, M.; Vérinaud, C.; Kestener, P.; Gray, M.; Petit, C.; Brulé, J.; Clénet, Y.; Ferreira, F.; Gendron, E.; Lainé, M.; Sevin, A.; Rousset, G.; Hammer, F.; Jégouzo, I.; Paillous, Michele; Taburet, S.; Yang, Y.; Beuzit, J.-L.; Carlotti, A.; Westphal, M.; Epinat, B.; Ferrari, M.; Gautrais, T.; Lambert, J. C.; Neichel, B.; Rodionov, S.

    2014-08-01

    The main objective of the COMPASS project is to provide a full scale end-to-end AO development platform, able to address the E-ELT scale and designed as a free, open source numerical tool with a long term maintenance plan. The development of this platform is based on a full integration of software with hardware and relies on an optimized implementation on heterogeneous hardware using GPUs as accelerators. In this paper, we present the overall platform, the various work packages of this project, the milestones to be reached, the results already obtained and the first output of the ongoing collaborations.

  4. Open-WiSe: a solar powered wireless sensor network platform.

    PubMed

    González, Apolinar; Aquino, Raúl; Mata, Walter; Ochoa, Alberto; Saldaña, Pedro; Edwards, Arthur

    2012-01-01

    Because battery-powered nodes are required in wireless sensor networks and energy consumption represents an important design consideration, alternate energy sources are needed to provide more effective and optimal function. The main goal of this work is to present an energy harvesting wireless sensor network platform, the Open Wireless Sensor node (WiSe). The design and implementation of the solar powered wireless platform is described including the hardware architecture, firmware, and a POSIX Real-Time Kernel. A sleep and wake up strategy was implemented to prolong the lifetime of the wireless sensor network. This platform was developed as a tool for researchers investigating Wireless sensor network or system integrators.

  5. Earth science vision: Platform technology challenges

    NASA Technical Reports Server (NTRS)

    Lemmerman, L.; Delin, K.; Hadaegh, F.; Lou, M.; Bhasin, K.; Bristow, J.; Connerton, R.; Pasciuto, M.

    2001-01-01

    Advanced new platform technologies are critical to the realization of the Earth Science Vision in the 2020 timeframe. Examples of the platform technology challenges and current state-of-the-art capabilities are present.

  6. Submerged tank aids platform stability

    SciTech Connect

    Compagnon, J.P.

    1985-05-01

    A new floating platform concept, proposed for the installation of a new lighthouse, 64 km off Ouessant Island, northwest France, in water 130 meters deep, is described. A series of model tests carried out in test tanks in 1983 demonstrated that this new concept is viable in the offshore business as an alternative for deep and rough seas. The key to the success of this design is primarily the location and shape of a large, submerged buoyancy tank - a floater sandwiched between a conventional rig topside and a rigid, vertically suspended counter-weight. The floater balanced by a counter-weight acts as a damper and minimizes the effect of most wave action. This configuration permits a considerable gain in structure weight, improves stability and allows the structure to support a very high deck load with or without storage facilities when used as a production platform.

  7. Stabilisation problem in biaxial platform

    NASA Astrophysics Data System (ADS)

    Lindner, Tymoteusz; Rybarczyk, Dominik; Wyrwał, Daniel

    2016-12-01

    The article describes investigation of rolling ball stabilization problem on a biaxial platform. The aim of the control system proposed here is to stabilize ball moving on a plane in equilibrium point. The authors proposed a control algorithm based on cascade PID and they compared it with another control method. The article shows the results of the accuracy of ball stabilization and influence of applied filter on the signal waveform. The application used to detect the ball position measured by digital camera has been written using a cross platform .Net wrapper to the OpenCV image processing library - EmguCV. The authors used the bipolar stepper motor with dedicated electronic controller. The data between the computer and the designed controller are sent with use of the RS232 standard. The control stand is based on ATmega series microcontroller.

  8. Radio interferometry from space platforms

    NASA Technical Reports Server (NTRS)

    Roberts, D. H.; Morgan, S. H.; Burke, B. F.; Jordan, J. F.; Preston, R. A.; Hamilton, E. C.

    1984-01-01

    While current VLBI observations are limited in their resolution by the earth diameter magnitude, which is the largest antenna separation available, as well as in their information content, because of the small number of antennas in use at a given time, the extension of VLBI to include one or more antennas in space will relieve both constraints and help to map distant radio sources with the highest possible resolution. Attention is given to the implementation of such an orbital VLBI system extension through (1) a Shuttle-launch mission, (2) a six-month to one-year near earth orbit mission based on a space platform associated with the Space Station, (3) a large orbit free flyer platform mission of more than 2-year duration, and (4) lunar and/or deep space orbits, aimed at reaching the resolution limits set by interstellar scattering.

  9. Shallow waters require platform innovation

    SciTech Connect

    Not Available

    1984-11-01

    Conventional platform designs generally apply to production facilities for relatively shallow-water oil and gas fields and consequently do not attract much attention in the offshore industry. But although new designs relate largely to deeper waters, specific requirements of a particular field in shallow water may well force designers to search for unconventional designs to meet a need for lower costs and rapid development. A central production facility is planned offshore at the drilling location AWG-1, approximately 3 km offshore and in a water depth of about six meters. The choice is governed by the optimum interfield pipeline configuration available at the AWG-1 location, taking into account the other locations required for adequate subsea well coverage. The platform is described.

  10. Offshore drilling platform protection device

    SciTech Connect

    Magill, J.M.

    1981-12-15

    A description is given of an offshore drilling platform protection device for use on an offshore oil well drilling vessel including a drilling platform supportable on a plurality of extendable legs wherein each leg is moved by a rack gear assembly. The rack gear assembly includes an otherwise exposed first gear which engages a second gear positioned in a housing having a rectangular corner opening through which the first gear extends, the protection device including first and second protective sections adapted for mounting over the first gear adjacent to the rectangular corner of the housing for the second gear, the first and second protective sections cooperating to provide an l-shaped opening which communicates with the opening at the second gear housing for protecting the first gear while allowing the first gear to mesh with the second gear.

  11. Science and Applications Space Platforms

    NASA Astrophysics Data System (ADS)

    Nein, Max E.; Ballance, James O.

    1981-04-01

    The advent of the "Space Shuttle Era" has spearheaded a new wave of thought in our approach to the exploitation of space. Through use of the Shuttle, science and applications payloads need no longer be abandoned at the scheduled end of a particular mission, or when struck with premature failure, or even when they simply become outdated through advancements in technology. Rather the option will now exist for on-orbit maintenance and/or recovery of the payload for potential reuse. The Shuttle itself can even serve as an operational base for the gathering of data. This will be accomplished primarily through the use of Spacelab and a multitude of "Spacelab Instruments," many of which are already being developed. Additionally, the Shuttle along with other members of the Space Transportation Systems. family, will allow the buildup of space structures which can be routinely maintained on-orbit, thereby allowing long-term technical and economic exploitation. One such structure being given increased consideration for use in Low Earth Orbit (LEO) is the "Space Platform." Such platforms are envisioned to have lifetimes of many years and to provide basic stability, various utilities, and on-orbit accessibility to a number of temporarily emplaced payloads. Some payloads, depending on the mission for which they are being flown, would operate from a few weeks or months to many years. This paper reports current planning efforts by NASA for these space platforms directed towards determining the technically most suitable concepts and the approaches which might be followed to evolve these platforms as a cost-effective extension of the Spacelab era.

  12. Modular Platforms for Optofluidic Systems

    NASA Astrophysics Data System (ADS)

    Brammer, Marko; Mappes, Timo

    2013-02-01

    Optofluidics is increasingly gaining impact in a number of different fields of research, namely biology and medicine, environmental monitoring and green energy. However, the market for optofluidic products is still in the early development phase. In this manuscript, we discuss modular platforms as a potential concept to facilitate the transfer of optofluidic sensing systems to an industrial implementation. We present microfluidic and optical networks as a basis for the interconnection of optofluidic sensor modules. Finally, we show the potential for entire optofluidic networks.

  13. Modular Platforms for Optofluidic Systems

    NASA Astrophysics Data System (ADS)

    Brammer, Marko; Mappes, Timo

    2014-01-01

    Optofluidics is increasingly gaining impact in a number of different fields of research, namely biology and medicine, environmental monitoring and green energy. However, the market for optofluidic products is still in the early development phase. In this manuscript, we discuss modular platforms as a potential concept to facilitate the transfer of optofluidic sensing systems to an industrial implementation. We present microfluidic and optical networks as a basis for the interconnection of optofluidic sensor modules. Finally, we show the potential for entire optofluidic networks

  14. A "clickable" titanium surface platform.

    PubMed

    Watson, Matthew A; Lyskawa, Joël; Zobrist, Cédric; Fournier, David; Jimenez, Maude; Traisnel, Michel; Gengembre, Léon; Woisel, Patrice

    2010-10-19

    A straightforward functionalization of a titanium surface using "click" chemistry is reported. A "clickable" titanium surface platform was prepared by the immobilization of an azide-functionalized electroactive catechol anchor and was subsequently derivatized with an electroactive or fluorinated probe via the CuAAC (copper-catalyzed azide-alkyne cycloaddition) reaction. The course of the reaction was investigated by contact angle, XPS, and electrochemical measurements.

  15. Clean access platform for orbiter

    NASA Technical Reports Server (NTRS)

    Morrison, H.; Harris, J.

    1990-01-01

    The design of the Clean Access Platform at the Kennedy Space Center, beginning with the design requirements and tracing the effort throughout development and manufacturing is described. Also examined are: (1) A system description; (2) Testing requirements and conclusions; (3) Safety and reliability features; (4) Major problems experienced during the project; and (5) Lessons learned, including features necessary for the effective design of mechanisms used in clean systems.

  16. Trajectory Optimization: OTIS 4

    NASA Technical Reports Server (NTRS)

    Riehl, John P.; Sjauw, Waldy K.; Falck, Robert D.; Paris, Stephen W.

    2010-01-01

    The latest release of the Optimal Trajectories by Implicit Simulation (OTIS4) allows users to simulate and optimize aerospace vehicle trajectories. With OTIS4, one can seamlessly generate optimal trajectories and parametric vehicle designs simultaneously. New features also allow OTIS4 to solve non-aerospace continuous time optimal control problems. The inputs and outputs of OTIS4 have been updated extensively from previous versions. Inputs now make use of objectoriented constructs, including one called a metastring. Metastrings use a greatly improved calculator and common nomenclature to reduce the user s workload. They allow for more flexibility in specifying vehicle physical models, boundary conditions, and path constraints. The OTIS4 calculator supports common mathematical functions, Boolean operations, and conditional statements. This allows users to define their own variables for use as outputs, constraints, or objective functions. The user-defined outputs can directly interface with other programs, such as spreadsheets, plotting packages, and visualization programs. Internally, OTIS4 has more explicit and implicit integration procedures, including high-order collocation methods, the pseudo-spectral method, and several variations of multiple shooting. Users may switch easily between the various methods. Several unique numerical techniques such as automated variable scaling and implicit integration grid refinement, support the integration methods. OTIS4 is also significantly more user friendly than previous versions. The installation process is nearly identical on various platforms, including Microsoft Windows, Apple OS X, and Linux operating systems. Cross-platform scripts also help make the execution of OTIS and post-processing of data easier. OTIS4 is supplied free by NASA and is subject to ITAR (International Traffic in Arms Regulations) restrictions. Users must have a Fortran compiler, and a Python interpreter is highly recommended.

  17. Graph processing platforms at scale: practices and experiences

    SciTech Connect

    Lim, Seung-Hwan; Lee, Sangkeun; Brown, Tyler C; Sukumar, Sreenivas R; Ganesh, Gautam

    2015-01-01

    Graph analysis unveils hidden associations of data in many phenomena and artifacts, such as road network, social networks, genomic information, and scientific collaboration. Unfortunately, a wide diversity in the characteristics of graphs and graph operations make it challenging to find a right combination of tools and implementation of algorithms to discover desired knowledge from the target data set. This study presents an extensive empirical study of three representative graph processing platforms: Pegasus, GraphX, and Urika. Each system represents a combination of options in data model, processing paradigm, and infrastructure. We benchmarked each platform using three popular graph operations, degree distribution, connected components, and PageRank over a variety of real-world graphs. Our experiments show that each graph processing platform shows different strength, depending the type of graph operations. While Urika performs the best in non-iterative operations like degree distribution, GraphX outputforms iterative operations like connected components and PageRank. In addition, we discuss challenges to optimize the performance of each platform over large scale real world graphs.

  18. Bacterial fermentation platform for producing artificial aromatic amines

    PubMed Central

    Masuo, Shunsuke; Zhou, Shengmin; Kaneko, Tatsuo; Takaya, Naoki

    2016-01-01

    Aromatic amines containing an aminobenzene or an aniline moiety comprise versatile natural and artificial compounds including bioactive molecules and resources for advanced materials. However, a bio-production platform has not been implemented. Here we constructed a bacterial platform for para-substituted aminobenzene relatives of aromatic amines via enzymes in an alternate shikimate pathway predicted in a Pseudomonad bacterium. Optimization of the metabolic pathway in Escherichia coli cells converted biomass glucose to 4-aminophenylalanine with high efficiency (4.4 g L−1 in fed-batch cultivation). We designed and produced artificial pathways that mimicked the fungal Ehrlich pathway in E. coli and converted 4-aminophenylalanine into 4-aminophenylethanol and 4-aminophenylacetate at 90% molar yields. Combining these conversion systems or fungal phenylalanine decarboxylases, the 4-aminophenylalanine-producing platform fermented glucose to 4-aminophenylethanol, 4-aminophenylacetate, and 4-phenylethylamine. This original bacterial platform for producing artificial aromatic amines highlights their potential as heteroatoms containing bio-based materials that can replace those derived from petroleum. PMID:27167511

  19. Communications platform payload definition study

    NASA Technical Reports Server (NTRS)

    Clopp, H. W.; Hawkes, T. A.; Bertles, C. R.; Pontano, B. A.; Kao, T.

    1986-01-01

    Large geostationary communications platforms were investigated in a number of studies since 1974 as a possible means to more effectively utilize the geostationary arc and electromagnetic spectrum and to reduce overall satellite communications system costs. The commercial feasibility of various communications platform payload concepts circa 1998 was addressed. Promising payload concepts were defined, recurring costs were estimated, and critical technologies needed to enable eventual commercialization were identified. Ten communications service aggregation scenarios describing potential groupings of service were developed for a range of conditions. Payload concepts were defined for four of these scenarios: (1) Land Mobile Satellite Service (LMSS) meets 100% of Contiguous United States (CONUS) plus Canada demand with a single platform; (2) Fixed Satellite Service (FSS) (trunking + Customer Premises Service (CPS)), meet 20% of CONUS demand;(3) FSS (trunking + CPS + video distribution), 10 to 13% of CONUS demand; and (4) FSS (20% of demand) + Inter Satellite Links (ISL) + Tracking and Data Relay Satellite System (TDRSS)/Tracking and Data Acquisition System (TDAS) Data Distribution.

  20. Smart Water: Energy-Water Optimization in Drinking Water Systems

    EPA Science Inventory

    This project aims to develop and commercialize a Smart Water Platform – Sensor-based Data-driven Energy-Water Optimization technology in drinking water systems. The key technological advances rely on cross-platform data acquisition and management system, model-based real-time sys...

  1. Unmanned Instrument Platform for Undersea Exploration

    NASA Technical Reports Server (NTRS)

    Paine, G.; Hansen, G. R.; Gulizia, R. W.; Paluzzi, P.

    1984-01-01

    Instruments accommodated on moving underwater platform. Towable underwater platform 3.2 meters long, 1.2 meters wide, 1.4 meters high and has mass of about 1,250 kilogram. Platform remotely operated and unmanned. Serves as test bed for development of ocean-measuring instruments and sonars at depths to 20,000 feet.

  2. Lightweight Integrated Optical Sensor for Atmospheric Measurements on Mobile Platforms

    SciTech Connect

    Parameswaran, Krishnan R.

    2013-12-02

    The goal of the Phase I program was to develop a novel open path sensor platform technology based on integration of semiconductor waveguides with efficient optoelectronic components on a monolithic platform. The successful Phase I effort resulted in demonstration of a novel optical resonator structure based on semiconductor high contrast gratings (HCGs) that will enable implementation of an ultra-compact, low-power gas sensor suitable for use on mobile platforms. Extensive numerical modeling was performed to design a device optimized for measuring CO2 at a wavelength for which a laser was available for proof of concept. Devices were fabricated and tested to match the target wavelength, angle, and operating temperature. This demonstration is the first implementation of HCGs at the wavelengths of interest and shows the flexibility of the proposed architecture for gas sensing applications. The measured cavity Q was lower than anticipated due to fabrication process challenges. The PSI and UC Berkeley team has identified solutions to these challenges and will produce optimized devices in a Phase II program where a prototype sensor will be fabricated and tested.

  3. Evaluating the enhancement and improvement of China's technology and financial services platform innovation strategy.

    PubMed

    Wu, Ching-Sung; Hu, Kuang-Hua; Chen, Fu-Hsiang

    2016-01-01

    The development of high-tech industry has been prosperous around the world in past decades, while technology and finance have already become the most significant issues in the information era. While high-tech firms are a major force behind a country's economic development, it requires a lot of money for the development process, as well as the financing difficulties for its potential problems, thus, how to evaluate and establish appropriate technology and financial services platforms innovation strategy has become one of the most critical and difficult issues. Moreover, how the chosen intertwined financial environment can be optimized in order that high-tech firms financing problems can be decided has seldom been addressed. Thus, this research aims to establish a technology and financial services platform innovation strategy improvement model, as based on the hybrid MADM model, which addresses the main causal factors and amended priorities in order to strengthen ongoing planning. A DEMATEL technique, as based on Analytic Network Process, as well as modified VIKOR, will be proposed for selecting and re-configuring the aspired technology and financial services platform. An empirical study, as based on China's technology and financial services platform innovation strategy, will be provided for verifying the effectiveness of this proposed methodology. Based on expert interviews, technology and financial services platforms innovation strategy improvement should be made in the following order: credit guarantee platform (C)_credit rating platform (B)_investment and finance platform (A).

  4. Development of an ASP (Air Stabilized Platform)

    NASA Astrophysics Data System (ADS)

    Seidl, L. H.

    1980-07-01

    A type of platform termed Air Stabilized Platform or ASP for short, was developed. The effect of the compressibility of air was given in terms of an air pocket factor f sub air. Functional relationships for f sub air with respect to internal draft of the airpocket and its geometry are developed. Several generic platform designs based on the ASP concept were designed and model tested. The platforms were moored by spread mooring, tension leg mooring or were free floating. Realistic applications of the ASP as support platforms for floating industrial plants were considered.

  5. Advanced propulsion for LEO and GEO platforms

    NASA Technical Reports Server (NTRS)

    Sovey, James S.; Pidgeon, David J.

    1990-01-01

    Mission requirements and mass savings applicable to specific low earth orbit and geostationary earth orbit platforms using three highly developed propulsion systems are described. Advanced hypergolic bipropellant thrusters and hydrazine arcjets can provide about 11 percent additional instrument payload to 14,000 kg LEO platforms. By using electric propulsion on a 8,000 kg class GEO platform, mass savings in excess of 15 percent of the beginning-of-life platform mass are obtained. Effects of large, advanced technology solar arrays and antennas on platform propulsion requirements are also discussed.

  6. Toward Optimal Transport Networks

    NASA Technical Reports Server (NTRS)

    Alexandrov, Natalia; Kincaid, Rex K.; Vargo, Erik P.

    2008-01-01

    Strictly evolutionary approaches to improving the air transport system a highly complex network of interacting systems no longer suffice in the face of demand that is projected to double or triple in the near future. Thus evolutionary approaches should be augmented with active design methods. The ability to actively design, optimize and control a system presupposes the existence of predictive modeling and reasonably well-defined functional dependences between the controllable variables of the system and objective and constraint functions for optimization. Following recent advances in the studies of the effects of network topology structure on dynamics, we investigate the performance of dynamic processes on transport networks as a function of the first nontrivial eigenvalue of the network's Laplacian, which, in turn, is a function of the network s connectivity and modularity. The last two characteristics can be controlled and tuned via optimization. We consider design optimization problem formulations. We have developed a flexible simulation of network topology coupled with flows on the network for use as a platform for computational experiments.

  7. Zero-Net Power, Low-Cost Sensor Platform

    SciTech Connect

    Hardy, J.E.

    2005-04-15

    Numerous national studies and working groups have identified very low-power, low-cost sensors as a critical technology for increasing energy efficiency, reducing waste, and optimizing processes. This research addressed that need by developing an ultra low-power, low-cost sensor platform based on microsensor (MS) arrays that includes MS sensors, very low-power electronics, signal processing, and two-way data communications, all integrated into a single package. MSs were developed to measure carbon dioxide and room occupancy. Advances were made in developing a coating for detecting carbon dioxide and sensing thermal energy with MSs with a low power electrical readout. In addition, robust algorithms were developed for communications within buildings over power lines and an integrated platform was realized that included gas sensing, temperature, humidity, and room occupancy with on-board communications.

  8. Turbine engine airfoil and platform assembly

    DOEpatents

    Campbell, Christian X [Oviedo, FL; James, Allister W [Chuluota, FL; Morrison, Jay A [Oviedo, FL

    2012-07-31

    A turbine airfoil (22A) is formed by a first process using a first material. A platform (30A) is formed by a second process using a second material that may be different from the first material. The platform (30A) is assembled around a shank (23A) of the airfoil. One or more pins (36A) extend from the platform into holes (28) in the shank (23A). The platform may be formed in two portions (32A, 34A) and placed around the shank, enclosing it. The two platform portions may be bonded to each other. Alternately, the platform (30B) may be cast around the shank (23B) using a metal alloy with better castability than that of the blade and shank, which may be specialized for thermal tolerance. The pins (36A-36D) or holes for them do not extend to an outer surface (31) of the platform, avoiding stress concentrations.

  9. The evolution of the geostationary platform concept

    NASA Technical Reports Server (NTRS)

    Edelson, Burton I.; Lovell, Robert R.; Cuccia, C. Louis

    1987-01-01

    The paper will review the conceptual development over the last decade of the use of very large spacecraft, i.e., 'platforms', in geostationary orbit. Geostationary platforms were originally conceived as an efficient means of increasing the capacity at a point in the geostationary orbital arc. Also, geostationary platforms have been suggested for mounting very large antennas as will be required for mobile communications, or high power sources as will be required for broadcast services to small terminals. More recently these 'large satellite' platforms were also envisioned as including earth observation and other science payloads. The advent of the Space Station, which can provide a staging base for platform assembly and test in space at low earth orbit prior to launch to geostationary earth orbit, will introduce a new dimension to practical platform design. This paper describes the evolution of concepts for geostationary platforms over the last decade based on both communications and science user scenarios developed worldwide.

  10. StreptoBase: An Oral Streptococcus mitis Group Genomic Resource and Analysis Platform

    PubMed Central

    Zheng, Wenning; Paterson, Ian C.; Mutha, Naresh V. R.; Siow, Cheuk Chuen; Tan, Shi Yang; Old, Lesley A.; Jakubovics, Nicholas S.; Choo, Siew Woh

    2016-01-01

    The oral streptococci are spherical Gram-positive bacteria categorized under the phylum Firmicutes which are among the most common causative agents of bacterial infective endocarditis (IE) and are also important agents in septicaemia in neutropenic patients. The Streptococcus mitis group is comprised of 13 species including some of the most common human oral colonizers such as S. mitis, S. oralis, S. sanguinis and S. gordonii as well as species such as S. tigurinus, S. oligofermentans and S. australis that have only recently been classified and are poorly understood at present. We present StreptoBase, which provides a specialized free resource focusing on the genomic analyses of oral species from the mitis group. It currently hosts 104 S. mitis group genomes including 27 novel mitis group strains that we sequenced using the high throughput Illumina HiSeq technology platform, and provides a comprehensive set of genome sequences for analyses, particularly comparative analyses and visualization of both cross-species and cross-strain characteristics of S. mitis group bacteria. StreptoBase incorporates sophisticated in-house designed bioinformatics web tools such as Pairwise Genome Comparison (PGC) tool and Pathogenomic Profiling Tool (PathoProT), which facilitate comparative pathogenomics analysis of Streptococcus strains. Examples are provided to demonstrate how StreptoBase can be employed to compare genome structure of different S. mitis group bacteria and putative virulence genes profile across multiple streptococcal strains. In conclusion, StreptoBase offers access to a range of streptococci genomic resources as well as analysis tools and will be an invaluable platform to accelerate research in streptococci. Database URL: http://streptococcus.um.edu.my. PMID:27138013

  11. Spacecraft platform cost estimating relationships

    NASA Technical Reports Server (NTRS)

    Gruhl, W. M.

    1972-01-01

    The three main cost areas of unmanned satellite development are discussed. The areas are identified as: (1) the spacecraft platform (SCP), (2) the payload or experiments, and (3) the postlaunch ground equipment and operations. The SCP normally accounts for over half of the total project cost and accurate estimates of SCP costs are required early in project planning as a basis for determining total project budget requirements. The development of single formula SCP cost estimating relationships (CER) from readily available data by statistical linear regression analysis is described. The advantages of single formula CER are presented.

  12. Education Platform at ZDM8

    PubMed Central

    Lyman Gingerich, Jamie S.; Pickart, Michael A.

    2016-01-01

    Abstract Interest among the zebrafish community in education and science accessibility for all ages has increased. At the 8th Annual Zebrafish Disease Models Conference (ZDM8), a specifically designed session enabled professional scientists, educators, and students to have a venue to present their science, discuss ideas in education, and partner to navigate a scientific meeting as an educational experience. This meeting report describes the format of the Platform Session as well as challenges and future plans to leverage impact of conferences on the local communities. PMID:26982162

  13. Optimizing Locomotion

    NASA Astrophysics Data System (ADS)

    Hosoi, Anette

    2006-11-01

    In this talk we will discuss two optimization topics related to low Reynolds number locomotion: optimal stroke patterns in linked swimmers and optimal fluid material properties in adhesive locomotion. In contrast to many optimization problems, we do not consider geometry, rather we optimize the swimming kinematics or fluid material properties for a given geometrical configuration. In the first case, we begin by optimizing stroke patterns for Purcell's 3-link swimmer. We model the swimmer as a jointed chain of three slender links moving in an inertialess flow. The swimmer is optimized for both efficiency and speed. In the second case, we analyze the adhesive locomotion used by common gastropods such as snails and slugs. Such organisms crawl on a solid substrate by propagating muscular waves of shear stress on a viscoelastic mucus. Using a simple mechanical model, we derive criteria for favorable fluid material properties to lower the energetic cost of locomotion.

  14. BESIU Physical Analysis on Hadoop Platform

    NASA Astrophysics Data System (ADS)

    Huo, Jing; Zang, Dongsong; Lei, Xiaofeng; Li, Qiang; Sun, Gongxing

    2014-06-01

    In the past 20 years, computing cluster has been widely used for High Energy Physics data processing. The jobs running on the traditional cluster with a Data-to-Computing structure, have to read large volumes of data via the network to the computing nodes for analysis, thereby making the I/O latency become a bottleneck of the whole system. The new distributed computing technology based on the MapReduce programming model has many advantages, such as high concurrency, high scalability and high fault tolerance, and it can benefit us in dealing with Big Data. This paper brings the idea of using MapReduce model to do BESIII physical analysis, and presents a new data analysis system structure based on Hadoop platform, which not only greatly improve the efficiency of data analysis, but also reduces the cost of system building. Moreover, this paper establishes an event pre-selection system based on the event level metadata(TAGs) database to optimize the data analyzing procedure.

  15. Turbulence control on an airborne laser platform

    NASA Technical Reports Server (NTRS)

    Gad-El-hak, Mohamed

    1987-01-01

    An active flow control device to generate large-scale, periodic structures in a turbulent shear flow is developed. Together with adaptive optics, the device may be used on airborne laser platforms to reduce or eliminate optical distortion caused by the turbulence in the aircraft's boundary layer. A cyclic jet issuing from a spanwise slot is used to collect the turbulent boundary layer for a finite time and then release all of the flow instantaneously in one large eddy that convects downstream. Flow visualization and hot-film probe measurements are used together with pattern recognition algorithms to demonstrate the viability of the flow control method. A flat plate towed in a water channel is used as a test bed. The instantaneous velocity signal is used to compute important statistical quantities of the random velocity field, such as the mean, the root-mean-square, the spectral distribution, and the probability density function. When optimized for a given boundary layer, it is shown that the cyclic jet will produce periodic structures that are similar to the random, naturally occurring ones. These structures seem to trigger the onset of bursting events near the wall of the plate. Thus, the present device generates periodic structures in both the outer and inner regions of a turbulent boundary layer.

  16. Rapid Development of Bespoke Unmanned Platforms for Atmospheric Science

    NASA Astrophysics Data System (ADS)

    Sobester, A.; Johnston, S. J.; Scanlan, J. P.; Hart, E. E.; O'Brien, N. S.

    2012-04-01

    The effective deployment of airborne atmospheric science instruments often hinges on the development cycle time of a suitable platform, one that is capable of delivering them to the desired altitude range for a specified amount of time, along a pre-determined trajectory. This could be driven by the need to respond rapidly to sudden, unexpected events (e.g., volcano eruptions, nuclear fallout, etc.) or simply to accommodate the iterative design and flight test cycle of the instrument developer. A shorter development cycle time would also afford us the ability to quickly adapt the hardware and control logic in response to unexpected results during an experimental campaign. We report on recent developments aimed at meeting this demand. As part of the Atmospheric Science Through Robotic Aircraft (ASTRA) initiative we have investigated the use of rapid prototyping technologies to this end, both on the 'airframe' of the platform itself and on the on-board systems. We show how fast multi-disciplinary design optimization techniques, coupled with computer-controlled additive manufacturing (3D printing) and laser cutting methods and electronic prototyping (using standard, modular, programmable building blocks) can lead to the delivery of a fully customized platform integrating a given instrument in a timescale of the order of ten days. Specific examples include the design and testing of a balloon-launched glider sensorcraft and a stratospheric balloon system. The 'vehicle' for the latter was built on a 3D printer using a copolymer thermoplastic material and fitted with a sacrificial protective 'cage' laser-cut from an open-cell foam. The data logging, tracking, sensor integration and communications services of the platform were constructed using the .net Gadgeteer open source hardware kit. The flight planning and eventual post-flight recovery of the system is enabled by a generic, stochastic trajectory simulation tool, also developed as part of the ASTRA initiative. This

  17. Thiolene and SIFEL-based Microfluidic Platforms for Liquid-Liquid Extraction

    PubMed Central

    Goyal, Sachit; Desai, Amit V.; Lewis, Robert W.; Ranganathan, David R.; Li, Hairong; Zeng, Dexing; Reichert, David E.; Kenis, Paul J.A.

    2014-01-01

    Microfluidic platforms provide several advantages for liquid-liquid extraction (LLE) processes over conventional methods, for example with respect to lower consumption of solvents and enhanced extraction efficiencies due to the inherent shorter diffusional distances. Here, we report the development of polymer-based parallel-flow microfluidic platforms for LLE. To date, parallel-flow microfluidic platforms have predominantly been made out of silicon or glass due to their compatibility with most organic solvents used for LLE. Fabrication of silicon and glass-based LLE platforms typically requires extensive use of photolithography, plasma or laser-based etching, high temperature (anodic) bonding, and/or wet etching with KOH or HF solutions. In contrast, polymeric microfluidic platforms can be fabricated using less involved processes, typically photolithography in combination with replica molding, hot embossing, and/or bonding at much lower temperatures. Here we report the fabrication and testing of microfluidic LLE platforms comprised of thiolene or a perfluoropolyether-based material, SIFEL, where the choice of materials was mainly guided by the need for solvent compatibility and fabrication amenability. Suitable designs for polymer-based LLE platforms that maximize extraction efficiencies within the constraints of the fabrication methods and feasible operational conditions were obtained using analytical modeling. To optimize the performance of the polymer-based LLE platforms, we systematically studied the effect of surface functionalization and of microstructures on the stability of the liquid-liquid interface and on the ability to separate the phases. As demonstrative examples, we report (i) a thiolene-based platform to determine the lipophilicity of caffeine, and (ii) a SIFEL-based platform to extract radioactive copper from an acidic aqueous solution. PMID:25246730

  18. Study of thermal management for space platform applications

    NASA Technical Reports Server (NTRS)

    Oren, J. A.

    1980-01-01

    Techniques for the management of the thermal energy of large space platforms using many hundreds of kilowatts over a 10 year life span were evaluated. Concepts for heat rejection, heat transport within the vehicle, and interfacing were analyzed and compared. The heat rejection systems were parametrically weight optimized over conditions for heat pipe and pumped fluid approaches. Two approaches to achieve reliability were compared for: performance, weight, volume, projected area, reliability, cost, and operational characteristics. Technology needs are assessed and technology advancement recommendations are made.

  19. Wind Turbine Controller to Mitigate Structural Loads on a Floating Wind Turbine Platform

    SciTech Connect

    Fleming, Paul A.; Peiffer, Antoine; Schlipf, David

    2016-06-24

    This paper summarizes the control design work that was performed to optimize the controller of a wind turbine on the WindFloat structure. The WindFloat is a semi-submersible floating platform designed to be a support structure for a multi-megawatt power-generating wind turbine. A controller developed for a bottom-fixed wind turbine configuration was modified for use when the turbine is mounted on the WindFloat platform. This results in an efficient platform heel resonance mitigation scheme. In addition several control modules, designed with a coupled linear model, were added to the fixed-bottom baseline controller. The approach was tested in a fully coupled nonlinear aero-hydroelastic simulation tool in which wind and wave disturbances were modeled. This testing yielded significant improvements in platform global performance and tower-base-bending loading.

  20. Tuning fractional PID controllers for a Steward platform based on frequency domain and artificial intelligence methods

    NASA Astrophysics Data System (ADS)

    Copot, Cosmin; Zhong, Yu; Ionescu, Clara; Keyser, Robin

    2013-06-01

    In this paper, two methods to tune a fractional-order PI λ D μ controller for a mechatronic system are presented. The first method is based on a genetic algorithm to obtain the parameter values for the fractionalorder PI λ D μ controller by global optimization. The second method used to design the fractional-order PI λ D μ controller relies on an auto-tuning approach by meeting some specifications in the frequency domain. The real-time experiments are conducted using a Steward platform which consists of a table tilted by six servo-motors with a ball on the top of the table. The considered system is a 6 degrees of freedom (d.o.f.) motion platform. The feedback on the position of the ball is obtained from images acquired by a visual sensor mounted above the platform. The fractional-order controllers were implemented and the performances of the steward platform are analyzed.

  1. Gas turbine bucket with impingement cooled platform

    DOEpatents

    Jones, Raphael Durand

    2002-01-01

    In a turbine bucket having an airfoil portion and a root portion, with a substantially planar platform at an interface between the airfoil portion and root portion, a platform cooling arrangement including at least one bore in the root portion and at least one impingement cooling tube seated in the bore, the tube extending beyond the bore with an outlet in close proximity to a targeted area on an underside of the platform.

  2. Bucket platform cooling scheme and related method

    DOEpatents

    Abuaf, Nesim; Barb, Kevin Joseph; Chopra, Sanjay; Kercher, David Max; Kellock, Iain Robertson; Lenahan, Dean Thomas; Nellian, Sankar; Starkweather, John Howard; Lupe, Douglas Arthur

    2002-01-01

    A turbine bucket includes an airfoil extending from a platform, having high and low pressure sides; a wheel mounting portion; a hollow shank portion located radially between the platform and the wheel mounting portion, the platform having an under surface. An impingement cooling plate is located in the hollow shank portion, spaced from the under surface, and the impingement plate is formed with a plurality of impingement cooling holes therein.

  3. Quantum photonics hybrid integration platform

    SciTech Connect

    Murray, E.; Floether, F. F.; Ellis, D. J. P.; Meany, T.; Bennett, A. J. Shields, A. J.; Lee, J. P.; Griffiths, J. P.; Jones, G. A. C.; Farrer, I.; Ritchie, D. A.

    2015-10-26

    Fundamental to integrated photonic quantum computing is an on-chip method for routing and modulating quantum light emission. We demonstrate a hybrid integration platform consisting of arbitrarily designed waveguide circuits and single-photon sources. InAs quantum dots (QD) embedded in GaAs are bonded to a SiON waveguide chip such that the QD emission is coupled to the waveguide mode. The waveguides are SiON core embedded in a SiO{sub 2} cladding. A tuneable Mach Zehnder interferometer (MZI) modulates the emission between two output ports and can act as a path-encoded qubit preparation device. The single-photon nature of the emission was verified using the on-chip MZI as a beamsplitter in a Hanbury Brown and Twiss measurement.

  4. Language Geography from Microblogging Platforms

    NASA Astrophysics Data System (ADS)

    Mocanu, Delia; Baronchelli, Andrea; Perra, Nicola; Gonçalves, Bruno; Vespignani, Alessandro

    2013-03-01

    Microblogging platforms have now become major open source indicators for complex social interactions. With the advent of smartphones, the everincreasing mobile Internet traffic gives us the unprecedented opportunity to complement studies of complex social phenomena with real-time location information. In this work, we show that the data nowadays accessible allows for detailed studies at different scales, ranging from country-level aggregate analysis to the analysis of linguistic communities withing specific neighborhoods. The high resolution and coverage of this data permits us to investigate such issues as the linguistic homogeneity of different countries, touristic seasonal patterns within countries, and the geographical distribution of different languages in bilingual regions. This work highlights the potentialities of geolocalized studies of open data sources that can provide an extremely detailed picture of the language geography.

  5. Particle platforms for cancer immunotherapy

    PubMed Central

    Serda, Rita Elena

    2013-01-01

    Elevated understanding and respect for the relevance of the immune system in cancer development and therapy has led to increased development of immunotherapeutic regimens that target existing cancer cells and provide long-term immune surveillance and protection from cancer recurrence. This review discusses using particles as immune adjuvants to create vaccines and to augment the anticancer effects of conventional chemotherapeutics. Several particle prototypes are presented, including liposomes, polymer nanoparticles, and porous silicon microparticles, the latter existing as either single- or multiparticle platforms. The benefits of using particles include immune-cell targeting, codelivery of antigens and immunomodulatory agents, and sustained release of the therapeutic payload. Nanotherapeutic-based activation of the immune system is dependent on both intrinsic particle characteristics and on the immunomodulatory cargo, which may include danger signals known as pathogen-associated molecular patterns and cytokines for effector-cell activation. PMID:23761969

  6. Fully human antibodies from transgenic mouse and phage display platforms.

    PubMed

    Lonberg, Nils

    2008-08-01

    Over the past two decades, technologies have emerged for generating monoclonal antibodies (MAbs) derived from human immunoglobulin gene sequences. These fully human MAbs provide an alternative to re-engineered, or de-immunized, rodent MAbs as a source of low immunogenicity therapeutic antibodies. There are now two marketed fully human therapeutic MAbs, adalimumab and panitumumab, and several dozen more in various stages of human clinical testing. Most of the drugs, including adalimumab and panitumumab, were generated using either phage display or transgenic mouse platforms. The reported clinical experience with fully human MAbs demonstrates that these two platforms are, and should continue to be, a significant source of active and well tolerated experimental therapeutics. While this body of reported clinical data does not yet provide a clear distinction between the platforms, the available descriptions of the drug discovery processes used to identify the clinical candidates highlight one difference. It appears that lead optimization is more commonly applied to phage display derived leads than transgenic mouse derived leads.

  7. A gene network engineering platform for lactic acid bacteria.

    PubMed

    Kong, Wentao; Kapuganti, Venkata S; Lu, Ting

    2016-02-29

    Recent developments in synthetic biology have positioned lactic acid bacteria (LAB) as a major class of cellular chassis for applications. To achieve the full potential of LAB, one fundamental prerequisite is the capacity for rapid engineering of complex gene networks, such as natural biosynthetic pathways and multicomponent synthetic circuits, into which cellular functions are encoded. Here, we present a synthetic biology platform for rapid construction and optimization of large-scale gene networks in LAB. The platform involves a copy-controlled shuttle for hosting target networks and two associated strategies that enable efficient genetic editing and phenotypic validation. By using a nisin biosynthesis pathway and its variants as examples, we demonstrated multiplex, continuous editing of small DNA parts, such as ribosome-binding sites, as well as efficient manipulation of large building blocks such as genes and operons. To showcase the platform, we applied it to expand the phenotypic diversity of the nisin pathway by quickly generating a library of 63 pathway variants. We further demonstrated its utility by altering the regulatory topology of the nisin pathway for constitutive bacteriocin biosynthesis. This work demonstrates the feasibility of rapid and advanced engineering of gene networks in LAB, fostering their applications in biomedicine and other areas.

  8. Study on the application of mobile internet cloud computing platform

    NASA Astrophysics Data System (ADS)

    Gong, Songchun; Fu, Songyin; Chen, Zheng

    2012-04-01

    The innovative development of computer technology promotes the application of the cloud computing platform, which actually is the substitution and exchange of a sort of resource service models and meets the needs of users on the utilization of different resources after changes and adjustments of multiple aspects. "Cloud computing" owns advantages in many aspects which not merely reduce the difficulties to apply the operating system and also make it easy for users to search, acquire and process the resources. In accordance with this point, the author takes the management of digital libraries as the research focus in this paper, and analyzes the key technologies of the mobile internet cloud computing platform in the operation process. The popularization and promotion of computer technology drive people to create the digital library models, and its core idea is to strengthen the optimal management of the library resource information through computers and construct an inquiry and search platform with high performance, allowing the users to access to the necessary information resources at any time. However, the cloud computing is able to promote the computations within the computers to distribute in a large number of distributed computers, and hence implement the connection service of multiple computers. The digital libraries, as a typical representative of the applications of the cloud computing, can be used to carry out an analysis on the key technologies of the cloud computing.

  9. Health-e-Child: a grid platform for european paediatrics

    NASA Astrophysics Data System (ADS)

    Skaburskas, K.; Estrella, F.; Shade, J.; Manset, D.; Revillard, J.; Rios, A.; Anjum, A.; Branson, A.; Bloodsworth, P.; Hauer, T.; McClatchey, R.; Rogulin, D.

    2008-07-01

    The Health-e-Child (HeC) project [1], [2] is an EC Framework Programme 6 Integrated Project that aims to develop a grid-based integrated healthcare platform for paediatrics. Using this platform biomedical informaticians will integrate heterogeneous data and perform epidemiological studies across Europe. The resulting Grid enabled biomedical information platform will be supported by robust search, optimization and matching techniques for information collected in hospitals across Europe. In particular, paediatricians will be provided with decision support, knowledge discovery and disease modelling applications that will access data in hospitals in the UK, Italy and France, integrated via the Grid. For economy of scale, reusability, extensibility, and maintainability, HeC is being developed on top of an EGEE/gLite [3] based infrastructure that provides all the common data and computation management services required by the applications. This paper discusses some of the major challenges in bio-medical data integration and indicates how these will be resolved in the HeC system. HeC is presented as an example of how computer science (and, in particular Grid infrastructures) originating from high energy physics can be adapted for use by biomedical informaticians to deliver tangible real-world benefits.

  10. Applications of thin-film sandwich crystallization platforms

    SciTech Connect

    Axford, Danny Aller, Pierre; Sanchez-Weatherby, Juan; Sandy, James

    2016-03-24

    Crystallization via sandwiches of thin polymer films is presented and discussed. Examples are shown of protein crystallization in, and data collection from, solutions sandwiched between thin polymer films using vapour-diffusion and batch methods. The crystallization platform is optimal for both visualization and in situ data collection, with the need for traditional harvesting being eliminated. In wells constructed from the thinnest plastic and with a minimum of aqueous liquid, flash-cooling to 100 K is possible without significant ice formation and without any degradation in crystal quality. The approach is simple; it utilizes low-cost consumables but yields high-quality data with minimal sample intervention and, with the very low levels of background X-ray scatter that are observed, is optimal for microcrystals.

  11. Jurassic platform development, northwestern Gulf of Mexico

    SciTech Connect

    Moore, C.H. Jr.

    1987-05-01

    Triassic and Early Jurassic rifting set the stage for the subsequent development of carbonate platforms in the Late Jurassic. These platforms formed along the interior margins of salt basins separated from the main ancestral Gulf of Mexico by a series of positive features. A major sea level rise, after deposition of the Louann Salt (late Callovian), drowned the interior salt basins around the margins of the Gulf of Mexico, leading to an anoxic event. Organic-rich sediments of the lower Smackover were deposited as a basin-fill sequence, forming one of the major hydrocarbon source rocks of the region. As sea level rise slowed in the late Oxfordian, carbonate production began to catch up with sea level rise along the basin margins, leading to the initial development of a rimmed carbonate platform. The platform margin was marked by high-energy ooid grainstones, while crustacean pellet muds were deposited in the platform interior. A high-energy ooid-dominated platform (upper Smackover) developed in the late Oxfordian when sea level reached a standstill. During the subsequent Kimmeridgian sea level rise, a second rimmed carbonate platform, the Haynesville, was developed. During the initial rise, grainstones were deposited on the platform margin, while the interior was dominated by evaporites (Buckner) and siliciclastics. As sea level slowed and reached a standstill, the platform margin facies extended shoreward (Gilmer) and a high-energy platform, analogous to the upper Smackover, was formed. The Smackover and Haynesville platforms of the northwestern gulf show a parallel evolution in response to cyclic changes in Upper Jurassic sea level.

  12. Helicopter flight simulation motion platform requirements

    NASA Astrophysics Data System (ADS)

    Schroeder, Jeffery Allyn

    Flight simulators attempt to reproduce in-flight pilot-vehicle behavior on the ground. This reproduction is challenging for helicopter simulators, as the pilot is often inextricably dependent on external cues for pilot-vehicle stabilization. One important simulator cue is platform motion; however, its required fidelity is unknown. To determine the required motion fidelity, several unique experiments were performed. A large displacement motion platform was used that allowed pilots to fly tasks with matched motion and visual cues. Then, the platform motion was modified to give cues varying from full motion to no motion. Several key results were found. First, lateral and vertical translational platform cues had significant effects on fidelity. Their presence improved performance and reduced pilot workload. Second, yaw and roll rotational platform cues were not as important as the translational platform cues. In particular, the yaw rotational motion platform cue did not appear at all useful in improving performance or reducing workload. Third, when the lateral translational platform cue was combined with visual yaw rotational cues, pilots believed the platform was rotating when it was not. Thus, simulator systems can be made more efficient by proper combination of platform and visual cues. Fourth, motion fidelity specifications were revised that now provide simulator users with a better prediction of motion fidelity based upon the frequency responses of their motion control laws. Fifth, vertical platform motion affected pilot estimates of steady-state altitude during altitude repositionings. This refutes the view that pilots estimate altitude and altitude rate in simulation solely from visual cues. Finally, the combined results led to a general method for configuring helicopter motion systems and for developing simulator tasks that more likely represent actual flight. The overall results can serve as a guide to future simulator designers and to today's operators.

  13. Public optimism towards nanomedicine

    PubMed Central

    Bottini, Massimo; Rosato, Nicola; Gloria, Fulvia; Adanti, Sara; Corradino, Nunziella; Bergamaschi, Antonio; Magrini, Andrea

    2011-01-01

    Background Previous benefit–risk perception studies and social experiences have clearly demonstrated that any emerging technology platform that ignores benefit–risk perception by citizens might jeopardize its public acceptability and further development. The aim of this survey was to investigate the Italian judgment on nanotechnology and which demographic and heuristic variables were most influential in shaping public perceptions of the benefits and risks of nanotechnology. Methods In this regard, we investigated the role of four demographic (age, gender, education, and religion) and one heuristic (knowledge) predisposing factors. Results The present study shows that gender, education, and knowledge (but not age and religion) influenced the Italian perception of how nanotechnology will (positively or negatively) affect some areas of everyday life in the next twenty years. Furthermore, the picture that emerged from our study is that Italian citizens, despite minimal familiarity with nanotechnology, showed optimism towards nanotechnology applications, especially those related to health and medicine (nanomedicine). The high regard for nanomedicine was tied to the perception of risks associated with environmental and societal implications (division among social classes and increased public expenses) rather than health issues. However, more highly educated people showed greater concern for health issues but this did not decrease their strong belief about the benefits that nanotechnology would bring to medical fields. Conclusion The results reported here suggest that public optimism towards nanomedicine appears to justify increased scientific effort and funding for medical applications of nanotechnology. It also obligates toxicologists, politicians, journalists, entrepreneurs, and policymakers to establish a more responsible dialog with citizens regarding the nature and implications of this emerging technology platform. PMID:22267931

  14. Functional Nanostructured Platforms for Chemical and Biological Sensing

    SciTech Connect

    Letant, S E

    2006-03-20

    The central goal of our work is to combine semiconductor nanotechnology and surface functionalization in order to build platforms for the selective detection of bio-organisms ranging in size from bacteria (micron range) down to viruses, as well as for the detection of chemical agents (nanometer range). We will show on three porous silicon platforms how pore geometry and pore wall chemistry can be combined and optimized to capture and detect specific targets. We developed a synthetic route allowing to directly anchor proteins on silicon surfaces and illustrated the relevance of this technique by immobilizing live enzymes onto electrochemically etched luminescent nano-porous silicon. The powerful association of the specific enzymes with the transducing matrix led to a selective hybrid platform for chemical sensing. We also used light-assisted electrochemistry to produce periodic arrays of through pores on pre-patterned silicon membranes with controlled diameters ranging from many microns down to tens of nanometers. We demonstrated the first covalently functionalized silicon membranes and illustrated their selective capture abilities with antibody-coated micro-beads. These engineered membranes are extremely versatile and could be adapted to specifically recognize the external fingerprints (size and coat composition) of target bio-organisms. Finally, we fabricated locally functionalized single nanopores using a combination of focused ion beam drilling and ion beam assisted oxide deposition. We showed how a silicon oxide ring can be grown around a single nanopore and how it can be functionalized with DNA probes to detect single viral-sized beads. The next step for this platform is the detection of whole viruses and bacteria.

  15. Functional nanostructured platforms for chemical and biological sensing

    NASA Astrophysics Data System (ADS)

    Létant, S. E.

    2006-05-01

    The central goal of our work is to combine semiconductor nanotechnology and surface functionalization in order to build platforms for the selective detection of bio-organisms ranging in size from bacteria (micron range) down to viruses, as well as for the detection of chemical agents (nanometer range). We will show on three porous silicon platforms how pore geometry and pore wall chemistry can be combined and optimized to capture and detect specific targets. We developed a synthetic route allowing to directly anchor proteins on silicon surfaces and illustrated the relevance of this technique by immobilizing live enzymes onto electrochemically etched luminescent nano-porous silicon. The powerful association of the specific enzymes with the transducing matrix led to a selective hybrid platform for chemical sensing. We also used light-assisted electrochemistry to produce periodic arrays of through pores on pre-patterned silicon membranes with controlled diameters ranging from many microns down to tens of nanometers. We demonstrated the first covalently functionalized silicon membranes and illustrated their selective capture abilities with antibody-coated micro-beads. These engineered membranes are extremely versatile and could be adapted to specifically recognize the external fingerprints (size and coat composition) of target bio-organisms. Finally, we fabricated locally functionalized single nanopores using a combination of focused ion beam drilling and ion beam assisted oxide deposition. We showed how a silicon oxide ring can be grown around a single nanopore and how it can be functionalized with DNA probes to detect single viral-sized beads. The next step for this platform is the detection of whole viruses and bacteria.

  16. Helicopter Flight Simulation Motion Platform Requirements

    NASA Technical Reports Server (NTRS)

    Schroeder, Jeffery Allyn

    1999-01-01

    To determine motion fidelity requirements, a series of piloted simulations was performed. Several key results were found. First, lateral and vertical translational platform cues had significant effects on fidelity. Their presence improved performance and reduced pilot workload. Second, yaw and roll rotational platform cues were not as important as the translational platform cues. In particular, the yaw rotational motion platform cue did not appear at all useful in improving performance or reducing workload. Third, when the lateral translational platform cue was combined with visual yaw rotational cues, pilots believed the platform was rotating when it was not. Thus, simulator systems can be made more efficient by proper combination of platform and visual cues. Fourth, motion fidelity specifications were revised that now provide simulator users with a better prediction of motion fidelity based upon the frequency responses of their motion control laws. Fifth, vertical platform motion affected pilot estimates of steady-state altitude during altitude repositioning. Finally, the combined results led to a general method for configuring helicopter motion systems and for developing simulator tasks that more likely represent actual flight. The overall results can serve as a guide to future simulator designers and to today's operators.

  17. Large communications platforms versus smaller satellites

    NASA Technical Reports Server (NTRS)

    1979-01-01

    Communications systems using large platforms are compared with systems using conventional satellites. Systems models were generated and compared for U.S. domestic application and for 1 INTELSAT's international and domestic transponder lease application. Technology advances were assumed the platforms and the evolution of conventional satellites.

  18. A Bioimpedance Analysis Platform for Amputee Residual Limb Assessment

    PubMed Central

    Sanders, JE; Moehring, MM; Rothlisberger, TM; Phillips, RH; Hartley, T; Dietrich, CR; Redd, CB; Gardner, DW; Cagle, JC

    2016-01-01

    Objective The objective of this research was to develop a bioimpedance platform for monitoring fluid volume in residual limbs of people with trans-tibial limb loss using prostheses. Methods A customized multi-frequency current stimulus profile was sent to thin flat electrodes positioned on the thigh and distal residual limb. The applied current signal and sensed voltage signals from four pairs of electrodes located on the anterior and posterior surfaces were demodulated into resistive and reactive components. An established electrical model (Cole) and segmental limb geometry model were used to convert results to extracellular and intracellular fluid volumes. Bench tests and testing on amputee participants were conducted to optimize the stimulus profile and electrode design and layout. Results The proximal current injection electrode needed to be at least 25 cm from the proximal voltage sensing electrode. A thin layer of hydrogel needed to be present during testing to ensure good electrical coupling. Using a burst duration of 2.0 ms, intermission interval of 100 μs, and sampling delay of 10 μs at each of 24 frequencies except 5 kHz which required a 200 μs sampling delay, the system achieved a sampling rate of 19.7 Hz. Conclusion The designed bioimpedance platform allowed system settings and electrode layouts and positions to be optimized for amputee limb fluid volume measurement. Significance The system will be useful towards identifying and ranking prosthetic design features and participant characteristics that impact residual limb fluid volume. PMID:26595906

  19. Venus Atmospheric Maneuverable Platform (VAMP)

    NASA Astrophysics Data System (ADS)

    Polidan, R.; Lee, G.; Sokol, D.; Griffin, K.; Bolisay, L.; Barnes, N.

    2014-04-01

    Over the past years we have explored a possible new approach to Venus upper atmosphere exploration by applying recent Northrop Grumman (non-NASA) development programs to the challenges associated with Venus upper atmosphere science missions. Our concept is a low ballistic coefficient (<50 Pa), semibuoyant aircraft that deploys prior to entering the Venus atmosphere, enters the Venus atmosphere without an aeroshell, and provides a long-lived (months to years), maneuverable vehicle capable of carrying science payloads to explore the Venus upper atmosphere. VAMP targets the global Venus atmosphere between 55 and 70 km altitude and would be a platform to address VEXAG goals I.A, I.B, and I.C. We will discuss the overall mission architecture and concept of operations from launch through Venus arrival, orbit, entry, and atmospheric science operations. We will present a strawman concept of VAMP, including ballistic coefficient, planform area, percent buoyancy, inflation gas, wing span, vehicle mass, power supply, propulsion, materials considerations, structural elements, subsystems, and packaging. The interaction between the VAMP vehicle and the supporting orbiter will also be discussed. In this context, we will specifically focus upon four key factors impacting the design and performance of VAMP: 1. Science payload accommodation, constraints, and opportunities 2. Characteristics of flight operations and performance in the Venus atmosphere: altitude range, latitude and longitude access, day/night performance, aircraft performance, performance sensitivity to payload weight 3. Feasibility of and options for the deployment of the vehicle in space 4. Entry into the Venus atmosphere, including descent profile, heat rate, total heat load, stagnation temperature, control, and entry into level flight We will discuss interdependencies of the above factors and the manner in which the VAMP strawman's characteristics affect the CONOPs and the science objectives. We will show how the

  20. Space Station Based Microacceleration Experiment Platform

    NASA Technical Reports Server (NTRS)

    Barber, Katy; Economopoulos, Tony; Evenson, Erik; Gonzalez, Raul; Henson, Steve; Parada, Enrique; Robinson, Rick; Scott, Mike; Spotz, Bill

    1990-01-01

    Normal Space Station Freedom activities, such as docking, astronauts' movement, equipment vibrations, and space station reboosts, exert forces on the structure, resulting in static or transient accelerations greater than many microgravity experiments can tolerate. A solution to this problem is to isolate experiments on a separate platform free from such disturbances. The Space Station Based Microacceleration Experiment Platform, a proposed solution to the Space Station microgravity experiment problem is described. It is modular in design and can be telerobotically assembled and operated. The Microacceleration Experiment Platform (MEP) consists of a minimum configuration platform to which power, propulsion, propellant, and experiment modules are added. The platform's layout is designed to take maximum advantage of the microgravity field structure in orbit.

  1. Apparatus to position a microelectromechanical platform

    SciTech Connect

    Miller, Samuel Lee; Rodgers, Murray Steven

    2003-09-23

    The present invention comprises a microelectromechanical positioner to achieve substantially translational positioning of a platform without rotational motion, thereby maintaining a constant angular orientation of the platform during movement. A linkage mechanism of the positioner can comprise parallelogram linkages to constrain the rotational motion of the platform. Such linkages further can comprise flexural hinges or other turning joints at the linkage pivots to eliminate the need for rubbing surfaces. A plurality of the linkage mechanisms can be used to enable translational motion of the platform with two degrees of freedom. A variety of means can be used to actuate the positioner. Independent actuation of the anchor links of the linkage mechanisms with rotary electrostatic actuators can be used to provide controlled translational movement of the platform.

  2. ESF Mine Power Center Platforms

    SciTech Connect

    T.A. Misiak

    2000-02-10

    The purpose and objective of this analysis is to structurally evaluate the existing Exploratory Studies Facility (ESF) mine power center (MPC) support frames and to design service platforms that will attach to the MPC support frames. This analysis follows the Development Plan titled ''Produce Additional Design for Title 111 Evaluation Report'' (CRWMS M&O 1999a). This analysis satisfies design recommended in the ''Title III Evaluation Report for the Surface and Subsurface Power System'' (CRWMS M&O 1999b, Section 7.6) and concurred with in the ''System Safety Evaluation of Title 111 Evaluation Reports Recommended Work'' (Gwyn 1999, Section 10.1.1). This analysis does not constitute a level-3 deliverable, a level-4 milestone, or a supporting work product. This document is not being prepared in support of the Monitored Geologic Repository (MGR) Site Recommendation (SR), Environmental Impact Statement (EIS), or License Application (LA) and should not be cited as a reference in the MGR SR, EIS, or LA.

  3. Distributed Optimization

    NASA Technical Reports Server (NTRS)

    Macready, William; Wolpert, David

    2005-01-01

    We demonstrate a new framework for analyzing and controlling distributed systems, by solving constrained optimization problems with an algorithm based on that framework. The framework is ar. information-theoretic extension of conventional full-rationality game theory to allow bounded rational agents. The associated optimization algorithm is a game in which agents control the variables of the optimization problem. They do this by jointly minimizing a Lagrangian of (the probability distribution of) their joint state. The updating of the Lagrange parameters in that Lagrangian is a form of automated annealing, one that focuses the multi-agent system on the optimal pure strategy. We present computer experiments for the k-sat constraint satisfaction problem and for unconstrained minimization of NK functions.

  4. Cross-species analysis of Fc engineered anti-Lewis-Y human IgG1 variants in human neonatal receptor transgenic mice reveal importance of S254 and Y436 in binding human neonatal Fc receptor

    PubMed Central

    Burvenich, Ingrid J. G.; Farrugia, William; Lee, Fook T.; Catimel, Bruno; Liu, Zhanqi; Makris, Dahna; Cao, Diana; O'Keefe, Graeme J.; Brechbiel, Martin W.; King, Dylan; Spirkoska, Violeta; Allan, Laura C.; Ramsland, Paul A.; Scott, Andrew M.

    2016-01-01

    ABSTRACT IgG has a long half-life through engagement of its Fc region with the neonatal Fc receptor (FcRn). The FcRn binding site on IgG1 has been shown to contain I253 and H310 in the CH2 domain and H435 in the CH3 domain. Altering the half-life of IgG has been pursued with the aim to prolong or reduce the half-life of therapeutic IgGs. More recent studies have shown that IgGs bind differently to mouse and human FcRn. In this study we characterize a set of hu3S193 IgG1 variants with mutations in the FcRn binding site. A double mutation in the binding site is necessary to abrogate binding to murine FcRn, whereas a single mutation in the FcRn binding site is sufficient to no longer detect binding to human FcRn and create hu3S193 IgG1 variants with a half-life similar to previously studied hu3S193 F(ab')2 (t1/2β, I253A, 12.23 h; H310A, 12.94; H435A, 12.57; F(ab')2, 12.6 h). Alanine substitutions in S254 in the CH2 domain and Y436 in the CH3 domain showed reduced binding in vitro to human FcRn and reduced elimination half-lives in huFcRn transgenic mice (t1/2β, S254A, 37.43 h; Y436A, 39.53 h; wild-type, 83.15 h). These variants had minimal effect on half-life in BALB/c nu/nu mice (t1/2β, S254A, 119.9 h; Y436A, 162.1 h; wild-type, 163.1 h). These results provide insight into the interaction of human Fc by human FcRn, and are important for antibody-based therapeutics with optimal pharmacokinetics for payload strategies used in the clinic. PMID:27030023

  5. Polymer-based platform for microfluidic systems

    DOEpatents

    Benett, William; Krulevitch, Peter; Maghribi, Mariam; Hamilton, Julie; Rose, Klint; Wang, Amy W.

    2009-10-13

    A method of forming a polymer-based microfluidic system platform using network building blocks selected from a set of interconnectable network building blocks, such as wire, pins, blocks, and interconnects. The selected building blocks are interconnectably assembled and fixedly positioned in precise positions in a mold cavity of a mold frame to construct a three-dimensional model construction of a microfluidic flow path network preferably having meso-scale dimensions. A hardenable liquid, such as poly (dimethylsiloxane) is then introduced into the mold cavity and hardened to form a platform structure as well as to mold the microfluidic flow path network having channels, reservoirs and ports. Pre-fabricated elbows, T's and other joints are used to interconnect various building block elements together. After hardening the liquid the building blocks are removed from the platform structure to make available the channels, cavities and ports within the platform structure. Microdevices may be embedded within the cast polymer-based platform, or bonded to the platform structure subsequent to molding, to create an integrated microfluidic system. In this manner, the new microfluidic platform is versatile and capable of quickly generating prototype systems, and could easily be adapted to a manufacturing setting.

  6. Ligand-binding assays: risk of using a platform supported by a single vendor.

    PubMed

    Yohrling, Jennifer

    2009-06-01

    The use of biological reagents in ligand-binding assays (LBAs) presents inherent challenges when measuring the concentration of large molecules in complex matrices. As a result, there are relatively few platforms that provide the accuracy, precision and robustness needed to determine the concentration of macromolecular therapies and biomarkers, and demonstrate the presence or absence of an immune response. Some bioanalytical laboratories use only one LBA platform to reduce costs, increase efficiency and maintain optimal assay performance. However, the business and regulatory risks of using a single platform supported by only one vendor should be considered. This article summarizes the immunological methods used to support bioanalysis for large molecules that are supported by a single vendor, the benefits of being dedicated to a single platform for bioanalysis used for regulatory filings, the costs associated with restructuring if an immunoassay platform is discontinued and recommendations to mitigate risk when using LBAs in drug development. The experience with the recent discontinuation of the BioVeris™ electrochemiluminescent-based platform is discussed.

  7. 30 CFR 250.911 - If my platform is subject to the Platform Verification Program, what must I do?

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 30 Mineral Resources 2 2014-07-01 2014-07-01 false If my platform is subject to the Platform Verification Program, what must I do? 250.911 Section 250.911 Mineral Resources BUREAU OF SAFETY AND... CONTINENTAL SHELF Platforms and Structures Platform Verification Program § 250.911 If my platform is...

  8. 30 CFR 250.911 - If my platform is subject to the Platform Verification Program, what must I do?

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 30 Mineral Resources 2 2013-07-01 2013-07-01 false If my platform is subject to the Platform Verification Program, what must I do? 250.911 Section 250.911 Mineral Resources BUREAU OF SAFETY AND... CONTINENTAL SHELF Platforms and Structures Platform Verification Program § 250.911 If my platform is...

  9. 30 CFR 250.911 - If my platform is subject to the Platform Verification Program, what must I do?

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 30 Mineral Resources 2 2012-07-01 2012-07-01 false If my platform is subject to the Platform Verification Program, what must I do? 250.911 Section 250.911 Mineral Resources BUREAU OF SAFETY AND... CONTINENTAL SHELF Platforms and Structures Platform Verification Program § 250.911 If my platform is...

  10. Reliability of plantar pressure platforms.

    PubMed

    Hafer, Jocelyn F; Lenhoff, Mark W; Song, Jinsup; Jordan, Joanne M; Hannan, Marian T; Hillstrom, Howard J

    2013-07-01

    Plantar pressure measurement is common practice in many research and clinical protocols. While the accuracy of some plantar pressure measuring devices and methods for ensuring consistency in data collection on plantar pressure measuring devices have been reported, the reliability of different devices when testing the same individuals is not known. This study calculated intra-mat, intra-manufacturer, and inter-manufacturer reliability of plantar pressure parameters as well as the number of plantar pressure trials needed to reach a stable estimate of the mean for an individual. Twenty-two healthy adults completed ten walking trials across each of two Novel emed-x(®) and two Tekscan MatScan(®) plantar pressure measuring devices in a single visit. Intraclass correlation (ICC) was used to describe the agreement between values measured by different devices. All intra-platform reliability correlations were greater than 0.70. All inter-emed-x(®) reliability correlations were greater than 0.70. Inter-MatScan(®) reliability correlations were greater than 0.70 in 31 and 52 of 56 parameters when looking at a 10-trial average and a 5-trial average, respectively. Inter-manufacturer reliability including all four devices was greater than 0.70 for 52 and 56 of 56 parameters when looking at a 10-trial average and a 5-trial average, respectively. All parameters reached a value within 90% of an unbiased estimate of the mean within five trials. Overall, reliability results are encouraging for investigators and clinicians who may have plantar pressure data sets that include data collected on different devices.

  11. A Multichannel Bioluminescence Determination Platform for Bioassays.

    PubMed

    Kim, Sung-Bae; Naganawa, Ryuichi

    2016-01-01

    The present protocol introduces a multichannel bioluminescence determination platform allowing a high sample throughput determination of weak bioluminescence with reduced standard deviations. The platform is designed to carry a multichannel conveyer, an optical filter, and a mirror cap. The platform enables us to near-simultaneously determine ligands in multiple samples without the replacement of the sample tubes. Furthermore, the optical filters beneath the multichannel conveyer are designed to easily discriminate colors during assays. This optical system provides excellent time- and labor-efficiency to users during bioassays.

  12. Space platform reference mission studies overview

    NASA Technical Reports Server (NTRS)

    Harrison, J. K.

    1981-01-01

    The design requirements for three major space platform systems are identified. The three were the Science and Applications Space Platform (SASP), the Geostationary Platform (GSP), and the Satellite Power System (SPS). Because the SASP and GSP were assumed to require no advanced technology for their development an advanced version of each was selected on which to base the design requirements. The SPS represented the opposite development state hence a nearer term test article was selected on which to base the requirements. The development period for these missions is estimated.

  13. A novel 3D integrated platform for the high-resolution study of cell migration plasticity.

    PubMed

    Schneider, Julian; Bachmann, Tobias; Franco, Davide; Richner, Patrizia; Galliker, Patrick; Tiwari, Manish K; Ferrari, Aldo; Poulikakos, Dimos

    2013-08-01

    Understanding the mechanisms of interstitial cancer migration is of great scientific and medical interest. Creating 3D platforms, conducive to optical microscopy and mimicking the physical parameters (in plane and out of plane) involved in interstitial migration, is a major step forward in this direction. Here, a novel approach is used to directly print free-form, 3D micropores on basal scaffolds containing microgratings optimized for contact guidance. The platforms so formed are validated by monitoring cancer cell migration and micropore penetration with high-resolution optical microscopy. The shapes, sizes and deformability of the micropores are controllable, paving the way to decipher their role in interstitial migration.

  14. U.S. Space Station platform - Configuration technology for customer servicing

    NASA Technical Reports Server (NTRS)

    Dezio, Joseph A.; Walton, Barbara A.

    1987-01-01

    Features of the Space Station coorbiting and polar orbiting platforms (COP and POP, respectively) are described that will allow them to be configured optimally to meet mission requirements and to be assembled, serviced, and modified on-orbit. Both of these platforms were designed to permit servicing at the Shuttle using the remote manipulator system with teleoperated end effectors; EVA was planned as a backup and for unplanned payload failure modes. Station-based servicing is discussed as well as expendable launch vehicle-based servicing concepts.

  15. Improving pandemic H5N1 influenza vaccines by combining different vaccine platforms.

    PubMed

    Luke, Catherine J; Subbarao, Kanta

    2014-07-01

    A variety of platforms are being explored for the development of vaccines for pandemic influenza. Observations that traditional inactivated subvirion vaccines and live-attenuated vaccines against H5 and some H7 influenza viruses were poorly immunogenic spurred efforts to evaluate new approaches, including whole virus vaccines, higher doses of antigen, addition of adjuvants and combinations of different vaccine modalities in heterologous prime-boost regimens to potentiate immune responses. Results from clinical trials of prime-boost regimens have been very promising. Further studies are needed to determine optimal combinations of platforms, intervals between doses of vaccines and the logistics of deployment in pre-pandemic and early pandemic settings.

  16. Prospective Optimization.

    PubMed

    Sejnowski, Terrence J; Poizner, Howard; Lynch, Gary; Gepshtein, Sergei; Greenspan, Ralph J

    2014-05-01

    Human performance approaches that of an ideal observer and optimal actor in some perceptual and motor tasks. These optimal abilities depend on the capacity of the cerebral cortex to store an immense amount of information and to flexibly make rapid decisions. However, behavior only approaches these limits after a long period of learning while the cerebral cortex interacts with the basal ganglia, an ancient part of the vertebrate brain that is responsible for learning sequences of actions directed toward achieving goals. Progress has been made in understanding the algorithms used by the brain during reinforcement learning, which is an online approximation of dynamic programming. Humans also make plans that depend on past experience by simulating different scenarios, which is called prospective optimization. The same brain structures in the cortex and basal ganglia that are active online during optimal behavior are also active offline during prospective optimization. The emergence of general principles and algorithms for goal-directed behavior has consequences for the development of autonomous devices in engineering applications.

  17. Prospective Optimization

    PubMed Central

    Sejnowski, Terrence J.; Poizner, Howard; Lynch, Gary; Gepshtein, Sergei; Greenspan, Ralph J.

    2014-01-01

    Human performance approaches that of an ideal observer and optimal actor in some perceptual and motor tasks. These optimal abilities depend on the capacity of the cerebral cortex to store an immense amount of information and to flexibly make rapid decisions. However, behavior only approaches these limits after a long period of learning while the cerebral cortex interacts with the basal ganglia, an ancient part of the vertebrate brain that is responsible for learning sequences of actions directed toward achieving goals. Progress has been made in understanding the algorithms used by the brain during reinforcement learning, which is an online approximation of dynamic programming. Humans also make plans that depend on past experience by simulating different scenarios, which is called prospective optimization. The same brain structures in the cortex and basal ganglia that are active online during optimal behavior are also active offline during prospective optimization. The emergence of general principles and algorithms for goal-directed behavior has consequences for the development of autonomous devices in engineering applications. PMID:25328167

  18. UAH/NASA Workshop on Space Science Platform

    NASA Technical Reports Server (NTRS)

    Wu, S. T. (Editor); Morgan, S. (Editor)

    1978-01-01

    The scientific user requirements for a space science platform were defined. The potential user benefits, technological implications and cost of space platforms were examined. Cost effectiveness of the platforms' capabilities were also examined.

  19. Translational research platforms integrating clinical and omics data: a review of publicly available solutions

    PubMed Central

    Canuel, Vincent; Avillach, Paul; Degoulet, Patrice; Burgun, Anita

    2015-01-01

    The rise of personalized medicine and the availability of high-throughput molecular analyses in the context of clinical care have increased the need for adequate tools for translational researchers to manage and explore these data. We reviewed the biomedical literature for translational platforms allowing the management and exploration of clinical and omics data, and identified seven platforms: BRISK, caTRIP, cBio Cancer Portal, G-DOC, iCOD, iDASH and tranSMART. We analyzed these platforms along seven major axes. (1) The community axis regrouped information regarding initiators and funders of the project, as well as availability status and references. (2) We regrouped under the information content axis the nature of the clinical and omics data handled by each system. (3) The privacy management environment axis encompassed functionalities allowing control over data privacy. (4) In the analysis support axis, we detailed the analytical and statistical tools provided by the platforms. We also explored (5) interoperability support and (6) system requirements. The final axis (7) platform support listed the availability of documentation and installation procedures. A large heterogeneity was observed in regard to the capability to manage phenotype information in addition to omics data, their security and interoperability features. The analytical and visualization features strongly depend on the considered platform. Similarly, the availability of the systems is variable. This review aims at providing the reader with the background to choose the platform best suited to their needs. To conclude, we discuss the desiderata for optimal translational research platforms, in terms of privacy, interoperability and technical features. PMID:24608524

  20. Optimal Fluoridation

    PubMed Central

    Lee, John R.

    1975-01-01

    Optimal fluoridation has been defined as that fluoride exposure which confers maximal cariostasis with minimal toxicity and its values have been previously determined to be 0.5 to 1 mg per day for infants and 1 to 1.5 mg per day for an average child. Total fluoride ingestion and urine excretion were studied in Marin County, California, children in 1973 before municipal water fluoridation. Results showed fluoride exposure to be higher than anticipated and fulfilled previously accepted criteria for optimal fluoridation. Present and future water fluoridation plans need to be reevaluated in light of total environmental fluoride exposure. PMID:1130041

  1. Future Role of Aerial Platforms at Venus

    NASA Astrophysics Data System (ADS)

    Cutts, J. A.; Pauken, M.; Hall, J. L.; Baines, K. H.; Grimm, R.

    2017-02-01

    This paper reviews the brief experience with deploying aerial platforms at Venus, the various mission concepts that have been proposed over the last three decades, and a vision for their application through 2050.

  2. 2011 Biomass Program Platform Peer Review: Algae

    SciTech Connect

    Yang, Joyce

    2012-02-01

    This document summarizes the recommendations and evaluations provided by an independent external panel of experts at the 2011 U.S. Department of Energy Biomass Program’s Algae Platform Review meeting.

  3. 2011 Biomass Program Platform Peer Review: Feedstock

    SciTech Connect

    McCann, Laura

    2012-02-01

    This document summarizes the recommendations and evaluations provided by an independent external panel of experts at the 2011 U.S. Department of Energy Biomass Program’s Feedstock Platform Review meeting.

  4. Summary of Fe opacity measurement platform

    SciTech Connect

    Nagayama, Taisuke

    2016-05-01

    This powerpoint presentation goes over the Fe opacity measurement platform, including how the experiment works, what can be gathered from the measurements, what can be gathered from the simulations, and the limitations of the experiment.

  5. 2011 Biomass Program Platform Peer Review. Infrastructure

    SciTech Connect

    Lindauer, Alicia

    2012-02-01

    This document summarizes the recommendations and evaluations provided by an independent external panel of experts at the 2011 U.S. Department of Energy Biomass Program’s Infrastructure Platform Review meeting.

  6. Parameters Identification for Motorcycle Simulator's Platform Characterization

    NASA Astrophysics Data System (ADS)

    Nehaoua, L.; Arioui, H.

    2008-06-01

    This paper presents the dynamics modeling and parameters identification of a motorcycle simulator's platform. This model begins with some suppositions which consider that the leg dynamics can be neglected with respect to the mobile platform one. The objectif is to synthesis a simplified control scheme, adapted to driving simulation application, minimising dealys and without loss of tracking performance. Electronic system of platform actuation is described. It's based on a CAN BUS communication which offers a large transmission robustness and error handling. Despite some disadvanteges, we adapted a control solution which overcome these inconvenients and preserve the quality of tracking trajectory. A bref description of the simulator's platform is given and results are shown and justified according to our specifications.

  7. 2011 Biomass Program Platform Peer Review: Analysis

    SciTech Connect

    Haq, Zia

    2012-02-01

    This document summarizes the recommendations and evaluations provided by an independent external panel of experts at the 2011 U.S. Department of Energy Biomass Program’s Analysis Platform Review meeting.

  8. 2011 Biomass Program Platform Peer Review. Sustainability

    SciTech Connect

    Eng, Alison Goss

    2012-02-01

    This document summarizes the recommendations and evaluations provided by an independent external panel of experts at the 2011 U.S. Department of Energy Biomass Program’s Sustainability Platform Review meeting.

  9. Cloud Based Applications and Platforms (Presentation)

    SciTech Connect

    Brodt-Giles, D.

    2014-05-15

    Presentation to the Cloud Computing East 2014 Conference, where we are highlighting our cloud computing strategy, describing the platforms on the cloud (including Smartgrid.gov), and defining our process for implementing cloud based applications.

  10. A Comprehensive Platform for NGS Data Analysis

    SciTech Connect

    Kravitz, Saul

    2010-06-03

    Saul Kravitz of CLC Bio discusses the company's Genomic Workbench and how it can be used with data from next generation sequencing platforms on June 3, 2010 at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM

  11. Virtual health platform for medical tourism purposes.

    PubMed

    Martinez, Debora; Ferriol, Pedro; Tous, Xisco; Cabrer, Miguel; Prats, Mercedes

    2008-01-01

    This paper introduces an overview of the Virtual Health Platform (VHP), an alternative approach to create a functional PHR system in a medical tourism environment. The proposed platform has been designed in order to be integrated with EHR infrastructures and in this way it expects to be useful and more advantageous to the patient or tourist. Use cases of the VHP and its potential benefits summarize the analysis.

  12. Creating Math Videos: Comparing Platforms and Software

    ERIC Educational Resources Information Center

    Abbasian, Reza O.; Sieben, John T.

    2016-01-01

    In this paper we present a short tutorial on creating mini-videos using two platforms--PCs and tablets such as iPads--and software packages that work with these devices. Specifically, we describe the step-by-step process of creating and editing videos using a Wacom Intuos pen-tablet plus Camtasia software on a PC platform and using the software…

  13. Secondary capping beams for offshore drilling platforms

    SciTech Connect

    Albaugh, E. K.

    1985-08-13

    A pair of I-shaped elongated girders secured to, and extending outwardly from, the capping beams of a four pile platform, to form cantilever secondary capping beams which support modified self-contained drilling rigs of a size and weight normally installed on eight pile platforms. Rig modifications comprise separation of pump and engine packages, a pipe rack extension, and a novel skidding system.

  14. Handheld Microneedle-Based Electrolyte Sensing Platform.

    SciTech Connect

    Miller, Philip R.; Rivas, Rhiana; Johnson, David; Edwards, Thayne L.; Koskelo, Markku; Shawa, Luay; Brener, Igal; Chavez, Victor H.; Polsky, Ronen

    2015-11-01

    Sandia National Laboratories will provide technical assistance, within time and budget, to Requester on testing and analyzing a microneedle-based electrolyte sensing platform. Hollow microneedles will be fabricated at Sandia and integrated with a fluidic chip using plastic laminate prototyping technology available at Sandia. In connection with commercial ion selective electrodes the sensing platform will be tested for detection of electrolytes (sodium and/or potassium) within physiological relevant concent ration ranges.

  15. Advanced control technology for LSST platform

    NASA Astrophysics Data System (ADS)

    Edmunds, R. S.

    1981-02-01

    Basic technology in the design, mechanization, and analysis of control systems for large flexible space structures was examined. The focus of the platform control effort was on pointing control. The reason for this emphasis was because of the unique problems in this area posed by multiple independent experiment packages operating simultaneously on a single platform. Attitude control and stationkeeping were also addressed for future consideration.

  16. Psychosocial burden among offshore drilling platform employees.

    PubMed

    Leszczyńska, Irena; Jeżewska, Maria

    2010-01-01

    Conditions of work on offshore drilling platforms are particularly hard due to extreme environmental situations created both by nature and technological processes. Oil drilling workers employed on the open sea are potentially exposed to permanently high stress. Apart from the obvious objective factors affecting drilling platform employees, a great role in the general work-related stress level is played by the working conditions and work-related psychosocial factors, defined according to Karask's concept as demands, control, and social support. A total of 184 drill platform workers were examined using objective and subjective research methods. The level of subjective stress among drilling platform workers is lower than the level of objective stress and the stress resulting from prognoses related with specificity of work in extremely hard conditions (audit). The examinations of drilling platform workers reveal a positive role of stress in psychological adaptation, being a special case of the "work ethos" and attachment to the firm. In such investigations of work-related stress on drilling platforms, which are very specific workplaces, a multi-aspect character, sociological and economic aspects, organizational culture conditions in the firm, and a tendency to conceal ailments and the stress experienced should be taken into account. It is important to apply measures referring to at least three different types of evidence (objective demands, subjective stress, health problems reported). Otherwise, the result reflecting work-related stress may not be objective and far from the truth.

  17. Nanopaper as an Optical Sensing Platform.

    PubMed

    Morales-Narváez, Eden; Golmohammadi, Hamed; Naghdi, Tina; Yousefi, Hossein; Kostiv, Uliana; Horák, Daniel; Pourreza, Nahid; Merkoçi, Arben

    2015-07-28

    Bacterial cellulose nanopaper (BC) is a multifunctional material known for numerous desirable properties: sustainability, biocompatibility, biodegradability, optical transparency, thermal properties, flexibility, high mechanical strength, hydrophilicity, high porosity, broad chemical-modification capabilities and high surface area. Herein, we report various nanopaper-based optical sensing platforms and describe how they can be tuned, using nanomaterials, to exhibit plasmonic or photoluminescent properties that can be exploited for sensing applications. We also describe several nanopaper configurations, including cuvettes, plates and spots that we printed or punched on BC. The platforms include a colorimetric-based sensor based on nanopaper containing embedded silver and gold nanoparticles; a photoluminescent-based sensor, comprising CdSe@ZnS quantum dots conjugated to nanopaper; and a potential up-conversion sensing platform constructed from nanopaper functionalized with NaYF4:Yb(3+)@Er(3+)&SiO2 nanoparticles. We have explored modulation of the plasmonic or photoluminescent properties of these platforms using various model biologically relevant analytes. Moreover, we prove that BC is and advantageous preconcentration platform that facilitates the analysis of small volumes of optically active materials (∼4 μL). We are confident that these platforms will pave the way to optical (bio)sensors or theranostic devices that are simple, transparent, flexible, disposable, lightweight, miniaturized and perhaps wearable.

  18. Gear optimization

    NASA Technical Reports Server (NTRS)

    Vanderplaats, G. N.; Chen, Xiang; Zhang, Ning-Tian

    1988-01-01

    The use of formal numerical optimization methods for the design of gears is investigated. To achieve this, computer codes were developed for the analysis of spur gears and spiral bevel gears. These codes calculate the life, dynamic load, bending strength, surface durability, gear weight and size, and various geometric parameters. It is necessary to calculate all such important responses because they all represent competing requirements in the design process. The codes developed here were written in subroutine form and coupled to the COPES/ADS general purpose optimization program. This code allows the user to define the optimization problem at the time of program execution. Typical design variables include face width, number of teeth and diametral pitch. The user is free to choose any calculated response as the design objective to minimize or maximize and may impose lower and upper bounds on any calculated responses. Typical examples include life maximization with limits on dynamic load, stress, weight, etc. or minimization of weight subject to limits on life, dynamic load, etc. The research codes were written in modular form for easy expansion and so that they could be combined to create a multiple reduction optimization capability in future.

  19. Hybrid laser integration for silicon photonics platform

    NASA Astrophysics Data System (ADS)

    Yang, Shuyu

    Silicon photonics has attracted extensive attention in both academia and industry in recent years, as an enabling technology to address the exponentially increasing demands for communication bandwidth. It brings state-of-the-art complementary metal-oxide-semiconductor (CMOS) processing technology to the field of photonic integration. The high yield and uniformity of silicon devices make it possible to build complex photonic systems-on-chip in large production volumes. Cutting-edge device performance has been demonstrated on this platform, including high-speed modulators, photodetectors, and passive devices such as the Y-junction, waveguide crossing, and arrayed waveguide gratings. As the device library quickly matures, an integrated laser source for a transmitter remains missing from the design kit. I demonstrated hybrid external cavity lasers by integrating reflective optical semiconductor amplifiers and silicon photonics chips. The gain chip and silicon chip can be designed and optimized independently, which is a significant advantage compared to bonding an III-V film on top of the silicon chip. Advanced optoelectronics packaging processes can be leveraged for chip alignment. Tunable C-Band (near 1550 nm) lasers with 10 mW on-chip power and less than 220 kHz bandwidth are demonstrated. O-Band lasers (operating near 1310 nm) as well as successful data transmission at 10 Gb/s and 40 Gb/s using the hybrid laser as the light source are also demonstrated. I designed a single cavity, multi wavelength laser by utilizing a quantum dot SOA, Sagnac loop and micro-ring based silicon photonics half cavity. Four lasing peaks with less than 3 dB power non-uniformity were measured, as well as 4 x 10 Gb/s error free data transmission. In addition to my main focus on RSOA/Silicon external cavity lasers, I propose and demonstrate a novel germanium-assisted grating coupler with low loss on-and-off chip fiber coupling. A coupling efficiency of 76% at 1.55 microm and 40 nm 1 d

  20. Composite nanowire networks for biological sensor platforms

    NASA Astrophysics Data System (ADS)

    Jabal, Jamie Marie Francisco

    The main goal of this research is to design, fabricate, and test a nanomaterial-based platform adequate for the measurement of physiological changes in living cells. The two primary objectives toward this end are (1) the synthesis and selection of a suitable nanomaterial and (2) the demonstration of cellular response to a direct stimulus. Determining a useful nanomaterial morphology and behavior within a sensor configuration presented challenges based on cellular integration and access to electrochemical characterization. The prospect for feasible optimization and eventual scale-up in technology were also significant. Constraining criteria are that the nanomaterial detector must (a) be cheap and relatively easy to fabricate controllably, (b) encourage cell attachment, (c) exhibit consistent wettability over time, and (d) facilitate electrochemical processes. The ultimate goal would be to transfer a proof-of-principle and proof-of-design for a whole-cell sensor technology that is cost effective and has a potential for hand-held packaging. Initial tasks were to determine an effective and highly-functional nanomaterial for biosensors by assessing wettability, morphology and conductivity behavior of several candidate materials: gallium nitride nanowires, silicon dioxide nanosprings and nanowires, and titania nanofibers. Electrospinning poly(vinyl pyrrolidone)-coated titania nano- and microfibers (O20 nm--2 microm) into a pseudo-random network is controllable to a uniformity of 1--2° in contact angle. The final electrode can be prepared with a precise wettability ranging from partial wetting to ultrahydrophobic (170°) on a variety of substrates: glass, indium tin oxide, silicon, and aluminum. Fiber mats exhibit excellent mechanical stability against rinsing, and support the incubation of epithelial (skin) and pancreatic cells. Impedance spectroscopy on the whole-cell sensor shows resistive changes attributed to cell growth as well as complex frequency

  1. Electric Propulsion Platforms at DFRC

    NASA Technical Reports Server (NTRS)

    Baraaclough, Jonathan

    2009-01-01

    NASA Dryden Flight Research Center is a world-class flight research facility located at Edwards AFB, CA. With access to a 44 sq. mile dry lakebed and 350 testable days per year, it is the ideal location for flight research. DFRC has been undertaking aircraft research for approximately six decades including the famous X-aircraft (X-1 through X-48) and many science and exploration platforms. As part of this impressive heritage, DFRC has garnered more hours of full-sized electric aircraft testing than any other facility in the US, and possibly the world. Throughout the 80 s and 90 s Dryden was the home of the Pathfinder, Pathfinder Plus, and Helios prototype solar-electric aircraft. As part of the ERAST program, these electric aircraft achieved a world record 97,000 feet altitude for propeller-driven aircraft. As a result of these programs, Dryden s staff has collected thousands of man-hours of electric aircraft research and testing. In order to better answer the needs of the US in providing aircraft technologies with lower fuel consumption, lower toxic emissions (NOx, CO, VOCs, etc.), lower greenhouse gas (GHG) emissions, and lower noise emissions, NASA has engaged in cross-discipline research under the Aeronautics Research Mission Directorate (ARMD). As a part of this overall effort, Mark Moore of LaRC has initiated a cross-NASA-center electric propulsion working group (EPWG) to focus on electric propulsion technologies as applied to aircraft. Electric propulsion technologies are ideally suited to overcome all of the obstacles mentioned above, and are at a sufficiently advanced state of development component-wise to warrant serious R&D and testing (TRL 3+). The EPWG includes participation from NASA Langley Research Center (LaRC), Glenn Research Center (GRC), Ames Research Center (ARC), and Dryden Flight Research Center (DFRC). Each of the center participants provides their own unique expertise to support the overall goal of advancing the state-of-the-art in aircraft

  2. An ultra-tunable platform for molecular engineering of high-performance crystalline porous materials

    DOE PAGES

    Zhai, Quan -Guo; Bu, Xianhui; Mao, Chengyu; ...

    2016-12-07

    Metal-organic frameworks are a class of crystalline porous materials with potential applications in catalysis, gas separation and storage, and so on. Of great importance is the development of innovative synthetic strategies to optimize porosity, composition and functionality to target specific applications. Here we show a platform for the development of metal-organic materials and control of their gas sorption properties. This platform can accommodate a large variety of organic ligands and homo- or hetero-metallic clusters, which allows for extraordinary tunability in gas sorption properties. Even without any strong binding sites, most members of this platform exhibit high gas uptake capacity. Asmore » a result, the high capacity is accomplished with an isosteric heat of adsorption as low as 20 kJ mol–1 for carbon dioxide, which could bring a distinct economic advantage because of the significantly reduced energy consumption for activation and regeneration of adsorbents.« less

  3. Exploring thermoelectric effects and Wiedemann-Franz violation in magnetic nanostructures via micromachined thermal platforms

    NASA Astrophysics Data System (ADS)

    Zink, B. L.; Avery, A. D.; Sultan, Rubina; Bassett, D.; Pufall, M. R.

    2010-04-01

    We describe the development and use of micromachined thermal isolation structures to explore thermoelectric effects in magnetic thin films and nanostructures. These unique measurement techniques allow fundamental studies that will help enable a wide range of spin-caloritronic devices that take advantage of the coupling between heat and magnetic degrees of freedom for useful effects. The thermal platform is capable of measuring thermal conductivity, k, thermopower (Seebeck coefficient), α, and electrical conductivity, σ, all on the same thin film sample. This also allows direct comparison of the measured thermal conductivity of a magnetic thin film to the prediction of the Wiedemann-Franz law based on measured electrical conductivity. In addition to describing the fabrication of the platforms and the basic principles of their operation, we present example data on nickel and nickel-iron alloy thin films, and briefly consider the range of samples that can be measured with both current techniques and future thermal platforms optimized for nanoscale samples.

  4. An ultra-tunable platform for molecular engineering of high-performance crystalline porous materials

    NASA Astrophysics Data System (ADS)

    Zhai, Quan-Guo; Bu, Xianhui; Mao, Chengyu; Zhao, Xiang; Daemen, Luke; Cheng, Yongqiang; Ramirez-Cuesta, Anibal J.; Feng, Pingyun

    2016-12-01

    Metal-organic frameworks are a class of crystalline porous materials with potential applications in catalysis, gas separation and storage, and so on. Of great importance is the development of innovative synthetic strategies to optimize porosity, composition and functionality to target specific applications. Here we show a platform for the development of metal-organic materials and control of their gas sorption properties. This platform can accommodate a large variety of organic ligands and homo- or hetero-metallic clusters, which allows for extraordinary tunability in gas sorption properties. Even without any strong binding sites, most members of this platform exhibit high gas uptake capacity. The high capacity is accomplished with an isosteric heat of adsorption as low as 20 kJ mol-1 for carbon dioxide, which could bring a distinct economic advantage because of the significantly reduced energy consumption for activation and regeneration of adsorbents.

  5. An ultra-tunable platform for molecular engineering of high-performance crystalline porous materials

    SciTech Connect

    Zhai, Quan -Guo; Bu, Xianhui; Mao, Chengyu; Zhao, Xiang; Daemen, Luke; Cheng, Yongqiang; Ramirez-Cuesta, Anibal J.; Feng, Pingyun

    2016-12-07

    Metal-organic frameworks are a class of crystalline porous materials with potential applications in catalysis, gas separation and storage, and so on. Of great importance is the development of innovative synthetic strategies to optimize porosity, composition and functionality to target specific applications. Here we show a platform for the development of metal-organic materials and control of their gas sorption properties. This platform can accommodate a large variety of organic ligands and homo- or hetero-metallic clusters, which allows for extraordinary tunability in gas sorption properties. Even without any strong binding sites, most members of this platform exhibit high gas uptake capacity. As a result, the high capacity is accomplished with an isosteric heat of adsorption as low as 20 kJ mol–1 for carbon dioxide, which could bring a distinct economic advantage because of the significantly reduced energy consumption for activation and regeneration of adsorbents.

  6. Technology assessment for an integrated PC-based platform for three telemedicine applications

    NASA Astrophysics Data System (ADS)

    Tohme, Walid G.; Hayes, Wendelin S.; Dai, Hailei L.; Komo, Darmadi; Pahira, John J.; Abernethy, Darrell R.; Rennert, Wolfgang; Kuehl, Karen S.; Hauser, Gabriel J.; Mun, Seong K.

    1996-05-01

    This paper investigates the design and technical efficacy of an integrated PC based platform for three different medical applications. The technical efficacy of such a telemedicine platform has not been evaluated in the literature and optimal technical requirements have not been developed. The first application, with the Department of Surgery, Division of Urology, tests the utility of a telemedicine platform including radiology images for a surgical stone disease consultation service from an off site location in West Virginia. The second application, with the Department of Internal Medicine, Division of Clinical Pharmacology, investigates the usefulness of telemedicine when used for a clinical pharmacology consultation service from an off-site location. The third application, with the Department of Pediatrics, will test telemedicine for trauma care triage service first within an off-site location in Virginia and then from there to Georgetown University Medical Center.

  7. Open-WiSe: A Solar Powered Wireless Sensor Network Platform

    PubMed Central

    González, Apolinar; Aquino, Raúl; Mata, Walter; Ochoa, Alberto; Saldaña, Pedro; Edwards, Arthur

    2012-01-01

    Because battery-powered nodes are required in wireless sensor networks and energy consumption represents an important design consideration, alternate energy sources are needed to provide more effective and optimal function. The main goal of this work is to present an energy harvesting wireless sensor network platform, the Open Wireless Sensor node (WiSe). The design and implementation of the solar powered wireless platform is described including the hardware architecture, firmware, and a POSIX Real-Time Kernel. A sleep and wake up strategy was implemented to prolong the lifetime of the wireless sensor network. This platform was developed as a tool for researchers investigating Wireless sensor network or system integrators. PMID:22969396

  8. An ultra-tunable platform for molecular engineering of high-performance crystalline porous materials

    PubMed Central

    Zhai, Quan-Guo; Bu, Xianhui; Mao, Chengyu; Zhao, Xiang; Daemen, Luke; Cheng, Yongqiang; Ramirez-Cuesta, Anibal J.; Feng, Pingyun

    2016-01-01

    Metal-organic frameworks are a class of crystalline porous materials with potential applications in catalysis, gas separation and storage, and so on. Of great importance is the development of innovative synthetic strategies to optimize porosity, composition and functionality to target specific applications. Here we show a platform for the development of metal-organic materials and control of their gas sorption properties. This platform can accommodate a large variety of organic ligands and homo- or hetero-metallic clusters, which allows for extraordinary tunability in gas sorption properties. Even without any strong binding sites, most members of this platform exhibit high gas uptake capacity. The high capacity is accomplished with an isosteric heat of adsorption as low as 20 kJ mol−1 for carbon dioxide, which could bring a distinct economic advantage because of the significantly reduced energy consumption for activation and regeneration of adsorbents. PMID:27924818

  9. Low Cost Hydrogen Production Platform

    SciTech Connect

    Timothy M. Aaron, Jerome T. Jankowiak

    2009-10-16

    A technology and design evaluation was carried out for the development of a turnkey hydrogen production system in the range of 2.4 - 12 kg/h of hydrogen. The design is based on existing SMR technology and existing chemical processes and technologies to meet the design objectives. Consequently, the system design consists of a steam methane reformer, PSA system for hydrogen purification, natural gas compression, steam generation and all components and heat exchangers required for the production of hydrogen. The focus of the program is on packaging, system integration and an overall step change in the cost of capital required for the production of hydrogen at small scale. To assist in this effort, subcontractors were brought in to evaluate the design concepts and to assist in meeting the overall goals of the program. Praxair supplied the overall system and process design and the subcontractors were used to evaluate the components and system from a manufacturing and overall design optimization viewpoint. Design for manufacturing and assembly (DFMA) techniques, computer models and laboratory/full-scale testing of components were utilized to optimize the design during all phases of the design development. Early in the program evaluation, a review of existing Praxair hydrogen facilities showed that over 50% of the installed cost of a SMR based hydrogen plant is associated with the high temperature components (reformer, shift, steam generation, and various high temperature heat exchange). The main effort of the initial phase of the program was to develop an integrated high temperature component for these related functions. Initially, six independent concepts were developed and the processes were modeled to determine overall feasibility. The six concepts were eventually narrowed down to the highest potential concept. A US patent was awarded in February 2009 for the Praxair integrated high temperature component design. A risk analysis of the high temperature component was

  10. A novel real time imaging platform to quantify macrophage phagocytosis.

    PubMed

    Kapellos, Theodore S; Taylor, Lewis; Lee, Heyne; Cowley, Sally A; James, William S; Iqbal, Asif J; Greaves, David R

    2016-09-15

    Phagocytosis of pathogens, apoptotic cells and debris is a key feature of macrophage function in host defense and tissue homeostasis. Quantification of macrophage phagocytosis in vitro has traditionally been technically challenging. Here we report the optimization and validation of the IncuCyte ZOOM® real time imaging platform for macrophage phagocytosis based on pHrodo® pathogen bioparticles, which only fluoresce when localized in the acidic environment of the phagolysosome. Image analysis and fluorescence quantification were performed with the automated IncuCyte™ Basic Software. Titration of the bioparticle number showed that the system is more sensitive than a spectrofluorometer, as it can detect phagocytosis when using 20× less E. coli bioparticles. We exemplified the power of this real time imaging platform by studying phagocytosis of murine alveolar, bone marrow and peritoneal macrophages. We further demonstrate the ability of this platform to study modulation of the phagocytic process, as pharmacological inhibitors of phagocytosis suppressed bioparticle uptake in a concentration-dependent manner, whereas opsonins augmented phagocytosis. We also investigated the effects of macrophage polarization on E. coli phagocytosis. Bone marrow-derived macrophage (BMDM) priming with M2 stimuli, such as IL-4 and IL-10 resulted in higher engulfment of bioparticles in comparison with M1 polarization. Moreover, we demonstrated that tolerization of BMDMs with lipopolysaccharide (LPS) results in impaired E. coli bioparticle phagocytosis. This novel real time assay will enable researchers to quantify macrophage phagocytosis with a higher degree of accuracy and sensitivity and will allow investigation of limited populations of primary phagocytes in vitro.

  11. Feasibility of a low-cost sounding rockoon platform

    NASA Astrophysics Data System (ADS)

    Okninski, Adam; Raurell, Daniel Sors; Mitre, Alberto Rodriguez

    2016-10-01

    This paper presents the results of analyses and simulations for the design of a small sounding platform, dedicated to conducting scientific atmospheric research and capable of reaching the von Kármán line by means of a rocket launched from it. While recent private initiatives have opted for the air launch concept to send small payloads to Low Earth Orbit, several historical projects considered the use of balloons as the first stage of orbital and suborbital platforms, known as rockoons. Both of these approaches enable the minimization of drag losses. This paper addresses the issue of utilizing stratospheric balloons as launch platforms to conduct sub-orbital rocket flights. Research and simulations have been conducted to demonstrate these capabilities and feasibility. A small sounding solid propulsion rocket using commercially-off-the-shelf hardware is proposed. Its configuration and design are analyzed with special attention given to the propulsion system and its possible mission-orientated optimization. The cost effectiveness of this approach is discussed. Performance calculation outcomes are shown. Additionally, sensitivity study results for different design parameters are given. Minimum mass rocket configurations for various payload requirements are presented. The ultimate aim is to enhance low-cost experimentation maintaining high mobility of the system and simplicity of operations. An easier and more affordable access to a space-like environment can be achieved with this system, thus allowing for widespread outreach of space science and technology knowledge. This project is based on earlier experience of the authors in LEEM Association of the Technical University of Madrid and the Polish Small Sounding Rocket Program developed at the Institute of Aviation and Warsaw University of Technology in Poland.

  12. Chemical and biochemical analysis using microfluidic-localized field platforms

    NASA Astrophysics Data System (ADS)

    Sepaniak, Michael; Abu-Hatab, Nahla; Wellman, Amber; John, Joshy; Connatser, Maggie

    2007-09-01

    Microfluidics offer the advantages of multiplexed analysis on small, inexpensive platforms. We describe herein two distinct optical detection techniques that have the common point of sequestering and measuring analyte signals in highly localized EM fields. The first technique mates a microfluidic polydimethylsiloxane (PDMS) platform with colloidal-based surface enhanced Raman scattering (SERS) in order to perform parallel, high throughput vibrational spectroscopy. Spectra are acquired for analytes localized in surface plasmon fields associated with conventional and uniquely synthesized cubic silver colloids. SERS studies such as pH of the colloidal solution, and the type of colloid are used to demonstrate the efficiency and applicability of the method. In addition, a facile passive pumping method is used to deliver Ag colloids and analytes into the channels where all SERS measurements were completed under nondestructive flowing conditions. With this approach, SERS signal reproducibility was found to be better than 7%. A calibration curve for the drug mitoxantrone (resonance enhanced) was generated. The second technique seeks to integrate a passively-pumped, microfluidic, PDMS platform and planar waveguide technology, utilizing magnetic beads as solid supports for fluoro-assays with direct detection of bound analyte within the sample mixture accomplished by selectively driving functionalized beads to a localized evanescent field. Because analyte binding occurs in free solution, the reaction is not diffusion limited and, once magnetically delivered to the evanescent wave, the analyte can be detected with fewer complications arising from non-optically homogeneous, biological matrices. Additionally, the evanescent sensing surface can be easily regenerated by simply removing the bead-retaining magnetic field. Initial testing, optimization and calibration were performed using a model sandwich immunoassay system for the detection of rabbit IgG, with which we demonstrate a

  13. New 3-D microarray platform based on macroporous polymer monoliths.

    PubMed

    Rober, M; Walter, J; Vlakh, E; Stahl, F; Kasper, C; Tennikova, T

    2009-06-30

    Polymer macroporous monoliths are widely used as efficient sorbents in different, mostly dynamic, interphase processes. In this paper, monolithic materials strongly bound to the inert glass surface are suggested as operative matrices at the development of three-dimensional (3-D) microarrays. For this purpose, several rigid macroporous copolymers differed by reactivity and hydrophobic-hydrophilic properties were synthesized and tested: (1) glycidyl methacrylate-co-ethylene dimethacrylate (poly(GMA-co-EDMA)), (2) glycidyl methacrylate-co-glycerol dimethacrylate (poly(GMA-co-GDMA)), (3) N-hydroxyphthalimide ester of acrylic acid-co-glycidyl methacrylate-co-ethylene dimethacrylate (poly(HPIEAA-co-GMA-co-EDMA)), (4) 2-cyanoethyl methacrylate-co-ethylene dimethacrylate (poly(CEMA-co-EDMA)), and (5) 2-cyanoethyl methacrylate-co-2-hydroxyethyl methacrylate-co-ethylene dimethacrylate (poly(CEMA-co-HEMA-co-EDMA)). The constructed devices were used as platforms for protein microarrays construction and model mouse IgG-goat anti-mouse IgG affinity pair was used to demonstrate the potential of developed test-systems, as well as to optimize microanalytical conditions. The offered microarray platforms were applied to detect the bone tissue marker osteopontin directly in cell culture medium.

  14. Diffuse optical tomography using multichannel robotic platform for interstitial PDT

    PubMed Central

    Sharikova, Anna V.; Liang, Xing; Zhu, Timothy C.

    2015-01-01

    In the operating room, time is extremely precious, and the speed of one’s data acquisition system often determines whether the data will be taken or not. Our multichannel robotic platform addresses this issue by optimizing source and detector scanning procedures. Up to 16 fibers can be moved independently with resolution of 0.05 mm and speed of 50 mm/s using motors with position feedback. The initial fiber alignment employs a light beam/optical detector system for identical positioning of all motors. Peak and edge detection algorithms, for point and linear sources, are used with multiple fibers simultaneously for fast realignment of sources and detectors. The robotic platform is used to perform Diffuse Optical Tomography (DOT) measurements in solid prostate phantoms with both homogenous and inhomogeneous Optical Properties (OP). Correct positioning is critical for the accurate recovery of the OP. The light fluence rate distribution is determined by scanning multiple detector fibers simultaneously along lit linear sources placed throughout the phantom volume inside catheter needles. The scanning time for the entire DOT is about 10 seconds after the initial alignment. The OP distribution reconstruction is based on the steady-state light diffusion equation. The inverse interstitial DOT problem is solved using NIRFAST. The optical properties are recovered by iterative minimization of the difference between measured and calculated light fluence rates. Recovered OP agree with the actual values within 10%. The OP corrections are used to significantly improve light fluence accuracy for the entire volume of bulk tumor. PMID:25999650

  15. An extensible imaging platform for optical imaging applications

    NASA Astrophysics Data System (ADS)

    Paladini, Gianluca; Azar, Fred S.

    2009-02-01

    The National Institutes of Health (NIH) has recently developed an extensible imaging platform (XIP), a new open-source software development platform. XIP can be used to rapidly develop imaging applications designed to meet the needs of the optical imaging community. XIP is a state-of-the-art set of visual 'drag and drop' programming tools and associated libraries for rapid prototyping and application development. The tools include modules tailored for medical imaging, many of which are GPU hardware accelerated. They also provide a friendlier environment for utilizing popular toolkits such as ITK and VTK, and enable the visualization and processing of optical imaging data and standard DICOM data. XIP has built-in functionality for multidimensional data visualization and processing, and enables the development of independently optimized and re-usable software modules, which can be seamlessly added and interconnected to build advanced applications. XIP applications can run "stand alone", including in client/server mode for remote access. XIP also supports the DICOM WG23 "Application Hosting" standard, which will enable plug-in XIP applications to run on any DICOM host workstation. Such interoperability will enable the optical imaging community to develop and deploy modular applications across all academic/clinical/industry partners with WG23 compliant imaging workstations.

  16. Design and development of synthetic microbial platform cells for bioenergy

    PubMed Central

    Lee, Sang Jun; Lee, Sang-Jae; Lee, Dong-Woo

    2013-01-01

    The finite reservation of fossil fuels accelerates the necessity of development of renewable energy sources. Recent advances in synthetic biology encompassing systems biology and metabolic engineering enable us to engineer and/or create tailor made microorganisms to produce alternative biofuels for the future bio-era. For the efficient transformation of biomass to bioenergy, microbial cells need to be designed and engineered to maximize the performance of cellular metabolisms for the production of biofuels during energy flow. Toward this end, two different conceptual approaches have been applied for the development of platform cell factories: forward minimization and reverse engineering. From the context of naturally minimized genomes,non-essential energy-consuming pathways and/or related gene clusters could be progressively deleted to optimize cellular energy status for bioenergy production. Alternatively, incorporation of non-indigenous parts and/or modules including biomass-degrading enzymes, carbon uptake transporters, photosynthesis, CO2 fixation, and etc. into chassis microorganisms allows the platform cells to gain novel metabolic functions for bioenergy. This review focuses on the current progress in synthetic biology-aided pathway engineering in microbial cells and discusses its impact on the production of sustainable bioenergy. PMID:23626588

  17. Design and development of synthetic microbial platform cells for bioenergy.

    PubMed

    Lee, Sang Jun; Lee, Sang-Jae; Lee, Dong-Woo

    2013-01-01

    The finite reservation of fossil fuels accelerates the necessity of development of renewable energy sources. Recent advances in synthetic biology encompassing systems biology and metabolic engineering enable us to engineer and/or create tailor made microorganisms to produce alternative biofuels for the future bio-era. For the efficient transformation of biomass to bioenergy, microbial cells need to be designed and engineered to maximize the performance of cellular metabolisms for the production of biofuels during energy flow. Toward this end, two different conceptual approaches have been applied for the development of platform cell factories: forward minimization and reverse engineering. From the context of naturally minimized genomes,non-essential energy-consuming pathways and/or related gene clusters could be progressively deleted to optimize cellular energy status for bioenergy production. Alternatively, incorporation of non-indigenous parts and/or modules including biomass-degrading enzymes, carbon uptake transporters, photosynthesis, CO2 fixation, and etc. into chassis microorganisms allows the platform cells to gain novel metabolic functions for bioenergy. This review focuses on the current progress in synthetic biology-aided pathway engineering in microbial cells and discusses its impact on the production of sustainable bioenergy.

  18. Geospatial Service Platform for Education and Research

    NASA Astrophysics Data System (ADS)

    Gong, J.; Wu, H.; Jiang, W.; Guo, W.; Zhai, X.; Yue, P.

    2014-04-01

    We propose to advance the scientific understanding through applications of geospatial service platforms, which can help students and researchers investigate various scientific problems in a Web-based environment with online tools and services. The platform also offers capabilities for sharing data, algorithm, and problem-solving knowledge. To fulfil this goal, the paper introduces a new course, named "Geospatial Service Platform for Education and Research", to be held in the ISPRS summer school in May 2014 at Wuhan University, China. The course will share cutting-edge achievements of a geospatial service platform with students from different countries, and train them with online tools from the platform for geospatial data processing and scientific research. The content of the course includes the basic concepts of geospatial Web services, service-oriented architecture, geoprocessing modelling and chaining, and problem-solving using geospatial services. In particular, the course will offer a geospatial service platform for handson practice. There will be three kinds of exercises in the course: geoprocessing algorithm sharing through service development, geoprocessing modelling through service chaining, and online geospatial analysis using geospatial services. Students can choose one of them, depending on their interests and background. Existing geoprocessing services from OpenRS and GeoPW will be introduced. The summer course offers two service chaining tools, GeoChaining and GeoJModelBuilder, as instances to explain specifically the method for building service chains in view of different demands. After this course, students can learn how to use online service platforms for geospatial resource sharing and problem-solving.

  19. A microbial biomanufacturing platform for natural and semisynthetic opioids.

    PubMed

    Thodey, Kate; Galanie, Stephanie; Smolke, Christina D

    2014-10-01

    Opiates and related molecules are medically essential, but their production via field cultivation of opium poppy Papaver somniferum leads to supply inefficiencies and insecurity. As an alternative production strategy, we developed baker's yeast Saccharomyces cerevisiae as a microbial host for the transformation of opiates. Yeast strains engineered to express heterologous genes from P. somniferum and bacterium Pseudomonas putida M10 convert thebaine to codeine, morphine, hydromorphone, hydrocodone and oxycodone. We discovered a new biosynthetic branch to neopine and neomorphine, which diverted pathway flux from morphine and other target products. We optimized strain titer and specificity by titrating gene copy number, enhancing cosubstrate supply, applying a spatial engineering strategy and performing high-density fermentation, which resulted in total opioid titers up to 131 mg/l. This work is an important step toward total biosynthesis of valuable benzylisoquinoline alkaloid drug molecules and demonstrates the potential for developing a sustainable and secure yeast biomanufacturing platform for opioids.

  20. Vertically Aligned Carbon Nanofiber based Biosensor Platform for Glucose Sensor

    SciTech Connect

    Al Mamun, Khandaker A.; Tulip, Fahmida S.; MacArthur, Kimberly; McFarlane, Nicole; Islam, Syed K.; Hensley, Dale

    2014-03-01

    Vertically aligned carbon nanofibers (VACNFs) have recently become an important tool for biosensor design. Carbon nanofibers (CNF) have excellent conductive and structural properties with many irregularities and defect sites in addition to exposed carboxyl groups throughout their surfaces. These properties allow a better immobilization matrix compared to carbon nanotubes and offer better resolution when compared with the FET-based biosensors. VACNFs can be deterministically grown on silicon substrates allowing optimization of the structures for various biosensor applications. Two VACNF electrode architectures have been employed in this study and a comparison of their performances has been made in terms of sensitivity, sensing limitations, dynamic range, and response time. The usage of VACNF platform as a glucose sensor has been verified in this study by selecting an optimum architecture based on the VACNF forest density. Read More: http://www.worldscientific.com/doi/abs/10.1142/S0129156414500062

  1. OSNAP! Introducing the open semantic network analysis platform

    NASA Astrophysics Data System (ADS)

    Radics, Peter J.; Polys, Nicholas F.; Neuman, Shawn P.; Lund, William H.

    2015-01-01

    Graph visualization continues to be a major challenge in the field of information visualization, meanwhile gaining importance due to the power of graph-based formulations across a wide variety of domains from knowledge representation to network flow, bioinformatics, and software optimization. We present the Open Semantic Network Analysis Platform (OSNAP), an open-source visualization framework designed for the flexible composition of 2D and 3D graph layouts. Analysts can filter and map a graph's attributes and structural properties to a variety of geometric forms including shape, color, and 3D position. Using the Provider Model software engineering pattern, developers can extend the framework with additional mappings and layout algorithms. We demonstrate the framework's flexibility by applying it to two separate domain ontologies and finally outline a research agenda to improve the value of semantic network visualization for human insight and analysis.

  2. The 2012 Lyrids from Non-traditional Observing Platforms

    NASA Technical Reports Server (NTRS)

    Moser, Danielle E.; Suggs, Robert M.; Cooke, W. J.; Blaauw, Rhiannon C.

    2013-01-01

    The NASA Meteoroid Environment Office (MEO) observed meteors during the Lyrid meteor shower peak on 22 April 2012 from three different observing platforms: the ground, a helium-filled balloon, and from the International Space Station (ISS). Even though the Lyrids are not noted for spectacular rates, the combination of New Moon and a favorable viewing geometry from ISS presented a unique opportunity to simultaneously image shower meteors from above the atmosphere and below it. In the end, however, no meteors were observed simultaneously, and it was impossible to identify Lyrids with 100% confidence among the 155 meteors observed from ISS and the 31 observed from the balloon. Still, this exercise proved successful in that meteors could be observed from a simple and inexpensive balloon-based payload and from less-than-optimal cameras on ISS.

  3. Multidisciplinary optimization

    SciTech Connect

    Dennis, J.; Lewis, R.M.; Cramer, E.J.; Frank, P.M.; Shubin, G.R.

    1994-12-31

    This talk will use aeroelastic design and reservoir characterization as examples to introduce some approaches to MDO, or Multidisciplinary Optimization. This problem arises especially in engineering design, where it is considered of paramount importance in today`s competitive global business climate. It is interesting to an optimizer because the constraints involve coupled dissimilar systems of parameterized partial differential equations each arising from a different discipline, like structural analysis, computational fluid dynamics, etc. Usually, these constraints are accessible only through pde solvers rather than through algebraic residual calculations as we are used to having. Thus, just finding a multidisciplinary feasible point is a daunting task. Many such problems have discrete variable disciplines, multiple objectives, and other challenging features. After discussing some interesting practical features of the design problem, we will give some standard ways to formulate the problem as well as some novel ways that lend themselves to divide-and-conquer parallelism.

  4. Integrated microfluidic platforms for investigating neuronal networks

    NASA Astrophysics Data System (ADS)

    Kim, Hyung Joon

    This dissertation describes the development and application of integrated microfluidics-based assay platforms to study neuronal activities in the nervous system in-vitro. The assay platforms were fabricated using soft lithography and micro/nano fabrication including microfluidics, surface patterning, and nanomaterial synthesis. The use of integrated microfluidics-based assay platform allows culturing and manipulating many types of neuronal tissues in precisely controlled microenvironment. Furthermore, they provide organized multi-cellular in-vitro model, long-term monitoring with live cell imaging, and compatibility with molecular biology techniques and electrophysiology experiment. In this dissertation, the integrated microfluidics-based assay platforms are developed for investigation of neuronal activities such as local protein synthesis, impairment of axonal transport by chemical/physical variants, growth cone path finding under chemical/physical cues, and synaptic transmission in neuronal circuit. Chapter 1 describes the motivation, objectives, and scope for developing in-vitro platform to study various neuronal activities. Chapter 2 introduces microfluidic culture platform for biochemical assay with large-scale neuronal tissues that are utilized as model system in neuroscience research. Chapter 3 focuses on the investigation of impaired axonal transport by beta-Amyloid and oxidative stress. The platform allows to control neuronal processes and to quantify mitochondrial movement in various regions of axons away from applied drugs. Chapter 4 demonstrates the development of microfluidics-based growth cone turning assay to elucidate the mechanism underlying axon guidance under soluble factors and shear flow. Using this platform, the behaviors of growth cone of mammalian neurons are verified under the gradient of inhibitory molecules and also shear flow in well-controlled manner. In Chapter 5, I combine in-vitro multicellular model with microfabricated MEA

  5. 29 CFR 1917.115 - Platforms and skids.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 29 Labor 7 2010-07-01 2010-07-01 false Platforms and skids. 1917.115 Section 1917.115 Labor... (CONTINUED) MARINE TERMINALS Terminal Facilities § 1917.115 Platforms and skids. (a) Platforms and skids... skid shall be protected from falling objects by a net stretched from the platform or skid to the...

  6. Rigid multipodal platforms for metal surfaces

    PubMed Central

    Valášek, Michal; Lindner, Marcin

    2016-01-01

    Summary In this review the recent progress in molecular platforms that form rigid and well-defined contact to a metal surface are discussed. Most of the presented examples have at least three anchoring units in order to control the spatial arrangement of the protruding molecular subunit. Another interesting feature is the lateral orientation of these foot structures which, depending on the particular application, is equally important as the spatial arrangement of the molecules. The numerous approaches towards assembling and organizing functional molecules into specific architectures on metal substrates are reviewed here. Particular attention is paid to variations of both, the core structures and the anchoring groups. Furthermore, the analytical methods enabling the investigation of individual molecules as well as monomolecular layers of ordered platform structures are summarized. The presented multipodal platforms bearing several anchoring groups form considerably more stable molecule–metal contacts than corresponding monopodal analogues and exhibit an enlarged separation of the functional molecules due to the increased footprint, as well as restrict tilting of the functional termini with respect to the metal surface. These platforms are thus ideally suited to tune important properties of the molecule–metal interface. On a single-molecule level, several of these platforms enable the control over the arrangement of the protruding rod-type molecular structures (e.g., molecular wires, switches, rotors, sensors) with respect to the surface of the substrate. PMID:27335731

  7. CC Pre-Amp Platform: Structural Analysis

    SciTech Connect

    Sakla, S.; /Fermilab

    1994-06-09

    The structure in question is an existing personnel access platform located in the D-Zero Assembly Building. This platform is used to access the preamplifiers located on the central calorimeter. The platform will need to be shortened to a 'fold-out' length of 36 in. due to some modifications recently made to the detector. The purpose of this note is to determine whether this modification affects the safety and the rated load of the platform. Three of the load carrying members were analyzed; the gusset supports, the hinge supports, and the hinge pins. The long and short beams which make up the platform's flooring were not analyzed. The long beams will not be affected by this modification because there is no change in the length of their moment arms. The short beams will be affected, but will see a smaller bending stress because of the decrease in the length of their moment arms. Any weld results previously found will also not be affected.

  8. Imputing gene expression to maximize platform compatibility.

    PubMed

    Zhou, Weizhuang; Han, Lichy; Altman, Russ B

    2017-02-15

    Microarray measurements of gene expression constitute a large fraction of publicly shared biological data, and are available in the Gene Expression Omnibus (GEO). Many studies use GEO data to shape hypotheses and improve statistical power. Within GEO, the Affymetrix HG-U133A and HG-U133 Plus 2.0 are the two most commonly used microarray platforms for human samples; the HG-U133 Plus 2.0 platform contains 54 220 probes and the HG-U133A array contains a proper subset (21 722 probes). When different platforms are involved, the subset of common genes is most easily compared. This approach results in the exclusion of substantial measured data and can limit downstream analysis. To predict the expression values for the genes unique to the HG-U133 Plus 2.0 platform, we constructed a series of gene expression inference models based on genes common to both platforms. Our model predicts gene expression values that are within the variability observed in controlled replicate studies and are highly correlated with measured data. Using six previously published studies, we also demonstrate the improved performance of the enlarged feature space generated by our model in downstream analysis.

  9. Cross-species and interassay comparisons of phytoestrogen action.

    PubMed Central

    Whitten, P L; Patisaul, H B

    2001-01-01

    This paper compiles animal and human data on the biologic effects and exposure levels of phytoestrogens in order to identify areas of research in which direct species comparisons can be made. In vitro and in vivo assays of phytoestrogen action and potency are reviewed and compared to actions, dose-response relationships, and estimates of exposure in human subjects. Binding studies show that the isoflavonoid phytoestrogens are high-affinity ligands for estrogen receptors (ERs), especially ER beta, but have lower potency in whole-cell assays, perhaps because of interactions with binding proteins. Many other enzymatic actions require concentrations higher than those normally seen in plasma. In vivo data show that phytoestrogens have a wide range of biologic effects at doses and plasma concentrations seen with normal human diets. Significant in vivoresponses have been observed in animal and human tests for bone, breast, ovary, pituitary, vasculature, prostate, and serum lipids. The doses reported to be biologically active in humans (0.4--10 mg/kg body weight/day) are lower than the doses generally reported to be active in rodents (10--100 mg/kg body weight/day), although some studies have reported rodent responses at lower doses. However, available estimates of bioavailability and peak plasma levels in rodents and humans are more similar. Steroidogenesis and the hypothalamic-pituitary-gonadal axis appear to be important loci of phytoestrogen actions, but these inferences must be tentative because good dose-response data are not available for many end points. The similarity of reported proliferative and antiproliferative doses illustrates the need for fuller examination of dose-response relationships and multiple end points in assessing phytoestrogen actions. PMID:11250801

  10. Superior cross-species reference genes: a blueberry case study.

    PubMed

    Die, Jose V; Rowland, Lisa J

    2013-01-01

    The advent of affordable Next Generation Sequencing technologies has had major impact on studies of many crop species, where access to genomic technologies and genome-scale data sets has been extremely limited until now. The recent development of genomic resources in blueberry will enable the application of high throughput gene expression approaches that should relatively quickly increase our understanding of blueberry physiology. These studies, however, require a highly accurate and robust workflow and make necessary the identification of reference genes with high expression stability for correct target gene normalization. To create a set of superior reference genes for blueberry expression analyses, we mined a publicly available transcriptome data set from blueberry for orthologs to a set of Arabidopsis genes that showed the most stable expression in a developmental series. In total, the expression stability of 13 putative reference genes was evaluated by qPCR and a set of new references with high stability values across a developmental series in fruits and floral buds of blueberry were identified. We also demonstrated the need to use at least two, preferably three, reference genes to avoid inconsistencies in results, even when superior reference genes are used. The new references identified here provide a valuable resource for accurate normalization of gene expression in Vaccinium spp. and may be useful for other members of the Ericaceae family as well.

  11. Nutritional regulation of glucokinase: a cross-species story.

    PubMed

    Panserat, Stéphane; Rideau, Nicole; Polakof, Sergio

    2014-06-01

    The glucokinase (GK) enzyme (EC 2.7.1.1.) is essential for the use of dietary glucose because it is the first enzyme to phosphorylate glucose in excess in different key tissues such as the pancreas and liver. The objective of the present review is not to fully describe the biochemical characteristics and the genetics of this enzyme but to detail its nutritional regulation in different vertebrates from fish to human. Indeed, the present review will describe the existence of the GK enzyme in different animal species that have naturally different levels of carbohydrate in their diets. Thus, some studies have been performed to analyse the nutritional regulation of the GK enzyme in humans and rodents (having high levels of dietary carbohydrates in their diets), in the chicken (moderate level of carbohydrates in its diet) and rainbow trout (no carbohydrate intake in its diet). All these data illustrate the nutritional importance of the GK enzyme irrespective of feeding habits, even in animals known to poorly use dietary carbohydrates (carnivorous species).

  12. Comparative cross-species alternative splicing in plants.

    PubMed

    Ner-Gaon, Hadas; Leviatan, Noam; Rubin, Eitan; Fluhr, Robert

    2007-07-01

    Alternative splicing (AS) can add significantly to genome complexity. Plants are thought to exhibit less AS than animals. An algorithm, based on expressed sequence tag (EST) pairs gapped alignment, was developed that takes advantage of the relatively small intron and exon size in plants and directly compares pairs of ESTs to search for AS. EST pairs gapped alignment was first evaluated in Arabidopsis (Arabidopsis thaliana), rice (Oryza sativa), and tomato (Solanum lycopersicum) for which annotated genome sequence is available and was shown to accurately predict splicing events. The method was then applied to 11 plant species that include 17 cultivars for which enough ESTs are available. The results show a large, 3.7-fold difference in AS rates between plant species with Arabidopsis and rice in the lower range and lettuce (Lactuca sativa) and sorghum (Sorghum bicolor) in the upper range. Hence, compared to higher animals, plants show a much greater degree of variety in their AS rates and in some plant species the rates of animal and plant AS are comparable although the distribution of AS types may differ. In eudicots but not monocots, a correlation between genome size and AS rates was detected, implying that in eudicots the mechanisms that lead to larger genomes are a driving force for the evolution of AS.

  13. Sim4cc: a cross-species spliced alignment program.

    PubMed

    Zhou, Leming; Pertea, Mihaela; Delcher, Arthur L; Florea, Liliana

    2009-06-01

    Advances in sequencing technologies have accelerated the sequencing of new genomes, far outpacing the generation of gene and protein resources needed to annotate them. Direct comparison and alignment of existing cDNA sequences from a related species is an effective and readily available means to determine genes in the new genomes. Current spliced alignment programs are inadequate for comparing sequences between different species, owing to their low sensitivity and splice junction accuracy. A new spliced alignment tool, sim4cc, overcomes problems in the earlier tools by incorporating three new features: universal spaced seeds, to increase sensitivity and allow comparisons between species at various evolutionary distances, and powerful splice signal models and evolutionarily-aware alignment techniques, to improve the accuracy of gene models. When tested on vertebrate comparisons at diverse evolutionary distances, sim4cc had significantly higher sensitivity compared to existing alignment programs, more than 10% higher than the closest competitor for some comparisons, while being comparable in speed to its predecessor, sim4. Sim4cc can be used in one-to-one or one-to-many comparisons of genomic and cDNA sequences, and can also be effectively incorporated into a high-throughput annotation engine, as demonstrated by the mapping of 64,000 Fagus grandifolia 454 ESTs and unigenes to the poplar genome.

  14. Evolutionary space platform concept study. Volume 2, part B: Manned space platform concepts

    NASA Technical Reports Server (NTRS)

    1982-01-01

    Logical, cost-effective steps in the evolution of manned space platforms are investigated and assessed. Tasks included the analysis of requirements for a manned space platform, identifying alternative concepts, performing system analysis and definition of the concepts, comparing the concepts and performing programmatic analysis for a reference concept.

  15. Optimal control for Rydberg quantum technology building blocks

    NASA Astrophysics Data System (ADS)

    Müller, Matthias M.; Pichler, Thomas; Montangero, Simone; Calarco, Tommaso

    2016-04-01

    We consider a platform for quantum technology based on Rydberg atoms in optical lattices where each atom encodes one qubit of information and external lasers can manipulate their state. We demonstrate how optimal control theory enables the functioning of two specific building blocks on this platform: We engineer an optimal protocol to perform a two-qubit phase gate and to transfer the information within the lattice among specific sites. These two elementary operations allow to design very general operations like storage of atoms and entanglement purification as, for example, needed for quantum repeaters.

  16. Application of simple adaptive control to rate gyroscope stable platform system

    NASA Astrophysics Data System (ADS)

    Hu, Yonghao; Song, Xueping; Li, Bangjun; Shi, Liping

    2013-09-01

    For a class of nonlinear systems with dynamic uncertainties, adaptive stabilization problem is considered in the rate gyroscope of stable platform system. Since the uncertainties are inevitable in the practical model of systems, the robust property of the systems in the presence of parametric uncertainties is important to be considered, such as modeling error, external disturbances, etc. Due to the strong nonlinearity and coupling characteristic of systems, it is difficult to obtain the precise model, and the nonlinearity cannot be cancelled exactly so that the controller performs badly. Adaptive control (AC) can adapt to parameter variations, but it is not applicable to the transition phase. A way to optimize the overall disturbances rejection performance of the AC system in the presence of unknown external disturbances existing in the stable platform system is provided in this paper. According to the construction of stable platform system based on gyroscope stabilized platform, the coordinate systems related to stable platform system are defined, and its mathematical model of stabilized platform is build up. Using the SIMULINK of MATLAB, the model is applied to the computer simulation of the stable platform system with good results. The author designed the control law of velocity-loop respective with the method of continuous correcting net and the AC. The simulation results show that the designed adaptive control law can satisfy the required criterion, it proves that the design method is feasible. In order to compare the above two method efficiently, the author gives the seeker system step response, square wave response especially. Adaptive control law is confirmed to give better tracking performance compared with correcting net control, and a control precision comparable to seeker system and higher robustness to parameter change, despite the simple controller. The research results ensure a wider application of simple AC in real mechanical systems.

  17. European research platform IPANEMA at the SOLEIL synchrotron for ancient and historical materials.

    PubMed

    Bertrand, L; Languille, M-A; Cohen, S X; Robinet, L; Gervais, C; Leroy, S; Bernard, D; Le Pennec, E; Josse, W; Doucet, J; Schöder, S

    2011-09-01

    IPANEMA, a research platform devoted to ancient and historical materials (archaeology, cultural heritage, palaeontology and past environments), is currently being set up at the synchrotron facility SOLEIL (Saint-Aubin, France; SOLEIL opened to users in January 2008). The new platform is open to French, European and international users. The activities of the platform are centred on two main fields: increased support to synchrotron projects on ancient materials and methodological research. The IPANEMA team currently occupies temporary premises at SOLEIL, but the platform comprises construction of a new building that will comply with conservation and environmental standards and of a hard X-ray imaging beamline today in its conceptual design phase, named PUMA. Since 2008, the team has supported synchrotron works at SOLEIL and at European synchrotron facilities on a range of topics including pigment degradation in paintings, composition of musical instrument varnishes, and provenancing of medieval archaeological ferrous artefacts. Once the platform is fully operational, user support will primarily take place within medium-term research projects for `hosted' scientists, PhDs and post-docs. IPANEMA methodological research is focused on advanced two-dimensional/three-dimensional imaging and spectroscopy and statistical image analysis, both optimized for ancient materials.

  18. Application and Removal of Strippable Coatings via Remote Platform - 13133

    SciTech Connect

    Shoffner, P.; Lagos, L.; Maggio, S.

    2013-07-01

    Florida International University's (FIU's) Applied Research Center is currently supporting the Department of Energy (DOE) Environmental Management Office of D and D and Facility Engineering program. FIU is supporting DOE's initiative to improve safety, reduce technical risks, and limit uncertainty within D and D operations by identifying technologies suitable to meet specific facility D and D requirements, assessing the readiness of those technologies for field deployment, and conducting feasibility studies and technology demonstrations of selected technologies and working with technology vendors to optimize the design of their current technologies to accomplish dangerous and demanding tasks during D and D operations. To meet one identified technology gap challenge for a technology to remotely apply strippable coatings, fixatives and decontamination gels, FIU identified and performed an initial demonstration of an innovative remote fixative sprayer platform from International Climbing Machines (ICM). The selected technology was demonstrated spraying fixative products at the hot cell mockup facility at the Applied Research Center at FIU in November 2008 under cold (non-radioactive) conditions. The remotely controlled platform was remotely operated and entered the facility and sprayed a fixative onto horizontal and vertical surfaces. Based on the initial FIU demonstration and the specific technical requirements identified at the DOE facilities, a follow-up demonstration was expanded to include strippable coatings and a decontamination gel, which was demonstrated in June 2010 at the ICM facility in Ithaca, NY. This second technology evaluation documented the ability of the remote system to spray the selected products on vertical stainless steel and concrete surfaces to a height of 3 meters (10 feet) and to achieve sufficient coverage and product thickness to promote the ability to peel/remove the strippable coatings and decontamination gel. The next challenge was to

  19. Development of novel microfluidic platforms for neural stem cell research

    NASA Astrophysics Data System (ADS)

    Chung, Bonggeun

    This dissertation describes the development and characterization of novel microfluidic platforms to study proliferation, differentiation, migration, and apoptosis of neural stem cells (NSCs). NSCs hold tremendous promise for fundamental biological studies and cell-based therapies in human disorders. NSCs are defined as cells that can self-renew yet maintain the ability to generate the three principal cell types of the central nervous system such as neurons, astrocytes, and oligodendrocytes. NSCs therefore have therapeutic possibilities in multiple neurodevelopmental and neurodegenerative diseases. Despite their promise, cell-based therapies are limited by the inability to precisely control their behavior in culture. Compared to traditional culture tools, microfluidic platforms can provide much greater control over cell microenvironments and optimize proliferation and differentiation conditions of cells exposed to combinatorial mixtures of growth factors. Human NSCs were cultured for more than 1 week in the microfluidic device while constantly exposed to a continuous gradient of a growth factor mixture. NSCs proliferated and differentiated in a graded and proportional fashion that varied directly with growth factor concentration. In parallel to the study of growth and differentiation of NSCs, we are interested in proliferation and apoptosis of mouse NSCs exposed to morphogen gradients. Morphogen gradients are fundamental to animal brain development. Nonetheless, much controversy remains about the mechanisms by which morphogen gradients act on the developing brain. To overcome limitations of in-vitro models of gradients, we have developed a hybrid microfluidic platform that can mimic morphogen gradient profiles. Bone morphogenetic protein (BMP) activity in the developing cortex is graded and cortical NSC responses to BMPs are highly dependent on concentration and gradient slope of BMPs. To make novel microfluidic devices integrated with multiple functions, we have

  20. Extending the BEAGLE library to a multi-FPGA platform

    PubMed Central

    2013-01-01

    Background Maximum Likelihood (ML)-based phylogenetic inference using Felsenstein’s pruning algorithm is a standard method for estimating the evolutionary relationships amongst a set of species based on DNA sequence data, and is used in popular applications such as RAxML, PHYLIP, GARLI, BEAST, and MrBayes. The Phylogenetic Likelihood Function (PLF) and its associated scaling and normalization steps comprise the computational kernel for these tools. These computations are data intensive but contain fine grain parallelism that can be exploited by coprocessor architectures such as FPGAs and GPUs. A general purpose API called BEAGLE has recently been developed that includes optimized implementations of Felsenstein’s pruning algorithm for various data parallel architectures. In this paper, we extend the BEAGLE API to a multiple Field Programmable Gate Array (FPGA)-based platform called the Convey HC-1. Results The core calculation of our implementation, which includes both the phylogenetic likelihood function (PLF) and the tree likelihood calculation, has an arithmetic intensity of 130 floating-point operations per 64 bytes of I/O, or 2.03 ops/byte. Its performance can thus be calculated as a function of the host platform’s peak memory bandwidth and the implementation’s memory efficiency, as 2.03 × peak bandwidth × memory efficiency. Our FPGA-based platform has a peak bandwidth of 76.8 GB/s and our implementation achieves a memory efficiency of approximately 50%, which gives an average throughput of 78 Gflops. This represents a ~40X speedup when compared with BEAGLE’s CPU implementation on a dual Xeon 5520 and 3X speedup versus BEAGLE’s GPU implementation on a Tesla T10 GPU for very large data sizes. The power consumption is 92 W, yielding a power efficiency of 1.7 Gflops per Watt. Conclusions The use of data parallel architectures to achieve high performance for likelihood-based phylogenetic inference requires high memory bandwidth and a design

  1. Flexible continuous manufacturing platforms for solid dispersion formulations

    NASA Astrophysics Data System (ADS)

    Karry-Rivera, Krizia Marie

    In 2013 16,000 people died in the US due to overdose from prescription drugs and synthetic narcotics. As of that same year, 90% of new molecular entities in the pharmaceutical drug pipeline are classified as poor water-soluble. The work in this dissertation aims to design, develop and validate platforms that solubilize weak acids and can potentially deter drug abuse. These platforms are based on processing solid dispersions via solvent-casting and hot-melt extrusion methods to produce oral transmucosal films and melt tablets. To develop these platforms, nanocrystalline suspensions and glassy solutions were solvent-casted in the form of films after physicochemical characterizations of drug-excipient interactions and design of experiment approaches. A second order model was fitted to the emulsion diffusion process to predict average nanoparticle size and for process optimization. To further validate the manufacturing flexibility of the formulations, glassy solutions were also extruded and molded into tablets. This process included a systematic quality-by-design (QbD) approach that served to identify the factors affecting the critical quality attributes (CQAs) of the melt tablets. These products, due to their novelty, lack discriminatory performance tests that serve as predictors to their compliance and stability. Consequently, Process Analytical Technology (PAT) tools were integrated into the continuous manufacturing platform for films. Near-infrared (NIR) spectroscopy, including chemical imaging, combined with deconvolution algorithms were utilized for a holistic assessment of the effect of formulation and process variables on the product's CQAs. Biorelevant dissolution protocols were then established to improve the in-vivo in-vitro correlation of the oral transmucosal films. In conclusion, the work in this dissertation supports the delivery of poor-water soluble drugs in products that may deter abuse. Drug nanocrystals ensured high bioavailability, while glassy

  2. Proposals for Future Virtual Environment Software Platforms

    NASA Astrophysics Data System (ADS)

    Steed, Anthony

    The past two decades have seen the development of a plethora of software solutions to support virtual environments. Many very capable software platforms, toolkits and libraries have been built, but the rate of development of new software continues to increase. There is very significant functional replication amongst these software, and there are few possibilities to migrate anything other than simple content from one piece of software to another. In this chapter we discuss why there are so many software solutions for virtual environments. We make some suggestions to software developers that might facilitate code re-use at the platform building stage, with the aim of moving towards platforms that support content re-use.

  3. GAVIP: a platform for Gaia data analysis

    NASA Astrophysics Data System (ADS)

    Vagg, Daniel; O'Callaghan, Derek; O'Hógáin, Fionn; McBreen, Sheila; Hanlon, Lorraine; Lynn, David; O'Mullane, William

    2016-07-01

    Gaia is a major European Space Agency (ESA) astrophysics mission designed to map and analyse 109 stars, ultimately generating more than 1 PetaByte of data-products. As Gaia data becomes publicly available and reaches a wider audience, there is an increasing need to facilitate the further use of Gaia products without needing to download large datasets. The Gaia Added Value Interface Platform (GAVIP) is designed to address this challenge by providing an innovative platform within which scientists can submit and deploy code, packaged as "Added Value Interfaces" (AVIs), which will be executed close to the data. Deployed AVIs and associated outputs may also be made available to other GAVIP platform users, thus providing a mechanism for scientific experiment reproducibility. This paper describes the capabilities and features of GAVIP.

  4. Development of a Zigbee platform for bioinstrumentation.

    PubMed

    Cifuentes, Carlos A; Gentiletti, Gabriel G; Suarez, Marco J; Rodriguez, Luis E

    2010-01-01

    This paper presents the development of a network platform which allows connecting multiple individual wireless devices for transmitting bioelectrics and biomechanics signals for application in a hospital network, or continuous monitoring in a patient's diary life. The Zigbee platform development proposal was made in three stages: 1) Hardware development, including the construction of a prototype network node and the integration of sensors, (2) Evaluation, in order to define the specifications of each node and scope of communication and (3) The Zigbee Network Implementation for bioinstrumentation based on ZigBee Health Care public application profile (ZHC). Finally, this work presents the experimental results based on measurements of Lost Packets and LQI (Link Quality Indicator), and the Zigbee Platform configuration for Bioinstrumentation in operation.

  5. Explosives remain preferred methods for platform abandonment

    SciTech Connect

    Pulsipher, A.; Daniel, W. IV; Kiesler, J.E.; Mackey, V. III

    1996-05-06

    Economics and safety concerns indicate that methods involving explosives remain the most practical and cost-effective means for abandoning oil and gas structures in the Gulf of Mexico. A decade has passed since 51 dead sea turtles, many endangered Kemp`s Ridleys, washed ashore on the Texas coast shortly after explosives helped remove several offshore platforms. Although no relationship between the explosions and the dead turtles was ever established, in response to widespread public concern, the US Minerals Management Service (MMS) and National Marine Fisheries Service (NMFS) implemented regulations limiting the size and timing of explosive charges. Also, more importantly, they required that operators pay for observers to survey waters surrounding platforms scheduled for removal for 48 hr before any detonations. If observers spot sea turtles or marine mammals within the danger zone, the platform abandonment is delayed until the turtles leave or are removed. However, concern about the effects of explosives on marine life remains.

  6. Communications platform payload definition study, executive summary

    NASA Technical Reports Server (NTRS)

    Clopp, H. W.; Hawkes, T. A.; Bertles, C. R.; Pontano, B. A.; Kao, T.

    1986-01-01

    Large geostationary communications platforms have been investigated in a number of studies since 1974 as a possible means to more effectively utilize the geostationary orbital arc and electromagnetic spectrum and to reduce overall satellite communications system costs. This NASA Lewis sponsored study addresses the commercial feasibility of various communications platform payload concepts circa 1998. It defines promising payload concepts, estimates recurring costs and identifies critical technologies needed to permit eventual commercialization. Ten communications service aggregation scenarios describing potential groupings of services were developed for a range of conditions. Payload concepts were defined for four of these scenarios: (1) Land Mobile Satellite Service (LMSS), meet 100% of CONUS plus Canada demand with a single platform; (2) Fixed Satellite Service (FSS) (Trunking + Customer Premises Service (CPS), meet 20% of CONUS demands; (3) FSS (Trunking + video distribution), 10 to 13% of CONUS demand; and (4) FSS (20% of demand) + Inter Satellite Links (ISL) + TDRSS/TDAS Data Distribution.

  7. Personnel evacuation apparatus for an offshore platform

    SciTech Connect

    Hunter, A.F.

    1987-04-28

    An apparatus is described for evacuating personnel from an offshore platform in all weather conditions to a position on the ocean surface a safe distance from the platform the apparatus comprising: a boat launching ramp; flotation means; boat means adapted to be supported and launched by the ramp; means for releasably securing the boat means within the ramp means adjacent the entry end; means for releasing the latch means to permit the flotation means to move the launching ramp from its stowed position to a deployed position; and means for releasing the boat securing means, thereby permitting the boat means to slide down the ramp and be launched from the exit end of the ramp onto the surface of the ocean a safe distance from the platform.

  8. Reconnaissance geophysical study of Diablo Platform, Texas

    SciTech Connect

    Crosby, G.W.; Neff, W.H.; Schlecht, R.D.; Knaus, J.R.

    1988-01-01

    The Diablo platform lies in the southeastern part of the Basin and Range province of North America. Production from several zones within the Paleozoic section has been established both in basins and shelf edges of the surrounding area. A thick sequence of volcanic rocks covers the platform in Jeff Davis County, Texas. These rocks effectively prevent seismic investigation of the presumed sedimentary section below. Gravity, magnetic, and sparse well data were used in constructing an initial geologic model. A magnetotelluric survey consisting of 18 sites showed shallow resistive anomalies in agreement with magnetic anomalies. The magnetotelluric field data were modeled using the initial geologic model. From well control data, resistivity values for the volcanic rocks, sediments, and basement were set. After successive geophysical modeling, a final geologic model was constructed, which is reconciled with the magnetotelluric, magnetic, and well control data. A possible reef is present on the northeast side of the platform.

  9. Optical detection strategies for centrifugal microfluidic platforms

    NASA Astrophysics Data System (ADS)

    King, Damien; O'Sullivan, Mary; Ducrée, Jens

    2014-01-01

    Centrifugal microfluidic systems have become one of the principal platforms for implementing bioanalytical assays, most notably for biomedical point-of-care diagnostics. These so-called 'lab-on-a-disc' systems primarily utilise the rotationally controlled centrifugal field in combination with capillary forces to automate a range of laboratory unit operations (LUOs) for sample preparation, such as metering, aliquoting, mixing and extraction for biofluids as well as sorting, isolation and counting of bioparticles. These centrifugal microfluidic LUOs have been regularly surveyed in the literature. However, even though absolutely essential to provide true sample-to-answer functionality of lab-on-a-disc platforms, systematic examination of associated, often optical, read-out technologies has been so far neglected. This review focusses on the history and state-of-the-art of optical read-out strategies for centrifugal microfluidic platforms, arising (commercial) application potential and future opportunities.

  10. Synthetic biology platform technologies for antimicrobial applications.

    PubMed

    Braff, Dana; Shis, David; Collins, James J

    2016-10-01

    The growing prevalence of antibiotic resistance calls for new approaches in the development of antimicrobial therapeutics. Likewise, improved diagnostic measures are essential in guiding the application of targeted therapies and preventing the evolution of therapeutic resistance. Discovery platforms are also needed to form new treatment strategies and identify novel antimicrobial agents. By applying engineering principles to molecular biology, synthetic biologists have developed platforms that improve upon, supplement, and will perhaps supplant traditional broad-spectrum antibiotics. Efforts in engineering bacteriophages and synthetic probiotics demonstrate targeted antimicrobial approaches that can be fine-tuned using synthetic biology-derived principles. Further, the development of paper-based, cell-free expression systems holds promise in promoting the clinical translation of molecular biology tools for diagnostic purposes. In this review, we highlight emerging synthetic biology platform technologies that are geared toward the generation of new antimicrobial therapies, diagnostics, and discovery channels.

  11. Command profile for Galileo scan platform control

    NASA Astrophysics Data System (ADS)

    Man, G. K.; Breckenridge, W. G.

    1981-08-01

    A recursive command profile is developed for the control of a two-degree-of-freedom scan platform mounted on a flexible structure. Perfect sensors and actuators are assumed for development and testing, and structural vibrations are minimized by actuator torque commands following a smooth torque-time profile. The integral of the smooth torque profile, the rate profile, is recursively generated by a piecewise constant second derivation, and the torque applied by the closk actuator is divided into three components. Results show that the smooth platform motion in response to the command profiles is what the Galileo control systems needs to avoid stator structural vibrations. Position, rate and acceleration profiles are also presented, and the resulting motion of the scan platform in response to command profiles is illustrated.

  12. Integrated electronic platforms for weight loss

    PubMed Central

    McCrady-Spitzer, Shelly K; Levine, James A

    2010-01-01

    What can be done to build effective weight loss solutions for the 1.5 billion people with obesity? It is self-evident that no one good solution exists for people who are overweight or obese, otherwise it would have been applied across the people who need it worldwide. There is, therefore, an urgent need for approaches that will afford weight loss; what is more, such approaches need to be scalable. For that reason, it is attractive to consider electronic platforms as an avenue for scalable weight loss solutions. Such platforms often do not require substantial investments but rather the integration of pre-existing off-the-shelf components. In this article we explore the concepts and design challenges for electronic platforms that precipitate weight loss. PMID:20214426

  13. Optimization of Actuating Origami Networks

    NASA Astrophysics Data System (ADS)

    Buskohl, Philip; Fuchi, Kazuko; Bazzan, Giorgio; Joo, James; Gregory, Reich; Vaia, Richard

    2015-03-01

    Origami structures morph between 2D and 3D conformations along predetermined fold lines that efficiently program the form, function and mobility of the structure. By leveraging design concepts from action origami, a subset of origami art focused on kinematic mechanisms, reversible folding patterns for applications such as solar array packaging, tunable antennae, and deployable sensing platforms may be designed. However, the enormity of the design space and the need to identify the requisite actuation forces within the structure places a severe limitation on design strategies based on intuition and geometry alone. The present work proposes a topology optimization method, using truss and frame element analysis, to distribute foldline mechanical properties within a reference crease pattern. Known actuating patterns are placed within a reference grid and the optimizer adjusts the fold stiffness of the network to optimally connect them. Design objectives may include a target motion, stress level, or mechanical energy distribution. Results include the validation of known action origami structures and their optimal connectivity within a larger network. This design suite offers an important step toward systematic incorporation of origami design concepts into new, novel and reconfigurable engineering devices. This research is supported under the Air Force Office of Scientific Research (AFOSR) funding, LRIR 13RQ02COR.

  14. Cross-Platform JavaScript Coding: Shifting Sand Dunes and Shimmering Mirages.

    ERIC Educational Resources Information Center

    Merchant, David

    1999-01-01

    Most libraries don't have the resources to cross-platform and cross-version test all of their JavaScript coding. Many turn to WYSIWYG; however, WYSIWYG editors don't generally produce optimized coding. Web developers should: test their coding on at least one 3.0 browser, code by hand using tools to help speed that process up, and include a simple…

  15. Evolutionary space platform concept study. Volume 1: Executive summary

    NASA Technical Reports Server (NTRS)

    1982-01-01

    The Evolutionary Space Platform Concept Study encompassed a 10 month effort to define, evaluate and compare approaches and concepts for evolving unmanned and manned capability platforms beyond the current Space Platform concepts to an evolutionary goal of establishing a permanent manned presence in space. Areas addressed included: special emphasis trade studies on the current unmanned concept, assessment of manned platform concepts, and utility analysis of a manned platform for defense related missions.

  16. A rapid automatic processing platform for bead label-assisted microarray analysis: application for genetic hearing-loss mutation detection.

    PubMed

    Zhu, Jiang; Song, Xiumei; Xiang, Guangxin; Feng, Zhengde; Guo, Hongju; Mei, Danyang; Zhang, Guohao; Wang, Dong; Mitchelson, Keith; Xing, Wanli; Cheng, Jing

    2014-04-01

    Molecular diagnostics using microarrays are increasingly being used in clinical diagnosis because of their high throughput, sensitivity, and accuracy. However, standard microarray processing takes several hours and involves manual steps during hybridization, slide clean up, and imaging. Here we describe the development of an integrated platform that automates these individual steps as well as significantly shortens the processing time and improves reproducibility. The platform integrates such key elements as a microfluidic chip, flow control system, temperature control system, imaging system, and automated analysis of clinical results. Bead labeling of microarray signals required a simple imaging system and allowed continuous monitoring of the microarray processing. To demonstrate utility, the automated platform was used to genotype hereditary hearing-loss gene mutations. Compared with conventional microarray processing procedures, the platform increases the efficiency and reproducibility of hybridization, speeding microarray processing through to result analysis. The platform also continuously monitors the microarray signals, which can be used to facilitate optimization of microarray processing conditions. In addition, the modular design of the platform lends itself to development of simultaneous processing of multiple microfluidic chips. We believe the novel features of the platform will benefit its use in clinical settings in which fast, low-complexity molecular genetic testing is required.

  17. Optimizing ELISAs for precision and robustness using laboratory automation and statistical design of experiments.

    PubMed

    Joelsson, Daniel; Moravec, Phil; Troutman, Matthew; Pigeon, Joseph; DePhillips, Pete

    2008-08-20

    Transferring manual ELISAs to automated platforms requires optimizing the assays for each particular robotic platform. These optimization experiments are often time consuming and difficult to perform using a traditional one-factor-at-a-time strategy. In this manuscript we describe the development of an automated process using statistical design of experiments (DOE) to quickly optimize immunoassays for precision and robustness on the Tecan EVO liquid handler. By using fractional factorials and a split-plot design, five incubation time variables and four reagent concentration variables can be optimized in a short period of time.

  18. Machine specific fracture optimization for JEOL e-beam mask writer

    NASA Astrophysics Data System (ADS)

    Yeap, Johnny; Kondepudy, Raghava; Kulkarni, Parikshit; Kawase, Yuichi; Cinque, Russell

    2010-05-01

    Traditionally, Mask Data Preparation (MDP) flow for Variable Shape E-Beam (VSB) writers has been optimized in a generic fashion to minimize slivers and reduce shot count while maintaining data symmetry. To date, this approach has been sufficient and allowed the mask industry to meet requirements for CD uniformity, registration, and write time. However, ever tighter error budgets and increasing pattern complexity are driving a need for writer-specific optimization of MDP. This paper summarizes the joint development effort between Synopsys and JEOL to optimize MDP fractures for the JEOL platform. The advantages and challenges of platform specific optimization are discussed.

  19. Reconcile: A Coreference Resolution Research Platform

    SciTech Connect

    Stoyanov, V; Cardie, C; Gilbert, N; Riloff, E; Buttler, D; Hysom, D

    2009-10-29

    Despite the availability of standard data sets and metrics, approaches to the problem of noun phrase coreference resolution are hard to compare empirically due to the different evaluation setting stemming, in part, from the lack of comprehensive coreference resolution research platforms. In this tech report we present Reconcile, a coreference resolution research platform that aims to facilitate the implementation of new approaches to coreference resolution as well as the comparison of existing approaches. We discuss Reconcile's architecture and give results of running Reconcile on six data sets using four evaluation metrics, showing that Reconcile's performance is comparable to state-of-the-art systems in coreference resolution.

  20. Bill Would Allow Platforms as Artificial Reefs

    NASA Astrophysics Data System (ADS)

    Showstack, Randy

    A 17 September U.S. congressional hearing on environmental aspects of oil and gas development focused primarily on potentially beneficial, alternative usages of thousands of decommissioned offshore oil and gas platforms in the Gulf of Mexico, and elsewhere. These platforms and associated rigs would be permitted to be used as artificial reefs for corals and fish populations, mariculture sites, and scientific research stations, under the Rigs to Reef Act, House Resolution 2654. The bill, introduced by Rep. David Vitter (R-Louisiana), currently is in referral in the Resources and in the Ways and Means committees of the House of Representatives.