Design and evaluation of a hybrid storage system in HEP environment

NASA Astrophysics Data System (ADS)

Xu, Qi; Cheng, Yaodong; Chen, Gang

2017-10-01

Nowadays, the High Energy Physics experiments produce a large amount of data. These data are stored in mass storage systems which need to balance the cost, performance and manageability. In this paper, a hybrid storage system including SSDs (Solid-state Drive) and HDDs (Hard Disk Drive) is designed to accelerate data analysis and maintain a low cost. The performance of accessing files is a decisive factor for the HEP computing system. A new deployment model of Hybrid Storage System in High Energy Physics is proposed which is proved to have higher I/O performance. The detailed evaluation methods and the evaluations about SSD/HDD ratio, and the size of the logic block are also given. In all evaluations, sequential-read, sequential-write, random-read and random-write are all tested to get the comprehensive results. The results show the Hybrid Storage System has good performance in some fields such as accessing big files in HEP.

HEP Software Foundation Community White Paper Working Group - Data Analysis and Interpretation

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

Bauerdick, Lothar

At the heart of experimental high energy physics (HEP) is the development of facilities and instrumentation that provide sensitivity to new phenomena. Our understanding of nature at its most fundamental level is advanced through the analysis and interpretation of data from sophisticated detectors in HEP experiments. The goal of data analysis systems is to realize the maximum possible scientific potential of the data within the constraints of computing and human resources in the least time. To achieve this goal, future analysis systems should empower physicists to access the data with a high level of interactivity, reproducibility and throughput capability. Asmore » part of the HEP Software Foundation Community White Paper process, a working group on Data Analysis and Interpretation was formed to assess the challenges and opportunities in HEP data analysis and develop a roadmap for activities in this area over the next decade. In this report, the key findings and recommendations of the Data Analysis and Interpretation Working Group are presented.« less

Impact of detector simulation in particle physics collider experiments

NASA Astrophysics Data System (ADS)

Daniel Elvira, V.

2017-06-01

Through the last three decades, accurate simulation of the interactions of particles with matter and modeling of detector geometries has proven to be of critical importance to the success of the international high-energy physics (HEP) experimental programs. For example, the detailed detector modeling and accurate physics of the Geant4-based simulation software of the CMS and ATLAS particle physics experiments at the European Center of Nuclear Research (CERN) Large Hadron Collider (LHC) was a determinant factor for these collaborations to deliver physics results of outstanding quality faster than any hadron collider experiment ever before. This review article highlights the impact of detector simulation on particle physics collider experiments. It presents numerous examples of the use of simulation, from detector design and optimization, through software and computing development and testing, to cases where the use of simulation samples made a difference in the precision of the physics results and publication turnaround, from data-taking to submission. It also presents estimates of the cost and economic impact of simulation in the CMS experiment. Future experiments will collect orders of magnitude more data with increasingly complex detectors, taxing heavily the performance of simulation and reconstruction software. Consequently, exploring solutions to speed up simulation and reconstruction software to satisfy the growing demand of computing resources in a time of flat budgets is a matter that deserves immediate attention. The article ends with a short discussion on the potential solutions that are being considered, based on leveraging core count growth in multicore machines, using new generation coprocessors, and re-engineering HEP code for concurrency and parallel computing.

Patients' mental models and adherence to outpatient physical therapy home exercise programs.

PubMed

Rizzo, Jon

2015-05-01

Within physical therapy, patient adherence usually relates to attending appointments, following advice, and/or undertaking prescribed exercise. Similar to findings for general medical adherence, patient adherence to physical therapy home exercise programs (HEP) is estimated between 35 and 72%. Adherence to HEPs is a multifactorial and poorly understood phenomenon, with no consensus regarding a common theoretical framework that best guides empirical or clinical efforts. Mental models, a construct used to explain behavior and decision-making in the social sciences, may serve as this framework. Mental models comprise an individual's tacit thoughts about how the world works. They include assumptions about new experiences and expectations for the future based on implicit comparisons between current and past experiences. Mental models play an important role in decision-making and guiding actions. This professional theoretical article discusses empirical research demonstrating relationships among mental models, prior experience, and adherence decisions in medical and physical therapy contexts. Specific issues related to mental models and physical therapy patient adherence are discussed, including the importance of articulation of patients' mental models, assessment of patients' mental models that relate to exercise program adherence, discrepancy between patient and provider mental models, and revision of patients' mental models in ways that enhance adherence. The article concludes with practical implications for physical therapists and recommendations for further research to better understand the role of mental models in physical therapy patient adherence behavior.

Analyzing How We Do Analysis and Consume Data, Results from the SciDAC-Data Project

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

Ding, P.; Aliaga, L.; Mubarak, M.

One of the main goals of the Dept. of Energy funded SciDAC-Data project is to analyze the more than 410,000 high energy physics datasets that have been collected, generated and defined over the past two decades by experiments using the Fermilab storage facilities. These datasets have been used as the input to over 5.6 million recorded analysis projects, for which detailed analytics have been gathered. The analytics and meta information for these datasets and analysis projects are being combined with knowledge of their part of the HEP analysis chains for major experiments to understand how modern computing and data deliverymore » is being used. We present the first results of this project, which examine in detail how the CDF, D0, NOvA, MINERvA and MicroBooNE experiments have organized, classified and consumed petascale datasets to produce their physics results. The results include analysis of the correlations in dataset/file overlap, data usage patterns, data popularity, dataset dependency and temporary dataset consumption. The results provide critical insight into how workflows and data delivery schemes can be combined with different caching strategies to more efficiently perform the work required to mine these large HEP data volumes and to understand the physics analysis requirements for the next generation of HEP computing facilities. In particular we present a detailed analysis of the NOvA data organization and consumption model corresponding to their first and second oscillation results (2014-2016) and the first look at the analysis of the Tevatron Run II experiments. We present statistical distributions for the characterization of these data and data driven models describing their consumption« less

Analyzing how we do Analysis and Consume Data, Results from the SciDAC-Data Project

NASA Astrophysics Data System (ADS)

Ding, P.; Aliaga, L.; Mubarak, M.; Tsaris, A.; Norman, A.; Lyon, A.; Ross, R.

2017-10-01

One of the main goals of the Dept. of Energy funded SciDAC-Data project is to analyze the more than 410,000 high energy physics datasets that have been collected, generated and defined over the past two decades by experiments using the Fermilab storage facilities. These datasets have been used as the input to over 5.6 million recorded analysis projects, for which detailed analytics have been gathered. The analytics and meta information for these datasets and analysis projects are being combined with knowledge of their part of the HEP analysis chains for major experiments to understand how modern computing and data delivery is being used. We present the first results of this project, which examine in detail how the CDF, D0, NOvA, MINERvA and MicroBooNE experiments have organized, classified and consumed petascale datasets to produce their physics results. The results include analysis of the correlations in dataset/file overlap, data usage patterns, data popularity, dataset dependency and temporary dataset consumption. The results provide critical insight into how workflows and data delivery schemes can be combined with different caching strategies to more efficiently perform the work required to mine these large HEP data volumes and to understand the physics analysis requirements for the next generation of HEP computing facilities. In particular we present a detailed analysis of the NOvA data organization and consumption model corresponding to their first and second oscillation results (2014-2016) and the first look at the analysis of the Tevatron Run II experiments. We present statistical distributions for the characterization of these data and data driven models describing their consumption.

On-demand provisioning of HEP compute resources on cloud sites and shared HPC centers

NASA Astrophysics Data System (ADS)

Erli, G.; Fischer, F.; Fleig, G.; Giffels, M.; Hauth, T.; Quast, G.; Schnepf, M.; Heese, J.; Leppert, K.; Arnaez de Pedro, J.; Sträter, R.

2017-10-01

This contribution reports on solutions, experiences and recent developments with the dynamic, on-demand provisioning of remote computing resources for analysis and simulation workflows. Local resources of a physics institute are extended by private and commercial cloud sites, ranging from the inclusion of desktop clusters over institute clusters to HPC centers. Rather than relying on dedicated HEP computing centers, it is nowadays more reasonable and flexible to utilize remote computing capacity via virtualization techniques or container concepts. We report on recent experience from incorporating a remote HPC center (NEMO Cluster, Freiburg University) and resources dynamically requested from the commercial provider 1&1 Internet SE into our intitute’s computing infrastructure. The Freiburg HPC resources are requested via the standard batch system, allowing HPC and HEP applications to be executed simultaneously, such that regular batch jobs run side by side to virtual machines managed via OpenStack [1]. For the inclusion of the 1&1 commercial resources, a Python API and SDK as well as the possibility to upload images were available. Large scale tests prove the capability to serve the scientific use case in the European 1&1 datacenters. The described environment at the Institute of Experimental Nuclear Physics (IEKP) at KIT serves the needs of researchers participating in the CMS and Belle II experiments. In total, resources exceeding half a million CPU hours have been provided by remote sites.

Introducing concurrency in the Gaudi data processing framework

NASA Astrophysics Data System (ADS)

Clemencic, Marco; Hegner, Benedikt; Mato, Pere; Piparo, Danilo

2014-06-01

In the past, the increasing demands for HEP processing resources could be fulfilled by the ever increasing clock-frequencies and by distributing the work to more and more physical machines. Limitations in power consumption of both CPUs and entire data centres are bringing an end to this era of easy scalability. To get the most CPU performance per watt, future hardware will be characterised by less and less memory per processor, as well as thinner, more specialized and more numerous cores per die, and rather heterogeneous resources. To fully exploit the potential of the many cores, HEP data processing frameworks need to allow for parallel execution of reconstruction or simulation algorithms on several events simultaneously. We describe our experience in introducing concurrency related capabilities into Gaudi, a generic data processing software framework, which is currently being used by several HEP experiments, including the ATLAS and LHCb experiments at the LHC. After a description of the concurrent framework and the most relevant design choices driving its development, we describe the behaviour of the framework in a more realistic environment, using a subset of the real LHCb reconstruction workflow, and present our strategy and the used tools to validate the physics outcome of the parallel framework against the results of the present, purely sequential LHCb software. We then summarize the measurement of the code performance of the multithreaded application in terms of memory and CPU usage.

Comparison of copper heptonate with copper oxide wire particles as copper supplements for sheep on pasture of high molybdenum content.

PubMed

Judson, G J; Babidge, P J

2002-10-01

To assess the effectiveness of intramuscular injection of copper heptonate (CuHep) and an oral dose of copper oxide wire particles (COWP) in preventing Cu inadequacy in adult and young sheep on pasture of high Mo content. Field experiments with flocks of mature Merino wethers and crossbred weaners. Adult wethers were given 25 or 37.5 mg Cu as CuHep, 2.5 g COWP or no Cu treatment. The weaners were given 12.5 or 25 mg Cu as CuHep, 1.25 g COWP or no Cu treatment. At intervals over the next 12 (adults) or 8 (weaners) months the sheep were weighed and samples of blood and liver were collected for trace element assay. Wool samples collected from the adults at the end of the experiment were assessed for physical characteristics. The higher dosage of CuHep raised liver Cu above control group values for at least 9 months in adults and 3 months in weaners. The lower dosage of CuHep was similarly effective for 3 months in adults but was without effect in weaners. In adults the response to COWP matched that to the higher dosage of CuHep; in weaners it was greater, lasting at least 5 months. No changes indicative of Cu deficiency, apart from a depressed body weight in adults, were seen. In sheep on pasture of high Mo content a single intramuscular injection of CuHep providing 37.5 mg Cu to adults or 25 mg Cu to weaners will raise liver Cu reserves for at least 9 and 3 months respectively and may be an acceptable alternative to COWP for preventing seasonal Cu deficiency in sheep in southern Australia.

HEP data analysis using jHepWork and Java.

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

Chekanov, S.; High Energy Physics

2009-03-23

A role of Java in high-energy physics (HEP) and recent progress in development of a platform-independent data-analysis framework, jHepWork, is discussed. The framework produces professional graphics and has many libraries for data manipulation.

High Energy Physics Exascale Requirements Review. An Office of Science review sponsored jointly by Advanced Scientific Computing Research and High Energy Physics, June 10-12, 2015, Bethesda, Maryland

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

Habib, Salman; Roser, Robert; Gerber, Richard

The U.S. Department of Energy (DOE) Office of Science (SC) Offices of High Energy Physics (HEP) and Advanced Scientific Computing Research (ASCR) convened a programmatic Exascale Requirements Review on June 10–12, 2015, in Bethesda, Maryland. This report summarizes the findings, results, and recommendations derived from that meeting. The high-level findings and observations are as follows. Larger, more capable computing and data facilities are needed to support HEP science goals in all three frontiers: Energy, Intensity, and Cosmic. The expected scale of the demand at the 2025 timescale is at least two orders of magnitude — and in some cases greatermore » — than that available currently. The growth rate of data produced by simulations is overwhelming the current ability of both facilities and researchers to store and analyze it. Additional resources and new techniques for data analysis are urgently needed. Data rates and volumes from experimental facilities are also straining the current HEP infrastructure in its ability to store and analyze large and complex data volumes. Appropriately configured leadership-class facilities can play a transformational role in enabling scientific discovery from these datasets. A close integration of high-performance computing (HPC) simulation and data analysis will greatly aid in interpreting the results of HEP experiments. Such an integration will minimize data movement and facilitate interdependent workflows. Long-range planning between HEP and ASCR will be required to meet HEP’s research needs. To best use ASCR HPC resources, the experimental HEP program needs (1) an established, long-term plan for access to ASCR computational and data resources, (2) the ability to map workflows to HPC resources, (3) the ability for ASCR facilities to accommodate workflows run by collaborations potentially comprising thousands of individual members, (4) to transition codes to the next-generation HPC platforms that will be available at ASCR facilities, (5) to build up and train a workforce capable of developing and using simulations and analysis to support HEP scientific research on next-generation systems.« less

Using S3 cloud storage with ROOT and CvmFS

NASA Astrophysics Data System (ADS)

Arsuaga-Ríos, María; Heikkilä, Seppo S.; Duellmann, Dirk; Meusel, René; Blomer, Jakob; Couturier, Ben

2015-12-01

Amazon S3 is a widely adopted web API for scalable cloud storage that could also fulfill storage requirements of the high-energy physics community. CERN has been evaluating this option using some key HEP applications such as ROOT and the CernVM filesystem (CvmFS) with S3 back-ends. In this contribution we present an evaluation of two versions of the Huawei UDS storage system stressed with a large number of clients executing HEP software applications. The performance of concurrently storing individual objects is presented alongside with more complex data access patterns as produced by the ROOT data analysis framework. Both Huawei UDS generations show a successful scalability by supporting multiple byte-range requests in contrast with Amazon S3 or Ceph which do not support these commonly used HEP operations. We further report the S3 integration with recent CvmFS versions and summarize the experience with CvmFS/S3 for publishing daily releases of the full LHCb experiment software stack.

Mapping modern software process engineering techniques onto an HEP development environment

NASA Astrophysics Data System (ADS)

Wellisch, J. P.

2003-04-01

One of the most challenging issues faced in HEP in recent years is the question of how to capitalise on software development and maintenance experience in a continuous manner. To capitalise means in our context to evaluate and apply new process technologies as they arise, and to further evolve technologies already widely in use. It also implies the definition and adoption of standards. The CMS off-line software improvement effort aims at continual software quality improvement, and continual improvement in the efficiency of the working environment with the goal to facilitate doing great new physics. To achieve this, we followed a process improvement program based on ISO-15504, and Rational Unified Process. This experiment in software process improvement in HEP has been progressing now for a period of 3 years. Taking previous experience from ATLAS and SPIDER into account, we used a soft approach of continuous change within the limits of current culture to create of de facto software process standards within the CMS off line community as the only viable route to a successful software process improvement program in HEP. We will present the CMS approach to software process improvement in this process R&D, describe lessons learned, and mistakes made. We will demonstrate the benefits gained, and the current status of the software processes established in CMS off-line software.

A Vision on the Status and Evolution of HEP Physics Software Tools

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

Canal, P.; Elvira, D.; Hatcher, R.

2013-07-28

This paper represents the vision of the members of the Fermilab Scientific Computing Division's Computational Physics Department (SCD-CPD) on the status and the evolution of various HEP software tools such as the Geant4 detector simulation toolkit, the Pythia and GENIE physics generators, and the ROOT data analysis framework. The goal of this paper is to contribute ideas to the Snowmass 2013 process toward the composition of a unified document on the current status and potential evolution of the physics software tools which are essential to HEP.

Target R and D for high power proton beam applications

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

Fabich, A.

High power targets are one of the major issues in an accelerator complex for future HEP physic studies. The paper will review status of studies worldwide. It will focus on the status of the MERIT mercury-jet target experiment at CERN.

Event visualization in ATLAS

NASA Astrophysics Data System (ADS)

Bianchi, R. M.; Boudreau, J.; Konstantinidis, N.; Martyniuk, A. C.; Moyse, E.; Thomas, J.; Waugh, B. M.; Yallup, D. P.; ATLAS Collaboration

2017-10-01

At the beginning, HEP experiments made use of photographical images both to record and store experimental data and to illustrate their findings. Then the experiments evolved and needed to find ways to visualize their data. With the availability of computer graphics, software packages to display event data and the detector geometry started to be developed. Here, an overview of the usage of event display tools in HEP is presented. Then the case of the ATLAS experiment is considered in more detail and two widely used event display packages are presented, Atlantis and VP1, focusing on the software technologies they employ, as well as their strengths, differences and their usage in the experiment: from physics analysis to detector development, and from online monitoring to outreach and communication. Towards the end, the other ATLAS visualization tools will be briefly presented as well. Future development plans and improvements in the ATLAS event display packages will also be discussed.

Scientometric indicators for Brazilian research on High Energy Physics, 1983-2013.

PubMed

Alvarez, Gonzalo R; Vanz, Samile A S; Barbosa, Marcia C

2017-01-01

This article presents an analysis of Brazilian research on High Energy Physics (HEP) indexed by Web of Science (WoS) from 1983 to 2013. Scientometric indicators for output, collaboration and impact were used to characterize the field under study. The results show that the Brazilian articles account for 3% of total HEP research worldwide and that the sharp rise in the scientific activity between 2009 and 2013 may have resulted from the consolidation of graduate programs, the increase of the funding and of the international collaboration as well as the implementation of the Rede Nacional de Física de Altas Energias (RENAFAE) in 2008. Our results also indicate that the collaboration patterns in terms of the authors, the institutions and the countries confirm the presence of Brazil in multinational Big Science experiments, which may also explain the prevalence of foreign citing documents (all types), emphasizing the international prestige and visibility of the output of Brazilian scientists. We concluded that the scientometric indicators suggested scientific maturity in the Brazilian HEP community due to its long history of experimental research.

Snowmass 2013 Young Physicists Science and Career Survey Report

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

Anderson, J.; Asaadi, J.; Carls, B.

2013-07-30

From April to July 2013 the Snowmass Young Physicists (SYP) administered an online survey collecting the opinions and concerns of the High Energy Physics (HEP) community. The aim of this survey is to provide input into the long term planning meeting known as the Community Summer Study (CSS), or Snowmass on the Mississippi. In total, 1112 respondents took part in the survey including 74 people who had received their training within HEP and have since left for non-academic jobs. This paper presents a summary of the survey results including demographic, career outlook, planned experiments and non-academic career path information collected.

Real-time UNIX in HEP data acquisition

NASA Astrophysics Data System (ADS)

Buono, S.; Gaponenko, I.; Jones, R.; Mapelli, L.; Mornacchi, G.; Prigent, D.; Sanchez-Corral, E.; Skiadelli, M.; Toppers, A.; Duval, P. Y.; Ferrato, D.; Le Van Suu, A.; Qian, Z.; Rondot, C.; Ambrosini, G.; Fumagalli, G.; Aguer, M.; Huet, M.

1994-12-01

Today's experimentation in high energy physics is characterized by an increasing need for sensitivity to rare phenomena and complex physics signatures, which require the use of huge and sophisticated detectors and consequently a high performance readout and data acquisition. Multi-level triggering, hierarchical data collection and an always increasing amount of processing power, distributed throughout the data acquisition layers, will impose a number of features on the software environment, especially the need for a high level of standardization. Real-time UNIX seems, today, the best solution for the platform independence, operating system interface standards and real-time features necessary for data acquisition in HEP experiments. We present the results of the evaluation, in a realistic application environment, of a Real-Time UNIX operating system: the EP/LX real-time UNIX system.

CMS Analysis and Data Reduction with Apache Spark

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

Gutsche, Oliver; Canali, Luca; Cremer, Illia

Experimental Particle Physics has been at the forefront of analyzing the world's largest datasets for decades. The HEP community was among the first to develop suitable software and computing tools for this task. In recent times, new toolkits and systems for distributed data processing, collectively called "Big Data" technologies have emerged from industry and open source projects to support the analysis of Petabyte and Exabyte datasets in industry. While the principles of data analysis in HEP have not changed (filtering and transforming experiment-specific data formats), these new technologies use different approaches and tools, promising a fresh look at analysis ofmore » very large datasets that could potentially reduce the time-to-physics with increased interactivity. Moreover these new tools are typically actively developed by large communities, often profiting of industry resources, and under open source licensing. These factors result in a boost for adoption and maturity of the tools and for the communities supporting them, at the same time helping in reducing the cost of ownership for the end-users. In this talk, we are presenting studies of using Apache Spark for end user data analysis. We are studying the HEP analysis workflow separated into two thrusts: the reduction of centrally produced experiment datasets and the end-analysis up to the publication plot. Studying the first thrust, CMS is working together with CERN openlab and Intel on the CMS Big Data Reduction Facility. The goal is to reduce 1 PB of official CMS data to 1 TB of ntuple output for analysis. We are presenting the progress of this 2-year project with first results of scaling up Spark-based HEP analysis. Studying the second thrust, we are presenting studies on using Apache Spark for a CMS Dark Matter physics search, comparing Spark's feasibility, usability and performance to the ROOT-based analysis.« less

High Energy Physics and Nuclear Physics Network Requirements

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

Dart, Eli; Bauerdick, Lothar; Bell, Greg

The Energy Sciences Network (ESnet) is the primary provider of network connectivity for the U.S. Department of Energy (DOE) Office of Science (SC), the single largest supporter of basic research in the physical sciences in the United States. In support of SC programs, ESnet regularly updates and refreshes its understanding of the networking requirements needed by instruments, facilities, scientists, and science programs that it serves. This focus has helped ESnet to be a highly successful enabler of scientific discovery for over 25 years. In August 2013, ESnet and the DOE SC Offices of High Energy Physics (HEP) and Nuclear Physicsmore » (NP) organized a review to characterize the networking requirements of the programs funded by the HEP and NP program offices. Several key findings resulted from the review. Among them: 1. The Large Hadron Collider?s ATLAS (A Toroidal LHC Apparatus) and CMS (Compact Muon Solenoid) experiments are adopting remote input/output (I/O) as a core component of their data analysis infrastructure. This will significantly increase their demands on the network from both a reliability perspective and a performance perspective. 2. The Large Hadron Collider (LHC) experiments (particularly ATLAS and CMS) are working to integrate network awareness into the workflow systems that manage the large number of daily analysis jobs (1 million analysis jobs per day for ATLAS), which are an integral part of the experiments. Collaboration with networking organizations such as ESnet, and the consumption of performance data (e.g., from perfSONAR [PERformance Service Oriented Network monitoring Architecture]) are critical to the success of these efforts. 3. The international aspects of HEP and NP collaborations continue to expand. This includes the LHC experiments, the Relativistic Heavy Ion Collider (RHIC) experiments, the Belle II Collaboration, the Large Synoptic Survey Telescope (LSST), and others. The international nature of these collaborations makes them heavily reliant on transoceanic connectivity, which is subject to longer term service disruptions than terrestrial connectivity. The network engineering aspects of undersea connectivity will continue to be a significant part of the planning, deployment, and operation of the data analysis infrastructure for HEP and NP experiments for the foreseeable future. Given their critical dependency on networking services, the experiments have expressed the need for tight integration (both technically and operationally) of the domestic and the transoceanic parts of the network infrastructure that supports the experiments. 4. The datasets associated with simulations continue to increase in size, and the need to move these datasets between analysis centers is placing ever-increasing demands on networks and on data management systems at the supercomputing centers. In addition, there is a need to harmonize cybersecurity practice with the data transfer performance requirements of the science. This report expands on these points, and addresses others as well. The report contains a findings section in addition to the text of the case studies discussed during the review.« less

One Year of FOS Measurements in CMS Experiment at CERN

NASA Astrophysics Data System (ADS)

Szillási, Zoltán; Buontempo, Salvatore; Béni, Noémi; Breglio, Giovanni; Cusano, Andrea; Laudati, Armando; Giordano, Michele; Saccomanno, Andrea; Druzhkin, Dmitry; Tsirou, Andromachi

Results are presented on the activity carried out by our research group, in collaboration with the SME Optosmart s.r.l. (an Italian spin-off company), on the application of Fiber Optic Sensor (FOS) techniques to monitor high-energy physics (HEP) detectors. Assuming that Fiber Bragg Grating sensors (FBGs) radiation hardness has been deeply studied for other field of application, we have applied the FBG technology to the HEP research domain. We present here the experimental evidences of the solid possibility to use such a class of sensors also in HEP detector very complex environmental side conditions. In particular we present more than one year data results of FBG measurements in the Compact Muon Solenoid (CMS) experiment set up at the CERN, where we have monitored temperatures (within CMS core) and strains in different locations by using FBG sensors during the detector operation with the Large Hadron Collider (LHC) collisions and high magnetic field. FOS data and FOS readout system stability and reliability is demonstrated, with continuous 24/24 h 7/7d data taking under severe and complex side conditions.

Development and validation of a new questionnaire for the assessment of subjective physical performance in adult patients with haemophilia--the HEP-Test-Q.

PubMed

von Mackensen, S; Czepa, D; Herbsleb, M; Hilberg, T

2010-01-01

Specific research studies for the investigation of physical performance in haemophilic patients are rare. However, these instruments become increasingly more important to evaluate therapeutic treatments. Within the frame of the Haemophilia & Exercise Project (HEP), a new questionnaire, namely HEP-Test-Q, has been developed for the assessment of subjective physical performance in haemophilic adults. In this article, the development and validation of the HEP-Test-Q is described. The development consisted of different phases including item collection, pilot testing and field testing. The preliminary version was pilot-tested in 24 German HEP-participants. Following evaluation and preliminary psychometric analysis, the HEP-Test-Q was revised. The final version consists of 25 items pertaining to the domains 'mobility', 'strength & coordination', 'endurance' and 'body perception', which was administered to 43 German haemophilic patients (43.8 +/- 11.2 years). Psychometric analysis included reliability and validity testing. Convergent validity was tested correlating the HEP-Test-Q with SF-36, Haem-A-QoL, HAL and the Orthopaedic Joint Score. Discriminant validity tested different clinical subgroups. Patients accepted the questionnaire and found it easy to fill in. Psychometric testing revealed good values for reliability in terms of internal consistency (Cronbach's alpha = 0.96) and test-retest reliability (r = 0.90) as well as for convergent validity correlating highly with Haem-A-QoL, HAL and SF-36. Discriminant validity testing showed significant differences for age, hepatitis A and hepatitis B and the number of target joints. HEP-Test-Q is a short and well-accepted questionnaire, assessing subjective physical performance of haemophiliacs, which might be combined with objective assessments to reveal aspects, which cannot be measured objectively, such as body perception.

Integrating Visualization Applications, such as ParaView, into HEP Software Frameworks for In-situ Event Displays

NASA Astrophysics Data System (ADS)

Lyon, A. L.; Kowalkowski, J. B.; Jones, C. D.

2017-10-01

ParaView is a high performance visualization application not widely used in High Energy Physics (HEP). It is a long standing open source project led by Kitware and involves several Department of Energy (DOE) and Department of Defense (DOD) laboratories. Futhermore, it has been adopted by many DOE supercomputing centers and other sites. ParaView is unique in speed and efficiency by using state-of-the-art techniques developed by the academic visualization community that are often not found in applications written by the HEP community. In-situ visualization of events, where event details are visualized during processing/analysis, is a common task for experiment software frameworks. Kitware supplies Catalyst, a library that enables scientific software to serve visualization objects to client ParaView viewers yielding a real-time event display. Connecting ParaView to the Fermilab art framework will be described and the capabilities it brings discussed.

Diversity in computing technologies and strategies for dynamic resource allocation

DOE PAGES

Garzoglio, G.; Gutsche, O.

2015-12-23

Here, High Energy Physics (HEP) is a very data intensive and trivially parallelizable science discipline. HEP is probing nature at increasingly finer details requiring ever increasing computational resources to process and analyze experimental data. In this paper, we discuss how HEP provisioned resources so far using Grid technologies, how HEP is starting to include new resource providers like commercial Clouds and HPC installations, and how HEP is transparently provisioning resources at these diverse providers.

HepML, an XML-based format for describing simulated data in high energy physics

NASA Astrophysics Data System (ADS)

Belov, S.; Dudko, L.; Kekelidze, D.; Sherstnev, A.

2010-10-01

In this paper we describe a HepML format and a corresponding C++ library developed for keeping complete description of parton level events in a unified and flexible form. HepML tags contain enough information to understand what kind of physics the simulated events describe and how the events have been prepared. A HepML block can be included into event files in the LHEF format. The structure of the HepML block is described by means of several XML Schemas. The Schemas define necessary information for the HepML block and how this information should be located within the block. The library libhepml is a C++ library intended for parsing and serialization of HepML tags, and representing the HepML block in computer memory. The library is an API for external software. For example, Matrix Element Monte Carlo event generators can use the library for preparing and writing a header of an LHEF file in the form of HepML tags. In turn, Showering and Hadronization event generators can parse the HepML header and get the information in the form of C++ classes. libhepml can be used in C++, C, and Fortran programs. All necessary parts of HepML have been prepared and we present the project to the HEP community. Program summaryProgram title: libhepml Catalogue identifier: AEGL_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEGL_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU GPLv3 No. of lines in distributed program, including test data, etc.: 138 866 No. of bytes in distributed program, including test data, etc.: 613 122 Distribution format: tar.gz Programming language: C++, C Computer: PCs and workstations Operating system: Scientific Linux CERN 4/5, Ubuntu 9.10 RAM: 1 073 741 824 bytes (1 Gb) Classification: 6.2, 11.1, 11.2 External routines: Xerces XML library ( http://xerces.apache.org/xerces-c/), Expat XML Parser ( http://expat.sourceforge.net/) Nature of problem: Monte Carlo simulation in high energy physics is divided into several stages. Various programs exist for these stages. In this article we are interested in interfacing different Monte Carlo event generators via data files, in particular, Matrix Element (ME) generators and Showering and Hadronization (SH) generators. There is a widely accepted format for data files for such interfaces - Les Houches Event Format (LHEF). Although information kept in an LHEF file is enough for proper working of SH generators, it is insufficient for understanding how events in the LHEF file have been prepared and which physical model has been applied. In this paper we propose an extension of the format for keeping additional information available in generators. We propose to add a new information block, marked up with XML tags, to the LHEF file. This block describes events in the file in more detail. In particular, it stores information about a physical model, kinematical cuts, generator, etc. This helps to make LHEF files self-documented. Certainly, HepML can be applied in more general context, not in LHEF files only. Solution method: In order to overcome drawbacks of the original LHEF accord we propose to add a new information block of HepML tags. HepML is an XML-based markup language. We designed several XML Schemas for all tags in the language. Any HepML document should follow rules of the Schemas. The language is equipped with a library for operation with HepML tags and documents. This C++ library, called libhepml, consists of classes for HepML objects, which represent a HepML document in computer memory, parsing classes, serializating classes, and some auxiliary classes. Restrictions: The software is adapted for solving problems, described in the article. There are no additional restrictions. Running time: Tests have been done on a computer with Intel(R) Core(TM)2 Solo, 1.4 GHz. Parsing of a HepML file: 6 ms (size of the HepML files is 12.5 Kb) Writing of a HepML block to file: 14 ms (file size 12.5 Kb) Merging of two HepML blocks and writing to file: 18 ms (file size - 25.0 Kb).

High Energy Physics Forum for Computational Excellence: Working Group Reports (I. Applications Software II. Software Libraries and Tools III. Systems)

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

Habib, Salman; Roser, Robert

Computing plays an essential role in all aspects of high energy physics. As computational technology evolves rapidly in new directions, and data throughput and volume continue to follow a steep trend-line, it is important for the HEP community to develop an effective response to a series of expected challenges. In order to help shape the desired response, the HEP Forum for Computational Excellence (HEP-FCE) initiated a roadmap planning activity with two key overlapping drivers -- 1) software effectiveness, and 2) infrastructure and expertise advancement. The HEP-FCE formed three working groups, 1) Applications Software, 2) Software Libraries and Tools, and 3)more » Systems (including systems software), to provide an overview of the current status of HEP computing and to present findings and opportunities for the desired HEP computational roadmap. The final versions of the reports are combined in this document, and are presented along with introductory material.« less

High Energy Physics Forum for Computational Excellence: Working Group Reports (I. Applications Software II. Software Libraries and Tools III. Systems)

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

Habib, Salman; Roser, Robert; LeCompte, Tom

2015-10-29

Computing plays an essential role in all aspects of high energy physics. As computational technology evolves rapidly in new directions, and data throughput and volume continue to follow a steep trend-line, it is important for the HEP community to develop an effective response to a series of expected challenges. In order to help shape the desired response, the HEP Forum for Computational Excellence (HEP-FCE) initiated a roadmap planning activity with two key overlapping drivers -- 1) software effectiveness, and 2) infrastructure and expertise advancement. The HEP-FCE formed three working groups, 1) Applications Software, 2) Software Libraries and Tools, and 3)more » Systems (including systems software), to provide an overview of the current status of HEP computing and to present findings and opportunities for the desired HEP computational roadmap. The final versions of the reports are combined in this document, and are presented along with introductory material.« less

Haemophilia & Exercise Project (HEP): subjective and objective physical performance in adult haemophilia patients--results of a cross-sectional study.

PubMed

Czepa, D; Von Mackensen, S; Hilberg, T

2012-01-01

Recurrent musculoskeletal haemorrhages in people with haemophilia (PWH) lead to restrictions in the locomotor system and consequently in physical performance. Patients' perceptions of their health status have gained an important role in the last few years. The assessment of subjective physical performance in PWH is a new approach. This study aimed to compare the subjective physical performance of PWH with healthy controls and to correlate the results with objective data. Subjective physical performance was assessed via the new questionnaire HEP-Test-Q, which consists of 25 items pertaining to four subscales 'mobility', 'strength & coordination', 'endurance' and 'body perception'. HEP-Test-Q subscales were compared with objective data in terms of range of motion, one-leg-stand and 12-minute walk test. Forty-eight patients (44 ± 11 years) with haemophilia A (43 severe, three moderate) or B (two severe) and 43 controls without haemophilia (42 ± 11 years) were enrolled. PWH showed an impaired subjective physical performance in all HEP-Test-Q subscales and in the total score (52 ± 20) compared with controls (77 ± 10; P ≤ 0.001). Correlation analyses for the total score of the HEP-Test-Q and objective data revealed values ranging from r = 0.403 (one-leg-stand) to r = 0.757 (12-minute walk test) (P ≤ 0.001). PWH evaluated their physical performance poorer in comparison with healthy people. As self-assessment did not always correlate highly with objective data, objective examinations of physical performance in PWH should be complemented with subjective perceptions. © 2011 Blackwell Publishing Ltd.

Analysis and Quantification of Coupling Mechanisms of External Signal Perturbations on Silicon Detectors for Particle Physics Experiments

NASA Astrophysics Data System (ADS)

Arteche, F.; Rivetta, C.; Iglesias, M.; Echeverria, I.

2016-05-01

Silicon detectors have been used in astrophysics satellites and particle detectors for high energy physics (HEP) experiments. For HEP applications, EMC studies have been conducted in silicon detectors to characterize the impact of external noise on the system. They have shown that problems associated with the new generation of silicon detectors are related with interferences generated by the power supplies and auxiliary equipment connected to the device. Characterization of these interferences along with the coupling and their propagation into the susceptible front-end circuits is required for a successful integration of these systems. This paper presents the analysis of the sensitivity curves and coupling mechanisms between the noise and the front-end electronics that have been observed during the characterization of two silicon detector prototypes: the CMS-Silicon tracker detector (CMS-ST) and Silicon Vertex Detector (Belle II-SVD). As a result of these studies, it is possible to identify critical elements in prototypes to take corrective actions in the design and improve the front-end electronics performance.

Editorial: Focus on Extra Space Dimensions

NASA Astrophysics Data System (ADS)

Agashe, Kaustubh; Pomarol, Alex

2010-07-01

Experiments at the Large Hadron Collider (LHC) have just started. In addition to verifying the Standard Model (SM) of particle physics, these experiments will probe a new energy frontier and test extensions of the SM. The existence of extra dimensions is one of the most attractive possibilities for physics beyond the SM. This focus issue contains a collection of articles addressing both theoretical and phenomenological aspects of extra-dimensional models. Focus on Extra Space Dimensions Contents Minimal universal extra dimensions in CalcHEP/CompHEP AseshKrishna Datta, Kyoungchul Kong and Konstantin T Matchev Disordered extra dimensions Karim Benakli Codimension-2 brane-bulk matching: examples from six and ten dimensions Allan Bayntun, C P Burgess and Leo van Nierop Gauge threshold corrections in warped geometry Kiwoon Choi, Ian-Woo Kim and Chang Sub Shin Holographic methods and gauge-Higgs unification in flat extra dimensions Marco Serone Soft-wall stabilization Joan A Cabrer, Gero von Gersdorff and Mariano Quirós Warped five-dimensional models: phenomenological status and experimental prospects Hooman Davoudiasl, Shrihari Gopalakrishna, Eduardo Pontón and José Santiago

HEPS Tool for Schools: A Guide for School Policy Development on Healthy Eating and Physical Activity

ERIC Educational Resources Information Center

Simovska, Venka; Dadaczynski, Kevin; Viig, Nina Grieg; Bowker, Sue; Woynarowska, Barbara; de Ruiter, Silvia; Buijs, Goof

2010-01-01

The HEPS Tool for Schools provides ideas, guidelines and suggested techniques to help schools in their development of school policy on healthy eating and physical activity. There is growing evidence that a comprehensive whole school policy on healthy eating and physical activity can lead to better academic outcomes of pupils as well as promoting…

U.S. Involvement in the LHC

DOE PAGES

Green, Dan

2016-12-14

The demise of the SSC in the U.S. created an upheaval in the U.S. high energy physics (HEP) community. Here, the subsequent redirection of HEP efforts to the CERN Large Hadron Collider (LHC) can perhaps be seen as informing on possible future paths for worldwide collaboration on future HEP megaprojects.

The path toward HEP High Performance Computing

NASA Astrophysics Data System (ADS)

Apostolakis, John; Brun, René; Carminati, Federico; Gheata, Andrei; Wenzel, Sandro

2014-06-01

High Energy Physics code has been known for making poor use of high performance computing architectures. Efforts in optimising HEP code on vector and RISC architectures have yield limited results and recent studies have shown that, on modern architectures, it achieves a performance between 10% and 50% of the peak one. Although several successful attempts have been made to port selected codes on GPUs, no major HEP code suite has a "High Performance" implementation. With LHC undergoing a major upgrade and a number of challenging experiments on the drawing board, HEP cannot any longer neglect the less-than-optimal performance of its code and it has to try making the best usage of the hardware. This activity is one of the foci of the SFT group at CERN, which hosts, among others, the Root and Geant4 project. The activity of the experiments is shared and coordinated via a Concurrency Forum, where the experience in optimising HEP code is presented and discussed. Another activity is the Geant-V project, centred on the development of a highperformance prototype for particle transport. Achieving a good concurrency level on the emerging parallel architectures without a complete redesign of the framework can only be done by parallelizing at event level, or with a much larger effort at track level. Apart the shareable data structures, this typically implies a multiplication factor in terms of memory consumption compared to the single threaded version, together with sub-optimal handling of event processing tails. Besides this, the low level instruction pipelining of modern processors cannot be used efficiently to speedup the program. We have implemented a framework that allows scheduling vectors of particles to an arbitrary number of computing resources in a fine grain parallel approach. The talk will review the current optimisation activities within the SFT group with a particular emphasis on the development perspectives towards a simulation framework able to profit best from the recent technology evolution in computing.

HEPS Inventory Tool: An Inventory Tool Including Quality Assessment of School Interventions on Healthy Eating and Physical Activity

ERIC Educational Resources Information Center

Dadaczynski, Kevin; Paulus, Peter; de Vries, Nanne; de Ruiter, Silvia; Buijs, Goof

2010-01-01

The HEPS Inventory Tool aims to support stakeholders working in school health promotion to promote high quality interventions on healthy eating and physical activity. As a tool it provides a step-by-step approach on how to develop a national or regional inventory of existing school based interventions on healthy eating and physical activity. It…

Exercise after Stroke: Patient Adherence and Beliefs after Discharge from Rehabilitation.

PubMed

Miller, Kristine K; Porter, Rebecca E; DeBaun-Sprague, Erin; Van Puymbroeck, Marieke; Schmid, Arlene A

2017-03-01

Most people complete post-stroke rehabilitation within the first 6 months after stroke even though benefits from exercise are believed to persist well beyond 6 months. Physical and Occupational therapists provide home exercise programs (HEP) to instruct patients on exercises to continue after discharge from rehabilitation. Unfortunately, there is little known about HEP adherence rates in adults with stroke. The objectives of this project were to (1) determine the adherence rate with post-rehabilitation HEP and reasons for non-adherence, (2) assess for interactions between HEP adherence and self-report of depression and fatigue, and (3) determine patient beliefs about the benefit of exercise during stroke recovery. This was a cross-sectional, survey study. A survey was developed and distributed during stroke support group meetings to determine adherence rates with post rehabilitation HEP, reasons for non-adherence, and patient beliefs about the benefit of exercise. Eighty-nine percent of participants reported receiving a HEP and 65.3% of those reported being adherent with at least part of the HEP. Several reasons for non-adherence were identified, including 'doing different exercises than the ones given by the physical therapist', as the most frequently given reason. Study participants identified positive roles of exercise in their recovery from stroke. Patient adherence with HEP after discharge from rehabilitation is less than ideal. Reasons for non-adherence are varied. Rehabilitation therapists need to be able to identify and help patients manage barriers to HEP adherence to promote management of residual deficits.

Integrating Visualization Applications, such as ParaView, into HEP Software Frameworks for In-situ Event Displays

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

Lyon, A. L.; Kowalkowski, J. B.; Jones, C. D.

ParaView is a high performance visualization application not widely used in High Energy Physics (HEP). It is a long standing open source project led by Kitware and involves several Department of Energy (DOE) and Department of Defense (DOD) laboratories. Futhermore, it has been adopted by many DOE supercomputing centers and other sites. ParaView is unique in speed and efficiency by using state-of-the-art techniques developed by the academic visualization community that are often not found in applications written by the HEP community. In-situ visualization of events, where event details are visualized during processing/analysis, is a common task for experiment software frameworks.more » Kitware supplies Catalyst, a library that enables scientific software to serve visualization objects to client ParaView viewers yielding a real-time event display. Connecting ParaView to the Fermilab art framework will be described and the capabilities it brings discussed.« less

``High energy Electron exPeriment (HEP)'' onboard the ERG satellite

NASA Astrophysics Data System (ADS)

Mitani, T.; Takashima, T.; Kasahara, S.; Miyake, W.; Hirahara, M.

2017-12-01

The Exploration of energization and Radiation in Geospace (ERG) satellite was successfully launched on December 20, 2016, and now explores how relativistic electrons in the radiation belts are generated during space storms. "High energy Electron exPeriment (HEP)" onboard the ERG satellite observes 70 keV - 2 MeV electrons and provides three-dimensional velocity distribution of electrons every spacecraft spin period. Electrons are observed by two types of camera designs, HEP-L and HEP-H, with regard to geometrical factor and energy range. HEP-L observes 0.1 - 1 MeV electrons and its geometrical factor (G-factor) is 10-3 cm2 str, and HEP-H observes 0.7 - 2 MeV and G-factor is 10-2 cm2 str. HEP-L and HEP-H each consist of three pin-hole type cameras, and each camera consist of mechanical collimator, stacked silicon semiconductor detectors and readout ASICs. HEP-H has larger opening angle of the collimator and more silicon detectors to observe higher energy electrons than HEP-L. The initial checkout in orbit was carried out in February 2017 and it was confirmed that there was no performance degradation by comparing the results of the initial checkout in orbit and the prelaunch function tests. Since late March, HEP has carried out normal observation. HEP observed losses and recovery of the outer radiation belt electrons several times up to now. In this presentation we introduce the HEP instrument design, prelaunch tests results and report the initial results in orbit.

Spark and HPC for High Energy Physics Data Analyses

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

Sehrish, Saba; Kowalkowski, Jim; Paterno, Marc

A full High Energy Physics (HEP) data analysis is divided into multiple data reduction phases. Processing within these phases is extremely time consuming, therefore intermediate results are stored in files held in mass storage systems and referenced as part of large datasets. This processing model limits what can be done with interactive data analytics. Growth in size and complexity of experimental datasets, along with emerging big data tools are beginning to cause changes to the traditional ways of doing data analyses. Use of big data tools for HEP analysis looks promising, mainly because extremely large HEP datasets can be representedmore » and held in memory across a system, and accessed interactively by encoding an analysis using highlevel programming abstractions. The mainstream tools, however, are not designed for scientific computing or for exploiting the available HPC platform features. We use an example from the Compact Muon Solenoid (CMS) experiment at the Large Hadron Collider (LHC) in Geneva, Switzerland. The LHC is the highest energy particle collider in the world. Our use case focuses on searching for new types of elementary particles explaining Dark Matter in the universe. We use HDF5 as our input data format, and Spark to implement the use case. We show the benefits and limitations of using Spark with HDF5 on Edison at NERSC.« less

Haemophilia & Exercise Project (HEP): the impact of 1-year sports therapy programme on physical performance in adult haemophilia patients.

PubMed

Czepa, D; von Mackensen, S; Hilberg, T

2013-03-01

Episodes of bleeding in people with haemophilia (PWH) are associated with reduced activity and limitations in physical performance. Within the scope of the 'Haemophilia & Exercise Project' (HEP) PWH were trained in a sports therapy programme. Aim of this study was to investigate subjective and objective physical performance in HEP-participants after 1 year training. Physical performance of 48 adult PWH was compared before and after sports therapy subjectively (HEP-Test-Q) and objectively regarding mobility (range of motion), strength and coordination (one-leg-stand) and endurance (12-min walk test). Sports therapy included an independent home training that had previously been trained in several collective sports camps. Forty-three controls without haemophilia and without training were compared to PWH. Of 48 PWH, 13 performed a regular training (active PWH); 12 HEP-participants were constantly passive (passive PWH). Twenty-three PWH and 24 controls dropped out because of incomplete data. The activity level increased by 100% in active PWH and remained constant in passive PWH, and in controls (P ≤ 0.05). Only mobility of the right knee was significantly improved in active PWH (+5.8 ± 5.3°) compared to passive PWH (-1.3 ± 8.6°). The 12-min walk test proved a longer walking distance for active PWH (+217 ± 199 m) compared to controls (-32 ± 217 m). Active PWH reported a better subjective physical performance in the HEP-Test-Q domains 'strength & coordination', 'endurance' and in the total score (+9.4 ± 13.8) compared to passive PWH (-5.3 ± 13.5) and controls (+3.7 ± 7.5). The 'mobility'-scale and one-leg-stand remained unchanged. Sports therapy increases the activity level and physical performance of PWH, whereby objective effects do not always correspond with subjective assessments. © 2012 Blackwell Publishing Ltd.

Open Access Publishing in High-Energy Physics: the SCOAP3 Initiative

NASA Astrophysics Data System (ADS)

Mele, S.

2010-10-01

Scholarly communication in High-Energy Physics (HEP) shows traits very similar to Astronomy and Astrophysics: pervasiveness of Open Access to preprints through community-based services; a culture of openness and sharing among its researchers; a compact number of yearly articles published by a relatively small number of journals which are dear to the community. These aspects have led HEP to spearhead an innovative model for the transition of its scholarly publishing to Open Access. The Sponsoring Consortium for Open Access Publishing in Particle Physics (SCOAP) aims to be a central body to finance peer-review service rather than the purchase of access to information as in the traditional subscription model, with all articles in the discipline eventually available in Open Access. Sustainable funding to SCOAP would come from libraries, library consortia and HEP funding agencies, through a re-direction of funds currently spent for subscriptions to HEP journals. This paper presents the cultural and bibliometric factors at the roots of SCOAP and the current status of this worldwide initiative.

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

Citterio, M.; Camplani, A.; Cannon, M.

SRAM based Field Programmable Gate Arrays (FPGAs) have been rarely used in High Energy Physics (HEP) due to their sensitivity to radiation. The last generation of commercial FPGAs based on 28 nm feature size and on Silicon On Insulator (SOI) technologies are more tolerant to radiation to the level that their use in front-end electronics is now feasible. FPGAs provide re-programmability, high-speed computation and fast data transmission through the embedded serial transceivers. They could replace custom application specific integrated circuits in front end electronics in locations with moderate radiation field. Finally, the use of a FPGA in HEP experiments ismore » only limited by our ability to mitigate single event effects induced by the high energy hadrons present in the radiation field.« less

HEPDOOP: High-Energy Physics Analysis using Hadoop

NASA Astrophysics Data System (ADS)

Bhimji, W.; Bristow, T.; Washbrook, A.

2014-06-01

We perform a LHC data analysis workflow using tools and data formats that are commonly used in the "Big Data" community outside High Energy Physics (HEP). These include Apache Avro for serialisation to binary files, Pig and Hadoop for mass data processing and Python Scikit-Learn for multi-variate analysis. Comparison is made with the same analysis performed with current HEP tools in ROOT.

Research in High Energy Physics at Duke University

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

Kotwal, Ashutosh V.; Goshaw, Al; Kruse, Mark

2013-07-29

This is the Closeout Report for the research grant in experimental elementary particle physics, carried out by the Duke University High Energy Physics (HEP) group. We re- port on physics results and detector development carried out under this grant, focussing on the recent three-year grant period (2010 to 2013). The Duke HEP group consisted of seven faculty members, two senior scientists, ve postdocs and eight graduate students. There were three thrusts of the research program. Measurements at the energy frontier at CDF and ATLAS were used to test aspects of elementary particle theory described by the Stan- dard Model (SM)more » and to search for new forces and particles beyond those contained within the SM. The neutrino sector was explored using data obtained from a large neutrino detector located in Japan, and R & D was conducted on new experiments to be built in the US. The measurements provided information about neutrino masses and the manner in which neutri- nos change species in particle beams. Two years ago we have started a new research program in rare processes based on the Mu2E experiment at Fermilab. This research is motivated by the search for the ! e transition with unprecedented sensitivity, a transition forbidden in the standard model but allowed in supersymmetric and other models of new physics. The high energy research program used proton and antiproton colliding beams. The experiments were done at the Fermilab Tevatron (proton-antiproton collisions at a center of mass energy of 1.96 TeV) and at the CERN Large Hadron Collider (proton-proton collisions at 7-8 TeV). The neutrino program used data obtained from the Super-Kamiokande detec- tor. This water- lled Cherenkov counter was used to detect and measure the properties of neutrinos produced in cosmic ray showers, and from neutrino beams produced from acceler- ators in Japan. The Mu2E experiment will use a special stopped muon beam to be built at Fermilab.« less

Research in High Energy Physics at Duke University

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

Goshaw, Alfred; Kotwal, Ashutosh; Kruse, Mark

2013-07-29

This is the Closeout Report for the research grant in experimental elementary particle physics, carried out by the Duke University High Energy Physics (HEP) group. We re- port on physics results and detector development carried out under this grant, focussing on the recent three-year grant period (2010 to 2013). The Duke HEP group consisted of seven faculty members, two senior scientists, five postdocs and eight graduate students. There were three thrusts of the research program. Measurements at the energy frontier at CDF and ATLAS were used to test aspects of elementary particle theory described by the Stan- dard Model (SM)more » and to search for new forces and particles beyond those contained within the SM. The neutrino sector was explored using data obtained from a large neutrino detector located in Japan, and R & D was conducted on new experiments to be built in the US. The measurements provided information about neutrino masses and the manner in which neutri- nos change species in particle beams. Two years ago we have started a new research program in rare processes based on the Mu2E experiment at Fermilab. This research is motivated by the search for the {mu} {yields} e transition with unprecedented sensitivity, a transition forbidden in the standard model but allowed in supersymmetric and other models of new physics. The high energy research program used proton and antiproton colliding beams. The experiments were done at the Fermilab Tevatron (proton-antiproton collisions at a center of mass energy of 1.96 TeV) and at the CERN Large Hadron Collider (proton-proton collisions at 7-8 TeV). The neutrino program used data obtained from the Super-Kamiokande detector. This water-filled Cherenkov counter was used to detect and measure the properties of neutrinos produced in cosmic ray showers, and from neutrino beams produced from acceler- ators in Japan. The Mu2E experiment will use a special stopped muon beam to be built at Fermilab.« less

Scidac-Data: Enabling Data Driven Modeling of Exascale Computing

DOE PAGES

Mubarak, Misbah; Ding, Pengfei; Aliaga, Leo; ...

2017-11-23

Here, the SciDAC-Data project is a DOE-funded initiative to analyze and exploit two decades of information and analytics that have been collected by the Fermilab data center on the organization, movement, and consumption of high energy physics (HEP) data. The project analyzes the analysis patterns and data organization that have been used by NOvA, MicroBooNE, MINERvA, CDF, D0, and other experiments to develop realistic models of HEP analysis workflows and data processing. The SciDAC-Data project aims to provide both realistic input vectors and corresponding output data that can be used to optimize and validate simulations of HEP analysis. These simulationsmore » are designed to address questions of data handling, cache optimization, and workflow structures that are the prerequisites for modern HEP analysis chains to be mapped and optimized to run on the next generation of leadership-class exascale computing facilities. We present the use of a subset of the SciDAC-Data distributions, acquired from analysis of approximately 71,000 HEP workflows run on the Fermilab data center and corresponding to over 9 million individual analysis jobs, as the input to detailed queuing simulations that model the expected data consumption and caching behaviors of the work running in high performance computing (HPC) and high throughput computing (HTC) environments. In particular we describe how the Sequential Access via Metadata (SAM) data-handling system in combination with the dCache/Enstore-based data archive facilities has been used to develop radically different models for analyzing the HEP data. We also show how the simulations may be used to assess the impact of design choices in archive facilities.« less

Scidac-Data: Enabling Data Driven Modeling of Exascale Computing

NASA Astrophysics Data System (ADS)

Mubarak, Misbah; Ding, Pengfei; Aliaga, Leo; Tsaris, Aristeidis; Norman, Andrew; Lyon, Adam; Ross, Robert

2017-10-01

The SciDAC-Data project is a DOE-funded initiative to analyze and exploit two decades of information and analytics that have been collected by the Fermilab data center on the organization, movement, and consumption of high energy physics (HEP) data. The project analyzes the analysis patterns and data organization that have been used by NOvA, MicroBooNE, MINERvA, CDF, D0, and other experiments to develop realistic models of HEP analysis workflows and data processing. The SciDAC-Data project aims to provide both realistic input vectors and corresponding output data that can be used to optimize and validate simulations of HEP analysis. These simulations are designed to address questions of data handling, cache optimization, and workflow structures that are the prerequisites for modern HEP analysis chains to be mapped and optimized to run on the next generation of leadership-class exascale computing facilities. We present the use of a subset of the SciDAC-Data distributions, acquired from analysis of approximately 71,000 HEP workflows run on the Fermilab data center and corresponding to over 9 million individual analysis jobs, as the input to detailed queuing simulations that model the expected data consumption and caching behaviors of the work running in high performance computing (HPC) and high throughput computing (HTC) environments. In particular we describe how the Sequential Access via Metadata (SAM) data-handling system in combination with the dCache/Enstore-based data archive facilities has been used to develop radically different models for analyzing the HEP data. We also show how the simulations may be used to assess the impact of design choices in archive facilities.

Scidac-Data: Enabling Data Driven Modeling of Exascale Computing

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

Mubarak, Misbah; Ding, Pengfei; Aliaga, Leo

Here, the SciDAC-Data project is a DOE-funded initiative to analyze and exploit two decades of information and analytics that have been collected by the Fermilab data center on the organization, movement, and consumption of high energy physics (HEP) data. The project analyzes the analysis patterns and data organization that have been used by NOvA, MicroBooNE, MINERvA, CDF, D0, and other experiments to develop realistic models of HEP analysis workflows and data processing. The SciDAC-Data project aims to provide both realistic input vectors and corresponding output data that can be used to optimize and validate simulations of HEP analysis. These simulationsmore » are designed to address questions of data handling, cache optimization, and workflow structures that are the prerequisites for modern HEP analysis chains to be mapped and optimized to run on the next generation of leadership-class exascale computing facilities. We present the use of a subset of the SciDAC-Data distributions, acquired from analysis of approximately 71,000 HEP workflows run on the Fermilab data center and corresponding to over 9 million individual analysis jobs, as the input to detailed queuing simulations that model the expected data consumption and caching behaviors of the work running in high performance computing (HPC) and high throughput computing (HTC) environments. In particular we describe how the Sequential Access via Metadata (SAM) data-handling system in combination with the dCache/Enstore-based data archive facilities has been used to develop radically different models for analyzing the HEP data. We also show how the simulations may be used to assess the impact of design choices in archive facilities.« less

Brane Physics in M-theory

NASA Astrophysics Data System (ADS)

Argurio, Riccardo

1998-07-01

The thesis begins with an introduction to M-theory (at a graduate student's level), starting from perturbative string theory and proceeding to dualities, D-branes and finally Matrix theory. The following chapter treats, in a self-contained way, of general classical p-brane solutions. Black and extremal branes are reviewed, along with their semi-classical thermodynamics. We then focus on intersecting extremal branes, the intersection rules being derived both with and without the explicit use of supersymmetry. The last three chapters comprise more advanced aspects of brane physics, such as the dynamics of open branes, the little theories on the world-volume of branes and how the four dimensional Schwarzschild black hole can be mapped to an extremal configuration of branes, thus allowing for a statistical interpretation of its entropy. The original results were already reported in hep-th/9701042, hep-th/9704190, hep-th/9710027 and hep-th/9801053.

Radiation testing campaign results for understanding the suitability of FPGAs in detector electronics

DOE PAGES

Citterio, M.; Camplani, A.; Cannon, M.; ...

2015-11-19

SRAM based Field Programmable Gate Arrays (FPGAs) have been rarely used in High Energy Physics (HEP) due to their sensitivity to radiation. The last generation of commercial FPGAs based on 28 nm feature size and on Silicon On Insulator (SOI) technologies are more tolerant to radiation to the level that their use in front-end electronics is now feasible. FPGAs provide re-programmability, high-speed computation and fast data transmission through the embedded serial transceivers. They could replace custom application specific integrated circuits in front end electronics in locations with moderate radiation field. Finally, the use of a FPGA in HEP experiments ismore » only limited by our ability to mitigate single event effects induced by the high energy hadrons present in the radiation field.« less

Studies for a 10 μs, thin, high resolution CMOS pixel sensor for future vertex detectors

NASA Astrophysics Data System (ADS)

Voutsinas, G.; Amar-Youcef, S.; Baudot, J.; Bertolone, G.; Brogna, A.; Chon-Sen, N.; Claus, G.; Colledani, C.; Dorokhov, A.; Dozière, G.; Dulinski, W.; Degerli, Y.; De Masi, R.; Deveaux, M.; Gelin, M.; Goffe, M.; Hu-Guo, Ch.; Himmi, A.; Jaaskelainen, K.; Koziel, M.; Morel, F.; Müntz, C.; Orsini, F.; Santos, C.; Schrader, C.; Specht, M.; Stroth, J.; Valin, I.; Wagner, F. M.; Winter, M.

2011-06-01

Future high energy physics (HEP) experiments require detectors with unprecedented performances for track and vertex reconstruction. These requirements call for high precision sensors, with low material budget and short integration time. The development of CMOS sensors for HEP applications was initiated at IPHC Strasbourg more than 10 years ago, motivated by the needs for vertex detectors at the International Linear Collider (ILC) [R. Turchetta et al, NIM A 458 (2001) 677]. Since then several other applications emerged. The first real scale digital CMOS sensor MIMOSA26 equips Flavour Tracker at RHIC, as well as for the microvertex detector of the CBM experiment at FAIR. MIMOSA sensors may also offer attractive performances for the ALICE upgrade at LHC. This paper will demonstrate the substantial performance improvement of CMOS sensors based on a high resistivity epitaxial layer. First studies for integrating the sensors into a detector system will be addressed and finally the way to go to a 10 μs readout sensor will be discussed.

High-energy electron experiments (HEP) aboard the ERG (Arase) satellite

NASA Astrophysics Data System (ADS)

Mitani, Takefumi; Takashima, Takeshi; Kasahara, Satoshi; Miyake, Wataru; Hirahara, Masafumi

2018-05-01

This paper reports the design, calibration, and operation of high-energy electron experiments (HEP) aboard the exploration of energization and radiation in geospace (ERG) satellite. HEP detects 70 keV-2 MeV electrons and generates a three-dimensional velocity distribution for these electrons in every period of the satellite's rotation. Electrons are detected by two instruments, namely HEP-L and HEP-H, which differ in their geometric factor (G-factor) and range of energies they detect. HEP-L detects 70 keV-1 MeV electrons and its G-factor is 9.3 × 10-4 cm2 sr at maximum, while HEP-H observes 0.7-2 MeV electrons and its G-factor is 9.3 × 10-3 cm2 sr at maximum. The instruments utilize silicon strip detectors and application-specific integrated circuits to readout the incident charge signal from each strip. Before the launch, we calibrated the detectors by measuring the energy spectra of all strips using γ-ray sources. To evaluate the overall performance of the HEP instruments, we measured the energy spectra and angular responses with electron beams. After HEP was first put into operation, on February 2, 2017, it was demonstrated that the instruments performed normally. HEP began its exploratory observations with regard to energization and radiation in geospace in late March 2017. The initial results of the in-orbit observations are introduced briefly in this paper.[Figure not available: see fulltext.

BES-HEP Connections: Common Problems in Condensed Matter and High Energy Physics, Round Table Discussion

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

Fradkin, Eduardo; Maldacena, Juan; Chatterjee, Lali

2015-02-02

On February 2, 2015 the Offices of High Energy Physics (HEP) and Basic Energy Sciences (BES) convened a Round Table discussion among a group of physicists on ‘Common Problems in Condensed Matter and High Energy Physics’. This was motivated by the realization that both fields deal with quantum many body problems, share many of the same challenges, use quantum field theoretical approaches and have productively interacted in the past. The meeting brought together physicists with intersecting interests to explore recent developments and identify possible areas of collaboration.... Several topics were identified as offering great opportunity for discovery and advancement inmore » both condensed matter physics and particle physics research. These included topological phases of matter, the use of entanglement as a tool to study nontrivial quantum systems in condensed matter and gravity, the gauge-gravity duality, non-Fermi liquids, the interplay of transport and anomalies, and strongly interacting disordered systems. Many of the condensed matter problems are realizable in laboratory experiments, where new methods beyond the usual quasi-particle approximation are needed to explain the observed exotic and anomalous results. Tools and techniques such as lattice gauge theories, numerical simulations of many-body systems, and tensor networks are seen as valuable to both communities and will likely benefit from collaborative development.« less

Experimental High Energy Physics Research: Direct Detection of Dark Matter

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

Witherell, Michael S.

2014-10-02

The grant supported research on an experimental search for evidence of dark matter interactions with normal matter. The PI carried out the research as a member of the LUX and LZ collaborations. The LUX research team collected a first data set with the LUX experiment, a large liquid xenon detector installed in the Sanford Underground Research Facility (SURF). The first results were published in Physical Review Letters on March 4, 2014. The journal Nature named the LUX result a scientific highlight of the year for 2013. In addition, the LZ collaboration submitted the full proposal for the Lux Zeplin experiment,more » which has since been approved by DOE-HEP as a second-generation dark matter experiment. Witherell is the Level 2 manager for the Outer Detector System on the LUX-Zeplin experiment.« less

SciDAC-Data, A Project to Enabling Data Driven Modeling of Exascale Computing

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

Mubarak, M.; Ding, P.; Aliaga, L.

The SciDAC-Data project is a DOE funded initiative to analyze and exploit two decades of information and analytics that have been collected by the Fermilab Data Center on the organization, movement, and consumption of High Energy Physics data. The project will analyze the analysis patterns and data organization that have been used by the NOvA, MicroBooNE, MINERvA and other experiments, to develop realistic models of HEP analysis workflows and data processing. The SciDAC-Data project aims to provide both realistic input vectors and corresponding output data that can be used to optimize and validate simulations of HEP analysis. These simulations aremore » designed to address questions of data handling, cache optimization and workflow structures that are the prerequisites for modern HEP analysis chains to be mapped and optimized to run on the next generation of leadership class exascale computing facilities. We will address the use of the SciDAC-Data distributions acquired from Fermilab Data Center’s analysis workflows and corresponding to around 71,000 HEP jobs, as the input to detailed queuing simulations that model the expected data consumption and caching behaviors of the work running in HPC environments. In particular we describe in detail how the Sequential Access via Metadata (SAM) data handling system in combination with the dCache/Enstore based data archive facilities have been analyzed to develop the radically different models of the analysis of HEP data. We present how the simulation may be used to analyze the impact of design choices in archive facilities.« less

The physics basis for ignition using indirect-drive targets on the National Ignition Facility

NASA Astrophysics Data System (ADS)

Lindl, John D.; Amendt, Peter; Berger, Richard L.; Glendinning, S. Gail; Glenzer, Siegfried H.; Haan, Steven W.; Kauffman, Robert L.; Landen, Otto L.; Suter, Laurence J.

2004-02-01

The 1990 National Academy of Science final report of its review of the Inertial Confinement Fusion Program recommended completion of a series of target physics objectives on the 10-beam Nova laser at the Lawrence Livermore National Laboratory as the highest-priority prerequisite for proceeding with construction of an ignition-scale laser facility, now called the National Ignition Facility (NIF). These objectives were chosen to demonstrate that there was sufficient understanding of the physics of ignition targets that the laser requirements for laboratory ignition could be accurately specified. This research on Nova, as well as additional research on the Omega laser at the University of Rochester, is the subject of this review. The objectives of the U.S. indirect-drive target physics program have been to experimentally demonstrate and predictively model hohlraum characteristics, as well as capsule performance in targets that have been scaled in key physics variables from NIF targets. To address the hohlraum and hydrodynamic constraints on indirect-drive ignition, the target physics program was divided into the Hohlraum and Laser-Plasma Physics (HLP) program and the Hydrodynamically Equivalent Physics (HEP) program. The HLP program addresses laser-plasma coupling, x-ray generation and transport, and the development of energy-efficient hohlraums that provide the appropriate spectral, temporal, and spatial x-ray drive. The HEP experiments address the issues of hydrodynamic instability and mix, as well as the effects of flux asymmetry on capsules that are scaled as closely as possible to ignition capsules (hydrodynamic equivalence). The HEP program also addresses other capsule physics issues associated with ignition, such as energy gain and energy loss to the fuel during implosion in the absence of alpha-particle deposition. The results from the Nova and Omega experiments approach the NIF requirements for most of the important ignition capsule parameters, including drive temperature, drive symmetry, and hydrodynamic instability. This paper starts with a review of the NIF target designs that have formed the motivation for the goals of the target physics program. Following that are theoretical and experimental results from Nova and Omega relevant to the requirements of those targets. Some elements of this work were covered in a 1995 review of indirect-drive [J. D. Lindl, ``Development of the indirect-drive approach to inertial confinement fusion and the target physics basis for ignition and gain,'' Phys. Plasmas 2, 3933 (1995)]. In order to present as complete a picture as possible of the research that has been carried out on indirect drive, key elements of that earlier review are also covered here, along with a review of work carried out since 1995.

HEP Computing

Science.gov Websites

Argonne National Laboratory High Energy Physics Division Windows Desktops Problem Report Service Request Password Help New Users Back to HEP Computing Email on ANL Exchange: See Windows Clients section (Outlook or Thunderbird recommended) Web Browsers: Web Browsers for Windows Desktops Software: Available

Patients' Perspectives on and Experiences of Home Exercise Programmes Delivered with a Mobile Application.

PubMed

Abramsky, Hillary; Kaur, Puneet; Robitaille, Mikale; Taggio, Leanna; Kosemetzky, Paul K; Foster, Hillary; Gibson Bmr Pt MSc PhD, Barbara E; Bergeron, Maggie; Jachyra, Patrick

2018-01-01

Purpose: We explored patients' perspectives on home exercise programmes (HEPs) and their experiences using a mobile application designed to facilitate home exercise. Method: Data were generated using qualitative, semi-structured, face-to-face interviews with 10 participants who were receiving outpatient physiotherapy. Results: Establishing a therapeutic partnership between physiotherapists and patients enabled therapists to customize the HEPs to the patients' lifestyles and preferences. Analysis suggests that using the mobile application improved participants' ability to integrate the HEP into their daily life and was overwhelmingly preferred to traditional paper handouts. Conclusions: The results suggest that efforts to engage patients in HEPs need to take their daily lives into account. To move in this direction, sample exercise prescription questions are offered. Mobile applications do not replace the clinical encounter, but they can be an effective tool and an extension of delivering personalized HEPs in an existing therapeutic partnership.

Gelsolin negatively regulates the activity of tumor suppressor p53 through their physical interaction in hepatocarcinoma HepG2 cells

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

An, Joo-Hee; Kim, Jung-Woong; Jang, Sang-Min

Highlights: {yields} The actin binding protein Gelsolin (GSN) interacts with transcription factor p53. {yields} GSN interacts with transactivation- and DNA binding domains of p53. {yields} GSN represses transactivity of p53 via inhibition of nuclear translocation of p53. {yields} GSN inhibits the p53-mediated apoptosis in hepatocarcinoma HepG2 cells. -- Abstract: As a transcription factor, p53 modulates several cellular responses including cell-cycle control, apoptosis, and differentiation. In this study, we have shown that an actin regulatory protein, gelsolin (GSN), can physically interact with p53. The nuclear localization of p53 is inhibited by GSN overexpression in hepatocarcinoma HepG2 cells. Additionally, we demonstrate thatmore » GSN negatively regulates p53-dependent transcriptional activity of a reporter construct, driven by the p21-promoter. Furthermore, p53-mediated apoptosis was repressed in GSN-transfected HepG2 cells. Taken together, these results suggest that GSN binds to p53 and this interaction leads to the inhibition of p53-induced apoptosis by anchoring of p53 in the cytoplasm in HepG2 cells.« less

Future HEP Accelerators: The US Perspective

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

Bhat, Pushpalatha; Shiltsev, Vladimir

2015-11-02

Accelerator technology has advanced tremendously since the introduction of accelerators in the 1930s, and particle accelerators have become indispensable instruments in high energy physics (HEP) research to probe Nature at smaller and smaller distances. At present, accelerator facilities can be classified into Energy Frontier colliders that enable direct discoveries and studies of high mass scale particles and Intensity Frontier accelerators for exploration of extremely rare processes, usually at relatively low energies. The near term strategies of the global energy frontier particle physics community are centered on fully exploiting the physics potential of the Large Hadron Collider (LHC) at CERN throughmore » its high-luminosity upgrade (HL-LHC), while the intensity frontier HEP research is focused on studies of neutrinos at the MW-scale beam power accelerator facilities, such as Fermilab Main Injector with the planned PIP-II SRF linac project. A number of next generation accelerator facilities have been proposed and are currently under consideration for the medium- and long-term future programs of accelerator-based HEP research. In this paper, we briefly review the post-LHC energy frontier options, both for lepton and hadron colliders in various regions of the world, as well as possible future intensity frontier accelerator facilities.« less

The Silverton Field Experience: A Model Geography Course for Achieving High-Impact Educational Practices (HEPs)

ERIC Educational Resources Information Center

Vogt, Brandon J.; Skop, Emily

2017-01-01

High-Impact Educational Practices (HEPs) are a set of specific teaching and learning approaches proven effective in university education. This paper focuses on the benefits derived from utilizing three particular HEPs (inquiry-based collaborative activities, undergraduate research, and experiential learning) while teaching a snow and ice field…

CompHEP: developments and applications

NASA Astrophysics Data System (ADS)

Boos, E. E.; Bunichev, V. E.; Dubinin, M. N.; Ilyin, V. A.; Savrin, V. I.; CompHEP Collaboration

2017-11-01

New developments of the CompHEP package and its applications to the top quark and the Higgs boson physics at the LHC collider are reviewed. These developments were motivated mainly by the needs of experimental searches of DO (Tevatron) and CMS (LHC) collaborations where identification of the top quark and the Higgs boson in the framework of the Standard Model (SM) or possible extensions of the SM played an important role. New useful features of the CompHEP Graphics User Interface (GUI) are described.

Screening of soy protein-derived hypotriglyceridemic di-peptides in vitro and in vivo

PubMed Central

2011-01-01

Background Soy protein and soy peptides have attracted considerable attention because of their potentially beneficial biological properties, including antihypertensive, anticarcinogenic, and hypolipidemic effects. Although soy protein isolate contains several bioactive peptides that have distinct physiological activities in lipid metabolism, it is not clear which peptide sequences are responsible for the triglyceride (TG)-lowering effects. In the present study, we investigated the effects of soy protein-derived peptides on lipid metabolism, especially TG metabolism, in HepG2 cells and obese Otsuka Long-Evans Tokushima fatty (OLETF) rats. Results In the first experiment, we found that soy crude peptide (SCP)-LD3, which was prepared by hydrolyze of soy protein isolate with endo-type protease, showed hypolipidemic effects in HepG2 cells and OLETF rats. In the second experiment, we found that hydrophilic fraction, separated from SCP-LD3 with hydrophobic synthetic absorbent, revealed lipid-lowering effects in HepG2 cells and OLETF rats. In the third experiment, we found that Fraction-C (Frc-C) peptides, fractionated from hydrophilic peptides by gel permeation chromatography-high performance liquid chromatography, significantly reduced TG synthesis and apolipoprotein B (apoB) secretion in HepG2 cells. In the fourth experiment, we found that the fraction with 0.1% trifluoroacetic acid, isolated from Frc-C peptides by octadecylsilyl column chromatography, showed hypolipidemic effects in HepG2 cells. In the final experiment, we found that 3 di-peptides, Lys-Ala, Val-Lys, and Ser-Tyr, reduced TG synthesis, and Ser-Tyr additionally reduced apoB secretion in HepG2 cells. Conclusion Novel active peptides with TG-lowering effects from soy protein have been isolated. PMID:21600040

Study on Desorption Process of n-Heptane and Methyl Cyclohexane Using UiO-66 with Hierarchical Pores.

PubMed

Chen, Sijia; Zhang, Lin; Zhang, Zhao; Qian, Gang; Liu, Zongjian; Cui, Qun; Wang, Haiyan

2018-06-06

UiO-66 (UiO for University of Oslo), is a zirconium-based MOF with reverse shape selectivity, gives an alternative way to produce high purity n-heptane used for the manufacture of high-purity pharmaceuticals. Couple of studies have shown that UiO-66 gives a high selectivity on the separation of n-/iso-alkanes. However, the microporous structure of UiO-66 causes poor mass transport during the desorption process. In this work, hierarchical-pore UiO-66 (H-UiO-66) was synthesized and utilized as an adsorbent of n-heptane (nHEP) and methyl cyclohexane (MCH) for systematically studying the desorption process of n/iso-alkanes. A suite of physical methods, including XRD patterns verified the UiO-66 structures and HRTEM showed the existence of hierarchical pores. N2 adsorption-desorption isotherms further confirmed the size distribution of hierarchical pores in H-UiO-66. Of particular note, the MCH/nHEP selectivity of H-UiO-66 is similar with UiO-66 in the same adsorption conditions, the desorption process of nHEP/MCH from H-UiO-66 is dramatically enhanced, viz, the desorption rates for nHEP/MCH from H-UiO-66 is enhanced by 30%/23% as comparing to UiO-66 at most. Moreover, desorption activation energy (Ed) derived from temperature-programmed desorption (TPD) experiments indicate that the Ed for nHEP/MCH is lower on H-UiO-66, i.e., the Ed of MCH on H-UiO-66 is ~37% lower than that on UiO-66 at most, leading to a milder condition for the desorption process. The introduction of hierarchical structures will be applicable for the optimization of desorption process during separation on porous materials.

Lipotoxicity in HepG2 cells triggered by free fatty acids

PubMed Central

Yao, Hong-Rui; Liu, Jun; Plumeri, Daniel; Cao, Yong-Bing; He, Ting; Lin, Ling; Li, Yu; Jiang, Yuan-Ying; Li, Ji; Shang, Jing

2011-01-01

The goal of this study was to investigate the lipid accumulation and lipotoxicity of free fatty acids (FFAs) induced in HepG2 cells. HepG2 cells were co-incubated with various concentrations of FFAs for 24h and the intracellular lipid contents were observed by Oil Red O and Nile Red staining methods. The lipotoxicity of HepG2 cells were then detected by Hoechest 33342/PI, Annexin V-FITC/PI double-staining and 3-(4,5-dimethylthiazol-2-yl)-2,5-di phenyltetrazolium bromide (MTT) experiment tests. The experiments showed a lipid accumulation and lipotoxicity by increasing FFA concentration gradients. Through cell morphological observation and quantitative analysis, FFAs have shown to increase in a dose-dependent manner compared with the control group. The data collected from hoechst 33342/PI, annexin V-FITC/PI double staining and also MTT experiments showed that cell apoptosis and necrosis significantly increased with increasing FFA concentrations. Apoptosis was not obvious in the 1 mM FFAs-treated group compared to the other two groups. In a certain concentration range, FFAs induced intracellular lipid accumulation and lipotoxicity of HepG2 cells in a dose-dependent manner. PMID:21654881

Evaluation results of xTCA equipment for HEP experiments at CERN

NASA Astrophysics Data System (ADS)

Di Cosmo, M.; Bobillier, V.; Haas, S.; Joos, M.; Mico, S.; Vasey, F.; Vichoudis, P.

2013-12-01

The MicroTCA and AdvancedTCA industry standards are candidate modular electronic platforms for the upgrade of the current generation of high energy physics experiments. The PH-ESE group at CERN launched in 2011 the xTCA evaluation project with the aim of performing technical evaluations and eventually providing support for commercially available components. Different devices from different vendors have been acquired, evaluated and interoperability tests have been performed. This paper presents the test procedures and facilities that have been developed and focuses on the evaluation results including electrical, thermal and interoperability aspects.

Networking: the view from HEP

NASA Astrophysics Data System (ADS)

McKee, Shawn

2017-10-01

Networks have played a critical role in high-energy physics (HEP), enabling us to access and effectively utilize globally distributed resources to meet the needs of our physicists. National and global-scale collaborations that characterize HEP would not be feasible without ubiquitous capable networks. Because of their importance in enabling our grid computing infrastructure many physicists have taken leading roles in research and education (R&E) networking, participating in, and even convening, network related meetings and research programs with the broader networking community worldwide. This has led to HEP benefiting from excellent global networking capabilities for little to no direct cost. However, as other science domains ramp-up their need for similar networking it becomes less clear that this situation will continue unchanged. This paper will briefly discuss the history of networking in HEP, the current activities and challenges we are facing, and try to provide some understanding of where networking may be going in the next 5 to 10 years.

How do particle physicists learn the programming concepts they need?

NASA Astrophysics Data System (ADS)

Kluth, S.; Pia, M. G.; Schoerner-Sadenius, T.; Steinbach, P.

2015-12-01

The ability to read, use and develop code efficiently and successfully is a key ingredient in modern particle physics. We report the experience of a training program, identified as “Advanced Programming Concepts”, that introduces software concepts, methods and techniques to work effectively on a daily basis in a HEP experiment or other programming intensive fields. This paper illustrates the principles, motivations and methods that shape the “Advanced Computing Concepts” training program, the knowledge base that it conveys, an analysis of the feedback received so far, and the integration of these concepts in the software development process of the experiments as well as its applicability to a wider audience.

The European Physical Society Conference on High Energy Physics

NASA Astrophysics Data System (ADS)

2017-07-01

The European Physical Society Conference on High Energy Physics (EPS- HEP) is one of the major international conferences that review the field. It takes place every other year since 1971. It is organized by the High Energy and Particle Physics Division of the European Physical Society in cooperation with an appointed European Local Institute of Research or an internationally recognized University or Academy Body. EPS-HEP 2017 was held on 5-12 July in Venice, Italy at Palazzo del Cinema and Palazzo del Casinò, located in the Lido island. The conference has been organized by the Istituto Nazionale di Fisica Nucleare (INFN) and by the Department of Physics and Astronomy of the University of Padova. Editorial Board: Paolo Checchia, Mauro Mezzetto, Giuseppina Salente, Michele Doro, Livia Conti, Caterina Braggio, Chiara Sirignano, Andrea Dainese, Martino Margoni, Roberto Rossin, Pierpaolo Mastrolia, Patrizia Azzi, Enrico Conti, Marco Zanetti, Luca Martucci, Sofia Talas Lucano Canton.

Detector Simulations with DD4hep

NASA Astrophysics Data System (ADS)

Petrič, M.; Frank, M.; Gaede, F.; Lu, S.; Nikiforou, N.; Sailer, A.

2017-10-01

Detector description is a key component of detector design studies, test beam analyses, and most of particle physics experiments that require the simulation of more and more different detector geometries and event types. This paper describes DD4hep, which is an easy-to-use yet flexible and powerful detector description framework that can be used for detector simulation and also extended to specific needs for a particular working environment. Linear collider detector concepts ILD, SiD and CLICdp as well as detector development collaborations CALICE and FCal have chosen to adopt the DD4hep geometry framework and its DDG4 pathway to Geant4 as its core simulation and reconstruction tools. The DDG4 plugins suite includes a wide variety of input formats, provides access to the Geant4 particle gun or general particles source and allows for handling of Monte Carlo truth information, eg. by linking hits and the primary particle that caused them, which is indispensable for performance and efficiency studies. An extendable array of segmentations and sensitive detectors allows the simulation of a wide variety of detector technologies. This paper shows how DD4hep allows to perform complex Geant4 detector simulations without compiling a single line of additional code by providing a palette of sub-detector components that can be combined and configured via compact XML files. Simulation is controlled either completely via the command line or via simple Python steering files interpreted by a Python executable. It also discusses how additional plugins and extensions can be created to increase the functionality.

Mitigated FPGA design of multi-gigabit transceivers for application in high radiation environments of High Energy Physics experiments

DOE PAGES

Brusati, M.; Camplani, A.; Cannon, M.; ...

2017-02-20

SRAM-ba8ed Field Programmable Gate Array (FPGA) logic devices arc very attractive in applications where high data throughput is needed, such as the latest generation of High Energy Physics (HEP) experiments. FPGAs have been rarely used in such experiments because of their sensitivity to radiation. The present paper proposes a mitigation approach applied to commercial FPGA devices to meet the reliability requirements for the front-end electronics of the Liquid Argon (LAr) electromagnetic calorimeter of the ATLAS experiment, located at CERN. Particular attention will be devoted to define a proper mitigation scheme of the multi-gigabit transceivers embedded in the FPGA, which ismore » a critical part of the LAr data acquisition chain. A demonstrator board is being developed to validate the proposed methodology. :!\\litigation techniques such as Triple Modular Redundancy (T:t\\IR) and scrubbing will be used to increase the robustness of the design and to maximize the fault tolerance from Single-Event Upsets (SEUs).« less

Two potential recombinant rabies vaccines expressing canine parvovirus virion protein 2 induce immunogenicity to canine parvovirus and rabies virus.

PubMed

Luo, Jun; Shi, Hehe; Tan, Yeping; Niu, Xuefeng; Long, Teng; Zhao, Jing; Tian, Qin; Wang, Yifei; Chen, Hao; Guo, Xiaofeng

2016-08-17

Both rabies virus (RABV) and canine parvovirus (CPV) cause lethal diseases in dogs. In this study, both high egg passage Flury (HEP-Flury) strains of RABV and recombinant RABV carrying double RABV glycoprotein (G) gene were used to express the CPV virion protein 2 (VP2) gene, and were designated rHEP-VP2 and, rHEP-dG-VP2 respectively. The two recombinant RABVs maintained optimal virus titration according to their viral growth kinetics assay compared with the parental strain HEP-Flury. Western blotting indicated that G protein and VP2 were expressed in vitro. The expression of VP2 in Crandell feline kidney cells post-infection by rHEP-VP2 and rHEP-dG-VP2 was confirmed by indirect immunofluorescence assay with antibody against VP2. Immunogenicity of recombinant rabies viruses was tested in Kunming mice. Both rHEP-VP2 and rHEP-dG-VP2 induced high levels of rabies antibody compared with HEP-Flury. Mice immunized with rHEP-VP2 and rHEP-dG-VP2 both had a high level of antibodies against VP2, which can protect against CPV infection. A challenge experiment indicated that more than 80% mice immunized with recombinant RABVs survived after infection of challenge virus standard 24 (CVS-24). Together, this study showed that recombinant RABVs expressing VP2 induced protective immune responses to RABV and CPV. Therefore, rHEP-VP2 and rHEP-dG-VP2 might be potential combined vaccines for RABV and CPV. Copyright © 2016 Elsevier Ltd. All rights reserved.

HappyFace as a generic monitoring tool for HEP experiments

NASA Astrophysics Data System (ADS)

Kawamura, Gen; Magradze, Erekle; Musheghyan, Haykuhi; Quadt, Arnulf; Rzehorz, Gerhard

2015-12-01

The importance of monitoring on HEP grid computing systems is growing due to a significant increase in their complexity. Computer scientists and administrators have been studying and building effective ways to gather information on and clarify a status of each local grid infrastructure. The HappyFace project aims at making the above-mentioned workflow possible. It aggregates, processes and stores the information and the status of different HEP monitoring resources into the common database of HappyFace. The system displays the information and the status through a single interface. However, this model of HappyFace relied on the monitoring resources which are always under development in the HEP experiments. Consequently, HappyFace needed to have direct access methods to the grid application and grid service layers in the different HEP grid systems. To cope with this issue, we use a reliable HEP software repository, the CernVM File System. We propose a new implementation and an architecture of HappyFace, the so-called grid-enabled HappyFace. It allows its basic framework to connect directly to the grid user applications and the grid collective services, without involving the monitoring resources in the HEP grid systems. This approach gives HappyFace several advantages: Portability, to provide an independent and generic monitoring system among the HEP grid systems. Eunctionality, to allow users to perform various diagnostic tools in the individual HEP grid systems and grid sites. Elexibility, to make HappyFace beneficial and open for the various distributed grid computing environments. Different grid-enabled modules, to connect to the Ganga job monitoring system and to check the performance of grid transfers among the grid sites, have been implemented. The new HappyFace system has been successfully integrated and now it displays the information and the status of both the monitoring resources and the direct access to the grid user applications and the grid collective services.

Nanoscale TiO₂-coated LPGs as radiation-tolerant humidity sensors for high-energy physics applications.

PubMed

Consales, Marco; Berruti, Gaia; Borriello, Anna; Giordano, Michele; Buontempo, Salvatore; Breglio, Giovanni; Makovec, Alajos; Petagna, Paolo; Cusano, Andrea

2014-07-15

This Letter deals with a feasibility analysis for the development of radiation-tolerant fiber-optic humidity sensors based on long-period grating (LPG) technology to be applied in high-energy physics (HEP) experiments currently running at the European Organization for Nuclear Research (CERN). In particular, here we propose a high-sensitivity LPG sensor coated with a finely tuned titanium dioxide (TiO₂) thin layer (~100 nm thick) through the solgel deposition method. Relative humidity (RH) monitoring in the range 0%-75% and at four different temperatures (in the range -10°C-25°C) was carried out to assess sensor performance in real operative conditions required in typical experiments running at CERN. Experimental results demonstrate the very high RH sensitivities of the proposed device (up to 1.4 nm/% RH in correspondence to very low humidity levels), which turned out to be from one to three orders of magnitude higher than those exhibited by fiber Bragg grating sensors coated with micrometer-thin polyimide overlays. The radiation tolerance capability of the TiO₂-coated LPG sensor is also investigated by comparing the sensing performance before and after its exposure to a 1 Mrad dose of γ-ionizing radiation. Overall, the results collected demonstrate the strong potential of the proposed technology with regard to its future exploitation in HEP applications as a robust and valid alternative to the commercial (polymer-based) hygrometers currently used.

A practical approach to virtualization in HEP

NASA Astrophysics Data System (ADS)

Buncic, P.; Aguado Sánchez, C.; Blomer, J.; Harutyunyan, A.; Mudrinic, M.

2011-01-01

In the attempt to solve the problem of processing data coming from LHC experiments at CERN at a rate of 15PB per year, for almost a decade the High Enery Physics (HEP) community has focused its efforts on the development of the Worldwide LHC Computing Grid. This generated large interest and expectations promising to revolutionize computing. Meanwhile, having initially taken part in the Grid standardization process, industry has moved in a different direction and started promoting the Cloud Computing paradigm which aims to solve problems on a similar scale and in equally seamless way as it was expected in the idealized Grid approach. A key enabling technology behind Cloud computing is server virtualization. In early 2008, an R&D project was established in the PH-SFT group at CERN to investigate how virtualization technology could be used to improve and simplify the daily interaction of physicists with experiment software frameworks and the Grid infrastructure. In this article we shall first briefly compare Grid and Cloud computing paradigms and then summarize the results of the R&D activity pointing out where and how virtualization technology could be effectively used in our field in order to maximize practical benefits whilst avoiding potential pitfalls.

MCdevelop - a universal framework for Stochastic Simulations

NASA Astrophysics Data System (ADS)

Slawinska, M.; Jadach, S.

2011-03-01

We present MCdevelop, a universal computer framework for developing and exploiting the wide class of Stochastic Simulations (SS) software. This powerful universal SS software development tool has been derived from a series of scientific projects for precision calculations in high energy physics (HEP), which feature a wide range of functionality in the SS software needed for advanced precision Quantum Field Theory calculations for the past LEP experiments and for the ongoing LHC experiments at CERN, Geneva. MCdevelop is a "spin-off" product of HEP to be exploited in other areas, while it will still serve to develop new SS software for HEP experiments. Typically SS involve independent generation of large sets of random "events", often requiring considerable CPU power. Since SS jobs usually do not share memory it makes them easy to parallelize. The efficient development, testing and running in parallel SS software requires a convenient framework to develop software source code, deploy and monitor batch jobs, merge and analyse results from multiple parallel jobs, even before the production runs are terminated. Throughout the years of development of stochastic simulations for HEP, a sophisticated framework featuring all the above mentioned functionality has been implemented. MCdevelop represents its latest version, written mostly in C++ (GNU compiler gcc). It uses Autotools to build binaries (optionally managed within the KDevelop 3.5.3 Integrated Development Environment (IDE)). It uses the open-source ROOT package for histogramming, graphics and the mechanism of persistency for the C++ objects. MCdevelop helps to run multiple parallel jobs on any computer cluster with NQS-type batch system. Program summaryProgram title:MCdevelop Catalogue identifier: AEHW_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEHW_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 48 136 No. of bytes in distributed program, including test data, etc.: 355 698 Distribution format: tar.gz Programming language: ANSI C++ Computer: Any computer system or cluster with C++ compiler and UNIX-like operating system. Operating system: Most UNIX systems, Linux. The application programs were thoroughly tested under Ubuntu 7.04, 8.04 and CERN Scientific Linux 5. Has the code been vectorised or parallelised?: Tools (scripts) for optional parallelisation on a PC farm are included. RAM: 500 bytes Classification: 11.3 External routines: ROOT package version 5.0 or higher ( http://root.cern.ch/drupal/). Nature of problem: Developing any type of stochastic simulation program for high energy physics and other areas. Solution method: Object Oriented programming in C++ with added persistency mechanism, batch scripts for running on PC farms and Autotools.

Impact of detector simulation in particle physics collider experiments

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

Elvira, V. Daniel

Through the last three decades, precise simulation of the interactions of particles with matter and modeling of detector geometries has proven to be of critical importance to the success of the international high-energy physics experimental programs. For example, the detailed detector modeling and accurate physics of the Geant4-based simulation software of the CMS and ATLAS particle physics experiments at the European Center of Nuclear Research (CERN) Large Hadron Collider (LHC) was a determinant factor for these collaborations to deliver physics results of outstanding quality faster than any hadron collider experiment ever before. This review article highlights the impact of detectormore » simulation on particle physics collider experiments. It presents numerous examples of the use of simulation, from detector design and optimization, through software and computing development and testing, to cases where the use of simulation samples made a difference in the accuracy of the physics results and publication turnaround, from data-taking to submission. It also presents the economic impact and cost of simulation in the CMS experiment. Future experiments will collect orders of magnitude more data, taxing heavily the performance of simulation and reconstruction software for increasingly complex detectors. Consequently, it becomes urgent to find solutions to speed up simulation software in order to cope with the increased demand in a time of flat budgets. The study ends with a short discussion on the potential solutions that are being explored, by leveraging core count growth in multicore machines, using new generation coprocessors, and re-engineering of HEP code for concurrency and parallel computing.« less

Impact of detector simulation in particle physics collider experiments

DOE PAGES

Elvira, V. Daniel

2017-06-01

Through the last three decades, precise simulation of the interactions of particles with matter and modeling of detector geometries has proven to be of critical importance to the success of the international high-energy physics experimental programs. For example, the detailed detector modeling and accurate physics of the Geant4-based simulation software of the CMS and ATLAS particle physics experiments at the European Center of Nuclear Research (CERN) Large Hadron Collider (LHC) was a determinant factor for these collaborations to deliver physics results of outstanding quality faster than any hadron collider experiment ever before. This review article highlights the impact of detectormore » simulation on particle physics collider experiments. It presents numerous examples of the use of simulation, from detector design and optimization, through software and computing development and testing, to cases where the use of simulation samples made a difference in the accuracy of the physics results and publication turnaround, from data-taking to submission. It also presents the economic impact and cost of simulation in the CMS experiment. Future experiments will collect orders of magnitude more data, taxing heavily the performance of simulation and reconstruction software for increasingly complex detectors. Consequently, it becomes urgent to find solutions to speed up simulation software in order to cope with the increased demand in a time of flat budgets. The study ends with a short discussion on the potential solutions that are being explored, by leveraging core count growth in multicore machines, using new generation coprocessors, and re-engineering of HEP code for concurrency and parallel computing.« less

Powerful inhibition of in-vivo growth of experimental hepatic cancers by bombesin/gastrin-releasing peptide antagonist RC-3940-II.

PubMed

Szepeshazi, Karoly; Schally, Andrew V; Rick, Ferenc G; Block, Norman L; Vidaurre, Irving; Halmos, Gabor; Szalontay, Luca

2012-10-01

Hepatic carcinoma is a major health problem worldwide. Its incidence is increasing in Western countries and there is currently no effective systemic therapy against it. Targeted treatment modalities developed in the past few years have provided very limited success. Development of new treatment strategies is therefore essential. We investigated the effects of bombesin/gastrin-releasing peptide (BN/GRP) antagonist RC-3940-II on experimental human liver cancers in nude mice. SK-Hep-1 and Hep-G2 cancers transplanted subcutaneously into nude mice were treated daily with 10 or 20 µg of RC-3940-II. Tumor growth was monitored for 50-184 days in five experiments. Tumor gene expression was analyzed with PCR array and protein expression by immunoblotting. Characteristics of BN/GRP receptors in the tumors were analyzed by binding assays. Effects of RC-3940-II on cell proliferation were investigated in vitro. RC-3940-II inhibited the growth of SK-Hep-1 cancers in nude mice by 65-98%, with total regression in 9 of 36 tumors in three experiments. The BN/GRP antagonist inhibited the growth of Hep-G2 cancers as well by 73-82% in two experiments, being effective even on originally large tumors. Gene expression analysis showed an increase in several angiogenesis inhibitors and decrease in proangiogenic genes after RC-3940-II treatment. Receptor assays demonstrated high-affinity binding sites for BN/GRP in both tumor lines. BN/GRP antagonist RC-3940-II powerfully inhibits growth of SK-Hep-1 and Hep-G2 cancers in nude mice. Its effect may be linked to changes in expression of those cancer genes important in angiogenesis, invasion, and metastasis. RC-3940-II may be considered for further investigations in treatment of liver cancers.

The HEP Software and Computing Knowledge Base

NASA Astrophysics Data System (ADS)

Wenaus, T.

2017-10-01

HEP software today is a rich and diverse domain in itself and exists within the mushrooming world of open source software. As HEP software developers and users we can be more productive and effective if our work and our choices are informed by a good knowledge of what others in our community have created or found useful. The HEP Software and Computing Knowledge Base, hepsoftware.org, was created to facilitate this by serving as a collection point and information exchange on software projects and products, services, training, computing facilities, and relating them to the projects, experiments, organizations and science domains that offer them or use them. It was created as a contribution to the HEP Software Foundation, for which a HEP S&C knowledge base was a much requested early deliverable. This contribution will motivate and describe the system, what it offers, its content and contributions both existing and needed, and its implementation (node.js based web service and javascript client app) which has emphasized ease of use for both users and contributors.

An FPGA-Based High-Speed Error Resilient Data Aggregation and Control for High Energy Physics Experiment

NASA Astrophysics Data System (ADS)

Mandal, Swagata; Saini, Jogender; Zabołotny, Wojciech M.; Sau, Suman; Chakrabarti, Amlan; Chattopadhyay, Subhasis

2017-03-01

Due to the dramatic increase of data volume in modern high energy physics (HEP) experiments, a robust high-speed data acquisition (DAQ) system is very much needed to gather the data generated during different nuclear interactions. As the DAQ works under harsh radiation environment, there is a fair chance of data corruption due to various energetic particles like alpha, beta, or neutron. Hence, a major challenge in the development of DAQ in the HEP experiment is to establish an error resilient communication system between front-end sensors or detectors and back-end data processing computing nodes. Here, we have implemented the DAQ using field-programmable gate array (FPGA) due to some of its inherent advantages over the application-specific integrated circuit. A novel orthogonal concatenated code and cyclic redundancy check (CRC) have been used to mitigate the effects of data corruption in the user data. Scrubbing with a 32-b CRC has been used against error in the configuration memory of FPGA. Data from front-end sensors will reach to the back-end processing nodes through multiple stages that may add an uncertain amount of delay to the different data packets. We have also proposed a novel memory management algorithm that helps to process the data at the back-end computing nodes removing the added path delays. To the best of our knowledge, the proposed FPGA-based DAQ utilizing optical link with channel coding and efficient memory management modules can be considered as first of its kind. Performance estimation of the implemented DAQ system is done based on resource utilization, bit error rate, efficiency, and robustness to radiation.

REPORT OF RESEARCH ACCOMPLISHMENTS AND FUTURE GOALS HIGH ENERGY PHYSICS

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

Wise, Mark B.; Kapustin, Anton N.; Schwarz, John Henry

Caltech High Energy Physics (HEP) has a broad program in both experimental and theoretical physics. We are known for our creativity and leadership. The future is uncertain and we strive to be involved in all the major areas of experimental and theoretical HEP physics so no matter where the important discoveries occur we are well positioned to play an important role. An outstanding group of postdoctoral scholars, graduate students, staff scientists, and technical and administrative personnel support our efforts in experimental and theoretical physics. The PI’s on this grant are involved in the following program of experimental and theoretical activities:more » I) EXPERIMENTAL PHYSICS Our CMS group, led by Harvey Newman and Maria Spiropulu, has played a key role in the discovery and interpretation of the Higgs boson and in searches for new physics. They have important hardware responsibilities in both ECAL and HCAL and are also involved in the upgrades needed for the High Luminosity LHC. Newman's group also develops and operates Grid-based computing, networking, and collaborative systems for CMS and the US HEP community. The charged lepton (Mu2e) and quark BaBar flavor physics group is led by David Hitlin and Frank Porter. On Mu2e they have been instrumental in the design of the calorimeter. Construction responsibilities include one third of the crystals and associated readout as well as the calibration system. They also will have responsibility for a major part of the online system software. Although data taking ceased in 2008 the Caltech BaBar group is active on several new forefront analyses. The neutrino group is led by Ryan Patterson. They are central to NOvA's core oscillation physics program, to calibration, and to detector readiness being responsible for the production and installation of 12,000 APD arrays. They have key roles in neutrino appearance and disappearance analysis in MINOS and MINOS+. Sunil Golwala leads the dark matter direct detection effort. Areas of activity include: CDMS II data analysis, contributions to SuperCDMS Soudan operations and analysis, R&D towards SuperCDMS SNOLAB, development of a novel screener for radiocontamination (the BetaCage), and development of new WIMP detector concepts. Ren-Yuan Zhu leads the HEP crystal laboratory for the advanced detector R&D effort. The crystal lab is involved in development of novel scintillating crystals and has proposed several crystal based detector concepts for future HEP experiments at the energy and intensity frontiers. Its current research effort is concentrated on development of fast crystal scintillators with good radiation hardness and low cost. II) THEORETICAL PHYSICS The main theme of Sergei Gukov's current research is the relation between the geometry of quantum group invariants and their categorification, on the one hand, and the physics of supersymmetric gauge theory and string theory, on the other. Anton Kapustin's research spans a variety of topics in non-perturbative Quantum Field Theory (QFT). His main areas of interest are supersymmetric gauge theories, non-perturbative dualities in QFT, disorder operators, Topological Quantum Field Theory, and non-relativistic QFT. He is also interested in the foundations and possible generalizations of Quantum Mechanics. Hirosi Ooguri's current research has two main components. One is to find exact results in Calabi-Yau compactification of string theory. Another is to explore applications of the AdS/CFT correspondence. He also plans to continue his project with Caltech postdoctoral fellows on BPS spectra of supersymmetric gauge theories in diverse dimensions. John Preskill works on quantum information science. This field may lead to important future technologies, and also lead to new understanding of issues in fundamental physics John Schwarz has been exploring a number of topics in superstring theory/M-theory, supersymmetric gauge theory, and their AdS/CFT relationships. Much of the motivation for these studies is the desire to gain a deeper understanding of superstring theory and M-theory. The research interests of Mark Wise span particle physics, cosmology and nuclear physics. His recent work has centered on extensions of the standard model where baryon number and lepton number are gauged and extensions of the standard model that have novel sources of baryon number violation and new sources of charged lepton flavor violation« less

Functional measures show improvements after a home exercise program following supervised balance training in older adults with elevated fall risk.

PubMed

Tisher, Kristen; Mann, Kimberly; VanDyke, Sarah; Johansson, Charity; Vallabhajosula, Srikant

2018-03-05

Supervised balance training shows immediate benefit for older adults at fall risk. The long-term effectiveness of such training can be enhanced by implementing a safe and simple home exercise program (HEP). We investigated the effects of a12-week unsupervised HEP following supervised clinic-based balance training on functional mobility, balance, fall risk, and gait. Six older adults with an elevated fall risk obtained an HEP and comprised the HEP group (HEPG) and five older adults who were not given an HEP comprised the no HEP group (NoHEPG). The HEP consisted of three static balance exercises: feet-together, single-leg stance, and tandem. Each exercise was to be performed twice for 30-60 s, once per day, 3 days per week for 12 weeks. Participants were educated on proper form, safety, and progression of exercises. Pre- and post-HEP testing included Berg Balance Scale (BBS), Timed Up and Go, Short Physical Performance Battery (SPPB) assessments, Activities-Balance Confidence, Late-Life Functional Disability Instrument and instrumented assessments of balance and gait (Limits of Stability, modified Clinical Test of Sensory Interaction on Balance, Gait). A healthy control group (HCG; n = 11) was also tested. For most of the measures, the HEPG improved to the level of HCG. Though task-specific improvements like BBS and SPPB components were seen, the results did not carry over to more dynamic assessments. Results provide proof of concept that a simple HEP can be independently implemented and effective for sustaining and/or improving balance in older adults at elevated fall-risk after they have undergone a clinic-based balance intervention.

Architecture of a general purpose embedded Slow-Control Adapter ASIC for future high-energy physics experiments

NASA Astrophysics Data System (ADS)

Gabrielli, Alessandro; Loddo, Flavio; Ranieri, Antonio; De Robertis, Giuseppe

2008-10-01

This work is aimed at defining the architecture of a new digital ASIC, namely Slow-Control Adapter (SCA), which will be designed in a commercial 130-nm CMOS technology. This chip will be embedded within a high-speed data acquisition optical link (GBT) to control and monitor the front-end electronics in future high-energy physics experiments. The GBT link provides a transparent transport layer between the SCA and control electronics in the counting room. The proposed SCA supports a variety of common bus protocols to interface with end-user general-purpose electronics. Between the GBT and the SCA a standard 100 Mb/s IEEE-802.3 compatible protocol will be implemented. This standard protocol allows off-line tests of the prototypes using commercial components that support the same standard. The project is justified because embedded applications in modern large HEP experiments require particular care to assure the lowest possible power consumption, still offering the highest reliability demanded by very large particle detectors.

Introducing HEP to schools through educational scenaria

NASA Astrophysics Data System (ADS)

Kourkoumelis, C.; Vourakis, S.

2015-05-01

Recent activities, towards the goal of introducing High Energy Physics in the school class, are reviewed. The most efficient method is a half or a full day workshop where the students are introduced to one of the large LHC experiments, follow a "virtual visit" to the experiment's Control Room and perform an interactive analysis of real data. Science cafes and visits to the CERN expositions are also very helpful, provided that the tours/discussions are led by an active scientist and/or a trained teacher. Several EU outreach projects provide databases rich with education scenaria and data analysis tools ready to be used by the teachers in order to bridge the gap between modern research and technology and school education.

HEPLIB `91: International users meeting on the support and environments of high energy physics computing

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

Johnstad, H.

The purpose of this meeting is to discuss the current and future HEP computing support and environments from the perspective of new horizons in accelerator, physics, and computing technologies. Topics of interest to the Meeting include (but are limited to): the forming of the HEPLIB world user group for High Energy Physic computing; mandate, desirables, coordination, organization, funding; user experience, international collaboration; the roles of national labs, universities, and industry; range of software, Monte Carlo, mathematics, physics, interactive analysis, text processors, editors, graphics, data base systems, code management tools; program libraries, frequency of updates, distribution; distributed and interactive computing, datamore » base systems, user interface, UNIX operating systems, networking, compilers, Xlib, X-Graphics; documentation, updates, availability, distribution; code management in large collaborations, keeping track of program versions; and quality assurance, testing, conventions, standards.« less

HEPLIB 91: International users meeting on the support and environments of high energy physics computing

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

Johnstad, H.

The purpose of this meeting is to discuss the current and future HEP computing support and environments from the perspective of new horizons in accelerator, physics, and computing technologies. Topics of interest to the Meeting include (but are limited to): the forming of the HEPLIB world user group for High Energy Physic computing; mandate, desirables, coordination, organization, funding; user experience, international collaboration; the roles of national labs, universities, and industry; range of software, Monte Carlo, mathematics, physics, interactive analysis, text processors, editors, graphics, data base systems, code management tools; program libraries, frequency of updates, distribution; distributed and interactive computing, datamore » base systems, user interface, UNIX operating systems, networking, compilers, Xlib, X-Graphics; documentation, updates, availability, distribution; code management in large collaborations, keeping track of program versions; and quality assurance, testing, conventions, standards.« less

Final Report: High Energy Physics Program (HEP), Physics Department, Princeton University

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

Callan, Curtis G.; Gubser, Steven S.; Marlow, Daniel R.

The activities of the Princeton Elementary particles group funded through Department of Energy Grant# DEFG02-91 ER40671 during the period October 1, 1991 through January 31, 2013 are summarized. These activities include experiments performed at Brookhaven National Lab; the CERN Lab in Geneva, Switzerland; Fermilab; KEK in Tsukuba City, Japan; the Stanford Linear Accelerator Center; as well as extensive experimental and the- oretical studies conducted on the campus of Princeton University. Funded senior personnel include: Curtis Callan, Stephen Gubser, Valerie Halyo, Daniel Marlow, Kirk McDonald, Pe- ter Meyers, James Olsen, Pierre Pirou e, Eric Prebys, A.J. Stewart Smith, Frank Shoemaker (deceased),more » Paul Steinhardt, David Stickland, Christopher Tully, and Liantao Wang.« less

Decorin-loaded poly lactic-co-glycolic acid nanoparticles modified by anti-alpha fetoprotein antibody: preparation, proliferation inhibition and induced apoptosis effects on HepG2 cells in vitro.

PubMed

Yang, Qiaoli; Wang, Shuyue; Wang, Yuan; Qu, Yane; Xue, Jun; Mi, Yang; Wang, Yanhong; Luo, Xuguang; Deng, Zhihua; Wang, Guiqin

2017-06-01

Decorin (DCN) is a negative regulatory factor for the growth of cancer cells and can inhibit the proliferation, metastasis of cancer cells and angiogenesis in cancer tissues. The aims of this study were to prepare the nanoparticles consisting of DCN and poly lactic-co-glycolic acid (PLGA) modified by anti-alpha fetoprotein (AFP) monoclonal antibody (mAb) and to examine the conventional physical properties, the in-vitro release of DCN and the targeting effect of these nanoparticles on HepG2 cells. The encapsulated plasmid was slowly and steadily released from the nanoparticles. The targeted PLGA nanoparticles were initiatively taken in HepG2 cells high-efficiently. According to the results of RT-PCR, DCN gene in AFPmAb-PLGA-rhDCN nanoparticles can be expressed in HepG2 cells successfully. These nanoparticles significantly inhibited the proliferation of HepG2 cells and induced apoptosis. The mRNA expression of Bcl-2 gene in the AFPmAb-PLGA-rhDCN-treated groups appeared significantly to decrease and the caspase-3 gene had the opposite trend as compared with that of control group (P < 0.01). These studies revealed that these nanoparticles were capable of specifically targeting the HepG2 cells and inhibiting the proliferation and they induce apoptosis of HepG2 cells in vitro, which was in a dose- and time-dependent manner. © 2017 Royal Pharmaceutical Society.

Enabling Research Network Connectivity to Clouds with Virtual Router Technology

NASA Astrophysics Data System (ADS)

Seuster, R.; Casteels, K.; Leavett-Brown, CR; Paterson, M.; Sobie, RJ

2017-10-01

The use of opportunistic cloud resources by HEP experiments has significantly increased over the past few years. Clouds that are owned or managed by the HEP community are connected to the LHCONE network or the research network with global access to HEP computing resources. Private clouds, such as those supported by non-HEP research funds are generally connected to the international research network; however, commercial clouds are either not connected to the research network or only connect to research sites within their national boundaries. Since research network connectivity is a requirement for HEP applications, we need to find a solution that provides a high-speed connection. We are studying a solution with a virtual router that will address the use case when a commercial cloud has research network connectivity in a limited region. In this situation, we host a virtual router in our HEP site and require that all traffic from the commercial site transit through the virtual router. Although this may increase the network path and also the load on the HEP site, it is a workable solution that would enable the use of the remote cloud for low I/O applications. We are exploring some simple open-source solutions. In this paper, we present the results of our studies and how it will benefit our use of private and public clouds for HEP computing.

PODIO: An Event-Data-Model Toolkit for High Energy Physics Experiments

NASA Astrophysics Data System (ADS)

Gaede, F.; Hegner, B.; Mato, P.

2017-10-01

PODIO is a C++ library that supports the automatic creation of event data models (EDMs) and efficient I/O code for HEP experiments. It is developed as a new EDM Toolkit for future particle physics experiments in the context of the AIDA2020 EU programme. Experience from LHC and the linear collider community shows that existing solutions partly suffer from overly complex data models with deep object-hierarchies or unfavorable I/O performance. The PODIO project was created in order to address these problems. PODIO is based on the idea of employing plain-old-data (POD) data structures wherever possible, while avoiding deep object-hierarchies and virtual inheritance. At the same time it provides the necessary high-level interface towards the developer physicist, such as the support for inter-object relations and automatic memory-management, as well as a Python interface. To simplify the creation of efficient data models PODIO employs code generation from a simple yaml-based markup language. In addition, it was developed with concurrency in mind in order to support the use of modern CPU features, for example giving basic support for vectorization techniques.

Special Colloquium : Looking at High Energy Physics from a gender studies perspective

ScienceCinema

Goetschel, Helene

2018-01-23

Human actors, workplace cultures and knowledge production: Gender studies analyse the social constructions and cultural representations of gender. Using methods and tools from the humanities and social science, we look at all areas, including the natural sciences and technology, science education and research labs. After a short introduction to gender studies, the main focus of my talk will be the presentation of selected research findings on gender and high energy physics. You will hear about an ongoing research project on women in neutrino physics and learn about a study on the world of high energy physicists characterised by "rites of passage" and "male tales" told during a life in physics. I will also present a study on how the HEP community communicates, and research findings on the naming culture in HEP. Getting to know findings from another field on your own might contribute to create a high energy physics culture that is fair and welcoming to all genders.

Special Colloquium : Looking at High Energy Physics from a gender studies perspective

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

Goetschel, Helene

Human actors, workplace cultures and knowledge production: Gender studies analyse the social constructions and cultural representations of gender. Using methods and tools from the humanities and social science, we look at all areas, including the natural sciences and technology, science education and research labs. After a short introduction to gender studies, the main focus of my talk will be the presentation of selected research findings on gender and high energy physics. You will hear about an ongoing research project on women in neutrino physics and learn about a study on the world of high energy physicists characterised by "rites ofmore » passage" and "male tales" told during a life in physics. I will also present a study on how the HEP community communicates, and research findings on the naming culture in HEP. Getting to know findings from another field on your own might contribute to create a high energy physics culture that is fair and welcoming to all genders.« less

From Physics to industry: EOS outside HEP

NASA Astrophysics Data System (ADS)

Espinal, X.; Lamanna, M.

2017-10-01

In the competitive market for large-scale storage solutions the current main disk storage system at CERN EOS has been showing its excellence in the multi-Petabyte high-concurrency regime. It has also shown a disruptive potential in powering the service in providing sync and share capabilities and in supporting innovative analysis environments along the storage of LHC data. EOS has also generated interest as generic storage solution ranging from university systems to very large installations for non-HEP applications.

Use of a Telehealth System to Enhance a Home Exercise Program for a Person With Parkinson Disease: A Case Report.

PubMed

Chatto, Charlotte A; York, Paul T; Slade, Catherine P; Hasson, Scott M

2018-01-01

This case addresses feasibility of a home-based telehealth system to enhance home exercise program (HEP) adherence for a patient with Parkinson disease (PD). We describe START-System for Technology-Augmented Rehabilitation and Training-and discuss outcomes after integrating START into the HEP component of an established therapy protocol, Lee Silverman Voice Technique BIG (LSVT BIG). The participant was a 67-year-old woman with PD at Hoehn and Yahr Stage II. During the first 4 weeks of a 4-month intervention, a physical therapist guided the participant through the LSVT BIG protocol. START was introduced at week 3; the participant was encouraged to complement her daily HEP through the end of the fourth month with START. Improvements in gait, endurance, balance confidence, and quality of life were observed from the start of the assessment to the end of month 1. By month 4, the participant maintained or improved with respect to these outcomes. Monitored by START, the rate of adherence to her twice-daily HEP prescription was 24%, but her daily participation rate was 78%. The participant's satisfaction with the START system was high, although autonomous feedback provided by START was a limiting concern. There were no technical issues or adverse events reported. This case supports START as a feasible HEP telehealth solution for physical therapy, given that increased long-term exercise adherence may improve health outcomes for people with PD. The outcomes of this case study support further investigation into the use of START for people with PD.Video Abstract available for more insights from the authors (see Video; Supplemental Digital Content 1, http://links.lww.com/JNPT/A192).

Early rehabilitation after total knee replacement surgery: a multicenter, noninferiority, randomized clinical trial comparing a home exercise program with usual outpatient care.

PubMed

Han, Annie S Y; Nairn, Lillias; Harmer, Alison R; Crosbie, Jack; March, Lyn; Parker, David; Crawford, Ross; Fransen, Marlene

2015-02-01

To determine, at 6 weeks postsurgery, if a monitored home exercise program (HEP) is not inferior to usual care rehabilitation for patients undergoing primary unilateral total knee replacement (TKR) surgery for osteoarthritis. We conducted a multicenter, randomized clinical trial. Patients ages 45-75 years were allocated at the time of hospital discharge to usual care rehabilitation (n = 196) or the HEP (n = 194). Outcomes assessed 6 weeks after surgery included the Western Ontario and McMaster Universities Osteoarthritis Index pain and physical function subscales, knee range of motion, and the 50-foot walk time. The upper bound of the 95% confidence interval (95% CI) mean difference favoring usual care was used to determine noninferiority. At 6 weeks after surgery there were no significant differences between usual care and HEP, respectively, for pain (7.4 and 7.2; 95% CI mean difference [MD] -0.7, 0.9), physical function (22.5 and 22.4; 95% CI MD -2.5, 2.6), knee flexion (96° and 97°; 95% CI MD -4°, 2°), knee extension (-7° and -6°; 95% CI MD -2°, 1°), or the 50-foot walk time (12.9 and 12.9 seconds; 95% CI MD -0.8, 0.7 seconds). At 6 weeks, 18 patients (9%) allocated to usual care and 11 (6%) to the HEP did not achieve 80° knee flexion. There was no difference between the treatment allocations in the number of hospital readmissions. The HEP was not inferior to usual care as an early rehabilitation protocol after primary TKR. Copyright © 2015 by the American College of Rheumatology.

Recent operation of the FNAL magnetron H- ion source

NASA Astrophysics Data System (ADS)

Karns, P. R.; Bollinger, D. S.; Sosa, A.

2017-08-01

This paper will detail changes in the operational paradigm of the Fermi National Accelerator Laboratory (FNAL) magnetron H- ion source due to upgrades in the accelerator system. Prior to November of 2012 the H- ions for High Energy Physics (HEP) experiments were extracted at ˜18 keV vertically downward into a 90 degree bending magnet and accelerated through a Cockcroft-Walton accelerating column to 750 keV. Following the upgrade in the fall of 2012 the H- ions are now directly extracted from a magnetron at 35 keV and accelerated to 750 keV by a Radio Frequency Quadrupole (RFQ). This change in extraction energy as well as the orientation of the ion source required not only a redesign of the ion source, but an updated understanding of its operation at these new values. Discussed in detail are the changes to the ion source timing, arc discharge current, hydrogen gas pressure, and cesium delivery system that were needed to maintain consistent operation at >99% uptime for HEP, with an increased ion source lifetime of over 9 months.

Experience with HEP analysis on mounted filesystems.

NASA Astrophysics Data System (ADS)

Fuhrmann, Patrick; Gasthuber, Martin; Kemp, Yves; Ozerov, Dmitry

2012-12-01

We present results on different approaches on mounted filesystems in use or under investigation at DESY. dCache, established since long as a storage system for physics data has implemented the NFS v4.1/pNFS protocol. New performance results will be shown with the most current version of the dCache server. In addition to the native usage of the mounted filesystem in a LAN environment, the results are given for the performance of the dCache NFS v4.1/pNFS in WAN case. Several commercial vendors are currently in alpha or beta phase of adding the NFS v4.1/pNFS protocol to their storage appliances. We will test some of these vendor solutions for their readiness for HEP analysis. DESY has recently purchased an IBM Sonas system. We will present the result of a thorough performance evaluation using the native protocols NFS (v3 or v4) and GPFS. As the emphasis is on the usability for end user analysis, we will use latest ROOT versions and current end user analysis code for benchmark scenarios.

A hydro-meteorological ensemble prediction system for real-time flood forecasting purposes in the Milano area

NASA Astrophysics Data System (ADS)

Ravazzani, Giovanni; Amengual, Arnau; Ceppi, Alessandro; Romero, Romualdo; Homar, Victor; Mancini, Marco

2015-04-01

Analysis of forecasting strategies that can provide a tangible basis for flood early warning procedures and mitigation measures over the Western Mediterranean region is one of the fundamental motivations of the European HyMeX programme. Here, we examine a set of hydro-meteorological episodes that affected the Milano urban area for which the complex flood protection system of the city did not completely succeed before the occurred flash-floods. Indeed, flood damages have exponentially increased in the area during the last 60 years, due to industrial and urban developments. Thus, the improvement of the Milano flood control system needs a synergism between structural and non-structural approaches. The flood forecasting system tested in this work comprises the Flash-flood Event-based Spatially distributed rainfall-runoff Transformation, including Water Balance (FEST-WB) and the Weather Research and Forecasting (WRF) models, in order to provide a hydrological ensemble prediction system (HEPS). Deterministic and probabilistic quantitative precipitation forecasts (QPFs) have been provided by WRF model in a set of 48-hours experiments. HEPS has been generated by combining different physical parameterizations (i.e. cloud microphysics, moist convection and boundary-layer schemes) of the WRF model in order to better encompass the atmospheric processes leading to high precipitation amounts. We have been able to test the value of a probabilistic versus a deterministic framework when driving Quantitative Discharge Forecasts (QDFs). Results highlight (i) the benefits of using a high-resolution HEPS in conveying uncertainties for this complex orographic area and (ii) a better simulation of the most of extreme precipitation events, potentially enabling valuable probabilistic QDFs. Hence, the HEPS copes with the significant deficiencies found in the deterministic QPFs. These shortcomings would prevent to correctly forecast the location and timing of high precipitation rates and total amounts at the catchment scale, thus impacting heavily the deterministic QDFs. In contrast, early warnings would have been possible within a HEPS context for the Milano area, proving the suitability of such system for civil protection purposes.

Citing and Reading Behaviors of High-Energy Physics or How a Community Stopped Worrying about Journals and Learned to Love Repositories

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

Gentil-Beccot, Anne; Mele, Salvatore; /CERN

Contemporary scholarly discourse follows many alternative routes in addition to the three-century old tradition of publication in peer-reviewed journals. The field of High-Energy Physics (HEP) has explored alternative communication strategies for decades, initially via the mass mailing of paper copies of preliminary manuscripts, then via the inception of the first online repositories and digital libraries. This field is uniquely placed to answer recurrent questions raised by the current trends in scholarly communication: is there an advantage for scientists to make their work available through repositories, often in preliminary form? Is there an advantage to publishing in Open Access journals? Domore » scientists still read journals or do they use digital repositories? The analysis of citation data demonstrates that free and immediate online dissemination of preprints creates an immense citation advantage in HEP, whereas publication in Open Access journals presents no discernible advantage. In addition, the analysis of clickstreams in the leading digital library of the field shows that HEP scientists seldom read journals, preferring preprints instead.« less

EDITORIAL: Metrological Aspects of Accelerator Technology and High Energy Physics Experiments

NASA Astrophysics Data System (ADS)

Romaniuk, Ryszard S.; Pozniak, Krzysztof T.

2007-08-01

The subject of this special feature in Measurement Science and Technology concerns measurement methods, devices and subsystems, both hardware and software aspects, applied in large experiments of high energy physics (HEP) and superconducting RF accelerator technology (SRF). These experiments concern mainly the physics of elementary particles or the building of new machines and detectors. The papers present practical examples of applied solutions in large, contemporary, international research projects such as HERA, LHC, FLASH, XFEL, ILC and others. These machines are unique in their global scale and consist of extremely dedicated apparatus. The apparatus is characterized by very large dimensions, a considerable use of resources and a high level of overall technical complexity. They possess a large number of measurement channels (ranging from thousands to over 100 million), are characterized by fast of processing of measured data and high measurement accuracies, and work in quite adverse environments. The measurement channels cooperate with a large number of different sensors of momenta, energies, trajectories of elementary particles, electron, proton and photon beam profiles, accelerating fields in resonant cavities, and many others. The provision of high quality measurement systems requires the designers to use only the most up-to-date technical solutions, measurement technologies, components and devices. Research work in these demanding fields is a natural birthplace of new measurement methods, new data processing and acquisition algorithms, complex, networked measurement system diagnostics and monitoring. These developments are taking place in both hardware and software layers. The chief intention of this special feature is that the papers represent equally some of the most current metrology research problems in HEP and SRF. The accepted papers have been divided into four topical groups: superconducting cavities (4 papers), low level RF systems (8 papers), ionizing radiation (5 papers) and HEP experiments (8 papers). The editors would like to thank cordially all the authors who accepted our invitation to present their very recent results. A number of authors of the papers in this issue are active in the 6th European Framework Research Program CARE—Coordinated Accelerators Research in Europe and ELAN—the European Linear Accelerator Network. Some authors are active in research programs of a global extent such as the LHC, ILC and GDE—the Global Design Effort for the International Linear Collider. We also would like to thank personally, as well as on behalf of all the authors, the Editorial Board of Measurement Science and Technology for accepting this very exciting field of contemporary metrology. This field seems to be really a birthplace of a host of new metrological technologies, where the driving force is the incredibly high technical requirements that must soon be fulfilled if we dream of building new accelerators for elementary particles, new biological materials and medicine alike. Special thanks are due to Professor R S Jachowicz of Warsaw University of Technology for initiating this issue and for continuous support and advice during our work.

Time-dependent effects of low-temperature atmospheric-pressure argon plasma on epithelial cell attachment, viability and tight junction formation in vitro

NASA Astrophysics Data System (ADS)

Hoentsch, Maxi; von Woedtke, Thomas; Weltmann, Klaus-Dieter; Nebe, J. Barbara

2012-01-01

The application of physical plasma to living tissues is expected to promote wound healing by plasma disinfection and stimulation of tissue regeneration. However, the effects of plasma on healthy cells must be studied and understood. In our experiments we used an argon plasma jet (kINPen®09) to gain insights into time-dependent plasma effects on cell attachment, viability and tight junction formation in vitro. Murine epithelial cells mHepR1 were suspended in complete cell culture medium and were irradiated with argon plasma (direct approach) for 30, 60 and 120 s. Suspecting that physical plasma may exert its effect via the medium, cell culture medium alone was first treated with argon plasma (indirect approach) and immediately afterwards, cells were added and also cultured for 24 h. Cell morphology and vitality were verified using light microscopy and an enzyme-linked immunosorbent assay. Already after 30 s of treatment the mHepR1 cells lost their capability to adhere and the cell vitality decreased with increasing treatment time. Interestingly, the same inhibitory effect was observed in the indirect approach. Furthermore, the argon plasma-treated culture medium-induced large openings of the cell's tight junctions, were verified by the zonula occludens protein ZO-1, which we observed for the first time in confluently grown epithelial cells.

ASCR/HEP Exascale Requirements Review Report

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

Habib, Salman; Roser, Robert; Gerber, Richard

This draft report summarizes and details the findings, results, and recommendations derived from the ASCR/HEP Exascale Requirements Review meeting held in June, 2015. The main conclusions are as follows. 1) Larger, more capable computing and data facilities are needed to support HEP science goals in all three frontiers: Energy, Intensity, and Cosmic. The expected scale of the demand at the 2025 timescale is at least two orders of magnitude -- and in some cases greater -- than that available currently. 2) The growth rate of data produced by simulations is overwhelming the current ability, of both facilities and researchers, tomore » store and analyze it. Additional resources and new techniques for data analysis are urgently needed. 3) Data rates and volumes from HEP experimental facilities are also straining the ability to store and analyze large and complex data volumes. Appropriately configured leadership-class facilities can play a transformational role in enabling scientific discovery from these datasets. 4) A close integration of HPC simulation and data analysis will aid greatly in interpreting results from HEP experiments. Such an integration will minimize data movement and facilitate interdependent workflows. 5) Long-range planning between HEP and ASCR will be required to meet HEP's research needs. To best use ASCR HPC resources the experimental HEP program needs a) an established long-term plan for access to ASCR computational and data resources, b) an ability to map workflows onto HPC resources, c) the ability for ASCR facilities to accommodate workflows run by collaborations that can have thousands of individual members, d) to transition codes to the next-generation HPC platforms that will be available at ASCR facilities, e) to build up and train a workforce capable of developing and using simulations and analysis to support HEP scientific research on next-generation systems.« less

ASCR/HEP Exascale Requirements Review Report

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

Habib, Salman; et al.

2016-03-30

This draft report summarizes and details the findings, results, and recommendations derived from the ASCR/HEP Exascale Requirements Review meeting held in June, 2015. The main conclusions are as follows. 1) Larger, more capable computing and data facilities are needed to support HEP science goals in all three frontiers: Energy, Intensity, and Cosmic. The expected scale of the demand at the 2025 timescale is at least two orders of magnitude -- and in some cases greater -- than that available currently. 2) The growth rate of data produced by simulations is overwhelming the current ability, of both facilities and researchers, tomore » store and analyze it. Additional resources and new techniques for data analysis are urgently needed. 3) Data rates and volumes from HEP experimental facilities are also straining the ability to store and analyze large and complex data volumes. Appropriately configured leadership-class facilities can play a transformational role in enabling scientific discovery from these datasets. 4) A close integration of HPC simulation and data analysis will aid greatly in interpreting results from HEP experiments. Such an integration will minimize data movement and facilitate interdependent workflows. 5) Long-range planning between HEP and ASCR will be required to meet HEP's research needs. To best use ASCR HPC resources the experimental HEP program needs a) an established long-term plan for access to ASCR computational and data resources, b) an ability to map workflows onto HPC resources, c) the ability for ASCR facilities to accommodate workflows run by collaborations that can have thousands of individual members, d) to transition codes to the next-generation HPC platforms that will be available at ASCR facilities, e) to build up and train a workforce capable of developing and using simulations and analysis to support HEP scientific research on next-generation systems.« less

Production of coagulation factor VII in human cell lines Sk-Hep-1 and HKB-11.

PubMed

Corrêa de Freitas, Marcela Cristina; Bomfim, Aline de Sousa; Mizukami, Amanda; Picanço-Castro, Virgínia; Swiech, Kamilla; Covas, Dimas Tadeu

2017-09-01

Recombinant factor VII (rFVII) is the main therapeutic choice for hemophilia patients who have developed inhibitory antibodies against conventional treatments (FVIII and FIX). Because of the post-translational modifications, rFVII needs to be produced in mammalian cell lines. In this study, for the first time, we have shown efficient rFVII production in HepG2, Sk-Hep-1, and HKB-11 cell lines. Experiments in static conditions for a period of 96 h showed that HepG2-FVII produced the highest amounts of rhFVII, with an average of 1843 ng/mL. Sk-hep-1-FVII cells reached a maximum protein production of 1432 ng/mL and HKB-11-FVII cells reached 1468 ng/mL. Sk-Hep-1-rFVII and HKB-11-rFVII were selected for the first step of scale-up. Over 10 days of spinner flask culture, HKB-11 and SK-Hep-1 cells showed a cumulative production of rFVII of 152 μg and 202.6 μg in 50 mL, respectively. Thus, these human cell lines can be used for an efficient production of recombinant FVII. With more investment in basic research, human cell lines can be optimized for the commercial production of different bio therapeutic proteins. Copyright © 2017 Elsevier Inc. All rights reserved.

Python and HPC for High Energy Physics Data Analyses

DOE PAGES

Sehrish, S.; Kowalkowski, J.; Paterno, M.; ...

2017-01-01

High level abstractions in Python that can utilize computing hardware well seem to be an attractive option for writing data reduction and analysis tasks. In this paper, we explore the features available in Python which are useful and efficient for end user analysis in High Energy Physics (HEP). A typical vertical slice of an HEP data analysis is somewhat fragmented: the state of the reduction/analysis process must be saved at certain stages to allow for selective reprocessing of only parts of a generally time-consuming workflow. Also, algorithms tend to to be modular because of the heterogeneous nature of most detectorsmore » and the need to analyze different parts of the detector separately before combining the information. This fragmentation causes difficulties for interactive data analysis, and as data sets increase in size and complexity (O10 TiB for a “small” neutrino experiment to the O10 PiB currently held by the CMS experiment at the LHC), data analysis methods traditional to the field must evolve to make optimum use of emerging HPC technologies and platforms. Mainstream big data tools, while suggesting a direction in terms of what can be done if an entire data set can be available across a system and analysed with high-level programming abstractions, are not designed with either scientific computing generally, or modern HPC platform features in particular, such as data caching levels, in mind. Our example HPC use case is a search for a new elementary particle which might explain the phenomenon known as “Dark Matter”. Here, using data from the CMS detector, we will use HDF5 as our input data format, and MPI with Python to implement our use case.« less

Isolation and characterization of HepP: a virulence-related Pseudomonas aeruginosa heparinase.

PubMed

Dzvova, Nyaradzo; Colmer-Hamood, Jane A; Griswold, John A; Hamood, Abdul N

2017-12-16

Pseudomonas aeruginosa is an opportunistic pathogen that causes serious infections in immunocompromised hosts including severely burned patients. In burn patients, P. aeruginosa infection often leads to septic shock and death. Despite numerous studies, the influence of severe thermal injuries on the pathogenesis of P. aeruginosa during systemic infection is not known. Through RNA-seq analysis, we recently showed that the growth of P. aeruginosa strain UCBPP-PA14 (PA14) in whole blood obtained from severely burned patients significantly altered the expression of the PA14 transcriptome when compared with its growth in blood from healthy volunteers. The expression of PA14_23430 and the adjacent gene, PA14_23420, was enhanced by seven- to eightfold under these conditions. Quantitative real-time PCR analysis confirmed the enhancement of expression of both PA14_23420 and PA14_23430 by growth of PA14 in blood from severely burned patients. Computer analysis revealed that PA14_23430 (hepP) encodes a potential heparinase while PA14_23420 (zbdP) codes for a putative zinc-binding dehydrogenase. This analysis further suggested that the two genes form an operon with zbdP first. Presence of the operon was confirmed by RT-PCR experiments. We characterized hepP and its protein product HepP. hepP was cloned from PA14 by PCR and overexpressed in E. coli. The recombinant protein (rHepP) was purified using nickel column chromatography. Heparinase assays using commercially available heparinase as a positive control, revealed that rHepP exhibits heparinase activity. Mutation of hepP resulted in delay of pellicle formation at the air-liquid interface by PA14 under static growth conditions. Biofilm formation by PA14ΔhepP was also significantly reduced. In the Caenorhabditis elegans model of slow killing, mutation of hepP resulted in a significantly lower rate of killing than that of the parent strain PA14. Changes within the blood of severely burned patients significantly induced expression of hepP in PA14. The heparinase encoded by hepP is a potential virulence factor for PA14 as HepP influences pellicle formation as well as biofilm development by PA14 and the protein is required for full virulence in the C. elegans model of slow killing.

Neutrino Interactions

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

Kamyshkov, Yuri; Handler, Thomas

The neutrino group of the University of Tennessee, Knoxville was involved from 05/01/2013 to 04/30/2015 in the neutrino physics research funded by DOE-HEP grant DE-SC0009861. Contributions were made to the Double Chooz nuclear reactor experiment in France where second detector was commissioned during this period and final series of measurements has been started. Although Double Chooz was smaller experimental effort than competitive Daya Bay and RENO experiments, its several advantages make it valuable for understanding of systematic errors in measurements of neutrino oscillations. Double Chooz was the first experiment among competing three that produced initial result for neutrino angle θmore » 13 measurement, giving other experiments the chance to improve measured value statistically. Graduate student Ben Rybolt defended his PhD thesis on the results of Double Chooz experiment in 2015. UT group has fulfilled all the construction and analysis commitments to Double Chooz experiment, and has withdrawn from the collaboration by the end of the mentioned period to start another experiment. Larger effort of UT neutrino group during this period was devoted to the participation in another DOE-HEP project - NOvA experiment. The 14,000-ton "FAR" neutrino detector was commissioned in northern Minnesota in 2014 together with 300-ton "NEAR" detector located at Fermilab. Following that, the physics measurement program has started when Fermilab accelerator complex produced the high-intensity neutrino beam propagating through Earth to detector in MInnessota. UT group contributed to NOvA detector construction and developments in several aspects. Our Research Associate Athanasios Hatzikoutelis was managing (Level 3 manager) the construction of the Detector Control System. This work was successfully accomplished in time with the commissioning of the detectors. Group was involved in the development of the on-line software and study of the signatures of the cosmic ray backgrounds. Flumerfelt and another graduate student Philip Mason were also studying the non-linearity properties of the NOvA liquid scintillator - information that will be essential at the final stages of NOvA data analysis. Philip Mason also studied the response of the FAR NOvA detector in correlation with solar flares. Flumerfelt and Mason successfully defended their PhD in 2015. Also, undergraduate student Cameron Blake Erickson has defended his undergraduate thesis on the NOvA liquid scintillator studies with Compton gamma spectrometer at UT.« less

The improvement of laser induced damage resistance of optical workpiece surface by hydrodynamic effect polishing

NASA Astrophysics Data System (ADS)

Peng, Wenqiang; Guan, Chaoliang; Li, Shengyi; Wang, Zhuo

2016-10-01

Surface and subsurface damage in optical element will greatly decrease the laser induced damage threshold (LIDT) in the intense laser optical system. Processing damage on the workpiece surface can be inevitably caused when the material is removed in brittle or plastic mode. As a non-contact polishing technology, hydrodynamic effect polishing (HEP) shows very good performance on generating an ultra-smooth surface without damage. The material is removed by chemisorption between nanoparticle and workpiece surface in the elastic mode in HEP. The subsurface damage and surface scratches can be effectively removed after the polishing process. Meanwhile ultra-smooth surface with atomic level surface roughness can be achieved. To investigate the improvement of LIDT of optical workpiece, polishing experiment was conducted on a magnetorheological finishing (MRF) silica glass sample. AFM measurement results show that all the MRF directional plastic marks have been removed clearly and the root-mean-square (rms) surface roughness has decreased from 0.673nm to 0.177nm after HEP process. Laser induced damage experiment was conducted with laser pulse of 1064nm wavelength and 10ns time width. Compared with the original state, the LEDT of the silica glass sample polished by HEP has increased from 29.78J/cm2 to 45.47J/cm2. It demonstrates that LIDT of optical element treated by HEP can be greatly improved for ultra low surface roughness and nearly defect-free surface/subsurface.

The Effects of Run-of-River Hydroelectric Power Schemes on Fish Community Composition in Temperate Streams and Rivers

PubMed Central

2016-01-01

The potential environmental impacts of large-scale storage hydroelectric power (HEP) schemes have been well-documented in the literature. In Europe, awareness of these potential impacts and limited opportunities for politically-acceptable medium- to large-scale schemes, have caused attention to focus on smaller-scale HEP schemes, particularly run-of-river (ROR) schemes, to contribute to meeting renewable energy targets. Run-of-river HEP schemes are often presumed to be less environmentally damaging than large-scale storage HEP schemes. However, there is currently a lack of peer-reviewed studies on their physical and ecological impact. The aim of this article was to investigate the effects of ROR HEP schemes on communities of fish in temperate streams and rivers, using a Before-After, Control-Impact (BACI) study design. The study makes use of routine environmental surveillance data collected as part of long-term national and international monitoring programmes at 23 systematically-selected ROR HEP schemes and 23 systematically-selected paired control sites. Six area-normalised metrics of fish community composition were analysed using a linear mixed effects model (number of species, number of fish, number of Atlantic salmon—Salmo salar, number of >1 year old Atlantic salmon, number of brown trout—Salmo trutta, and number of >1 year old brown trout). The analyses showed that there was a statistically significant effect (p<0.05) of ROR HEP construction and operation on the number of species. However, no statistically significant effects were detected on the other five metrics of community composition. The implications of these findings are discussed in this article and recommendations are made for best-practice study design for future fish community impact studies. PMID:27191717

The Effects of Run-of-River Hydroelectric Power Schemes on Fish Community Composition in Temperate Streams and Rivers.

PubMed

Bilotta, Gary S; Burnside, Niall G; Gray, Jeremy C; Orr, Harriet G

2016-01-01

The potential environmental impacts of large-scale storage hydroelectric power (HEP) schemes have been well-documented in the literature. In Europe, awareness of these potential impacts and limited opportunities for politically-acceptable medium- to large-scale schemes, have caused attention to focus on smaller-scale HEP schemes, particularly run-of-river (ROR) schemes, to contribute to meeting renewable energy targets. Run-of-river HEP schemes are often presumed to be less environmentally damaging than large-scale storage HEP schemes. However, there is currently a lack of peer-reviewed studies on their physical and ecological impact. The aim of this article was to investigate the effects of ROR HEP schemes on communities of fish in temperate streams and rivers, using a Before-After, Control-Impact (BACI) study design. The study makes use of routine environmental surveillance data collected as part of long-term national and international monitoring programmes at 23 systematically-selected ROR HEP schemes and 23 systematically-selected paired control sites. Six area-normalised metrics of fish community composition were analysed using a linear mixed effects model (number of species, number of fish, number of Atlantic salmon-Salmo salar, number of >1 year old Atlantic salmon, number of brown trout-Salmo trutta, and number of >1 year old brown trout). The analyses showed that there was a statistically significant effect (p<0.05) of ROR HEP construction and operation on the number of species. However, no statistically significant effects were detected on the other five metrics of community composition. The implications of these findings are discussed in this article and recommendations are made for best-practice study design for future fish community impact studies.

Gaseous Electron Multiplier (GEM) Detectors

NASA Astrophysics Data System (ADS)

Gnanvo, Kondo

2017-09-01

Gaseous detectors have played a pivotal role as tracking devices in the field of particle physics experiments for the last fifty years. Recent advances in photolithography and micro processing techniques have enabled the transition from Multi Wire Proportional Chambers (MWPCs) and Drift Chambers to a new family of gaseous detectors refer to as Micro Pattern Gaseous Detectors (MPGDs). MPGDs combine the basic gas amplification principle with micro-structure printed circuits to provide detectors with excellent spatial and time resolution, high rate capability, low material budget and high radiation tolerance. Gas Electron Multiplier (GEMs) is a well-established MPGD technology invented by F. Sauli at CERN in 1997 and deployed various high energy physics (HEP) and nuclear NP experiment for tracking systems of current and future NP experiments. GEM detector combines an exceptional high rate capability (1 MHz / mm2) and robustness against harsh radiation environment with excellent position and timing resolution performances. Recent breakthroughs over the past decade have allowed the possibility for large area GEMs, making them cost effective and high-performance detector candidates to play pivotal role in current and future particle physics experiments. After a brief introduction of the basic principle of GEM technology, I will give a brief overview of the GEM detectors used in particle physics experiments over the past decades and especially in the NP community at Thomas Jefferson National Laboratory (JLab) and Brookhaven National Laboratory (BNL). I will follow by a review of state of the art of the new GEM development for the next generation of colliders such as Electron Ion Collider (EIC) or High Luminosity LHC and future Nuclear Physics experiments. I will conclude with a presentation of the CERN-based RD51 collaboration established in 2008 and its major achievements regarding technological developments and applications of MPGDs.

A potent approach for the development of FPGA based DAQ system for HEP experiments

NASA Astrophysics Data System (ADS)

Khan, Shuaib Ahmad; Mitra, Jubin; David, Erno; Kiss, Tivadar; Nayak, Tapan Kumar

2017-10-01

With ever increasing particle beam energies and interaction rates in modern High Energy Physics (HEP) experiments in the present and future accelerator facilities, there has always been the demand for robust Data Acquisition (DAQ) schemes which perform in the harsh radiation environment and handle high data volume. The scheme is required to be flexible enough to adapt to the demands of future detector and electronics upgrades, and at the same time keeping the cost factor in mind. To address these challenges, in the present work, we discuss an efficient DAQ scheme for error resilient, high speed data communication on commercially available state-of-the-art FPGA with optical links. The scheme utilises GigaBit Transceiver (GBT) protocol to establish radiation tolerant communication link between on-detector front-end electronics situated in harsh radiation environment to the back-end Data Processing Unit (DPU) placed in a low radiation zone. The acquired data are reconstructed in DPU which reduces the data volume significantly, and then transmitted to the computing farms through high speed optical links using 10 Gigabit Ethernet (10GbE). In this study, we focus on implementation and testing of GBT protocol and 10GbE links on an Intel FPGA. Results of the measurements of resource utilisation, critical path delays, signal integrity, eye diagram and Bit Error Rate (BER) are presented, which are the indicators for efficient system performance.

Neutrino oscillation parameter sampling with MonteCUBES

NASA Astrophysics Data System (ADS)

Blennow, Mattias; Fernandez-Martinez, Enrique

2010-01-01

We present MonteCUBES ("Monte Carlo Utility Based Experiment Simulator"), a software package designed to sample the neutrino oscillation parameter space through Markov Chain Monte Carlo algorithms. MonteCUBES makes use of the GLoBES software so that the existing experiment definitions for GLoBES, describing long baseline and reactor experiments, can be used with MonteCUBES. MonteCUBES consists of two main parts: The first is a C library, written as a plug-in for GLoBES, implementing the Markov Chain Monte Carlo algorithm to sample the parameter space. The second part is a user-friendly graphical Matlab interface to easily read, analyze, plot and export the results of the parameter space sampling. Program summaryProgram title: MonteCUBES (Monte Carlo Utility Based Experiment Simulator) Catalogue identifier: AEFJ_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEFJ_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public Licence No. of lines in distributed program, including test data, etc.: 69 634 No. of bytes in distributed program, including test data, etc.: 3 980 776 Distribution format: tar.gz Programming language: C Computer: MonteCUBES builds and installs on 32 bit and 64 bit Linux systems where GLoBES is installed Operating system: 32 bit and 64 bit Linux RAM: Typically a few MBs Classification: 11.1 External routines: GLoBES [1,2] and routines/libraries used by GLoBES Subprograms used:Cat Id ADZI_v1_0, Title GLoBES, Reference CPC 177 (2007) 439 Nature of problem: Since neutrino masses do not appear in the standard model of particle physics, many models of neutrino masses also induce other types of new physics, which could affect the outcome of neutrino oscillation experiments. In general, these new physics imply high-dimensional parameter spaces that are difficult to explore using classical methods such as multi-dimensional projections and minimizations, such as those used in GLoBES [1,2]. Solution method: MonteCUBES is written as a plug-in to the GLoBES software [1,2] and provides the necessary methods to perform Markov Chain Monte Carlo sampling of the parameter space. This allows an efficient sampling of the parameter space and has a complexity which does not grow exponentially with the parameter space dimension. The integration of the MonteCUBES package with the GLoBES software makes sure that the experimental definitions already in use by the community can also be used with MonteCUBES, while also lowering the learning threshold for users who already know GLoBES. Additional comments: A Matlab GUI for interpretation of results is included in the distribution. Running time: The typical running time varies depending on the dimensionality of the parameter space, the complexity of the experiment, and how well the parameter space should be sampled. The running time for our simulations [3] with 15 free parameters at a Neutrino Factory with O(10) samples varied from a few hours to tens of hours. References:P. Huber, M. Lindner, W. Winter, Comput. Phys. Comm. 167 (2005) 195, hep-ph/0407333. P. Huber, J. Kopp, M. Lindner, M. Rolinec, W. Winter, Comput. Phys. Comm. 177 (2007) 432, hep-ph/0701187. S. Antusch, M. Blennow, E. Fernandez-Martinez, J. Lopez-Pavon, arXiv:0903.3986 [hep-ph].

Social and Physical Environments and Disparities in Risk for Cardiovascular Disease: The Healthy Environments Partnership Conceptual Model

PubMed Central

Schulz, Amy J.; Kannan, Srimathi; Dvonch, J. Timothy; Israel, Barbara A.; Allen, Alex; James, Sherman A.; House, James S.; Lepkowski, James

2005-01-01

The Healthy Environments Partnership (HEP) is a community-based participatory research effort investigating variations in cardiovascular disease risk, and the contributions of social and physical environments to those variations, among non-Hispanic black, non-Hispanic white, and Hispanic residents in three areas of Detroit, Michigan. Initiated in October 2000 as a part of the National Institute of Environmental Health Sciences’ Health Disparities Initiative, HEP is affiliated with the Detroit Community–Academic Urban Research Center. The study is guided by a conceptual model that considers race-based residential segregation and associated concentrations of poverty and wealth to be fundamental factors influencing multiple, more proximate predictors of cardiovascular risk. Within this model, physical and social environments are identified as intermediate factors that mediate relationships between fundamental factors and more proximate factors such as physical activity and dietary practices that ultimately influence anthropomorphic and physiologic indicators of cardiovascular risk. The study design and data collection methods were jointly developed and implemented by a research team based in community-based organizations, health service organizations, and academic institutions. These efforts include collecting and analyzing airborne particulate matter over a 3-year period; census and administrative data; neighborhood observation checklist data to assess aspects of the physical and social environment; household survey data including information on perceived stressors, access to social support, and health-related behaviors; and anthropometric, biomarker, and self-report data as indicators of cardiovascular health. Through these collaborative efforts, HEP seeks to contribute to an understanding of factors that contribute to racial and socioeconomic health inequities, and develop a foundation for efforts to eliminate these disparities in Detroit. PMID:16330371

!CHAOS: A cloud of controls

NASA Astrophysics Data System (ADS)

Angius, S.; Bisegni, C.; Ciuffetti, P.; Di Pirro, G.; Foggetta, L. G.; Galletti, F.; Gargana, R.; Gioscio, E.; Maselli, D.; Mazzitelli, G.; Michelotti, A.; Orrù, R.; Pistoni, M.; Spagnoli, F.; Spigone, D.; Stecchi, A.; Tonto, T.; Tota, M. A.; Catani, L.; Di Giulio, C.; Salina, G.; Buzzi, P.; Checcucci, B.; Lubrano, P.; Piccini, M.; Fattibene, E.; Michelotto, M.; Cavallaro, S. R.; Diana, B. F.; Enrico, F.; Pulvirenti, S.

2016-01-01

The paper is aimed to present the !CHAOS open source project aimed to develop a prototype of a national private Cloud Computing infrastructure, devoted to accelerator control systems and large experiments of High Energy Physics (HEP). The !CHAOS project has been financed by MIUR (Italian Ministry of Research and Education) and aims to develop a new concept of control system and data acquisition framework by providing, with a high level of aaabstraction, all the services needed for controlling and managing a large scientific, or non-scientific, infrastructure. A beta version of the !CHAOS infrastructure will be released at the end of December 2015 and will run on private Cloud infrastructures based on OpenStack.

Graphics Processing Units for HEP trigger systems

NASA Astrophysics Data System (ADS)

Ammendola, R.; Bauce, M.; Biagioni, A.; Chiozzi, S.; Cotta Ramusino, A.; Fantechi, R.; Fiorini, M.; Giagu, S.; Gianoli, A.; Lamanna, G.; Lonardo, A.; Messina, A.; Neri, I.; Paolucci, P. S.; Piandani, R.; Pontisso, L.; Rescigno, M.; Simula, F.; Sozzi, M.; Vicini, P.

2016-07-01

General-purpose computing on GPUs (Graphics Processing Units) is emerging as a new paradigm in several fields of science, although so far applications have been tailored to the specific strengths of such devices as accelerator in offline computation. With the steady reduction of GPU latencies, and the increase in link and memory throughput, the use of such devices for real-time applications in high-energy physics data acquisition and trigger systems is becoming ripe. We will discuss the use of online parallel computing on GPU for synchronous low level trigger, focusing on CERN NA62 experiment trigger system. The use of GPU in higher level trigger system is also briefly considered.

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

Shiltsev, Vladimir

The 2014 P5 report indicated the accelerator-based neutrino and rare decay physics research as a centerpiece of the US domestic HEP program. Operation, upgrade and development of the accelerators for the near-term and longer-term particle physics program at the Intensity Frontier face formidable challenges. Here we discuss key elements of the accelerator physics and technology R&D program toward future multi-MW proton accelerators.

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

Brusati, M.; Camplani, A.; Cannon, M.

SRAM-ba8ed Field Programmable Gate Array (FPGA) logic devices arc very attractive in applications where high data throughput is needed, such as the latest generation of High Energy Physics (HEP) experiments. FPGAs have been rarely used in such experiments because of their sensitivity to radiation. The present paper proposes a mitigation approach applied to commercial FPGA devices to meet the reliability requirements for the front-end electronics of the Liquid Argon (LAr) electromagnetic calorimeter of the ATLAS experiment, located at CERN. Particular attention will be devoted to define a proper mitigation scheme of the multi-gigabit transceivers embedded in the FPGA, which ismore » a critical part of the LAr data acquisition chain. A demonstrator board is being developed to validate the proposed methodology. :!\\litigation techniques such as Triple Modular Redundancy (T:t\\IR) and scrubbing will be used to increase the robustness of the design and to maximize the fault tolerance from Single-Event Upsets (SEUs).« less

Biofilm formation and sanitizer resistance of Escherichia coli 0157:H7 strains isolated from "High Event Period" meat contamination

USDA-ARS?s Scientific Manuscript database

In the meat industry, a “High Event Period” (HEP) is defined as a time period during which commercial meat plants experience a higher than usual rate of E. coli O157:H7 contamination. Genetic analysis indicated that within a HEP, most of the E. coli O157:H7 strains belong to a singular dominant str...

[Effects of stable ANO1 overexpression on biological behaviors of human laryngeal squamous cell carcinoma Hep-2 cells in vitro].

PubMed

Li, Yadong; Zhang, Jinsong; Yang, Kai; Zhang, Fujun; Chen, Rui; Chen, Dan

2014-02-01

To detect the effects of ANO1 overexpression on the biological behaviors of human laryngeal squamous cell carcinoma Hep-2 cells. A Hep-2 cell line stably overexpressing ANO1 were examined with flow cytometry, soft agar assay, wound healing assay, siRNA experiments, and chloride channel block with DIDS to observe the effect of ANO1 overexpression on the growth, migration and invasion of the cells. Flow cytometry revealed a comparable cell percentage in G0/G1 phase between ANO1-overexpressing cells and the control cells (P>0.05). The two cells showed no significant difference in soft agar assay (P>0.05), but in wound healing experiments, ANO1-overexpressing cells showed significantly accelerated migration (P<0.05), whereas siRNA-mediated silencing of ANO1 significantly inhibited the cell migration (P<0.05). Treatment with DIDS resulted in an effective block of the ANO1 chloride channel activity and obviously decreased the migration speed of Hep-2 cells. ANO1 overexpression does not significantly affect the proliferation of cancer cells, but can enhance the migration ability of head and neck squamous cell carcinoma, suggesting the value of ANO1 as a new gene therapy target for head and neck squamous cell carcinoma.

HEP Computing

Science.gov Websites

Argonne National Laboratory High Energy Physics Division Email Information Problem Report Service outlook.office365.com. Your mailbox on this server is created along with your ANL Domain account. All of your

The swiss army knife of job submission tools: grid-control

NASA Astrophysics Data System (ADS)

Stober, F.; Fischer, M.; Schleper, P.; Stadie, H.; Garbers, C.; Lange, J.; Kovalchuk, N.

2017-10-01

grid-control is a lightweight and highly portable open source submission tool that supports all common workflows in high energy physics (HEP). It has been used by a sizeable number of HEP analyses to process tasks that sometimes consist of up to 100k jobs. grid-control is built around a powerful plugin and configuration system, that allows users to easily specify all aspects of the desired workflow. Job submission to a wide range of local or remote batch systems or grid middleware is supported. Tasks can be conveniently specified through the parameter space that will be processed, which can consist of any number of variables and data sources with complex dependencies on each other. Dataset information is processed through a configurable pipeline of dataset filters, partition plugins and partition filters. The partition plugins can take the number of files, size of the work units, metadata or combinations thereof into account. All changes to the input datasets or variables are propagated through the processing pipeline and can transparently trigger adjustments to the parameter space and the job submission. While the core functionality is completely experiment independent, full integration with the CMS computing environment is provided by a small set of plugins.

A Security Monitoring Framework For Virtualization Based HEP Infrastructures

NASA Astrophysics Data System (ADS)

Gomez Ramirez, A.; Martinez Pedreira, M.; Grigoras, C.; Betev, L.; Lara, C.; Kebschull, U.; ALICE Collaboration

2017-10-01

High Energy Physics (HEP) distributed computing infrastructures require automatic tools to monitor, analyze and react to potential security incidents. These tools should collect and inspect data such as resource consumption, logs and sequence of system calls for detecting anomalies that indicate the presence of a malicious agent. They should also be able to perform automated reactions to attacks without administrator intervention. We describe a novel framework that accomplishes these requirements, with a proof of concept implementation for the ALICE experiment at CERN. We show how we achieve a fully virtualized environment that improves the security by isolating services and Jobs without a significant performance impact. We also describe a collected dataset for Machine Learning based Intrusion Prevention and Detection Systems on Grid computing. This dataset is composed of resource consumption measurements (such as CPU, RAM and network traffic), logfiles from operating system services, and system call data collected from production Jobs running in an ALICE Grid test site and a big set of malware samples. This malware set was collected from security research sites. Based on this dataset, we will proceed to develop Machine Learning algorithms able to detect malicious Jobs.

Computing at DESY — current setup, trends and strategic directions

NASA Astrophysics Data System (ADS)

Ernst, Michael

1998-05-01

Since the HERA experiments H1 and ZEUS started data taking in '92, the computing environment at DESY has changed dramatically. Running a mainframe centred computing for more than 20 years, DESY switched to a heterogeneous, fully distributed computing environment within only about two years in almost every corner where computing has its applications. The computing strategy was highly influenced by the needs of the user community. The collaborations are usually limited by current technology and their ever increasing demands is the driving force for central computing to always move close to the technology edge. While DESY's central computing has a multidecade experience in running Central Data Recording/Central Data Processing for HEP experiments, the most challenging task today is to provide for clear and homogeneous concepts in the desktop area. Given that lowest level commodity hardware draws more and more attention, combined with the financial constraints we are facing already today, we quickly need concepts for integrated support of a versatile device which has the potential to move into basically any computing area in HEP. Though commercial solutions, especially addressing the PC management/support issues, are expected to come to market in the next 2-3 years, we need to provide for suitable solutions now. Buying PC's at DESY currently at a rate of about 30/month will otherwise absorb any available manpower in central computing and still will leave hundreds of unhappy people alone. Though certainly not the only region, the desktop issue is one of the most important one where we need HEP-wide collaboration to a large extent, and right now. Taking into account that there is traditionally no room for R&D at DESY, collaboration, meaning sharing experience and development resources within the HEP community, is a predominant factor for us.

The Effect of Chair Yoga on Biopsychosocial Changes in English- and Spanish-Speaking Community-Dwelling Older Adults with Lower-Extremity Osteoarthritis.

PubMed

Park, Juyoung; Newman, David; McCaffrey, Ruth; Garrido, Jacinto J; Riccio, Mary Lou; Liehr, Patricia

Chair yoga (CY), a mind-body therapy, is a safe nonpharmacological approach for managing osteoarthritis (OA) in older adults who cannot participate in standing exercise. However, there is no linguistically tailored CY program for those with limited English proficiency (LEP). This 2-arm randomized controlled trial compared the effects of a linguistically tailored yoga program (English and Spanish versions) on the outcomes of pain, physical function, and psychosocial factors compared to the effects of a linguistically tailored Health Education Program (HEP; English and Spanish versions). Participants with lower-extremity OA, recruited from 2 community sites, completed the Spanish (n = 40) or English (n = 60) version of twice-weekly 45-min CY or HEP sessions for 8 weeks. Data were collected at baseline, 4 weeks, 8 weeks, and 1- and 3-month follow-ups. English and Spanish CY groups (but neither HEP language group) showed significant decreases in pain interference. Measures of OA symptoms, balance, depression, and social activities were not significantly different between English and Spanish versions of CY and English and Spanish versions of HEP. It was concluded that the Spanish and English versions of CY and HEP were equivalent. Linguistically tailored CY could be implemented in aging-serving communities for persons with LEP.

Countries' interest in a hepatitis B vaccine licensed for the controlled temperature chain; survey results from African and Western Pacific regions.

PubMed

Petit, Dörte; Tevi-Benissan, Carole; Woodring, Joseph; Hennessey, Karen; Kahn, Anna-Lea

2017-12-14

Chronic hepatitis B infection can be prevented by hepatitis B vaccine birth dose (hepB-BD) given within 24 h after birth, followed by two hepatitis B vaccinations within the first year of life. Yet nearly half of World Health Organization (WHO) Member States do not provide a hepB-BD. Barriers are primarily attributed to vaccine storage and transportation, as well as high rates of home births. Delivering the vaccine outside the cold chain could potentially increase coverage. To do this, WHO recommends vaccines be licensed for use in a "controlled temperature chain" (CTC), which requires a given product to tolerate temperature excursions up to at least 40 °C for a minimum of three days. To date, no hepB vaccine is labelled for CTC. To inform dialogue with manufacturers, WHO conducted a survey among countries in the African and Western Pacific Regions (AFR and WPR) to assess demand for a hepatitis B product licensed for use in a CTC. Twenty-five (44%) countries responded, with 8 of 11 (73%) from the WPR and 17 of 46 (37%) from the AFR. Of these responding countries, 5 in AFR and all 8 in WPR have introduced universal hepB-BD. Seventy-two percent indicated that CTC would facilitate the provision of hepB-BD. While no overall difference in responses was detected between countries either providing or not providing hepB-BD, countries that already introduced hepB-BD but had low hepB-BD coverage were particularly interested in CTC. Irrespective of hepB-BD policy, responding countries suggested that a CTC-licenced product would be beneficial, though the price of such a vaccine would influence procurement decisions. This survey was beneficial to inform the CTC agenda. However, countries' lack of experience with HepB-BD as well as with CTC and the fact that countries were commenting on a product that is not yet on the market should be acknowledged. Copyright © 2017. Published by Elsevier Ltd.

A high-energy Compton polarimeter for the POET SMEX mission

NASA Astrophysics Data System (ADS)

Bloser, Peter F.; McConnell, Mark L.; Legere, Jason S.; Ertley, Camden D.; Hill, Joanne E.; Kippen, Marc; Ryan, James M.

2014-07-01

The primary science goal of the Polarimeters for Energetic Transients (POET) mission is to measure the polarization of gamma-ray bursts over a wide energy range, from X rays to soft gamma rays. The higher-energy portion of this band (50 - 500 keV) will be covered by the High Energy Polarimeter (HEP) instrument, a non-imaging, wide field of view Compton polarimeter. Incident high-energy photons will Compton scatter in low-Z, plastic scintillator detector elements and be subsequently absorbed in high-Z, CsI(Tl) scintillator elements; polarization is detected by measuring an asymmetry in the azimuthal scatter angle distribution. The HEP design is based on our considerable experience with the development and flight of the Gamma-Ray Polarimeter Experiment (GRAPE) balloon payload. We present the design of the POET HEP instrument, which incorporates lessons learned from the GRAPE balloon design and previous work on Explorer proposal efforts, and its expected performance on a two-year SMEX mission.

Probabilistic risk assessment for a loss of coolant accident in McMaster Nuclear Reactor and application of reliability physics model for modeling human reliability

NASA Astrophysics Data System (ADS)

Ha, Taesung

A probabilistic risk assessment (PRA) was conducted for a loss of coolant accident, (LOCA) in the McMaster Nuclear Reactor (MNR). A level 1 PRA was completed including event sequence modeling, system modeling, and quantification. To support the quantification of the accident sequence identified, data analysis using the Bayesian method and human reliability analysis (HRA) using the accident sequence evaluation procedure (ASEP) approach were performed. Since human performance in research reactors is significantly different from that in power reactors, a time-oriented HRA model (reliability physics model) was applied for the human error probability (HEP) estimation of the core relocation. This model is based on two competing random variables: phenomenological time and performance time. The response surface and direct Monte Carlo simulation with Latin Hypercube sampling were applied for estimating the phenomenological time, whereas the performance time was obtained from interviews with operators. An appropriate probability distribution for the phenomenological time was assigned by statistical goodness-of-fit tests. The human error probability (HEP) for the core relocation was estimated from these two competing quantities: phenomenological time and operators' performance time. The sensitivity of each probability distribution in human reliability estimation was investigated. In order to quantify the uncertainty in the predicted HEPs, a Bayesian approach was selected due to its capability of incorporating uncertainties in model itself and the parameters in that model. The HEP from the current time-oriented model was compared with that from the ASEP approach. Both results were used to evaluate the sensitivity of alternative huinan reliability modeling for the manual core relocation in the LOCA risk model. This exercise demonstrated the applicability of a reliability physics model supplemented with a. Bayesian approach for modeling human reliability and its potential usefulness of quantifying model uncertainty as sensitivity analysis in the PRA model.

Current Grid operation and future role of the Grid

NASA Astrophysics Data System (ADS)

Smirnova, O.

2012-12-01

Grid-like technologies and approaches became an integral part of HEP experiments. Some other scientific communities also use similar technologies for data-intensive computations. The distinct feature of Grid computing is the ability to federate heterogeneous resources of different ownership into a seamless infrastructure, accessible via a single log-on. Like other infrastructures of similar nature, Grid functioning requires not only technologically sound basis, but also reliable operation procedures, monitoring and accounting. The two aspects, technological and operational, are closely related: weaker is the technology, more burden is on operations, and other way around. As of today, Grid technologies are still evolving: at CERN alone, every LHC experiment uses an own Grid-like system. This inevitably creates a heavy load on operations. Infrastructure maintenance, monitoring and incident response are done on several levels, from local system administrators to large international organisations, involving massive human effort worldwide. The necessity to commit substantial resources is one of the obstacles faced by smaller research communities when moving computing to the Grid. Moreover, most current Grid solutions were developed under significant influence of HEP use cases, and thus need additional effort to adapt them to other applications. Reluctance of many non-HEP researchers to use Grid negatively affects the outlook for national Grid organisations, which strive to provide multi-science services. We started from the situation where Grid organisations were fused with HEP laboratories and national HEP research programmes; we hope to move towards the world where Grid will ultimately reach the status of generic public computing and storage service provider and permanent national and international Grid infrastructures will be established. How far will we be able to advance along this path, depends on us. If no standardisation and convergence efforts will take place, Grid will become limited to HEP; if however the current multitude of Grid-like systems will converge to a generic, modular and extensible solution, Grid will become true to its name.

Quasiperiodic modulations of energetic electron fluxes in the ULF range observed by the ERG satellite

NASA Astrophysics Data System (ADS)

Teramoto, M.; Hori, T.; Kurita, S.; Yoshizumi, M.; Saito, S.; Higashio, N.; Mitani, T.; Matsuoka, A.; Park, I.; Takashima, T.; Nomura, R.; Nose, M.; Fujimoto, A.; Tanaka, Y.; Shinohara, M.; Shinohara, I.

2017-12-01

Exploration of energization and Radiation in Geospace (ERG) satellite was successfully launched on December 20, 2016. The Extremely High-Energy Electron Experiment (XEP) and High-Energy Electron Experiments (HEP-L and HEP-H) are carried by the ERG satellite to observe energetic electrons. These instruments frequently observed quasiperiodic modulations of energetic electron fluxes with period of 100-600 sec. Continuous flux modulations with the period of 600 s appeared in the 700keV-3.6MeV energy range during the period 0920UT-1120UT on March 31, 2017 when the ERG satellite was located at L 5.5-6.1 and MLT 3-4 h. We compare these flux modulations with the magnetic field observed by the Magnetic Field Experiment (MGF) on the ERG satellite. It is found that these flux modulations are not accompanied by corresponding magnetic signatures. It indicates that these quasiperiodic flux modulations are not caused by drift-resonant interactions between ULF waves and energetic electrons, at least locally. In this study, we will show several events and discuss possible mechanism for quasiperiodic flux modulations of energetic electrons on XEP and HEP.

Next Generation Workload Management and Analysis System for Big Data

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

De, Kaushik

We report on the activities and accomplishments of a four-year project (a three-year grant followed by a one-year no cost extension) to develop a next generation workload management system for Big Data. The new system is based on the highly successful PanDA software developed for High Energy Physics (HEP) in 2005. PanDA is used by the ATLAS experiment at the Large Hadron Collider (LHC), and the AMS experiment at the space station. The program of work described here was carried out by two teams of developers working collaboratively at Brookhaven National Laboratory (BNL) and the University of Texas at Arlingtonmore » (UTA). These teams worked closely with the original PanDA team – for the sake of clarity the work of the next generation team will be referred to as the BigPanDA project. Their work has led to the adoption of BigPanDA by the COMPASS experiment at CERN, and many other experiments and science projects worldwide.« less

[Study on alkaloids of Corydalis ochotensis and their antitumor bioactivity].

PubMed

Yu, Jia-jia; Cong, Deng-li; Jiang, Ying; Zhou, Yuan; Wang, Yan; Zhao, Chun-fang

2014-10-01

To investigate the chemical constituents of Corydalis ochotensis and their antitumor bioactivity. The compounds were isolated by silica gel column chromatography and recrystallization. Their structures were identified by spectroscopic analysis (NMR) and physicochemical properties. Their cytotoxic activity was studied by MTT. Six compounds were elucidated as protopine (1), ochotensimine (2), fumariline (3), sanguinarine (4), tetrahydroberberine (5) and berberine (6). Compound 1 had excellent inhibitory activity on HepG2, SW480 and A549 cells, and compound 4 had excellent inhibitory activity on Hep2, HepG2, SW480 and A549 cells. Compounds 3, 4 and 5 are isolated from this plant for the first time; In the MTT antitumor experiments,compounds 1 and 4 show an antitumor activity.

The Open Science Grid - Support for Multi-Disciplinary Team Science - the Adolescent Years

NASA Astrophysics Data System (ADS)

Bauerdick, Lothar; Ernst, Michael; Fraser, Dan; Livny, Miron; Pordes, Ruth; Sehgal, Chander; Würthwein, Frank; Open Science Grid

2012-12-01

As it enters adolescence the Open Science Grid (OSG) is bringing a maturing fabric of Distributed High Throughput Computing (DHTC) services that supports an expanding HEP community to an increasingly diverse spectrum of domain scientists. Working closely with researchers on campuses throughout the US and in collaboration with national cyberinfrastructure initiatives, we transform their computing environment through new concepts, advanced tools and deep experience. We discuss examples of these including: the pilot-job overlay concepts and technologies now in use throughout OSG and delivering 1.4 Million CPU hours/day; the role of campus infrastructures- built out from concepts of sharing across multiple local faculty clusters (made good use of already by many of the HEP Tier-2 sites in the US); the work towards the use of clouds and access to high throughput parallel (multi-core and GPU) compute resources; and the progress we are making towards meeting the data management and access needs of non-HEP communities with general tools derived from the experience of the parochial tools in HEP (integration of Globus Online, prototyping with IRODS, investigations into Wide Area Lustre). We will also review our activities and experiences as HTC Service Provider to the recently awarded NSF XD XSEDE project, the evolution of the US NSF TeraGrid project, and how we are extending the reach of HTC through this activity to the increasingly broad national cyberinfrastructure. We believe that a coordinated view of the HPC and HTC resources in the US will further expand their impact on scientific discovery.

Pattern of (Multi)strange (Anti)baryon Production and Search for Deconfinement

NASA Astrophysics Data System (ADS)

Rafelski, Johann

1998-04-01

We study (multi)strange particle abundances obtained recently in relativistic heavy ion collisions and determine thermal and chemical source parameters(J. Letessier et al., Phys. Lett. B410 (1997) 315--322 hep-ph/9710310 and: Acta Physica Polonica in press, hep- ph/9710340). These are primarily constrained by (multi)strange (anti)baryon relative abundances, which have been measured for Pb--Pb 158 A GeV interactions(I. Kralik, for WA97 collaboration, QM97 Tsukuba, to appear in Nucl. Phys. A) and S-S/W/Pb 200 A GeV interactions(See: proceedings of S'96-Budapest, APH N.S., Heavy Ion Physics 4 (1996) vii--x). We have extended our analysis and have now determined the properties of the particle source using the fitted macro canonical parameters, allowing as required for non-equilibrium dynamics of the locally thermal fireball. We find that in the 158 A GeV Pb--Pb collisions the entropy per baryon, energy per baryon, strangeness per baryon implied by particle spectra are all in the range of values associated commonly with the deconfined QGP phase.

miR-203a is involved in HBx-induced inflammation by targeting Rap1a

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

Wu, AiRong; Chen, Huo; Xu, ChunFang

Hepatitis B virus (HBV) causes acute and chronic hepatitis, and is one of the major causes of cirrhosis and hepatocellular carcinoma. Accumulating evidence suggests that inflammation is the key factor for liver cirrhosis and hepatocellular carcinoma. MicroRNAs play important roles in many biological processes. Here, we aim to explore the function of microRNAs in the HBX-induced inflammation. First, microarray experiment showed that HBV{sup +} liver samples expressed higher level of miR-203a compared to HBV{sup -} liver samples. To verify these alterations, HBx-coding plasmid was transfected into HepG2 cells to overexpress HBx protein. The real-time PCR results suggested that over-expression ofmore » HBx could induce up-regulation of miR-203a. To define how up-regulation of miR-203a can induce liver cells inflammation, we over-expressed miR-203a in HepG2 cells. Annexin V staining and BrdU staining suggested that overexpression of miR-203a significantly increased the cell apoptosis and proliferation, meanwhile, over-expression of miR-203a could lead to a decrease in G0/G1 phase cells and an increase in G2/M phase cells. Some cytokines production including IL-6 and IL-8 were significantly increased, but TGFβ and IFNγ were decreased in miR-203a over-expressed HepG2 cells. Luciferase reporter assay experiments, protein mass-spectrum assay and real-time PCR all together demonstrated that Rap1a was the target gene of miR-203a. Further experiments showed that these alterations were modulated through PI3K/ERK/p38/NFκB pathways. These data suggested that HBV-infection could up-regulate the expression of miR-203a, thus down regulated the expression of Rap1a and affected the PI3K/ERK/p38/NFκB pathways, finally induced the hepatitis inflammation. - Highlights: • HBX induces the over-expression of miR-203a in HepG2 cells. • miR-203a targets Rap1a to induce the inflammation in HepG2 cells. • miR-203a regulates the apoptosis and cell cycles of HepG2 cells. • miR-203a alters the MAPK signaling pathway by down-regulating the Rap1a.« less

Manual physical therapy and exercise versus supervised home exercise in the management of patients with inversion ankle sprain: a multicenter randomized clinical trial.

PubMed

Cleland, Joshua A; Mintken, Paul E; McDevitt, Amy; Bieniek, Melanie L; Carpenter, Kristin J; Kulp, Katherine; Whitman, Julie M

2013-01-01

Randomized clinical trial. To compare the effectiveness of manual therapy and exercise (MTEX) to a home exercise program (HEP) in the management of individuals with an inversion ankle sprain. An in-clinic exercise program has been found to yield similar outcomes as an HEP for individuals with an inversion ankle sprain. However, no studies have compared an MTEX approach to an HEP. Patients with an inversion ankle sprain completed the Foot and Ankle Ability Measure (FAAM) activities of daily living subscale, the FAAM sports subscale, the Lower Extremity Functional Scale, and the numeric pain rating scale. Patients were randomly assigned to either an MTEX or an HEP treatment group. Outcomes were collected at baseline, 4 weeks, and 6 months. The primary aim (effects of treatment on pain and disability) was examined with a mixed-model analysis of variance. The hypothesis of interest was the 2-way interaction (group by time). Seventy-four patients (mean ± SD age, 35.1 ± 11.0 years; 48.6% female) were randomized into the MTEX group (n = 37) or the HEP group (n = 37). The overall group-by-time interaction for the mixed-model analysis of variance was statistically significant for the FAAM activities of daily living subscale (P<.001), FAAM sports subscale (P<.001), Lower Extremity Functional Scale (P<.001), and pain (P ≤.001). Improvements in all functional outcome measures and pain were significantly greater at both the 4-week and 6-month follow-up periods in favor of the MTEX group. The results suggest that an MTEX approach is superior to an HEP in the treatment of inversion ankle sprains. Registered at clinicaltrials.gov (NCT00797368). Therapy, level 1b-.

Role of CD137 signaling in dengue virus-mediated apoptosis

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

Nagila, Amar; Department of Biochemistry, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok; Netsawang, Janjuree

Highlights: {yields} For the first time the role of CD137 in dengue virus (DENV) infection. {yields} Induction of DENV-mediated apoptosis by CD137 signaling. {yields} Sensitization to CD137-mediated apoptosis by dengue virus capsid protein (DENV C). {yields} Nuclear localization of DENV C is required for CD137-mediated apoptosis. -- Abstract: Hepatic dysfunction is a well recognized feature of dengue virus (DENV) infection. However, molecular mechanisms of hepatic injury are still poorly understood. A complex interaction between DENV and the host immune response contributes to DENV-mediated tissue injury. DENV capsid protein (DENV C) physically interacts with the human death domain-associated protein Daxx. Amore » double substitution mutation in DENV C (R85A/K86A) abrogates Daxx interaction, nuclear localization and apoptosis. Therefore we compared the expression of cell death genes between HepG2 cells expressing DENV C and DENV C (R85A/K86A) using a real-time PCR array. Expression of CD137, which is a member of the tumor necrosis factor receptor family, increased significantly in HepG2 cells expressing DENV C compared to HepG2 cells expressing DENV C (R85A/K86A). In addition, CD137-mediated apoptotic activity in HepG2 cells expressing DENV C was significantly increased by anti-CD137 antibody compared to that of HepG2 cells expressing DENV C (R85A/K86A). In DENV-infected HepG2 cells, CD137 mRNA and CD137 positive cells significantly increased and CD137-mediated apoptotic activity was increased by anti-CD137 antibody. This work is the first to demonstrate the contribution of CD137 signaling to DENV-mediated apoptosis.« less

A Roadmap for HEP Software and Computing R&D for the 2020s

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

Alves, Antonio Augusto, Jr; et al.

Particle physics has an ambitious and broad experimental programme for the coming decades. This programme requires large investments in detector hardware, either to build new facilities and experiments, or to upgrade existing ones. Similarly, it requires commensurate investment in the R&D of software to acquire, manage, process, and analyse the shear amounts of data to be recorded. In planning for the HL-LHC in particular, it is critical that all of the collaborating stakeholders agree on the software goals and priorities, and that the efforts complement each other. In this spirit, this white paper describes the R&D activities required to preparemore » for this software upgrade.« less

Investigating free radical generation in HepG2 cells using immuno-spin trapping.

PubMed

Horinouchi, Yuya; Summers, Fiona A; Ehrenshaft, Marilyn; Kawazoe, Kazuyoshi; Tsuchiya, Koichiro; Tamaki, Toshiaki; Mason, Ronald P

2014-10-01

Oxidative stress can induce the generation of free radicals, which are believed to play an important role in both physiological and pathological processes and a number of diseases such as cancer. Therefore, it is important to identify chemicals which are capable of inducing oxidative stress. In this study, we evaluated the ability of four environmental chemicals, aniline, nitrosobenzene (NB), N,N-dimethylaniline (DMA) and N,N-dimethyl-4-nitrosoaniline (DMNA), to induce free radicals and cellular damage in the hepatoma cell line HepG2. Cytotoxicity was assessed using lactate dehydrogenase (LDH) assays and morphological changes were observed using phase contrast microscopy. Free radicals were detected by immuno-spin trapping (IST) in in-cell western experiments or in confocal microscopy experiments to determine the subcellular localization of free radical generation. DMNA induced free radical generation, LDH release and morphological changes in HepG2 cells whereas aniline, NB and DMA did not. Confocal microscopy showed that DMNA induced free radical generation mainly in the cytosol. Preincubation of HepG2 cells with N-acetylcysteine and 2,2'-dipyridyl significantly prevented free radical generation upon subsequent incubation with DMNA, whereas preincubation with apocynin and dimethyl sulfoxide did not. These results suggest that DMNA induces oxidative stress and that reactive oxygen species, metals and free radical generation play a critical role in DMNA-induced cytotoxicity. Copyright © 2014. Published by Elsevier Inc.

CalcHEP 3.4 for collider physics within and beyond the Standard Model

NASA Astrophysics Data System (ADS)

Belyaev, Alexander; Christensen, Neil D.; Pukhov, Alexander

2013-07-01

We present version 3.4 of the CalcHEP software package which is designed for effective evaluation and simulation of high energy physics collider processes at parton level. The main features of CalcHEP are the computation of Feynman diagrams, integration over multi-particle phase space and event simulation at parton level. The principle attractive key-points along these lines are that it has: (a) an easy startup and usage even for those who are not familiar with CalcHEP and programming; (b) a friendly and convenient graphical user interface (GUI); (c) the option for the user to easily modify a model or introduce a new model by either using the graphical interface or by using an external package with the possibility of cross checking the results in different gauges; (d) a batch interface which allows to perform very complicated and tedious calculations connecting production and decay modes for processes with many particles in the final state. With this features set, CalcHEP can efficiently perform calculations with a high level of automation from a theory in the form of a Lagrangian down to phenomenology in the form of cross sections, parton level event simulation and various kinematical distributions. In this paper we report on the new features of CalcHEP 3.4 which improves the power of our package to be an effective tool for the study of modern collider phenomenology. Program summaryProgram title: CalcHEP Catalogue identifier: AEOV_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEOV_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 78535 No. of bytes in distributed program, including test data, etc.: 818061 Distribution format: tar.gz Programming language: C. Computer: PC, MAC, Unix Workstations. Operating system: Unix. RAM: Depends on process under study Classification: 4.4, 5. External routines: X11 Nature of problem: Implement new models of particle interactions. Generate Feynman diagrams for a physical process in any implemented theoretical model. Integrate phase space for Feynman diagrams to obtain cross sections or particle widths taking into account kinematical cuts. Simulate collisions at modern colliders and generate respective unweighted events. Mix events for different subprocesses and connect them with the decays of unstable particles. Solution method: Symbolic calculations. Squared Feynman diagram approach Vegas Monte Carlo algorithm. Restrictions: Up to 2→4 production (1→5 decay) processes are realistic on typical computers. Higher multiplicities sometimes possible for specific 2→5 and 2→6 processes. Unusual features: Graphical user interface, symbolic algebra calculation of squared matrix element, parallelization on a pbs cluster. Running time: Depends strongly on the process. For a typical 2→2 process it takes seconds. For 2→3 processes the typical running time is of the order of minutes. For higher multiplicities it could take much longer.

Effects of task-specific and impairment-based training compared with usual care on functional walking ability after inpatient stroke rehabilitation: LEAPS Trial.

PubMed

Nadeau, Stephen E; Wu, Samuel S; Dobkin, Bruce H; Azen, Stanley P; Rose, Dorian K; Tilson, Julie K; Cen, Steven Y; Duncan, Pamela W

2013-05-01

After inpatient stroke rehabilitation, many people still cannot participate in community activities because of limited walking ability. To compare the effectiveness of 2 conceptually different, early physical therapy (PT) interventions to usual care (UC) in improving walking 6 months after stroke. The locomotor experience applied post-stroke (LEAPS) study was a single-blind, randomized controlled trial conducted in 408 adults with disabling hemiparetic stroke. Participants were stratified at baseline (2 months) by impairment in walking speed: severe (<0.4 m/s) or moderate (0.4 to <0.8 m/s). Between 2 and 6 months, they received either only UC (n = 143) or UC plus 36 therapist-provided sessions of either (1) walking training on a treadmill using body-weight support and practice overground at clinics (locomotor training program [LTP], n = 139) or (2) impairment-based strength and balance exercise at home (home exercise program [HEP], n = 126). LTP participants were 18% more likely to transition to a higher functional walking level: severe to >0.4 m/s and moderate to >0.8 m/s than UC participants (95% confidence interval [CI] = 7%-29%), and HEP participants were 17% more likely to transition (95% CI = 5%-29%). Mean gain in walking speed in LTP participants was 0.13 m/s greater (95% CI = 0.09-0.18) and in HEP participants, 0.10 m/s greater (95% CI = 0.05-0.14) than in UC participants. Progressive PT, using either walking training on a treadmill and overground, conducted in a clinic, or strength and balance exercises conducted at home, was superior to UC in improving walking, regardless of severity of initial impairment.

Giving pandas ROOT to chew on: experiences with the XENON1T Dark Matter experiment

NASA Astrophysics Data System (ADS)

Remenska, D.; Tunnell, C.; Aalbers, J.; Verhoeven, S.; Maassen, J.; Templon, J.

2017-10-01

In preparation for the XENON1T Dark Matter data acquisition, we have prototyped and implemented a new computing model. The XENON signal and data processing software is developed fully in Python 3, and makes extensive use of generic scientific data analysis libraries, such as the SciPy stack. A certain tension between modern “Big Data” solutions and existing HEP frameworks is typically experienced in smaller particle physics experiments. ROOT is still the “standard” data format in our field, defined by large experiments (ATLAS, CMS). To ease the transition, our computing model caters to both analysis paradigms, leaving the choice of using ROOT-specific C++ libraries, or alternatively, Python and its data analytics tools, as a front-end choice of developing physics algorithms. We present our path on harmonizing these two ecosystems, which allowed us to use off-the-shelf software libraries (e.g., NumPy, SciPy, scikit-learn, matplotlib) and lower the cost of development and maintenance. To analyse the data, our software allows researchers to easily create “mini-trees” small, tabular ROOT structures for Python analysis, which can be read directly into pandas DataFrame structures. One of our goals was making ROOT available as a cross-platform binary for an easy installation from the Anaconda Cloud (without going through the “dependency hell”). In addition to helping us discover dark matter interactions, lowering this barrier helps shift the particle physics toward non-domain-specific code.

GSDC: A Unique Data Center in Korea for HEP research

NASA Astrophysics Data System (ADS)

Ahn, Sang-Un

2017-04-01

Global Science experimental Data hub Center (GSDC) at Korea Institute of Science and Technology Information (KISTI) is a unique data center in South Korea established for promoting the fundamental research fields by supporting them with the expertise on Information and Communication Technology (ICT) and the infrastructure for High Performance Computing (HPC), High Throughput Computing (HTC) and Networking. GSDC has supported various research fields in South Korea dealing with the large scale of data, e.g. RENO experiment for neutrino research, LIGO experiment for gravitational wave detection, Genome sequencing project for bio-medical, and HEP experiments such as CDF at FNAL, Belle at KEK, and STAR at BNL. In particular, GSDC has run a Tier-1 center for ALICE experiment using the LHC at CERN since 2013. In this talk, we present the overview on computing infrastructure that GSDC runs for the research fields and we discuss on the data center infrastructure management system deployed at GSDC.

Dynamic provisioning of local and remote compute resources with OpenStack

NASA Astrophysics Data System (ADS)

Giffels, M.; Hauth, T.; Polgart, F.; Quast, G.

2015-12-01

Modern high-energy physics experiments rely on the extensive usage of computing resources, both for the reconstruction of measured events as well as for Monte-Carlo simulation. The Institut fur Experimentelle Kernphysik (EKP) at KIT is participating in both the CMS and Belle experiments with computing and storage resources. In the upcoming years, these requirements are expected to increase due to growing amount of recorded data and the rise in complexity of the simulated events. It is therefore essential to increase the available computing capabilities by tapping into all resource pools. At the EKP institute, powerful desktop machines are available to users. Due to the multi-core nature of modern CPUs, vast amounts of CPU time are not utilized by common desktop usage patterns. Other important providers of compute capabilities are classical HPC data centers at universities or national research centers. Due to the shared nature of these installations, the standardized software stack required by HEP applications cannot be installed. A viable way to overcome this constraint and offer a standardized software environment in a transparent manner is the usage of virtualization technologies. The OpenStack project has become a widely adopted solution to virtualize hardware and offer additional services like storage and virtual machine management. This contribution will report on the incorporation of the institute's desktop machines into a private OpenStack Cloud. The additional compute resources provisioned via the virtual machines have been used for Monte-Carlo simulation and data analysis. Furthermore, a concept to integrate shared, remote HPC centers into regular HEP job workflows will be presented. In this approach, local and remote resources are merged to form a uniform, virtual compute cluster with a single point-of-entry for the user. Evaluations of the performance and stability of this setup and operational experiences will be discussed.

Healthy Eating and Physical Activity in Schools in Europe: A Toolkit for Policy Development and Its Implementation

ERIC Educational Resources Information Center

Simovska, Venka; Dadaczynski, Kevin; Woynarowska, Barbara

2012-01-01

Purpose: The purpose of this paper is to introduce the HEPS project ("H"ealthy "E"ating and "P"hysical Activity in "S"chools) and discuss initial steps of the project implementation within EU countries. On the basis of the Health Promoting School approach as a conceptual foundation for the project, HEPS…

Online production validation in a HEP environment

NASA Astrophysics Data System (ADS)

Harenberg, T.; Kuhl, T.; Lang, N.; Mättig, P.; Sandhoff, M.; Schwanenberger, C.; Volkmer, F.

2017-03-01

In high energy physics (HEP) event simulations, petabytes of data are processed and stored requiring millions of CPU-years. This enormous demand for computing resources is handled by centers distributed worldwide, which form part of the LHC computing grid. The consumption of such an important amount of resources demands for an efficient production of simulation and for the early detection of potential errors. In this article we present a new monitoring framework for grid environments, which polls a measure of data quality during job execution. This online monitoring facilitates the early detection of configuration errors (specially in simulation parameters), and may thus contribute to significant savings in computing resources.

Final Report for U.S. DOE GRANT No. DEFG02-96ER41015 November 1, 2010 - April 30, 2013 entitled HIGH ENERGY ACCELERATOR AND COLLIDING BEAM USER GROUP at the UNIVERSITY of MARYLAND

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

Hadley, Nicholas; Jawahery, Abolhassan; Eno, Sarah C

2013-07-26

We have finished the third year of a three year grant cycle with the U.S. Department of Energy for which we were given a five month extension (U.S. D.O.E. Grant No. DEFG02-96ER41015). This document is the fi nal report for this grant and covers the period from November 1, 2010 to April 30, 2013. The Maryland program is administered as a single task with Professor Nicholas Hadley as Principal Investigator. The Maryland experimental HEP group is focused on two major research areas. We are members of the CMS experiment at the LHC at CERN working on the physics of themore » Energy Frontier. We are also analyzing the data from the Babar experiment at SLAC while doing design work and R&D towards a Super B experiment as part of the Intensity Frontier. We have recently joined the LHCb experiment at CERN. We concluded our activities on the D experiment at Fermilab in 2009.« less

HEP Division Argonne National Laboratory

Science.gov Websites

Argonne National Laboratory Environmental Safety & Health DOE Logo Home Division ES&H ... Search Argonne Home >High Energy Physics> Environmental Safety & Health Environmental Safety & Health New Employee Training */ ?> Office Safety: Checklist (Submitted Checklists) Submitted

Differences in hypolipidaemic effects of two statins on Hep G2 cells or human hepatocytes in primary culture.

PubMed Central

Clerc, T.; Sbarra, V.; Domingo, N.; Rault, J. P.; Diaconescu, N.; Moutardier, V.; Hasselot, N.; Lafont, H.; Jadot, G.; Laruelle, C.; Chanussot, F.

1996-01-01

1. The objective of this study was to compare in cultured human hepatocytes or Hep G2 cells, changes in the fate of unesterified low density lipoprotein (LDL)-cholesterol induced by crilvastatin, a new cholesterol lowering drug and a reference statin, simvastatin. 2. The experiments were carried out for 20 h, each well contained 4.2 x 10(5)/cm2 Hep G2 cells or 0.5 x 10(5)/Cm2 human hepatocytes, 130 microM ursodeoxycholate, 0.68 microCi or 1.59 microCi unesterified human [14C]-LDL-cholesterol, crilvastatin or simvastatin at 0 or 50 microM (both cell types) or 300 microM (Hep-G2 cells). Incubation with the two drugs resulted in increased amounts of unesterified [14C]-LDL-cholesterol taken by the two cell types, compared to control. 3. Crilvastatin 50 microM led to significantly higher quantities of [14C]-glyco-tauro-conjugated bile salts, compared to simvastatin. Statins reduced the apo B100 level secreted by the two cell types (simvastatin) or human hepatocytes (crilvastatin). Crilvastatin enhanced both the level of apo A1 secreted by the Hep G2 cells and the level of APF, a high density lipoprotein (HDL) and biliary apoprotein. 4. Crilvastatin not only acts by stimulating LDL-cholesterol uptake by hepatocytes, but also by enhancing the catabolism of LDL-cholesterol in bile salts and probably by stimulating HDL and/or bile component secretion. Such a mechanism was not previously described for HMG CoA reductase inhibitors. Our results on APF show that this apoprotein could be considered also as an indicator of changes in bile and/or HDL compartments. 5. The human hepatocyte model appeared to be a suitable and relevant model in the pharmacological-metabolic experiments carried out in this study. It led to more consistent data than those obtained with Hep G2 cells. Images Figure 1 Figure 2 Figure 3 Figure 4 Figure 5 PMID:8842455

HEP in Greek Classes

NASA Astrophysics Data System (ADS)

Fassouliotis, Dimitris; Kourkoumelis, Christine; Vourakis, Stylianos

2017-03-01

The HEP Inquiry learning resources created over the last four years by the European outreach projects are reviewed. The resources are mostly addressed to high school students and the purpose is to ignite their interest on science. In addition, at the University of Athens for the last four years we have been using the HYPATIA online event analysis tool as a lab course for fourth year undergraduate physics students, majoring in HEP. Each year 40-50 students highly appreciated the course, since they get a direct involvement in the actual toplevel research. Up to now, the course was limited to visual inspection of a few tens of ATLAS events. Recently we have enriched the course with additional analysis exercises, which involve large samples of events. The students, through a user friendly interface can analyze the samples (both signal and background ones) and optimize the cut selection in order to search for the Higgs decay H □ 4 leptons. Recently ATLAS released 1/fb of data, so starting now the students analyse real data.

Verification of Electromagnetic Physics Models for Parallel Computing Architectures in the GeantV Project

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

Amadio, G.; et al.

An intensive R&D and programming effort is required to accomplish new challenges posed by future experimental high-energy particle physics (HEP) programs. The GeantV project aims to narrow the gap between the performance of the existing HEP detector simulation software and the ideal performance achievable, exploiting latest advances in computing technology. The project has developed a particle detector simulation prototype capable of transporting in parallel particles in complex geometries exploiting instruction level microparallelism (SIMD and SIMT), task-level parallelism (multithreading) and high-level parallelism (MPI), leveraging both the multi-core and the many-core opportunities. We present preliminary verification results concerning the electromagnetic (EM) physicsmore » models developed for parallel computing architectures within the GeantV project. In order to exploit the potential of vectorization and accelerators and to make the physics model effectively parallelizable, advanced sampling techniques have been implemented and tested. In this paper we introduce a set of automated statistical tests in order to verify the vectorized models by checking their consistency with the corresponding Geant4 models and to validate them against experimental data.« less

Cellular Responses Modulated by FGF-2 Adsorbed on Albumin/Heparin Layer-by-Layer Assemblies.

PubMed

Kumorek, Marta; Kubies, Dana; Filová, Elena; Houska, Milan; Kasoju, Naresh; Mázl Chánová, Eliška; Matějka, Roman; Krýslová, Markéta; Bačáková, Lucie; Rypáček, František

2015-01-01

In a typical cell culture system, growth factors immobilized on the cell culture surfaces can serve as a reservoir of bio-signaling molecules, without the need to supplement them additionally into the culture medium. In this paper, we report on the fabrication of albumin/heparin (Alb/Hep) assemblies for controlled binding of basic fibroblast growth factor (FGF-2). The surfaces were constructed by layer-by-layer adsorption of polyelectrolytes albumin and heparin and were subsequently stabilized by covalent crosslinking with glutaraldehyde. An analysis of the surface morphology by atomic force microscopy showed that two Alb/Hep bilayers are required to cover the surface of substrate. The formation of the Alb/Hep assemblies was monitored by the surface plasmon resonance (SPR), the infrared multiinternal reflection spectroscopy (FTIR MIRS) and UV/VIS spectroscopy. The adsorption of FGF-2 on the cross-linked Alb/Hep was followed by SPR. The results revealed that FGF-2 binds to the Alb/Hep assembly in a dose and time-dependent manner up to the surface concentration of 120 ng/cm(2). The bioactivity of the adsorbed FGF-2 was assessed in experiments in vitro, using calf pulmonary arterial endothelial cells (CPAE). CPAE cells could attach and proliferate on Alb/Hep surfaces. The adsorbed FGF-2 was bioactive and stimulated both the proliferation and the differentiation of CPAE cells. The improvement was more pronounced at a lower FGF-2 surface concentration (30 ng/cm(2)) than on surfaces with a higher concentration of FGF-2 (120 ng/cm(2)).

Cellular Responses Modulated by FGF-2 Adsorbed on Albumin/Heparin Layer-by-Layer Assemblies

PubMed Central

Kumorek, Marta; Kubies, Dana; Filová, Elena; Houska, Milan; Kasoju, Naresh; Mázl Chánová, Eliška; Matějka, Roman; Krýslová, Markéta; Bačáková, Lucie; Rypáček, František

2015-01-01

In a typical cell culture system, growth factors immobilized on the cell culture surfaces can serve as a reservoir of bio-signaling molecules, without the need to supplement them additionally into the culture medium. In this paper, we report on the fabrication of albumin/heparin (Alb/Hep) assemblies for controlled binding of basic fibroblast growth factor (FGF-2). The surfaces were constructed by layer-by-layer adsorption of polyelectrolytes albumin and heparin and were subsequently stabilized by covalent crosslinking with glutaraldehyde. An analysis of the surface morphology by atomic force microscopy showed that two Alb/Hep bilayers are required to cover the surface of substrate. The formation of the Alb/Hep assemblies was monitored by the surface plasmon resonance (SPR), the infrared multiinternal reflection spectroscopy (FTIR MIRS) and UV/VIS spectroscopy. The adsorption of FGF-2 on the cross-linked Alb/Hep was followed by SPR. The results revealed that FGF-2 binds to the Alb/Hep assembly in a dose and time-dependent manner up to the surface concentration of 120 ng/cm2. The bioactivity of the adsorbed FGF-2 was assessed in experiments in vitro, using calf pulmonary arterial endothelial cells (CPAE). CPAE cells could attach and proliferate on Alb/Hep surfaces. The adsorbed FGF-2 was bioactive and stimulated both the proliferation and the differentiation of CPAE cells. The improvement was more pronounced at a lower FGF-2 surface concentration (30 ng/cm2) than on surfaces with a higher concentration of FGF-2 (120 ng/cm2). PMID:25945799

Novel Interconnections in Lipid Metabolism Revealed by Overexpression of Sphingomyelin Synthase-1*

PubMed Central

Deevska, Gergana M.; Dotson, Patrick P.; Karakashian, Alexander A.; Isaac, Giorgis; Wrona, Mark; Kelly, Samuel B.; Merrill, Alfred H.; Nikolova-Karakashian, Mariana N.

2017-01-01

This study investigates the consequences of elevating sphingomyelin synthase 1 (SMS1) activity, which generates the main mammalian sphingolipid, sphingomyelin. HepG2 cells stably transfected with SMS1 (HepG2-SMS1) exhibit elevated enzyme activity in vitro and increased sphingomyelin content (mainly C22:0- and C24:0-sphingomyelin) but lower hexosylceramide (Hex-Cer) levels. HepG2-SMS1 cells have fewer triacylglycerols than controls but similar diacylglycerol acyltransferase activity, triacylglycerol secretion, and mitochondrial function. Treatment with 1 mm palmitate increases de novo ceramide synthesis in both cell lines to a similar degree, causing accumulation of C16:0-ceramide (and some C18:0-, C20:0-, and C22:0-ceramides) as well as C16:0- and C18:0-Hex-Cers. In these experiments, the palmitic acid is delivered as a complex with delipidated BSA (2:1, mol/mol) and does not induce significant lipotoxicity. Based on precursor labeling, the flux through SM synthase also increases, which is exacerbated in HepG2-SMS1 cells. In contrast, palmitate-induced lipid droplet formation is significantly reduced in HepG2-SMS1 cells. [14C]Choline and [3H]palmitate tracking shows that SMS1 overexpression apparently affects the partitioning of palmitate-enriched diacylglycerol between the phosphatidylcholine and triacylglycerol pathways, to the benefit of the former. Furthermore, triacylglycerols from HepG2-SMS1 cells are enriched in polyunsaturated fatty acids, which is indicative of active remodeling. Together, these results delineate novel metabolic interactions between glycerolipids and sphingolipids. PMID:28087695

UFMulti: A new parallel processing software system for HEP

NASA Astrophysics Data System (ADS)

Avery, Paul; White, Andrew

1989-12-01

UFMulti is a multiprocessing software package designed for general purpose high energy physics applications, including physics and detector simulation, data reduction and DST physics analysis. The system is particularly well suited for installations where several workstation or computers are connected through a local area network (LAN). The initial configuration of the software is currently running on VAX/VMS machines with a planned extension to ULTRIX, using the new RISC CPUs from Digital, in the near future.

Characterization of Escherichia coli O157:H7 strains from contaminated raw beef trim during "high event periods".

PubMed

Arthur, Terrance M; Bono, James L; Kalchayanand, Norasak

2014-01-01

The development and implementation of effective antimicrobial interventions by the beef processing industry in the United States have dramatically reduced the incidence of beef trim contamination by Escherichia coli O157:H7. However, individual processing plants still experience sporadic peaks in contamination rates where multiple E. coli O157:H7-positive lots are clustered in a short time frame. These peaks have been referred to as "high event periods" (HEP) of contamination. The results reported here detail the characterization of E. coli O157:H7 isolates from 21 HEP across multiple companies and processing plants to gain insight regarding the mechanisms causing these incidents. Strain genotypes were determined by pulsed-field gel electrophoresis, and isolates were investigated for characteristics linking them to human illness. Through these analyses, it was determined that individual HEP show little to no diversity in strain genotypes. Hence, each HEP has one strain type that makes up most, if not all, of the contamination. This is shown to differ from the genotypic diversity of E. coli O157:H7 found on the hides of cattle entering processing plants. In addition, it was found that a large proportion (81%) of HEP are caused by strain types associated with human illness. These results pose a potential challenge to the current model for finished product contamination during beef processing.

Design exploration and verification platform, based on high-level modeling and FPGA prototyping, for fast and flexible digital communication in physics experiments

NASA Astrophysics Data System (ADS)

Magazzù, G.; Borgese, G.; Costantino, N.; Fanucci, L.; Incandela, J.; Saponara, S.

2013-02-01

In many research fields as high energy physics (HEP), astrophysics, nuclear medicine or space engineering with harsh operating conditions, the use of fast and flexible digital communication protocols is becoming more and more important. The possibility to have a smart and tested top-down design flow for the design of a new protocol for control/readout of front-end electronics is very useful. To this aim, and to reduce development time, costs and risks, this paper describes an innovative design/verification flow applied as example case study to a new communication protocol called FF-LYNX. After the description of the main FF-LYNX features, the paper presents: the definition of a parametric SystemC-based Integrated Simulation Environment (ISE) for high-level protocol definition and validation; the set up of figure of merits to drive the design space exploration; the use of ISE for early analysis of the achievable performances when adopting the new communication protocol and its interfaces for a new (or upgraded) physics experiment; the design of VHDL IP cores for the TX and RX protocol interfaces; their implementation on a FPGA-based emulator for functional verification and finally the modification of the FPGA-based emulator for testing the ASIC chipset which implements the rad-tolerant protocol interfaces. For every step, significant results will be shown to underline the usefulness of this design and verification approach that can be applied to any new digital protocol development for smart detectors in physics experiments.

Clopper-Pearson bounds from HEP data cuts

NASA Astrophysics Data System (ADS)

Berg, B. A.

2001-08-01

For the measurement of Ns signals in N events rigorous confidence bounds on the true signal probability pexact were established in a classical paper by Clopper and Pearson [Biometrica 26, 404 (1934)]. Here, their bounds are generalized to the HEP situation where cuts on the data tag signals with probability Ps and background data with likelihood Pb

[Primary study on fluro [ 19F] berberine derivative for human hepatocellular carcinoma targetting in vitro].

PubMed

Zhang, Tong; Wu, Xiaoai; Cai, Huawei; Liang, Meng; Fan, Chengzhong

2017-04-01

[ 18 F]HX-01, a Fluorine-18 labeled berberine derivative, is a potential positron emission tomography (PET) tumor imaging agent, while [ 19 F]HX-01 is a nonradioactive reference substance with different energy state and has the same physical and chemical properties. In order to collect data for further study of [ 18 F]HX-01 PET imaging of hepatocellular carcinoma in vivo , this study compared the uptake of [ 19 F]HX-01 by human hepatocellular carcinoma and normal hepatocytes in vitro . The target compound, [ 19 F]HX-01, was synthesized in one step using berberrubine and 3-fluoropropyl 4-methylbenzenesulfonate. Cellular uptake and localization of [ 19 F]HX-01 were performed by a fluorescence microscope in human hepatocellular carcinoma HepG2, SMMC-7721 and human normal hepatocyte HL-7702. Cellular proliferation inhibition and cell cytotoxicity assay of the [ 19 F]HX-01 were conducted using cell counting kit-8 (CCK-8) on HepG2, SMMC-7721 and HL-7702 cells. Fluorescent microscopy showed that the combining ability of [ 19 F]HX-01 to the carcinoma SMMC-7721 and HepG2 was higher than that to the normal HL-7702. Cellular proliferation inhibition assay demonstrated that [ 19 F]HX-01 leaded to a dose-dependent inhibition on SMMC-7721, HepG2, and HL-7702 proliferation. Cell cytotoxicity assay presented that the cytotoxicity of [ 19 F]HX-01 to SMMC-7721 and HepG2 was obviously higher than that to HL-7702. This in vitro study showed that [ 19 F]HX-01 had a higher selectivity on human hepatocellular carcinoma cells (SMMC-7721, HepG2) but has less toxicity to normal hepatocytes (HL-7702). This could set up the idea that the radioactive reference substance [ 18 F]HX-01 may be worthy of further development as a potential molecular probe targeting human hepatocellular carcinoma using PET.

Inhibition of Aurora A Kinase by Alisertib Induces Autophagy and Cell Cycle Arrest and Increases Chemosensitivity in Human Hepatocellular Carcinoma HepG2 Cells.

PubMed

Zhu, Qiaohua; Yu, Xinfa; Zhou, Zhi-Wei; Zhou, Chengyu; Chen, Xiao-Wu; Zhou, Shu-Feng

2017-01-01

Aurora A kinase represent a feasible target in cancer therapy. To evaluate the proteomic response of human liver carcinoma cells to alisertib (ALS) and identify the molecular targets of ALS, we examined the effects of ALS on the proliferation, cell cycle, autophagy, apoptosis, and chemosensitivity in HepG2 cells. The stable-isotope labeling by amino acids in cell culture (SILAC) based quantitative proteomic study was performed to evaluate the proteomic response to ALS. Cell cycle distribution and apoptosis were assessed using flow cytometry and autophagy was determined using flow cytometry and confocal microscopy. Our SILAC proteomic study showed that ALS regulated the expression of 914 proteins, with 407 molecules being up-regulated and 507 molecules being down-regulated in HepG2 cells. Ingenuity pathway analysis (IPA) and KEGG pathway analysis identified 146 and 32 signaling pathways were regulated by ALS, respectively, which were associated with cell survival, programmed cell death, and nutrition-energy metabolism. Subsequently, the verification experiments showed that ALS remarkably arrested HepG2 cells in G2/M phase and led to an accumulation of aneuploidy via regulating the expression of key cell cycle regulators. ALS induced a marked autophagy in a concentration- and time-dependent manner via the phosphatidylinositol 3-kinase (PI3K)/protein kinase B (Akt)/mammalian target of rapamycin (mTOR) signaling pathway. Autophagy inhibition promoted the pro-apoptotic effect of ALS, indicating a cyto-protective role of ALS-induced autophagy. ALS increased the chemosensitivity of HepG2 cells to cisplatin and doxorubicin. Taken together, ALS induces autophagy and cell cycle arrest in HepG2 cells via PI3K/Akt/mTOR-mediated pathway. Autophagy inhibition may promote the anticancer effect of ALS and sensitize the chemotherapy in HepG2 cells. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

OSBP-related protein 8 (ORP8) interacts with Homo sapiens sperm associated antigen 5 (SPAG5) and mediates oxysterol interference of HepG2 cell cycle

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

Zhong, Wenbin; Zhou, You; Li, Jiwei

We earlier identified OSBP-related protein 8 (ORP8) as an endoplasmic reticulum/nuclear envelope oxysterol-binding protein implicated in cellular lipid homeostasis, migration, and organization of the microtubule cytoskeleton. Here, a yeast two-hybrid screen identified Homo sapiens sperm associated antigen 5 (SPAG5)/Astrin as interaction partner of ORP8. The putative interaction was further confirmed by pull-down and co-immunoprecipitation assays. ORP8 did not colocalize with kinetochore-associated SPAG5 in mitotic HepG2 or HuH7 cells, but overexpressed ORP8 was capable of recruiting SPAG5 onto endoplasmic reticulum membranes in interphase cells. In our experiments, 25-hydroxycholesterol (25OHC) retarded the HepG2 cell cycle, causing accumulation in G2/M phase; ORP8 overexpressionmore » resulted in the same phenotype. Importantly, ORP8 knock-down dramatically inhibited the oxysterol effect on HepG2 cell cycle, suggesting a mediating role of ORP8. Furthermore, knock-down of SPAG5 significantly reduced the effects of both ORP8 overexpression and 25OHC on the cell cycle, placing SPAG5 downstream of the two cell-cycle interfering factors. Taken together, the present results suggest that ORP8 may via SPAG5 mediate oxysterol interference of the HepG2 cell cycle. - Highlights: • The oxysterol-binding protein ORP8 was found to interact with the mitotic regulator SPAG5/Astrin. • Treatment of HepG2 cells with 25-hydroxycholesterol caused cell cycle retardation in G2/M. • ORP8 overexpression caused a similar G2/M accumulation, and ORP8 knock-down reversed the 25-hydroxycholesterol effect. • Reduction of cellular of SPAG5/Astrin reversed the cell cycle effects of both 25-hydroxycholesterol and ORP8 overexpression. • Our results suggest that ORP8 mediates via SPAG5/Astrin the oxysterol interference of HepG2 cell cycle.« less

Use of the WWW as a Collaborative Tool in a Large HEP Collaboration

NASA Astrophysics Data System (ADS)

Bower, G.; Dubois, R.; Johnson, A. S.; Moss, L.; Perl, J.; Langston, M.; Weiss, E.

As the phenomenal growth of the WWW continues it is easy to view it purely as a tool for PR and advertising, and to forget its roots as a collaborative tool for HEP research. The SLD collaboration has made extensive use of WWW in this latter role, using it to allow collaborators to sign up for shifts, to monitor physics data-taking in near real time, and as a tool to educate and inform collaborators. By their nature such tools are accessible to all collaborators wherever they are located. In this talk we will describe our current system and comment on its effectiveness, and discuss possible enhancements based on forthcoming more powerful web browsers.

Characterization of PbWO4 crystals for high-energy physics experiments

NASA Astrophysics Data System (ADS)

Kim, M. J.; Park, H.; Kim, H. J.

2016-09-01

High-energy physics (HEP) experiments have employed many new types of scintillators. Specifically, bismuth germanate, thallium-doped cesium iodide, and lead tungstate (PbWO4, PWO) have been used for the L3 experiment; CLEO II, Belle and BES-III; and CMS, respectively. PWO has particularly beneficial properties, such as high density, fast decay time, short radiation length and radiation hardness. In this study, we tested the PWO crystals at low temperatures to determine their applicability in future calorimeters. Various crystals from the Proton Antiproton Annihilations at Darmstadt (PANDA) experiment in Giessen, the Bogoroditsk Techno-Chemical Plant (BTCP) in Russia and by Shanghai Institute of Ceramics, Chinese Academy of Sciences (SICCAS) in China were investigated. We studied the scintillation properties of PWO crystals, such as their X-ray luminescence, relative light yields, absolute light yields, energy resolutions, decay times and longitudinal uniformities of their light yields. In addition, we measured the temperature dependences of the light yields and decay times by using a 137Cs γ-ray source. The emission spectra of the PWO crystals consisted of a broad band from 350 nm to 700 nm, and the peak emission wavelength in each spectrum was 420 nm. The emission spectra of the PWO crystals from SICCAS were slightly shifted to longer wavelengths compared with those of the crystals from the other institutions.

FERMILAB ACCELERATOR R&D PROGRAM TOWARDS INTENSITY FRONTIER ACCELERATORS : STATUS AND PROGRESS

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

Shiltsev, Vladimir

2016-11-15

The 2014 P5 report indicated the accelerator-based neutrino and rare decay physics research as a centrepiece of the US domestic HEP program at Fermilab. Operation, upgrade and development of the accelerators for the near- term and longer-term particle physics program at the Intensity Frontier face formidable challenges. Here we discuss key elements of the accelerator physics and technology R&D program toward future multi-MW proton accelerators and present its status and progress. INTENSITY FRONTIER ACCELERATORS

SDN-NGenIA, a software defined next generation integrated architecture for HEP and data intensive science

NASA Astrophysics Data System (ADS)

Balcas, J.; Hendricks, T. W.; Kcira, D.; Mughal, A.; Newman, H.; Spiropulu, M.; Vlimant, J. R.

2017-10-01

The SDN Next Generation Integrated Architecture (SDN-NGeNIA) project addresses some of the key challenges facing the present and next generations of science programs in HEP, astrophysics, and other fields, whose potential discoveries depend on their ability to distribute, process and analyze globally distributed Petascale to Exascale datasets. The SDN-NGenIA system under development by Caltech and partner HEP and network teams is focused on the coordinated use of network, computing and storage infrastructures, through a set of developments that build on the experience gained in recently completed and previous projects that use dynamic circuits with bandwidth guarantees to support major network flows, as demonstrated across LHC Open Network Environment [1] and in large scale demonstrations over the last three years, and recently integrated with PhEDEx and Asynchronous Stage Out data management applications of the CMS experiment at the Large Hadron Collider. In addition to the general program goals of supporting the network needs of the LHC and other science programs with similar needs, a recent focus is the use of the Leadership HPC facility at Argonne National Lab (ALCF) for data intensive applications.

Extreme I/O on HPC for HEP using the Burst Buffer at NERSC

NASA Astrophysics Data System (ADS)

Bhimji, Wahid; Bard, Debbie; Burleigh, Kaylan; Daley, Chris; Farrell, Steve; Fasel, Markus; Friesen, Brian; Gerhardt, Lisa; Liu, Jialin; Nugent, Peter; Paul, Dave; Porter, Jeff; Tsulaia, Vakho

2017-10-01

In recent years there has been increasing use of HPC facilities for HEP experiments. This has initially focussed on less I/O intensive workloads such as generator-level or detector simulation. We now demonstrate the efficient running of I/O-heavy analysis workloads on HPC facilities at NERSC, for the ATLAS and ALICE LHC collaborations as well as astronomical image analysis for DESI and BOSS. To do this we exploit a new 900 TB NVRAM-based storage system recently installed at NERSC, termed a Burst Buffer. This is a novel approach to HPC storage that builds on-demand filesystems on all-SSD hardware that is placed on the high-speed network of the new Cori supercomputer. We describe the hardware and software involved in this system, and give an overview of its capabilities, before focusing in detail on how the ATLAS, ALICE and astronomical workflows were adapted to work on this system. We describe these modifications and the resulting performance results, including comparisons to other filesystems. We demonstrate that we can meet the challenging I/O requirements of HEP experiments and scale to many thousands of cores accessing a single shared storage system.

GLoBES: General Long Baseline Experiment Simulator

NASA Astrophysics Data System (ADS)

Huber, Patrick; Kopp, Joachim; Lindner, Manfred; Rolinec, Mark; Winter, Walter

2007-09-01

GLoBES (General Long Baseline Experiment Simulator) is a flexible software package to simulate neutrino oscillation long baseline and reactor experiments. On the one hand, it contains a comprehensive abstract experiment definition language (AEDL), which allows to describe most classes of long baseline experiments at an abstract level. On the other hand, it provides a C-library to process the experiment information in order to obtain oscillation probabilities, rate vectors, and Δχ-values. Currently, GLoBES is available for GNU/Linux. Since the source code is included, the port to other operating systems is in principle possible. GLoBES is an open source code that has previously been described in Computer Physics Communications 167 (2005) 195 and in Ref. [7]). The source code and a comprehensive User Manual for GLoBES v3.0.8 is now available from the CPC Program Library as described in the Program Summary below. The home of GLobES is http://www.mpi-hd.mpg.de/~globes/. Program summaryProgram title: GLoBES version 3.0.8 Catalogue identifier: ADZI_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADZI_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 145 295 No. of bytes in distributed program, including test data, etc.: 1 811 892 Distribution format: tar.gz Programming language: C Computer: GLoBES builds and installs on 32bit and 64bit Linux systems Operating system: 32bit or 64bit Linux RAM: Typically a few MBs Classification: 11.1, 11.7, 11.10 External routines: GSL—The GNU Scientific Library, www.gnu.org/software/gsl/ Nature of problem: Neutrino oscillations are now established as the leading flavor transition mechanism for neutrinos. In a long history of many experiments, see, e.g., [1], two oscillation frequencies have been identified: The fast atmospheric and the slow solar oscillations, which are driven by the respective mass squared differences. In addition, there could be interference effects between these two oscillations, provided that the coupling given by the small mixing angle θ is large enough. Such interference effects include, for example, leptonic CP violation. In order to test the unknown oscillation parameters, i.e. the mixing angle θ, the leptonic CP phase, and the neutrino mass hierarchy, new long-baseline and reactor experiments are proposed. These experiments send an artificial neutrino beam to a detector, or detect the neutrinos produced by a nuclear fission reactor. However, the presence of multiple solutions which are intrinsic to neutrino oscillation probabilities [2-5] affect these measurements. Thus optimization strategies are required which maximally exploit complementarity between experiments. Therefore, a modern, complete experiment simulation and analysis tool does not only need to have a highly accurate beam and detector simulation, but also powerful means to analyze correlations and degeneracies, especially for the combination of several experiments. The GLoBES software package is such a tool [6,7]. Solution method: GLoBES is a flexible software tool to simulate and analyze neutrino oscillation long-baseline and reactor experiments using a complete three-flavor description. On the one hand, it contains a comprehensive abstract experiment definition language (AEDL), which makes it possible to describe most classes of long baseline and reactor experiments at an abstract level. On the other hand, it provides a C-library to process the experiment information in order to obtain oscillation probabilities, rate vectors, and Δχ-values. In addition, it provides a binary program to test experiment definitions very quickly, before they are used by the application software. Restrictions: Currently restricted to discrete sets of sources and detectors. For example, the simulation of an atmospheric neutrino flux is not supported. Unusual features: Clear separation between experiment description and the simulation software. Additional comments: To find information on the latest version of the software and user manual, please check the author's web site, http://www.mpi-hd.mpg.de/~globes Running time: The examples included in the distribution take only a few minutes to complete. More sophisticated problems can take up to several days. References [1] V. Barger, D. Marfatia, K. Whisnant, Int. J. Mod. Phys. E 12 (2003) 569, hep-ph/0308123, and references therein. [2] G.L. Fogli, E. Lisi, Phys. Rev. D 54 (1996) 3667, hep-ph/9604415. [3] J. Burguet-Castell, M.B. Gavela, J.J. Gomez-Cadenas, P. Hernandez, O. Mena, Nucl. Phys. B 608 (2001) 301, hep-ph/0103258. [4] H. Minakata, H. Nunokawa, JHEP 0110 (2001) 001, hep-ph/0108085. [5] V. Barger, D. Marfatia, K. Whisnant, Phys. Rev. D 65 (2002) 073023, hep-ph/0112119. [6] P. Huber, M. Lindner, W. Winter, Comput. Phys. Commun. 167 (2005) 195. [7] P. Huber, J. Kopp, M. Lindner, M. Rolinec, W. Winter, Comput. Phys. Commun. 177 (2007) 432.

Design and performance of an electromagnetic calorimeter for a FCC-hh experiment

NASA Astrophysics Data System (ADS)

Zaborowska, A.

2018-03-01

The physics reach and feasibility of the Future Circular Collider are currently under investigation. The goal is to collide protons with centre-of-mass energies up to 100 TeV, extending the research carried out at the current HEP facilities. The detectors designed for the FCC experiments need to tackle harsh conditions of the unprecedented collision energy and luminosity. The baseline technology for the calorimeter system of the FCC-hh detector is described. The electromagnetic calorimeter in the barrel, as well as the electromagnetic and hadronic calorimeters in the endcaps and the forward regions, are based on the liquid argon as active material. The detector layout in the barrel region combines the concept of a high granularity calorimeter with precise energy measurements. The calorimeters have to meet the requirements of high radiation hardness and must be able to deal with a very high number of collisions per bunch crossings (pile-up). A very good energy and angular resolution for a wide range of electrons' and photons' momentum is needed in order to meet the demands based on the physics benchmarks. First results of the performance studies with the new liquid argon calorimeter are presented, meeting the energy resolution goal.

[Study on transient absorption spectrum of tungsten nanoparticle with HepG2 tumor cell].

PubMed

Cao, Lin; Shu, Xiao-Ning; Liang, Dong; Wang, Cong

2014-07-01

Significance of this study lies in tungsten nano materials can be used as a preliminary innovative medicines applied basic research. This paper investigated the inhibition of tungsten nanoparticles which effected on human hepatoma HepG2 cells by MTT. The authors use transient absorption spectroscopy (TAS) technology absorption and emission spectra characterization of charge transfer between nanoparticles and tumor cell. The authors discussed the role of the tungsten nanoparticles in the tumor early detection of the disease and its anti-tumor properties. In the HepG2 experiments system, 100-150 microg x mL(-1) is the best drug concentration of anti-tumor activity which recact violently within 6 hours and basically completed in 24 hours. The results showed that transient absorption spectroscopy can be used as tumor detection methods and characterization of charge transfer between nano-biosensors and tumor cells. Tungsten nanoparticles have potential applications as anticancer drugs.

The polysaccharides from fermented Ganoderma lucidum mycelia induced miRNAs regulation in suppressed HepG2 cells.

PubMed

Shen, Jie; Park, Hyeon-soo; Xia, Yong-mei; Kim, Gon-sup; Cui, Steve W

2014-03-15

Medicinal mushroom polysaccharides such as Ganoderma lucidum polysaccharides (GLPs) have been commonly hypothesized to suppress tumor cells proliferation through immune effects. To verify this hypothesis through investigating comprehensive miRNA expression in polysaccharide treated cancer cells, an anticancer mycelia GLP was employed to disclose miRNA differential expression of human hepatocarcinoma cells (HepG2), by using a miRNA microarray assay based on Sanger miR-Base Release 16. The experiment and the analysis result indicates that among the 61 differential expressed miRNAs (p ≤ 0.01), 17 of them were regulated significantly. GLP can inhibit HepG2 cells directly through regulation of hepatocarcinoma genes. A newly found miR-3131 exhibited the strongest upregulation (92-folds, Log2 = 6.53, p = 0.000016). The miRNAs responded synergistically in both hepatocarcinoma and immune-related aspects. Copyright © 2014 Elsevier Ltd. All rights reserved.

Physical-mechanical image of the cell surface on the base of AFM data in contact mode

NASA Astrophysics Data System (ADS)

Starodubtseva, M. N.; Starodubtsev, I. E.; Yegorenkov, N. I.; Kuzhel, N. S.; Konstantinova, E. E.; Chizhik, S. A.

2017-10-01

Physical and mechanical properties of the cell surface are well-known markers of a cell state. The complex of the parameters characterizing the cell surface properties, such as the elastic modulus (E), the parameters of adhesive (Fa), and friction (Ff) forces can be measured using atomic force microscope (AFM) in a contact mode and form namely the physical-mechanical image of the cell surface that is a fundamental element of the cell mechanical phenotype. The paper aims at forming the physical-mechanical images of the surface of two types of glutaraldehyde-fixed cancerous cells (human epithelial cells of larynx carcinoma, HEp-2c cells, and breast adenocarcinoma, MCF-7 cells) based on the data obtained by AFM in air and revealing the basic difference between them. The average values of friction, elastic and adhesive forces, and the roughness of lateral force maps, as well as dependence of the fractal dimension of lateral force maps on Z-scale factor have been studied. We have revealed that the response of microscale areas of the HEp-2c cell surface having numerous microvilli to external mechanical forces is less expressed and more homogeneous in comparison with the response of MCF-7 cell surface.

Achieving production-level use of HEP software at the Argonne Leadership Computing Facility

NASA Astrophysics Data System (ADS)

Uram, T. D.; Childers, J. T.; LeCompte, T. J.; Papka, M. E.; Benjamin, D.

2015-12-01

HEP's demand for computing resources has grown beyond the capacity of the Grid, and these demands will accelerate with the higher energy and luminosity planned for Run II. Mira, the ten petaFLOPs supercomputer at the Argonne Leadership Computing Facility, is a potentially significant compute resource for HEP research. Through an award of fifty million hours on Mira, we have delivered millions of events to LHC experiments by establishing the means of marshaling jobs through serial stages on local clusters, and parallel stages on Mira. We are running several HEP applications, including Alpgen, Pythia, Sherpa, and Geant4. Event generators, such as Sherpa, typically have a split workload: a small scale integration phase, and a second, more scalable, event-generation phase. To accommodate this workload on Mira we have developed two Python-based Django applications, Balsam and ARGO. Balsam is a generalized scheduler interface which uses a plugin system for interacting with scheduler software such as HTCondor, Cobalt, and TORQUE. ARGO is a workflow manager that submits jobs to instances of Balsam. Through these mechanisms, the serial and parallel tasks within jobs are executed on the appropriate resources. This approach and its integration with the PanDA production system will be discussed.

Cetuximab-conjugated nanodiamonds drug delivery system for enhanced targeting therapy and 3D Raman imaging.

PubMed

Li, Dandan; Chen, Xin; Wang, Hong; Liu, Jie; Zheng, Meiling; Fu, Yang; Yu, Yuan; Zhi, Jinfang

2017-12-01

In this study, a multicomponent nanodiamonds (NDs)-based targeting drug delivery system, cetuximab-NDs-cisplatin bioconjugate, combining both specific targeting and enhanced therapeutic efficacy capabilities, is developed and characterized. The specific targeting ability of cetuximab-NDs-cisplatin system on human liver hepatocellular carcinoma (HepG2) cells is evaluated through epidermal growth factor receptor (EGFR) blocking experiments, since EGFR is over-expressed on HepG2 cell membrane. Besides, cytotoxic evaluation confirms that cetuximab-NDs-cisplatin system could significantly inhibit the growth of HepG2 cells, and the therapeutic activity of this system is proven to be better than that of both nonspecific NDs-cisplatin conjugate and specific EGF-NDs-cisplatin conjugate. Furthermore, a 3-dimensional (3D) Raman imaging technique is utilized to visualize the targeting efficacy and enhanced internalization of cetuximab-NDs-cisplatin system in HepG2 cells, using the NDs existing in the bioconjugate as Raman probes, based on the characteristic Raman signal of NDs at 1332 cm -1 . These advantageous properties of cetuximab-NDs-cisplatin system propose a prospective imaging and treatment tool for further diagnostic and therapeutic purposes. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Comparative study of physicochemical properties and bioactivity of Hericium erinaceus polysaccharides at different solvent extractions.

PubMed

Yan, Jing-Kun; Ding, Zhi-Chao; Gao, Xianli; Wang, Yao-Yao; Yang, Yan; Wu, Di; Zhang, He-Nan

2018-08-01

In this study, hot water, 0.9% NaCl, citric acid, and 1.25 M NaOH/0.05% NaBH 4 were separately used for the extraction of water-soluble H. erinaceus polysaccharides (HEPs; HEP-W, HEP-S, HEP-C, and HEP-A) from the fruit body of Hericium erinaceus. The physicochemical properties and biological activities were then investigated and compared. Results showed that the extraction solvents exhibited significant effects on the extraction yields, molecular weights, monosaccharide compositions, preliminary structural characteristics, microstructures of HEPs and on their contents, such as neutral sugar, uronic acid, protein, and β-(1 → 3)-glucan. In vitro antioxidant activity assays indicated that HEP-C extracted with citric acid solution showed stronger scavenging abilities on hydroxyl and DPPH radicals and antioxidant capacities than HEP-W and HEP-S. Moreover, HEP-C exhibited the strongest inhibitory effects on α-glycosidase and α-amylase activities. Therefore, HEP-C extracted with citric acid can be developed as a potential bioactive ingredient for applications in food, medicine, and cosmetics industries. Copyright © 2018 Elsevier Ltd. All rights reserved.

Physiotherapy home exercise program for haemophiliacs.

PubMed

Pierstorff, K; Seuser, A; Weinspach, S; Laws, H-J

2011-05-01

Regular physiotherapy can improve the stability and flexibility of joints and decrease the bleeding risk in patients with haemophilia. To reduce the appointments for the patients and to make exercising a part of daily live, an individualized home exercise program (HEP) was designed. Retrospectively the number of bleedings during the HEP was compared to number of bleedings before. 8 patients aged between 4 and 16 years with haemophilia A were evaluated. At start and after 13 month patients had a motion analysis via topographic ultrasound. According to the results and clinical findings an individualized HEP was created. Standardised scores for clinical evaluation and the patient based evaluation of exercises were designed. At every appointment exercises were individually adjusted. Patients exercised in median 1.7 times a week. No training related bleeds occurred. 7 of 8 patients showed reduced joint and/or muscle bleeds (p<0.02). Clinical scores raised slightly in every patient. However the second motion analysis of squat and gait showed a worsening in 7 of 8 patients (p>0.05). A HEP can help to advance in physical fitness and coordination and may reduce bleeding tendency, but needs to be accomplished regularly. Patients are interested but the motivation to exercise at home is low. Disorders measured by motion analysis seem not to be sufficiently influenced by our surrogate training program. © Georg Thieme Verlag KG Stuttgart · New York.

A comparison of mindfulness-based stress reduction and an active control in modulation of neurogenic inflammation

PubMed Central

Rosenkranz, Melissa A.; Davidson, Richard J.; MacCoon, Donal G.; Sheridan, John F.; Kalin, Ned H.; Lutz, Antoine

2012-01-01

Psychological stress is a major provocative factor of symptoms in chronic inflammatory conditions. In recent years, interest in addressing stress responsivity through meditation training in health-related domains has increased astoundingly, despite a paucity of evidence that reported benefits are specific to meditation practice. We designed the present study to rigorously compare an 8-week Mindfulness-Based Stress Reduction (MBSR) intervention to a well-matched active control intervention, the Health Enhancement Program (HEP) in ability to reduce psychological stress and experimentally-induced inflammation. The Trier Social Stress Test (TSST) was used to induce psychological stress and inflammation was produced using topical application of capsaicin cream to forearm skin. Immune and endocrine measures of inflammation and stress were collected both before and after MBSR training. Results show those randomized to MBSR and HEP training had comparable post-training stress-evoked cortisol responses, as well as equivalent reductions in self-reported psychological distress and physical symptoms. However, MBSR training resulted in a significantly smaller post-stress inflammatory response compared to HEP, despite equivalent levels of stress hormones. These results suggest behavioral interventions designed to reduce emotional reactivity may be of therapeutic benefit in chronic inflammatory conditions. Moreover, mindfulness practice, in particular, may be more efficacious in symptom relief than the well-being promoting activities cultivated in the HEP program. PMID:23092711

HEPCloud, a New Paradigm for HEP Facilities: CMS Amazon Web Services Investigation

DOE PAGES

Holzman, Burt; Bauerdick, Lothar A. T.; Bockelman, Brian; ...

2017-09-29

Historically, high energy physics computing has been performed on large purpose-built computing systems. These began as single-site compute facilities, but have evolved into the distributed computing grids used today. Recently, there has been an exponential increase in the capacity and capability of commercial clouds. Cloud resources are highly virtualized and intended to be able to be flexibly deployed for a variety of computing tasks. There is a growing interest among the cloud providers to demonstrate the capability to perform large-scale scientific computing. In this paper, we discuss results from the CMS experiment using the Fermilab HEPCloud facility, which utilized bothmore » local Fermilab resources and virtual machines in the Amazon Web Services Elastic Compute Cloud. We discuss the planning, technical challenges, and lessons learned involved in performing physics workflows on a large-scale set of virtualized resources. Additionally, we will discuss the economics and operational efficiencies when executing workflows both in the cloud and on dedicated resources.« less

HEPCloud, a New Paradigm for HEP Facilities: CMS Amazon Web Services Investigation

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

Holzman, Burt; Bauerdick, Lothar A. T.; Bockelman, Brian

Historically, high energy physics computing has been performed on large purpose-built computing systems. These began as single-site compute facilities, but have evolved into the distributed computing grids used today. Recently, there has been an exponential increase in the capacity and capability of commercial clouds. Cloud resources are highly virtualized and intended to be able to be flexibly deployed for a variety of computing tasks. There is a growing interest among the cloud providers to demonstrate the capability to perform large-scale scientific computing. In this paper, we discuss results from the CMS experiment using the Fermilab HEPCloud facility, which utilized bothmore » local Fermilab resources and virtual machines in the Amazon Web Services Elastic Compute Cloud. We discuss the planning, technical challenges, and lessons learned involved in performing physics workflows on a large-scale set of virtualized resources. Additionally, we will discuss the economics and operational efficiencies when executing workflows both in the cloud and on dedicated resources.« less

Argonne HEP Lunch Seminars

Science.gov Websites

Argonne HEP Lunch Seminar Schedule ANL home | HEP Division | Theory group | HEP Division seminars | HEP Theory seminars | Chicago seminars The ANL HEP Lunchtime Seminar is held regularly on Tuesdays at Phenomena in Astrophysics and Cosmology November 15, 2005 Harry Lipkin Update on Pentaquark theory and

An overview of the DII-HEP OpenStack based CMS data analysis

NASA Astrophysics Data System (ADS)

Osmani, L.; Tarkoma, S.; Eerola, P.; Komu, M.; Kortelainen, M. J.; Kraemer, O.; Lindén, T.; Toor, S.; White, J.

2015-05-01

An OpenStack based private cloud with the Cluster File System has been built and used with both CMS analysis and Monte Carlo simulation jobs in the Datacenter Indirection Infrastructure for Secure High Energy Physics (DII-HEP) project. On the cloud we run the ARC middleware that allows running CMS applications without changes on the job submission side. Our test results indicate that the adopted approach provides a scalable and resilient solution for managing resources without compromising on performance and high availability. To manage the virtual machines (VM) dynamically in an elastic fasion, we are testing the EMI authorization service (Argus) and the Execution Environment Service (Argus-EES). An OpenStackplugin has been developed for Argus-EES. The Host Identity Protocol (HIP) has been designed for mobile networks and it provides a secure method for IP multihoming. HIP separates the end-point identifier and locator role for IP address which increases the network availability for the applications. Our solution leverages HIP for traffic management. This presentation gives an update on the status of the work and our lessons learned in creating an OpenStackbased cloud for HEP.

Immunomodulatory effects of hydroxyethylated Hericium erinaceus polysaccharide on macrophages RAW264.7.

PubMed

Ren, Zhe; Qin, Tao; Qiu, Fuan; Song, Yulong; Lin, Dandan; Ma, Yufang; Li, Jian; Huang, Yifan

2017-12-01

Hericium erinaceus polysaccharide (HEP) has been shown to possess a variety of biological activities. In present study, HEP was successfully modified to obtain its hydroxyethylated derivative hHEP. Its potential immunomodulatory activities on RAW264.7 macrophages were investigated. Results showed that the hHEP were significantly stronger than that of the corresponding unmodified polysaccharide, HEP. Meanwhile, the NO, IL-6 and TNF-α production activities of macrophages were enhanced in the RAW264.7 macrophages by stimulation of hHEP. In addition, the hHEP increase significantly higher iNOS expression than HEP. These results indicated that the hydroxyethylated derivative hHEP could enhance the activation of peritoneal macrophages, and hydroxyethylation modification can enhance the immunomodulation function of HEP. Copyright © 2017 Elsevier B.V. All rights reserved.

Selenizing Hericium erinaceus polysaccharides induces dendritic cells maturation through MAPK and NF-κB signaling pathways.

PubMed

Qin, Tao; Ren, Zhe; Huang, Yifan; Song, Yulong; Lin, Dandan; Li, Jian; Ma, Yufang; Wu, Xiuqin; Qiu, Fuan; Xiao, Qi

2017-04-01

In this study, polysaccharides extracted from Hericium erinaceus were modified to obtain its nine selenium derivatives, sHEP 1 -sHEP 9 . Their structures were identified, yields and selenium contents were determined, the phenotypic and functional maturation of murine bone marrow-derived dendritic cells (DCs) and relevant mechanisms were compared taking unmodified HEP as control. The results revealed that the selenylation were successful. sHEP 1 , sHEP 2 and sHEP 8 treatment of DCs increased their surface expression of MHC-II and CD86 and indicated that sHEP 1 , sHEP 2 and sHEP 8 induced DC maturation. Furthermore, sHEP 2 and sHEP 8 also significantly decreased DCs endocytosis and significantly enhanced cytokine (IL-12 and IFN-γ) production. In line with TLR4 activation, sHEP 2 increased the phosphorylation of ERK, p38, and JNK, and the nuclear translocation of p-c-Jun, p-CREB, and c-Fos. sHEP 2 also activated NF-κB signaling, as evidenced by degradation of IκBα/β and nuclear translocation of p65 and p50. Together, these results suggest that sHEP is a strong immunostimulant. Copyright © 2017 Elsevier B.V. All rights reserved.

Impact of exercise capacity on myocardial high-energy phosphate metabolism.

PubMed

Klug, G; Zwick, R H; Frick, M; Wolf, C; Schocke, M F H; Conci, E; Jaschke, W; Pachinger, O; Metzler, B

2007-08-01

31-Phosphorous magnetic resonance spectroscopy (31P MRS) is a unique tool to investigate IN VIVO high-energy phosphates (HEP) in the human heart. We hypothesized that physical capacity may be associated with myocardial HEP status. Healthy, male volunteers (n = 105, mean age 51 +/- 7 years) underwent bicycle ergometry with a stepwise increasing workload to determine maximal working capacity (MWC). Heart rate (HR) and blood pressure (BP) were measured continuously during exercise and 4 minutes of recovery. Further 31-Phosphorous 2-dimensional chemical shift imaging (31P 2D CSI) MRS was performed to assess myocardial HEP metabolism by determining phosphocreatinine to beta-ATP ratios (PCr/b-ATP) using a 1.5 tesla scanner. Volunteers with MWC > 230 Watt had significantly higher PCr/b-ATP ratios than those with MWC < 200 Watt (1.93 +/- 0.36 vs. 1.59 +/- 0.35; p < 0.001). Additionally, those with a recovery systolic (S)BP < 195 mmHg had significantly higher ratios than those with a recovery SBP > 195 mmHg (1.74 +/- 0.3 vs. 1.51 +/- 0.2; p < 0.05). We observed a linear correlation between the PCr/b-ATP ratio and MWC (r = 0.411; p < 0.001) and recovery SBP (r = - 0.290; p < 0.01). After statistical correction for age, these correlations remained significant. In this study, we observed a correlation of parameters of physical fitness determined by bicycle exercise testing and cardiac PCr/b-ATP ratios.

Oklahoma Center for High Energy Physics (OCHEP)

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

Nandi, S; Strauss, M J; Snow, J

2012-02-29

The DOE EPSCoR implementation grant, with the support from the State of Oklahoma and from the three universities, Oklahoma State University, University of Oklahoma and Langston University, resulted in establishing of the Oklahoma Center for High Energy Physics (OCHEP) in 2004. Currently, OCHEP continues to flourish as a vibrant hub for research in experimental and theoretical particle physics and an educational center in the State of Oklahoma. All goals of the original proposal were successfully accomplished. These include foun- dation of a new experimental particle physics group at OSU, the establishment of a Tier 2 computing facility for the Largemore » Hadron Collider (LHC) and Tevatron data analysis at OU and organization of a vital particle physics research center in Oklahoma based on resources of the three universities. OSU has hired two tenure-track faculty members with initial support from the grant funds. Now both positions are supported through OSU budget. This new HEP Experimental Group at OSU has established itself as a full member of the Fermilab D0 Collaboration and LHC ATLAS Experiment and has secured external funds from the DOE and the NSF. These funds currently support 2 graduate students, 1 postdoctoral fellow, and 1 part-time engineer. The grant initiated creation of a Tier 2 computing facility at OU as part of the Southwest Tier 2 facility, and a permanent Research Scientist was hired at OU to maintain and run the facility. Permanent support for this position has now been provided through the OU university budget. OCHEP represents a successful model of cooperation of several universities, providing the establishment of critical mass of manpower, computing and hardware resources. This led to increasing Oklahoma's impact in all areas of HEP, theory, experiment, and computation. The Center personnel are involved in cutting edge research in experimental, theoretical, and computational aspects of High Energy Physics with the research areas ranging from the search for new phenomena at the Fermilab Tevatron and the CERN Large Hadron Collider to theoretical modeling, computer simulation, detector development and testing, and physics analysis. OCHEP faculty members participating on the D0 collaboration at the Fermilab Tevatron and on the ATLAS collaboration at the CERN LHC have made major impact on the Standard Model (SM) Higgs boson search, top quark studies, B physics studies, and measurements of Quantum Chromodynamics (QCD) phenomena. The OCHEP Grid computing facility consists of a large computer cluster which is playing a major role in data analysis and Monte Carlo productions for both the D0 and ATLAS experiments. Theoretical efforts are devoted to new ideas in Higgs bosons physics, extra dimensions, neutrino masses and oscillations, Grand Unified Theories, supersymmetric models, dark matter, and nonperturbative quantum field theory. Theory members are making major contributions to the understanding of phenomena being explored at the Tevatron and the LHC. They have proposed new models for Higgs bosons, and have suggested new signals for extra dimensions, and for the search of supersymmetric particles. During the seven year period when OCHEP was partially funded through the DOE EPSCoR implementation grant, OCHEP members published over 500 refereed journal articles and made over 200 invited presentations at major conferences. The Center is also involved in education and outreach activities by offering summer research programs for high school teachers and college students, and organizing summer workshops for high school teachers, sometimes coordinating with the Quarknet programs at OSU and OU. The details of the Center can be found in http://ochep.phy.okstate.edu.« less

Pharmacological characterization of the inhibitory activity of beta h-endorphin (beta h-EP), [Arg9,19,24,28,29]-beta h-EP, [Gln8,Gly31]-beta h-EP-Gly-Gly-NH2, in the neuroeffector junction of the mouse vas deferens.

PubMed

Valenzuela, R; Li, C H; Huidobro-Toro, J P

1991-08-01

The inhibitory opioid activities of beta h-endorphin (beta h-EP), its structurally related peptide analogues [Gln8,Gly31]-beta h-EP-Gly-Gly-NH2 (Gly-Gly-beta h-EP), [Arg9,19,24,28,29]-beta h-EP (Arg-beta h-EP) and methionine enkephalin have been examined in the electrically stimulated mouse vas deferens bioassay. All four peptides behaved as full agonists; methionine enkephalin was the most potent followed by Arg-beta h-EP, beta h-EP and Gly-Gly-beta h-EP. Neither Gly-Gly-beta h-EP nor Arg-beta h-EP antagonized the inhibitory action of beta h-EP or methionine enkephalin. An hour of tissue exposure to 30 nM beta-funaltrexamine followed by thorough washing, displaced to the right, in a parallel fashion, the concentration-response curves of beta h-EP and analogues. Whereas the displacement of the concentration response curves was 8 to 10-fold for beta h-EP and Arg-beta h-EP, it was only about 3-fold for Gly-Gly-beta h-EP and methionine enkephalin. Naltrindole was the most potent antagonist of methionine enkephalin with an apparent pA2 of 9.4; its potency as an antagonist of beta h-EP and related analogues was approximately one-tenth of this with pA2 values approximately 8.5. Norbinaltorphimine also antagonized the action of the opioid peptides with pA2 values close to 7.8.

ACTS: from ATLAS software towards a common track reconstruction software

NASA Astrophysics Data System (ADS)

Gumpert, C.; Salzburger, A.; Kiehn, M.; Hrdinka, J.; Calace, N.; ATLAS Collaboration

2017-10-01

Reconstruction of charged particles’ trajectories is a crucial task for most particle physics experiments. The high instantaneous luminosity achieved at the LHC leads to a high number of proton-proton collisions per bunch crossing, which has put the track reconstruction software of the LHC experiments through a thorough test. Preserving track reconstruction performance under increasingly difficult experimental conditions, while keeping the usage of computational resources at a reasonable level, is an inherent problem for many HEP experiments. Exploiting concurrent algorithms and using multivariate techniques for track identification are the primary strategies to achieve that goal. Starting from current ATLAS software, the ACTS project aims to encapsulate track reconstruction software into a generic, framework- and experiment-independent software package. It provides a set of high-level algorithms and data structures for performing track reconstruction tasks as well as fast track simulation. The software is developed with special emphasis on thread-safety to support parallel execution of the code and data structures are optimised for vectorisation to speed up linear algebra operations. The implementation is agnostic to the details of the detection technologies and magnetic field configuration which makes it applicable to many different experiments.

Quantifying the Digital Divide: A Scientific Overview of Network Connectivity and Grid Infrastructure in South Asian Countries

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

Khan, Shahryar Muhammad; /SLAC /NUST, Rawalpindi; Cottrell, R.Les

2007-10-30

The future of Computing in High Energy Physics (HEP) applications depends on both the Network and Grid infrastructure. South Asian countries such as India and Pakistan are making significant progress by building clusters as well as improving their network infrastructure However to facilitate the use of these resources, they need to manage the issues of network connectivity to be among the leading participants in Computing for HEP experiments. In this paper we classify the connectivity for academic and research institutions of South Asia. The quantitative measurements are carried out using the PingER methodology; an approach that induces minimal ICMP trafficmore » to gather active end-to-end network statistics. The PingER project has been measuring the Internet performance for the last decade. Currently the measurement infrastructure comprises of over 700 hosts in more than 130 countries which collectively represents approximately 99% of the world's Internet-connected population. Thus, we are well positioned to characterize the world's connectivity. Here we present the current state of the National Research and Educational Networks (NRENs) and Grid Infrastructure in the South Asian countries and identify the areas of concern. We also present comparisons between South Asia and other developing as well as developed regions. We show that there is a strong correlation between the Network performance and several Human Development indices.« less

Final Report for Research in High Energy Physics (University of Hawaii)

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

Browder, Thomas E.

2013-08-31

Here we present a final report for the DOE award for the University of Hawaii High Energy Physics Group (UHHEPG) for the period from December 1, 2009 to May 31, 2013 (including a period of no-cost extension). The high energy physics (HEP) group at the University of Hawaii (UH) has been engaged in experiments at the intensity frontier studying flavor physics (Task A: Belle, Belle-II and Task B: BES) and neutrinos (Task C: SuperK, LBNE, Double Chooz, DarkSide, and neutrino R\\&D). On the energy frontier, new types of pixel detectors were developed for upgrades of the ATLAS experiment at themore » LHC (Task D). On the cosmic frontier, there were investigations of ultra high-energy neutrino astrophysics and the highest energy cosmic rays using special radio detection techniques (Task E: AMBER, ANITA R\\&D) and results of the analysis of ANITA data. In addition, we have developed new types of sophisticated and cutting edge instrumentation based on novel ``oscilloscope on a chip'' electronics (Task F). Theoretical physics research (Task G) is phenomenologically oriented and has studied experimental consequences of existing and proposed new theories relevant to the energy, cosmic and intensity frontiers. The senior investigators for proposal were T. E. Browder (Task A), F. A. Harris (Task B), P. Gorham (Task E), J. Kumar (Task G), J. Maricic (Task C), J. G. Learned (Task C), S. Pakvasa (Task G), S. Parker (Task D), S. Matsuno (Task C), X. Tata (Task G) and G. S. Varner (Tasks F, A, E).« less

QuarkNet Stories

Science.gov Websites

      Stories of QuarkNet Teachers and Students   and labs 18 HEP experiments 475 high schools in 28 states 60 ,000 students per year The focus of QuarkNet is to involve teachers and students in our experiments: Teachers do research with us and bring

ProMC: Input-output data format for HEP applications using varint encoding

NASA Astrophysics Data System (ADS)

Chekanov, S. V.; May, E.; Strand, K.; Van Gemmeren, P.

2014-10-01

A new data format for Monte Carlo (MC) events, or any structural data, including experimental data, is discussed. The format is designed to store data in a compact binary form using variable-size integer encoding as implemented in the Google's Protocol Buffers package. This approach is implemented in the PROMC library which produces smaller file sizes for MC records compared to the existing input-output libraries used in high-energy physics (HEP). Other important features of the proposed format are a separation of abstract data layouts from concrete programming implementations, self-description and random access. Data stored in PROMC files can be written, read and manipulated in a number of programming languages, such C++, JAVA, FORTRAN and PYTHON.

HEP Outreach, Inreach, and Web 2.0

NASA Astrophysics Data System (ADS)

Goldfarb, Steven

2011-12-01

I report on current usage of multimedia and social networking "Web 2.0" tools for Education and Outreach in high-energy physics, and discuss their potential for internal communication within large worldwide collaborations, such as those of the LHC. Following a brief description of the history of Web 2.0 development, I present a survey of the most popular sites and describe their usage in HEP to disseminate information to students and the general public. I then discuss the potential of certain specific tools, such as document and multimedia sharing sites, for boosting the speed and effectiveness of information exchange within the collaborations. I conclude with a brief discussion of the successes and failures of these tools, and make suggestions for improved usage in the future.

Randomized controlled trial of concurrent hepatitis A and B vaccination.

PubMed

Bryan, J P; McCardle, P; South-Paul, J E; Fogarty, J P; Legters, L J; Perine, P L

2001-02-01

Hepatitis A and B viruses are threats to deployed military forces. The objective of this study was to determine the feasibility of concurrent vaccination against hepatitis A and B viruses. One hundred five healthy persons, 20 to 49 years of age and without serologic markers to hepatitis A or B viruses, were randomized to receive an inactivated hepatitis A vaccine (HEP A; 25 units in 0.5 mL), recombinant hepatitis B vaccine (HEP B; 10 micrograms in 1.0 mL), or both (HEP A & B) concurrently in separate arms. Vaccines were administered intramuscularly at 0, 1, and 6 months. Sera obtained at 1, 2, 6, 7, and 12 months after the first dose were tested for quantitative antibody to hepatitis A virus (anti-HAV) and antibody to hepatitis B surface antigen. Local reactions (e.g., pain) were reported by less than half of the volunteers and were similar at the site of HEP A, whether given alone or concurrently. However, more persons complained of pain (usually mild) at the HEP B site when HEP B was given concurrently with HEP A compared with HEP B alone (43% vs. 15%, 34% vs. 9%, and 42% vs. 15% for doses 1, 2, and 3, respectively; p < 0.05 for each dose). Among persons immunized with HEP A alone or HEP A & B, the proportion with > or = 10 mIU/mL anti-HAV was 83% in both groups 1 month after dose 1 and 100% at months 2, 7, and 12. The geometric mean concentrations of anti-HAV increased from 21 mIU/mL at month 1 to 2,649 and 2,312 mIU/mL in the HEP A and HEP A & B groups, respectively, at month 7. The response to HEP B was similar whether administered alone or concurrently. Antibody responses were similar in those receiving HEP A or HEP B concurrently or alone, but more subjects reported pain (usually mild) at the HEP B site after concurrent vaccination than after HEP B alone. Further work should be conducted to approve HEP A for patients younger than 2 years of age and to develop combined HEP A and HEP B vaccines in the United States.

Standardized Solution for Management Controller for MTCA.4

NASA Astrophysics Data System (ADS)

Makowski, D.; Fenner, M.; Ludwig, F.; Mavrič, U.; Mielczarek, A.; Napieralski, A.; Perek, P.; Schlarb, H.

2015-06-01

The Micro Telecommunications Computing Architecture (MTCA) standard is a modern platform that is gaining popularity in the area of High Energy Physics (HEP) experiments. The standard provides extensive management, monitoring and diagnostics functionalities. The hardware control and monitoring is based on the Intelligent Platform Management Interface (IPMI), that was initially developed for supervision of complex computers operation. The original IPMI specification was extended to support functions required by the MTCA specification. The Module Management Controller (MMC) is required on each Advanced Mezzanine Card (AMC) installed in MTCA chassis. The Rear Transition Modules (RTMs) have to be equipped with RTM Management Controllers (RMCs) which is required by the MTCA.4 subsidiary specification. The commercially available implementations of MMC and RMC are expensive and do not provide the complete functionality that is required by specific HEP applications. Therefore, many research centers and commercial companies work on their own implementation of AMC and RTM controllers. The available implementations suffer because of lack of common approach and interoperability problems. Since both Lodz University of Technology (TUL) and Deutsches Elektronen-Synchrotron (DESY) have long-term experience in developing ATCA and MTCA hardware, the authors decided to develop a unified solution of management controller fully compliant with AMC and MTCA.4 standards. The MMC v1.00 solution is dedicated for management of AMC and RTM modules. The MMC v1.00 is based on Atmel ATxmega MCUs and can be fully customized by the user or used as a drop-in-module without any modifications. The paper discusses the functionality of the MMC v1.00 solution. The implementation was verified with developed evaluation kits for AMC and RTM cards.

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

Sehrish, S.; Kowalkowski, J.; Paterno, M.

High level abstractions in Python that can utilize computing hardware well seem to be an attractive option for writing data reduction and analysis tasks. In this paper, we explore the features available in Python which are useful and efficient for end user analysis in High Energy Physics (HEP). A typical vertical slice of an HEP data analysis is somewhat fragmented: the state of the reduction/analysis process must be saved at certain stages to allow for selective reprocessing of only parts of a generally time-consuming workflow. Also, algorithms tend to to be modular because of the heterogeneous nature of most detectorsmore » and the need to analyze different parts of the detector separately before combining the information. This fragmentation causes difficulties for interactive data analysis, and as data sets increase in size and complexity (O10 TiB for a “small” neutrino experiment to the O10 PiB currently held by the CMS experiment at the LHC), data analysis methods traditional to the field must evolve to make optimum use of emerging HPC technologies and platforms. Mainstream big data tools, while suggesting a direction in terms of what can be done if an entire data set can be available across a system and analysed with high-level programming abstractions, are not designed with either scientific computing generally, or modern HPC platform features in particular, such as data caching levels, in mind. Our example HPC use case is a search for a new elementary particle which might explain the phenomenon known as “Dark Matter”. Here, using data from the CMS detector, we will use HDF5 as our input data format, and MPI with Python to implement our use case.« less

Surface quality of silicon wafer improved by hydrodynamic effect polishing

NASA Astrophysics Data System (ADS)

Peng, Wenqiang; Guan, Chaoliang; Li, Shengyi

2014-08-01

Differing from the traditional pad polishing, hydrodynamic effect polishing (HEP) is non-contact polishing with the wheel floated on the workpiece. A hydrodynamic lubricated film is established between the wheel and the workpiece when the wheel rotates at a certain speed in HEP. Nanoparticles mixed with deionized water are employed as the polishing slurry, and with action of the dynamic pressure, nanoparticles with high chemisorption due to the high specific surface area can easily reacted with the surface atoms forming a linkage with workpiece surface. The surface atoms are dragged away when nanoparticles are transported to separate by the flow shear stress. The development of grand scale integration put extremely high requirements on the surface quality on the silicon wafer with surface roughness at subnanometer and extremely low surface damage. In our experiment a silicon sample was processed by HEP, and the surface topography before and after polishing was observed by the atomic force microscopy. Experiment results show that plastic pits and bumpy structures on the initial surface have been removed away clearly with the removal depth of 140nm by HEP process. The processed surface roughness has been improved from 0.737nm RMS to 0.175nm RMS(10μm×10μm) and the section profile shows peaks of the process surface are almost at the same height. However, the machining ripples on the wheel surface will duplicate on the silicon surface under the action of the hydrodynamic effect. Fluid dynamic simulation demonstrated that the coarse surface on the wheel has greatly influence on the distribution of shear stress and dynamic pressure on the workpiece surface.

Analytical Research to Determine the effects of the Components of ONGABO on the Viability of HepG2 Cancer Cells by Using the Sovereign, Minister, Assistant and Courier Principle (君臣佐使論)

PubMed Central

Shin, Jeong-Hun; Jun, Seung-lyul; Hwang, Sung-Yeoun; Ahn, Seong-Hun

2012-01-01

Objectives: This study used the basic principle of Oriental medicine, the sovereign, minister, assistant and courier principle (君臣佐使論) to investigate the effects of the component of ONGABO, which is composed of Ginseng Radix (Red Ginseng), Angelica Gigantis Radix, Schisandrae Fructus, Cuscuta Semen and Curcumae tuber on the viability of HepG2 cells. Methods: Single and mixed extracts of the component of ONGABO were prepared by lypohilizing powder of Red Ginseng (6-year root from Kanghwa), Angelica Gigantis Radix, Schisandrae Fructus, Cuscuta Semen, Curcumae Tuber (from Omniherb Co., Ltd., Korea) at the laboratory of herbal medicine in Woosuk University and were eluted after being macerated with 100% ethanol for three days. The cell viability of HepG2 was determined by using an absorptiometric analysis with PrestoBlue (Invitrogen) reagent after the plate had been incubated for 48 hours. All of the experiments were repeated three times to obtain the average value and standard deviation. The statistical analysis was done and the correlation factor was obtained by using Microsoft Office Excel 2007 and Origin 6.0 software. Results: Although Ginseng Radix (Red Ginseng) and Schisandrae Fructus did not enhance the viability of HepG2 cells, they were shown to provide protection of those cells. On the other hand, Angelica Gigantis Radix decreased the viability of HepG2 cells significantly, Cuscuta Semen and Curcumae Tuber had a small or no effect on the viability of HepG2 cells. Conclusions: In the sovereign, minister, assistant and courier principle (君臣佐使論), Ginseng Radix (Red Ginseng) corresponds to the sovereign component because it provides cell protection effects, Angelica Gigantis Radix corresponds to minister medicinal because it kills cells, Schisandrae Fructus corresponds to the assistant medicinal to help red ginseng having cell protect effects. Cuscuta Semen and Curcumae Tuber correspond to the courier medicinal having no effect in cell viability in HepG2. We hope this study provides motivation for advanced research on the sovereign, minister, assistant and courier principle. PMID:25780653

Analytical Research to Determine the effects of the Components of ONGABO on the Viability of HepG2 Cancer Cells by Using the Sovereign, Minister, Assistant and Courier Principle ().

PubMed

Shin, Jeong-Hun; Jun, Seung-Lyul; Hwang, Sung-Yeoun; Ahn, Seong-Hun

2012-12-01

This study used the basic principle of Oriental medicine, the sovereign, minister, assistant and courier principle () to investigate the effects of the component of ONGABO, which is composed of Ginseng Radix (Red Ginseng), Angelica Gigantis Radix, Schisandrae Fructus, Cuscuta Semen and Curcumae tuber on the viability of HepG2 cells. Single and mixed extracts of the component of ONGABO were prepared by lypohilizing powder of Red Ginseng (6-year root from Kanghwa), Angelica Gigantis Radix, Schisandrae Fructus, Cuscuta Semen, Curcumae Tuber (from Omniherb Co., Ltd., Korea) at the laboratory of herbal medicine in Woosuk University and were eluted after being macerated with 100% ethanol for three days. The cell viability of HepG2 was determined by using an absorptiometric analysis with PrestoBlue (Invitrogen) reagent after the plate had been incubated for 48 hours. All of the experiments were repeated three times to obtain the average value and standard deviation. The statistical analysis was done and the correlation factor was obtained by using Microsoft Office Excel 2007 and Origin 6.0 software. Although Ginseng Radix (Red Ginseng) and Schisandrae Fructus did not enhance the viability of HepG2 cells, they were shown to provide protection of those cells. On the other hand, Angelica Gigantis Radix decreased the viability of HepG2 cells significantly, Cuscuta Semen and Curcumae Tuber had a small or no effect on the viability of HepG2 cells. In the sovereign, minister, assistant and courier principle (), Ginseng Radix (Red Ginseng) corresponds to the sovereign component because it provides cell protection effects, Angelica Gigantis Radix corresponds to minister medicinal because it kills cells, Schisandrae Fructus corresponds to the assistant medicinal to help red ginseng having cell protect effects. Cuscuta Semen and Curcumae Tuber correspond to the courier medicinal having no effect in cell viability in HepG2. We hope this study provides motivation for advanced research on the sovereign, minister, assistant and courier principle.

Diagnostic layer integration in FPGA-based pipeline measurement systems for HEP experiments

NASA Astrophysics Data System (ADS)

Pozniak, Krzysztof T.

2007-08-01

Integrated triggering and data acquisition systems for high energy physics experiments may be considered as fast, multichannel, synchronous, distributed, pipeline measurement systems. A considerable extension of functional, technological and monitoring demands, which has recently been imposed on them, forced a common usage of large field-programmable gate array (FPGA), digital signal processing-enhanced matrices and fast optical transmission for their realization. This paper discusses modelling, design, realization and testing of pipeline measurement systems. A distribution of synchronous data stream flows is considered in the network. A general functional structure of a single network node is presented. A suggested, novel block structure of the node model facilitates full implementation in the FPGA chip, circuit standardization and parametrization, as well as integration of functional and diagnostic layers. A general method for pipeline system design was derived. This method is based on a unified model of the synchronous data network node. A few examples of practically realized, FPGA-based, pipeline measurement systems were presented. The described systems were applied in ZEUS and CMS.

Enabling IPv6 at FZU - WLCG Tier2 in Prague

NASA Astrophysics Data System (ADS)

Kouba, Tomáš; Chudoba, Jiří; Eliáš, Marek

2014-06-01

The usage of the new IPv6 protocol in production is becoming reality in the HEP community and the Computing Centre of the Institute of Physics in Prague participates in many IPv6 related activities. Our contribution presents experience with monitoring in HEPiX distributed IPv6 testbed which includes 11 remote sites. We use Nagios to check availability of services and Smokeping for monitoring the network latency. Since it is not always trivial to setup DNS in a dual stack environment properly, we developed a Nagios plugin for checking whether a domain name is resolvable when using only IP protocol version 6 and only version 4. We will also present local area network monitoring and tuning related to IPv6 performance. One of the most important software for a grid site is a batch system for a job execution. We will present our experience with configuring and running Torque batch system in a dual stack environment. We also discuss the steps needed to run VO specific jobs in our IPv6 testbed.

The in vivo antitumor effects of type I-interferon against hepatocellular carcinoma: the suppression of tumor cell growth and angiogenesis.

PubMed

Enomoto, Hirayuki; Tao, Lihua; Eguchi, Ryoji; Sato, Ayuko; Honda, Masao; Kaneko, Shuichi; Iwata, Yoshinori; Nishikawa, Hiroki; Imanishi, Hiroyasu; Iijima, Hiroko; Tsujimura, Tohru; Nishiguchi, Shuhei

2017-09-22

Type I-interferon (IFN) is considered to exert antitumor effects through the inhibition of cancer cell proliferation and angiogenesis. Based on the species-specific biological activity of IFN, we evaluated each antitumor mechanism separately. We further examined the antitumor effects of type I-IFN combined with sorafenib. Human IFN (hIFN) significantly inhibited the proliferation of human hepatocellular carcinoma (HCC) Hep3B cells and the tube formation of human umbilical vein endothelial cells (HUVECs) in vitro. Although mouse IFN (mIFN) did not inhibit the proliferation of Hep3B cells in vitro, mIFN, as well as hIFN, showed significant antitumor effects in mouse Hep3B cell-xenograft model. Furthermore, mIFN treatment amplified the antitumor effects of sorafenib in vivo with the suppression of angiogenesis. The DNA chip analysis showed that the mIFN treatment promoted the antitumor signal pathways of sorafenib, including anti-angiogenic effects. Unlike the effects observed in in vitro experiments, mIFN showed an antitumor effect in the mouse Hep3B cell-xenograft model, suggesting a role of the anti-angiogenic activity in the in vivo tumoricidal effects of type I-IFN. In addition, our findings suggested the clinical utility of combination therapy with type І-IFN and sorafenib for HCC.

HEP Computing Tools, Grid and Supercomputers for Genome Sequencing Studies

NASA Astrophysics Data System (ADS)

De, K.; Klimentov, A.; Maeno, T.; Mashinistov, R.; Novikov, A.; Poyda, A.; Tertychnyy, I.; Wenaus, T.

2017-10-01

PanDA - Production and Distributed Analysis Workload Management System has been developed to address ATLAS experiment at LHC data processing and analysis challenges. Recently PanDA has been extended to run HEP scientific applications on Leadership Class Facilities and supercomputers. The success of the projects to use PanDA beyond HEP and Grid has drawn attention from other compute intensive sciences such as bioinformatics. Recent advances of Next Generation Genome Sequencing (NGS) technology led to increasing streams of sequencing data that need to be processed, analysed and made available for bioinformaticians worldwide. Analysis of genomes sequencing data using popular software pipeline PALEOMIX can take a month even running it on the powerful computer resource. In this paper we will describe the adaptation the PALEOMIX pipeline to run it on a distributed computing environment powered by PanDA. To run pipeline we split input files into chunks which are run separately on different nodes as separate inputs for PALEOMIX and finally merge output file, it is very similar to what it done by ATLAS to process and to simulate data. We dramatically decreased the total walltime because of jobs (re)submission automation and brokering within PanDA. Using software tools developed initially for HEP and Grid can reduce payload execution time for Mammoths DNA samples from weeks to days.

Low doses of TiO2-polyethylene glycol nanoparticles stimulate proliferation of hepatocyte cells

NASA Astrophysics Data System (ADS)

Sun, Qingqing; Kanehira, Koki; Taniguchi, Akiyoshi

2016-01-01

This paper describes the effect of low concentrations of 100 nm polyethylene glycol-modified TiO2 nanoparticles (TiO2-PEG NPs) on HepG2 hepatocellular carcinoma cells. Proliferation of HepG2 cells increased significantly when the cells were exposed to low doses (<100 μg ml-1) of TiO2-PEG NPs. These results were further confirmed by cell counting experiments and cell cycle assays. Cellular uptake assays were performed to determine why HepG2 cells proliferate with low-dose exposure to TiO2-PEG NPs. The results showed that exposure to lower doses of NPs led to less cellular uptake, which in turn decreased cytotoxicity. We therefore hypothesized that TiO2-PEG NPs could affect the activity of hepatocyte growth factor receptors (HGFRs), which bind to hepatocyte growth factor and stimulate cell proliferation. The localization of HGFRs on the surface of the cell membrane was detected via immunofluorescence staining and confocal microscopy. The results showed that HGFRs aggregate after exposure to TiO2-PEG NPs. In conclusion, our results indicate that TiO2-PEG NPs have the potential to promote proliferation of HepG2 cells through HGFR aggregation and suggest that NPs not only exhibit cytotoxicity but also affect cellular responses.

Enhanced reactive oxygen species overexpression by CuO nanoparticles in poorly differentiated hepatocellular carcinoma cells

NASA Astrophysics Data System (ADS)

Kung, Mei-Lang; Hsieh, Shu-Ling; Wu, Chih-Chung; Chu, Tian-Huei; Lin, Yu-Chun; Yeh, Bi-Wen; Hsieh, Shuchen

2015-01-01

Copper oxide nanoparticles (CuO NPs) are known to exhibit toxic effects on a variety of cell types and organs. To determine the oxidative impact of CuO NPs on hepatocellular carcinoma (HCC) cells, well-differentiated (HepG2) and poorly differentiated (SK-Hep-1) cells were exposed to CuO NPs. Cell viability assay showed that the median inhibition concentration (IC50) for SK-Hep-1 and HepG2 cells was 25 μg ml-1 and 85 μg ml-1, respectively. Cellular fluorescence intensity using DCFH-DA staining analysis revealed significant intracellular reactive oxygen species (ROS) generation of up to 242% in SK-Hep-1 cells, compared with 86% in HepG2 cells. HPLC analysis demonstrated that a CuO NP treatment caused cellular GSH depletion of 58% and a GSH/GSSG ratio decrease to ~0.1 in SK-Hep-1 cells. The oxidative stress caused by enhanced superoxide anion production was observed in both HepG2 (146%) and SK-Hep-1 (192%) cells. The Griess assay verified that CuO NPs induced NO production (170%) in SK-Hep-1 cells. Comet assay and western blot further demonstrated that CuO NPs induced severe DNA strand breakage (70%) in SK-Hep-1 cells and caused DNA damage via increased γ-H2AX levels. These results suggest that well-differentiated HepG2 cells possess a robust antioxidant defense system against CuO NP-induced ROS stress and exhibit more tolerance to oxidative stress. Conversely, poorly differentiated SK-Hep-1 cells exhibited a deregulated antioxidant defense system that allowed accumulation of CuO NP-induced ROS and resulted in severe cytotoxicity.Copper oxide nanoparticles (CuO NPs) are known to exhibit toxic effects on a variety of cell types and organs. To determine the oxidative impact of CuO NPs on hepatocellular carcinoma (HCC) cells, well-differentiated (HepG2) and poorly differentiated (SK-Hep-1) cells were exposed to CuO NPs. Cell viability assay showed that the median inhibition concentration (IC50) for SK-Hep-1 and HepG2 cells was 25 μg ml-1 and 85 μg ml-1, respectively. Cellular fluorescence intensity using DCFH-DA staining analysis revealed significant intracellular reactive oxygen species (ROS) generation of up to 242% in SK-Hep-1 cells, compared with 86% in HepG2 cells. HPLC analysis demonstrated that a CuO NP treatment caused cellular GSH depletion of 58% and a GSH/GSSG ratio decrease to ~0.1 in SK-Hep-1 cells. The oxidative stress caused by enhanced superoxide anion production was observed in both HepG2 (146%) and SK-Hep-1 (192%) cells. The Griess assay verified that CuO NPs induced NO production (170%) in SK-Hep-1 cells. Comet assay and western blot further demonstrated that CuO NPs induced severe DNA strand breakage (70%) in SK-Hep-1 cells and caused DNA damage via increased γ-H2AX levels. These results suggest that well-differentiated HepG2 cells possess a robust antioxidant defense system against CuO NP-induced ROS stress and exhibit more tolerance to oxidative stress. Conversely, poorly differentiated SK-Hep-1 cells exhibited a deregulated antioxidant defense system that allowed accumulation of CuO NP-induced ROS and resulted in severe cytotoxicity. Electronic supplementary information (ESI) available. See DOI: 10.1039/c4nr05843g

Effect of Home Exercise Program Performance in Patients with Osteoarthritis of the Knee or the Spine on the Visual Analog Scale after Discharge from Physical Therapy

ERIC Educational Resources Information Center

Chen, Hamilton; Onishi, Kentaro

2012-01-01

The aim of our study was to assess the effect of the frequency of home exercise program (HEP) performance on pain [10-point visual analog scale (VAS)] in patients with osteoarthritis of the spine or knee after more than 6 months discharge from physical therapy (PT). We performed a retrospective chart review of 48 adult patients with a clinical…

Crambescin C1 Exerts a Cytoprotective Effect on HepG2 Cells through Metallothionein Induction

PubMed Central

Roel, María; Rubiolo, Juan A.; Ternon, Eva; Thomas, Olivier P.; Vieytes, Mercedes R.; Botana, Luis M.

2015-01-01

The Mediterranean marine sponge Crambe crambe is the source of two families of guanidine alkaloids known as crambescins and crambescidins. Some of the biological effects of crambescidins have been previously reported while crambescins have undergone little study. Taking this into account, we performed comparative transcriptome analysis to examine the effect of crambescin-C1 (CC1) on human tumor hepatocarcinoma cells HepG2 followed by validation experiments to confirm its predicted biological activities. We report herein that, while crambescin-A1 has a minor effect on these cells, CC1 protects them against oxidative injury by means of metallothionein induction even at low concentrations. Additionally, at high doses, CC1 arrests the HepG2 cell cycle in G0/G1 and thus inhibits tumor cell proliferation. The findings presented here provide the first detailed approach regarding the different effects of crambescins on tumor cells and provide a basis for future studies on other possible cellular mechanisms related to these bioactivities. PMID:26225985

Applying deep neural networks to HEP job classification

NASA Astrophysics Data System (ADS)

Wang, L.; Shi, J.; Yan, X.

2015-12-01

The cluster of IHEP computing center is a middle-sized computing system which provides 10 thousands CPU cores, 5 PB disk storage, and 40 GB/s IO throughput. Its 1000+ users come from a variety of HEP experiments. In such a system, job classification is an indispensable task. Although experienced administrator can classify a HEP job by its IO pattern, it is unpractical to classify millions of jobs manually. We present how to solve this problem with deep neural networks in a supervised learning way. Firstly, we built a training data set of 320K samples by an IO pattern collection agent and a semi-automatic process of sample labelling. Then we implemented and trained DNNs models with Torch. During the process of model training, several meta-parameters was tuned with cross-validations. Test results show that a 5- hidden-layer DNNs model achieves 96% precision on the classification task. By comparison, it outperforms a linear model by 8% precision.

Argonne HEP Lunch Seminars

Science.gov Websites

reactor neutrino experiment July 29, 2008 August 5, 2008 Adam Clark (Rockhurst University) and Teng Jian August 12, 2008 Peter de Maagt THz Technology August 19, 2008 Razmick Mirzoyan Recent Developments on Low

Argonne Physics Division - Theory Group

Science.gov Websites

Gamma-ray Telescopes October 7 Ken Nollett (PHY) Discussion of the Astro2010 Astronomy and Astrophysics (HEP) Gamma-ray astronomy and VERITAS July 2 Francesca Primas (European Southern Observatory ) Recent Results in TeV Gamma-Ray Astronomy December 1 Kaori Otsuki (U of C) Astrophysical site for the r

[Biological characteristics of a chimeric rabies virus expressing canine parvovirus VP2 protein].

PubMed

Niu, Xue-Feng; Liu, Xiao-Hui; Sun, Zhao-Jin; Shi, He-He; Chen, Jing; Jiang, Bido; Sun, Jing-Chen; Guo, Xiao-Feng

2009-09-01

To obtain a bivalence vaccine against canine rabies virus and canine parvovirus, a chimeric rabies virus expressing canine parvovirus VP2 protein was generated by the technique of reverse genetics. It was shown that the chimeric virus designated as HEP-Flury (VP2) grew well on BHK-21 cells and the VP2 gene could still be stably expressed after ten passages on BHK-21 cells. Experiments on the mice immunized with the chimeric virus HEP-Flury (VP2) demonstrated that specific antibodies against rabies virus and canine parvovirus were induced in immunized mice after vaccination with the live chimeric virus.

Opportunities and choice in a new vector era

NASA Astrophysics Data System (ADS)

Nowak, A.

2014-06-01

This work discusses the significant changes in computing landscape related to the progression of Moore's Law, and the implications on scientific computing. Particular attention is devoted to the High Energy Physics domain (HEP), which has always made good use of threading, but levels of parallelism closer to the hardware were often left underutilized. Findings of the CERN openlab Platform Competence Center are reported in the context of expanding "performance dimensions", and especially the resurgence of vectors. These suggest that data oriented designs are feasible in HEP and have considerable potential for performance improvements on multiple levels, but will rarely trump algorithmic enhancements. Finally, an analysis of upcoming hardware and software technologies identifies heterogeneity as a major challenge for software, which will require more emphasis on scalable, efficient design.

Structure characterization of a novel polysaccharide from Hericium erinaceus fruiting bodies and its immunomodulatory activities.

PubMed

Wu, Fangfang; Zhou, Chunhui; Zhou, Dandan; Ou, Shiyi; Zhang, Xiaoai; Huang, Huihua

2018-01-24

A novel polysaccharide fraction (HEP-S) was extracted and isolated from the fruiting bodies of Hericium erinaceus. Structural characterization revealed that HEP-S had an average molecular weight of 1.83 × 10 4 Da and consisted of rhamnose, fucose, mannose, glucose and galactose at a molar ratio of 1.47 : 0.93 : 1.36 : 8.68 : 4.08. Periodate oxidation-Smith degradation and NMR analysis showed that the main linkage types of HEP-S were composed of (1→)-α-d-Glc, (1→3,4)-α-d-Glc, (1→6)-α-d-Gal, (1→3,4)-β-d-Man, (1→3,6)-α-Rha and (1→2)-β-l-Fuc. The immunomodulatory assay indicated that HEP-S could significantly enhance the pinocytic and phagocytic capacity and promote the secretion of nitric oxide and pro-inflammatory cytokines by activating the corresponding mRNA and protein expression in RAW 264.7 cells involving a toll-like receptor 2 membrane receptor. Besides, HEP-S was also found to improve the adaptive immune function by enhancing T and B lymphocyte proliferation and increasing the interleukin-2, interleukin-4 and interferon-γ secretion in spleen lymphocytes. These results suggested that HEP-S could be used as a potential immunoregulatory agent in functional foods.

The GeantV project: Preparing the future of simulation

DOE PAGES

Amadio, G.; J. Apostolakis; Bandieramonte, M.; ...

2015-12-23

Detector simulation is consuming at least half of the HEP computing cycles, and even so, experiments have to take hard decisions on what to simulate, as their needs greatly surpass the availability of computing resources. New experiments still in the design phase such as FCC, CLIC and ILC as well as upgraded versions of the existing LHC detectors will push further the simulation requirements. Since the increase in computing resources is not likely to keep pace with our needs, it is therefore necessary to explore innovative ways of speeding up simulation in order to sustain the progress of High Energymore » Physics. The GeantV project aims at developing a high performance detector simulation system integrating fast and full simulation that can be ported on different computing architectures, including CPU accelerators. After more than two years of R&D the project has produced a prototype capable of transporting particles in complex geometries exploiting micro-parallelism, SIMD and multithreading. Portability is obtained via C++ template techniques that allow the development of machine- independent computational kernels. Furthermore, a set of tables derived from Geant4 for cross sections and final states provides a realistic shower development and, having been ported into a Geant4 physics list, can be used as a basis for a direct performance comparison.« less

Grid Computing Environment using a Beowulf Cluster

NASA Astrophysics Data System (ADS)

Alanis, Fransisco; Mahmood, Akhtar

2003-10-01

Custom-made Beowulf clusters using PCs are currently replacing expensive supercomputers to carry out complex scientific computations. At the University of Texas - Pan American, we built a 8 Gflops Beowulf Cluster for doing HEP research using RedHat Linux 7.3 and the LAM-MPI middleware. We will describe how we built and configured our Cluster, which we have named the Sphinx Beowulf Cluster. We will describe the results of our cluster benchmark studies and the run-time plots of several parallel application codes that were compiled in C on the cluster using the LAM-XMPI graphics user environment. We will demonstrate a "simple" prototype grid environment, where we will submit and run parallel jobs remotely across multiple cluster nodes over the internet from the presentation room at Texas Tech. University. The Sphinx Beowulf Cluster will be used for monte-carlo grid test-bed studies for the LHC-ATLAS high energy physics experiment. Grid is a new IT concept for the next generation of the "Super Internet" for high-performance computing. The Grid will allow scientist worldwide to view and analyze huge amounts of data flowing from the large-scale experiments in High Energy Physics. The Grid is expected to bring together geographically and organizationally dispersed computational resources, such as CPUs, storage systems, communication systems, and data sources.

Impact of a 1-year lifestyle modification program on cholesterol efflux capacities in men with abdominal obesity and dyslipidemia.

PubMed

Boyer, Marjorie; Mitchell, Patricia L; Poirier, Dr Paul; Alméras, Natalie; Tremblay, Angelo; Bergeron, Jean; Despres, Jean-Pierre; Arsenault, Benoit J

2018-06-05

Cholesterol efflux capacities (CECs) are negatively associated with cardiovascular disease risk, irrespective of plasma high-density lipoprotein (HDL) cholesterol levels. Whether interventions targeting lifestyle improve HDL-CECs is unknown. Our objective was to determine whether improving dietary quality and increasing physical activity levels improves HDL-CECs in abdominally obese men with dyslipidemia. Our study sample included men (488.5 years) with an elevated waist circumference ({greater than or equal to}90 cm) associated with dyslipidemia (triglycerides {greater than or equal to}1.69 and/or HDL cholesterol <1.03 mmol/l); 113 men completed a 1-year intervention, consisting of a healthy eating and physical activity/exercise program and 32 were included in a control group. An oral lipid tolerance test (OLTT) was performed in a subsample of 28 men who completed the intervention and blood was collected every 2 hours during 8 hours. HDL-CECs were measured using 3 H cholesterol labeled J774 macrophages and HepG2 hepatocytes. The lifestyle modification program led to an overall improvement in the cardiometabolic risk profile, increases in J774-HDL-CEC by 14.1% (+0.881.09%, p<0.0001), HepG2-HDL-CEC by 3.4% (+0.170.75%, p=0.01), HDL-C and apolipoprotein A-1 levels (13.5%, p<0.0001 and 14.9%, p<0.0001, respectively). J774-HDL-CECs and HepG2-HDL-CECs did not change in the control group. The best predictor for changes in HDL-CEC was Apo A1 level. The lifestyle modification program also improved HDL-CECs response in postprandial lipemia during an OLTT. HDL-CEC did not change during the OLTT. Our results suggest that increasing physical activity levels and improving diet quality can have a positive impact on both HDL quantity and quality in abdominally obese men with dyslipidemia.

Quantum Sensing for High Energy Physics

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

van Bibber, Karl; Boshier, Malcolm; Demarteau, Marcel

The Coordinating Panel for Advanced Detectors (CPAD) of the APS Division of Particles and Fields organized a first workshop on Quantum Sensing for High Energy Physics (HEP) in early December 2017 at Argonne National Laboratory. Participants from universities and national labs were drawn from the intersecting fields of Quantum Information Science (QIS), high energy physics, atomic, molecular and optical physics, condensed matter physics, nuclear physics and materials science. Quantum-enabled science and technology has seen rapid technical advances and growing national interest and investments over the last few years. The goal of the workshop was to bring the various communities togethermore » to investigate pathways to integrate the expertise of these two disciplines to accelerate the mutual advancement of scientific progress.« less

Mind-body therapy via videoconferencing in patients with neurofibromatosis: An RCT.

PubMed

Vranceanu, Ana-Maria; Riklin, Eric; Merker, Vanessa L; Macklin, Eric A; Park, Elyse R; Plotkin, Scott R

2016-08-23

To test, within a single-blind randomized controlled trial, the feasibility, acceptability, efficacy, and durability of a mind-body program (the Relaxation Response Resiliency Program for neurofibromatosis [3RP-NF]) vs an attention placebo control (Health Enhancement Program for NF [HEP-NF]), both delivered via group videoconferencing. Sixty-three patients completed baseline assessments and were randomized. Primary outcomes were physical health and psychological quality of life (QoL), measured by the WHOQOL-BREF (World Health Organization QoL abbreviated instrument). Secondary outcomes were social relations and environment QoL, depression, anxiety, pain intensity, and pain interference. Sixty-three participants completed the intervention (100%) and 52 the 6-month follow-up (82.5%). Acceptability was 4.1 (5-point scale). Patients in the 3RP-NF showed greater improvement in physical health QoL (7.69; 95% confidence interval [CI]: 0.29-15.10; p = 0.040), psychological QoL (5.57; 95% CI: 0.17-11.34; p = 0.056), social relations QoL (10.95; 95% CI: 1.57-20.31; p = 0.021), environment QoL (8.02; 95% CI: 2.57-13.48; p = 0.005), and anxiety (-2.32; 95% CI: -3.96 to 0.69; p = 0.006) compared to those in HEP-NF, and gains were maintained at follow-up. Patients in the 3RP-NF did not improve more than those in HEP-NF on depression, with both groups showing improvement. Patients in the 3RP-NF with baseline pain ≥5 of 10 showed improvement in pain intensity from baseline to posttest (1.30; 95% CI: -2.26 to -0.34; p = 0.009) with effects maintained at follow-up; this improvement was not greater than that in HEP-NF. There were more treatment responders in the 3RP-NF group (p < 0.05). The 3RP-NF delivered via videoconferencing was highly feasible and accepted by patients, and resulted in sustained improvement in QoL. This study provides Class II evidence that for patients with NF, a mind-body program is superior to an attention placebo control in improving QoL. © 2016 American Academy of Neurology.

An untargeted multi-technique metabolomics approach to studying intracellular metabolites of HepG2 cells exposed to 2,3,7,8-tetrachlorodibenzo-p-dioxin.

PubMed

Ruiz-Aracama, Ainhoa; Peijnenburg, Ad; Kleinjans, Jos; Jennen, Danyel; van Delft, Joost; Hellfrisch, Caroline; Lommen, Arjen

2011-05-20

In vitro cell systems together with omics methods represent promising alternatives to conventional animal models for toxicity testing. Transcriptomic and proteomic approaches have been widely applied in vitro but relatively few studies have used metabolomics. Therefore, the goal of the present study was to develop an untargeted methodology for performing reproducible metabolomics on in vitro systems. The human liver cell line HepG2, and the well-known hepatotoxic and non-genotoxic carcinogen 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), were used as the in vitro model system and model toxicant, respectively. The study focused on the analysis of intracellular metabolites using NMR, LC-MS and GC-MS, with emphasis on the reproducibility and repeatability of the data. State of the art pre-processing and alignment tools and multivariate statistics were used to detect significantly altered levels of metabolites after exposing HepG2 cells to TCDD. Several metabolites identified using databases, literature and LC-nanomate-Orbitrap analysis were affected by the treatment. The observed changes in metabolite levels are discussed in relation to the reported effects of TCDD. Untargeted profiling of the polar and apolar metabolites of in vitro cultured HepG2 cells is a valid approach to studying the effects of TCDD on the cell metabolome. The approach described in this research demonstrates that highly reproducible experiments and correct normalization of the datasets are essential for obtaining reliable results. The effects of TCDD on HepG2 cells reported herein are in agreement with previous studies and serve to validate the procedures used in the present work.

ABCC6 knockdown in HepG2 cells induces a senescent-like cell phenotype.

PubMed

Miglionico, Rocchina; Ostuni, Angela; Armentano, Maria Francesca; Milella, Luigi; Crescenzi, Elvira; Carmosino, Monica; Bisaccia, Faustino

2017-01-01

Pseudoxanthoma elasticum (PXE) is characterized by progressive ectopic mineralization of elastic fibers in dermal, ocular and vascular tissues. No effective treatment exists. It is caused by inactivating mutations in the gene encoding for the ATP-binding cassette, sub-family C member 6 transporter (ABCC6), which is mainly expressed in the liver. The ABCC6 substrate (s) and the PXE pathomechanism remain unknown. Recent studies have shown that overexpression of ABCC6 in HEK293 cells results in efflux of ATP, which is rapidly converted into nucleoside monophosphates and pyrophosphate (PPi). Since the latter inhibits mineralization, it was proposed that the absence of circulating PPi in PXE patients results in the characteristic ectopic mineralization. These studies also demonstrated that the presence of ABCC6 modifies cell secretory activity and suggested that ABCC6 can change the cell phenotype. Stable ABCC6 knockdown HepG2 clones were generated using small hairpin RNA (shRNA) technology. The intracellular glutathione and ROS levels were determined. Experiments using cell cycle analysis, real-time PCR and western blot were performed on genes involved in the senescence phenotype. To shed light on the physiological role of ABCC6, we focused on the phenotype of HepG2 cells that lack ABCC6 activity. Interestingly, we found that ABCC6 knockdown HepG2 cells show: 1) intracellular reductive stress; 2) cell cycle arrest in G1 phase; 3) upregulation of p21 Cip p53 independent; and 4) downregulation of lamin A/C. These findings show that the absence of ABCC6 profoundly changes the HepG2 phenotype, suggesting that the PXE syndrome is a complex metabolic disease that is not exclusively related to the absence of pyrophosphate in the bloodstream.

Feasibility and Biocompatibility of 3D-Printed Photopolymerized and Laser Sintered Polymers for Neuronal, Myogenic, and Hepatic Cell Types.

PubMed

Rimington, Rowan P; Capel, Andrew J; Player, Darren J; Bibb, Richard J; Christie, Steven D R; Lewis, Mark P

2018-06-13

The integration of additive manufacturing (AM) technology within biological systems holds significant potential, specifically when refining the methods utilized for the creation of in vitro models. Therefore, examination of cellular interaction with the physical/physicochemical properties of 3D-printed polymers is critically important. In this work, skeletal muscle (C 2 C 12 ), neuronal (SH-SY5Y) and hepatic (HepG2) cell lines are utilized to ascertain critical evidence of cellular behavior in response to 3D-printed candidate polymers: Clear-FL (stereolithography, SL), PA-12 (laser sintering, LS), and VeroClear (PolyJet). This research outlines initial critical evidence for a framework of polymer/AM process selection when 3D printing biologically receptive scaffolds, derived from industry standard, commercially available AM instrumentation. C 2 C 12 , SH-SY5Y, and HepG2 cells favor LS polymer PA-12 for applications in which cellular adherence is necessitated. However, cell type specific responses are evident when cultured in the chemical leachate of photopolymers (Clear-FL and VeroClear). With the increasing prevalence of 3D-printed biointerfaces, the development of rigorous cell type specific biocompatibility data is imperative. Supplementing the currently limited database of functional 3D-printed biomaterials affords the opportunity for experiment-specific AM process and polymer selection, dependent on biological application and intricacy of design features required. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

UPR/Mayaguez High Energy Physics

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

Mendez, Hector

This year the University of Puerto Rico at Mayaguez (UPRM) High Energy Physics (HEP) group continued with the ongoing research program outlined in the grant proposal. The program is centered on the Compact Muon Solenoid (CMS) experiment at the proton-proton (pp) collisions at the Large Hadron Collider (LHC) at CERN in Geneva, Switzerland. The main research focus is on data analysis and on the preparation for the High Luminosity (HL) LHC or experiment detector upgrade. The physics data analysis included Higgs Doublet Search and measurement of the (1) Λ 0 b branching fraction, (2) B meson mass, and (3) hyperonmore » θ - b lifetime. The detector upgrade included work on the preparations for the Forward Pixel (FPIX) detector Silicon Sensor Testing in a production run at Fermilab. In addition, the group has taken responsibilities on the Software Release through our former research associate Dr. Eric Brownson who acted until last December as a Level Two Offline Manager for the CMS Upgrade. In support of the CMS data analysis activities carried out locally, the UPRM group has built and maintains an excellent Tier3 analysis center in Mayaguez. This allowed us to analyze large data samples and to continue the development of algorithms for the upgrade tracking robustness we started several years ago, and we plan to resume in the near future. This project involves computer simulation of the radiation damage to be suffered at the higher luminosities of the upgraded LHC. This year we continued to serve as a source of outstanding students for the field of high energy physics. Three of our graduate students finished their MS work in May, 2014, Their theses research were on data analysis of heavy quark b-physics. All of them are currently enrolled at Ph.D. physics program across the nation. One of them (Hector Moreno) at New Mexico University (Hector Moreno), one at University of New Hampshire (Sandra Santiesteban) and one at University of Puerto Rico-Rio Piedras (Carlos Malca). The students H. Moreno and C. Malca has been directly supervised by Dr. Mendez and S. Santiesteban supervised by Dr. Ramirez. During the last 13 years, our group have graduated 23 MS students on experimental High Energy Physics data analysis and applied hardware techniques. Most of the students have been supported by DOE grants, included this grant. Since 2001, Dr. Mendez have directly supervised eleven students, Dr. Ramirez three students and the former PI (Dr. Lopez) nine students. These theses work are fully documented in the group web page (http://charma.uprm.edu). The High Energy Physics group at Mayaguez is small and presently consists of three Physics faculty members, the Senior Investigators Dr. Hector Mendez (Professor) and Dr. Juan Eduardo Ramirez (Professor), and Dr. Sudhir Malik who was just hired in July 2014. Dr. Ramirez is in charge of the UPRM Tier-3 computing and will be building the network bandwidth infrastructure for the campus, while Dr. Mendez will continues his effort in finishing the heavy quark physics data analysis and moving to work on SUSY analysis for the 2015 data. Our last grant application in 2012 was awarded only for 2013-2014. As a result our postdoc position was lost last month of March. Since then, we have hired Dr. Malik as a new faculty in order to reinforce the group and to continue our efforts with the CMS experiment. Our plan is to hire another junior faculty in the next two years to strengthen the HEP group even further. Dr. Mendez continues with QuarkNet activities involving an ever larger group of high school physics teachers from all around Puerto Rico.« less

HepG2 human hepatocarcinomas cells sensitization by endogenous porphyrins

NASA Astrophysics Data System (ADS)

Vonarx-Coinsmann, Veronique; Foultier, Marie-Therese; de Brito, Leonor X.; Morlet, Laurent; Patrice, Thierry

1995-03-01

We assessed the ability of the human hepatocarcinoma cell line HepG2 to synthesize PpIX in vitro from exogenous ALA and analyzed ALA-induced toxicity and phototoxicity on this cell line. ALA induced a slight dose-dependent dark toxicity, with 79 and 66% cell survival respectively for ALA 50 and 100 mg/ml after 3-h incubation. Whereas the same treatment followed by laser irradiation (l equals 632 nm, 25 J/sq cm) induced dose-dependent phototoxicity, with 54 and 19% cell survival 24 h after PDT. Whatever the incubation time with ALA, a 3-h delay before light exposure was found optimal to reach a maximal phototoxicity. Photoproducts induced by porphyrin light irradiation absorbed light in the red spectral region at longer wavelengths than did the original porphyrins. The possible enhancement of PDT effects after ALA HepG2 cell incubation was investigated by irradiating cells successively with red light (l equals 632 nm) and light (l equals 650 nm). Total fluence was kept constant at 25 J/sq cm. Phototoxicity was lower when cells were irradiated for increased periods of l equals 650 nm light than with l equals 632 nm light alone. Any photoproducts involved had either a short life or were poorly photoreactive. HepG2 cells, synthesizing enzymes and precursors of endogenous porphyrin synthesis, represent a good in vitro model for experiments using ALA-PpIX-PDT.

Implementing the birth dose of hepatitis B vaccine in rural Indonesia.

PubMed

Creati, Mick; Saleh, Asmaniar; Ruff, Tilman A; Stewart, Tony; Otto, Bradley; Sutanto, Agustinus; Clements, C John

2007-08-10

Reaching mothers and their newborn infants around the time of birth with adequate health services has long been a difficult problem in developing countries. In parallel, similar problems have arisen in attempting to deliver hepatitis B (HepB) vaccine to infants born at home in many countries where mother-to-infant transmission is common. It is logical, and supported by experience in Indonesia, to find a combined solution for both problems. The World Health Organization (WHO) recommends that a timely birth dose of HepB vaccine be given, particularly in areas of high vertical transmission of hepatitis B virus (HBV). This can be achieved relatively easily in situations where almost all births occur in health facilities. But where a significant proportion of births occur at home and without birth attendants able to give injections, this is much more difficult. Barriers to the timely administration of the birth dose of HepB vaccine include weakness in policy development and implementation, difficulties in reliably supplying potent vaccine to community level, limited transport, poor communication, limited cold chain capacity, lack of effective training, and lack of a clear delineation of responsibility between health care professionals. Demonstration projects, such as those in Indonesia, suggest that there are significant opportunities to improve the timely delivery of HepB vaccine birth dose in existing maternal and child health programmes where health workers are trained to provide home delivery care.

Low doses of TiO2-polyethylene glycol nanoparticles stimulate proliferation of hepatocyte cells

PubMed Central

Sun, Qingqing; Kanehira, Koki; Taniguchi, Akiyoshi

2016-01-01

Abstract This paper describes the effect of low concentrations of 100 nm polyethylene glycol-modified TiO2 nanoparticles (TiO2-PEG NPs) on HepG2 hepatocellular carcinoma cells. Proliferation of HepG2 cells increased significantly when the cells were exposed to low doses (<100 μg ml–1) of TiO2-PEG NPs. These results were further confirmed by cell counting experiments and cell cycle assays. Cellular uptake assays were performed to determine why HepG2 cells proliferate with low-dose exposure to TiO2-PEG NPs. The results showed that exposure to lower doses of NPs led to less cellular uptake, which in turn decreased cytotoxicity. We therefore hypothesized that TiO2-PEG NPs could affect the activity of hepatocyte growth factor receptors (HGFRs), which bind to hepatocyte growth factor and stimulate cell proliferation. The localization of HGFRs on the surface of the cell membrane was detected via immunofluorescence staining and confocal microscopy. The results showed that HGFRs aggregate after exposure to TiO2-PEG NPs. In conclusion, our results indicate that TiO2-PEG NPs have the potential to promote proliferation of HepG2 cells through HGFR aggregation and suggest that NPs not only exhibit cytotoxicity but also affect cellular responses. PMID:27877913

Argonne/HEP Dark Energy Survey Group

Science.gov Websites

Kuehn U of C Summer School at Yerkes Observatory 2012-07 Kuehn Lemont High 2012-02 Kuehn Canada-America -Mexico Physics Grad Student Conference 2012-02 Bernstein ANL QuarkNet 2011-03 Kuhlmann Rockford High Kids2Work 2010-04 Kuhlmann Rockford High School 2010-02 Bernstein ANL QuarkNet 2010-02 Kuhlmann Rockford

Impact of Duality Violations on Spectral Sum Rule analyses

NASA Astrophysics Data System (ADS)

Catà, Oscar

2007-02-01

Recent sum rule analyses on the two-point correlator have led to significant discrepancies in the values found for the OPE condensates, most dramatically in the dimension eight condensate and to a lesser extent in the dimension six one [R. Barate et al., ALEPH Collaboration, Eur. Phys. J. C 4 (1998) 409; K. Ackerstaff et al., OPAL Collaboration, Eur. Phys. J. C 7 (1999) 571, arXiv:hep-ex/9808019; S. Peris, B. Phily and E. de Rafael, Phys. Rev. Lett. 86 (2001) 14, arXiv:hep-ph/0007338; S. Friot, D. Greynat and E. de Rafael, JHEP 0410 (2004) 043, arXiv:hep-ph/0408281; M. Davier, L. Girlanda, A. Hocker and J. Stern, Phys. Rev. D 58 (1998) 096014, arXiv:hep-ph/9802447; B.L. Ioffe and K.N. Zyablyuk, Nucl. Phys. A 687 (2001) 437, arXiv:hep-ph/0010089. K.N. Zyablyuk, Eur. Phys. J. C 38 (2004) 215, arXiv:hep-ph/0404230; J. Bijnens, E. Gamiz and J. Prades, JHEP 0110 (2001) 009, arXiv:hep-ph/0108240; C.A. Dominguez and K. Schilcher, Phys. Lett. B 581 (2004) 193, arXiv:hep-ph/0309285; J. Rojo and J. I. Latorre, JHEP 0401 (2004) 055, arXiv:hep-ph/0401047; V. Cirigliano, E. Golowich and K. Maltman, Phys. Rev. D 68 (2003) 054013, arXiv:hep-ph/0305118; S. Ciulli, C. Sebu, K. Schilcher and H. Spiesberger, Phys. Lett. B 595 (2004) 359, arXiv:hep-ph/0312212. S. Narison, arXiv:hep-ph/0412152]. Precise knowledge of these condensates is of relevance in kaon decays [M. Knecht, S. Peris and E. de Rafael, Phys. Lett. B 457 (1999) 227, arXiv:hep-ph/9812471; J.F. Donoghue and E. Golowich, Phys. Lett. B 478 (2000) 172, arXiv:hep-ph/9911309; M. Knecht, S. Peris and E. de Rafael, Phys. Lett. B 508 (2001) 117, arXiv:hep-ph/0102017] and therefore it seems mandatory to assess the actual impact of what is commonly neglected in spectral sum rules, most prominently the issue of duality violations. We will explicitly compute them in a toy model and show that they are a priori non-negligible.

Volunteer Clouds and Citizen Cyberscience for LHC Physics

NASA Astrophysics Data System (ADS)

Aguado Sanchez, Carlos; Blomer, Jakob; Buncic, Predrag; Chen, Gang; Ellis, John; Garcia Quintas, David; Harutyunyan, Artem; Grey, Francois; Lombrana Gonzalez, Daniel; Marquina, Miguel; Mato, Pere; Rantala, Jarno; Schulz, Holger; Segal, Ben; Sharma, Archana; Skands, Peter; Weir, David; Wu, Jie; Wu, Wenjing; Yadav, Rohit

2011-12-01

Computing for the LHC, and for HEP more generally, is traditionally viewed as requiring specialized infrastructure and software environments, and therefore not compatible with the recent trend in "volunteer computing", where volunteers supply free processing time on ordinary PCs and laptops via standard Internet connections. In this paper, we demonstrate that with the use of virtual machine technology, at least some standard LHC computing tasks can be tackled with volunteer computing resources. Specifically, by presenting volunteer computing resources to HEP scientists as a "volunteer cloud", essentially identical to a Grid or dedicated cluster from a job submission perspective, LHC simulations can be processed effectively. This article outlines both the technical steps required for such a solution and the implications for LHC computing as well as for LHC public outreach and for participation by scientists from developing regions in LHC research.

Future computing platforms for science in a power constrained era

DOE PAGES

Abdurachmanov, David; Elmer, Peter; Eulisse, Giulio; ...

2015-12-23

Power consumption will be a key constraint on the future growth of Distributed High Throughput Computing (DHTC) as used by High Energy Physics (HEP). This makes performance-per-watt a crucial metric for selecting cost-efficient computing solutions. For this paper, we have done a wide survey of current and emerging architectures becoming available on the market including x86-64 variants, ARMv7 32-bit, ARMv8 64-bit, Many-Core and GPU solutions, as well as newer System-on-Chip (SoC) solutions. We compare performance and energy efficiency using an evolving set of standardized HEP-related benchmarks and power measurement techniques we have been developing. In conclusion, we evaluate the potentialmore » for use of such computing solutions in the context of DHTC systems, such as the Worldwide LHC Computing Grid (WLCG).« less

RCT - subjective physical performance and quality of life after a 6-month programmed sports therapy (PST) in patients with haemophilia.

PubMed

Runkel, B; Von Mackensen, S; Hilberg, T

2017-01-01

Musculoskeletal bleedings lead to limitations in the locomotor system and consequently, in health-related quality of life (HRQoL) in patients with haemophilia (PwH). Sports therapy is increasingly recommended to improve their physical performance. Until today, randomised controlled studies investigating changes in physical performance in PwH are rare. This study investigates the impact of programmed sports therapy on the subjective physical performance and the HRQoL in PwH. A randomised controlled trial (RCT) was conducted with a training intervention for over 6 months. For this purpose, 64 PwH with moderate (n = 5) or severe (n = 59) haemophilia A (n = 57) or B (n = 7) were randomised into two groups - intervention (IG) or control group (CG). The HRQoL was assessed with the SF-36 questionnaire and the disease-specific Haem-A-QoL before and after the intervention. The subjective physical performance was tested by the HEP-Test-Q. After the 6-month training intervention, PwH in the IG subjectively reported significant better 'endurance' (P = 0.000) in the HEP-Test-Q compared to the CG. In the SF-36, a significant difference in the domains 'general health perceptions' (P = 0.005) and 'mental health' (P = 0.001) was detected. The haemophilia-specific HRQoL questionnaire showed a significant improvement in the dimensions 'feeling' (P = 0.049), 'work' (P = 0.046) and 'family' (P = 0.040). In the first RCT evaluating the impact of a 6-month training intervention on the subjective perception of PwH, an increase in subjective physical performance and some domains of HRQoL was demonstrated in the IG. Specific sports therapy should be included into the comprehensive treatment under supervision and monitoring by experienced staff. © 2016 John Wiley & Sons Ltd.

Combination with CK19 Might Increase the Prognostic Power of Hep Par 1 in Hepatocellular Carcinoma after Curative Resection.

PubMed

Jin, Ye; Liang, Zhi-Yong; Zhou, Wei-Xun; Zhou, Li

2017-07-31

Hepatocyte Paraffin 1 (Hep Par 1) and cytokeratin 19 (CK19) were shown to be associated with post-surgical prognosis of hepatocellular carcinoma (HCC). However, further validation might be needed. Besides, their combined evaluation has not been reported. The present study was designed to address the issues. Expressions of Hep Par 1 and CK19 were detected using tissue microarray-based immunohistochemical staining in 79 patients with HCC underwent curative hepatectomy. Their associations with cliniopathologic variables, overall and recurrence-free survival were analyzed. Hep Par 1 was highly expressed in 61 patients (77.2%), whereas CK19 was positive in 8 patients (10.1%). Moreover, expressions of these two proteins were all associated with tumor-node-metastasis (TNM) stage and vascular invasion. It was found that high Hep Par 1 expression was univariately associated with good overall and recurrence-free survival, while CK19 was marginally prognostic. Also in univariate analyses, combination of the two markers more effectively predicted for long-term prognosis in HCC than Hep Par 1 did. However, neither Hep Par 1 nor Hep Par 1/CK19 was multivariately significant. Finally, Hep Par 1/CK19 combined with TNM stage might obtain more satisfactory outcome prediction, especially for overall survival. Combination of CK19 with Hep Par 1 might have higher prognostic power, which might be further improved by adding TNM stage, than Hep Par 1 alone, in resected HCC. Of course, subsequent confirmation is necessary.

Reports to the Vaccine Adverse Event Reporting System after hepatitis A and hepatitis AB vaccines in pregnant women.

PubMed

Moro, Pedro L; Museru, Oidda I; Niu, Manette; Lewis, Paige; Broder, Karen

2014-06-01

To characterize adverse events (AEs) after hepatitis A vaccines (Hep A) and hepatitis A and hepatitis B combination vaccine (Hep AB) in pregnant women reported to the Vaccine Adverse Event Reporting System (VAERS), a spontaneous reporting surveillance system. We searched VAERS for AEs reports in pregnant women who received Hep A or Hep AB from Jan. 1, 1996-April 5, 2013. Clinicians reviewed all reports and available medical records. VAERS received 139 reports of AEs in pregnant women; 7 (5.0%) were serious; no maternal or infant deaths were identified. Sixty-five (46.8%) did not describe any AEs. For those women whose gestational age was available, most were vaccinated during the first trimester, 50/60 (83.3%) for Hep A and 18/21 (85.7%) for Hep AB. The most common pregnancy-specific outcomes following Hep A or Hep AB vaccinations were spontaneous abortion in 15 (10.8%) reports, elective termination in 10 (7.2%), and preterm delivery in 7 (5.0%) reports. The most common nonpregnancy specific outcome was urinary tract infection and nausea/vomiting with 3 (2.2%) reports each. One case of amelia of the lower extremities was reported in an infant following maternal Hep A immunization. This review of VAERS reports did not identify any concerning pattern of AEs in pregnant women or their infants following maternal Hep A or Hep AB immunizations during pregnancy. Published by Mosby, Inc.

A Pilot Randomized Controlled Trial of the Effects of Chair Yoga on Pain and Physical Function Among Community-Dwelling Older Adults With Lower Extremity Osteoarthritis

PubMed Central

Park, Juyoung; McCaffrey, Ruth; Newman, David; Liehr, Patricia; Ouslander, Joseph G.

2016-01-01

Objectives To determine effects of Sit ‘N’ Fit Chair Yoga, compared to a Health Education program (HEP), on pain and physical function in older adults with lower extremity osteoarthritis (OA) who could not participate in standing exercise Design Two-arm randomized controlled trial Setting One HUD senior housing facility and one day senior center in south Florida Participants Community-dwelling older adults (N = 131) were randomly assigned to chair yoga (n = 66) or HEP (n = 65). Thirteen dropped after assignment but prior to the intervention; 6 dropped during the intervention; 106 of 112 completed at least 12 of 16 sessions (95% retention rate). Interventions Participants attended either chair yoga or HEP. Both interventions consisted of twice-weekly 45-minute sessions for 8 weeks. Measurements Primary: pain, pain interference; secondary: balance, gait speed, fatigue, functional ability measured at baseline, after 4 weeks of intervention, at the end of the 8-week intervention, and post-intervention (1 and 3 months). Results The chair yoga group showed greater reduction in pain interference during the intervention (p = .01), sustained through 3 months (p = .022). WOMAC pain (p = .048), gait speed (p = .024), and fatigue (p = .037) were improved in the yoga group during the intervention (p = .048) but improvements were not sustained post intervention. Chair yoga had no effect on balance. Conclusion An 8-week chair yoga program was associated with reduction in pain, pain interference, and fatigue, and improvement in gait speed, but only the effects on pain interference were sustained 3 months post intervention. Chair yoga should be further explored as a nonpharmacologic intervention for older people with OA in the lower extremities. Trial Registration ClinicalTrials.gov: NCT02113410 PMID:28008603

[Pseudolaric acid B induces G2/M arrest and inhibits invasion and migration in HepG2 hepatoma cells].

PubMed

Li, Shuai; Guo, Lianyi

2018-01-01

Objective To investigate the mechanisms of pseudolaric acid B (PAB) blocks cell cycle and inhibits invasion and migration in human hepatoma HepG2 cells. Methods The proliferation effect of PAB on HepG2 cells was evaluated by MTT assay. The effect of PAB on the cell cycle of HepG2 cells was analyzed by flow cytometry. Immunofluorescence cytochemical staining was applied to observe the effect of PAB on the α-tubulin polymerization and expression in HepG2 cells. Transwell TM chamber invasion assay and wound healing assay were performed to detect the influence of PAB on the migration and invasion ability of HepG2 cells. Western blotting was used to determine the expressions of α-tubulin, E-cadherin and MMP-9 in HepG2 cells after treated with PAB. Results PAB inhibited the proliferation of HepG2 cells in a dose-dependent manner and blocked the cell cycle in G2/M phase. PAB significantly changed the polymerization and decreased the expression of α-tubulin. The capacities of invasion and migration of HepG2 cells treated by PAB were significantly depressed. The protein levels of α-tubulin and MMP-9 decreased while the E-cadherin protein level increased. Conclusion PAB can inhibits the proliferation of HepG2 cells by down-regulating the expression of α-tubulin and influencing its polymerization, arresting HepG2 cells in G2/M phase. Meanwhile, PAB also can inhibit the invasion and migration of HepG2 cells by lowering cytoskeleton α-tubulin and MMP-9, and increasing E-cadherin.

Named Data Networking in Climate Research and HEP Applications

NASA Astrophysics Data System (ADS)

Shannigrahi, Susmit; Papadopoulos, Christos; Yeh, Edmund; Newman, Harvey; Jerzy Barczyk, Artur; Liu, Ran; Sim, Alex; Mughal, Azher; Monga, Inder; Vlimant, Jean-Roch; Wu, John

2015-12-01

The Computing Models of the LHC experiments continue to evolve from the simple hierarchical MONARC[2] model towards more agile models where data is exchanged among many Tier2 and Tier3 sites, relying on both large scale file transfers with strategic data placement, and an increased use of remote access to object collections with caching through CMS's AAA, ATLAS' FAX and ALICE's AliEn projects, for example. The challenges presented by expanding needs for CPU, storage and network capacity as well as rapid handling of large datasets of file and object collections have pointed the way towards future more agile pervasive models that make best use of highly distributed heterogeneous resources. In this paper, we explore the use of Named Data Networking (NDN), a new Internet architecture focusing on content rather than the location of the data collections. As NDN has shown considerable promise in another data intensive field, Climate Science, we discuss the similarities and differences between the Climate and HEP use cases, along with specific issues HEP faces and will face during LHC Run2 and beyond, which NDN could address.

Immunomodulatory Activities of a Fungal Protein Extracted from Hericium erinaceus through Regulating the Gut Microbiota.

PubMed

Diling, Chen; Chaoqun, Zheng; Jian, Yang; Jian, Li; Jiyan, Su; Yizhen, Xie; Guoxiao, Lai

2017-01-01

A single-band protein (HEP3) was isolated from Hericium erinaceus using a chemical separation combined with pharmacodynamic evaluation methods. This protein exhibited immunomodulatory activity in lipopolysaccharide-activated RAW 264.7 macrophages by decreasing the overproduction of tumor necrosis factor-α, interleukin (IL)-1β, and IL-6, and downregulating the expression of inducible nitric oxide synthase and nuclear factor-κB p65. Further researches revealed that HEP3 could improve the immune system via regulating the composition and metabolism of gut microbiota to activate the proliferation and differentiation of T cells, stimulate the intestinal antigen-presenting cells in high-dose cyclophosphamide-induced immunotoxicity in mice, and play a prebiotic role in the case of excessive antibiotics in inflammatory bowel disease model mice. Aided experiments also showed that HEP3 could be used as an antitumor immune inhibitor in tumor-burdened mice. The results of the present study suggested that fungal protein from H. erinaceus could be used as a drug or functional food ingredient for immunotherapy because of its immunomodulatory activities.

Immunomodulatory Activities of a Fungal Protein Extracted from Hericium erinaceus through Regulating the Gut Microbiota

PubMed Central

Diling, Chen; Chaoqun, Zheng; Jian, Yang; Jian, Li; Jiyan, Su; Yizhen, Xie; Guoxiao, Lai

2017-01-01

A single-band protein (HEP3) was isolated from Hericium erinaceus using a chemical separation combined with pharmacodynamic evaluation methods. This protein exhibited immunomodulatory activity in lipopolysaccharide-activated RAW 264.7 macrophages by decreasing the overproduction of tumor necrosis factor-α, interleukin (IL)-1β, and IL-6, and downregulating the expression of inducible nitric oxide synthase and nuclear factor-κB p65. Further researches revealed that HEP3 could improve the immune system via regulating the composition and metabolism of gut microbiota to activate the proliferation and differentiation of T cells, stimulate the intestinal antigen-presenting cells in high-dose cyclophosphamide-induced immunotoxicity in mice, and play a prebiotic role in the case of excessive antibiotics in inflammatory bowel disease model mice. Aided experiments also showed that HEP3 could be used as an antitumor immune inhibitor in tumor-burdened mice. The results of the present study suggested that fungal protein from H. erinaceus could be used as a drug or functional food ingredient for immunotherapy because of its immunomodulatory activities. PMID:28713364

Hepatitis A and Hepatitis B vaccination coverage among adults with chronic liver disease

PubMed Central

Yue, Xin; Black, Carla L.; O’Halloran, Alissa; Lu, Peng-Jun; Williams, Walter W.; Nelson, Noele P.

2018-01-01

Background Infection with hepatitis A and hepatitis B virus can increase the risk of morbidity and mortality in persons with chronic liver disease (CLD). The Advisory Committee on Immunization Practices recommends hepatitis A (HepA) and hepatitis B (HepB) vaccination for persons with CLD. Methods Data from the 2014 and 2015 National Health Interview Surveys (NHIS), nationally representative, in-person interview surveys of the non-institutionalized US civilian population, were used to assess self-reported HepA (≥1 and ≥2 doses) and HepB vaccination (≥1 and ≥3 doses) coverage among adults who reported a chronic or long-term liver condition. Multivariable logistic regression was used to identify factors independently associated with HepA and HepB vaccination among adults with CLD. Results Overall, 19.4% and 11.5% of adults aged ≥18 years with CLD reported receiving ≥1 dose and ≥2 doses of HepA vaccine, respectively, compared with 14.7% and 9.1% of adults without CLD (p<0.05 comparing those with and without CLD, ≥1dose). Age, education, geographic region, and international travel were associated with receipt of ≥2 doses HepA vaccine among adults with CLD. Overall, 35.7% and 29.1% of adults with CLD reported receiving ≥1 dose and ≥3 doses of HepB vaccine, respectively, compared with 30.2% and 24.7% of adults without CLD (p<0.05 comparing those with and without CLD, ≥1 dose). Age, education, and receipt of influenza vaccination in the past 12 months were associated with receipt of ≥3 doses HepB vaccine among adults with CLD. Among adults with CLD and ≥10 provider visits, only 13.8% and 35.3% had received ≥2 doses HepA and ≥3 doses HepB vaccine, respectively. Conclusions HepA and HepB vaccination among adults with CLD is suboptimal and missed opportunities to vaccinate occurred. Providers should adhere to recommendations to vaccinate persons with CLD to increase vaccination among this population. PMID:29395521

Hepatitis A and hepatitis B vaccination coverage among adults with chronic liver disease.

PubMed

Yue, Xin; Black, Carla L; O'Halloran, Alissa; Lu, Peng-Jun; Williams, Walter W; Nelson, Noele P

2018-02-21

Infection with hepatitis A and hepatitis B virus can increase the risk of morbidity and mortality in persons with chronic liver disease (CLD). The Advisory Committee on Immunization Practices recommends hepatitis A (HepA) and hepatitis B (HepB) vaccination for persons with CLD. Data from the 2014 and 2015 National Health Interview Surveys (NHIS), nationally representative, in-person interview surveys of the non-institutionalized US civilian population, were used to assess self-reported HepA (≥1 and ≥2 doses) and HepB vaccination (≥1 and ≥3 doses) coverage among adults who reported a chronic or long-term liver condition. Multivariable logistic regression was used to identify factors independently associated with HepA and HepB vaccination among adults with CLD. Overall, 19.4% and 11.5% of adults aged ≥ 18 years with CLD reported receiving ≥1 dose and ≥2 doses of HepA vaccine, respectively, compared with 14.7% and 9.1% of adults without CLD (p < .05 comparing those with and without CLD, ≥1dose). Age, education, geographic region, and international travel were associated with receipt of ≥2 doses HepA vaccine among adults with CLD. Overall, 35.7% and 29.1% of adults with CLD reported receiving ≥1 dose and ≥3 doses of HepB vaccine, respectively, compared with 30.2% and 24.7% of adults without CLD (p < .05 comparing those with and without CLD, ≥1 dose). Age, education, and receipt of influenza vaccination in the past 12 months were associated with receipt of ≥3 doses HepB vaccine among adults with CLD. Among adults with CLD and ≥10 provider visits, only 13.8% and 35.3% had received ≥2 doses HepA and ≥3 doses HepB vaccine, respectively. HepA and HepB vaccination among adults with CLD is suboptimal and missed opportunities to vaccinate occurred. Providers should adhere to recommendations to vaccinate persons with CLD to increase vaccination among this population. Copyright © 2018 Elsevier Ltd. All rights reserved.

Safety of currently licensed hepatitis B surface antigen vaccines in the United States, Vaccine Adverse Event Reporting System (VAERS), 2005-2015.

PubMed

Haber, Penina; Moro, Pedro L; Ng, Carmen; Lewis, Paige W; Hibbs, Beth; Schillie, Sarah F; Nelson, Noele P; Li, Rongxia; Stewart, Brock; Cano, Maria V

2018-01-25

Currently four recombinant hepatitis B (HepB) vaccines are in use in the United States. HepB vaccines are recommended for infants, children and adults. We assessed adverse events (AEs) following HepB vaccines reported to the Vaccine Adverse Event Reporting System (VAERS), a national spontaneous reporting system. We searched VAERS for reports of AEs following single antigen HepB vaccine and HepB-containing vaccines (either given alone or with other vaccines), from January 2005 - December 2015. We conducted descriptive analyses and performed empirical Bayesian data mining to assess disproportionate reporting. We reviewed serious reports including reports of special interest. VAERS received 20,231 reports following HepB or HepB-containing vaccines: 10,291 (51%) in persons <2 years of age; 2588 (13%) in persons 2-18 years and 5867 (29%) in persons >18 years; for 1485 (7.3%) age was missing. Dizziness and nausea (8.4% each) were the most frequently reported AEs following a single antigen HepB vaccine: fever (23%) and injection site erythema (11%) were most frequent following Hep-containing vaccines. Of the 4444 (22%) reports after single antigen HepB vaccine, 303 (6.8%) were serious, including 45 deaths. Most commonly reported cause of death was Sudden Infant Death Syndrome (197). Most common non-death serious reports following single antigen HepB vaccines among infants aged <1 month, were nervous system disorders (15) among children aged 1-23 months; infections and infestation (8) among persons age 2-18 years blood and lymphatic systemic disorders; and general disorders and administration site conditions among persons age >18 years. Most common vaccination error following single antigen HepB was incorrect product storage. Review current U.S.-licensed HepB vaccines administered alone or in combination with other vaccines did not reveal new or unexpected safety concerns. Vaccination errors were identified which indicate the need for training and education of providers on HepB vaccine indications and recommendations. Published by Elsevier Ltd.

Batch calculations in CalcHEP

NASA Astrophysics Data System (ADS)

Pukhov, A.

2003-04-01

CalcHEP is a clone of the CompHEP project which is developed by the author outside of the CompHEP group. CompHEP/CalcHEP are packages for automatic calculations of elementary particle decay and collision properties in the lowest order of perturbation theory. The main idea prescribed into the packages is to make available passing on from the Lagrangian to the final distributions effectively with a high level of automation. According to this, the packages were created as a menu driven user friendly programs for calculations in the interactive mode. From the other side, long-time calculations should be done in the non-interactive regime. Thus, from the beginning CompHEP has a problem of batch calculations. In CompHEP 33.23 the batch session was realized by mean of interactive menu which allows to the user to formulate the task for batch. After that the not-interactive session was launched. This way is too restricted, not flexible, and leads to doubling in programming. In this article I discuss another approach how one can force an interactive program to work in non-interactive mode. This approach was realized in CalcHEP 2.1 disposed on http://theory.sinp.msu.ru/~pukhov/calchep.html.

Anti-fatigue activities of polysaccharides extracted from Hericium erinaceus.

PubMed

Liu, Jianqing; DU, Congxin; Wang, Yifei; Yu, Zhihua

2015-02-01

Hericium erinaceus (HEP) is a notable medicinal fungus grown in China and other oriental countries. Polysaccharides from HEP have recently attracted considerable attention due to their numerous physiological activities. The objective of this study was to evaluate the anti-fatigue activity of HEP in a mouse model. After one week of acclimation, mice were randomly divided into four groups: a control group, a low-dose HEP-treated group, a moderate-dose HEP-treated group, and a high-dose HEP-treated group. The treated groups received HEP (50, 100 and 200 mg/kg, ig), while the control group received saline solution. Following treatment for 28 days, the mice performed a forced swimming test until they were exhausted, then the exhaustive swimming time was recorded along with certain biochemical parameters related to fatigue, including blood lactic acid (BLA), serum urea nitrogen (SUN), tissue glycogen, superoxide dismutase (SOD), glutathione peroxidase (GPx) and malondialdehyde (MDA). These results suggested that HEP has significant anti-fatigue activity by decreasing BLA, SUN and MDA content, as well as increasing tissue glycogen content and antioxidant enzyme activity. Based on these results, this study provided theoretical support for the application of HEP in the field of sports nutrition.

Anti-fatigue activities of polysaccharides extracted from Hericium erinaceus

PubMed Central

LIU, JIANQING; DU, CONGXIN; WANG, YIFEI; YU, ZHIHUA

2015-01-01

Hericium erinaceus (HEP) is a notable medicinal fungus grown in China and other oriental countries. Polysaccharides from HEP have recently attracted considerable attention due to their numerous physiological activities. The objective of this study was to evaluate the anti-fatigue activity of HEP in a mouse model. After one week of acclimation, mice were randomly divided into four groups: a control group, a low-dose HEP-treated group, a moderate-dose HEP-treated group, and a high-dose HEP-treated group. The treated groups received HEP (50, 100 and 200 mg/kg, ig), while the control group received saline solution. Following treatment for 28 days, the mice performed a forced swimming test until they were exhausted, then the exhaustive swimming time was recorded along with certain biochemical parameters related to fatigue, including blood lactic acid (BLA), serum urea nitrogen (SUN), tissue glycogen, superoxide dismutase (SOD), glutathione peroxidase (GPx) and malondialdehyde (MDA). These results suggested that HEP has significant anti-fatigue activity by decreasing BLA, SUN and MDA content, as well as increasing tissue glycogen content and antioxidant enzyme activity. Based on these results, this study provided theoretical support for the application of HEP in the field of sports nutrition. PMID:25574220

The status of hepatitis B control in the African region

PubMed Central

Breakwell, Lucy; Tevi-Benissan, Carol; Childs, Lana; Mihigo, Richard; Tohme, Rania

2017-01-01

The World Health Organization (WHO) African Region has approximately 100 million people with chronic hepatitis B virus (HBV) infection. This review describes the status of hepatitis B control in the Region. We present hepatitis B vaccine (HepB) coverage data and from available data in the published literature, the impact of HepB vaccination on hepatitis B surface antigen (HBsAg) prevalence, a marker of chronic infection, among children, HBsAg prevalence in pregnant women, and risk of perinatal transmission. Lastly, we describe challenges with HepB birth dose (HepB-BD) introduction reported in the Region, and propose strategies to increase coverage. In 2015, regional three dose HepB coverage was 76%, and 16(34%) of 47 countries reported ≥ 90% coverage. Overall, 11 countries introduced HepB-BD; only nine provide universal HepB-BD, and of these, five reported ≥ 80% coverage. From non-nationally representative serosurveys among children, HBsAg prevalence was lower among children born after HepB introduction compared to those born before HepB introduction. However, some studies still found HBsAg prevalence to be above 2%. From limited surveys among pregnant women, the median HBsAg prevalence varied by country, ranging from 1.9% (Madagascar) to 16.1% (Niger); hepatitis B e antigen (HBeAg) prevalence among HBsAg-positive women ranged from 3.3% (Zimbabwe) to 28.5% (Nigeria). Studies in three countries indicated that the risk of perinatal HBV transmission was associated with HBeAg expression or high HBV DNA viral load. Major challenges for timely HepB-BD administration were poor knowledge of or lack of national HepB-BD vaccination guidelines, high prevalence of home births, and unreliable vaccine supply. Overall, substantial progress has been made in the region. However, countries need to improve HepB3 coverage and some countries might need to consider introducing the HepB-BD to help achieve the regional hepatitis B control goal of < 2% HBsAg prevalence among children < 5 years old by 2020. To facilitate HepB-BD introduction and improve timely coverage, strategies are needed to reach both facility-based and home births. Strong political commitment, clear policy recommendations and staff training on HepB-BD administration are also required. Furthermore, high quality nationally representative serosurveys among children are needed to inform decision makers about progress towards the regional control goal. PMID:29296152

A recombinant rabies virus carrying GFP between N and P affects viral transcription in vitro.

PubMed

Luo, Jun; Zhao, Jing; Tian, Qin; Mo, Weiyu; Wang, Yifei; Chen, Hao; Guo, Xiaofeng

2016-06-01

Several studies have demonstrated the rabies virus to be a perfect potential vaccine vector to insert foreign genes into the target genome. For this study, a green fluorescent protein (GFP) gene was cloned into the rabies virus (RABV) genome between the N and P gene. CT dinucleotide was inserted as intergenic region. The recombinant high egg passage Flury strain (HEP-Flury) of RABV, carrying GFP (rHEP-NP-GFP), was generated in BHK-21 cells using reverse genetics. According to the viral growth kinetics assay, the addition of GFP between N and P gene has little effect on the viral growth compared to the parental strain HEP-Flury. Quantitative real-time PCR (qPCR) indicated that rHEP-NP-GFP showed different viral gene transcription, especially for G gene, compared to HEP-Flury. The same is true for one other recombinant RABV carrying GFP between G and L gene in NA cells. In addition, parent HEP-Flury showed more expression of innate immune-related molecules in NA cells. Compared to HEP-Flury, Western blotting (WB) indicated that insertion of a foreign gene following N gene enhanced the expression of M and G proteins. According to the qPCR and WB, GFP expression levels of rHEP-NP-GFP were significantly higher than rHEP-GFP. This study indicates HEP-Flury as valid vector to express exogenous genes between N and P.

ApoB-100 secretion by HepG2 cells is regulated by the rate of triglyceride biosynthesis but not by intracellular lipid pools.

PubMed

Benoist, F; Grand-Perret, T

1996-10-01

Triglycerides (TGs), cholesteryl esters (CEs), cholesterol, and phosphatidylcholine have been independently proposed as playing regulatory roles in apoB-100 secretion; the results depended on the cellular model used. In this study, we reinvestigate the role of lipids in apoB-100 production in HepG2 cells and in particular, we clarify the respective roles of intracellular mass and the biosynthesis of lipids in the regulation of apoB-100 production. In a first set of experiments, the pool size of cholesterol, CEs, and TGs was modulated by a 3-day treatment with either lipid precursors or inhibitors of enzymes involved in lipid synthesis. We used simvastatin (a hydroxymethylglutaryl coenzyme A reductase inhibitor), 58-035 (an acyl coenzyme A cholesterol acyltransferase inhibitor), 5-tetradecyloxy-2-furancarboxylic acid (TOFA, an inhibitor of fatty acid synthesis), and oleic acid. The secretion rate of apoB-100 was not affected by the large modulation of lipid mass induced by these various pre-treatments. In a second set of experiments, the same lipid modulators were added during a 4-hour labeling period. Simvastatin and 58-035 inhibited cholesterol and CE synthesis without affecting apoB-100 secretion. By contrast, treatment of HepG2 cells with TOFA resulted in the inhibition of TG synthesis and apoB-100 secretion. This effect was highly specific for apoB-100 and was reversed by adding oleic acid, which stimulated both TG synthesis and apoB-100 secretion. Moreover, a combination of oleic acid and 58-035 inhibited CE biosynthesis and increased both TG synthesis and apoB-100 secretion. These results show that in HepG2 cells TG biosynthesis regulates apoB-100 secretion, whereas the rate of cholesterol or CE biosynthesis has no effect.

HL-LHC and HE-LHC Upgrade Plans and Opportunities for US Participation

NASA Astrophysics Data System (ADS)

Apollinari, Giorgio

2017-01-01

The US HEP community has identified the exploitation of physics opportunities at the High Luminosity-LHC (HL-LHC) as the highest near-term priority. Thanks to multi-year R&D programs, US National Laboratories and Universities have taken the leadership in the development of technical solutions to increase the LHC luminosity, enabling the HL-LHC Project and uniquely positioning this country to make critical contributions to the LHC luminosity upgrade. This talk will describe the shaping of the US Program to contribute in the next decade to HL-LHC through newly developed technologies such as Nb3Sn focusing magnets or superconducting crab cavities. The experience gained through the execution of the HL-LHC Project in the US will constitute a pool of knowledge and capabilities allowing further developments in the future. Opportunities for US participations in proposed hadron colliders, such as a possible High Energy-LHC (HE-LHC), will be described as well.

Development of AC-coupled, poly-silicon biased, p-on-n silicon strip detectors in India for HEP experiments

NASA Astrophysics Data System (ADS)

Jain, Geetika; Dalal, Ranjeet; Bhardwaj, Ashutosh; Ranjan, Kirti; Dierlamm, Alexander; Hartmann, Frank; Eber, Robert; Demarteau, Marcel

2018-02-01

P-on-n silicon strip sensors having multiple guard-ring structures have been developed for High Energy Physics applications. The study constitutes the optimization of the sensor design, and fabrication of AC-coupled, poly-silicon biased sensors of strip width of 30 μm and strip pitch of 55 μm. The silicon wafers used for the fabrication are of 4 inch n-type, having an average resistivity of 2-5 k Ω cm, with a thickness of 300 μm. The electrical characterization of these detectors comprises of: (a) global measurements of total leakage current, and backplane capacitance; (b) strip and voltage scans of strip leakage current, poly-silicon resistance, interstrip capacitance, interstrip resistance, coupling capacitance, and dielectric current; and (c) charge collection measurements using ALiBaVa setup. The results of the same are reported here.

CephFS: a new generation storage platform for Australian high energy physics

NASA Astrophysics Data System (ADS)

Borges, G.; Crosby, S.; Boland, L.

2017-10-01

This paper presents an implementation of a Ceph file system (CephFS) use case at the ARC Center of Excellence for Particle Physics at the Terascale (CoEPP). CoEPP’s CephFS provides a posix-like file system on top of a Ceph RADOS object store, deployed on commodity hardware and without single points of failure. By delivering a unique file system namespace at different CoEPP centres spread across Australia, local HEP researchers can store, process and share data independently of their geographical locations. CephFS is also used as the back-end file system for a WLCG ATLAS user area at the Australian Tier-2. Dedicated SRM and XROOTD services, deployed on top of CoEPP’s CephFS, integrates it in ATLAS data distributed operations. This setup, while allowing Australian HEP researchers to trigger data movement via ATLAS grid tools, also enables local posix-like read access providing greater control to scientists of their data flows. In this article we will present details on CoEPP’s Ceph/CephFS implementation and report performance I/O metrics collected during the testing/tuning phase of the system.

The Inspiring Science Education project and the resources for HEP analysis by university students

NASA Astrophysics Data System (ADS)

Fassouliotis, Dimitris; Kourkoumelis, Christine; Vourakis, Stylianos

2016-11-01

The Inspiring Science Education outreach project has been running for more than two years, creating a large number of inquiry based educational resources for high-school teachers and students. Its goal is the promotion of science education in schools though new methods built on the inquiry based education techniques, involving large consortia of European partners and implementation of large-scale pilots in schools. Recent hands-on activities, developing and testing the above mentioned innovative applications are reviewed. In general, there is a lack for educational scenaria and laboratory courses earmarked for more advanced, namely university, students. At the University of Athens for the last four years, the HYPATIA on-line event analysis tool has been used as a lab course for fourth year undergraduate physics students, majoring in HEP. Up to now, the course was limited to visual inspection of a few tens of ATLAS events. Recently the course was enriched with additional analysis exercises, which involve large samples of events. The students through a user friendly interface can analyse the samples and optimize the cut selection in order to search for new physics. The implementation of this analysis is described.

Experimental Neutrino Physics

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

Wilkes, Richard Jeffrey

The University of Washington (UW) HEP neutrino group performed experimental research on the physics of neutrinos, using the capabilities offered by the T2K Experiment and the Super-Kamiokande Neutrino Observatory. The UW group included senior investigator R. J. Wilkes, two PhD students, four MS degree students, and a research engineer, all of whom are members of the international scientific collaborations for T2K and Super-Kamiokande. During the period of support, within T2K we pursued new precision studies sensitive to new physics, going beyond the limits of current measurements of the fundamental neutrino oscillation parameters (mass differences and mixing angles). We began effortsmore » to measure (or significantly determine the absence of) 1 the CP-violating phase parameter δCP and determine the neutrino mass hierarchy. Using the Super-Kamiokande (SK) detector we pursued newly increased precision in measurement of neutrino oscillation parameters with atmospheric neutrinos, and extended the current reach in searches for proton decay, in addition to running the most sensitive supernova watch instrument [Scholberg 2012], performing other astrophysical neutrino studies, and analyzing beam-induced events from T2K. Overall, the research addressed central questions in the field of particle physics. It included the training of graduate students (both PhD and professional MS degree students), and postdoctoral researchers. Undergraduate students also participated as laboratory assistants.« less

Experimental High Energy Physics Research

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

Hohlmann, Marcus

This final report summarizes activities of the Florida Tech High Energy Physics group supported by DOE under grant #DE-SC0008024 during the period June 2012 – March 2015. We focused on one of the main HEP research thrusts at the Energy Frontier by participating in the CMS experiment. We were exploiting the tremendous physics opportunities at the Large Hadron Collider (LHC) and prepared for physics at its planned extension, the High-Luminosity LHC. The effort comprised a physics component with analysis of data from the first LHC run and contributions to the CMS Phase-2 upgrades in the muon endcap system (EMU) formore » the High-Luminosity LHC. The emphasis of our hardware work was the development of large-area Gas Electron Multipliers (GEMs) for the CMS forward muon upgrade. We built a production and testing site for such detectors at Florida Tech to complement future chamber production at CERN. The first full-scale CMS GE1/1 chamber prototype ever built outside of CERN was constructed at Florida Tech in summer 2013. We conducted two beam tests with GEM prototype chambers at CERN in 2012 and at FNAL in 2013 and reported the results at conferences and in publications. Principal Investigator Hohlmann served as chair of the collaboration board of the CMS GEM collaboration and as co-coordinator of the GEM detector working group. He edited and authored sections of the detector chapter of the Technical Design Report (TDR) for the GEM muon upgrade, which was approved by the LHCC and the CERN Research Board in 2015. During the course of the TDR approval process, the GEM project was also established as an official subsystem of the muon system by the CMS muon institution board. On the physics side, graduate student Kalakhety performed a Z' search in the dimuon channel with the 2011 and 2012 CMS datasets that utilized 20.6 fb⁻¹ of p-p collisions at √s = 8 TeV. For the dimuon channel alone, the 95% CL lower limits obtained on the mass of a Z' resonance are 2770 GeV for a Z' with the same standard-model couplings as the Z boson. Our student team operated a Tier-3 cluster on the Open Science Grid (OSG) to support local CMS physics analysis and remote OSG activity. As a service to the HEP community, Hohlmann participated in the Snowmass effort over the course of 2013. Specifically, he acted as a liaison for gaseous detectors between the Instrumentation Frontier and the Energy Frontier and contributed to five papers and reports submitted to the summer study.« less

Enhancing cisplatin delivery to hepatocellular carcinoma HepG2 cells using dual sensitive smart nanocomposite.

PubMed

Salimi, Farzaneh; Dilmaghani, Karim Akbari; Alizadeh, Effat; Akbarzadeh, Abolfazl; Davaran, Soodabeh

2017-07-07

Targeted entrance and accumulation of higher doses of drugs into malignant cells could help in intensification of tumor specific cytotoxicity. A dual-responsive nanogel, poly(N-isopropylacrylamide)-co-poly(N,N-(dimethylamino)ethyl methacrylate) [P(NIPAM-co-DMA)] containing N-isopropylacrylamide (NIPAM) as thermoresponsive monomer and N,N-(dimethylamino)ethyl methacrylate (DMA) as pH-responsive monomer and methylene-bis-acrylamide (MBA) as cross-linking agent, was synthesized by free radical emulsion polymerization. Cisplatin along with magnetic Fe 3 O 4 nanoparticles (MNPs) was loaded into the nanogel by physically embedding the magnetic nanoparticles into hydrogel matrix after gelation to obtain drug-loaded magnetic nanocomposite [P(NIPAM-co-DMA)/Fe 3 O 4 ]. Drug loading efficiencies and drug release profiles of cisplatin-loaded P(NIPAM-co-DMA) nanogel and P(NIPAM-co-DMA)/Fe 3 O 4 nanocomposite were evaluated in vitro for controlled drug delivery in different temperature and pH conditions. Finally, the anticancer activity of P(NIPAM-co-DMA)/Fe 3 O 4 nanocomposite on human liver HepG2 cells was evaluated. Nanogel and nanocomposite showed significantly higher (p < .05) cisplatin release at 40 °C compared to 37 °C and at pH 5.7 compared to pH 7.4, demonstrating their temperature and pH sensitivity, respectively. The cytotoxicity assay of drug free nanogel on HepG2 cell line indicated that the nanogel is biocompatible and suitable as drug carrier. Moreover, MTT assay revealed that the cisplatin-loaded nanocomposite represented significant superior cytotoxicity (p < .05) to HepG2 cells as compared with free cisplatin.

Dechlorination and chlorine rearrangement of 1,2,5,5,6,9,10-heptachlorodecane mediated by the whole pumpkin seedlings.

PubMed

Li, Yanlin; Hou, Xingwang; Yu, Miao; Zhou, Qunfang; Liu, Jiyan; Schnoor, Jerald L; Jiang, Guibin

2017-05-01

Short chain chlorinated paraffins (SCCPs) are ubiquitously present as persistent organic pollutants in the environment. However, little information on the interaction of SCCPs with plants is currently available. In this work, young pumpkin plants (Cucurbita maxima × C. Moschata) were hydroponically exposed to the congener of chlorinated decane, 1,2,5,5,6,9,10-heptachlorodecane (1,2,5,5,6,9,10-HepCD), to investigate the uptake, translocation and transformation of chlorinated decanes in the intact plants. It was found that parent HepCD was taken up by the pumpkin roots, translocated from root to shoots, and phytovolatilized from pumpkin plants to air via the plant transpiration flux. Our data suggested that dechlorination of 1,2,5,5,6,9,10-HepCD to lower chlorinated decanes and rearrangement of chlorine atoms in the molecule were all mediated by the whole pumpkin seedlings. Chlorinated decanes were found in the shoots and roots of blank controls, indicating that chlorinated decanes in the air could be absorbed by leaves and translocated from shoots to roots. Lower chlorinated congeners (C 10 H 17 Cl 5 ) tended to detain in air compared to higher chlorinated congeners (C 10 H 16 Cl 6 and other C 10 H 15 Cl 7 ). Potential transformation pathway and behavior of 1,2,5,5,6,9,10-HepCD in pumpkin were proposed based on these experiments. Copyright © 2017 Elsevier Ltd. All rights reserved.

Electron Production and Collective Field Generation in Intense Particle Beams

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

Molvik, A W; Vay, J; Cohen, R

Electron cloud effects (ECEs) are increasingly recognized as important, but incompletely understood, dynamical phenomena, which can severely limit the performance of present electron colliders, the next generation of high-intensity rings, such as PEP-II upgrade, LHC, and the SNS, the SIS 100/200, or future high-intensity heavy ion accelerators such as envisioned in Heavy Ion Inertial Fusion (HIF). Deleterious effects include ion-electron instabilities, emittance growth, particle loss, increase in vacuum pressure, added heat load at the vacuum chamber walls, and interference with certain beam diagnostics. Extrapolation of present experience to significantly higher beam intensities is uncertain given the present level of understanding.more » With coordinated LDRD projects at LLNL and LBNL, we undertook a comprehensive R&D program including experiments, theory and simulations to better understand the phenomena, establish the essential parameters, and develop mitigating mechanisms. This LDRD project laid the essential groundwork for such a program. We developed insights into the essential processes, modeled the relevant physics, and implemented these models in computational production tools that can be used for self-consistent study of the effect on ion beams. We validated the models and tools through comparison with experimental data, including data from new diagnostics that we developed as part of this work and validated on the High-Current Experiment (HCX) at LBNL. We applied these models to High-Energy Physics (HEP) and other advanced accelerators. This project was highly successful, as evidenced by the two paragraphs above, and six paragraphs following that are taken from our 2003 proposal with minor editing that mostly consisted of changing the tense. Further benchmarks of outstanding performance are: we had 13 publications with 8 of them in refereed journals, our work was recognized by the accelerator and plasma physics communities by 8 invited papers and we have 5 additional invitations for invited papers at upcoming conferences, we attracted collaborators who had SBIR funding, we are collaborating with scientists at CERN and GSI Darmstadt on gas desorption physics for submission to Physical Review Letters, and another PRL on absolute measurements of electron cloud density and Phys. Rev. ST-AB on electron emission physics are also being readied for submission.« less

A Recombinant Rabies Virus Encoding Two Copies of the Glycoprotein Gene Confers Protection in Dogs against a Virulent Challenge

PubMed Central

Sun, Zhaojin; Chen, Jing; Ai, Jun; Dun, Can; Fu, Zhen F.; Niu, Xuefeng; Guo, Xiaofeng

2014-01-01

The rabies virus (RABV) glycoprotein (G) is the principal antigen responsible for the induction of virus neutralizing antibodies (VNA) and is the major modality of protective immunity in animals. A recombinant RABV HEP-Flury strain was generated by reverse genetics to encode two copies of the G-gene (referred to as HEP-dG). The biological properties of HEP-dG were compared to those of the parental virus (HEP-Flury strain). The HEP-dG recombinant virus grew 100 times more efficiently in BHK-21 cell than the parental virus, yet the virulence of the dG recombinant virus in suckling mice was lower than the parental virus. The HEP-dG virus can improve the expression of G-gene mRNA and the G protein and produce more offspring viruses in cells. The amount of G protein revealed a positive relationship with immunogenicity in mice and dogs. The inactivated HEP-dG recombinant virus induced higher levels of VNA and conferred better protection against virulent RABV in mice and dogs than the inactivated parental virus and a commercial vaccine. The protective antibody persisted for at least 12 months. These data demonstrate that the HEP-dG is stable, induces a strong VNA response and confers protective immunity more effectively than the RABV HEP-Flury strain. HEP-dG could be a potential candidate in the development of novel inactivated rabies vaccines PMID:24498294

RAPPORT: running scientific high-performance computing applications on the cloud.

PubMed

Cohen, Jeremy; Filippis, Ioannis; Woodbridge, Mark; Bauer, Daniela; Hong, Neil Chue; Jackson, Mike; Butcher, Sarah; Colling, David; Darlington, John; Fuchs, Brian; Harvey, Matt

2013-01-28

Cloud computing infrastructure is now widely used in many domains, but one area where there has been more limited adoption is research computing, in particular for running scientific high-performance computing (HPC) software. The Robust Application Porting for HPC in the Cloud (RAPPORT) project took advantage of existing links between computing researchers and application scientists in the fields of bioinformatics, high-energy physics (HEP) and digital humanities, to investigate running a set of scientific HPC applications from these domains on cloud infrastructure. In this paper, we focus on the bioinformatics and HEP domains, describing the applications and target cloud platforms. We conclude that, while there are many factors that need consideration, there is no fundamental impediment to the use of cloud infrastructure for running many types of HPC applications and, in some cases, there is potential for researchers to benefit significantly from the flexibility offered by cloud platforms.

{sup 64}Cu levels from the {sup 62 }Ni({sup 3}He,p) reaction at 18 MeV

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

Basak, A.K.; Basher, M.A.; Mondal, A.S.

1997-10-01

The ({sup 3}He,p) reaction has been studied on {sup 62}Ni using a beam of 18 MeV {sup 3}He particles. Angular distributions of the outgoing protons have been measured for 65 levels including the new levels at 2.323, 3.231, 5.043, and 7.339 MeV and the analog states at 6.821 MeV (0{sup + };4) and 8.188 MeV (2{sup +};4) in the angular range {theta}{sub lab}=5{degree}{endash}80 {degree}. Data have been analyzed in terms of the distorted-wave Born approximation (DWBA). The L transfers have been obtained, J{sup {pi}} limits have been assigned, and the normalization constant has been deduced for several low-lying states. {copyright}more » {ital 1997} {ital The American Physical Society}« less

Moles of a Substance per Cell Is a Highly Informative Dosing Metric in Cell Culture

PubMed Central

Wagner, Brett A.; Buettner, Garry R.

2015-01-01

Background The biological consequences upon exposure of cells in culture to a dose of xenobiotic are not only dependent on biological variables, but also the physical aspects of experiments e.g. cell number and media volume. Dependence on physical aspects is often overlooked due to the unrecognized ambiguity in the dominant metric used to express exposure, i.e. initial concentration of xenobiotic delivered to the culture medium over the cells. We hypothesize that for many xenobiotics, specifying dose as moles per cell will reduce this ambiguity. Dose as moles per cell can also provide additional information not easily obtainable with traditional dosing metrics. Methods Here, 1,4-benzoquinone and oligomycin A are used as model compounds to investigate moles per cell as an informative dosing metric. Mechanistic insight into reactions with intracellular molecules, differences between sequential and bolus addition of xenobiotic and the influence of cell volume and protein content on toxicity are also investigated. Results When the dose of 1,4-benzoquinone or oligomycin A was specified as moles per cell, toxicity was independent of the physical conditions used (number of cells, volume of medium). When using moles per cell as a dose-metric, direct quantitative comparisons can be made between biochemical or biological endpoints and the dose of xenobiotic applied. For example, the toxicity of 1,4-benzoquinone correlated inversely with intracellular volume for all five cell lines exposed (C6, MDA-MB231, A549, MIA PaCa-2, and HepG2). Conclusions Moles per cell is a useful and informative dosing metric in cell culture. This dosing metric is a scalable parameter that: can reduce ambiguity between experiments having different physical conditions; provides additional mechanistic information; allows direct comparison between different cells; affords a more uniform platform for experimental design; addresses the important issue of repeatability of experimental results, and could increase the translatability of information gained from in vitro experiments. PMID:26172833

An Interactive and Comprehensive Working Environment for High-Energy Physics Software with Python and Jupyter Notebooks

NASA Astrophysics Data System (ADS)

Braun, N.; Hauth, T.; Pulvermacher, C.; Ritter, M.

2017-10-01

Today’s analyses for high-energy physics (HEP) experiments involve processing a large amount of data with highly specialized algorithms. The contemporary workflow from recorded data to final results is based on the execution of small scripts - often written in Python or ROOT macros which call complex compiled algorithms in the background - to perform fitting procedures and generate plots. During recent years interactive programming environments, such as Jupyter, became popular. Jupyter allows to develop Python-based applications, so-called notebooks, which bundle code, documentation and results, e.g. plots. Advantages over classical script-based approaches is the feature to recompute only parts of the analysis code, which allows for fast and iterative development, and a web-based user frontend, which can be hosted centrally and only requires a browser on the user side. In our novel approach, Python and Jupyter are tightly integrated into the Belle II Analysis Software Framework (basf2), currently being developed for the Belle II experiment in Japan. This allows to develop code in Jupyter notebooks for every aspect of the event simulation, reconstruction and analysis chain. These interactive notebooks can be hosted as a centralized web service via jupyterhub with docker and used by all scientists of the Belle II Collaboration. Because of its generality and encapsulation, the setup can easily be scaled to large installations.

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

Dykstra, Dave; Garzoglio, Gabriele; Kim, Hyunwoo

As of 2012, a number of US Department of Energy (DOE) National Laboratories have access to a 100 Gb/s wide-area network backbone. The ESnet Advanced Networking Initiative (ANI) project is intended to develop a prototype network, based on emerging 100 Gb/s Ethernet technology. The ANI network will support DOE's science research programs. A 100 Gb/s network test bed is a key component of the ANI project. The test bed offers the opportunity for early evaluation of 100Gb/s network infrastructure for supporting the high impact data movement typical of science collaborations and experiments. In order to make effective use of thismore » advanced infrastructure, the applications and middleware currently used by the distributed computing systems of large-scale science need to be adapted and tested within the new environment, with gaps in functionality identified and corrected. As a user of the ANI test bed, Fermilab aims to study the issues related to end-to-end integration and use of 100 Gb/s networks for the event simulation and analysis applications of physics experiments. In this paper we discuss our findings from evaluating existing HEP Physics middleware and application components, including GridFTP, Globus Online, etc. in the high-speed environment. These will include possible recommendations to the system administrators, application and middleware developers on changes that would make production use of the 100 Gb/s networks, including data storage, caching and wide area access.« less

BelleII@home: Integrate volunteer computing resources into DIRAC in a secure way

NASA Astrophysics Data System (ADS)

Wu, Wenjing; Hara, Takanori; Miyake, Hideki; Ueda, Ikuo; Kan, Wenxiao; Urquijo, Phillip

2017-10-01

The exploitation of volunteer computing resources has become a popular practice in the HEP computing community as the huge amount of potential computing power it provides. In the recent HEP experiments, the grid middleware has been used to organize the services and the resources, however it relies heavily on the X.509 authentication, which is contradictory to the untrusted feature of volunteer computing resources, therefore one big challenge to utilize the volunteer computing resources is how to integrate them into the grid middleware in a secure way. The DIRAC interware which is commonly used as the major component of the grid computing infrastructure for several HEP experiments proposes an even bigger challenge to this paradox as its pilot is more closely coupled with operations requiring the X.509 authentication compared to the implementations of pilot in its peer grid interware. The Belle II experiment is a B-factory experiment at KEK, and it uses DIRAC for its distributed computing. In the project of BelleII@home, in order to integrate the volunteer computing resources into the Belle II distributed computing platform in a secure way, we adopted a new approach which detaches the payload running from the Belle II DIRAC pilot which is a customized pilot pulling and processing jobs from the Belle II distributed computing platform, so that the payload can run on volunteer computers without requiring any X.509 authentication. In this approach we developed a gateway service running on a trusted server which handles all the operations requiring the X.509 authentication. So far, we have developed and deployed the prototype of BelleII@home, and tested its full workflow which proves the feasibility of this approach. This approach can also be applied on HPC systems whose work nodes do not have outbound connectivity to interact with the DIRAC system in general.

Pharmacological intervention against bubble-induced platelet aggregation in a rat model of decompression sickness

PubMed Central

Vallée, Nicolas; Ignatescu, Mihaela; Bourdon, Lionel

2011-01-01

Decompression sickness (DCS) with alterations in coagulation system and formation of platelet thrombi occurs when a subject is subjected to a reduction in environmental pressure. Blood platelet consumption after decompression is clearly linked to bubble formation in humans and offers an index for evaluating DCS severity in animal models. Previous studies highlighted a predominant involvement of platelet activation and thrombin generation in bubble-induced platelet aggregation (BIPA). To study the mechanism of the BIPA in DCS, we examined the effect of acetylsalicylic acid (ASA), heparin (Hep), and clopidogrel (Clo), with anti-thrombotic dose pretreatment in a rat model of DCS. Male Sprague-Dawley rats (n = 208) were randomly assigned to one experimental group treated before the hyperbaric exposure and decompression protocol either with ASA (3×100 mg·kg−1·day−1, n = 30), Clo (50 mg·kg−1·day−1, n = 60), Hep (500 IU/kg, n = 30), or to untreated group (n = 49). Rats were first compressed to 1,000 kPa (90 msw) for 45 min and then decompressed to surface in 38 min. In a control experiment, rats were treated with ASA (n = 13), Clo (n = 13), or Hep (n = 13) and maintained at atmospheric pressure for an equivalent period of time. Onset of DCS symptoms and death were recorded during a 60-min observation period after surfacing. DCS evaluation included pulmonary and neurological signs. Blood samples for platelet count (PC) were taken 30 min before hyperbaric exposure and 30 min after surfacing. Clo reduces the DCS mortality risk (mortality rate: 3/60 with Clo, 15/30 with ASA, 21/30 with Hep, and 35/49 in the untreated group) and DCS severity (neurological DCS incidence: 9/60 with Clo, 6/30 with ASA, 5/30 with Hep, and 12/49 in the untreated group). Clo reduced fall in platelet count and BIPA (−4,5% with Clo, −19.5% with ASA, −19,9% with Hep, and −29,6% in the untreated group). ASA, which inhibits the thromboxane A2 pathway, and Hep, which inhibits thrombin generation, have no protective effect on DCS incidence. Clo, a specific ADP-receptor antagonist, reduces post-decompression platelet consumption. These results point to the predominant involvement of the ADP release in BIPA but cannot differentiate definitively between bubble-induced vessel wall injury and bubble-blood component interactions in DCS. PMID:21212250

``Recent experiences and future expectations in data storage technology''

NASA Astrophysics Data System (ADS)

Pfister, Jack

1990-08-01

For more than 10 years the conventional media for High Energy Physics has been 9 track magnetic tape in various densities. More recently, especially in Europe, the IBM 3480 technology has been adopted while in the United States, especially at Fermilab, 8 mm is being used by the largest experiments as a primary recording media and where possible they are using 8 mm for the production, analysis and distribution of data summary tapes. VHS and Digital Audio tape have recurrently appeared but seem to serve primarily as a back-up storage media. The reasons for what appear to be a radical departure are many. Economics (media and controllers are inexpensive), form factor (two gigabytes per shirt pocket), and convenience (fewer mounts/dismounts per minute) are dominant among the reasons. The traditional data media suppliers seem to have been content to evolve the traditional media at their own pace with only modest enhancements primarily in ``value engineering'' of extant products. Meanwhile, start-up companies providing small system and workstations sought other media both to reduce the price of their offerings and respond to the real need of lower cost back-up for lower cost systems. This happening in a market context where traditional computer systems vendors were leaving the tape market altogether or shifting to ``3480'' technology which has certainly created a climate for reconsideration and change. The newest data storage products, in most cases, are not coming from the technologies developed by the computing industry but by the audio and video industry. Just where these flopticals, opticals, 19 mm tape and the new underlying technologies, such as, ``digital paper'' may fit in the HEP computing requirement picture will be reviewed. What these technologies do for and to HEP will be discussed along with some suggestions for a methodology for tracking and evaluating extant and emerging technologies.

External validation of the HIT Expert Probability (HEP) score.

PubMed

Joseph, Lee; Gomes, Marcelo P V; Al Solaiman, Firas; St John, Julie; Ozaki, Asuka; Raju, Manjunath; Dhariwal, Manoj; Kim, Esther S H

2015-03-01

The diagnosis of heparin-induced thrombocytopenia (HIT) can be challenging. The HIT Expert Probability (HEP) Score has recently been proposed to aid in the diagnosis of HIT. We sought to externally and prospectively validate the HEP score. We prospectively assessed pre-test probability of HIT for 51 consecutive patients referred to our Consultative Service for evaluation of possible HIT between August 1, 2012 and February 1, 2013. Two Vascular Medicine fellows independently applied the 4T and HEP scores for each patient. Two independent HIT expert adjudicators rendered a diagnosis of HIT likely or unlikely. The median (interquartile range) of 4T and HEP scores were 4.5 (3.0, 6.0) and 5 (3.0, 8.5), respectively. There were no significant differences between area under receiver-operating characteristic curves of 4T and HEP scores against the gold standard, confirmed HIT [defined as positive serotonin release assay and positive anti-PF4/heparin ELISA] (0.74 vs 0.73, p = 0.97). HEP score ≥ 2 was 100 % sensitive and 16 % specific for determining the presence of confirmed HIT while a 4T score > 3 was 93 % sensitive and 35 % specific. In conclusion, the HEP and 4T scores are excellent screening pre-test probability models for HIT, however, in this prospective validation study, test characteristics for the diagnosis of HIT based on confirmatory laboratory testing and expert opinion are similar. Given the complexity of the HEP scoring model compared to that of the 4T score, further validation of the HEP score is warranted prior to widespread clinical acceptance.

Alteration of mitochondrial membrane potential by Spirulina platensis C-phycocyanin induces apoptosis in the doxorubicinresistant human hepatocellular-carcinoma cell line HepG2.

PubMed

Roy, Karnati R; Arunasree, Kalle M; Reddy, Nishant P; Dheeraj, Bhavanasi; Reddy, Gorla Venkateswara; Reddanna, Pallu

2007-07-01

C-PC (C-phycocyanin) is a water-soluble biliprotein from the filamentous cyanobacterium Spirulina platensis with potent antioxidant, anti-inflammatory and anticancerous properties. In the present study, the effect of C-PC was tested on the proliferation of doxorubicin-sensitive (S-HepG2) and -resistant (R-HepG2) HCC (hepatocellular carcinoma) cell lines. These studies indicate a 50% decrease in the proliferation of S- and R-HepG2 cells treated with 40 and 50 microM C-PC for 24 h respectively. C-PC also enhanced the sensitivity of R-HepG2 cells to doxorubicin. R-HepG2 cells treated with C-PC showed typical apoptotic features such as membrane blebbing and DNA fragmentation. Flow-cytometric analysis of R-HepG2 cells treated with 10, 25 and 50 microM C-PC for 24 h showed 18.8, 39.72 and 65.64% cells in sub-G(0)/G(1)-phase respectively. Cytochrome c release, decrease in membrane potential, caspase 3 activation and PARP [poly(ADP-ribose) polymerase] cleavage were observed in C-PC-treated R-HepG2 cells. These studies also showed down-regulation of the anti-apoptotic protein Bcl-2 and up-regulation of the pro-apoptotic Bax (Bcl2-associated X-protein) protein in the R-HepG2 cells treated with C-PC. The present study thus demonstrates that C-PC induces apoptosis in R-HepG2 cells and its potential as an anti-HCC agent.

Physician Knowledge and Attitudes About Hepatitis A and Current Practices Regarding Hepatitis A Vaccination Delivery.

PubMed

Nelson, Noele P; Allison, Mandy A; Lindley, Megan C; Brtnikova, Michaela; Crane, Lori A; Beaty, Brenda L; Hurley, Laura P; Kempe, Allison

2017-07-01

To assess physicians': 1) knowledge and attitudes about hepatitis A disease and hepatitis A (HepA) vaccine, 2) child care and school HepA vaccine mandates, 3) practices related to HepA vaccine delivery, 4) factors associated with strongly recommending HepA vaccine to all 1- to 2-year-olds, and 5) feasibility of implementing HepA catch-up vaccination at health maintenance visits. A national survey was conducted among representative networks of pediatricians and family medicine physicians (FMs) from March to June, 2014 via e-mail or mail on the basis of provider preference. Response rates were 81% (356 of 440) among pediatricians and 75% (348 of 464) among FMs. Less than 50% correctly identified that hepatitis A virus (HAV) infection is usually asymptomatic in young children and that morbidity from HAV disease increases with age. Ninety-two percent of pediatricians and 59% of FMs strongly recommend HepA vaccine for all 1- to 2-year-olds. In addition to practice specialty, belief that HepA vaccine is required for kindergarten enrollment was the most robust predictor of strong physician recommendation. Gaps in knowledge regarding HAV infection and hepatitis A recommendations and lack of a strong recommendation for routine HepA vaccination of young children among FMs likely contribute to suboptimal coverage. Closing knowledge gaps and addressing barriers that prevent all physicians from strongly recommending HepA vaccine to 1- to 2-year-olds could help increase HepA vaccine coverage and ultimately improve population protection against HAV infection. Published by Elsevier Inc.

The Interface of Clinical Decision-Making With Study Protocols for Knowledge Translation From a Walking Recovery Trial.

PubMed

Hershberg, Julie A; Rose, Dorian K; Tilson, Julie K; Brutsch, Bettina; Correa, Anita; Gallichio, Joann; McLeod, Molly; Moore, Craig; Wu, Sam; Duncan, Pamela W; Behrman, Andrea L

2017-01-01

Despite efforts to translate knowledge into clinical practice, barriers often arise in adapting the strict protocols of a randomized, controlled trial (RCT) to the individual patient. The Locomotor Experience Applied Post-Stroke (LEAPS) RCT demonstrated equal effectiveness of 2 intervention protocols for walking recovery poststroke; both protocols were more effective than usual care physical therapy. The purpose of this article was to provide knowledge-translation tools to facilitate implementation of the LEAPS RCT protocols into clinical practice. Participants from 2 of the trial's intervention arms: (1) early Locomotor Training Program (LTP) and (2) Home Exercise Program (HEP) were chosen for case presentation. The two cases illustrate how the protocols are used in synergy with individual patient presentations and clinical expertise. Decision algorithms and guidelines for progression represent the interface between implementation of an RCT standardized intervention protocol and clinical decision-making. In each case, the participant presents with a distinct clinical challenge that the therapist addresses by integrating the participant's unique presentation with the therapist's expertise while maintaining fidelity to the LEAPS protocol. Both participants progressed through an increasingly challenging intervention despite their own unique presentation. Decision algorithms and exercise progression for the LTP and HEP protocols facilitate translation of the RCT protocol to the real world of clinical practice. The two case examples to facilitate translation of the LEAPS RCT into clinical practice by enhancing understanding of the protocols, their progression, and their application to individual participants.Video Abstract available for more insights from the authors (see Supplemental Digital Content 1, available at: http://links.lww.com/JNPT/A147).

WLCG and IPv6 - The HEPiX IPv6 working group

DOE PAGES

Campana, S.; K. Chadwick; Chen, G.; ...

2014-06-11

The HEPiX (http://www.hepix.org) IPv6 Working Group has been investigating the many issues which feed into the decision on the timetable for the use of IPv6 (http://www.ietf.org/rfc/rfc2460.txt) networking protocols in High Energy Physics (HEP) Computing, in particular in the Worldwide Large Hadron Collider (LHC) Computing Grid (WLCG). RIPE NCC, the European Regional Internet Registry (RIR), ran out ofIPv4 addresses in September 2012. The North and South America RIRs are expected to run out soon. In recent months it has become more clear that some WLCG sites, including CERN, are running short of IPv4 address space, now without the possibility of applyingmore » for more. This has increased the urgency for the switch-on of dual-stack IPv4/IPv6 on all outward facing WLCG services to allow for the eventual support of IPv6-only clients. The activities of the group include the analysis and testing of the readiness for IPv6 and the performance of many required components, including the applications, middleware, management and monitoring tools essential for HEP computing. Many WLCG Tier 1/2 sites are participants in the group's distributed IPv6 testbed and the major LHC experiment collaborations are engaged in the testing. We are constructing a group web/wiki which will contain useful information on the IPv6 readiness of the various software components and a knowledge base (http://hepix-ipv6.web.cern.ch/knowledge-base). Furthermore, this paper describes the work done by the working group and its future plans.« less

WLCG and IPv6 - the HEPiX IPv6 working group

NASA Astrophysics Data System (ADS)

Campana, S.; Chadwick, K.; Chen, G.; Chudoba, J.; Clarke, P.; Eliáš, M.; Elwell, A.; Fayer, S.; Finnern, T.; Goossens, L.; Grigoras, C.; Hoeft, B.; Kelsey, D. P.; Kouba, T.; López Muñoz, F.; Martelli, E.; Mitchell, M.; Nairz, A.; Ohrenberg, K.; Pfeiffer, A.; Prelz, F.; Qi, F.; Rand, D.; Reale, M.; Rozsa, S.; Sciaba, A.; Voicu, R.; Walker, C. J.; Wildish, T.

2014-06-01

The HEPiX (http://www.hepix.org) IPv6 Working Group has been investigating the many issues which feed into the decision on the timetable for the use of IPv6 (http://www.ietf.org/rfc/rfc2460.txt) networking protocols in High Energy Physics (HEP) Computing, in particular in the Worldwide Large Hadron Collider (LHC) Computing Grid (WLCG). RIPE NCC, the European Regional Internet Registry (RIR), ran out ofIPv4 addresses in September 2012. The North and South America RIRs are expected to run out soon. In recent months it has become more clear that some WLCG sites, including CERN, are running short of IPv4 address space, now without the possibility of applying for more. This has increased the urgency for the switch-on of dual-stack IPv4/IPv6 on all outward facing WLCG services to allow for the eventual support of IPv6-only clients. The activities of the group include the analysis and testing of the readiness for IPv6 and the performance of many required components, including the applications, middleware, management and monitoring tools essential for HEP computing. Many WLCG Tier 1/2 sites are participants in the group's distributed IPv6 testbed and the major LHC experiment collaborations are engaged in the testing. We are constructing a group web/wiki which will contain useful information on the IPv6 readiness of the various software components and a knowledge base (http://hepix-ipv6.web.cern.ch/knowledge-base). This paper describes the work done by the working group and its future plans.

Online reverse phase-high-performance liquid chromatography-fluorescence detection-electrospray ionization-mass spectrometry separation and characterization of heparan sulfate, heparin, and low-molecular weight-heparin disaccharides derivatized with 2-aminoacridone.

PubMed

Galeotti, Fabio; Volpi, Nicola

2011-09-01

A high-resolution online reverse-phase-high-performance liquid chromatography (RP-HPLC)-fluorescence detector (Fd)-electrospray ionization-mass spectrometry (ESI-MS) separation and structural characterization of disaccharides prepared from heparin (Hep), heparan sulfate (HS), and various low-molecular-weight (LMW)-Hep using heparin lyases and derivatization with 2-aminoacridone (AMAC) are described. A total of 12 commercially available Hep/HS-derived unsaturated disaccharides were separated and unambiguously identified on the basis of their retention times and mass spectra. The constituent disaccharides of various samples, including unfractionated Hep/HS, fast-moving and slow-moving Hep components, and several marketed products, were characterized. Furthermore, for the first time, the saturated trisulfated disaccharide belonging to the nonreducing end of Heps was detected as being approximately 2% in unfractionated samples and ~15-21% in LMW-Heps prepared by nitrous acid depolymerization. No desalting of the commercial products prior to enzymatic digestion or prepurification steps to eliminate any excess of AMAC reagent or interference from proteins, peptides, and other sample impurities before RP-HPLC-Fd-ESI-MS injection were necessary. This method has applicability for the rapid differentiation of pharmaceutical Heps and LMW-Heps prepared by means of different depolymerization processes and for compositional analysis of small amounts of samples derived from biological sources by using the highly sensitive fluorescence detector.

Immobilization of heparin/poly-(L)-lysine nanoparticles on dopamine-coated surface to create a heparin density gradient for selective direction of platelet and vascular cells behavior.

PubMed

Liu, Tao; Liu, Yang; Chen, Yuan; Liu, Shihui; Maitz, Manfred F; Wang, Xue; Zhang, Kun; Wang, Jian; Wang, Yuan; Chen, Junying; Huang, Nan

2014-05-01

Restenosis, thrombosis formation and delayed endothelium regeneration continue to be problematic for coronary artery stent therapy. To improve the hemocompatibility of the cardiovascular implants and selectively direct vascular cell behavior, a novel kind of heparin/poly-l-lysine (Hep/PLL) nanoparticle was developed and immobilized on a dopamine-coated surface. The stability and structural characteristics of the nanoparticles changed with the Hep:PLL concentration ratio. A Hep density gradient was created on a surface by immobilizing nanoparticles with various Hep:PLL ratios on a dopamine-coated surface. Antithrombin III binding quantity was significantly enhanced, and in plasma the APTT and TT times as coagulation tests were prolonged, depending on the Hep density. A low Hep density is sufficient to prevent platelet adhesion and activation. The sensitivity of vascular cells to the Hep density is very different: high Hep density inhibits the growth of all vascular cells, while low Hep density could selectively inhibit smooth muscle cell hyperplasia but promote endothelial progenitor cells and endothelial cell proliferation. These observations provide important guidance for modification of surface heparinization. We suggest that this method will provide a potential means to construct a suitable platform on a stent surface for selective direction of vascular cell behavior with low side effects. Copyright © 2013 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Aroused with heart: Modulation of heartbeat evoked potential by arousal induction and its oscillatory correlates

PubMed Central

Luft, Caroline Di Bernardi; Bhattacharya, Joydeep

2015-01-01

Recent studies showed that the visceral information is constantly processed by the brain, thereby potentially influencing cognition. One index of such process is the heartbeat evoked potential (HEP), an ERP component related to the cortical processing of the heartbeat. The HEP is sensitive to a number of factors such as motivation, attention, pain, which are associated with higher levels of arousal. However, the role of arousal and its associated brain oscillations on the HEP has not been characterized, yet it could underlie the previous findings. Here we analysed the effects of high- (HA) and low-arousal (LA) induction on the HEP. Further, we investigated the brain oscillations and their role in the HEP in response to HA and LA inductions. As compared to LA, HA was associated with a higher HEP and lower alpha oscillations. Interestingly, individual differences in the HEP modulation by arousal induction were correlated with alpha oscillations. In particular, participants with higher alpha power during the arousal inductions showed a larger HEP in response to HA compared to LA. In summary, we demonstrated that arousal induction affects the cortical processing of heartbeats; and that the alpha oscillations may modulate this effect. PMID:26503014

Mitochondria are required for ATM activation by extranuclear oxidative stress in cultured human hepatoblastoma cell line Hep G2 cells

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

Morita, Akinori, E-mail: morita@tokushima-u.ac.jp; Department of Radiological Science, Institute of Health Biosciences, The University of Tokushima Graduate School, Tokushima 770-8509; Tanimoto, Keiji

2014-01-24

Highlights: • Oxidative ATM activation can occur in the absence of nuclear DNA damage response. • The oxidized Hep G2 cells were subjected to subcellular fractionation. • The obtained results suggest that the ATM activation occurs in mitochondria. • ATM failed to respond to oxidative stress in mitochondria-depleted Hep G2 cells. • Mitochondria are required for the oxidative activation of ATM. - Abstract: Ataxia–telangiectasia mutated (ATM) is a serine/threonine protein kinase that plays a central role in DNA damage response (DDR). A recent study reported that oxidized ATM can be active in the absence of DDR. However, the issue ofmore » where ATM is activated by oxidative stress remains unclear. Regarding the localization of ATM, two possible locations, namely, mitochondria and peroxisomes are possible. We report herein that ATM can be activated when exposed to hydrogen peroxide without inducing nuclear DDR in Hep G2 cells, and the oxidized cells could be subjected to subcellular fractionation. The first detergent-based fractionation experiment revealed that active, phosphorylated ATM was located in the second fraction, which also contained both mitochondria and peroxisomes. An alternative fractionation method involving homogenization and differential centrifugation, which permits the light membrane fraction containing peroxisomes to be produced, but not mitochondria, revealed that the light membrane fraction contained only traces of ATM. In contrast, the heavy membrane fraction, which mainly contained mitochondrial components, was enriched in ATM and active ATM, suggesting that the oxidative activation of ATM occurs in mitochondria and not in peroxisomes. In Rho 0-Hep G2 cells, which lack mitochondrial DNA and functional mitochondria, ATM failed to respond to hydrogen peroxide, indicating that mitochondria are required for the oxidative activation of ATM. These findings strongly suggest that ATM can be activated in response to oxidative stress in mitochondria and that this occurs in a DDR-independent manner.« less

Human beta-endorphin: synthesis and biological activity of analogs with substitutions in positions 2, 9, 18, 27 and 31.

PubMed

Yeung, H W; Yamashiro, D; Tseng, L F; Chang, W C; Li, C H

1981-02-01

Four analogs of the opioid peptide human beta-endorphin (Bh-EP) have been synthesized: [D-Lys9, Phe27, Gly31]-beta h-EP, [D-PHe18,Phe27,Gly31]-beta h-EP, [D-Thr2,D-Lys9,Phe27,Gly31]-beta h-EP, and [D-Thr2,D-Phe18,Phe27,Gly31]-beta h-EP. All are practically indistinguishable from beta h-EP in the guinea pig ileum assay. All show diminished analgesic potency in the mouse tail-flick assay.

Polydatin inhibits cell proliferation and induces apoptosis in laryngeal cancer and HeLa cells via suppression of the PDGF/AKT signaling pathway.

PubMed

Li, Haixia; Shi, Baoyuan; Li, Yanyun; Yin, Fengfang

2017-07-01

Polydatin (PD), a stilbene compound extracted from Polygonum cuspidatum, is suggested to possess anti-cancer activities, including inhibition of cell proliferation, cell cycle arrest, and induction of apoptosis. The platelet-derived growth factor (PDGF)/AKT signaling pathway plays complex roles in tumor suppression. However, the effect of PD on the PDGF/AKT signaling pathway in laryngeal cancer and HeLa cells has not been explored. MTT assay and flow cytometry showed that PD inhibited cell proliferation and induced apoptosis in Hep-2 and AMC-HN-8 cells. Western blot analysis indicated that PD inhibited the expression levels of PDGF-B and phosphorylated AKT (p-AKT) in both cells. Treatment of PDGF-B siRNA or PDGFR inhibitor found that after the PDGF signaling was inactivated, p-AKT expression was significantly decreased in Hep-2 cells. Tumor xenograft experiment in nude mice indicated PD significantly inhibited the growth of Hep-2 cells in vivo. In conclusion, PD inhibited cell proliferation and induced apoptosis in laryngeal cancer and HeLa cells via inactivation of the PDGF/AKT signaling pathway. © 2017 Wiley Periodicals, Inc.

[Stimulation of human hepatic stellate cells by cytochrome P4502E1-mediated oxidative stress].

PubMed

Li, Jing; Liu, Tian-hui; You, Hong; Xu, You-qing; Wang, Chen

2010-08-01

To explore the stimulation of human hepatic stellate cells by Cytochrome P4502E1-mediated oxidative stress. HepG2-line was transfected with human CYP2E1 plasmid (HepG2/CYP2E1) and empty plasmid (HepG2/PCI) respectively. The CYP2E1 expression was evaluated with RT-PCR and Western blot. MDA was measured in culture medium of HepG2 cell lines. LX2 was co-incubated with HepG2/CYP2E1, HepG2/PCI and HepG2 respectively. The level of hydroxyproline in culture medium was examined in 48 hours and the cells were lysated and total RNA and protein were extracted. COL-1 and MMP2 mRNA levels were detected by RT-PCR and analyzed semi-quantitatively. PICP proteins were measured by ELISA. Zymography was performed to investigate MMP2 enzymatic activities. (1) MDA from the HepG2 which (HepG2/CYP2E1)express human CYP2E1 (6.51+/-0.25) was significantly higher than that from the HepG2 which do not (HepG2/PCI) express human CYP2E1 (3.07+/-0.29) and HepG2 alone (2.57+/-0.29). (F=22.66, all P<0.01). (2) After co-incubated for 48 hours,the level of hydroxyproline in culture medium (35.24+/-3.52) excreted from CYP2E1/LX2 could significantly increase (F=58.89, P is less than 0.01). PICP protein (540.01+/-11.38) excreted from CYP2E1/LX2 was significantly increased (F=124.97, P<0.01). Zymography showed MMP2 gene expression and enzymatic activities of MMP2 had no difference among the groups (F=0.29, P>0.05) (F=0.33, P>0.05). CYP2E1 derived oxidative stress mediated stimulation of collagen I synthesis by hepatic stellate cells. Hydroxyproline excreted by LX2 was increased by CYP2E1. COL-1mRNA had no difference among the groups (F=0.73, P>0.05).

Prokaryotic arsenate reductase enhances arsenate resistance in Mammalian cells.

PubMed

Wu, Dan; Tao, Xuanyu; Wu, Gaofeng; Li, Xiangkai; Liu, Pu

2014-01-01

Arsenic is a well-known heavy metal toxicant in the environment. Bioremediation of heavy metals has been proposed as a low-cost and eco-friendly method. This article described some of recent patents on transgenic plants with enhanced heavy metal resistance. Further, to test whether genetic modification of mammalian cells could render higher arsenic resistance, a prokaryotic arsenic reductase gene arsC was transfected into human liver cancer cell HepG2. In the stably transfected cells, the expression level of arsC gene was determined by quantitative real-time PCR. Results showed that arsC was expressed in HepG2 cells and the expression was upregulated by 3 folds upon arsenate induction. To further test whether arsC has function in HepG2 cells, the viability of HepG2-pCI-ArsC cells exposed to arsenite or arsenate was compared to that of HepG2-pCI cells without arsC gene. The results indicated that arsC increased the viability of HepG2 cells by 25% in arsenate, but not in arsenite. And the test of reducing ability of stably transfected cells revealed that the concentration of accumulated trivalent arsenic increased by 25% in HepG2-pCI-ArsC cells. To determine the intracellular localization of ArsC, a fusion vector with fluorescent marker pEGFP-N1-ArsC was constructed and transfected into.HepG2. Laser confocal microscopy showed that EGFP-ArsC fusion protein was distributed throughout the cells. Taken together, these results demonstrated that prokaryotic arsenic resistant gene arsC integrated successfully into HepG2 genome and enhanced arsenate resistance of HepG2, which brought new insights of arsenic detoxification in mammalian cells.

Antioxidant and anticancer activity of Artemisia princeps var. orientalis extract in HepG2 and Hep3B hepatocellular carcinoma cells.

PubMed

Choi, Eun-Jeong; Kim, Gun-Hee

2013-10-01

The aim of the present study was to investigate antioxidant and the anticancerigen activity of a methanol extract from Artemisia princeps var. orientalis (APME), a well-known traditional herbal medicine in Asia, in hepatocellular cancer cells. To evaluate the antioxidant activity of APME, reactive oxygen species (ROS) and the antioxidant enzymes, superoxide dismutase (SOD) and catalase were investigated in HepG2 cells exposed to APME (5, 100, and 200 µg/mL) for 72 h. Then, to evaluate the anticancer activity of APME, we investigated the proliferation and apoptosis induction of HepG2 and Hep3B cells exposed to APME (1-200 µg/mL) for 24, 48, and 72 h. APME dose-dependently reduced the generation of ROS in the presence of H2O2 compared with control cells. Furthermore, it increased catalase and SOD activity. Moreover, APME inhibited cell proliferation in a dose- and time-dependent manner, but at concentrations lower than 100 µg/mL, the inhibition was less dose-dependent than time-dependent. HepG2 and Hep3B cells exposed to 5, 100, and 200 µg/mL APME for 72 h underwent cell cycle arrest and apoptosis. Exposure to APME resulted in a significant increase in the number of cells in G1 phase and a decrease in the G2/M phase cell population. In addition, APME induced P53 expression of HepG2 cells in a dose-dependent manner, and played a role in the downregulation of Bcl-2 and upregulation of Bax in both HepG2 and Hep3B cells. These results indicate the potential role of APME as an antioxidant and anticancerigen agent in hepatocarcinoma cell lines.

HEP Computing

Science.gov Websites

Computing Visitors who do not need a HEP linux account Visitors with laptops can use wireless network HEP linux account Step 1: Click Here for New Account Application After submitting the application, you

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

Varma, Shailly; Shrivastav, Anuraag; Health Research Division, Saskatchewan Cancer Agency, Saskatoon, SK S7N 4H4

Protein kinase B (Akt/PKB) is a Ser/Thr kinase that is involved in the regulation of cell proliferation/survival through mammalian target of rapamycin (mTOR) and the regulation of glycogen metabolism through glycogen synthase kinase 3{beta} (GSK-3{beta}) and glycogen synthase (GS). Rapamycin is an inhibitor of mTOR. The objective of this study was to investigate the effects of rapamycin pretreatment on the insulin mediated phosphorylation of Akt/PKB phosphorylation and GS activity in parental HepG2 and HepG2 cells with overexpression of constitutively active Akt1/PKB-{alpha} (HepG2-CA-Akt/PKB). Rapamycin pretreatment resulted in a decrease (20-30%) in the insulin mediated phosphorylation of Akt1 (Ser 473) in parentalmore » HepG2 cells but showed an upregulation of phosphorylation in HepG2-CA-Akt/PKB cells. Rictor levels were decreased (20-50%) in parental HepG2 cells but were not significantly altered in the HepG2-CA-Akt/PKB cells. Furthermore, rictor knockdown decreased the phosphorylation of Akt (Ser 473) by 40-60% upon rapamycin pretreatment. GS activity followed similar trends as that of phosphorylated Akt and so with rictor levels in these cells pretreated with rapamycin; parental HepG2 cells showed a decrease in GS activity, whereas as HepG2-CA-Akt/PKB cells showed an increase in GS activity. The changes in the levels of phosphorylated Akt/PKB (Ser 473) correlated with GS and protein phoshatase-1 activity.« less

Integration of Grid and Local Batch Resources at DESY

NASA Astrophysics Data System (ADS)

Beyer, Christoph; Finnern, Thomas; Gellrich, Andreas; Hartmann, Thomas; Kemp, Yves; Lewendel, Birgit

2017-10-01

As one of the largest resource centres DESY has to support differing work flows of users from various scientific backgrounds. Users can be for one HEP experiments in WLCG or Belle II as well as local HEP users but also physicists from other fields as photon science or accelerator development. By abandoning specific worker node setups in favour of generic flat nodes with middleware resources provided via CVMFS, we gain flexibility to subsume different use cases in a homogeneous environment. Grid jobs and the local batch system are managed in a HTCondor based setup, accepting pilot, user and containerized jobs. The unified setup allows dynamic re-assignment of resources between the different use cases. Monitoring is implemented on global batch system metrics as well as on a per job level utilizing corresponding cgroup information.

Free radical generation from an aniline derivative in HepG2 cells: a possible captodative effect.

PubMed

Horinouchi, Yuya; Summers, Fiona A; Ehrenshaft, Marilyn; Mason, Ronald P

2015-01-01

Xenobiotic metabolism can induce the generation of protein radicals, which are believed to play an important role in the toxicity of chemicals and drugs. It is therefore important to identify chemical structures capable of inducing macromolecular free radical formation in living cells. In this study, we evaluated the ability of four structurally related environmental chemicals, aniline, nitrosobenzene, N,N-dimethylaniline, and N,N-dimethyl-4-nitrosoaniline (DMNA), to induce free radicals and cellular damage in the hepatoma cell line HepG2. Cytotoxicity was assessed using lactate dehydrogenase assays, and morphological changes were observed using phase contrast microscopy. Protein free radicals were detected by immuno-spin trapping using in-cell western experiments and confocal microscopy to determine the subcellular locale of free radical generation. DMNA induced free radical generation, lactate dehydrogenase release, and morphological changes in HepG2 cells, whereas aniline, nitrosobenzene, N,N-dimethylaniline did not. Confocal microscopy showed that DMNA induced free radical generation mainly in the cytosol. Preincubation of HepG2 cells with N-acetylcysteine and 2,2'-dipyridyl significantly prevented free radical generation on subsequent incubation with DMNA, whereas preincubation with apocynin and dimethyl sulfoxide had no effect. These results suggest that DMNA is metabolized to reactive free radicals capable of generating protein radicals which may play a critical role in DMNA toxicity. We propose that the captodative effect, the combined action of the electron-releasing dimethylamine substituent, and the electron-withdrawing nitroso substituent, leads to a thermodynamically stabilized radical, facilitating enhanced protein radical formation by DMNA. Copyright © 2014 Elsevier Inc. All rights reserved.

Hepatoprotective effect of Cirsium arisanense Kitamura in tacrine-treated hepatoma Hep 3B cells and C57BL mice.

PubMed

Ku, Kuo-Lung; Tsai, Chu-Tsai; Chang, Wei-Min; Shen, Mei-Lin; Wu, Chia-Tien; Liao, Hui-Fen

2008-01-01

Cirsium arisanense Kitamura (Compositae) has been used for hundreds of years in Taiwan as a folk medicine for hepatoprotection. However, no scientific research has demonstrated this effect. In the present study, we extracted the phenol-containing aqueous components of C. arisanense roots (CaR) and leaves/stem (CaL), and then assessed their hepatoprotective activities in both human hepatocellular carcinoma Hep 3B cells and C57BL/6 mice strain. High performance liquid chromatography (HPLC) analysis revealed that the components of CaR and CaL differed from those of the positive control silymarin. CaR exhibited a higher phenolic content and antioxidant capacity than CaL. Hep 3B cells treated with silymarin (0-200 microg/ml) demonstrated a concentration-dependent decrease in viability; however, both CaR and CaL did not exhibit any apparent cytotoxicity. Silymarin at 100 microg/ml, as well as CaR and CaL, not only protect Hep 3B cells from tacrine-induced hepatotoxicity but also decrease the expression of hepatitis B surface antigen (HBsAg). Moreover, an animal experiment demonstrated that CaR, CaL, and silymarin have hepatoprotective effects in C57BL/6 mice injected with tacrine, and they significantly decrease the levels of plasma alanine aminotransferase (ALT) and aspartate aminotransferase (AST). These effects of CaR and silymarin, but not of CaL, may occur via an increase in the hepatic glutathione level and the elimination of the nitric oxide production. In conclusion, the phenol-containing aqueous components from C. arisanense have potential in hepatoprotection.

Altered Hepa1-6 cells by dimethyl sulfoxide (DMSO)-treatment induce anti-tumor immunity in vivo.

PubMed

Jiang, Zhengyu; Zhang, Hongxia; Wang, Ye; Yu, Bin; Wang, Chen; Liu, Changcheng; Lu, Juan; Chen, Fei; Wang, Minjun; Yu, Xinlu; Lin, Jiahao; Pan, Xinghua; Wang, Pin; Zhu, Haiying

2016-02-23

Cancer immunotherapy is the use of the immune system to treat cancer. Our current research proposed an optional strategy of activating immune system involving in cancer immunotherapy. When being treated with 2% DMSO in culture medium, Hepa1-6 cells showed depressed proliferation with no significant apoptosis or decreased viability. D-hep cells, Hepa1-6 cells treated with DMSO for 7 days, could restore to the higher proliferation rate in DMSO-free medium, but alteration of gene expression profile was irreversible. Interestingly, tumors from D-hep cells, not Hepa1-6 cells, regressed in wild-type C57BL/6 mice whereas D-hep cells exhibited similar tumorigenesis as Hep1-6 cells in immunodeficient mice. As expected, additional Hepa1-6 cells failed to form tumors in the D-hep-C57 mice in which D-hep cells were eliminated. Further research confirmed that D-hep-C57 mice established anti-tumor immunity against Hepa1-6 cells. Our research proposed viable tumor cells with altered biological features by DMSO-treatment could induce anti-tumor immunity in vivo.

Cortisol rapidly affects amplitudes of heartbeat-evoked brain potentials--implications for the contribution of stress to an altered perception of physical sensations?

PubMed

Schulz, André; Strelzyk, Florian; Ferreira de Sá, Diana S; Naumann, Ewald; Vögele, Claus; Schächinger, Hartmut

2013-11-01

Little is known about the impact of stress and stress hormones on the processing of visceral-afferent signals. Clinical data suggest that cortisol may lower the threshold for interoceptive stimuli, while a pharmacological administration of cortisol decreases the sensitivity for physical symptoms. To clarify the role of cortisol for the processing of interoceptive signals, we investigated 16 healthy men on two occasions, once during the infusion of 4 mg of cortisol and once during the infusion of a placebo substance. Heartbeat-evoked potentials (HEP; derived from resting EEG and ECG, during open and closed eyes), which are psychophysiological indicators for the cortical processing of cardioceptive signals, were measured over 6-min periods once before, and four times after the infusion (1-7, 11-17, 21-27 and 31-37 min). We found that HEP amplitudes were higher during open than during closed eyes between 1 and 17 min after cortisol infusion. There was no effect of cortisol on heart rate. We conclude that cortisol may rapidly modulate the cortical processing of cardioceptive neural signals. These results may have relevance for the effects of stress on the development and maintenance of psychosomatic symptoms. Copyright © 2013 Elsevier Ltd. All rights reserved.

On the incidence of meteorological and hydrological processors: Effect of resolution, sharpness and reliability of hydrological ensemble forecasts

NASA Astrophysics Data System (ADS)

Abaza, Mabrouk; Anctil, François; Fortin, Vincent; Perreault, Luc

2017-12-01

Meteorological and hydrological ensemble prediction systems are imperfect. Their outputs could often be improved through the use of a statistical processor, opening up the question of the necessity of using both processors (meteorological and hydrological), only one of them, or none. This experiment compares the predictive distributions from four hydrological ensemble prediction systems (H-EPS) utilising the Ensemble Kalman filter (EnKF) probabilistic sequential data assimilation scheme. They differ in the inclusion or not of the Distribution Based Scaling (DBS) method for post-processing meteorological forecasts and the ensemble Bayesian Model Averaging (ensemble BMA) method for hydrological forecast post-processing. The experiment is implemented on three large watersheds and relies on the combination of two meteorological reforecast products: the 4-member Canadian reforecasts from the Canadian Centre for Meteorological and Environmental Prediction (CCMEP) and the 10-member American reforecasts from the National Oceanic and Atmospheric Administration (NOAA), leading to 14 members at each time step. Results show that all four tested H-EPS lead to resolution and sharpness values that are quite similar, with an advantage to DBS + EnKF. The ensemble BMA is unable to compensate for any bias left in the precipitation ensemble forecasts. On the other hand, it succeeds in calibrating ensemble members that are otherwise under-dispersed. If reliability is preferred over resolution and sharpness, DBS + EnKF + ensemble BMA performs best, making use of both processors in the H-EPS system. Conversely, for enhanced resolution and sharpness, DBS is the preferred method.

[Anti-proliferation Effect of Taraxacum mongolicum Extract in HepG2 Cells and Its Mechanism].

PubMed

Guo, Jun-bin; Ye, Hai-hong; Chen, Jian-feng

2015-10-01

To study the anti-proliferation effect of Taraxacum mongolicum extract in HepG2 cells and its mechanism. The total proteins of HepG2 cells treated with Taraxacum mongolicum extract were. extracted and mitochondria-mediated apoptosis-related proteins (Survivin, Mcl-1, BCL-xL, BCL-2, Smac, BAX, Bad, Cytochrome c and Caspase-3/7/9) were detected by Western blot. Taraxacum mongolicum extract obviously inhibited the proliferation of HepG2 cells and the expression of anti-apoptotic proteins (Survivin, BCL-xL and BCL-2), increased the expression of pro-apoptotic proteins (Smac and Caspase-3/7/9), and promoted the release of Cytochrome c from mitochondria to cytoplasm in HepG2 cells. The effects were in a dose-independent mode. Taraxacum mongolicum extract can inhibit the proliferation of HepG2 cells and the anti-proliferation mechanism is related to mitochondria-mediated apoptosis.

The HAAPI (Home Arm Assistance Progression Initiative) Trial: A Novel Robotics Delivery Approach in Stroke Rehabilitation.

PubMed

Wolf, Steven L; Sahu, Komal; Bay, R Curtis; Buchanan, Sharon; Reiss, Aimee; Linder, Susan; Rosenfeldt, Anson; Alberts, Jay

2015-01-01

Geographical location, socioeconomic status, and logistics surrounding transportation impede access of poststroke individuals to comprehensive rehabilitative services. Robotic therapy may enhance telerehabilitation by delivering consistent and state-of-the art therapy while allowing remote monitoring and adjusting therapy for underserved populations. The Hand Mentor Pro (HMP) was incorporated within a home exercise program (HEP) to improve upper-extremity (UE) functional capabilities poststroke. To determine the efficacy of a home-based telemonitored robotic-assisted therapy as part of a HEP compared with a dose-matched HEP-only intervention among individuals less than 6 months poststroke and characterized as underserved. In this prospective, single-blinded, multisite, randomized controlled trial, 99 hemiparetic participants with limited access to UE rehabilitation were randomized to either (1) the experimental group, which received combined HEP and HMP for 3 h/d ×5 days ×8 weeks, or (2) the control group, which received HEP only at an identical dosage. Weekly communication between the supervising therapist and participant promoted compliance and progression of the HEP and HMP prescription. The Action Research Arm Test and Wolf Motor Function Test along with the Fugl-Meyer Assessment (UE) were primary and secondary outcome measures, respectively, undertaken before and after the interventions. Both groups demonstrated improvement across all UE outcomes. Robotic + HEP and HEP only were both effectively delivered remotely. There was no difference between groups in change in motor function over time. Additional research is necessary to determine the appropriate dosage of HMP and HEP. © The Author(s) 2015.

The HAAPI (Home Arm Assistance Progression Initiative) Trial: - A Novel Robotics Delivery Approach in Stroke Rehabilitation

PubMed Central

Wolf, Steven L.; Sahu, Komal; Bay, R. Curtis; Buchanan, Sharon; Reiss, Aimee; Linder, Susan; Rosenfeldt, Anson; Alberts, Jay

2015-01-01

Background Geographical location, socioeconomic status and logistics surrounding transportation impede access of post-stroke individuals to comprehensive rehabilitative services. Robotic therapy may enhance telerehabilitation by delivering consistent and state-of-the art therapy while allowing for the remote monitoring and adjusting therapy for underserved populations. The Hand Mentor Pro (HMP), was incorporated within a home exercise program (HEP) to improve upper extremity functional capabilities post-stroke. Objective To determine the efficacy of a home-based telemonitored robotic-assisted therapy as part of a HEP compared with a dose-matched HEP-only intervention among individuals less than 6 months post-stroke and characterized as underserved. Methods In this prospective, single-blinded, multisite, randomized controlled trial, 99 hemiparetic participants with limited access to upper extremity rehabilitation were randomized to the: 1) experimental group which received combined HEP and HMP for 3 hrs/day x 5 days x 8 weeks; or 2) control group which received HEP only at an identical dosage. Weekly communication between the supervising therapist and participant promoted compliance and progression of the HEP and HMP prescription. The Action Research Arm Test and Wolf Motor Function Test along with the Fugl Meyer Assessment (upper extremity) were primary and secondary outcome measures respectively, undertaken before and after the interventions. Results Both groups demonstrated improvement across all upper extremity outcomes. Conclusions Robotic+HEP and HEP only were both effectively delivered remotely. There was no difference between groups in change in motor function over time, additional research is necessary to determine appropriate dosage of HMP and HEP. PMID:25782693

Software Aspects of IEEE Floating-Point Computations for Numerical Applications in High Energy Physics

ScienceCinema

Arnold, Jeffrey

2018-05-14

Floating-point computations are at the heart of much of the computing done in high energy physics. The correctness, speed and accuracy of these computations are of paramount importance. The lack of any of these characteristics can mean the difference between new, exciting physics and an embarrassing correction. This talk will examine practical aspects of IEEE 754-2008 floating-point arithmetic as encountered in HEP applications. After describing the basic features of IEEE floating-point arithmetic, the presentation will cover: common hardware implementations (SSE, x87) techniques for improving the accuracy of summation, multiplication and data interchange compiler options for gcc and icc affecting floating-point operations hazards to be avoided. About the speaker: Jeffrey M Arnold is a Senior Software Engineer in the Intel Compiler and Languages group at Intel Corporation. He has been part of the Digital->Compaq->Intel compiler organization for nearly 20 years; part of that time, he worked on both low- and high-level math libraries. Prior to that, he was in the VMS Engineering organization at Digital Equipment Corporation. In the late 1980s, Jeff spent 2½ years at CERN as part of the CERN/Digital Joint Project. In 2008, he returned to CERN to spent 10 weeks working with CERN/openlab. Since that time, he has returned to CERN multiple times to teach at openlab workshops and consult with various LHC experiments. Jeff received his Ph.D. in physics from Case Western Reserve University.

Label-free Proteomic Analysis of Exosomes Derived from Inducible Hepatitis B Virus-Replicating HepAD38 Cell Line*

PubMed Central

Jia, Xiaofang; Chen, Jieliang; Megger, Dominik A.; Zhang, Xiaonan; Kozlowski, Maya; Zhang, Lijun; Fang, Zhong; Li, Jin; Chu, Qiaofang; Wu, Min; Li, Yaming; Sitek, Barbara; Yuan, Zhenghong

2017-01-01

Hepatitis B virus (HBV) infection is a major health problem worldwide. Recent evidence suggests that some viruses can manipulate the infection process by packing specific viral and cellular components into exosomes, small nanometer-sized (30–150 nm) vesicles secreted from various cells. However, the impact of HBV replication on the content of exosomes produced by hepatocytes has not been fully delineated. In this work, an HBV-inducible cell line HepAD38 was used to directly compare changes in the protein content of exosomes secreted from HepAD38 cells with or without HBV replication. Exosomes were isolated from supernantants of HepAD38 cells cultured with or without doxycycline (dox) and their purity was confirmed by transmission electron microscopy (TEM) and Western immunoblotting assays. Ion-intensity based label-free LC-MS/MS quantitation technologies were applied to analyze protein content of exosomes from HBV replicating cells [referred as HepAD38 (dox−)-exo] and from HBV nonreplicating cells [referred as HepAD38 (dox+)-exo]. A total of 1412 exosomal protein groups were identified, among which the abundance of 35 proteins was significantly changed following HBV replication. Strikingly, 5 subunit proteins from the 26S proteasome complex, including PSMC1, PSMC2, PSMD1, PSMD7 and PSMD14 were consistently enhanced in HepAD38 (dox−)-exo. Bioinformatic analysis of differential exosomal proteins confirmed the significant enrichment of components involved in the proteasomal catabolic process. Proteasome activity assays further suggested that HepAD38 (dox−)-exo had enhanced proteolytic activity compared with HepAD38 (dox+)-exo. Furthermore, human peripheral monocytes incubated with HepAD38 (dox−)-exo induced a significantly lower level of IL-6 secretion compared with IL-6 levels from HepAD38 (dox+)-exo. Irreversible inhibition of proteasomal activity within exosomes restored higher production of IL-6 by monocytes, suggesting that transmission of proteasome subunit proteins by HepAD38 (dox−)-exo might modulate the production of pro-inflammatory molecules in the recipient monocytes. These results revealed the composition and potential function of exosomes produced during HBV replication, thus providing a new perspective on the role of exosomes in HBV-host interaction. PMID:28242843

Lack of mixed agonist-antagonist properties of [Gln8-Gly31]-beta h-EP-Gly-Gly-NH2 and [Arg9,19,24,28,29]-beta h-EP in the rat vas deferens neuroeffector junction: studies with naloxone, beta-funaltrexamine and ICI 174,864.

PubMed

Valenzuela, R; Li, C H; Huidobro-Toro, J P

1989-02-01

The 1-27 truncated fragment of beta h-endorphin (beta h-EP) as well as [Gln8,Gly31]-beta h-EP-Gly-Gly-NH2 or [Arg9,19,24,28,29]-beta h-EP exhibited opiate agonist activity in the rat vas deferens bioassay; the potency of these peptides was 3 to 6 times less than that of beta h-EP. None of these compounds exhibited any degree of antagonism towards the inhibitory action of beta h-EP. Naloxone antagonized and reversed the inhibitory action of beta h-EP and its analogues though with varying potencies. The apparent naloxone-pA2 value for beta h-EP was 8.94; that for [Gln8-Gly31]-beta h-EP-Gly-Gly-NH2 was 8.08 and that for [Arg9,19,24,28,29]-beta h-EP was 8.38. beta-Funaltrexamine (beta-FNA) potently antagonized the inhibitory action of beta h-EP following non-equilibrium kinetics. Tissue preincubation with 10 nM beta-FNA for 60 min followed by extensive washing caused a 10-fold increase in the beta h-EP IC50. However, 10 nM beta-FNA caused only a 1.2 increase in the IC50 of [Gln8,Gly31]-beta h-EP-Gly-Gly-NH2 and a 4.1-fold increase in the IC50 of [Arg9,19,24,28,29]-beta h-EP. In contrast, preincubation of the tissue with 3 microM ICI 174,864 did not modify the potency of beta h-EP or its structural analogues. However, a 60 min pretreatment with 10 microM beta-FNA followed by the addition of 3 microM ICI 174,864 revealed a further decrease in the potency of the opiopeptins compared with tissues exposed to beta-FNA alone or ICI 174,864 alone. In conclusion, the inhibitory action of these peptides is remarkably sensitive to beta-FNA antagonism; in addition the peptides act as pure opiate agonists in marked contrast with the agonist-antagonist properties described in the CNS.

Label-free Proteomic Analysis of Exosomes Derived from Inducible Hepatitis B Virus-Replicating HepAD38 Cell Line.

PubMed

Jia, Xiaofang; Chen, Jieliang; Megger, Dominik A; Zhang, Xiaonan; Kozlowski, Maya; Zhang, Lijun; Fang, Zhong; Li, Jin; Chu, Qiaofang; Wu, Min; Li, Yaming; Sitek, Barbara; Yuan, Zhenghong

2017-04-01

Hepatitis B virus (HBV) infection is a major health problem worldwide. Recent evidence suggests that some viruses can manipulate the infection process by packing specific viral and cellular components into exosomes, small nanometer-sized (30-150 nm) vesicles secreted from various cells. However, the impact of HBV replication on the content of exosomes produced by hepatocytes has not been fully delineated. In this work, an HBV-inducible cell line HepAD38 was used to directly compare changes in the protein content of exosomes secreted from HepAD38 cells with or without HBV replication. Exosomes were isolated from supernantants of HepAD38 cells cultured with or without doxycycline (dox) and their purity was confirmed by transmission electron microscopy (TEM) and Western immunoblotting assays. Ion-intensity based label-free LC-MS/MS quantitation technologies were applied to analyze protein content of exosomes from HBV replicating cells [referred as HepAD38 (dox - )-exo] and from HBV nonreplicating cells [referred as HepAD38 (dox + )-exo]. A total of 1412 exosomal protein groups were identified, among which the abundance of 35 proteins was significantly changed following HBV replication. Strikingly, 5 subunit proteins from the 26S proteasome complex, including PSMC1, PSMC2, PSMD1, PSMD7 and PSMD14 were consistently enhanced in HepAD38 (dox - )-exo. Bioinformatic analysis of differential exosomal proteins confirmed the significant enrichment of components involved in the proteasomal catabolic process. Proteasome activity assays further suggested that HepAD38 (dox - )-exo had enhanced proteolytic activity compared with HepAD38 (dox + )-exo. Furthermore, human peripheral monocytes incubated with HepAD38 (dox - )-exo induced a significantly lower level of IL-6 secretion compared with IL-6 levels from HepAD38 (dox + )-exo. Irreversible inhibition of proteasomal activity within exosomes restored higher production of IL-6 by monocytes, suggesting that transmission of proteasome subunit proteins by HepAD38 (dox - )-exo might modulate the production of pro-inflammatory molecules in the recipient monocytes. These results revealed the composition and potential function of exosomes produced during HBV replication, thus providing a new perspective on the role of exosomes in HBV-host interaction. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Prokaryotic degradation of high molecular weight dissolved organic matter in the deep-sea waters of NW Mediterranean Sea under in situ temperature and pressure conditions during contrasted hydrological conditions

NASA Astrophysics Data System (ADS)

Tamburini, C.; Boutrif, M.; Garel, M.; Sempéré, R.; Repeta, D.; Charriere, B.; Nerini, D.; Panagiotopoulos, C.

2016-02-01

The contribution of the semi-labile dissolved organic carbon (DOC) to the global prokaryotic production has been assessed in very few previous studies. Some experiments show rapid utilization of semi-reactive DOC by prokaryotes, while other experiments show almost no utilization at all. However, all these studies did not take into account the role of hydrostatic pressure for the degradation of organic matter. In this study, we investigate (1) the degradation of "natural" high molecular weight DOM HMW-DOM (obtained after ultrafiltration) and (2) the uptake of labeled extracellular polymeric substances (3H-EPS) incubated with deep-sea water samples (2000 m-depth, NW Mediterranean Sea) under in situ pressure conditions (HP) and under atmospheric compression after decompression of the deep samples (ATM) during stratified and mixed water conditions (deep sea convection). Our results indicated that during HP incubations DOC exhibited the highest degradation rates (kHP DOC = 0.82 d-1) compared to the ATM conditions were no or few degradation was observed (kATM DOC= 0.007 d-1). An opposite trend was observed for the HP incubations from mixed deep water masses. HP incubation measurements displayed the lowest DOC degradation (kHP DOC=0.031 d-1) compared to the ATM conditions (kATM DOC=0.62 d-1). These results imply the presence of allochthonous prokaryotic cells in deep-sea samples after a winter water mass convection. Same trends were found using 3H-EPS uptake rates which were higher at HP than at ATM conditions during stratified period conditions whereas the opposite patterns were observed during deep-sea convection event. Moreover, we found than Euryarchaea were the main contributors to 3H-EPS assimilation at 2000m-depth, representing 58% of the total cells actively assimilating 3H-EPS. This study demonstrates that remineralization rates of semi-labile DOC in deep NW Med. Sea are controlled by the prokaryotic communities, which are influenced by the hydrological conditions of the water column.

Thyroid hormone upregulates zinc-α2-glycoprotein production in the liver but not in adipose tissue.

PubMed

Simó, Rafael; Hernández, Cristina; Sáez-López, Cristina; Soldevila, Berta; Puig-Domingo, Manel; Selva, David M

2014-01-01

Overproduction of zinc-α2-glycoprotein by adipose tissue is crucial in accounting for the lipolysis occurring in cancer cachexia of certain malignant tumors. The main aim of this study was to explore whether thyroid hormone could enhance zinc-α2-glycoprotein production in adipose tissue. In addition, the regulation of zinc-α2-glycoprotein by thyroid hormone in the liver was investigated. We performed in vitro (HepG2 cells and primary human adipocytes) and in vivo (C57BL6/mice) experiments addressed to examine the effect of thyroid hormone on zinc-α2-glycoprotein production (mRNA and protein levels) in liver and visceral adipose tissue. We also measured the zinc-α2-glycoprotein serum levels in a cohort of patients before and after controlling their hyperthyroidism. Our results showed that thyroid hormone up-regulates zinc-α2-glycoprotein production in HepG2 cells in a dose-dependent manner. In addition, the zinc-α2-glycoprotein proximal promoter contains functional thyroid hormone receptor binding sites that respond to thyroid hormone treatment in luciferase reporter gene assays in HepG2 cells. Furthermore, zinc-α2-glycoprotein induced lipolysis in HepG2 in a dose-dependent manner. Our in vivo experiments in mice confirmed the up-regulation of zinc-α2-glycoprotein induced by thyroid hormone in the liver, thus leading to a significant increase in zinc-α2-glycoprotein circulating levels. However, thyroid hormone did not regulate zinc-α2-glycoprotein production in either human or mouse adipocytes. Finally, in patients with hyperthyroidism a significant reduction of zinc-α2-glycoprotein serum levels was detected after treatment but was unrelated to body weight changes. We conclude that thyroid hormone up-regulates the production of zinc-α2-glycoprotein in the liver but not in the adipose tissue. The neutral effect of thyroid hormones on zinc-α2-glycoprotein expression in adipose tissue could be the reason why zinc-α2-glycoprotein is not related to weight loss in hyperthyroidism.

Wee1 Kinase Inhibitor AZD1775 Radiosensitizes Hepatocellular Carcinoma Regardless of TP53 Mutational Status Through Induction of Replication Stress

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

Cuneo, Kyle C., E-mail: kcuneo@umich.edu; Morgan, Meredith A.; Davis, Mary A.

2016-06-01

Purpose: Wee1 kinase inhibitors are effective radiosensitizers in cells lacking a G{sub 1} checkpoint. In this study we examined the potential effect of Wee1 kinase inhibition on inducing replication stress in hepatocellular carcinoma (HCC). Methods and Materials: Five independent datasets from the Oncomine database comparing gene expression in HCC compared to normal tissue were combined and specific markers associated with Wee1 sensitivity were analyzed. We then performed a series of in vitro experiments to study the effect of Wee1 inhibition on irradiated HCC cell lines with varying p53 mutational status. Clonogenic survival assays and flow cytometry using anti-γH2AX and phospho-histone H3more » antibodies with propidium iodide were performed to study the effect of AZD1775 on survival, cell cycle, and DNA repair. Additionally, nucleoside enriched medium was used to examine the effect of altering nucleotide pools on Wee1 targeted radiation sensitization. Results: Our analysis of the Oncomine database found high levels of CDK1 and other cell cycle regulators indicative of Wee1 sensitivity in HCC. In our in vitro experiments, treatment with AZD1775 radiosensitized and chemosensitized Hep3B, Huh7, and HepG2 cell lines and was associated with delayed resolution of γH2AX foci and the induction of pan-nuclear γH2AX staining. Wee1 inhibition attenuated radiation-induced G{sub 2} arrest in the Hep3B (TP53 null) and Huh7 (TP53 mutant) cell lines but not in the TP53 wild-type cell line HepG2. Supplementation with nucleosides reversed the radiation-sensitizing effect of AZD1775 and reduced the amount of cells with pan-nuclear γH2AX staining after radiation. Conclusions: Radiation sensitization with Wee1 inhibition occurs in cells regardless of their p53 mutational status. In this study we show for the first time that replication stress via the overconsumption of nucleotides plays an important role in AZD1775-induced radiation sensitization.« less

Thyroid Hormone Upregulates Zinc-α2-glycoprotein Production in the Liver but Not in Adipose Tissue

PubMed Central

Simó, Rafael; Hernández, Cristina; Sáez-López, Cristina; Soldevila, Berta; Puig-Domingo, Manel; Selva, David M.

2014-01-01

Overproduction of zinc-α2-glycoprotein by adipose tissue is crucial in accounting for the lipolysis occurring in cancer cachexia of certain malignant tumors. The main aim of this study was to explore whether thyroid hormone could enhance zinc-α2-glycoprotein production in adipose tissue. In addition, the regulation of zinc-α2-glycoprotein by thyroid hormone in the liver was investigated. We performed in vitro (HepG2 cells and primary human adipocytes) and in vivo (C57BL6/mice) experiments addressed to examine the effect of thyroid hormone on zinc-α2-glycoprotein production (mRNA and protein levels) in liver and visceral adipose tissue. We also measured the zinc-α2-glycoprotein serum levels in a cohort of patients before and after controlling their hyperthyroidism. Our results showed that thyroid hormone up-regulates zinc-α2-glycoprotein production in HepG2 cells in a dose-dependent manner. In addition, the zinc-α2-glycoprotein proximal promoter contains functional thyroid hormone receptor binding sites that respond to thyroid hormone treatment in luciferase reporter gene assays in HepG2 cells. Furthermore, zinc-α2-glycoprotein induced lipolysis in HepG2 in a dose-dependent manner. Our in vivo experiments in mice confirmed the up-regulation of zinc-α2-glycoprotein induced by thyroid hormone in the liver, thus leading to a significant increase in zinc-α2-glycoprotein circulating levels. However, thyroid hormone did not regulate zinc-α2-glycoprotein production in either human or mouse adipocytes. Finally, in patients with hyperthyroidism a significant reduction of zinc-α2-glycoprotein serum levels was detected after treatment but was unrelated to body weight changes. We conclude that thyroid hormone up-regulates the production of zinc-α2-glycoprotein in the liver but not in the adipose tissue. The neutral effect of thyroid hormones on zinc-α2-glycoprotein expression in adipose tissue could be the reason why zinc-α2-glycoprotein is not related to weight loss in hyperthyroidism. PMID:24465683

A Pilot Randomized Controlled Trial of the Effects of Chair Yoga on Pain and Physical Function Among Community-Dwelling Older Adults With Lower Extremity Osteoarthritis.

PubMed

Park, Juyoung; McCaffrey, Ruth; Newman, David; Liehr, Patricia; Ouslander, Joseph G

2017-03-01

To determine effects of Sit 'N' Fit Chair Yoga, compared to a Health Education program (HEP), on pain and physical function in older adults with lower extremity osteoarthritis (OA) who could not participate in standing exercise. Two-arm randomized controlled trial. One HUD senior housing facility and one day senior center in south Florida. Community-dwelling older adults (N = 131) were randomly assigned to chair yoga (n = 66) or HEP (n = 65). Thirteen dropped after assignment but prior to the intervention; six dropped during the intervention; 106 of 112 completed at least 12 of 16 sessions (95% retention rate). Participants attended either chair yoga or HEP. Both interventions consisted of twice-weekly 45-minute sessions for 8 weeks. Primary: pain, pain interference; secondary: balance, gait speed, fatigue, functional ability measured at baseline, after 4 weeks of intervention, at the end of the 8-week intervention, and post-intervention (1 and 3 months). The chair yoga group showed greater reduction in pain interference during the intervention (P = .01), sustained through 3 months (P = .022). WOMAC pain (P = .048), gait speed (P = .024), and fatigue (P = .037) were improved in the yoga group during the intervention (P = .048) but improvements were not sustained post intervention. Chair yoga had no effect on balance. An 8-week chair yoga program was associated with reduction in pain, pain interference, and fatigue, and improvement in gait speed, but only the effects on pain interference were sustained 3 months post intervention. Chair yoga should be further explored as a nonpharmacologic intervention for older people with OA in the lower extremities. ClinicalTrials.gov: NCT02113410. © 2016, Copyright the Authors Journal compilation © 2016, The American Geriatrics Society.

Longitudinal Changes in Cholesterol Efflux Capacities in Patients With Coronary Artery Disease Undergoing Lifestyle Modification Therapy.

PubMed

Boyer, Marjorie; Lévesque, Valérie; Poirier, Paul; Marette, André; Mitchell, Patricia L; Mora, Samia; Mathieu, Patrick; Després, Jean-Pierre; Larose, Éric; Arsenault, Benoit J

2018-06-01

Our objective was to identify the determinants of high-density lipoprotein cholesterol efflux capacity (HDL-CEC) changes in patients with coronary artery disease who participated in a lifestyle modification program aimed at increasing physical activity levels and improving diet quality. A total of 86 men with coronary artery disease aged between 35 and 80 years participated in a 1-year lifestyle modification program that aimed to achieve a minimum of 150 minutes of aerobic physical activity weekly and improve diet quality. HDL-CECs were measured before and after the 1-year intervention using 3 H-cholesterol-labeled J774 and HepG2 cells. Visceral, subcutaneous, and cardiac adipose tissue levels were assessed before and after the intervention using magnetic resonance imaging. Lipoprotein particle size and concentrations were measured by proton nuclear magnetic resonance spectroscopy and a complete lipoprotein-lipid profile was obtained. At baseline, the best correlate of HDL-CECs were apolipoprotein AI ( R 2 =0.35, P <0.0001) and high-density lipoprotein cholesterol ( R 2 =0.21, P <0.0001) for J774-HDL-CECs and HepG2-HDL-CECs, respectively. Baseline and longitudinal changes in HDL-CECs were associated with several lipoprotein size and concentration indices, although high-density lipoprotein cholesterol was the best predictor of longitudinal changes in J774-HDL-CECs ( R 2 =0.18, P =0.002) and apolipoprotein AI was found to be the best predictor of longitudinal changes in HepG2 cholesterol efflux capacities ( R 2 =0.21, P =0.002). Results of this study suggest that increases in high-density lipoprotein cholesterol and apolipoprotein AI levels typically observed in patients with coronary artery disease undergoing healthy lifestyle modification therapy may be indicative of higher plasma concentrations of functional high-density lipoprotein particles. © 2018 The Authors. Published on behalf of the American Heart Association, Inc., by Wiley.

Chalcone-Induced Apoptosis through Caspase-Dependent Intrinsic Pathways in Human Hepatocellular Carcinoma Cells.

PubMed

Ramirez-Tagle, Rodrigo; Escobar, Carlos A; Romero, Valentina; Montorfano, Ignacio; Armisén, Ricardo; Borgna, Vincenzo; Jeldes, Emanuel; Pizarro, Luis; Simon, Felipe; Echeverria, Cesar

2016-02-22

Hepatocellular carcinoma (HCC) is one of the most commonly diagnosed cancers worldwide. Chemoprevention of HCC can be achieved through the use of natural or synthetic compounds that reverse, suppress or prevent the development of cancer progression. In this study, we investigated the antiproliferative effects and the mechanism of action of two compounds, 2,3,4'-trimethoxy-2'-hydroxy-chalcone (CH1) and 3'-bromo-3,4-dimethoxy-chalcone (CH2), over human hepatoma cells (HepG2 and Huh-7) and cultured mouse hepatocytes (HepM). Cytotoxic effects were observed over the HepG2 and Huh-7, and no effects were observed over the HepM. For HepG2 cells, treated separately with each chalcone, typical apoptotic laddering and nuclear condensation were observed. Additionally, the caspases and Bcl-2 family proteins activation by using Western blotting and immunocytochemistry were studied. Caspase-8 was not activated, but caspase-3 and -9 were both activated by chalcones in HepG2 cells. Chalcones also induced reactive oxygen species (ROS) accumulation after 4, 8 and 24 h of treatment in HepG2 cells. These results suggest that apoptosis in HepG2 was induced through: (i) a caspase-dependent intrinsic pathway; and (ii) by alterations in the cellular levels of Bcl-2 family proteins, and also, that the chalcone moiety could be a potent candidate as novel anticancer agents acting on human hepatomas.

Toll-like receptor-4 is a target for suppression of proliferation and chemoresistance in HepG2 hepatoblastoma cells.

PubMed

Hsiao, Chih-Cheng; Chen, Po-Han; Cheng, Cheng-I; Tsai, Ming-Shian; Chang, Chih-Yang; Lu, Shang-Chieh; Hsieh, Ming-Chu; Lin, Yu-Chun; Lee, Po-Huang; Kao, Ying-Hsien

2015-11-01

Toll-like receptor-4 (TLR4) is known to influence growth and migration of hepatocellular tumors; however, its role in hepatoblastoma remains poorly understood. This study investigated the regulatory role of TLR4 in proliferation and chemoresistance of HepG2 hepatoblastoma cells. Treatment with lipopolysaccharide (LPS), a TLR4 agonist, was found to significantly upregulate TLR4 expression in HepG2 cells, but not in malignant Huh-7 and Sk-Hep1 hepatocellular carcinoma cells. Additionally, IL-6 enhanced LPS-induced TLR4 upregulation. LPS-stimulated TLR4 activation increased proliferation, nitric oxide synthase (NOS) expression, and NO production in HepG2 cells. Chemotherapeutic agents, cisplatin and doxorubicin, effectively inhibited TLR4 expression in HepG2 cells. Characterization of LPS-induced signaling activation and blockade with kinase inhibitors revealed the involvement of Akt and MAPK pathways in LPS-enhanced NO release from, and proliferation of HepG2 cells. Mechanistically, gene modifications as a result of TLR4 transfection and siRNA-mediated knockdown further demonstrated a crucial role for TLR4 in the regulation of NOS expression, cell proliferation, and chemoresistance in HepG2 cells. These findings suggest that targeting TLR4 expression and its cognate signaling may modulate proliferation and chemosensitivity in hepatoblastoma cells and serve as a potential therapeutic target. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Loss of confidence in vaccines following media reports of infant deaths after hepatitis B vaccination in China.

PubMed

Yu, Wenzhou; Liu, Dawei; Zheng, Jingshan; Liu, Yanmin; An, Zhijie; Rodewald, Lance; Zhang, Guomin; Su, Qiru; Li, Keli; Xu, Disha; Wang, Fuzhen; Yuan, Ping; Xia, Wei; Ning, Guijun; Zheng, Hui; Chu, Yaozhu; Cui, Jian; Duan, Mengjuan; Hao, Lixin; Zhou, Yuqing; Wu, Zhenhua; Zhang, Xuan; Cui, Fuqiang; Li, Li; Wang, Huaqing

2016-04-01

China reduced hepatitis B virus (HBV) infection by 90% among children under 5 years old with safe and effective hepatitis B vaccines (HepB). In December 2013, this success was threatened by widespread media reports of infant deaths following HepB administration. Seventeen deaths and one case of anaphylactic shock following HBV vaccination had been reported. We conducted a telephone survey to measure parental confidence in HepB in eleven provinces at four points in time; reviewed maternal HBV status and use of HepB for newborns in birth hospitals in eight provinces before and after the event; and monitored coverage with hepatitis B vaccine and other programme vaccines in ten provinces. HepB from the implicated company was suspended during the investigation, which showed that the deaths were not caused by HepB vaccination. Before the event, 85% respondents regarded domestic vaccines as safe, decreasing to 26.7% during the event. During the height of the crisis, 30% of parents reported being hesitant to vaccinate and 18.4% reported they would refuse HepB. Use of HepB in the monitored provinces decreased by 18.6%, from 53 653 doses the week before the event to 43 688 doses during the week that Biokangtai HepB was suspended. Use of HepB within the first day of life decreased by 10% among infants born to HBsAg-negative mothers, and by 6% among infants born to HBsAg-positive mothers. Vaccine refusal and HepB birth dose rates returned to baseline within 2 months; confidence increased, but remained below baseline. The HBV vaccine event resulted in the suspension of a safe vaccine, which was associated with a decline of parental confidence, and refusal of vaccination. Suspension of a vaccine can lead to loss of confidence that is difficult to recover. Timely and credible investigation, accompanied by proactive outreach to stakeholders and the media, may help mitigate negative impact of future coincidental adverse events following immunization. © The Author 2016; all rights reserved. Published by Oxford University Press on behalf of the International Epidemiological Association.

Experiences with http/WebDAV protocols for data access in high throughput computing

NASA Astrophysics Data System (ADS)

Bernabeu, Gerard; Martinez, Francisco; Acción, Esther; Bria, Arnau; Caubet, Marc; Delfino, Manuel; Espinal, Xavier

2011-12-01

In the past, access to remote storage was considered to be at least one order of magnitude slower than local disk access. Improvement on network technologies provide the alternative of using remote disk. For those accesses one can today reach levels of throughput similar or exceeding those of local disks. Common choices as access protocols in the WLCG collaboration are RFIO, [GSI]DCAP, GRIDFTP, XROOTD and NFS. HTTP protocol shows a promising alternative as it is a simple, lightweight protocol. It also enables the use of standard technologies such as http caching or load balancing which can be used to improve service resilience and scalability or to boost performance for some use cases seen in HEP such as the "hot files". WebDAV extensions allow writing data, giving it enough functionality to work as a remote access protocol. This paper will show our experiences with the WebDAV door for dCache, in terms of functionality and performance, applied to some of the HEP work flows in the LHC Tier1 at PIC.

The HEP.TrkX Project: deep neural networks for HL-LHC online and offline tracking

DOE PAGES

Farrell, Steven; Anderson, Dustin; Calafiura, Paolo; ...

2017-08-08

Particle track reconstruction in dense environments such as the detectors of the High Luminosity Large Hadron Collider (HL-LHC) is a challenging pattern recognition problem. Traditional tracking algorithms such as the combinatorial Kalman Filter have been used with great success in LHC experiments for years. However, these state-of-the-art techniques are inherently sequential and scale poorly with the expected increases in detector occupancy in the HL-LHC conditions. The HEP.TrkX project is a pilot project with the aim to identify and develop cross-experiment solutions based on machine learning algorithms for track reconstruction. Machine learning algorithms bring a lot of potential to this problemmore » thanks to their capability to model complex non-linear data dependencies, to learn effective representations of high-dimensional data through training, and to parallelize easily on high-throughput architectures such as GPUs. This contribution will describe our initial explorations into this relatively unexplored idea space. Furthermore, we will discuss the use of recurrent (LSTM) and convolutional neural networks to find and fit tracks in toy detector data.« less

The HEP.TrkX Project: deep neural networks for HL-LHC online and offline tracking

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

Farrell, Steven; Anderson, Dustin; Calafiura, Paolo

Particle track reconstruction in dense environments such as the detectors of the High Luminosity Large Hadron Collider (HL-LHC) is a challenging pattern recognition problem. Traditional tracking algorithms such as the combinatorial Kalman Filter have been used with great success in LHC experiments for years. However, these state-of-the-art techniques are inherently sequential and scale poorly with the expected increases in detector occupancy in the HL-LHC conditions. The HEP.TrkX project is a pilot project with the aim to identify and develop cross-experiment solutions based on machine learning algorithms for track reconstruction. Machine learning algorithms bring a lot of potential to this problemmore » thanks to their capability to model complex non-linear data dependencies, to learn effective representations of high-dimensional data through training, and to parallelize easily on high-throughput architectures such as GPUs. This contribution will describe our initial explorations into this relatively unexplored idea space. Furthermore, we will discuss the use of recurrent (LSTM) and convolutional neural networks to find and fit tracks in toy detector data.« less

The HEP.TrkX Project: deep neural networks for HL-LHC online and offline tracking

NASA Astrophysics Data System (ADS)

Farrell, Steven; Anderson, Dustin; Calafiura, Paolo; Cerati, Giuseppe; Gray, Lindsey; Kowalkowski, Jim; Mudigonda, Mayur; Prabhat; Spentzouris, Panagiotis; Spiropoulou, Maria; Tsaris, Aristeidis; Vlimant, Jean-Roch; Zheng, Stephan

2017-08-01

Particle track reconstruction in dense environments such as the detectors of the High Luminosity Large Hadron Collider (HL-LHC) is a challenging pattern recognition problem. Traditional tracking algorithms such as the combinatorial Kalman Filter have been used with great success in LHC experiments for years. However, these state-of-the-art techniques are inherently sequential and scale poorly with the expected increases in detector occupancy in the HL-LHC conditions. The HEP.TrkX project is a pilot project with the aim to identify and develop cross-experiment solutions based on machine learning algorithms for track reconstruction. Machine learning algorithms bring a lot of potential to this problem thanks to their capability to model complex non-linear data dependencies, to learn effective representations of high-dimensional data through training, and to parallelize easily on high-throughput architectures such as GPUs. This contribution will describe our initial explorations into this relatively unexplored idea space. We will discuss the use of recurrent (LSTM) and convolutional neural networks to find and fit tracks in toy detector data.

Cancer-associated fibroblasts in a human HEp-2 established laryngeal xenografted tumor are not derived from cancer cells through epithelial-mesenchymal transition, phenotypically activated but karyotypically normal.

PubMed

Wang, Mei; Wu, Chun-Ping; Pan, Jun-Yan; Zheng, Wen-Wei; Cao, Xiao-Juan; Fan, Guo-Kang

2015-01-01

Cancer-associated fibroblasts (CAFs) play a crucial role in cancer progression and even initiation. However, the origins of CAFs in various cancer types remain controversial, and one of the important hypothesized origins is through epithelial-mesenchymal transition (EMT) from cancer cells. In this study, we investigated whether the HEp-2 laryngeal cancer cells are able to generate CAFs via EMT during tumor formation, which is now still unknown. The laryngeal xenografted tumor model was established by inoculating the HEp-2 laryngeal cancer cell line in nude mice. Primary cultured CAFs from the tumor nodules and matched normal fibroblasts (NFs) from the adjacent connective tissues were subcultured, purified, and verified by immunofluorescence. Migration, invasion, and proliferation potentials were compared between the CAFs and NFs. A co-culture of CAFs with HEp-2 cells and a co-injection of CAFs with HEp-2 cells in nude mice were performed to examine the cancer-promoting potential of CAFs to further verify their identity. Karyotypic analyses of the CAFs, NFs, and HEp-2 cells were conducted. A co-culture of NFs with HEp-2 cells was also performed to examine the expression of activated markers of CAFs. A pathological examination confirmed that the laryngeal xenografted tumor model was successfully established, containing abundant CAFs. Immunocytochemical staining verified the purities and identities of the CAFs and NFs. Although the CAFs manifested higher migration, invasion, proliferation, and cancer-promoting capacities compared with the NFs, an analysis of chromosomes revealed that both the CAFs and NFs showed typical normal mouse karyotypes. In addition, the NFs co-cultured with HEp-2 cells did not show induced expressions of activated markers of CAFs. Our findings reveal that the CAFs in the HEp-2 established laryngeal xenografted tumor are not of laryngeal cancer origin but of mouse origin, indicating that the HEp-2 laryngeal cancer cells cannot generate their own CAFs via EMT in this model.

Findings from a hepatitis B birth dose assessment in health facilities in the Philippines: opportunities to engage the private sector.

PubMed

Patel, Minal K; Capeding, Rosario Z; Ducusin, Joyce U; de Quiroz Castro, Maricel; Garcia, Luzviminda C; Hennessey, Karen

2014-09-03

Hepatitis B vaccination in the Philippines was introduced in 1992 to reduce the high burden of chronic hepatitis B virus (HBV) infection in the population; in 2007, a birth dose (HepB-BD) was introduced to decrease perinatal HBV transmission. Timely HepB-BD coverage, defined as doses given within 24h of birth, was 40% nationally in 2011. A first step in improving timely HepB-BD coverage is to ensure that all newborns born in health facilities are vaccinated. In order to assess ways of improving the Philippines' HepB-BD program, we evaluated knowledge, attitudes, and practices surrounding HepB-BD administration in health facilities. Teams visited selected government clinics, government hospitals, and private hospitals in regions with low reported HepB-BD coverage and interviewed immunization and maternity staff. HepB-BD coverage was calculated in each facility for a 3-month period in 2011. Of the 142 health facilities visited, 12 (8%) did not provide HepB-BD; seven were private hospitals and five were government hospitals. Median timely HepB-BD coverage was 90% (IQR 80%-100%) among government clinics, 87% (IQR 50%-97%) among government hospitals, and 50% (IQR 0%-90%) among private hospitals (p=0.02). The private hospitals were least likely to receive supervision (53% vs. 6%-31%, p=0.0005) and to report vaccination data to the national Expanded Programme on Immunization (36% vs. 96%-100%, p<0.0001). Private sector hospitals in the Philippines, which deliver 18% of newborns, had the lowest timely HepB-BD coverage. Multiple avenues exist to engage the private sector in hepatitis B prevention including through existing laws, newborn health initiatives, hospital accreditation processes, and raising awareness of the government's free vaccine program. Copyright © 2013 World Health Organization (WHO). Published by Elsevier Ltd.. All rights reserved.

The effects of different dosage levels of hepatitis B vaccine as booster on anti-HBs-negative children 5–15 y after primary immunization; China, 2009–2010

PubMed Central

Chen, Yongdi; Lv, Huakun; Gu, Hua; Cui, Fujiang; Wang, Fuzhen; Yao, Jun; Xia, Shichang; Liang, Xiaofeng

2014-01-01

The changes in lgG antibody levels to hepatitis B surface antigen (HBsAg) and in antibody to HBsAg (anti-HBs) seroconversion rates due to different dosages of hepatitis B vaccine (HepB) were compared in 2106 children. Children who had been previously vaccinated as infants with HepB were revaccinated at 5–15 y of age, after which the antibody titers were determined. After the first booster dose, the anti-HBs seroconversion rate (defined as an anti-HBs ≥10 mIU/ml) with 10 μg of HepB (93.6%) was significantly greater than the rate with 5 µg of HepB (90.3%) (P < 0.05); the anti-HBs seroconversion rate in 10–15-y-old boys vaccinated with 10 μg of HepB (90.9%) was significantly greater than the rate with 5 µg of HepB (84.3%) (P < 0.05). The anti-HBs seroconversion rates after the third booster dose with 5 or 10 μg of HepB were greater than those after the first booster dose (99.6% and 99.7%, vs. 90.3% and 93.6%, P < 0.05); as was the corresponding GMTs (658 ± 4 mIU/ml and 2599 ± 3 mIU/ml, vs. 255 ± 11 mIU/ml and 877 ± 11 mIU/ml [P < 0.05]). The immunization effects of booster vaccination with 3 doses of HepB with 5 or 10 µg are effective; a single booster dose with 10 µg of HepB for 10–15-y-old boys and with 5 or 10 µg of HepB for 5–9 y old boys and for 5–15-y-old girls are effective in generating protective antibody against HBV; however, for anti-HBs-negative children after a single dose of booster, 3 doses are needed. PMID:24192508

The effects of different dosage levels of hepatitis B vaccine as booster on anti-HBs-negative children 5-15 y after primary immunization; China, 2009-2010.

PubMed

Chen, Yongdi; Lv, Huakun; Gu, Hua; Cui, Fujiang; Wang, Fuzhen; Yao, Jun; Xia, Shichang; Liang, Xiaofeng

2014-01-01

The changes in lgG antibody levels to hepatitis B surface antigen (HBsAg) and in antibody to HBsAg (anti-HBs) seroconversion rates due to different dosages of hepatitis B vaccine (HepB) were compared in 2106 children. Children who had been previously vaccinated as infants with HepB were revaccinated at 5-15 y of age, after which the antibody titers were determined. After the first booster dose, the anti-HBs seroconversion rate (defined as an anti-HBs ≥10 mIU/ml) with 10 μg of HepB (93.6%) was significantly greater than the rate with 5 µg of HepB (90.3%) (P<0.05); the anti-HBs seroconversion rate in 10-15-y-old boys vaccinated with 10 μg of HepB (90.9%) was significantly greater than the rate with 5 µg of HepB (84.3%) (P<0.05). The anti-HBs seroconversion rates after the third booster dose with 5 or 10 μg of HepB were greater than those after the first booster dose (99.6% and 99.7%, vs. 90.3% and 93.6%, P<0.05); as was the corresponding GMTs (658 ± 4 mIU/ml and 2599 ± 3 mIU/ml, vs. 255 ± 11 mIU/ml and 877 ± 11 mIU/ml [P<0.05]). The immunization effects of booster vaccination with 3 doses of HepB with 5 or 10 µg are effective; a single booster dose with 10 µg of HepB for 10-15-y-old boys and with 5 or 10 µg of HepB for 5-9 y old boys and for 5-15-y-old girls are effective in generating protective antibody against HBV; however, for anti-HBs-negative children after a single dose of booster, 3 doses are needed.

Antioxidant and anticancer activity of Artemisia princeps var. orientalis extract in HepG2 and Hep3B hepatocellular carcinoma cells

PubMed Central

Choi, Eun-Jeong

2013-01-01

Objective The aim of the present study was to investigate antioxidant and the anticancerigen activity of a methanol extract from Artemisia princeps var. orientalis (APME), a well-known traditional herbal medicine in Asia, in hepatocellular cancer cells. Methods To evaluate the antioxidant activity of APME, reactive oxygen species (ROS) and the antioxidant enzymes, superoxide dismutase (SOD) and catalase were investigated in HepG2 cells exposed to APME (5, 100, and 200 µg/mL) for 72 h. Then, to evaluate the anticancer activity of APME, we investigated the proliferation and apoptosis induction of HepG2 and Hep3B cells exposed to APME (1-200 µg/mL) for 24, 48, and 72 h. Results APME dose-dependently reduced the generation of ROS in the presence of H2O2 compared with control cells. Furthermore, it increased catalase and SOD activity. Moreover, APME inhibited cell proliferation in a dose- and time-dependent manner, but at concentrations lower than 100 µg/mL, the inhibition was less dose-dependent than time-dependent. HepG2 and Hep3B cells exposed to 5, 100, and 200 µg/mL APME for 72 h underwent cell cycle arrest and apoptosis. Exposure to APME resulted in a significant increase in the number of cells in G1 phase and a decrease in the G2/M phase cell population. In addition, APME induced P53 expression of HepG2 cells in a dose-dependent manner, and played a role in the downregulation of Bcl-2 and upregulation of Bax in both HepG2 and Hep3B cells. Conclusions These results indicate the potential role of APME as an antioxidant and anticancerigen agent in hepatocarcinoma cell lines. PMID:24255577

Fluorophore-assisted carbohydrate electrophoresis for the determination of molecular mass of heparins and low-molecular-weight (LMW) heparins.

PubMed

Buzzega, Dania; Maccari, Francesca; Volpi, Nicola

2008-11-01

We report the use of fluorophore-assisted carbohydrate electrophoresis (FACE) to determine the molecular mass (M) values of heparins (Heps) and low-molecular-weight (LMW)-Hep derivatives. Hep are labeled with 8-aminonaphthalene-1,3,6-trisulfonic acid and FACE is able to resolve each fraction as a discrete band depending on their M. After densitometric acquisition, the migration distance of each Hep standard is acquired and the third-grade polynomial calibration standard curve is determined by plotting the logarithms of the M values as a function of migration ratio. Purified Hep samples having different properties, pharmaceutical Heps and various LMW-Heps were analyzed by both FACE and conventional high-performance size-exclusion liquid chromatography (HPSEC) methods. The molecular weight value on the top of the chromatographic peak (Mp), the number-average Mn, weight-average Mw and polydispersity (Mw/Mn) were examined by both techniques and found to be similar. This approach offers certain advantages over the HPSEC method. The derivatization process with 8-aminonaphthalene-1,3,6-trisulfonic acid is complete after 4 h so that many samples may be analyzed in a day also considering that multiple samples can be run simultaneously and in parallel and that a single FACE analysis requires approx. 15 min. Furthermore, FACE is a very sensitive method as it requires approx. 5-10 microg of Heps, about 10-100-fold lower than samples and standards used in HPSEC evaluation. Finally, the utilization of mini-gels allows the use of very low amounts of reagents with neither expensive equipment nor any complicated procedures having to be applied. This study demonstrates that FACE analysis is a sensitive method for the determination of the M values of Heps and LMW-Heps with possible utilization in virtually any kind of research and development such as quality control laboratories due to its rapid, parallel analysis of multiple samples by means of common and simple largely used analytical laboratory equipment.

West Foster Creek Expansion Project 2007 HEP Report.

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

Ashley, Paul R.

During April and May 2007, the Columbia Basin Fish and Wildlife Authority's (CBFWA) Regional HEP Team (RHT) conducted baseline Habitat Evaluation Procedures (HEP) (USFWS 1980, 1980a) analyses on five parcels collectively designated the West Foster Creek Expansion Project (3,756.48 acres). The purpose of the HEP analyses was to document extant habitat conditions and to determine how many baseline/protection habitat units (HUs) to credit Bonneville Power Administration (BPA) for funding maintenance and enhancement activities on project lands as partial mitigation for habitat losses associated with construction of Grand Coulee and Chief Joseph Dams. HEP evaluation models included mule deer (Odocoileus hemionus),more » western meadowlark (Sturnella neglecta), sharp-tailed grouse, (Tympanuchus phasianellus), Bobcat (Lynx rufus), mink (Neovison vison), mallard (Anas platyrhynchos), and black-capped chickadee (Parus atricapillus). Combined 2007 baseline HEP results show that 4,946.44 habitat units were generated on 3,756.48 acres (1.32 HUs per acre). HEP results/habitat conditions were generally similar for like cover types at all sites. Unlike crediting of habitat units (HUs) on other WDFW owned lands, Bonneville Power Administration received full credit for HUs generated on these sites.« less

NTCP-Reconstituted In Vitro HBV Infection System.

PubMed

Sun, Yinyan; Qi, Yonghe; Peng, Bo; Li, Wenhui

2017-01-01

Sodium taurocholate cotransporting polypeptide (NTCP) has been identified as a functional receptor for hepatitis B virus (HBV). Expressing human NTCP in human hepatoma HepG2 cells (HepG2-NTCP) renders these cells susceptible for HBV infection. The HepG2-NTCP stably transfected cell line provides a much-needed and easily accessible platform for studying the virus. HepG2-NTCP cells could also be used to identify chemicals targeting key steps of the virus life cycle including HBV covalent closed circular (ccc) DNA, and enable the development of novel antivirals against the infection.Many factors may contribute to the efficiency of HBV infection on HepG2-NTCP cells, with clonal differences among cell line isolates, the source of viral inoculum, and infection medium among the most critical ones. Here, we provide detailed protocols for efficient HBV infection of HepG2-NTCP cells in culture; generation and selection of single cell clones of HepG2-NTCP; production of infectious HBV virion stock through DNA transfection of recombinant plasmid that enables studying primary clinical HBV isolates; and assessing the infection with immunostaining of HBV antigens and Southern blot analysis of HBV cccDNA.

Pirfenidone Inhibits Proliferation and Promotes Apoptosis of Hepatocellular Carcinoma Cells by Inhibiting the Wnt/β-Catenin Signaling Pathway.

PubMed

Zou, Wei-Jie; Huang, Zhi; Jiang, Tian-Peng; Shen, Ya-Ping; Zhao, An-Su; Zhou, Shi; Zhang, Shuai

2017-12-25

BACKGROUND Hepatocellular carcinoma (HCC) is the most important cause of cancer-related deaths worldwide. Pirfenidone is an orally available small molecule with therapeutic potential for fibrotic diseases. MATERIAL AND METHODS In this study, we analyzed the effects of different pirfenidone concentrations on the proliferation of HepG2 HCC cells using Cell Counting Kit-8 (CCK-8) and colony formation assays. Flow cytometry was performed to measure the apoptotic effects of pirfenidone on HepG2 cells. Western blot analysis was performed to detect the expression of β-catenin and p-β-catenin. RESULTS Pirfenidone inhibited proliferation and promoted HepG2 cell apoptosis. In addition, Western blot results indicated that pirfenidone suppressed b-catenin expression in HepG2 cells. To assess the mechanism, we treated HepG2 cells with pirfenidone, and pirfenidone plus the β-catenin activator, SB-216763. The results revealed that SB-216763 accelerated proliferation and inhibited apoptosis in HepG2 cells treated with pirfenidone. Western blot results showed that SB-216763 upregulated β-catenin expression in HepG2 cells treated with pirfenidone. CONCLUSIONS In conclusions, pirfenidone may be a potential drug for HCC treatment.

CosmoSIS: A system for MC parameter estimation

DOE PAGES

Bridle, S.; Dodelson, S.; Jennings, E.; ...

2015-12-23

CosmoSIS is a modular system for cosmological parameter estimation, based on Markov Chain Monte Carlo and related techniques. It provides a series of samplers, which drive the exploration of the parameter space, and a series of modules, which calculate the likelihood of the observed data for a given physical model, determined by the location of a sample in the parameter space. While CosmoSIS ships with a set of modules that calculate quantities of interest to cosmologists, there is nothing about the framework itself, nor in the Markov Chain Monte Carlo technique, that is specific to cosmology. Thus CosmoSIS could bemore » used for parameter estimation problems in other fields, including HEP. This paper describes the features of CosmoSIS and show an example of its use outside of cosmology. Furthermore, it also discusses how collaborative development strategies differ between two different communities: that of HEP physicists, accustomed to working in large collaborations, and that of cosmologists, who have traditionally not worked in large groups.« less

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

Lu, Yanxin; Biomedical Research Institute, Shenzhen-PKU-HKUST Medical Center, Guangdong Province, Shenzhen 518036; Yue, Xupeng

Highlights: •miR-124 is down-regulated in hepatocellular carcinoma HepG2 cells. •Over-expression of miR-124 suppresses proliferation and induces apoptosis in HepG2 cells. •miR-124 inhibits xenograft tumor growth in nude mice implanted with HepG2 cells by reducing STAT3 expression. •STATs function as a novel target of miR-124 in HCC HepG2 cells. -- Abstract: The aberrant expression of microRNAs is associated with development and progression of cancers. Down-regulation of miR-124 has been demonstrated in the hepatocellular carcinoma (HCC), but the underlying mechanism by which miR-124 suppresses tumorigenesis in HCC remains elusive. In this study, we found that miR-124 suppresses the tumor growth of HCCmore » through targeting the signal transducers and activators of transcription 3 (STAT3). Overexpression of miR-124 suppressed proliferation and induced apoptosis in HepG-2 cells. Luciferase assay confirmed that miR-124 binding to the 3′-UTR region of STAT3 inhibited the expression of STAT3 and phosphorylated STAT3 proteins in HepG-2 cells. Knockdown of STAT3 by siRNA in HepG-2 cells mimicked the effect induced by miR-124. Overexpression of STAT3 in miR-124-transfected HepG-2 cells effectively rescued the inhibition of cell proliferation caused by miR-124. Furthermore, miR-124 suppressed xenograft tumor growth in nude mice implanted with HepG-2 cells by reducing STAT3 expression. Taken together, our findings show that miR-124 functions as tumor suppressor in HCC by targeting STAT3, and miR-124 may therefore serve as a biomarker for diagnosis and therapeutics in HCC.« less

High molecular weight of polysaccharides from Hericium erinaceus against amyloid beta-induced neurotoxicity.

PubMed

Cheng, Jai-Hong; Tsai, Chia-Ling; Lien, Yi-Yang; Lee, Meng-Shiou; Sheu, Shyang-Chwen

2016-06-07

Hericium erinaceus (HE) is a well-known mushroom in traditional Chinese food and medicine. HE extracts from the fruiting body and mycelia not only exhibit immunomodulatory, antimutagenic and antitumor activity but also have neuroprotective properties. Here, we purified HE polysaccharides (HEPS), composed of two high molecular weight polysaccharides (1.7 × 10(5) Da and 1.1 × 10(5) Da), and evaluated their protective effects on amyloid beta (Aβ)-induced neurotoxicity in rat pheochromocytoma PC12 cells. HEPS were prepared and purified using a 95 % ethanol extraction method. The components of HEPS were analyzed and the molecular weights of the polysaccharides were determined using high-pressure liquid chromatography (HPLC). The neuroprotective effects of the polysaccharides were evaluated through a 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging assay and an MTT assay and by quantifying reactive oxygen species (ROS) and mitochondrial membrane potentials (MMP) of Aβ-induced neurotoxicity in cells. Our results showed that 250 μg/ml HEPS was harmless and promoted cell viability with 1.2 μM Aβ treatment. We observed that the free radical scavenging rate exceeded 90 % when the concentration of HEPS was higher than 1 mg/mL in cells. The HEPS decreased the production of ROS from 80 to 58 % in a dose-dependent manner. Cell pretreatment with 250 μg/mL HEPS significantly reduced Aβ-induced high MMPs from 74 to 51 % and 94 to 62 % at 24 and 48 h, respectively. Finally, 250 μg/mL of HEPS prevented Aβ-induced cell shrinkage and nuclear degradation of PC12 cells. Our results demonstrate that HEPS exhibit antioxidant and neuroprotective effects on Aβ-induced neurotoxicity in neurons.

The human escort protein Hep binds to the ATPase domain of mitochondrial hsp70 and regulates ATP hydrolysis.

PubMed

Zhai, Peng; Stanworth, Crystal; Liu, Shirley; Silberg, Jonathan J

2008-09-19

Hsp70 escort proteins (Hep) have been implicated as essential for maintaining the function of yeast mitochondrial hsp70 molecular chaperones (mtHsp70), but the role that escort proteins play in regulating mammalian chaperone folding and function has not been established. We present evidence that human mtHsp70 exhibits limited solubility due to aggregation mediated by its ATPase domain and show that human Hep directly enhances chaperone solubility through interactions with this domain. In the absence of Hep, mtHsp70 was insoluble when expressed in Escherichia coli, as was its isolated ATPase domain and a chimera having this domain fused to the peptide-binding domain of HscA, a soluble monomeric chaperone. In contrast, these proteins all exhibited increased solubility when expressed in the presence of Hep. In vitro studies further revealed that purified Hep regulates the interaction of mtHsp70 with nucleotides. Full-length mtHsp70 exhibited slow intrinsic ATP hydrolysis activity (6.8+/-0.2 x 10(-4) s(-1)) at 25 degrees C, which was stimulated up to 49-fold by Hep. Hep also stimulated the activity of the isolated ATPase domain, albeit to a lower maximal extent (11.5-fold). In addition, gel-filtration studies showed that formation of chaperone-escort protein complexes inhibited mtHsp70 self-association, and they revealed that Hep binding to full-length mtHsp70 and its isolated ATPase domain is strongest in the absence of nucleotides. These findings provide evidence that metazoan escort proteins regulate the catalytic activity and solubility of their cognate chaperones, and they indicate that both forms of regulation arise from interactions with the mtHsp70 ATPase domain.

The Human Escort Protein Hep Binds to the ATPase Domain of Mitochondrial Hsp70 and Regulates ATP Hydrolysis*

PubMed Central

Zhai, Peng; Stanworth, Crystal; Liu, Shirley; Silberg, Jonathan J.

2008-01-01

Hsp70 escort proteins (Hep) have been implicated as essential for maintaining the function of yeast mitochondrial hsp70 molecular chaperones (mtHsp70), but the role that escort proteins play in regulating mammalian chaperone folding and function has not been established. We present evidence that human mtHsp70 exhibits limited solubility due to aggregation mediated by its ATPase domain and show that human Hep directly enhances chaperone solubility through interactions with this domain. In the absence of Hep, mtHsp70 was insoluble when expressed in Escherichia coli, as was its isolated ATPase domain and a chimera having this domain fused to the peptide-binding domain of HscA, a soluble monomeric chaperone. In contrast, these proteins all exhibited increased solubility when expressed in the presence of Hep. In vitro studies further revealed that purified Hep regulates the interaction of mtHsp70 with nucleotides. Full-length mtHsp70 exhibited slow intrinsic ATP hydrolysis activity (6.8 ± 0.2 × 10-4 s-1) at 25 °C, which was stimulated up to 49-fold by Hep. Hep also stimulated the activity of the isolated ATPase domain, albeit to a lower maximal extent (11.5-fold). In addition, gel-filtration studies showed that formation of chaperone-escort protein complexes inhibited mtHsp70 self-association, and they revealed that Hep binding to full-length mtHsp70 and its isolated ATPase domain is strongest in the absence of nucleotides. These findings provide evidence that metazoan escort proteins regulate the catalytic activity and solubility of their cognate chaperones, and they indicate that both forms of regulation arise from interactions with the mtHsp70 ATPase domain. PMID:18632665

Expression of interleukin-6 by a recombinant rabies virus enhances its immunogenicity as a potential vaccine.

PubMed

Luo, Jun; Zhang, Boyue; Wu, Yuting; Tian, Qin; Zhao, Jing; Lyu, Ziyu; Zhang, Qiong; Mei, Mingzhu; Luo, Yongwen; Guo, Xiaofeng

2017-02-07

Several studies have confirmed that interleukin-6 (IL6) mediates multiple biological effects that enhance immune responses when used as an adjuvant. In the present study, recombinant rabies virus (RABV) expressing canine IL6 (rHEP-CaIL6) was rescued and its pathogenicity and immunogenicity were investigated in mice. We demonstrated that mice received a single intramuscular immunization with rHEP-CaIL6 showed an earlier increase and higher maximum titres of virus-neutralizing antibody (VNA) as well as anti-RABV antibodies compared with mice immunized with the parent strain. Moreover, survival rates of mice immunized with rHEP-CaIL6 were higher compared with mice immunized with parent HEP-Flury according to the challenge assay. Flow cytometry further confirmed that immunization with rHEP-CaIL6 induced the strong recruitment of mature B cells and CD8 + T cells to lymph nodes, which may partially explain the high levels of VNA and enhanced cellular immunity. Quantitative real-time PCR indicated that rHEP-CaIL6 induced stronger inflammatory and immune responses in the central nervous system, which might have allowed virus clearance in the early infection phase. Furthermore, mice infected intranasally with rHEP-CaIL6 developed no clinical symptoms while mice infected with HEP-Flury showed piloerection. In summary, these data indicate that rHEP-CaIL6 induces a strong, protective immune response with a good safety profile. Therefore, a recombinant RABV strain expressing canine IL6 may aid the development of an effective, safe attenuated rabies vaccine. Copyright © 2017 Elsevier Ltd. All rights reserved.

CYP3A4-dependent cellular response does not relate to CYP3A4-catalysed metabolites of C-1748 and C-1305 acridine antitumor agents in HepG2 cells.

PubMed

Augustin, Ewa; Niemira, Magdalena; Hołownia, Adam; Mazerska, Zofia

2014-11-01

High CYP3A4 expression sensitizes tumor cells to certain antitumor agents while for others it can lower their therapeutic efficacy. We have elucidated the influence of CYP3A4 overexpression on the cellular response induced by antitumor acridine derivatives, C-1305 and C-1748, in two hepatocellular carcinoma (HepG2) cell lines, Hep3A4 stably transfected with CYP3A4 isoenzyme, and HepC34 expressing empty vector. The compounds were selected considering their different chemical structures and different metabolic pathways seen earlier in human and rat liver microsomes C-1748 was transformed to several metabolites at a higher rate in Hep3A4 than in HepC34 cells. In contrast, C-1305 metabolism in Hep3A4 cells was unchanged compared to HepC34 cells, with each cell line producing a single metabolite of comparable concentration. C-1748 resulted in a progressive appearance of sub-G1 population to its high level in both cell lines. In turn, the sub-G1 fraction was dominated in CYP3A4-overexpressing cells following C-1305 exposure. Both compounds induced necrosis and to a lesser extent apoptosis, which were more pronounced in Hep3A4 than in wild-type cells. In conclusion, CYP3A4-overexpressing cells produce higher levels of C-1748 metabolites, but they do not affect the cellular responses to the drug. Conversely, cellular response was modulated following C-1305 treatment in CYP3A4-overexpressing cells, although metabolism of this drug was unaltered. © 2014 International Federation for Cell Biology.

beta-Endorphin-induced analgesia is inhibited by synthetic analogs of beta-endorphin.

PubMed

Nicolas, P; Hammonds, R G; Li, C H

1984-05-01

Competitive antagonism of human beta-endorphin (beta h-EP)-induced analgesia by synthetic beta h-EP analogs with high in vitro opiate receptor binding to in vivo analgesic potency ratio has been demonstrated. A parallel shift of the dose-response curve for analgesia to the right was observed when either beta h-EP or [ Trp27 ] -beta h-EP was coinjected with various doses of [Gln8, Gly31 ]-beta h-EP-Gly-Gly-NH2, [Arg9,19,24,28,29]-beta h-EP, or [ Cys11 ,26, Phe27 , Gly31 ]-beta h-EP. It was estimated that the most potent antagonist, [Gln8, Gly31 ]-beta h-EP-Gly-NH2, is at least 200 times more potent than naloxone.

Hydroxyethyl Pachyman as a novel excipient for sustained-release matrix tablets.

PubMed

Zhou, Xiaoju; Wang, Pengyu; Wang, Jiong; Liu, Zhi; Hong, Xuechuan; Xiao, Yuling; Liu, Peng; Hu, Xianming

2016-12-10

This paper addressed the application of hydroxyethyl pachyman (HEP) as a novel matrix for sustained - release tablets, using diclofenac sodium (DS) as a model drug. The studies showed the HEP tablets prepared by wet granulation had much slower drug release as compared to those prepared by direct compression. Meanwhile, increasing the percentage of HEP in the formulations caused a decrease in drug release rates. Moreover, DS release from the HEP tablets was much higher at high pH (6.8) than that at low pH (1.2). Morphology studies proved the HEP tablet formed a continuous gel layer with porous inner structure in the dissolution media. Analysis of DS release profiles revealed that diffusion and matrix erosion occurred in simulated intestinal fluid(SIF, pH=6.8) for all the tablets. The experimental results predict HEP has a potential as a hydrophilic matrix in tablets to prolong drug release. Copyright © 2016 Elsevier Ltd. All rights reserved.

Induction of Apoptosis by Berberine in Hepatocellular Carcinoma HepG2 Cells via Downregulation of NF-κB.

PubMed

Li, Min; Zhang, Mao; Zhang, Zhi-Lang; Liu, Ning; Han, Xiao-Yu; Liu, Qin-Cheng; Deng, Wei-Jun; Liao, Cai-Xian

2017-01-26

Hepatocellular carcinoma (HCC) is highly resistant to traditional chemotherapeutic approaches, which causes difficulty in the development of effective drugs for the treatment of HCC. Berberine, a major ingredient of Rhizoma coptidis, is a natural alkaloid used in traditional Chinese medicine. Berberine exhibits potent antitumor activity against HCC due to its high efficiency and low toxicity. In the present study, we found that berberine sensitized HepG cells to NF-κB-mediated apoptosis. Berberine exhibited a significant antiproliferation effect on the HepG2 cells and promoted apoptosis. Both qRT-PCR and immunofluorescence staining revealed that berberine reduced the NF-κB p65 levels in HepG2 cells. Moreover, p65 overexpression rescued berberine-induced cell proliferation and prevented HepG2 cells from undergoing apoptosis. These results suggest that berberine inhibits the growth of HepG2 cells by promoting apoptosis through the NF-κB p65 pathway.

Fabrication of doxorubicin and heparin co-loaded microcapsules for synergistic cancer therapy.

PubMed

Chen, Jing-Xiao; Liang, Yan; Liu, Wen; Huang, Jin; Chen, Jing-Hua

2014-08-01

In this study, a layer-by-layer (LbL) assembly (HEP/CHI)5 microcapsule with doxorubicin hydrochloride (DOX) encapsulating inside was fabricated via alternatively depositing heparin (HEP) and chitosan (CHI) onto DOX-loaded CaCO3 templates. The microcapsules were of stable architecture and had good dispersity in aqueous medium. Fluorescence observation showed that DOX distributed both in the wall and in the cavity of microcapsules, while HEP presented in the capsule wall. The release rate of DOX increased at acidic pH as compared with that at basic pH, suggesting a pH-responsive drug release behavior. The microcapsules with positively charged CHI lying on the outer layer could protect HEP from heparanase degradation and achieve intracellular co-delivery of both DOX and HEP. Thus, the DOX-loaded microcapsules could have improved inhibition activity against A549 cells by combining pharmacological actions of DOX and HEP. Copyright © 2014 Elsevier B.V. All rights reserved.

Preparation, characterization, and anti-Helicobacter pylori activity of Bi3+-Hericium erinaceus polysaccharide complex.

PubMed

Zhu, Yang; Chen, Yao; Li, Qian; Zhao, Ting; Zhang, Ming; Feng, Weiwei; Takase, Mohammed; Wu, Xueshan; Zhou, Zhaoxiang; Yang, Liuqing; Wu, Xiangyang

2014-09-22

Two new Bi3+-Hericium erinaceus polysaccharide (BiHEP) complexes were prepared using Bi3+ and two purified polysaccharides from H. erinaceus (HEPs), respectively. The complexes were characterized by elemental analysis, FT-IR, CD, SEM, AFM, XRD, and TG. The anti-Helicobacter pylori (Hp) activities in vitro by agar dilution assay of the complexes were evaluated. The molecular weights of HEPs were 197 and 20 kDa, respectively. All the analyses confirmed the formation of new BiHEP complexes with lower content of Bi3+ compared with colloidal bismuth subcitrate (CBS), the most utilized bismuth preparation clinically. Furthermore, HEPs themselves have definite inhibition effects on Hp, and BiHEP complexes have lower content of Bi exhibited strong inhibition effects on Hp (MIC=20 μg/mL), similar to that of CBS with higher content of Bi. The study provides a basis for further development of multiple treatments of Hp infection or new medicines. Copyright © 2014 Elsevier Ltd. All rights reserved.

Networks in ATLAS

NASA Astrophysics Data System (ADS)

McKee, Shawn; ATLAS Collaboration

2017-10-01

Networks have played a critical role in high-energy physics (HEP), enabling us to access and effectively utilize globally distributed resources to meet the needs of our physicists. Because of their importance in enabling our grid computing infrastructure many physicists have taken leading roles in research and education (R&E) networking, participating in, and even convening, network related meetings and research programs with the broader networking community worldwide. This has led to HEP benefiting from excellent global networking capabilities for little to no direct cost. However, as other science domains ramp-up their need for similar networking it becomes less clear that this situation will continue unchanged. What this means for ATLAS in particular needs to be understood. ATLAS has evolved its computing model since the LHC started based upon its experience with using globally distributed resources. The most significant theme of those changes has been increased reliance upon, and use of, its networks. We will report on a number of networking initiatives in ATLAS including participation in the global perfSONAR network monitoring and measuring efforts of WLCG and OSG, the collaboration with the LHCOPN/LHCONE effort, the integration of network awareness into PanDA, the use of the evolving ATLAS analytics framework to better understand our networks and the changes in our DDM system to allow remote access to data. We will also discuss new efforts underway that are exploring the inclusion and use of software defined networks (SDN) and how ATLAS might benefit from: • Orchestration and optimization of distributed data access and data movement. • Better control of workflows, end to end. • Enabling prioritization of time-critical vs normal tasks • Improvements in the efficiency of resource usage

Hepatitis A vaccination coverage among adults 18-49 years traveling to a country of high or intermediate endemicity, United States.

PubMed

Lu, Peng-Jun; Byrd, Kathy K; Murphy, Trudy V

2013-05-01

Since 1996, hepatitis A vaccine (HepA) has been recommended for adults at increased risk for infection including travelers to high or intermediate hepatitis A endemic countries. In 2009, travel outside the United States and Canada was the most common exposure nationally reported for persons with hepatitis A virus (HAV) infection. To assess HepA vaccination coverage among adults 18-49 years traveling to a country of high or intermediate endemicity in the United States. We analyzed data from the 2010 National Health Interview Survey (NHIS), to determine self-reported HepA vaccination coverage (≥1 dose) and series completion (≥2 dose) among persons 18-49 years who traveled, since 1995, to a country of high or intermediate HAV endemicity. Multivariable logistic regression and predictive marginal analyses were conducted to identify factors independently associated with HepA vaccine receipt. In 2010, approximately 36.6% of adults 18-49 years reported traveling to high or intermediate hepatitis A endemic countries; among this group unadjusted HepA vaccination coverage was 26.6% compared to 12.7% among non-travelers (P-values<0.001) and series completion were 16.9% and 7.6%, respectively (P-values<0.001). On multivariable analysis among all respondents, travel status was an independent predictor of HepA coverage and series completion (both P-values<0.001). Among travelers, HepA coverage and series completion (≥2 doses) were higher for travelers 18-25 years (prevalence ratios 2.3, 2.8, respectively, P-values<0.001) and for travelers 26-39 years (prevalence ratios 1.5, 1.5, respectively, P-value<0.001, P-value=0.002, respectively) compared to travelers 40-49 years. Other characteristics independently associated with a higher likelihood of HepA receipt among travelers included Asian race/ethnicity, male sex, never having been married, having a high school or higher education, living in the western United States, having greater number of physician contacts or receipt of influenza vaccination in the previous year. HepB vaccination was excluded from the model because of the significant correlation between receipt of HepA vaccination and HepB vaccination could distort the model. Although travel to a country of high or intermediate hepatitis A endemicity was associated with higher likelihood of HepA vaccination in 2010 among adults 18-49 years, self-reported HepA vaccination coverage was low among adult travelers to these areas. Healthcare providers should ask their patients' upcoming travel plans and recommend and offer travel related vaccinations to their patients. Published by Elsevier Ltd.

Selective killing of hepatocellular carcinoma HepG2 cells by three-dimensional nanographene nanoparticles based on triptycene

NASA Astrophysics Data System (ADS)

Xiong, Xiaoqin; Gan, Lu; Liu, Ying; Zhang, Chun; Yong, Tuying; Wang, Ziyi; Xu, Huibi; Yang, Xiangliang

2015-03-01

Carbon-based materials have been widely used in the biomedical fields including drug delivery and cancer therapies. In this paper, a recently synthesized three-dimensional nanographene (NG) based on triptycene self-assembles into nanoparticles which selectively kill human hepatocellular carcinoma HepG2 cells as compared to human normal liver HL7702 cells. Obvious differences in cellular accumulation, the endocytic pathway and intracellular trafficking of NG nanoparticles are observed in HepG2 cells and HL7702 cells. Further studies reveal that NG nanoparticles significantly increase the levels of reactive oxygen species (ROS) in HepG2 cells, but not in HL7702 cells. NG nanoparticle-induced ROS result in apoptosis induction and the decrease in mitochondrial membrane potential in HepG2 cells. Moreover, IKK/nuclear factor-κB (NF-κB) signaling is found to be activated by NG nanoparticle-induced ROS and serves to antagonize NG nanoparticle-induced apoptosis in HepG2 cells. Our studies show that the distinct behaviors of cellular uptake and ROS-mediated cytotoxicity are responsible for the selective killing of HepG2 cells. This study provides a foundation for understanding the mechanism of selective induction of apoptosis in cancer cells by NG nanoparticles and designing more effective chemotherapeutical agents.Carbon-based materials have been widely used in the biomedical fields including drug delivery and cancer therapies. In this paper, a recently synthesized three-dimensional nanographene (NG) based on triptycene self-assembles into nanoparticles which selectively kill human hepatocellular carcinoma HepG2 cells as compared to human normal liver HL7702 cells. Obvious differences in cellular accumulation, the endocytic pathway and intracellular trafficking of NG nanoparticles are observed in HepG2 cells and HL7702 cells. Further studies reveal that NG nanoparticles significantly increase the levels of reactive oxygen species (ROS) in HepG2 cells, but not in HL7702 cells. NG nanoparticle-induced ROS result in apoptosis induction and the decrease in mitochondrial membrane potential in HepG2 cells. Moreover, IKK/nuclear factor-κB (NF-κB) signaling is found to be activated by NG nanoparticle-induced ROS and serves to antagonize NG nanoparticle-induced apoptosis in HepG2 cells. Our studies show that the distinct behaviors of cellular uptake and ROS-mediated cytotoxicity are responsible for the selective killing of HepG2 cells. This study provides a foundation for understanding the mechanism of selective induction of apoptosis in cancer cells by NG nanoparticles and designing more effective chemotherapeutical agents. Electronic supplementary information (ESI) available. See DOI: 10.1039/c4nr07248k

Hepatitis A vaccination coverage among adults 18–49 years traveling to a country of high or intermediate endemicity, United States

PubMed Central

Lu, Peng-jun; Byrd, Kathy K.; Murphy, Trudy V.

2018-01-01

Background Since 1996, hepatitis A vaccine (HepA) has been recommended for adults at increased risk for infection including travelers to high or intermediate hepatitis A endemic countries. In 2009, travel outside the United States and Canada was the most common exposure nationally reported for persons with hepatitis A virus (HAV) infection. Objective To assess HepA vaccination coverage among adults 18–49 years traveling to a country of high or intermediate endemicity in the United States. Methods We analyzed data from the 2010 National Health Interview Survey (NHIS), to determine self-reported HepA vaccination coverage (≥1 dose) and series completion (≥2 dose) among persons 18–49 years who traveled, since 1995, to a country of high or intermediate HAV endemicity. Multivariable logistic regression and predictive marginal analyses were conducted to identify factors independently associated with HepA vaccine receipt. Results In 2010, approximately 36.6% of adults 18–49 years reported traveling to high or intermediate hepatitis A endemic countries; among this group unadjusted HepA vaccination coverage was 26.6% compared to 12.7% among non-travelers (P-values < 0.001) and series completion were 16.9% and 7.6%, respectively (P-values < 0.001). On multivariable analysis among all respondents, travel status was an independent predictor of HepA coverage and series completion (both P-values < 0.001). Among travelers, HepA coverage and series completion (≥2 doses) were higher for travelers 18–25 years (prevalence ratios 2.3, 2.8, respectively, P-values < 0.001) and for travelers 26–39 years (prevalence ratios 1.5, 1.5, respectively, P-value < 0.001, P-value = 0.002, respectively) compared to travelers 40–49 years. Other characteristics independently associated with a higher likelihood of HepA receipt among travelers included Asian race/ethnicity, male sex, never having been married, having a high school or higher education, living in the western United States, having greater number of physician contacts or receipt of influenza vaccination in the previous year. HepB vaccination was excluded from the model because of the significant correlation between receipt of HepA vaccination and HepB vaccination could distort the model. Conclusions Although travel to a country of high or intermediate hepatitis A endemicity was associated with higher likelihood of HepA vaccination in 2010 among adults 18–49 years, self-reported HepA vaccination coverage was low among adult travelers to these areas. Healthcare providers should ask their patients’ upcoming travel plans and recommend and offer travel related vaccinations to their patients. PMID:23523408

Effects of β-glucan extracted from Agaricus blazei on the expression of ERCC5, CASP9, and CYP1A1 genes and metabolic profile in HepG2 cells.

PubMed

da Silva, A F; Sartori, D; Macedo, F C; Ribeiro, L R; Fungaro, M H P; Mantovani, M S

2013-06-01

The polysaccharide β-glucan has biological properties that stimulate the immune system and can prevent chronic pathologies, including cancer. It has been shown to prevent damage to DNA caused by the chemical and physical agents to which humans are exposed. However, the mechanism of β-glucan remains poorly understood. The objective of the present study was to verify the protective effect of β-glucan on the expression of the genes ERCC5 (involved in excision repair of DNA damage), CASP9 (involved in apoptosis), and CYP1A1 (involved in the metabolism of xenobiotics) using real-time polymerase chain reaction and perform metabolic profile measurements on the HepG2 cells. Cells were exposed to only benzo[a]pyrene (B[a]P), β-glucan, or a combination of B[a]P with β-glucan. The results demonstrated that 50 µg/mL β-glucan significantly repressed the expression of the ERCC5 gene when compared with the untreated control cells in these conditions. No change was found in the CASP9 transcript level. However, the CYP1A1 gene expression was also induced by HepG2 cells exposed to B[a]P only or in association with β-glucan, showing its effective protector against damage caused by B[a]P, while HepG2 cells exposed to only β-glucan did not show CYP1A1 modulation. The metabolic profiles showed moderate bioenergetic metabolism with an increase in the metabolites involved in bioenergetic metabolism (alanine, glutamate, creatine and phosphocholine) in cells treated with β-glucan and to a lesser extent treated with B[a]P. Thus, these results demonstrate that the chemopreventive activity of β-glucan may modulate bioenergetic metabolism and gene expression.

Machine Protection System Research and Development for the Fermilab PIP-II Proton Linac

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

Warner, Arden; Carmichael, Linden; Harrison, Beau

PIP-II is a high intensity proton linac being design to support a world-leading physics program at Fermilab. Initially it will provide high intensity beams for Fermilab's neutrino program with a future extension to other applications requiring an upgrade to CW linac operation (e.g. muon experiments). The machine is conceived to be 2 mA CW, 800 MeV H⁻ linac capable of working initially in a pulse (0.55 ms, 20 Hz) mode for injection into the existing Booster. The planned upgrade to CW operation implies that the total beam current and damage potential will be greater than in any present HEP hadronmore » linac. To mitigate the primary technical risk and challenges associated PIP-II an integrated system test for the PIP-II front-end technology is being developed. As part of the R&D a robust machine protection system (MPS) is being designed. This paper describes the progress and challenges associated with the MPS.« less

How Much Higher Can HTCondor Fly?

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

Fajardo, E. M.; Dost, J. M.; Holzman, B.

The HTCondor high throughput computing system is heavily used in the high energy physics (HEP) community as the batch system for several Worldwide LHC Computing Grid (WLCG) resources. Moreover, it is the backbone of GlidelnWMS, the pilot system used by the computing organization of the Compact Muon Solenoid (CMS) experiment. To prepare for LHC Run 2, we probed the scalability limits of new versions and configurations of HTCondor with a goal of reaching 200,000 simultaneous running jobs in a single internationally distributed dynamic pool.In this paper, we first describe how we created an opportunistic distributed testbed capable of exercising runsmore » with 200,000 simultaneous jobs without impacting production. This testbed methodology is appropriate not only for scale testing HTCondor, but potentially for many other services. In addition to the test conditions and the testbed topology, we include the suggested configuration options used to obtain the scaling results, and describe some of the changes to HTCondor inspired by our testing that enabled sustained operations at scales well beyond previous limits.« less

Gamow-Teller transitions and neutron-proton-pair transfer reactions

NASA Astrophysics Data System (ADS)

Van Isacker, P.; Macchiavelli, A. O.

2018-05-01

We propose a schematic model of nucleons moving in spin-orbit partner levels, j = l ± 1/2, to explain Gamow-Teller and two-nucleon transfer data in N = Z nuclei above 40Ca. Use of the LS coupling scheme provides a more transparent approach to interpret the structure and reaction data. We apply the model to the analysis of charge-exchange, 42Ca(3He,t)42Sc, and np-transfer, 40Ca(3He,p)42Sc, reactions data to define the elementary modes of excitation in terms of both isovector and isoscalar pairs, whose properties can be determined by adjusting the parameters of the model (spin-orbit splitting, isovector pairing strength and quadrupole matrix element) to the available data. The overall agreement with experiment suggests that the approach captures the main physics ingredients and provides the basis for a boson approximation that can be extended to heavier nuclei. Our analysis also reveals that the SU(4)-symmetry limit is not realized in 42Sc.

Graphical processors for HEP trigger systems

NASA Astrophysics Data System (ADS)

Ammendola, R.; Biagioni, A.; Chiozzi, S.; Cotta Ramusino, A.; Di Lorenzo, S.; Fantechi, R.; Fiorini, M.; Frezza, O.; Lamanna, G.; Lo Cicero, F.; Lonardo, A.; Martinelli, M.; Neri, I.; Paolucci, P. S.; Pastorelli, E.; Piandani, R.; Pontisso, L.; Rossetti, D.; Simula, F.; Sozzi, M.; Vicini, P.

2017-02-01

General-purpose computing on GPUs is emerging as a new paradigm in several fields of science, although so far applications have been tailored to employ GPUs as accelerators in offline computations. With the steady decrease of GPU latencies and the increase in link and memory throughputs, time is ripe for real-time applications using GPUs in high-energy physics data acquisition and trigger systems. We will discuss the use of online parallel computing on GPUs for synchronous low level trigger systems, focusing on tests performed on the trigger of the CERN NA62 experiment. Latencies of all components need analysing, networking being the most critical. To keep it under control, we envisioned NaNet, an FPGA-based PCIe Network Interface Card (NIC) enabling GPUDirect connection. Moreover, we discuss how specific trigger algorithms can be parallelised and thus benefit from a GPU implementation, in terms of increased execution speed. Such improvements are particularly relevant for the foreseen LHC luminosity upgrade where highly selective algorithms will be crucial to maintain sustainable trigger rates with very high pileup.

How "Discover the COSMOS", "PATHWAY", "Go-Lab" and "Inspiring Science Education" are changing the science education in European high schools

NASA Astrophysics Data System (ADS)

Kourkoumelis, Christine

2014-04-01

It has been noted by various reports that during recent years, there has been an alarming decline in young people's interest for science studies and mathematics. Since it is believed that the traditional teaching methods often fail to foster positive attitudes towards learning science, the European Commission has made intensive efforts to promote science education in schools though new methods based on the inquiry methodology of learning: questions, search and answers. This should be coupled to laboratories and hands-on experience which should be structured and scaffolded in a pedagogically meaningful way. "PATHWAY", "Discover the COSMOS" and "ISE" have been providing the lesson plans and the best practices for teachers and students and "Go-lab" is working towards an integrated set up of on-line labs for large scale use in science education. In the next sections some concrete examples which aim to bring the High Energy Physics (HEP) frontier research to schools will be given.

Expression and characterization of an enhanced recombinant heparinase I with chitin binding domain.

PubMed

Xu, Shuqin; Qiu, Meiling; Zhang, Xuanyue; Chen, Jinghua

2017-12-01

Heparinase I (Hep I) can efficiently depolymerize heparin and heparin sulfate to oligosaccharides or unsaturated disaccharides, which resulted in loss of physiological function such as blood coagulation. In order to realize the immobilization of Hep I on chitin carriers, we cloned Hep I with the chitin binding domain (ChBD) as a chitin-affinity tag, and the Small Ubiquitin-like MOdifier (SUMO) linker as a solvation enhancer in different fusion sequence. DNA and protein gels suggested that 4 kinds of recombinants were successfully constructed and expressed in Escherichia coli (E. coli). And the triple functional heparinases isolated from cell lysate could be efficiently purified by chitin beads. After optimizing fermentation conditions, it gave the specific enzyme activities of 1.88±0.11, 3.69±0.45, 3.44±0.38, and 2.73±0.29IU/mg total proteins for ChBD-Hep I, ChBD-SUMO-Hep I, SUMO-ChBD-Hep I, and ChBD-Hep I-SUMO, respectively, with unfractionated heparin as substrate. The optimal reaction temperature and pH were determined to be 30°C and 7.0 for all the fusion enzymes. ChBD-SUMO-Hep I exhibited the maximum half-life (48min) at 30°C and best thermo-stability under 15-50°C. All the fusion enzymes showed broad pH-stability in the range of 5.4-9.0. Copyright © 2017 Elsevier B.V. All rights reserved.

Chalcone-Induced Apoptosis through Caspase-Dependent Intrinsic Pathways in Human Hepatocellular Carcinoma Cells

PubMed Central

Ramirez-Tagle, Rodrigo; Escobar, Carlos A.; Romero, Valentina; Montorfano, Ignacio; Armisén, Ricardo; Borgna, Vincenzo; Jeldes, Emanuel; Pizarro, Luis; Simon, Felipe; Echeverria, Cesar

2016-01-01

Hepatocellular carcinoma (HCC) is one of the most commonly diagnosed cancers worldwide. Chemoprevention of HCC can be achieved through the use of natural or synthetic compounds that reverse, suppress or prevent the development of cancer progression. In this study, we investigated the antiproliferative effects and the mechanism of action of two compounds, 2,3,4′-trimethoxy-2′-hydroxy-chalcone (CH1) and 3′-bromo-3,4-dimethoxy-chalcone (CH2), over human hepatoma cells (HepG2 and Huh-7) and cultured mouse hepatocytes (HepM). Cytotoxic effects were observed over the HepG2 and Huh-7, and no effects were observed over the HepM. For HepG2 cells, treated separately with each chalcone, typical apoptotic laddering and nuclear condensation were observed. Additionally, the caspases and Bcl-2 family proteins activation by using Western blotting and immunocytochemistry were studied. Caspase-8 was not activated, but caspase-3 and -9 were both activated by chalcones in HepG2 cells. Chalcones also induced reactive oxygen species (ROS) accumulation after 4, 8 and 24 h of treatment in HepG2 cells. These results suggest that apoptosis in HepG2 was induced through: (i) a caspase-dependent intrinsic pathway; and (ii) by alterations in the cellular levels of Bcl-2 family proteins, and also, that the chalcone moiety could be a potent candidate as novel anticancer agents acting on human hepatomas. PMID:26907262

Upgrading cytochrome P450 activity in HepG2 cells co-transfected with adenoviral vectors for drug hepatotoxicity assessment.

PubMed

Tolosa, Laia; Donato, M Teresa; Pérez-Cataldo, Gabriela; Castell, José Vicente; Gómez-Lechón, M José

2012-12-01

In a number of adverse drug reactions leading to hepatotoxicity, drug metabolism is thought to be involved by the generation of reactive metabolites from non-toxic drugs. The use of hepatoma cell lines, such as HepG2 cell line, for the evaluation of drug-induced hepatotoxicity is hampered by their low cytochrome P450 expression which makes impossible the study of the toxicity produced by bioactivable compounds. Genetically manipulated cells constitute promising tools for hepatotoxicity applications. HepG2 cells were simultaneously transfected with recombinant adenoviruses encoding CYP1A2, CYP2C9 and CYP3A4 to confer them drug-metabolic competence. Upgraded cells (Adv-HepG2) were highly able to metabolize the toxin studied in contrast to the reduced metabolic capacity of HepG2 cells. Aflatoxin B1-induced hepatotoxicity was studied as a proof of concept in metabolically competent and non-competent HepG2 cells by using high content screening technology. Significant differences in mitochondrial membrane potential, intracellular calcium concentration, nuclear morphology and cell viability after treatment with aflatoxin B1 were observed in Adv-HepG2 when compared to HepG2 cells. Rotenone (non bioactivable) and citrate (non hepatotoxic) were analysed as negative controls. This cell model showed to be a suitable hepatic model to test hepatotoxicity of bioactivable drugs and constitutes a valuable alternative for hepatotoxicity testing. Copyright © 2011 Elsevier Ltd. All rights reserved.

Antitumor activities of extracts from selected desert plants against HepG2 human hepatocellular carcinoma cells.

PubMed

Thoppil, Roslin J; Harlev, Eli; Mandal, Animesh; Nevo, Eviatar; Bishayee, Anupam

2013-05-01

Phytochemicals are produced by desert plants to protect themselves against stressful environments. They have been shown to be useful in preventing and fighting adverse pathophysiological conditions and complex diseases, including cancer. Although many desert plants have been investigated for their antitumor properties, a large number of them still remain to be explored for possible therapeutic applications in oncologic diseases. To screen the antitumor effects of selected desert plants, namely Achillea fragrantissima (Forssk.) Sch. Bip. (Compositae), Ochradenus baccatus Delile (Resedaceae), Origanum dayi Post (Lamiaceae), Phlomis platystegia Post (Lamiaceae) and Varthemia iphionoides Boiss (Compositae), against an in vitro tumor model utilizing HepG2 human hepatocellular carcinoma cells. The aqueous extracts of aerial parts of the aforementioned plants were prepared and used for the in vitro experiments. The HepG2 cells were exposed to varying concentrations (0-4 mg/mL) of each plant extract for 24 or 48 h and the cytotoxicity was measured by the MTT assay. Following 24 h exposure, O. dayi extract exhibited a substantial antiproliferative effect in HepG2 cells (IC50 = 1.0 mg/mL) followed by O. baccatus (IC50 = 1.5 mg/mL). All plant extracts displayed cytotoxicity following 48 h exposure. Nevertheless, a substantial effect was observed with O. dayi (IC50 = 0.35 mg/mL) or O. baccatus (IC50 = 0.83 mg/mL). The aqueous extracts from aerial parts of O. dayi and O. baccatus possess antitumor effects against human liver cancer cells. These desert plants represent valuable resources for the development of potential anticancer agents.

Transfer of free polymannose-type oligosaccharides from the cytosol to lysosomes in cultured human hepatocellular carcinoma HepG2 cells.

PubMed

Saint-Pol, A; Bauvy, C; Codogno, P; Moore, S E

1997-01-13

Large, free polymannose oligosaccharides generated during glycoprotein biosynthesis rapidly appear in the cytosol of HepG2 cells where they undergo processing by a cytosolic endo H-like enzyme and a mannosidase to yield the linear isomer of Man5GlcNAc (Man[alpha 1-2]Man[alpha 1-2]Man[alpha 1-3][Man alpha 1-6]Man[beta 1-4] GlcNAc). Here we have examined the fate of these partially trimmed oligosaccharides in intact HepG2 cells. Subsequent to pulse-chase incubations with D-[2-3H]mannose followed by permeabilization of cells with streptolysin O free oligosaccharides were isolated from the resulting cytosolic and membrane-bound compartments. Control pulse-chase experiments revealed that total cellular free oligosaccharides are lost from HepG2 cells with a half-life of 3-4 h. In contrast use of the vacuolar H+/ATPase inhibitor, concanamycin A, stabilized total cellular free oligosaccharides and enabled us to demonstrate a translocation of partially trimmed oligosaccharides from the cytosol into a membrane-bound compartment. This translocation process was unaffected by inhibitors of autophagy but inhibited if cells were treated with either 100 microM swainsonine, which provokes a cytosolic accumulation of large free oligosaccharides bearing 8-9 residues of mannose, or agents known to reduce cellular ATP levels which lead to the accumulation of the linear isomer of Man5GlcNAc in the cytosol. Subcellular fractionation studies on Percoll density gradients revealed that the cytosol-generated linear isomer of Man5GlcNAc is degraded in a membrane-bound compartment that cosediments with lysosomes.

Herpes simplex virus 2 modulates apoptosis and stimulates NF-{kappa}B nuclear translocation during infection in human epithelial HEp-2 cells

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

Yedowitz, Jamie C.; Blaho, John A.

2005-11-25

Virus-mediated apoptosis is well documented in various systems, including herpes simplex virus 1 (HSV-1). HSV-2 is closely related to HSV-1 but its apoptotic potential during infection has not been extensively scrutinized. We report that (i) HEp-2 cells infected with HSV-2(G) triggered apoptosis, assessed by apoptotic cellular morphologies, oligosomal DNA laddering, chromatin condensation, and death factor processing when a translational inhibitor (CHX) was added at 3 hpi. Thus, HSV-2 induced apoptosis but was unable to prevent the process from killing cells. (ii) Results from a time course of CHX addition experiment indicated that infected cell protein produced between 3 and 5more » hpi, termed the apoptosis prevention window, are required for blocking virus-induced apoptosis. This corresponds to the same prevention time frame as reported for HSV-1. (iii) Importantly, CHX addition prior to 3 hpi led to less apoptosis than that at 3 hpi. This suggests that proteins produced immediately upon infection are needed for efficient apoptosis induction by HSV-2. This finding is different from that observed previously with HSV-1. (iv) Infected cell factors produced during the HSV-2(G) prevention window inhibited apoptosis induced by external TNF{alpha} plus cycloheximide treatment. (v) NF-{kappa}B translocated to nuclei and its presence in nuclei correlated with apoptosis prevention during HSV-2(G) infection. (vi) Finally, clinical HSV-2 isolates induced and prevented apoptosis in HEp-2 cells in a manner similar to that of laboratory strains. Thus, while laboratory and clinical HSV-2 strains are capable of modulating apoptosis in human HEp-2 cells, the mechanism of HSV-2 induction of apoptosis differs from that of HSV-1.« less

Human scFv antibody fragments specific for hepatocellular carcinoma selected from a phage display library.

PubMed

Yu, Bing; Ni, Ming; Li, Wen-Han; Lei, Ping; Xing, Wei; Xiao, Dai-Wen; Huang, Yu; Tang, Zhen-Jie; Zhu, Hui-Fen; Shen, Guan-Xin

2005-07-14

To identify the scFv antibody fragments specific for hepatocellular carcinoma by biopanning from a large human naive scFv phage display library. A large human naive scFv phage library was used to search for the specific targets by biopanning with the hepatocellular carcinoma cell line HepG2 for the positive-selecting and the normal liver cell line L02 for the counter-selecting. After three rounds of biopanning, individual scFv phages binding selectively to HepG2 cells were picked out. PCR was carried out for identification of the clones containing scFv gene sequence. The specific scFv phages were selected by ELISA and flow cytometry. DNA sequences of positive clones were analyzed by using Applied Biosystem Automated DNA sequencers 3 730. The expression proteins of the specific scFv antibody fragments in E.coli HB2151 were purified by the affinity chromatography and detected by SDS-PAGE, Western blot and ELISA. The biological effect of the soluble antibody fragments on the HepG2 cells was investigated by observing the cell proliferation. Two different positive clones were obtained and the functional variable sequences were identified. Their DNA sequences of the scFv antibody fragments were submitted to GenBank (accession nos: AY686498 and AY686499). The soluble scFv antibody fragments were successfully expressed in E.coli HB2151. The relative molecular mass of the expression products was about 36 ku, according to its predicted M(r) value. The two soluble scFv antibody fragments also had specific binding activity and obvious growth inhibition properties to HepG2 cells. The phage library biopanning permits identification of specific antibody fragments for hepatocellular carcinoma and affords experiment evidence for its immunotherapy study.

Improving Design Efficiency for Large-Scale Heterogeneous Circuits

NASA Astrophysics Data System (ADS)

Gregerson, Anthony

Despite increases in logic density, many Big Data applications must still be partitioned across multiple computing devices in order to meet their strict performance requirements. Among the most demanding of these applications is high-energy physics (HEP), which uses complex computing systems consisting of thousands of FPGAs and ASICs to process the sensor data created by experiments at particles accelerators such as the Large Hadron Collider (LHC). Designing such computing systems is challenging due to the scale of the systems, the exceptionally high-throughput and low-latency performance constraints that necessitate application-specific hardware implementations, the requirement that algorithms are efficiently partitioned across many devices, and the possible need to update the implemented algorithms during the lifetime of the system. In this work, we describe our research to develop flexible architectures for implementing such large-scale circuits on FPGAs. In particular, this work is motivated by (but not limited in scope to) high-energy physics algorithms for the Compact Muon Solenoid (CMS) experiment at the LHC. To make efficient use of logic resources in multi-FPGA systems, we introduce Multi-Personality Partitioning, a novel form of the graph partitioning problem, and present partitioning algorithms that can significantly improve resource utilization on heterogeneous devices while also reducing inter-chip connections. To reduce the high communication costs of Big Data applications, we also introduce Information-Aware Partitioning, a partitioning method that analyzes the data content of application-specific circuits, characterizes their entropy, and selects circuit partitions that enable efficient compression of data between chips. We employ our information-aware partitioning method to improve the performance of the hardware validation platform for evaluating new algorithms for the CMS experiment. Together, these research efforts help to improve the efficiency and decrease the cost of the developing large-scale, heterogeneous circuits needed to enable large-scale application in high-energy physics and other important areas.

Smart nanovehicles based on pH-triggered disassembly of supramolecular peptide-amphiphiles for efficient intracellular drug delivery.

PubMed

Xu, Xianghui; Li, Yunkun; Li, Haiping; Liu, Rong; Sheng, Mingming; He, Bin; Gu, Zhongwei

2014-03-26

A novel type of nanovehicle (NV) based on stimuli-responsive supramolecular peptide-amphiphiles (SPAs, dendritic poly (L-lysine) non-covalently linked poly (L-leucine)) is developed for intracellular drug delivery. To determine the pH-dependent mechanism, the supramolecular peptide-amphiphile system (SPAS) is investigated at different pH conditions using a variety of physical and chemical approaches. The pH-triggered disassembly of SPAS can be attributed to the disappearance of non-covalent interactions within SPAs around the isoelectric point of poly (L-leucine). SPAS is found to encapsulate guest molecules at pH 7.4 but release them at pH 6.2. In this way, SPAS is able to act as a smart NV to deliver its target to tumor cells using intracellular pH as a trigger. The DOX-loaded NVs are approximately 150 nm in size. In vitro release profiles and confocal laser scanning microscopy (CLSM) images of HepG2 cells confirm that lower pH conditions can trigger the disassembly of NVs and so achieve pH-dependent intracellular DOX delivery. In vitro cytotoxicity of the DOX-loaded NVs to HepG2 cells demonstrate that the smart NVs enhance the efficacy of hydrophobic DOX. Fluorescence-activated cell sorting (FACS) and CLSM results show that the NVs can enhance the endocytosis of DOX into HepG2 cells considerably and deliver DOX to the nuclei. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Synergistic anticancer effect of the extracts from Polyalthia evecta caused apoptosis in human hepatoma (HepG2) cells

PubMed Central

Machana, Sasipawan; Weerapreeyakul, Natthida; Barusrux, Sahapat; Thumanu, Kanjana; Tanthanuch, Waraporn

2012-01-01

Objective To evaluate the anticancer activity of the extract fraction of Polyalthia evecta (P. evecta) (Pierre) Finet & Gagnep and the synergistic anticancer effect of the extracts from P. evecta by using the ATR/FT-IR spectroscopy. Methods The 50% ethanol-water crude leaf extract of P. evecta (EW-L) was prepared and was further fractionated to isolate various fractions. The anticancer activity was investigated from cytotoxicity against HepG2 using a neutral red assay and apoptosis induction by evaluation of nuclei morphological changes after DAPI staining. Synergistic anticancer effects of the extracts from P. evecta were performed using the ATR/FT-IR spectroscopy. Results The result showed that the EW-L showed higher cytotoxicity and apoptosis induction in HepG2 cells than its fractionated extracts. The hexane extract exhibited higher cytotoxicity and apoptosis induction than the water extracts, but less than the EW-L. The combined water and hexane extracts apparently increased cytotoxicity and apoptosis induction. The %apoptotic cells induced by the extract mixture were increased about 2-fold compared to the single hexane extract. Conclusions The polar extract fraction is necessary for the anticancer activity of the non-polar extract fraction. The ATR/FT-IR spectra illustrates the physical interaction among the constituents in the extract mixture and reveals the presence of polyphenolic constituents in the EW-L, which might play a role for the synergistic anticancer effect. PMID:23569977

beta-Endorphin: synthesis of analogs modified at the carboxyl terminus with increased activites.

PubMed Central

Li, C H; Yamashiro, D; Tseng, L F; Chang, W C; Ferrara, P

1979-01-01

Three analogs of human beta-endorphin (beta h-EP) have been synthesized: [Gly31]beta h-EP, [Gly31]beta h-endorphinamide, and [Gly31]beta h-endorphinylglycine. All are more active than beta h-EP in both the guinea pig ileum bioassay and the opiate receptor binding assay. The last two analogs are about twice as active as beta h-EP in an assay for analgesia. Modification at position 31 and extension at the COOH terminus may afford a route toward analogs with even greater biological activity. PMID:226965

beta-Endorphin: synthesis of analogs modified at the carboxyl terminus with increased activites.

PubMed

Li, C H; Yamashiro, D; Tseng, L F; Chang, W C; Ferrara, P

1979-07-01

Three analogs of human beta-endorphin (beta h-EP) have been synthesized: [Gly31]beta h-EP, [Gly31]beta h-endorphinamide, and [Gly31]beta h-endorphinylglycine. All are more active than beta h-EP in both the guinea pig ileum bioassay and the opiate receptor binding assay. The last two analogs are about twice as active as beta h-EP in an assay for analgesia. Modification at position 31 and extension at the COOH terminus may afford a route toward analogs with even greater biological activity.

Medical Surveillance Monthly Report (MSMR). Volume 13, Number 2, February/March 2007

DTIC Science & Technology

2007-03-01

13/No. 2 1 10 100 1,000 10,000 100,000 Influenza Varicella Hep B Pertussis Hep A Mumps Meningococcal disease Vaccine-preventable disease R ep or te... pertussis (ICD- 9: 033), mumps (ICD-9: 072), influenza (ICD-9: 487), hepatitis B (ICD-9: 070.2, 070.3), and hepatitis A (ICD- 9: 070.0, 070.1) were defined by...Influenza Varicella Hep B w/o coma Pertussis Hep A w/o coma MSMR 17Vol. 13/No. 2 conditions should account for potential changes in case ascertainment and

beta-Endorphin-induced analgesia is inhibited by synthetic analogs of beta-endorphin.

PubMed Central

Nicolas, P; Hammonds, R G; Li, C H

1984-01-01

Competitive antagonism of human beta-endorphin (beta h-EP)-induced analgesia by synthetic beta h-EP analogs with high in vitro opiate receptor binding to in vivo analgesic potency ratio has been demonstrated. A parallel shift of the dose-response curve for analgesia to the right was observed when either beta h-EP or [ Trp27 ] -beta h-EP was coinjected with various doses of [Gln8, Gly31 ]-beta h-EP-Gly-Gly-NH2, [Arg9,19,24,28,29]-beta h-EP, or [ Cys11 ,26, Phe27 , Gly31 ]-beta h-EP. It was estimated that the most potent antagonist, [Gln8, Gly31 ]-beta h-EP-Gly-NH2, is at least 200 times more potent than naloxone. PMID:6328494

[Cytotoxicity of the secondary metabolites of Marine Mangrove Fungus Paecilomyces sp. tree 1-7 on human hepatoma cell line HepG2].

PubMed

Cai, Xiao-Ling; Gao, Jun-Ping; Li, Qing; Wen, Lu; She, Zhi-Gang; Lin, Yong-Cheng

2008-06-01

To study the cytotoxicity of the secondary metabolites of Marine Mangrove Fungus Paecilomyces sp. Tree 1-7 on human hepatoma cell line HepG2 cultured in vitro. Three groups were divided: compounds group, 5-Fu group and control group. The cytotoxicity was measured by MTT method when HepG2 cells were treated by different concentration of the secondary metabolites of Paecilomyces sp. Tree 1-7. Secalonic acid A, tenellic acid A and alternin inhibited the growth of human hepatoma cell line HepG2, the IC50 separately were 2.0, 62.1 and 7.0 microg/ml. Secalonic acid A and alternin have strong cytotoxicity on HepG2 cultured in vitro.

VCC-1 over-expression inhibits cisplatin-induced apoptosis in HepG2 cells

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

Zhou, Zhitao; Lu, Xiao; Zhu, Ping

Highlights: Black-Right-Pointing-Pointer VCC-1 is hypothesized to be associated with carcinogenesis. Black-Right-Pointing-Pointer Levels of VCC-1 are increased significantly in HCC. Black-Right-Pointing-Pointer Over-expression of VCC-1 could promotes cellular proliferation rate. Black-Right-Pointing-Pointer Over-expression of VCC-1 inhibit the cisplatin-provoked apoptosis in HepG2 cells. Black-Right-Pointing-Pointer VCC-1 plays an important role in control the tumor growth and apoptosis. -- Abstract: Vascular endothelial growth factor-correlated chemokine 1 (VCC-1), a recently described chemokine, is hypothesized to be associated with carcinogenesis. However, the molecular mechanisms by which aberrant VCC-1 expression determines poor outcomes of cancers are unknown. In this study, we found that VCC-1 was highly expressed in hepatocellularmore » carcinoma (HCC) tissue. It was also associated with proliferation of HepG2 cells, and inhibition of cisplatin-induced apoptosis of HepG2 cells. Conversely, down-regulation of VCC-1 in HepG2 cells increased cisplatin-induced apoptosis of HepG2 cells. In summary, these results suggest that VCC-1 is involved in cisplatin-induced apoptosis of HepG2 cells, and also provides some evidence for VCC-1 as a potential cellular target for chemotherapy.« less

The targeted inhibition of mitochondrial Hsp90 overcomes the apoptosis resistance conferred by Bcl-2 in Hep3B cells via necroptosis

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

Yan, Chunlan; Department of Physiology, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058; Oh, Joon Seok

Previous studies have reported that a Gamitrinib variant containing triphenylphosphonium (G-TPP) binds to mitochondrial Hsp90 and rapidly inhibits its activity, thus inducing the apoptotic pathway in the cells. Accordingly, G-TPP shows a potential as a promising drug for the treatment of cancer. A cell can die from different types of cell death such as apoptosis, necrosis, necroptosis, and autophagic cell death. In this study, we further investigated the mechanisms and modes of cell death in the G-TPP-treated Hep3B and U937 cell lines. We discovered that G-TPP kills the U937 cells through the apoptotic pathway and the overexpression of Bcl-2 significantlymore » inhibits U937 cell death to G-TPP. We further discovered that G-TPP kills the Hep3B cells by activating necroptosis in combination with the partial activation of caspase-dependent apoptosis. Importantly, G-TPP overcomes the apoptosis resistance conferred by Bcl-2 in Hep3B cells via necroptosis. We also observed that G-TPP induces compensatory autophagy in the Hep3B cell line. We further found that whereas there is a Bcl-2-Beclin 1 interaction in response to G-TPP, silencing the beclin 1 gene failed to block LC3-II accumulation in the Hep3B cells, indicating that G-TPP triggers Beclin 1-independent protective autophagy in Hep3B cells. Taken together, these data reveal that G-TPP induces cell death through a combination of death pathways, including necroptosis and apoptosis, and overcomes the apoptosis resistance conferred by Bcl-2 in Hep3B cells via necroptosis. These findings are important for the therapeutic exploitation of necroptosis as an alternative cell death program to bypass the resistance to apoptosis. Highlights: ► G-TPP binds to mitochondrial Hsp90. ► G-TPP induces apoptosis in U937 human leukemia cancer cells. ► G-TPP induces combination of death pathways in Hep3B cell. ► G-TPP overcomes the resistance conferred by Bcl-2 in Hep3B cells via necroptosis. ► G-TPP triggers Beclin 1-independent protective autophagy in Hep3B cells.« less

The orphan receptor hepatic nuclear factor 4 functions as a transcriptional activator for tissue-specific and hypoxia-specific erythropoietin gene expression and is antagonized by EAR3/COUP-TF1.

PubMed

Galson, D L; Tsuchiya, T; Tendler, D S; Huang, L E; Ren, Y; Ogura, T; Bunn, H F

1995-04-01

The erythropoietin (Epo) gene is regulated by hypoxia-inducible cis-acting elements in the promoter and in a 3' enhancer, both of which contain consensus hexanucleotide hormone receptor response elements which are important for function. A group of 11 orphan nuclear receptors, transcribed and translated in vitro, were screened by the electrophoretic mobility shift assay. Of these, hepatic nuclear factor 4 (HNF-4), TR2-11, ROR alpha 1, and EAR3/COUP-TF1 bound specifically to the response elements in the Epo promoter and enhancer and, except for ROR alpha 1, formed DNA-protein complexes that had mobilities similar to those observed in nuclear extracts of the Epo-producing cell line Hep3B. Moreover, both anti-HNF-4 and anti-COUP antibodies were able to supershift complexes in Hep3B nuclear extracts. Like Epo, HNF-4 is expressed in kidney, liver, and Hep3B cells but not in HeLa cells. Transfection of a plasmid expressing HNF-4 into HeLa cells enabled an eightfold increase in the hypoxic induction of a luciferase reporter construct which contains the minimal Epo enhancer and Epo promoter, provided that the nuclear hormone receptor consensus DNA elements in both the promoter and the enhancer were intact. The augmentation by HNF-4 in HeLa cells could be abrogated by cotransfection with HNF-4 delta C, which retains the DNA binding domain of HNF-4 but lacks the C-terminal activation domain. Moreover, the hypoxia-induced expression of the endogenous Epo gene was significantly inhibited in Hep3B cells stably transfected with HNF-4 delta C. On the other hand, cotransfection of EAR3/COUP-TF1 and the Epo reporter either with HNF-4 into HeLa cells or alone into Hep3B cells suppressed the hypoxia induction of the Epo reporter. These electrophoretic mobility shift assay and functional experiments indicate that HNF-4 plays a critical positive role in the tissue-specific and hypoxia-inducible expression of the Epo gene, whereas the COUP family has a negative modulatory role.

Induction of AhR-Mediated Gene Transcription by Coffee

PubMed Central

Ishikawa, Toshio; Takahashi, Satoshi; Morita, Koji; Okinaga, Hiroko; Teramoto, Tamio

2014-01-01

Background Aryl hydrocarbon receptor (AhR) is classically known to be activated by xenobiotics such as dioxins and polycyclic aromatic hydrocarbons (PAHs). Although it has been reported that PAHs are contained in roasted coffee beans, in general coffee beverages are not considered to be AhR activators. We tested whether exposure to coffee would activate AhR in cultured cells. Methods HepG2 cells stably expressing an AhR-responsive reporter gene were treated with coffee samples. Also, expression of CYP1A1, an endogenous AhR-responsive gene, was quantitated by RT-PCR and Western blotting in HepG2, Caco-2, and MCF-7 cells, after treatment with coffee. In order to obtain sensitive and reproducible results, all the experiments were performed with the cells placed in either phosphate-buffered saline (PBS) or pure serum, instead of routinely-used culture medium, whose intrinsic AhR-stimulating activity turned out to be so strong as to interfere with the analyses. Results All the coffee samples tested robustly stimulated AhR-mediated transcription in the reporter gene assays. Of note, to what extent coffee and other AhR agonists activated AhR was different, depending on whether the experiments were done in PBS or serum. CYP1A1 mRNA was induced by coffee, in HepG2, Caco-2, and MCF-7 cells placed in either PBS or serum. CYP1A1 protein expression, which was not detected in these cells incubated in PBS, was also increased by coffee in cells placed in serum. Conclusions By using culture medium-free experimental settings, we have shown that coffee is a strong AhR activator. Our observation may help elucidate as-yet-unrecognized effects of coffee on human health. PMID:25007155

Benchmarking worker nodes using LHCb productions and comparing with HEPSpec06

NASA Astrophysics Data System (ADS)

Charpentier, P.

2017-10-01

In order to estimate the capabilities of a computing slot with limited processing time, it is necessary to know with a rather good precision its “power”. This allows for example pilot jobs to match a task for which the required CPU-work is known, or to define the number of events to be processed knowing the CPU-work per event. Otherwise one always has the risk that the task is aborted because it exceeds the CPU capabilities of the resource. It also allows a better accounting of the consumed resources. The traditional way the CPU power is estimated in WLCG since 2007 is using the HEP-Spec06 benchmark (HS06) suite that was verified at the time to scale properly with a set of typical HEP applications. However, the hardware architecture of processors has evolved, all WLCG experiments moved to using 64-bit applications and use different compilation flags from those advertised for running HS06. It is therefore interesting to check the scaling of HS06 with the HEP applications. For this purpose, we have been using CPU intensive massive simulation productions from the LHCb experiment and compared their event throughput to the HS06 rating of the worker nodes. We also compared it with a much faster benchmark script that is used by the DIRAC framework used by LHCb for evaluating at run time the performance of the worker nodes. This contribution reports on the finding of these comparisons: the main observation is that the scaling with HS06 is no longer fulfilled, while the fast benchmarks have a better scaling but are less precise. One can also clearly see that some hardware or software features when enabled on the worker nodes may enhance their performance beyond expectation from either benchmark, depending on external factors.

The activation of peroxisome proliferator-activated receptor γ is regulated by Krüppel-like transcription factors 6 & 9 under steatotic conditions

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

Escalona-Nandez, Ivonne; Guerrero-Escalera, Dafne; Estanes-Hernández, Alma

2015-03-20

Liver steatosis is characterised by lipid droplet deposition in hepatocytes that can leads to an inflammatory and fibrotic phenotype. Peroxisome proliferator-activated receptors (PPARs) play key roles in energetic homeostasis by regulating lipid metabolism in hepatic tissue. In adipose tissue PPARγ regulates the adipocyte differentiation by promoting the expression of lipid-associated genes. Within the liver PPARγ is up-regulated under steatotic conditions; however, which transcription factors participate in its expression is not completely understood. Krüppel-like transcription factors (KLFs) regulate various cellular mechanisms, such as cell proliferation and differentiation. KLFs are key components of adipogenesis by regulating the expression of PPARγ and othermore » proteins such as the C-terminal enhancer binding protein (C/EBP). Here, we demonstrate that the transcript levels of Klf6, Klf9 and Pparγ are increased in response to a steatotic insult in vitro. Chromatin immunoprecipitation (ChIp) experiments showed that klf6 and klf9 are actively recruited to the Pparγ promoter region under these conditions. Accordingly, the loss-of-function experiments reduced cytoplasmic triglyceride accumulation. Here, we demonstrated that KLF6 and KLF9 proteins directly regulate PPARγ expression under steatotic conditions. - Highlights: • Palmitic acid promotes expression of KlF6 & KLF9 in HepG2 cells. • KLF6 and KLF9 promote the expression of PPARγ in response to palmitic acid. • Binding of KLF6 and KLF9 to the PPARγ promoter promotes steatosis in HepG2 cells. • KLF6 and KLF9 loss-of function diminishes the steatosis in HepG2 cells.« less

Hyperecho PROPELLER-MRI: Application to rapid high-resolution motion-insensitive T2 -weighted black-blood imaging of the carotid arterial vessel wall and plaque.

PubMed

Yoneyama, Masami; Nakamura, Masanobu; Obara, Makoto; Okuaki, Tomoyuki; Sashi, Ryuji; Sawano, Seishi; Tatsuno, Satoshi; Van Cauteren, Marc

2017-02-01

To demonstrate the usefulness of hyperecho and PROPELLER (HEP) for carotid arterial vessel wall imaging by using a quantitative comparison with conventional methods. PROPELLER is a motion-insensitive turbo spin-echo (TSE) sequence and has recently been utilized in magnetic resonance (MR) plaque imaging instead of double inversion recovery TSE (DIR-TSE). Wider blade-width, higher k-space density, and an improved blood suppression effect result in better image quality. In this study we introduce a new combination of HEP. A total of 17 subjects were examined on a 3.0T system. We conducted quantitative comparisons for signal-to-noise ratio (SNR), contrast-to-noise-ratio, and image sharpness among HEP, DIR-TSE, and conventional PROPELLER (c-PROPELLER). Subsequently, images obtained with DIR-TSE, c-PROPELLER, and HEP were visually evaluated using a three-point scale by two board-certified radiologists. HEP showed high SNR similar to c-PROPELLER, good T 2 contrast approximating DIR-TSE, and better blood suppression compared with the other two methods (P < 0.05). The image sharpness of HEP (2.55 ± 0.53) was higher than that of DIR-TSE (1.89 ± 0.33) and the absence of ghost or streak artifacts in HEP (2.89 ± 0.33) was better than that in both other methods (2.22 ± 0.83 for DIR-TSE and 2.00 ± 0.50 for c-PROPELLER) (P < 0.05). Furthermore, the degree of blood suppression, particularly in cases of slow or turbulent flow close to the atherosclerotic plaque, was identical for HEP (2.80 ± 0.45) and DIR-TSE (2.80 ± 0.45) but was significantly better than for c-PROPELLER (1.60 ± 0.55) (P < 0.05). This study demonstrates the usefulness of HEP in the carotid arteries. HEP can provide higher-resolution T 2 -weighted black-blood imaging without flow- and/or motion-related artifacts, compared to conventional techniques. 3 J. Magn. Reson. Imaging 2017;45:515-524. © 2016 International Society for Magnetic Resonance in Medicine.

Cancer-Associated Fibroblasts in a Human HEp-2 Established Laryngeal Xenografted Tumor Are Not Derived from Cancer Cells through Epithelial-Mesenchymal Transition, Phenotypically Activated but Karyotypically Normal

PubMed Central

Wang, Mei; Wu, Chun-Ping; Pan, Jun-Yan; Zheng, Wen-Wei; Cao, Xiao-Juan; Fan, Guo-Kang

2015-01-01

Cancer-associated fibroblasts (CAFs) play a crucial role in cancer progression and even initiation. However, the origins of CAFs in various cancer types remain controversial, and one of the important hypothesized origins is through epithelial-mesenchymal transition (EMT) from cancer cells. In this study, we investigated whether the HEp-2 laryngeal cancer cells are able to generate CAFs via EMT during tumor formation, which is now still unknown. The laryngeal xenografted tumor model was established by inoculating the HEp-2 laryngeal cancer cell line in nude mice. Primary cultured CAFs from the tumor nodules and matched normal fibroblasts (NFs) from the adjacent connective tissues were subcultured, purified, and verified by immunofluorescence. Migration, invasion, and proliferation potentials were compared between the CAFs and NFs. A co-culture of CAFs with HEp-2 cells and a co-injection of CAFs with HEp-2 cells in nude mice were performed to examine the cancer-promoting potential of CAFs to further verify their identity. Karyotypic analyses of the CAFs, NFs, and HEp-2 cells were conducted. A co-culture of NFs with HEp-2 cells was also performed to examine the expression of activated markers of CAFs. A pathological examination confirmed that the laryngeal xenografted tumor model was successfully established, containing abundant CAFs. Immunocytochemical staining verified the purities and identities of the CAFs and NFs. Although the CAFs manifested higher migration, invasion, proliferation, and cancer-promoting capacities compared with the NFs, an analysis of chromosomes revealed that both the CAFs and NFs showed typical normal mouse karyotypes. In addition, the NFs co-cultured with HEp-2 cells did not show induced expressions of activated markers of CAFs. Our findings reveal that the CAFs in the HEp-2 established laryngeal xenografted tumor are not of laryngeal cancer origin but of mouse origin, indicating that the HEp-2 laryngeal cancer cells cannot generate their own CAFs via EMT in this model. PMID:25658113

Shillapoo Wildlife Area 2007 Follow-up HEP Report.

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

Ashley, Paul R.

In April and May 2007 the Regional HEP Team (RHT) conducted a follow-up HEP analysis on the Egger (612 acres) and Herzog (210 acres) parcels located at the north end of the Shillapoo Wildlife Area. The Egger and Herzog parcels have been managed with Bonneville Power Administration funds since acquired in 1998 and 2001 respectively. Slightly more than 936 habitat units (936.47) or 1.14 HUs per acre was generated as an outcome of the 2007 follow-up HEP surveys. Results included 1.65 black-capped chickadee HUs, 280.57 great blue heron HUs, 581.45 Canada goose HUs, 40 mallard HUs, and 32.80 mink HUs.more » Introduction A follow-up Habitat Evaluation Procedures (HEP) (USFWS 1980) analysis was conducted by the Columbia Basin Fish and Wildlife Authority's (CBFWA) Regional HEP Team (RHT) during April and May 2007 to document changes in habitat quality and to determine the number of habitat units (HUs) to credit Bonneville Power Administration (BPA) for providing operation and maintenance (O&M) funds since WDFW acquired the parcels. The 2007 follow-up HEP evaluation was limited to Shillapoo Wildlife Area (SWA) parcels purchased with Bonneville Power Administration funds. D. Budd (pers. comm.) reported WDFW purchased the 612 acre Egger Farms parcel on November 2, 1998 for $1,737,0001 and the 210 acre Herzog acquisition on June 21, 2001 for $500,000 with Memorandum of Agreement funds (BPA and WDFW 1996) as partial fulfillment of BPA's wildlife mitigation obligation for construction of Bonneville and John Day Dams (Rasmussen and Wright 1989). Anticipating the eventual acquisition of the Egger and Herzog properties, WDFW conducted HEP surveys on these lands in 1994 to determine the potential number of habitat units to be credited to BPA. As a result, HEP surveys and habitat unit calculations were completed as much as seven years prior to acquiring the sites. The term 'Shillapoo Wildlife Area' will be used to describe only the Herzog and Egger parcels in this document. Details and results of the HEP analysis are included in this report.« less

Apigenin suppresses GLUT-1 and p-AKT expression to enhance the chemosensitivity to cisplatin of laryngeal carcinoma Hep-2 cells: an in vitro study

PubMed Central

Xu, Ying-Ying; Wu, Ting-Ting; Zhou, Shui-Hong; Bao, Yang-Yang; Wang, Qin-Ying; Fan, Jun; Huang, Ya-Ping

2014-01-01

Glucose transporter-1 (GLUT-1) and PI3K/Akt are known to be closely involved in resistance to chemotherapy. Co-targeted therapy reducing GLUT-1 expression and PI3K/Akt pathway activity may overcome the chemoresistance of human cancers. Apigenin may inhibit the expression of GLUT-1 and the PI3K/Akt pathway. We hypothesized that over-expression of GLUT-1 and p-Akt was associated with the resistance to cisplatin of laryngeal carcinoma Hep-2 cells. We explored whether apigenin inhibited GLUT-1 and p-Akt, resulting in sensitization of laryngeal carcinoma Hep-2 cells to cisplatin. Real-time RT-PCR and Western blotting confirmed the presence of GLUT-1 mRNA, and GLUT-1 and p-Akt proteins in Hep-2 cells. We found that resistance or insensitivity of Hep-2 cells to cisplatin might be associated with such expression. Apigenin markedly enhanced the cisplatin-induced suppression of Hep-2 cell growth. This effect was concentration- and time-dependent. Thus apigenin may significantly reduce the levels of GLUT-1 mRNA, and GLUT-1 and p-Akt proteins, in cisplatin-treated Hep-2 cells, in a concentration- and time-dependent manner. To conclude, overexpression of GLUT-1 mRNA may be associated with the resistance to cisplatin of laryngeal carcinoma Hep-2 cells. Apigenin may enhance the sensitivity to cisplatin of laryngeal carcinoma cells via inhibition of GLUT-1 and p-Akt expression. PMID:25120770

Cytotoxicity of β-D-glucose/sucrose-coated silver nanoparticles depends on cell type, nanoparticles concentration and time of incubation

NASA Astrophysics Data System (ADS)

Vergallo, Cristian; Panzarini, Elisa; Carata, Elisabetta; Ahmadi, Meysam; Mariano, Stefania; Tenuzzo, Bernardetta Anna; Dini, Luciana

2016-06-01

The use of silver NanoParticles (AgNPs) in several consumer commercialized products, like food contact materials, medical devices and cosmetics has increased significantly, owing to their antibacterial and antifungal properties. Even though the NPs are widely diffused, due to the great variety in size, coating or shape, controversial data on their possible detrimental health effects still exist. Herein, by performing an easy and fast green method synthesis, we used β-D-glucose/sucrose to stabilize AgNPs and avoid the release of cytotoxic soluble silver ions Ag+ in the culture medium. The cytotoxic effects of these β-D-Glucose/Sucrose-Coated AgNPs (AgNPs-GS) was assessed on two cell culture models, which are human liver HepG2 and human Peripheral Blood Lymphocytes (PBLs) cells. AgNPs-GS, as determined by Transmission Electron Microscopy (TEM) analyses, had an average diameter of 30±5 nm, a spherical shape and were well-dispersed in the freshly-prepared solution. In addition, they were found spectrophotometrically stable throughout the experiment. Cytotoxicity, determined by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) reduction assay, was evaluated by using two AgNPs-GS amounts, indicated as highest (10×103 of NPs/cell) and lowest (2×103 NPs/cell) concentration for 6, 12 and 24 h. The highest concentration of AgNPs-GS was significantly cytotoxic for both HepG2 and PBLs cells at all times, when compared with the negative control; conversely, the lowest amount of AgNPs-GS was toxic only for HepG2 cells. A significant increase of Reactive Oxygen Species (ROS) levels, determined by Nitro Blue Tetrazolium (NBT) reduction assay, was observed only in PBLs after treatment with NPs, by reaching maximum levels after the incubation with the lowest amount of NPs for 24 h. Significant morphological changes, depending on NPs/cell amount, characteristic of cell toxicity, like shape, cytoplasm, and nucleus alterations, were observed in lymphocytes and HepG2 cells exposed to AgNPs. The results indicate that HepG2 cells are more responsive to AgNPs treatment than PBLs. It is generally believed that cellular oxidative stress induces toxicity of NPs; however, in this study we did not detect any AgNPs-induced oxidative stress in HepG2, thus suggesting an alternative mechanism of toxicity in this cell line. In the whole, our findings suggest that AgNPs-GS-induced toxicity strictly depends on cell type, NPs amount and time of treatment.

Induction of apoptosis in human liver carcinoma HepG2 cell line by 5-allyl-7-gen-difluoromethylenechrysin.

PubMed

Tan, Xiang-Wen; Xia, Hong; Xu, Jin-Hua; Cao, Jian-Guo

2009-05-14

To investigate the effect of 5-allyl-7-gen-difluoromethylenechrysin (ADFMChR) on apoptosis of human liver carcinoma HepG2 cell line and the molecular mechanisms involved. HepG2 cells and L-02 cells were cultured in vitro and the inhibitory effect of ADFMChR on their proliferation was measured by MTT assay. The apoptosis of HepG2 cells was determined by flow cytometry (FCM) using propidium iodide (PI) fluorescence staining. DNA ladder bands were observed by DNA agarose gel electrophoresis. The influence of ADFMChR on the proxisome proliferator-activated receptor gamma (PPARgamma), NF-kappaB, Bcl-2 and Bax protein expression of HepG2 cells were analyzed by Western blotting. MTT assay showed that ADFMChR significantly inhibited proliferation of HepG2 cells in a dose-dependent manner, with little effect on growth of L-02 cells, and when IC(50) was measured as 8.45 micromol/L and 191.55 micromol/L respectively, the potency of ADFMChR to HepG2 cells, was found to be similar to 5-fluorouracil (5-FU, IC(50) was 9.27 micromol/L). The selective index of ADFMChR cytotoxicity to HepG2 cells was 22.67 (191.55/8.45), higher than 5-FU (SI was 7.05 (65.37/9.27). FCM with PI staining demonstrated that the apoptosis rates of HepG2 cells treated with 3.0, 10.0 and 30.0 micromol/L ADFMChR for 48 h were 5.79%, 9.29% and 37.8%, respectively, and were significantly higher when treated with 30.0 micromol/L ADFMChR than when treated with 30.0 micromol/L ChR (16.0%) (P < 0.05) and were similar to those obtained with 30.0 micromol/L 5-FU (41.0%). DNA agarose gel electrophoresis showed that treatment of HepG2 cells with 10.0 micromol/L ADFMChR for 48 h and 72 h resulted in typical DNA ladders which could be reversed by 10.00 micromol/L GW9662, a blocker of PPARgamma. Western blotting analysis revealed that after 24 h of treatment with 3.0, 10.0, 30.0 micromol/L ADFMChR, PPARgamma and Bax protein expression in HepG2 cells increased but Bcl-2 and NF-kappaB expression decreased; however, pre-incubation with 10.0 micromol/L GW9662 could efficiently antagonize and weaken the regulatory effect of 3.0, 30.0 micromol/L ADFMChR on PPARgamma and NF-kappaB protein expression in HepG2 cells. ADFMChR induces apoptosis of HepG2 cell lines by activating PPARgamma, inhibiting protein expression of Bcl-2 and NF-kappaB, and increasing Bax expression.

Algorithm for fast event parameters estimation on GEM acquired data

NASA Astrophysics Data System (ADS)

Linczuk, Paweł; Krawczyk, Rafał D.; Poźniak, Krzysztof T.; Kasprowicz, Grzegorz; Wojeński, Andrzej; Chernyshova, Maryna; Czarski, Tomasz

2016-09-01

We present study of a software-hardware environment for developing fast computation with high throughput and low latency methods, which can be used as back-end in High Energy Physics (HEP) and other High Performance Computing (HPC) systems, based on high amount of input from electronic sensor based front-end. There is a parallelization possibilities discussion and testing on Intel HPC solutions with consideration of applications with Gas Electron Multiplier (GEM) measurement systems presented in this paper.

Application of particle accelerators in research.

PubMed

Mazzitelli, Giovanni

2011-07-01

Since the beginning of the past century, accelerators have started to play a fundamental role as powerful tools to discover the world around us, how the universe has evolved since the big bang and to develop fundamental instruments for everyday life. Although more than 15 000 accelerators are operating around the world only a very few of them are dedicated to fundamental research. An overview of the present high energy physics (HEP) accelerator status and prospectives is presented.

Identification of centrarchid hepcidins and evidence that 17β-estradiol disrupts constitutive expression of hepcidin-1 and inducible expression of hepcidin-2 in largemouth bass (Micropterus salmoides)

USGS Publications Warehouse

Robertson, L.S.; Iwanowicz, L.R.; Marranca, J.M.

2009-01-01

Hepcidin is a highly conserved antimicrobial peptide and iron-regulatory hormone. Here, we identify two hepcidin genes (hep-1 and hep-2) in largemouth bass (Micropterus salmoides) and smallmouth bass (Micropterus dolomieu). Hepcidin-1 contains a putative ATCUN metal-binding site in the amino-terminus that is missing in hepcidin-2, suggesting that hepcidin-1 may function as an iron-regulatory hormone. Both hepcidins are predominately expressed in the liver of largemouth bass, similar to other fish and mammals. Experimental exposure of pond-raised largemouth bass to 17β-estradiol and/or the bacteria Edwardsiella ictaluri led to distinct changes in expression of hep-1 and hep-2. Estradiol reduced the constitutive expression of hep-1 in the liver. Bacterial exposure induced expression of hep-2, suggesting that hepcidin-2 may have an antimicrobial function, and this induction was abolished by estradiol. To our knowledge, this is the first report of the regulation of hepcidin expression by estradiol in either fish or mammals.

Identification of centrarchid hepcidins and evidence that 17beta-estradiol disrupts constitutive expression of hepcidin-1 and inducible expression of hepcidin-2 in largemouth bass (Micropterus salmoides).

PubMed

Robertson, Laura S; Iwanowicz, Luke R; Marranca, Jamie Marie

2009-06-01

Hepcidin is a highly conserved antimicrobial peptide and iron-regulatory hormone. Here, we identify two hepcidin genes (hep-1 and hep-2) in largemouth bass (Micropterus salmoides) and smallmouth bass (Micropterus dolomieu). Hepcidin-1 contains a putative ATCUN metal-binding site in the amino-terminus that is missing in hepcidin-2, suggesting that hepcidin-1 may function as an iron-regulatory hormone. Both hepcidins are predominately expressed in the liver of largemouth bass, similar to other fish and mammals. Experimental exposure of pond-raised largemouth bass to 17beta-estradiol and/or the bacteria Edwardsiella ictaluri led to distinct changes in expression of hep-1 and hep-2. Estradiol reduced the constitutive expression of hep-1 in the liver. Bacterial exposure induced expression of hep-2, suggesting that hepcidin-2 may have an antimicrobial function, and this induction was abolished by estradiol. To our knowledge, this is the first report of the regulation of hepcidin expression by estradiol in either fish or mammals.

Evaluation of storing hepatitis B vaccine outside the cold chain in the Solomon Islands: Identifying opportunities and barriers to implementation.

PubMed

Breakwell, Lucy; Anga, Jenniffer; Dadari, Ibrahim; Sadr-Azodi, Nahad; Ogaoga, Divinal; Patel, Minal

2017-05-15

Monovalent Hepatitis B vaccine (HepB) is heat stable, making it suitable for storage outside cold chain (OCC) at 37°C for 1month. We conducted an OCC project in the Solomon Islands to determine the feasibility of and barriers to national implementation and to evaluate impact on coverage. Healthcare workers at 13 facilities maintained monovalent HepB birth dose (HepB-BD) OCC for up to 28days over 7months. Vaccination data were recorded for children born during the project and those born during 7months before the project. Timely HepB-BD coverage among facility and home births increased from 30% to 68% and from 4% to 24%, respectively. Temperature excursions above 37°C were rare, but vaccine wastage was high and shortages common. Storing HepB OCC can increase HepB-BD coverage in countries with insufficient cold chain capacity or numerous home births. High vaccine wastage and unreliable vaccine supply must be addressed for successful implementation. Published by Elsevier Ltd.

Enhancing the functional maturity of induced pluripotent stem cell-derived human hepatocytes by controlled presentation of cell-cell interactions in vitro.

PubMed

Berger, Dustin R; Ware, Brenton R; Davidson, Matthew D; Allsup, Samuel R; Khetani, Salman R

2015-04-01

Induced pluripotent stem cell-derived human hepatocyte-like cells (iHeps) could provide a powerful tool for studying the mechanisms underlying human liver development and disease, testing the efficacy and safety of pharmaceuticals across different patients (i.e., personalized medicine), and enabling cell-based therapies in the clinic. However, current in vitro protocols that rely upon growth factors and extracellular matrices (ECMs) alone yield iHeps with low levels of liver functions relative to adult primary human hepatocytes (PHHs). Moreover, these low hepatic functions in iHeps are difficult to maintain for prolonged times (weeks to months) in culture. Here, we engineered a micropatterned coculture (iMPCC) platform in a multiwell format that, in contrast to conventional confluent cultures, significantly enhanced the functional maturation and longevity of iHeps in culture for at least 4 weeks in vitro when benchmarked against multiple donors of PHHs. In particular, iHeps were micropatterned onto collagen-coated domains of empirically optimized dimensions, surrounded by 3T3-J2 murine embryonic fibroblasts, and then sandwiched with a thin layer of ECM gel (Matrigel). We assessed iHep maturity by global gene expression profiles, hepatic polarity, secretion of albumin and urea, basal cytochrome P450 (CYP450) activities, phase II conjugation, drug-mediated CYP450 induction, and drug-induced hepatotoxicity. Controlling both homotypic interactions between iHeps and heterotypic interactions with stromal fibroblasts significantly matures iHep functions and maintains them for several weeks in culture. In the future, iMPCCs could prove useful for drug screening, studying molecular mechanisms underlying iHep differentiation, modeling liver diseases, and integration into human-on-a-chip systems being designed to assess multiorgan responses to compounds. © 2014 by the American Association for the Study of Liver Diseases.

Roles of hepatocyte and myeloid CXC chemokine receptor-2 in liver recovery and regeneration after ischemia/reperfusion in mice.

PubMed

Van Sweringen, Heather L; Sakai, Nozomu; Quillin, Ralph C; Bailey, Jeff; Schuster, Rebecca; Blanchard, John; Goetzman, Holly; Caldwell, Charles C; Edwards, Michael J; Lentsch, Alex B

2013-01-01

Previous studies have demonstrated the significance of signaling through the CXC chemokine receptor-2 (CXCR2) receptor in the process of recovery and regeneration of functional liver mass after hepatic ischemia/reperfusion (I/R). CXCR2 is constitutively expressed on both neutrophils and hepatocytes; however, the cell-specific roles of this receptor are unknown. In the present study, chimeric mice were created through bone marrow transplantation (BMT) using wild-type and CXCR2-knockout mice, yielding selective expression of CXCR2 on hepatocytes (Hep) and/or myeloid cells (My) in the following combinations: Hep+/My+; Hep-/My+; Hep+/My-; and Hep-/My-. These tools allowed us to assess the contributions of myeloid and hepatocyte CXCR2 in the recovery of the liver after I/R injury. Flow cytometry confirmed the adoption of the donor phenotype in neutrophils. Interestingly, Kupffer cells from all chimeras lacked CXCR2 expression. Recovery/regeneration of hepatic parenchyma was assessed by histologic assessment and measurement of hepatocyte proliferation. CXCR2(Hep+/My+) mice showed the least amount of liver recovery and hepatocyte proliferation, whereas CXCR2(Hep-/My-) mice had the greatest liver recovery and hepatocyte proliferation. CXCR2(Hep+/My-) mice had enhanced liver recovery, with hepatocyte proliferation similar to CXCR2(Hep-/My-) mice. Myeloid expression of CXCR2 directly regulated CXC chemokine expression levels after hepatic I/R, such that mice lacking myeloid CXCR2 had markedly increased chemokine expression, compared with mice expressing CXCR2 on myeloid cells. The data suggest that CXCR2 on myeloid cells is the predominant regulator of liver recovery and regeneration after I/R injury, whereas hepatocyte CXCR2 plays a minor, secondary role. These findings suggest that myeloid cell-directed therapy may significantly affect liver regeneration after liver resection or transplantation. Copyright © 2012 American Association for the Study of Liver Diseases.

β3-Adrenoceptor activation upregulates apolipoprotein A-I expression in HepG2 cells, which might further promote cholesterol efflux from macrophage foam cells.

PubMed

Gao, Xia-Qing; Li, Yan-Fang; Jiang, Zhi-Li

2017-01-01

The aim of this study was to explore the effects of β 3 -adrenoceptor (β 3 -AR) activation on HepG2 cells and its influence on cholesterol efflux from macrophage foam cells. HepG2 cells were cultured and treated with the β 3 -AR agonist, BRL37344, and antagonist, SR52390A, and the expression of apolipoprotein (Apo) A-I, ApoA-II, ApoB, and β 3 -AR in the supernatants and cells was determined. The expression of peroxisome proliferator-activated receptor (PPAR) γ and PPARα in the HepG2 cells was also assessed. Next, using the RAW264.7 macrophage foam cell model, we also assessed the influence of the HepG2 cell supernatants on lipid efflux. The cholesterol content of the foam cells was also measured, and the cholesterol efflux from the macrophages was examined by determining 3 H-labeled cholesterol levels. Expression of ATP-binding cassette transporter (ABC) A1 and ABCG1 of the macrophage foam cells was also assessed. β 3 -AR activation increased ApoA-I expression in both the HepG2 cells and the supernatants; PPARγ expression was upregulated, but PPARα expression was not. Treatment with GW9662 abolished the increased expression of ApoA-I induced by the β 3 -AR agonist. The HepG2 cell supernatants decreased the lipid accumulation and increased the cholesterol efflux from the macrophage foam cells. ABCA1 expression, but not ABCG1 expression, increased in the macrophage foam cells treated with BRL37344-treated HepG2 cell supernatants. Activation of β 3 -AR in HepG2 cells upregulates ApoA-I expression, which might further promote cholesterol efflux from macrophage foam cells. PPARγ might be required for the induction of ApoA-I expression.

In vitro and in vivo study of phloretin-induced apoptosis in human liver cancer cells involving inhibition of type II glucose transporter.

PubMed

Wu, Chih-Hsiung; Ho, Yuan-Soon; Tsai, Chia-Yi; Wang, Ying-Jan; Tseng, How; Wei, Po-Li; Lee, Chia-Hwa; Liu, Ren-Shyan; Lin, Shyr-Yi

2009-05-01

Phloretin (Ph), a natural product found in apples and pears with glucose transporter (GLUT) inhibitory activity, exerts antitumor effects. However, little is known about its effects on human liver cancer. The purpose of this study is to test the cytotoxic effects of Ph on HepG2 cells and to identify the underlying molecular pathways. Human hepatocellular carcinoma specimens and HepG2 show a high level of GLUT2 transporter activity in the cell membrane. Real-time PCR and MTT assays demonstrate that Ph-induced cytotoxicity correlates with the expression of GLUT2. Flow cytometry and DNA fragmentation studies show that 200 microM Ph induces apoptosis in HepG2, which was reversed by glucose pretreatment. GLUT2 siRNA knockdown induced HepG2 apoptosis, which was not reversed by glucose. Western blot analysis demonstrates that both intrinsic and extrinsic apoptotic pathways in addition to Akt and Bcl-2 family signaling pathways are involved in Ph-induced cell death in HepG2 cells. Furthermore, using flow cytometry analysis, a mitochondrial membrane potential assay and Western blot analysis, we show that cytochalasin B, a glucose transport inhibitor, enhances the Ph-induced apoptotic effect on HepG2 cells, which was reversed by pretreatment with glucose. Furthermore, we found significant antitumor effects in vivo by administering Ph at 10 mg/kg intraperitoneally to severe combined immune deficiency mice carrying a HepG2 xenograft. A microPET study in the HepG2 tumor-bearing mice showed a 10-fold decrease in (18)F-FDG uptake in Ph-treated tumors compared to controls. Taken together, these results suggest that Ph-induced apoptosis in HepG2 cells involves inhibition of GLUT2 glucose transport mechanisms. (c) 2008 Wiley-Liss, Inc.

Quick assessment of the influence of the Hepatitis B vaccine event on children's vaccination.

PubMed

Yue, Chenyan; Sun, Xiaojin; Wei, Ning; Yu, Wenzhou; Cui, Fuqiang; Wang, Huaqing; Li, Li; Zhang, Lijie; Shi, Guoqing; An, Zhijie

2016-10-02

From December 2013 to January 2014, a large number of medias in China reported negative information about Hepatitis B vaccine (HepB) safety issues using eye-catching titles, such as "3 infants in Hunan inoculated with HepB occurred adverse event, and 2 died," and that caused crisis of confidence in vaccination, which we called "HepB event." The progress of "HepB event" could be divided into 3 stages which were initiation, peak and ending stages. In order to evaluate the influence of "HepB event" on the attitudes of participants toward Hepatitis B vaccine safety and their intention of vaccinating their children in different stages, and provide evidence for authority departments as soon as possible to take measures to prevent decrease of HepB coverage rate, a quick field investigation was carried out. Using convenience sampling methods during the initiation, peak and ending stages of the "HepB event." In the 3 stages of the "HepB event," the awareness rate of the event among participants was rapidly rising, showing that the participants paid great attention to the event, and the information was spread very quickly. The proportion of participants who knew the event but thought that the Hepatitis B vaccine was unsafe were 31%, 37% and 26% respectively in 3 stages. In addition, the acceptance of vaccination by the participants was influenced, the proportion of participants who would like to delay or reject vaccinating their children was up to 43% in the peak stage of the event. The "HepB event" had impacted on the participants' confidence in the safety of Hepatitis B vaccine. For such event, relevant authority departments need effectively communicate with the media and the public, and promptly issue positive information and the investigation result, thereby reducing the negative impact of the event, and improve the vaccine confidence among the public.

Cytotoxic prenylated flavones from the stem and root bark of Daphne giraldii.

PubMed

Sun, Qian; Wang, Di; Li, Fei-Fei; Yao, Guo-Dong; Li, Xue; Li, Ling-Zhi; Huang, Xiao-Xiao; Song, Shao-Jiang

2016-08-15

Three new prenylated flavones (1-3), along with three known analogues (4-6), were isolated from the stem and root bark of Daphne giraldii. Their structures were determined by comprehensive NMR and HRESIMS spectroscopic data analyses. The absolute configurations of compounds 2 and 3 were assigned by optical rotation comparison, CD and [Rh2(OCOCF3)4]-induced CD spectral methods. The in vitro cytotoxicity experiments carried out involving five cancer cell lines (U251, A549, HepG2, MCF-7 and Bcap37) showed that 2 markedly inhibited the proliferation of all tested cells with IC50 values ranging from 4.26 to 20.82μM. The preliminary structure-activity relationships of these flavones are discussed. In addition, compound 2 was found to effectively induce apoptosis in HepG2 cells according to a flow cytometry analysis. Copyright © 2016 Elsevier Ltd. All rights reserved.

Evaluation of synthesized platinum nanoparticles on the MCF-7 and HepG-2 cancer cell lines

NASA Astrophysics Data System (ADS)

Mohammadi, Hadi; Abedi, Anita; Akbarzadeh, Azim; Mokhtari, Mohammad Javad; Shahmabadi, Hasan Ebrahimi; Mehrabi, Mohamad Reza; Javadian, Saifuddin; Chiani, Mohsen

2013-04-01

Platinum nanoparticles (PNPs) were synthesized by chemical reduction of potassium hexachloroplatinate (IV) with trisodium citrate under vigorous stirring and addition of sodium dodecyl sulfate as stabilizer reagent. Reducing agent was chosen depending on the oxidation reactions and potential values of the chemical materials used in the experiment. The aim of this study is to investigate the effects of PNPs on the different cancer cell lines and cytotoxicity study of this nanomaterial. The morphology of PNPs was investigated by scanning electron microscope (XL30, Philips Electronics, Amsterdam, The Netherlands) with the ability to perform elemental analysis by EDX. Malvern Zetasizer 3000 HSA (Malvern Instruments, Worcestershire, UK) was used to determine the distribution of particle size and zeta potential of PNPs. The cytotoxicity property of the nanoparticles was evaluated by MTT assay on MCF-7 and HepG-2 cell lines, and the cytotoxic concentration 50% values were determined for 24 h.

Analysis of microRNA and gene expression profiling in triazole fungicide-treated HepG2 cell line.

PubMed

An, Yu Ri; Kim, Seung Jun; Oh, Moon-Ju; Kim, Hyun-Mi; Shim, Il-Seob; Kim, Pil-Je; Choi, Kyunghee; Hwang, Seung Yong

2013-01-07

MicroRNA (miRNA) plays an important role in various diseases and in cellular and molecular responses to toxicants. In the present study, we investigated differential expression of miRNAs in response to three triazole fungicides (myclobutanil, propiconazole, and triadimefon). The human hepatoma cell line (HepG2) was treated with the above triazoles for 3 h or 48 h. miRNA-based microarray experiments were carried out using the Agilent human miRNA v13 array. At early exposure (3h), six miRNAs were differentially expressed and at late exposure (48 h), three miRNAs were significantly expressed. Overall, this study provides an array of potential biomarkers for the above triazole fungicides. Furthermore, these miRNAs induced by triazoles could be the foundation for the development of a miRNA-based toxic biomarker library that can predict environmental toxicity. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

Metastatic breast cancer to the liver with hepatoid features and Hep Par 1 antibody positive mimicking hepatocellular carcinoma.

PubMed

Affleck, Authur; Lyman, William B; Jacobs, W Carl; Livasy, Chad A; Martinie, John B; Iannitti, David A; Vrochides, Dionisios

2018-05-09

The hepatocyte paraffin 1 antibody (Hep Par 1) has a high positive predictive value for differentiating hepatocellular carcinoma from cholangiocarcinoma and metastatic carcinoma. 1 We report a case of metastatic breast cancer to the liver with hepatoid histology and strong positive staining for Hep Par 1 mimicking hepatocellular carcinoma. To our knowledge, primary breast carcinoma staining Hep Par 1 positive has not been reported in the setting of hepatic metastasis. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Expression and chromatin structures of cellulolytic enzyme gene regulated by heterochromatin protein 1.

PubMed

Zhang, Xiujun; Qu, Yinbo; Qin, Yuqi

2016-01-01

Heterochromatin protein 1 (HP1, homologue HepA in Penicillium oxalicum ) binding is associated with a highly compact chromatin state accompanied by gene silencing or repression. HP1 loss leads to the derepression of gene expression. We investigated HepA roles in regulating cellulolytic enzyme gene expression, as an increasingly number of studies have suggested that cellulolytic enzyme gene expression is not only regulated by transcription factors, but is also affected by the chromatin status. Among the genes that exhibited significant differences between the hepA deletion strain (Δ hepA ) and the wild type (WT), most (95.0 %) were upregulated in Δ hepA compared with WT. The expression of the key transcription factor for cellulolytic enzyme gene (e.g., repressor CreA and activator ClrB) increased significantly. However, the deletion of hepA led to downregulation of prominent extracellular cellulolytic enzyme genes. Among the top 10 extracellular glycoside hydrolases (Amy15A, Amy13A, Cel7A/CBHI, Cel61A, Chi18A, Cel3A/BGLI, Xyn10A, Cel7B/EGI, Cel5B/EGII, and Cel6A/CBHII), in which secretion amount is from the highest to the tenth in P . oxalicum secretome, eight genes, including two amylase genes ( amy15A and amy13A ), all five cellulase genes ( cel7A / cbh1 , cel6A / cbh2 , cel7B / eg1 , cel5B / eg2 , and cel3A / bgl1 ), and the cellulose-active LPMO gene ( cel61A ) expression were downregulated. Results of chromatin accessibility real-time PCR (CHART-PCR) showed that the chromatin of all three tested upstream regions opened specifically because of the deletion of hepA in the case of two prominent cellulase genes cel7A/cbh1 and cel7B/eg1 . However, the open chromatin status did not occur along with the activation of cellulolytic enzyme gene expression. The overexpression of hepA upregulated the cellulolytic enzyme gene expression without chromatin modification. The overexpression of hepA remarkably activated the cellulolytic enzyme synthesis, not only in WT (~150 % filter paper activity (FPA) increase), but also in the industry strain RE-10 (~20-30 % FPA increase). HepA is required for chromatin condensation of prominent cellulase genes. However, the opening of chromatin mediated by the deletion of hepA was not positively correlated with cellulolytic enzyme gene activation. HepA is actually a positive regulator for cellulolytic enzyme gene expression and could be a promising target for genetic modification to improve cellulolytic enzyme synthesis.

Geant4 Computing Performance Benchmarking and Monitoring

DOE PAGES

Dotti, Andrea; Elvira, V. Daniel; Folger, Gunter; ...

2015-12-23

Performance evaluation and analysis of large scale computing applications is essential for optimal use of resources. As detector simulation is one of the most compute intensive tasks and Geant4 is the simulation toolkit most widely used in contemporary high energy physics (HEP) experiments, it is important to monitor Geant4 through its development cycle for changes in computing performance and to identify problems and opportunities for code improvements. All Geant4 development and public releases are being profiled with a set of applications that utilize different input event samples, physics parameters, and detector configurations. Results from multiple benchmarking runs are compared tomore » previous public and development reference releases to monitor CPU and memory usage. Observed changes are evaluated and correlated with code modifications. Besides the full summary of call stack and memory footprint, a detailed call graph analysis is available to Geant4 developers for further analysis. The set of software tools used in the performance evaluation procedure, both in sequential and multi-threaded modes, include FAST, IgProf and Open|Speedshop. In conclusion, the scalability of the CPU time and memory performance in multi-threaded application is evaluated by measuring event throughput and memory gain as a function of the number of threads for selected event samples.« less

Cytostatic and genotoxic effect of temephos in human lymphocytes and HepG2 cells.

PubMed

Benitez-Trinidad, A B; Herrera-Moreno, J F; Vázquez-Estrada, G; Verdín-Betancourt, F A; Sordo, M; Ostrosky-Wegman, P; Bernal-Hernández, Y Y; Medina-Díaz, I M; Barrón-Vivanco, B S; Robledo-Marenco, M L; Salazar, A M; Rojas-García, A E

2015-06-01

Temephos is an organophosphorus pesticide that is used in control campaigns against Aedes aegypti mosquitoes, which transmit dengue. In spite of the widespread use of temephos, few studies have examined its genotoxic potential. The aim of this study was to evaluate the cytotoxic, cytostatic and genotoxic effects of temephos in human lymphocytes and hepatoma cells (HepG2). The cytotoxicity was evaluated with simultaneous staining (FDA/EtBr). The cytostatic and genotoxic effects were evaluated using comet assays and the micronucleus technique. We found that temephos was not cytotoxic in either lymphocytes or HepG2 cells. Regarding the cytostatic effect in human lymphocytes, temephos (10 μM) caused a significant decrease in the percentage of binucleated cells and in the nuclear division index as well as an increase in the apoptotic cell frequency, which was not the case for HepG2 cells. The comet assay showed that temephos increased the DNA damage levels in human lymphocytes, but it did not increase the MN frequency. In contrast, in HepG2 cells, temephos increased the tail length, tail moment and MN frequency in HepG2 cells compared to control cells. In conclusion, temephos causes stable DNA damage in HepG2 cells but not in human lymphocytes. These findings suggest the importance of temephos biotransformation in its genotoxic effect. Copyright © 2015. Published by Elsevier Ltd.

Xanthorrhizol induced DNA fragmentation in HepG2 cells involving Bcl-2 family proteins

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

Tee, Thiam-Tsui, E-mail: thiamtsu@yahoo.com; Cheah, Yew-Hoong; Bioassay Unit, Herbal Medicine Research Center, Institute for Medical Research, Jalan Pahang, Kuala Lumpur

Highlights: Black-Right-Pointing-Pointer We isolated xanthorrhizol, a sesquiterpenoid compound from Curcuma xanthorrhiza. Black-Right-Pointing-Pointer Xanthorrhizol induced apoptosis in HepG2 cells as observed using SEM. Black-Right-Pointing-Pointer Apoptosis in xanthorrhizol-treated HepG2 cells involved Bcl-2 family proteins. Black-Right-Pointing-Pointer DNA fragmentation was observed in xanthorrhizol-treated HepG2 cells. Black-Right-Pointing-Pointer DNA fragmentation maybe due to cleavage of PARP and DFF45/ICAD proteins. -- Abstract: Xanthorrhizol is a plant-derived pharmacologically active sesquiterpenoid compound isolated from Curcuma xanthorrhiza. Previously, we have reported that xanthorrhizol inhibited the proliferation of HepG2 human hepatoma cells by inducing apoptotic cell death via caspase activation. Here, we attempt to further elucidate the mode of action ofmore » xanthorrhizol. Apoptosis in xanthorrhizol-treated HepG2 cells as observed by scanning electron microscopy was accompanied by truncation of BID; reduction of both anti-apoptotic Bcl-2 and Bcl-X{sub L} expression; cleavage of PARP and DFF45/ICAD proteins and DNA fragmentation. Taken together, these results suggest xanthorrhizol as a potent antiproliferative agent on HepG2 cells by inducing apoptosis via Bcl-2 family members. Hence we proposed that xanthorrhizol could be used as an anti-liver cancer drug for future studies.« less

Galactomannan from Schizolobium amazonicum seed and its sulfated derivatives impair metabolism in HepG2 cells.

PubMed

Cunha de Padua, Monique Meyenberg; Suter Correia Cadena, Silvia Maria; de Oliveira Petkowicz, Carmen Lucia; Martinez, Glaucia Regina; Rodrigues Noleto, Guilhermina

2017-08-01

This study evaluated the effects of native galactomannan from Schizolobium amazonicum seeds and its sulfated forms on certain metabolic parameters of HepG2 cells. Aqueous extraction from S. amazonicum seeds furnished galactomannan with 3.2:1 Man:Gal ratio (SAGM) and molar mass of 4.34×10 5 g/mol. The SAGM fraction was subjected to sulfation using chlorosulfonic acid to obtain SAGMS1 and SAGMS2 with DS of 0.4 and 0.6, respectively. Cytotoxicity of SAGM, SAGMS1, and SAGMS2 was evaluated in human hepatocellular carcinoma cells (HepG2). After 72h, SAGM decreased the viability of HepG2 cells by 50% at 250μg/mL, while SAGMS1 reduced it by 30% at the same concentration. SAGM, SAGMS1, and SAGMS2 promoted a reduction in oxygen consumption and an increase in lactate production in non-permeabilized HepG2 cells after 72h of treatment. These results suggest that SAGM, SAGMS1, and SAGMS2 could be recognized by HepG2 cells and might trigger alterations that impair its survival. These effects could be implicated in the modification of the oxidative phosphorylation process in HepG2 cells and activation of the glycolytic pathway. Copyright © 2017 Elsevier B.V. All rights reserved.

Umbilical cord-derived mesenchymal stem cells inhibit growth and promote apoptosis of HepG2 cells.

PubMed

Tang, Ying-Mei; Bao, Wei-Min; Yang, Jin-Hui; Ma, Lin-Kun; Yang, Jing; Xu, Ying; Yang, Li-Hong; Sha, Feng; Xu, Zhi-Yuan; Wu, Hua-Mei; Zhou, Wei; Li, Yan; Li, Yu-Hua

2016-09-01

Hepatocellular carcinoma is the fifth most common type of cancer worldwide and remains difficult to treat. The aim of this study was to investigate the effects of mesenchymal stem cells (MSCs) derived from the umbilical cord (UC‑MSCs) on HepG2 hepatocellular carcinoma cells. UC‑MSCs were co‑cultured with HepG2 cells and biomarkers of UC‑MSCs were analyzed by flow cytometry. mRNA and protein expression of genes were determined by reverse transcription‑polymerase chain reaction and flow cytometry, respectively. Passage three and seven UC‑MSCs expressed CD29, CD44, CD90 and CD105, whereas CD34 and CD45 were absent on these cells. Co‑culture with UC‑MSCs inhibited proliferation and promoted apoptosis of HepG2 cells in a time‑dependent manner. The initial seeding density of UC‑MSCs also influenced the proliferation and apoptosis of HepG2 cells, with an increased number of UC‑MSCs causing enhanced proliferation inhibition and cell apoptosis. Co‑culture with UC‑MSCs downregulated mRNA and protein expression of α‑fetoprotein (AFP), Bcl‑2 and Survivin in HepG2 cells. Thus, UC‑MSCs may inhibit growth and promote apoptosis of HepG2 cells through downregulation of AFP, Bcl‑2 and Survivin. US-MSCs may be used as a novel therapy for treating hepatocellular carcinoma in the future.

l-Lactate metabolism in HEP G2 cell mitochondria due to the l-lactate dehydrogenase determines the occurrence of the lactate/pyruvate shuttle and the appearance of oxaloacetate, malate and citrate outside mitochondria.

PubMed

Pizzuto, Roberto; Paventi, Gianluca; Porcile, Carola; Sarnataro, Daniela; Daniele, Aurora; Passarella, Salvatore

2012-09-01

As part of an ongoing study of l-lactate metabolism both in normal and in cancer cells, we investigated whether and how l-lactate metabolism occurs in mitochondria of human hepatocellular carcinoma (Hep G2) cells. We found that Hep G2 cell mitochondria (Hep G2-M) possess an l-lactate dehydrogenase (ml-LDH) restricted to the inner mitochondrial compartments as shown by immunological analysis, confocal microscopy and by assaying ml-LDH activity in solubilized mitochondria. Cytosolic and mitochondrial l-LDHs were found to differ from one another in their saturation kinetics. Having shown that l-lactate itself can enter Hep G2 cells, we found that Hep G2-M swell in ammonium l-lactate, but not in ammonium pyruvate solutions, in a manner inhibited by mersalyl, this showing the occurrence of a carrier-mediated l-lactate transport in these mitochondria. Occurrence of the l-lactate/pyruvate shuttle and the appearance outside mitochondria of oxaloacetate, malate and citrate arising from l-lactate uptake and metabolism together with the low oxygen consumption and membrane potential generation are in favor of an anaplerotic role for l-LAC in Hep G2-M. Copyright © 2012 Elsevier B.V. All rights reserved.

Regorafenib inhibits tumor progression through suppression of ERK/NF-κB activation in hepatocellular carcinoma bearing mice.

PubMed

Weng, Mao-Chi; Wang, Mei-Hui; Tsai, Jai-Jen; Kuo, Yu-Cheng; Liu, Yu-Chang; Hsu, Fei-Ting; Wang, Hsin-Ell

2018-06-29

Regorafenib has been demonstrated in our previous study to trigger apoptosis through suppression of extracellular signal-regulated kinase (ERK)/nuclear factor-κB (NF-κB) activation in hepatocellular carcinoma (HCC) SK-Hep1 cells in vitro However, the effect of regorafenib on NF-κB-modulated tumor progression in HCC in vivo is ambiguous. The aim of the present study is to investigate the effect of regorafenib on NF-κB-modulated tumor progression in HCC bearing mouse model. pGL4.50 luciferase reporter vector transfected SK-Hep1 (SK-Hep1/ luc2 ) and Hep3B 2.1-7 tumor bearing mice were established and used for the present study. Mice were treated with vehicle or regorafenib (20 mg/kg/day by gavage) for 14 days. Effects of regorafenib on tumor growth and protein expression together with toxicity of regorafenib were evaluated with digital caliper and bioluminescence imaging (BLI), ex vivo Western blotting immunohistochemistry (IHC) staining, and measurement of body weight and pathological examination of liver tissue, respectively, in SK-Hep1/ luc2 and Hep3B 2.1-7 tumor bearing mice. The results indicated regorafenib significantly reduced tumor growth and expression of phosphorylated ERK, NF-κB p65 (Ser536), phosphorylated AKT, and tumor progression-associated proteins. In addition, we found regorafenib induced both extrinsic and intrinsic apoptotic pathways. Body weight and liver morphology were not affected by regorafenib treatment. Our findings present the mechanism of tumor progression inhibition by regorafenib is linked to suppression of ERK/NF-κB signaling in SK-Hep1/ luc2 and Hep3B 2.1-7 tumor bearing mice. © 2018 The Author(s).

Citral, A Monoterpene Protect Against High Glucose Induced Oxidative Injury in HepG2 Cell In Vitro-An Experimental Study.

PubMed

Subramaniyan, Sri Devi; Natarajan, Ashok Kumar

2017-08-01

Diabetes mellitus, a major metabolic disorder associated with hyperglycaemia is one of the leading cause of death in many developed countries. However, use of natural phytochemicals have been proved to have a protective effect against oxidative damage. To investigate the effect of citral, a monoterpene on high glucose induced cytotoxicity and oxidative stress in human hepatocellular liver carcinoma (Hep G2) cell line. Cells were treated with 50 mM concentration of glucose for 24 hours incubation following citral (30 μM) was added to confluent HepG2 cells. Cell viability, Reactive Oxygen Species (ROS) generation, DNA damage, lipid peroxidation, antioxidants and Mitogen Activated Protein Kinases (MAPKs) signaling were assessed in citral and/or high glucose induced HepG2 cells. Cells treated with glucose (50 mM), resulted in increased cytotoxicity, ROS generation, DNA damage, lipid peroxidation and depletion of enzymatic and non enzymatic antioxidants. In contrast, treatment with citral (30 μM) significantly decreased cell cytotoxicity, ROS generation, DNA damage, lipid peroxidation and increased antioxidants enzymes in high glucose induced HepG2 cells. In addition, the present study highlighted that high glucose treated cells showed increased expression of Extracellular Signal Regulated Protein Kinase-1 (ERK-1), c-Jun N-terminal Kinase (JNK) and p38 in HepG2 cells. On the other hand treatment with citral significantly suppressed the expression of ERK-1, JNK and p38 in high glucose induced HepG2 cells. Citral protects against high glucose induced oxidative stress through inhibiting ROS activated MAPK signaling pathway in HepG2 cells.

HepG2 cells biospecific extraction and HPLC-ESI-MS analysis for screening potential antiatherosclerotic active components in Bupeuri radix.

PubMed

Liu, Shuqiang; Tan, Zhibin; Li, Pingting; Gao, Xiaoling; Zeng, Yuaner; Wang, Shuling

2016-03-20

HepG2 cells biospecific extraction method and high performance liquid chromatography-electrospray ionization-mass spectrometry (HPLC-ESI-MS) analysis was proposed for screening of potential antiatherosclerotic active components in Bupeuri radix, a well-known Traditional Chinese Medicine (TCM). The hypothesis suggested that when cells are incubated together with the extracts of TCM, the potential bioactive components in the TCM should selectively combine with the receptor or channel of HepG2 cells, then the eluate which contained biospecific component binding to HepG2 cells was identified using HPLC-ESI-MS analysis. The potential bioactive components of Bupeuri radix were investigated using the proposed approach. Five compounds in the saikosaponins of Bupeuri radix were detected as these components selectively combined with HepG2 cells, among these compounds, two potentially bioactive compounds namely saikosaponin b1 and saikosaponin b2 (SSb2) were identified by comparing with the chromatography of the standard sample and analysis of the structural clearance characterization of MS. Then SSb2 was used to assess the uptake of DiI-high density lipoprotein (HDL) in HepG2 cells for antiatherosclerotic activity. The results have showed that SSb2, with indicated concentrations (5, 15, 25, and 40 μM) could remarkably uptake dioctadecylindocarbocyanine labeled- (DiI) -HDL in HepG2 cells (Vs control group, *P<0.01). In conclusion, the application of HepG2 biospecific extraction coupled with HPLC-ESI-MS analysis is a rapid, convenient, and reliable method for screening potential bioactive components in TCM and SSb2 may be a valuable novel drug agent for the treatment of atherosclerosis. Copyright © 2016 Elsevier B.V. All rights reserved.

NOR1 promotes hepatocellular carcinoma cell proliferation and migration through modulating the Notch signaling pathway

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

You, Kun; Sun, Peisheng; Yue, Zhongyi

Hepatocellular carcinoma (HCC) is one of the most common malignant tumors worldwide. Previous studies have reported that the oxidored-nitro domain containing protein 1 (NOR1) is a novel tumor suppressor in several tumors. Recent evidence suggests that NOR1 is strongly expressed in HCC cells. However, its role and mechanism in HCC are unclear. In the current study, Western blot and qPCR detected strong NOR1 mRNA and protein expression in HepG2 and Hep3B cells. After transfection with NOR1 siRNA or pcDNA3.1-myc-his-NOR1, the proliferation and migration of HepG2 and Hep3B cells were analyzed in vitro. HepG2 or Hep3B cells overexpressing NOR1 showed anmore » increased proliferation and migration, whereas siRNA-mediated silencing of NOR1 showed the opposite effect. Furthermore, NOR1 activated the Notch signaling pathway, indicated by increased levels of Notch1, NICD, Hes1, and Hey1 in protein. Importantly, the Notch inhibitor DAPT downregulated Notch activation and further enhanced siNOR1-induced reduction of cell proliferation and migration in HepG2 and Hep3B cells, whereas DAPT reversed the effect of NOR1 overexpression on cell proliferation and migration. In conclusion, these results indicate that NOR1 may be involved in the progression of HCC and thus may be a potential target for the treatment of liver cancer. - Highlights: • NOR1 expression is up-regulated in HCC cells. • NOR1 promotes the proliferation and migration of HCC cells. • NOR1 promotes the progression of HCC cells by activating Notch pathway.« less

Identification of p90 Ribosomal S6 Kinase 2 as a Novel Host Protein in HBx Augmenting HBV Replication by iTRAQ-Based Quantitative Comparative Proteomics.

PubMed

Yan, Li-Bo; Yu, You-Jia; Zhang, Qing-Bo; Tang, Xiao-Qiong; Bai, Lang; Huang, FeiJun; Tang, Hong

2018-05-01

The aim of this study was to screen for novel host proteins that play a role in HBx augmenting Hepatitis B virus (HBV) replication. Three HepG2 cell lines stably harboring different functional domains of HBx (HBx, HBx-Cm6, and HBx-Cm16) were cultured. ITRAQ technology integrated with LC-MS/MS analysis was applied to identify the proteome differences among these three cell lines. In brief, a total of 70 different proteins were identified among HepG2-HBx, HepG2-HBx-Cm6, and HepG2-HBx-Cm16 by double repetition. Several differentially expressed proteins, including p90 ribosomal S6 kinase 2 (RSK2), were further validated. RSK2 was expressed at higher levels in HepG2-HBx and HepG2-HBx-Cm6 compared with HepG2-HBx-Cm16. Furthermore, levels of HBV replication intermediates were decreased after silencing RSK2 in HepG2.2.15. An HBx-minus HBV mutant genome led to decreased levels of HBV replication intermediates and these decreases were restored to levels similar to wild-type HBV by transient ectopic expression of HBx. After silencing RSK2 expression, the levels of HBV replication intermediates synthesized from the HBx-minus HBV mutant genome were not restored to levels that were observed with wild-type HBV by transient HBx expression. Based on iTRAQ quantitative comparative proteomics, RSK2 was identified as a novel host protein that plays a role in HBx augmenting HBV replication. © 2018 The Authors. Proteomics - Clinical Application Published by WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Propagation of Human Hepatocytes in uPA/SCID Mice: Producing Chimeric Mice with Humanized Liver.

PubMed

Ohshita, Hiroki; Tateno, Chise

2017-01-01

Primary or cryopreserved human hepatocytes (h-heps) have been used as the gold standard for in vitro metabolism and hepatotoxicity studies; however, the supply of h-heps is limited and they cannot grow in vitro. We achieved approximately 1000-fold propagation of h-heps in the liver of albumin promoter/enhancer-driven urokinase-type plasminogen activator transgenic/severe combined immunodeficiency disease (uPA/SCID) mice with genetically induced liver disease and immunodeficiency. When h-heps are transplanted into the uPA/SCID mouse liver via the spleen, the h-heps engraft in the mouse liver, resulting in its repopulation with h-heps. We have named this model "chimeric mouse with humanized liver, PXB-mouse ® ." Fresh h-heps can be isolated from the chimeric mice (PXB-cells ® ) and have been used for in vitro studies.The efficacy and safety of chemical entities for use in humans are estimated using experimental animals such as rats and mice. The drug development of many chemical entities has been halted because of metabolic differences between humans and animals during clinical studies. Therefore, chimeric mice with humanized liver have been used to predict human-type metabolism and safety conditions for h-heps. In addition, until recently there were no suitable hepatitis B or C virus (HBV or HCV) susceptible animal models aside from chimpanzees. Chimeric mice are the sole persistent infectious small animal model for HBV and HCV and they have been used to investigate the efficacy of new anti-HBV or HCV agents.In this chapter, we describe a method for producing chimeric mice with humanized liver using uPA/SCID mice.

The Science Training Program for Young Italian Physicists and Engineers at Fermilab

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

Barzi, Emanuela; Bellettini, Giorgio; Donati, Simone

2015-03-12

Since 1984 Fermilab has been hosting a two-month summer training program for selected undergraduate and graduate Italian students in physics and engineering. Building on the traditional close collaboration between the Italian National Institute of Nuclear Physics (INFN) and Fermilab, the program is supported by INFN, by the DOE and by the Scuola Superiore di Sant`Anna of Pisa (SSSA), and is run by the Cultural Association of Italians at Fermilab (CAIF). This year the University of Pisa has qualified it as a “University of Pisa Summer School”, and will grant successful students with European Supplementary Credits. Physics students join the Fermilabmore » HEP research groups, while engineers join the Particle Physics, Accelerator, Technical, and Computing Divisions. Some students have also been sent to other U.S. laboratories and universities for special trainings. The programs cover topics of great interest for science and for social applications in general, like advanced computing, distributed data analysis, nanoelectronics, particle detectors for earth and space experiments, high precision mechanics, applied superconductivity. In the years, over 350 students have been trained and are now employed in the most diverse fields in Italy, Europe, and the U.S. In addition, the existing Laurea Program in Fermilab Technical Division was extended to the whole laboratory, with presently two students in Master’s thesis programs on neutrino physics and detectors in the Neutrino Division. And finally, a joint venture with the Italian Scientists and Scholars North-America Foundation (ISSNAF) provided this year 4 professional engineers free of charge for Fermilab. More details on all of the above can be found below.« less

Effects of Lidocaine-Mediated CPEB3 Upregulation in Human Hepatocellular Carcinoma Cell Proliferation In Vitro

PubMed Central

Liu, Hongjun; Wang, Yiru; Chen, Bing

2018-01-01

Lidocaine displays antitumor activity by inducing apoptosis and suppressing tumor growth in human hepatocellular carcinoma (HepG2) cells in vitro. However, the molecular mechanism underlying lidocaine-mediated antitumor activity is unclear. In this study, HepG2 cells were treated with lidocaine, and cell proliferation and colony-forming ability were assessed. The expression level of cytoplasmic polyadenylation element binding protein 3 (CPEB3) was detected by real-time quantitative PCR and western blot. Lidocaine treatment resulted in decreased HepG2 cell viability and colony formation in a dose-dependent manner. In hepatocellular carcinoma patient samples, CPEB3 was downregulated and was associated with poor prognosis and high-grade malignancy. Additionally, CPEB3 was a critical mediator of lidocaine-induced repression of HepG2 cell proliferation. These results demonstrated that lidocaine decreased cell viability and colony-forming ability of HepG2 cells by upregulating CPEB3 expression.

Specific binding of tubeimoside-2 with proteins in hepatocarcinoma HepG2 cells: investigation by molecular spectroscopy

NASA Astrophysics Data System (ADS)

Yang, Sun; Shi-Sheng, Sun; Ying-Yong, Zhao; Jun, Fan

2012-07-01

In this study, we compared different binding interactions of TBMS2 with proteins both in hepatocarcinoma HepG2 cells and in normal embryo hepatic L02 cells by using fluorescence, absorption, and CD spectroscopy. The fluorescence data revealed that the fluorescence intensity of proteins in the HepG2 and L02 cells decreased in the presence of TBMS2 by 30.79% and 12.01%, respectively. Binding constants and thermodynamic parameters were obtained for systems of TBMS2 with the two kinds of cell proteins. The results indicated that HepG2 cell proteins had a higher TBMS2 binding activity than those in the L02 cells. Analysis of the TBMS2 cytotoxic activities showed that TBMS2 could selectively induce apoptosis of HepG2 cells by binding to them, while its apoptotic effect on L02 cells was relatively weaker.

Linoleic acid-menthyl ester reduces the secretion of apolipoprotein B100 in HepG2 cells.

PubMed

Inoue, Nao; Yamano, Naomi; Sakata, Kotaro; Arao, Keisuke; Kobayashi, Takashi; Nagao, Toshihiro; Shimada, Yuji; Nagao, Koji; Yanagita, Teruyoshi

2009-01-01

The effect of linoleic acid-menthyl ester (LAME) on lipid metabolism were assessed in HepG2 cells. It is well known that high level of apolipoprotein (apo) B100 in the serum is risk for atherosclerosis. Although linoleic acid (LA) treatment and LA plus L-mentol treatment increased apo B100 secretion, LAME treatment significantly decreased apo B100 secretion in HepG2 cells compared with control medium. The hypolipidemic effect of LAME was attributable to the suppression of triglyceride synthesis in HepG2 cells. It is also known that the risk of coronary heart disease is negatively related to the concentration of serum apo A-1. In the present study, LAME treatment increased apo A-1 secretion as compared with LA treatment in HepG2 cells. These results suggest that mentyl-esterification of fatty acids may be beneficial in anti-atherogenic dietary therapy.

Immunomodulatory effects of Hericium erinaceus derived polysaccharides are mediated by intestinal immunology.

PubMed

Sheng, Xiaotong; Yan, Jingmin; Meng, Yue; Kang, Yuying; Han, Zhen; Tai, Guihua; Zhou, Yifa; Cheng, Hairong

2017-03-22

This study was aimed at investigating the immunomodulating activity of Hericium erinaceus polysaccharide (HEP) in mice, by assessing splenic lymphocyte proliferation (cell-mediated immunity), serum hemolysin levels (humoral immunity), phagocytic capacity of peritoneal cavity phagocytes (macrophage phagocytosis), and NK cell activity. ELISA of immunoglobulin A (SIgA) in the lamina propria, and western blotting of small intestinal proteins were also performed to gain insight into the mechanism by which HEP affects the intestinal immune system. Here, we report that HEP improves immune function by functionally enhancing cell-mediated and humoral immunity, macrophage phagocytosis, and NK cell activity. In addition, HEP was found to upregulate the secretion of SIgA and activate the MAPK and AKT cellular signaling pathways in the intestine. In conclusion, all these results allow us to postulate that the immunomodulatory effects of HEP are most likely attributed to the effective regulation of intestinal mucosal immune activity.

PanDA: Exascale Federation of Resources for the ATLAS Experiment at the LHC

NASA Astrophysics Data System (ADS)

Barreiro Megino, Fernando; Caballero Bejar, Jose; De, Kaushik; Hover, John; Klimentov, Alexei; Maeno, Tadashi; Nilsson, Paul; Oleynik, Danila; Padolski, Siarhei; Panitkin, Sergey; Petrosyan, Artem; Wenaus, Torre

2016-02-01

After a scheduled maintenance and upgrade period, the world's largest and most powerful machine - the Large Hadron Collider(LHC) - is about to enter its second run at unprecedented energies. In order to exploit the scientific potential of the machine, the experiments at the LHC face computational challenges with enormous data volumes that need to be analysed by thousand of physics users and compared to simulated data. Given diverse funding constraints, the computational resources for the LHC have been deployed in a worldwide mesh of data centres, connected to each other through Grid technologies. The PanDA (Production and Distributed Analysis) system was developed in 2005 for the ATLAS experiment on top of this heterogeneous infrastructure to seamlessly integrate the computational resources and give the users the feeling of a unique system. Since its origins, PanDA has evolved together with upcoming computing paradigms in and outside HEP, such as changes in the networking model, Cloud Computing and HPC. It is currently running steadily up to 200 thousand simultaneous cores (limited by the available resources for ATLAS), up to two million aggregated jobs per day and processes over an exabyte of data per year. The success of PanDA in ATLAS is triggering the widespread adoption and testing by other experiments. In this contribution we will give an overview of the PanDA components and focus on the new features and upcoming challenges that are relevant to the next decade of distributed computing workload management using PanDA.

Tertiary particle physics with ELI: from challenge to chance (Conference Presentation)

NASA Astrophysics Data System (ADS)

Drska, Ladislav

2017-05-01

nteraction of high-intensity laser pulses with solid state targets results in generation of intense pulses of secondary particles via electromagnetic interaction : electrons, ions, hard x-rays. The beams of these particles can be used to produce various types of third-generation particles, beyond electromagnetic also other types of fundamental interactions can be involved in this process [1]. As the most interesting tertiary particles could be mentioned positrons, neutron, muons. This paper shall extend our previous analysis of this topic [2]: it discusses selected technical problems of design and realization of applicable sources of these particles and presents some more elaborated proposals for potential meaningful / hopefuly realistic exploitations of this technology. (1)Tertiary Sources (TS) : First Development Steps. This part of the presentation includes the topics as follows: (11) Pulsed positron sources: Verified solutions of laser-driven positron sources [3] [4] [5], development towards applicable facilities. Some unconventional concepts of application of lasers for positron production [6]. Techniques for realization of low/very-low energy positrons. (12) Taylored neutron sources [7]: Neutron sources with demanded space distribution, strongly beamed and isotropic solutions [8] [9]. Neutron generation with taylored energy distribution. Problem of the direct production of neutrons with very low energy [10] [11]. (13) Potential muon sources: Proof-of-principle laser experiment on electron / photon driven muon production [12] [13]. Study of the possibility of effective generation of surface muons. Problems of the production of muons with very low energy. (2) Fundamental & Applied Physics with TS: This part of the talk presents the themes: (21) Diagnostic potential of TS: Lepton emission as a signature of processes in extreme systems. Passive and active diagnostics using positrons, problems of detection and evaluation. Potential diagnostic applications of muons. Concrete application study: muon tomography. (22) Antilepton gravity studies [14]: Possibility of antimattter gravity research using positronium and muonium [15] [16]. Lepton / antilepton gravity studiesactive with relativistic particle beams [17]. First-phase practical application : positron production for filling (commertial) particle traps, development base for multiple microtrap systems. (23) Hidden world searching [18] : Potential laser-based production / detection of selected dark mattter particles - axions, hidden photons [19] [20]. Search for hidden particles in nuclear decay processes [21]. Potential application output: intense positronium source. Conclusion: The extensive feasibility study confirms the potential of ELI to contribute to the solution of Grand Challenge Problems of physics. Laser-produced tertiary particles will play important role in this effort. : References [1] L.Drska et al.: Physics of Extreme Systems. Course ATHENS CTU18, Prague 12 - 19 Nov., 2016. http://vega.fjfi.cvut.cz/docs/athens2016/ [2] L.Drska : Lepton Diagnostics and Antimatter Physics. In: SPIE Optics+Optoelectronics, Prague, April 13 - 16, 2015 . [3] H. Chen et al.: Scaling the Yield of Laser-Driven Electron-Positron Jets to Laboratory Astrophysics Applications. Rep. LLNL-JRNL-665381, Dec. 11, 2014. [4] E Liang et al.: High e+ / e- Ratio Dense Pair Creation with 1022 W.cm-2 Laser Irradiating Solid Targets. Scientific Reports, Sept. 14, 2015. www.nature.com/scientificreports [5] G. Sarri et al.: Spectral and Spatial Characterization of Laser-driven Positron Beams. Plasma Phys. Control. Fusion 59 (2017) 014015. [6] B. Schoch: A Method to Produce Intense Positron Beams via Electro Pair Production on Electrons. arXiv:1607.03847v1 [physics.acc-ph] [7] I. Pomerantz: Laser Generation of Neutrons: Science and Applications. In: ELI-NP Summer School, Magurele, Sept. 21 - 25, 2015. http://www.eli-np.ro/2015-summer-school/presentations/23.09/Pomerantz_Eli-NP-Summer-school-2015.pdf [8] V.P. Kovalev: Secondary Radiation of Electron Accelerators (in Russian). Atomizdat 1969. [9] M. Lebois et al.: Development of a Kinematically Focused Neutron Source with p(Li7,n)Be7 Inverse Reaction. Nucl. Instr. Meth. Phys. Res. A 735 (2014), 145. [10] D. Habs et al.: Neutron Halo Isomers in Stable Nuclei and their Possible Application for the Production of Low Energy, Pulsed, Polarized Neutron Beams of High Intensity and High Brilliance. Appl. Phys B103 (2011),485. [11] T. Masuda et al.: A New Method of Creating High/Intensity Neutron Source. arXiv:1604.02818v1[nucl-ex] [12] A.I. Titov et al.: Dimuon Production by Laser-wakefield Accelerated Electrons. Phys. Rev. ST Accel. Beams 12 (2009) 111301. [13] W. Dreesen et al.: Detection of Petawatt Laser-Induced Muon Source for Rapid High-Gamma Material Detection. DOE/NV/25946-2262. [14] F. Castelli: Positronium and Fundamental Physics: What Next ? In: What Next, Florence 2015. [15] G. Dufour et al. : Prospects for Studies of the Free Fall and Gravitation Quantum States of Antimatter. Advances in High Energy Physics 2015 (2015) 379642. [16] D.M. Kaplan et al.. Antimatter Gravity with Muonium. IIT-CAPP-16-1. arXiv:1601.07222v2 [physics.ins-det] [17] T. Kalaydzhyan: Gravitational Mass of Positron from LEP Synchrotron Losses. arXiv:1508.04377v3 [hep-ph] [18] J. Alexander et al.: Dark Sector 2016 Workshop: Community Report. arXiv:1608.08632[hep-ph] [19] M.A. Wahud et al.: Axion-like Particle Production in a Laser-Induced Dynamical Spacertime. arXiv:1612.07743v1 [hep-ph] [20] V. Kozhuharov et al: New Projects on Dark Photon Search. arXiv:1610.04389v1 [hep-ex] [21] A.J. Krasznahorkay et al.: Observation of Anomalous Internal Pair Creation in Be8: A Possible Signature of a Light, Neutral Boson. arXiv:1504.01527v1 [nucl-ex

Differential genomic effects of six different TiO2 nanomaterials on human liver HepG2 cells

EPA Science Inventory

Engineered nanoparticles are reported to cause liver toxicity in vivo. To better assess the mechanism of the in vivo liver toxicity, we used the human hepatocarcinoma cells (HepG2) as a model system. Human HepG2 cells were exposed to 6 TiO2 nanomaterials (with dry primary partic...

Does the Intel Xeon Phi processor fit HEP workloads?

NASA Astrophysics Data System (ADS)

Nowak, A.; Bitzes, G.; Dotti, A.; Lazzaro, A.; Jarp, S.; Szostek, P.; Valsan, L.; Botezatu, M.; Leduc, J.

2014-06-01

This paper summarizes the five years of CERN openlab's efforts focused on the Intel Xeon Phi co-processor, from the time of its inception to public release. We consider the architecture of the device vis a vis the characteristics of HEP software and identify key opportunities for HEP processing, as well as scaling limitations. We report on improvements and speedups linked to parallelization and vectorization on benchmarks involving software frameworks such as Geant4 and ROOT. Finally, we extrapolate current software and hardware trends and project them onto accelerators of the future, with the specifics of offline and online HEP processing in mind.

Simultaneous detection of MCF-7 and HepG2 cells in blood by ICP-MS with gold nanoparticles and quantum dots as elemental tags.

PubMed

Li, Xiaoting; Chen, Beibei; He, Man; Wang, Han; Xiao, Guangyang; Yang, Bin; Hu, Bin

2017-04-15

In this work, we demonstrate a novel method based on inductively coupled plasma mass spectrometry (ICP-MS) detection with gold nanoparticles (Au NPs) and quantum dots (QDs) labeling for the simultaneous counting of two circulating tumor cell lines (MCF-7 and HepG2 cells) in human blood. MCF-7 and HepG2 cells were captured by magnetic beads coupled with anti-EpCAM and then specifically labeled by CdSe QDs-anti-ASGPR and Au NPs-anti-MUC1, respectively, which were used as signal probes for ICP-MS measurement. Under the optimal experimental conditions, the limits of detection of 50 MCF-7, 89 HepG2 cells and the linear ranges of 200-40000 MCF-7, 300-30000 HepG2 cells were obtained, and the relative standard deviations for seven replicate detections of 800 MCF-7 and HepG2 cells were 4.6% and 5.7%, respectively. This method has the advantages of high sensitivity, low sample consumption, wide linear range and can be extended to the simultaneous detection of multiple CTC lines in human peripheral blood. Copyright © 2016 Elsevier B.V. All rights reserved.

Arctigenin Inhibits Liver Cancer Tumorigenesis by Inhibiting Gankyrin Expression via C/EBPα and PPARα

PubMed Central

Sun, Ying; Tan, Yu-jun; Lu, Zhan-zhao; Li, Bing-bing; Sun, Cheng-hong; Li, Tao; Zhao, Li-li; Liu, Zhong; Zhang, Gui-min; Yao, Jing-chun; Li, Jie

2018-01-01

Burdock (Arctium lappa) is a popular vegetable in China and Japan that is consumed for its general health benefits. The principal active component of burdock is arctigenin, which shows a range of bioactivities in vivo and in vitro. Here, we investigated the potential anti-tumor effects of arctigenin using two human hepatocellular carcinoma (HCC) cell lines, HepG2 and Hep3B, and sought to elucidate its potential mechanisms of action. Our results showed that arctigenin treatment inhibited cell growth in both HepG2 and Hep3B cell lines (IC50 of 4.74 nM for HepG2 cells, and of 59.27 nM for Hep3B cells). In addition, migration, invasion, and colony formation by HepG2 cells were significantly inhibited by arctigenin. By contrast, treatment of Hep3B cells with arctigenin did not alter these parameters. Arctigenin also significantly reduced the levels of gankyrin mRNA and protein in HepG2 cells, but not in Hep3B cells. A luciferase assay indicated that arctigenin targeted the -450 to -400 region of the gankyrin promoter. This region is also the potential binding site for both C/EBPα and PPARα, as predicted and confirmed by an online software analysis and ChIP assay. Additionally, a co-immunoprecipitation (Co-IP) assay showed that binding between C/EBPα and PPARα was increased in the presence of arctigenin. However, arctigenin did not increase the expression of C/EBPα or PPARα protein. A binding screening assay and liquid chromatography–mass spectrometry (LC–MS) were performed to identify the mechanisms by which arctigenin regulates gankyrin expression. The results suggested that arctigenin could directly increase C/EBPα binding to the gankyrin promoter (-432 to -422 region), but did not affect PPARα binding. Expression of gankyrin, C/EBPα, and PPARα were analyzed in tumor tissues of patients using real-time PCR. Both C/EBPα and PPARα showed negative correlations with gankyrin. In tumor-bearing mice, arctigenin had a significant inhibitory effect on HCC growth. In conclusion, our results suggested that arctigenin could inhibit liver cancer growth by directly recruiting C/EBPα to the gankyrin promoter. PPARα subsequently bound to C/EBPα, and both had a negative regulatory effect on gankyrin expression. This study has identified a new mechanism of action of arctigenin against liver cancer growth. PMID:29636686

Arctigenin Inhibits Liver Cancer Tumorigenesis by Inhibiting Gankyrin Expression via C/EBPα and PPARα.

PubMed

Sun, Ying; Tan, Yu-Jun; Lu, Zhan-Zhao; Li, Bing-Bing; Sun, Cheng-Hong; Li, Tao; Zhao, Li-Li; Liu, Zhong; Zhang, Gui-Min; Yao, Jing-Chun; Li, Jie

2018-01-01

Burdock ( Arctium lappa ) is a popular vegetable in China and Japan that is consumed for its general health benefits. The principal active component of burdock is arctigenin, which shows a range of bioactivities in vivo and in vitro . Here, we investigated the potential anti-tumor effects of arctigenin using two human hepatocellular carcinoma (HCC) cell lines, HepG2 and Hep3B, and sought to elucidate its potential mechanisms of action. Our results showed that arctigenin treatment inhibited cell growth in both HepG2 and Hep3B cell lines (IC 50 of 4.74 nM for HepG2 cells, and of 59.27 nM for Hep3B cells). In addition, migration, invasion, and colony formation by HepG2 cells were significantly inhibited by arctigenin. By contrast, treatment of Hep3B cells with arctigenin did not alter these parameters. Arctigenin also significantly reduced the levels of gankyrin mRNA and protein in HepG2 cells, but not in Hep3B cells. A luciferase assay indicated that arctigenin targeted the -450 to -400 region of the gankyrin promoter. This region is also the potential binding site for both C/EBPα and PPARα, as predicted and confirmed by an online software analysis and ChIP assay. Additionally, a co-immunoprecipitation (Co-IP) assay showed that binding between C/EBPα and PPARα was increased in the presence of arctigenin. However, arctigenin did not increase the expression of C/EBPα or PPARα protein. A binding screening assay and liquid chromatography-mass spectrometry (LC-MS) were performed to identify the mechanisms by which arctigenin regulates gankyrin expression. The results suggested that arctigenin could directly increase C/EBPα binding to the gankyrin promoter (-432 to -422 region), but did not affect PPARα binding. Expression of gankyrin, C/EBPα , and PPARα were analyzed in tumor tissues of patients using real-time PCR. Both C/EBPα and PPARα showed negative correlations with gankyrin. In tumor-bearing mice, arctigenin had a significant inhibitory effect on HCC growth. In conclusion, our results suggested that arctigenin could inhibit liver cancer growth by directly recruiting C/EBPα to the gankyrin promoter. PPARα subsequently bound to C/EBPα, and both had a negative regulatory effect on gankyrin expression. This study has identified a new mechanism of action of arctigenin against liver cancer growth.

Changes in hepatitis A and B vaccination rates in adult patients with chronic liver diseases and diabetes in the U.S. population.

PubMed

Younossi, Zobair M; Stepanova, Maria

2011-10-01

Professional societies recommend hepatitis A and hepatitis B immunization for individuals with chronic liver disease (CLD), but the degree of implementation is unknown. Data were obtained from the National Health and Nutrition Examination Surveys (NHANES) conducted in 1999-2008. For the entire study population and for those with CLD and diabetes, we determined the rates and independent predictors of history of hepatitis A and hepatitis B (HepA and HepB) vaccinations, of their effectiveness, and of seroprevalence of hepatitis A antibody and anti-HB surface antibody. In total, 24,871 participants from NHANES were included: 14,886 (1999-2004) and 9,985 (2005-2008). Of these individuals, 14.0% had CLD and 8.6% had diabetes. During the study period, HepA vaccination in CLD increased from 13.3% ± 1.0% to 20.0% ± 1.5%, HepB vaccination increased from 23.4% ± 1.2% to 32.1% ± 1.5%. Of subtypes of CLD, HepA vaccination rates increased only in nonalcoholic fatty liver disease (NAFLD), whereas HepB vaccination increased for patients with hepatitis C and nonalcoholic fatty liver disease. In the diabetic cohort, HepA vaccination rates increased from 9.3% ± 1.1% to 15.4% ± 1.7% and HepB rates increased from 15.2% ± 1.5% to 22.4% ± 1.7%. All changes were similar to those observed in the general population. The quality measure (QM) for HepA in the general population decreased from 44.4% ± 1.2% in 1999-2004 to 41.7% ± 1.9% in 2005-2008, and similar changes were noted for all subcohorts. On the other hand, QM for HepB increased from 31.7% ± 0.9% to 40.7% ± 1.0% in the population, whereas no changes in QM were noted in any diagnostic cohort except for NAFLD. Although vaccination rates in CLD and diabetic cohorts are increasing, they remain low. Given the public health implications of acute hepatitis A and hepatitis B in patients with CLD, better implementation of the vaccination recommendations for these populations is warranted. Copyright © 2011 American Association for the Study of Liver Diseases.

Identification of the C-terminal domain of Daxx acts as a potential regulator of intracellular cholesterol synthesis in HepG2 cells

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

Sun, Shaowei; Medical School, Hunan University of Chinese Medicine, Changsha 410208, Hunan; Wen, Juan

Daxx is a highly conserved nuclear transcriptional factor, which has been implicated in many nuclear processes including transcription and cell cycle regulation. Our previous study demonstrated Daxx also plays a role in regulation of intracellular cholesterol content. Daxx contains several domains that are essential for interaction with a growing number of proteins. To delineate the underlying mechanism of hypocholesterolemic activity of Daxx, we constructed a set of plasmids which can be used to overexpress different fragments of Daxx and transfected to HepG2 cells. We found that the C- terminal region Daxx626–740 clearly reduced intracellular cholesterol levels and inhibited the expressionmore » of SREBPs and SCAP. In GST pull-down experiments and Double immunofluorescence assays, Daxx626–740 was demonstrated to bind directly to androgen receptor (AR). Our findings suggest that the interaction of Daxx626-740 and AR abolishes the AR-mediated activation of SCAP/SREBPs pathway, which suppresses the de novo cholesterol synthesis. Thus, C-terminal domain of Daxx acts as a potential regulator of intracellular cholesterol content in HepG2 cells. - Highlights: • Daxx C-terminal domain reduces cholesterol levels. • Daxx C-terminal domain binds directly to AR. • The interaction of Daxx C-terminal domain and AR suppresses cholesterol synthesis.« less

Heparin conjugated quantum dots for in vitro imaging applications.

PubMed

Maguire, Ciaran Manus; Mahfoud, Omar Kazem; Rakovich, Tatsiana; Gerard, Valerie Anne; Prina-Mello, Adriele; Gun'ko, Yurii; Volkov, Yuri

2014-11-01

In this work heparin-gelatine multi-layered cadmium telluride quantum dots (QDgel/hep) were synthesised using a novel 'one-pot' method. The QDs produced were characterised using various spectroscopic and physiochemical techniques. Suitable QDs were then selected and compared to thioglycolic acid stabilised quantum dots (QDTGA) and gelatine coated quantum dots (QDgel) for utilisation in in vitro imaging experiments on live and fixed permeabilised THP-1, A549 and Caco-2 cell lines. Exposure of live THP-1 cells to QDgel/hep resulted in localisation of the QDs to the nucleus of the cells. QDgel/hep show affinity for the nuclear compartment of fixed permeabilised THP-1 and A549 cells but remain confined to cytoplasm of fixed permeabilised Caco-2 cells. It is postulated that heparin binding to the CD11b receptor facilitates the internalisation of the QDs into the nucleus of THP-1 cells. In addition, the heparin layer may reduce the unfavourable thrombogenic nature of quantum dots observed in vivo. In this study, heparin conjugated quantum dots were found to have superior imaging properties compared to its native counterparts. The authors postulate that heparin binding to the CD11b receptor facilitates QD internalization to the nucleus, and the heparin layer may reduce the in vivo thrombogenic properties of quantum dots. Copyright © 2014 Elsevier Inc. All rights reserved.

The Compound of Mangiferin-Berberine Salt Has Potent Activities in Modulating Lipid and Glucose Metabolisms in HepG2 Cells

PubMed Central

Wang, Can; Jiang, Jian-Dong; Wu, Wei; Kong, Wei-Jia

2016-01-01

The mangiferin-berberine (MB) salt was synthesized by ionic bonding of mangiferin (M) and berberine (B) at an equal molecular ratio. This study aimed to investigate the activities of MB salt in modulating lipid and glucose metabolisms in HepG2 cells. After 24 h treatment of the studying compounds, cellular AMP-activated protein kinase α (AMPKα)/acetyl-CoA carboxylase (ACC) protein levels and carnitine palmitoyltransferase (CPT) 1 activities, intracellular lipid contents, mRNA expression levels of target genes, glucose consumption, and glucose production amounts were determined. Compound C (CC) was used in the blocking experiments. Our results showed that MB salt increased p-AMPKα (Thr172)/p-ACC (Ser79) levels and CPT1 activity and suppressed oleic acid- (OA-) induced lipid accumulation and upregulation of lipogenic genes potently in HepG2 cells. The above activities of MB salt were AMPK dependent and were superior to those of M or B when administered at an equal molar concentration. MB salt enhanced basal and insulin-stimulated glucose consumption and suppressed gluconeogenesis more potently than M or B alone. The inhibiting activity of MB salt on cellular gluconeogenesis was AMPK dependent. Our results may support MB salt as a new kind of agent for the development of novel lipid or glucose-lowering drugs in the future. PMID:27123455

Advances in Grid Computing for the FabrIc for Frontier Experiments Project at Fermialb

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

Herner, K.; Alba Hernandex, A. F.; Bhat, S.

The FabrIc for Frontier Experiments (FIFE) project is a major initiative within the Fermilab Scientic Computing Division charged with leading the computing model for Fermilab experiments. Work within the FIFE project creates close collaboration between experimenters and computing professionals to serve high-energy physics experiments of diering size, scope, and physics area. The FIFE project has worked to develop common tools for job submission, certicate management, software and reference data distribution through CVMFS repositories, robust data transfer, job monitoring, and databases for project tracking. Since the projects inception the experiments under the FIFE umbrella have signicantly matured, and present an increasinglymore » complex list of requirements to service providers. To meet these requirements, the FIFE project has been involved in transitioning the Fermilab General Purpose Grid cluster to support a partitionable slot model, expanding the resources available to experiments via the Open Science Grid, assisting with commissioning dedicated high-throughput computing resources for individual experiments, supporting the eorts of the HEP Cloud projects to provision a variety of back end resources, including public clouds and high performance computers, and developing rapid onboarding procedures for new experiments and collaborations. The larger demands also require enhanced job monitoring tools, which the project has developed using such tools as ElasticSearch and Grafana. in helping experiments manage their large-scale production work ows. This group in turn requires a structured service to facilitate smooth management of experiment requests, which FIFE provides in the form of the Production Operations Management Service (POMS). POMS is designed to track and manage requests from the FIFE experiments to run particular work ows, and support troubleshooting and triage in case of problems. Recently a new certicate management infrastructure called Distributed Computing Access with Federated Identities (DCAFI) has been put in place that has eliminated our dependence on a Fermilab-specic third-party Certicate Authority service and better accommodates FIFE collaborators without a Fermilab Kerberos account. DCAFI integrates the existing InCommon federated identity infrastructure, CILogon Basic CA, and a MyProxy service using a new general purpose open source tool. We will discuss the general FIFE onboarding strategy, progress in expanding FIFE experiments presence on the Open Science Grid, new tools for job monitoring, the POMS service, and the DCAFI project.« less

Advances in Grid Computing for the Fabric for Frontier Experiments Project at Fermilab

NASA Astrophysics Data System (ADS)

Herner, K.; Alba Hernandez, A. F.; Bhat, S.; Box, D.; Boyd, J.; Di Benedetto, V.; Ding, P.; Dykstra, D.; Fattoruso, M.; Garzoglio, G.; Kirby, M.; Kreymer, A.; Levshina, T.; Mazzacane, A.; Mengel, M.; Mhashilkar, P.; Podstavkov, V.; Retzke, K.; Sharma, N.; Teheran, J.

2017-10-01

The Fabric for Frontier Experiments (FIFE) project is a major initiative within the Fermilab Scientific Computing Division charged with leading the computing model for Fermilab experiments. Work within the FIFE project creates close collaboration between experimenters and computing professionals to serve high-energy physics experiments of differing size, scope, and physics area. The FIFE project has worked to develop common tools for job submission, certificate management, software and reference data distribution through CVMFS repositories, robust data transfer, job monitoring, and databases for project tracking. Since the projects inception the experiments under the FIFE umbrella have significantly matured, and present an increasingly complex list of requirements to service providers. To meet these requirements, the FIFE project has been involved in transitioning the Fermilab General Purpose Grid cluster to support a partitionable slot model, expanding the resources available to experiments via the Open Science Grid, assisting with commissioning dedicated high-throughput computing resources for individual experiments, supporting the efforts of the HEP Cloud projects to provision a variety of back end resources, including public clouds and high performance computers, and developing rapid onboarding procedures for new experiments and collaborations. The larger demands also require enhanced job monitoring tools, which the project has developed using such tools as ElasticSearch and Grafana. in helping experiments manage their large-scale production workflows. This group in turn requires a structured service to facilitate smooth management of experiment requests, which FIFE provides in the form of the Production Operations Management Service (POMS). POMS is designed to track and manage requests from the FIFE experiments to run particular workflows, and support troubleshooting and triage in case of problems. Recently a new certificate management infrastructure called Distributed Computing Access with Federated Identities (DCAFI) has been put in place that has eliminated our dependence on a Fermilab-specific third-party Certificate Authority service and better accommodates FIFE collaborators without a Fermilab Kerberos account. DCAFI integrates the existing InCommon federated identity infrastructure, CILogon Basic CA, and a MyProxy service using a new general purpose open source tool. We will discuss the general FIFE onboarding strategy, progress in expanding FIFE experiments presence on the Open Science Grid, new tools for job monitoring, the POMS service, and the DCAFI project.

[Arginase inhibitor nor-NOHA induces apoptosis and inhibits invasion and migration of HepG2 cells].

PubMed

Li, Xiangnan; Zhu, Fangyu; He, Yongsong; Luo, Fang

2017-04-01

Objective To investigate the cell inhibitory effect of arginase inhibitor nor-NOHA on HepG2 hepatocellular carcinoma cells and related mechanism. Methods CCK-8 assay was used to detect the cell proliferation and flow cytometry to detect the apoptosis of HepG2 cells treated with (0, 0.5, 1.0, 2.0, 3.0) ng/μL nor-NOHA. The protein levels of arginase 1 (Arg1), P53, matrix metalloproteinase-2 (MMP-2), E-cadherin (ECD) were determined by Western blotting. Real time quantitative PCR was employed to examine the changes in the mRNA level of inducible nitric oxide synthase (iNOS). Griess assay was used to measure the concentration of nitric oxide (NO) in HepG2 cells. Transwell TM assay and wound-healing assay were performed to evaluate the changes of the cell invasion and migration ability, respectively. Results nor-NOHA inhibited the proliferation and induced the apoptosis of HepG2 cells. It also decreased the expression levels of Arg1 and MMP-2, increased the expression levels of P53 and ECD as well as the production of NO; in addition, nor-NOHA inhibited the invasion and migration of HepG2 cells. Conclusion Nor-NOHA can induce cell apoptosis and inhibit the ability of invasion and migration of HepG2 cells by inhibiting Arg1, which is related with the increase of iNOS expression and the high concentration of NO.

Effects of High-energy Particles on Accretion Flows onto a Supermassive Black Hole

NASA Astrophysics Data System (ADS)

Kimura, Shigeo S.; Toma, Kenji; Takahara, Fumio

2014-08-01

We study the effects of high-energy particles (HEPs) on the accretion flows onto a supermassive black hole and luminosities of escaping particles such as protons, neutrons, gamma rays, and neutrinos. We formulate a one-dimensional model of the two-component accretion flow consisting of thermal particles and HEPs, supposing that some fraction of the released energy is converted to the acceleration of HEPs. The thermal component is governed by fluid dynamics while the HEPs obey the moment equations of the diffusion-convection equation. By solving the time evolution of these equations, we obtain advection-dominated flows as the steady state solutions. The effects of the HEPs on the flow structures turn out to be small even if the pressure of the HEPs dominates over the thermal pressure. For a model in which the escaping protons take away almost all the energy released, the HEPs have a large enough influence to make the flow have a Keplerian angular velocity at the inner region. We calculate the luminosities of the escaping particles for these steady solutions. The escaping particles can extract the energy from about 10^{-4}\\dot{M} c^2 to 10^{-2}\\dot{M} c^2, where \\dot{M} is the mass accretion rate. The luminosities of the escaping particles depend on parameters such as the injection Lorentz factors, the mass accretion rates, and the diffusion coefficients. We also discuss some implications on the relativistic jet production by the escaping particles.

Autophagy in anti-apoptotic effect of augmenter of liver regeneration in HepG2 cells.

PubMed

Shi, Hong-Bo; Sun, Hai-Qing; Shi, Hong-Lin; Ren, Feng; Chen, Yu; Chen, De-Xi; Lou, Jin-Li; Duan, Zhong-Ping

2015-05-07

To investigate the role of autophagy in the anti-apoptotic effect of augmenter of liver regeneration (ALR). Autophagy was induced through serum deprivation. An ALR-expressing plasmid was transfected into HepG2 cells, and autophagic flux was determined using fluorescence microscopy, electron microscopy, Western blot and quantitative polymerase chain reaction (qPCR) assays. After ALR-expressing plasmid transfection, an autophagy inhibitor [3-methyladenine (3-MA)] was added to HepG2 cells, and apoptosis was observed using fluorescence microscopy and flow cytometry. Autophagy was activated in HepG2 cells, peaking at 24 h after serum deprivation. Microtubule-associated protein light chain three-II levels were higher in HepG2 cells treated with ALR than in control cells, fluorescence microscopy, electron microscopy and qPCR studies showed the similar trend, and p62 levels showed the opposite trend, which indicated that ALR may play an important role in increasing autophagy flux. The numbers of apoptotic cells were substantially higher in HepG2 cells treated with both ALR and 3-MA than in cells treated with ALR alone. Therefore, the protective effect of ALR was significantly attenuated or abolished when autophagy was inhibited, indicating that the anti-apoptotic effect of ALR may be related to autophagy. ALR protects cells from apoptosis partly through increased autophagy in HepG2 cells and may be valuable as a new therapeutic treatment for liver disease.

A Randomized Controlled Trial of Mindfulness-Based Cognitive Therapy for Treatment-Resistant Depression.

PubMed

Eisendrath, Stuart J; Gillung, Erin; Delucchi, Kevin L; Segal, Zindel V; Nelson, J Craig; McInnes, L Alison; Mathalon, Daniel H; Feldman, Mitchell D

2016-01-01

Due to the clinical challenges of treatment-resistant depression (TRD), we evaluated the efficacy of mindfulness-based cognitive therapy (MBCT) relative to a structurally equivalent active comparison condition as adjuncts to treatment-as-usual (TAU) pharmacotherapy in TRD. This single-site, randomized controlled trial compared 8-week courses of MBCT and the Health Enhancement Program (HEP), comprising physical fitness, music therapy and nutritional education, as adjuncts to TAU pharmacotherapy for outpatient adults with TRD. The primary outcome was change in depression severity, measured by percent reduction in the total score on the 17-item Hamilton Depression Rating Scale (HAM-D17), with secondary depression indicators of treatment response and remission. We enrolled 173 adults; mean length of a current depressive episode was 6.8 years (SD = 8.9). At the end of 8 weeks of treatment, a multivariate analysis showed that relative to the HEP condition, the MBCT condition was associated with a significantly greater mean percent reduction in the HAM-D17 (36.6 vs. 25.3%; p = 0.01) and a significantly higher rate of treatment responders (30.3 vs. 15.3%; p = 0.03). Although numerically superior for MBCT than for HEP, the rates of remission did not significantly differ between treatments (22.4 vs. 13.9%; p = 0.15). In these models, state anxiety, perceived stress and the presence of personality disorder had adverse effects on outcomes. MBCT significantly decreased depression severity and improved treatment response rates at 8 weeks but not remission rates. MBCT appears to be a viable adjunct in the management of TRD. © 2016 S. Karger AG, Basel.

Large Scale Computing and Storage Requirements for High Energy Physics

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

Gerber, Richard A.; Wasserman, Harvey

2010-11-24

The National Energy Research Scientific Computing Center (NERSC) is the leading scientific computing facility for the Department of Energy's Office of Science, providing high-performance computing (HPC) resources to more than 3,000 researchers working on about 400 projects. NERSC provides large-scale computing resources and, crucially, the support and expertise needed for scientists to make effective use of them. In November 2009, NERSC, DOE's Office of Advanced Scientific Computing Research (ASCR), and DOE's Office of High Energy Physics (HEP) held a workshop to characterize the HPC resources needed at NERSC to support HEP research through the next three to five years. Themore » effort is part of NERSC's legacy of anticipating users needs and deploying resources to meet those demands. The workshop revealed several key points, in addition to achieving its goal of collecting and characterizing computing requirements. The chief findings: (1) Science teams need access to a significant increase in computational resources to meet their research goals; (2) Research teams need to be able to read, write, transfer, store online, archive, analyze, and share huge volumes of data; (3) Science teams need guidance and support to implement their codes on future architectures; and (4) Projects need predictable, rapid turnaround of their computational jobs to meet mission-critical time constraints. This report expands upon these key points and includes others. It also presents a number of case studies as representative of the research conducted within HEP. Workshop participants were asked to codify their requirements in this case study format, summarizing their science goals, methods of solution, current and three-to-five year computing requirements, and software and support needs. Participants were also asked to describe their strategy for computing in the highly parallel, multi-core environment that is expected to dominate HPC architectures over the next few years. The report includes a section that describes efforts already underway or planned at NERSC that address requirements collected at the workshop. NERSC has many initiatives in progress that address key workshop findings and are aligned with NERSC's strategic plans.« less

Development of self-forming doxorubicin-loaded polymeric depots as an injectable drug delivery system for liver cancer chemotherapy.

PubMed

Nittayacharn, Pinunta; Nasongkla, Norased

2017-07-01

The objective of this work was to develop self-forming doxorubicin-loaded polymeric depots as an injectable drug delivery system for liver cancer chemotherapy and studied the release profiles of doxorubicin (Dox) from different depot formulations. Tri-block copolymers of poly(ε-caprolactone), poly(D,L-lactide) and poly(ethylene glycol) named PLECs were successfully used as a biodegradable material to encapsulate Dox as the injectable local drug delivery system. Depot formation and encapsulation efficiency of these depots were evaluated. Results show that depots could be formed and encapsulate Dox with high drug loading content. For the release study, drug loading content (10, 15 and 20% w/w) and polymer concentration (25, 30, and 35% w/v) were varied. It could be observed that the burst release occurred within 1-2 days and this burst release could be reduced by physical mixing of hydroxypropyl-beta-cyclodextrin (HP-β-CD) into the depot system. The degradation at the surface and cross-section of the depots were examined by Scanning Electron Microscope (SEM). In addition, cytotoxicity of Dox-loaded depots and blank depots were tested against human liver cancer cell lines (HepG2). Dox released from depots significantly exhibited potent cytotoxic effect against HepG2 cell line compared to that of blank depots. Results from this study reveals an important insight in the development of injectable drug delivery system for liver cancer chemotherapy. Schematic diagram of self-forming doxorubicin-loaded polymeric depots as an injectable drug delivery system and in vitro characterizations. (a) Dox-loaded PLEC depots could be formed with more than 90% of sustained-release Dox at 25% polymer concentration and 20% Dox-loading content. The burst release occurred within 1-2 days and could be reduced by physical mixing of hydroxypropyl-beta-cyclodextrin (HP-β-CD) into the depot system. (b) Dox released from depots significantly exhibited potent cytotoxic effect against human liver cancer cell lines (HepG2 cell line) compared to that of blank depots. (c) Dox-loaded depots showed bulk erosion with hollow core at day 60.

The Subcellular Location of Ovalbumin in Plasmodium berghei Blood Stages Influences the Magnitude of T-Cell Responses

PubMed Central

Lin, Jing-Wen; Shaw, Tovah N.; Annoura, Takeshi; Fougère, Aurélie; Bouchier, Pascale; Chevalley-Maurel, Séverine; Kroeze, Hans; Franke-Fayard, Blandine; Janse, Chris J.; Couper, Kevin N.

2014-01-01

Model antigens are frequently introduced into pathogens to study determinants that influence T-cell responses to infections. To address whether an antigen's subcellular location influences the nature and magnitude of antigen-specific T-cell responses, we generated Plasmodium berghei parasites expressing the model antigen ovalbumin (OVA) either in the parasite cytoplasm or on the parasitophorous vacuole membrane (PVM). For cytosolic expression, OVA alone or conjugated to mCherry was expressed from a strong constitutive promoter (OVAhsp70 or OVA::mCherryhsp70); for PVM expression, OVA was fused to HEP17/EXP1 (OVA::Hep17hep17). Unexpectedly, OVA expression in OVAhsp70 parasites was very low, but when OVA was fused to mCherry (OVA::mCherryhsp70), it was highly expressed. OVA expression in OVA::Hep17hep17 parasites was strong but significantly less than that in OVA::mCherryhsp70 parasites. These transgenic parasites were used to examine the effects of antigen subcellular location and expression level on the development of T-cell responses during blood-stage infections. While all OVA-expressing parasites induced activation and proliferation of OVA-specific CD8+ T cells (OT-I) and CD4+ T cells (OT-II), the level of activation varied: OVA::Hep17hep17 parasites induced significantly stronger splenic and intracerebral OT-I and OT-II responses than those of OVA::mCherryhsp70 parasites, but OVA::mCherryhsp70 parasites promoted stronger OT-I and OT-II responses than those of OVAhsp70 parasites. Despite lower OVA expression levels, OVA::Hep17hep17 parasites induced stronger T-cell responses than those of OVA::mCherryhsp70 parasites. These results indicate that unconjugated cytosolic OVA is not stably expressed in Plasmodium parasites and, importantly, that its cellular location and expression level influence both the induction and magnitude of parasite-specific T-cell responses. These parasites represent useful tools for studying the development and function of antigen-specific T-cell responses during malaria infection. PMID:25156724

[Knockdown of STAT3 inhibits proliferation and migration of HepG2 hepatoma cells induced by IFN1].

PubMed

Li, Xiaofang; Wang, Yuqi; Yan, Ben; Fang, Peipei; Ma, Chao; Xu, Ning; Fu, Xiaoyan; Liang, Shujuan

2018-02-01

Objective To prepare lentiviruses expressing shRNA sequences targeting human signal transducer and activator of transcription 3 (STAT3) and detect the effect of STAT3 knockdown on type I interferon (IFN1)-induced proliferation and migration in HepG2 cells. Methods Four STAT3-targeting shRNA sequences (shRNA1-shRNA4) and one control sequence (Ctrl shRNA) were selected and cloned respectively into pLKO.1-sp6-pgk-GFP to construct shRNA-expressing vectors. Along with backbone psPAX2 and pMD2.G vectors, they were separately transfected into HEK293T cells to prepare lentiviruses. HepG2 cells were infected with the lentiviruses. Cytoplastic STAT3 level was detected by Western blotting to screen effective shRNA sequence(s) targeting STAT3. Proliferation and migration of HepG2 cells were analyzed by CCK-8 assay and Transwell TM migration and scratching assay, respectively. To detect the effect of IFN1 on cell proliferation and migration of HepG2 cells, the cells were treated with 2000 U/mL IFNα2b for indicated time and the activation of IFN-triggered STAT1 signal transduction was assayed by Western blotting. Results Two most effective STAT3-targeting shRNA sequences shRNA1 and shRNA2 were selected, and the expression of both STAT3 shRNA significantly decreased proliferation and migration of HepG2 cells. When treated with IFNα2b, 2000 U/mL of IFN1 showed more competent in attenuating growth and migration of HepG2 cells. Our data further proved that knockdown of STAT3 increased the phosphorylation of STAT1, and IFNα2b further enhanced the activation of STAT1 signaling in HepG2 cells. Conclusion Knockdown of STAT3 inhibits cell migration and growth, and rescues IFN response through up-regulating STAT1 signal transduction in HepG2 hepatoma cells.

Effect of heparin and heparan sulphate on open promoter complex formation for a simple tandem gene model using ex situ atomic force microscopy.

PubMed

Chammas, Oliver; Bonass, William A; Thomson, Neil H

2017-05-01

The influence of heparin and heparan sulphate (HepS) on the appearance and analysis of open promoter complex (RP o ) formation by E. coli RNA polymerase (RNAP) holoenzyme (σ 70 RNAP) on linear DNA using ex situ imaging by atomic force microscopy (AFM) has been investigated. Introducing heparin or HepS into the reaction mix significantly reduces non-specific interactions of the σ 70 RNAP and RNAP after RP o formation allowing for better interpretation of complexes shown within AFM images, particularly on DNA templates containing more than one promoter. Previous expectation was that negatively charged polysaccharides, often used as competitive inhibitors of σRNAP binding and RP o formation, would also inhibit binding of the DNA template to the mica support surface and thereby lower the imaging yield of active RNAP-DNA complexes. We found that the reverse of this was true, and that the yield of RP o formation detected by AFM, for a simple tandem gene model containing two λ PR promoters, increased. Moreover and unexpectedly, HepS was more efficient than heparin, with both of them having a dispersive effect on the sample, minimising unwanted RNAP-RNAP interactions as well as non-specific interactions between the RNAP and DNA template. The success of this method relied on the observation that E. coli RNAP has the highest affinity for the mica surface of all the molecular components. For our system, the affinity of the three constituent biopolymers to muscovite mica was RNAP>Heparin or HepS>DNA. While we observed that heparin and HepS can inhibit DNA binding to the mica, the presence of E. coli RNAP overcomes this effect allowing a greater yield of RP o s for AFM analysis. This method can be extended to other DNA binding proteins and enzymes, which have an affinity to mica higher than DNA, to improve sample preparation for AFM studies. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

IRE1α links Nck1 deficiency to attenuated PTP1B expression in HepG2 cells.

PubMed

Li, Hui; Li, Bing; Larose, Louise

2017-08-01

PTP1B, a prototype of the non-receptor subfamily of the protein tyrosine phosphatase superfamily, plays a key role in regulating intracellular signaling from various receptor and non-receptor protein tyrosine kinases. Previously, we reported that silencing Nck1 in human hepatocellular carcinoma HepG2 cells enhances basal and growth factor-induced activation of the PI3K-Akt pathway through attenuating PTP1B expression. However, the underlying mechanism by which Nck1 depletion represses PTP1B expression remains unclear. In this study, we found that silencing Nck1 attenuates PTP1B expression in HepG2 cells through down-regulation of IRE1α. Indeed, we show that silencing Nck1 in HepG2 cells leads to decreased IRE1α expression and signaling. Accordingly, IRE1α depletion using siRNA in HepG2 cells enhances PI3K-dependent basal and growth factor-induced Akt activation, reproducing the effects of silencing Nck1 on activation of this pathway. In addition, depletion of IRE1α also leads to reduced PTP1B expression, which was rescued by ectopic expression of IRE1α in Nck1-depleted cells. Mechanistically, we found that silencing either Nck1 or IRE1α in HepG2 cells decreases PTP1B mRNA levels and stability. However, despite miR-122 levels, a miRNA targeting PTP1B 3' UTR and inducing PTP1B mRNA degradation in HepG2 cells, are increased in both Nck1- and IRE1α-depleted HepG2 cells, a miR-122 antagomir did not rescue PTP1B expression in these cells. Overall, this study highlights an important role for Nck1 in fine-tuning IRE1α expression and signaling that regulate PTP1B expression and subsequent activation of the PI3K-Akt pathway in HepG2 cells. Copyright © 2017 Elsevier Inc. All rights reserved.

Bridging the Particle Physics and Big Data Worlds

NASA Astrophysics Data System (ADS)

Pivarski, James

2017-09-01

For decades, particle physicists have developed custom software because the scale and complexity of our problems were unique. In recent years, however, the ``big data'' industry has begun to tackle similar problems, and has developed some novel solutions. Incorporating scientific Python libraries, Spark, TensorFlow, and machine learning tools into the physics software stack can improve abstraction, reliability, and in some cases performance. Perhaps more importantly, it can free physicists to concentrate on domain-specific problems. Building bridges isn't always easy, however. Physics software and open-source software from industry differ in many incidental ways and a few fundamental ways. I will show work from the DIANA-HEP project to streamline data flow from ROOT to Numpy and Spark, to incorporate ideas of functional programming into histogram aggregation, and to develop real-time, query-style manipulations of particle data.

beta-endorphin: synthesis of analogs with extension at the carboxyl terminus with high radioreceptor binding activity.

PubMed

Yamashiro, D; Ferrara, P; Li, C H

1980-07-01

Four analogs of human beta-endorphin (beta h-EP) have been synthesized: [Gly31]-Beta h-EP-Gly-NH2, [CH3(CH2)4NH231]-beta h-EP, [Gly31]-beta h-EP-Gly-Gly-NH2, and [Gln8, Gly31]-betah-EP-Gly-Gly-NH2. All are more active than beta h-EP in an opiate receptor binding assay. Stepwise extension at the COOH-terminus shows a progressive increase in binding activity. The last analog, which combines extension at the COOH-terminus with elimination of the remaining anionic charge in beta h-EP, is nine times more active than the parent molecule.

Beta-Endorphin: dissociation of receptor binding activity from analgesic potency.

PubMed

Li, C H; Tseng, L F; Ferrara, P; Yamashiro, D

1980-04-01

Biological activities of synthetic camel beta-endorphin and human beta-endorphin (beta h-EP) have been measured by the radioreceptor binding assay, using [Tyr27-3H]-beta h-EP as the primary ligand and by the tail-flick test for analgesic potency. Four synthetic analogs of beta h-EP, namely [Gly31]-beta h-EP-Gly-NH2, [Gly31]-beta h-EP-Gly-Gly-NH2, [Gln8,Gly31]-beta h-EP-Gly-Gly-NH2, and [CH3(CH2)4NH231]-beta h-EP, have also been assayed by the same procedures. Results indicate a clear dissociation of radioreceptor binding activity from analgesic potency.

Beta-Endorphin: dissociation of receptor binding activity from analgesic potency.

PubMed Central

Li, C H; Tseng, L F; Ferrara, P; Yamashiro, D

1980-01-01

Biological activities of synthetic camel beta-endorphin and human beta-endorphin (beta h-EP) have been measured by the radioreceptor binding assay, using [Tyr27-3H]-beta h-EP as the primary ligand and by the tail-flick test for analgesic potency. Four synthetic analogs of beta h-EP, namely [Gly31]-beta h-EP-Gly-NH2, [Gly31]-beta h-EP-Gly-Gly-NH2, [Gln8,Gly31]-beta h-EP-Gly-Gly-NH2, and [CH3(CH2)4NH231]-beta h-EP, have also been assayed by the same procedures. Results indicate a clear dissociation of radioreceptor binding activity from analgesic potency. PMID:6246537

Reconfigurable PCI Express cards for low-latency data transport in HEP experiments

NASA Astrophysics Data System (ADS)

Ammendola, R.; Biagioni, A.; Cretaro, P.; Frezza, O.; Lamanna, G.; Lo Cicero, F.; Lonardo, A.; Martinelli, M.; Paolucci, P. S.; Pastorelli, E.; Pontisso, L.; Simula, F.; Vicini, P.

2017-01-01

State-of-the-art technology supports the High Energy Physics community in addressing the problem of managing an overwhelming amount of experimental data. From the point of view of communication between the detectors' readout system and computing nodes, the critical issues are the following: latency, moving data in a deterministic and low amount of time; bandwidth, guaranteeing the maximum capability of the link and communication protocol adopted; endpoint consolidation, tight aggregation of channels on a single board. This contribution describes the status and performances of the NaNet project, whose goal is the design of a family of FPGA-based PCIe network interface cards. The efforts of the team are focused on implementing a low-latency, real-time data transport mechanism between the board network multi-channel system and CPU and GPU accelerators memories on the host. Several opportunities concerning technical solutions and scientific applications have been explored: NaNet-1 with a single GbE I/O interface, and NaNet-10, offering four 10GbE ports, for activities related to the GPU-based real-time trigger of NA62 experiment at CERN; NaNet ^3 , with four 2.5Gbit optical channels, developed for the KM3NeT-ITALIA underwater neutrino telescope.

Characterization of E. coli O157:H7 strains isolated from “High Event Period” beef trim contamination

USDA-ARS?s Scientific Manuscript database

Introduction: A “High Event Period” (HEP) is defined as a time period in which commercial plants experience a higher than usual rate of E. coli O157:H7 contamination of beef trims. Our previous studies suggested that instead of being a direct result of bacteria on animal hides, in-plant biofilm for...

Beta-endorphin. Biological activity of synthetic analogs with analgesia inhibiting property in rat vas deferens and guinea pig ileum assays.

PubMed

Ho, C L; Li, C H

1985-03-01

Three synthetic analogs of human beta-endorphin (beta h-EP) (I, [Gln8, Gly31]-beta h-EP-Gly-Gly-NH2; II, [Arg9,12,24,28,29]-beta h-EP and III, [Cys11,26, Phe27, Gly31]-beta h-EP), which have been shown to possess potent inhibiting activity to beta h-EP-induced analgesia, were assayed in rat vas deferens and guinea pig ileum bioassay systems. In the rat vas deferens assay, relative potencies of these analogs were beta h-EP, 100; I, 30; II, 40; III, 1, whereas in the guinea pig ileum assay: beta h-EP, 100; I, 184; II, 81; III, 163. From previous studies on their analgesia potency in mice and opiate receptor-binding activity in rat brain membranes, their activity in rat vas deferens correlates well with the analgesic potency and the activity from guinea pig ileum assay shows good correlations with that from the opiate receptor-binding assay.

Sustained release of hepatocyte growth factor by cationic self-assembling peptide/heparin hybrid hydrogel improves β-cell survival and function through modulating inflammatory response

PubMed Central

Liu, Shuyun; Zhang, Lanlan; Cheng, Jingqiu; Lu, Yanrong; Liu, Jingping

2016-01-01

Inflammatory response is a major cause of grafts dysfunction in islet transplantation. Hepatocyte growth factor (HGF) had shown anti-inflammatory activity in multiple diseases. In this study, we aim to deliver HGF by self-assembling peptide/heparin (SAP/Hep) hybrid gel to protect β-cell from inflammatory injury. The morphological and slow release properties of SAPs were analyzed. Rat INS-1 β-cell line was treated with tumor necrosis factor α in vitro and transplanted into rat kidney capsule in vivo, and the viability, apoptosis, function, and inflammation of β-cells were evaluated. Cationic KLD1R and KLD2R self-assembled to nanofiber hydrogel, which showed higher binding affinity for Hep and HGF because of electrostatic interaction. Slow release of HGF from cationic SAP/Hep gel is a two-step mechanism involving binding affinity with Hep and molecular diffusion. In vitro and in vivo results showed that HGF-loaded KLD2R/Hep gel promoted β-cell survival and insulin secretion, and inhibited cell apoptosis, cytokine release, T-cell infiltration, and activation of NFκB/p38 MAPK pathways in β-cells. This study suggested that SAP/Hep gel is a promising carrier for local delivery of bioactive proteins in islet transplantation. PMID:27729786

NF-κB mediates the antiproliferative and proapoptotic effects of bergamot juice in HepG2 cells.

PubMed

Ferlazzo, Nadia; Cirmi, Santa; Russo, Marina; Trapasso, Elena; Ursino, Maria Rita; Lombardo, Giovanni Enrico; Gangemi, Sebastiano; Calapai, Gioacchino; Navarra, Michele

2016-02-01

Among cancers, hepatocellular carcinoma is one of the commonest worldwide, and its incidence is increasing around the world. A lot of evidence underlines that natural substances usually consumed in the diet can have an important role in the prevention of cancer. In this study we investigated the molecular mechanisms underlying the antiproliferative activity of Citrus bergamia (bergamot) juice (BJ) in human hepatocellular carcinoma HepG2 cells. HepG2 cells were exposed to BJ and then cell proliferation, cell cycle progression, apoptosis and NF-κB nuclear translocation were evaluated. Here we present results demonstrating that BJ reduced the growth rate of human hepatocellular carcinoma HepG2 cells in a time- and concentration-dependent manner, by a mechanism involving the activation of apoptotic machinery via both intrinsic and extrinsic pathways. Moreover, BJ increased expression of P53 and P21 proteins that may be responsible for the HepG2 cell cycle arrest in G2 phase. In addition, BJ reduced NF-κB nuclear translocation. Our data demonstrate the ability of BJ in reducing the growth of HepG2 cells, revealing its mechanism of action and suggesting a promising role as anticancer drugs. Copyright © 2016 Elsevier Inc. All rights reserved.

Heterochromatin influences the secondary metabolite profile in the plant pathogen Fusarium graminearum

PubMed Central

Reyes-Dominguez, Yazmid; Boedi, Stefan; Sulyok, Michael; Wiesenberger, Gerlinde; Stoppacher, Norbert; Krska, Rudolf; Strauss, Joseph

2012-01-01

Chromatin modifications and heterochromatic marks have been shown to be involved in the regulation of secondary metabolism gene clusters in the fungal model system Aspergillus nidulans. We examine here the role of HEP1, the heterochromatin protein homolog of Fusarium graminearum, for the production of secondary metabolites. Deletion of Hep1 in a PH-1 background strongly influences expression of genes required for the production of aurofusarin and the main tricothecene metabolite DON. In the Hep1 deletion strains AUR genes are highly up-regulated and aurofusarin production is greatly enhanced suggesting a repressive role for heterochromatin on gene expression of this cluster. Unexpectedly, gene expression and metabolites are lower for the trichothecene cluster suggesting a positive function of Hep1 for DON biosynthesis. However, analysis of histone modifications in chromatin of AUR and DON gene promoters reveals that in both gene clusters the H3K9me3 heterochromatic mark is strongly reduced in the Hep1 deletion strain. This, and the finding that a DON-cluster flanking gene is up-regulated, suggests that the DON biosynthetic cluster is repressed by HEP1 directly and indirectly. Results from this study point to a conserved mode of secondary metabolite (SM) biosynthesis regulation in fungi by chromatin modifications and the formation of facultative heterochromatin. PMID:22100541

Mitochondrial Dysfunction and Ca(2+) Overload Contributes to Hesperidin Induced Paraptosis in Hepatoblastoma Cells, HepG2.

PubMed

Yumnam, Silvia; Hong, Gyeong Eun; Raha, Suchismita; Saralamma, Venu Venkatarame Gowda; Lee, Ho Jeong; Lee, Won-Sup; Kim, Eun-Hee; Kim, Gon Sup

2016-06-01

Paraptosis is a programmed cell death which is morphologically and biochemically different from apoptosis. In this study, we have investigated the role of Ca(2+) in hesperidin-induced paraptotic cell death in HepG2 cells. Increase in mitochondrial Ca(2+) level was observed in hesperidin treated HepG2 cells but not in normal liver cancer cells. Inhibition of inositol-1,4,5-triphosphate receptor (IP3 R) and ryanodine receptor also block the mitochondrial Ca(2+) accumulation suggesting that the release of Ca(2+) from the endoplasmic reticulum (ER) may probably lead to the increase in mitochondrial Ca(2+) level. Pretreatment with ruthenium red (RuRed), a Ca(2+) uniporter inhibitor inhibited the hesperidin-induced mitochondrial Ca(2+) overload, swelling of mitochondria, and cell death in HepG2 cells. It has also been demonstrated that mitochondrial Ca(2+) influxes act upstream of ROS and mitochondrial superoxide production. The increased ROS production further leads to mitochondrial membrane loss in hesperidin treated HepG2 cells. Taken together our results show that IP3 R and ryanodine receptor mediated release of Ca(2+) from the ER and its subsequent influx through the uniporter into mitochondria contributes to hesperidin-induced paraptosis in HepG2 cells. © 2015 Wiley Periodicals, Inc.

[Inhibitory effect of Biejiajian pills on HepG2 cell xenograft growth and expression of β-catenin and Tbx3 in nude mice].

PubMed

Wen, Bin; Sun, Hai-Tao; He, Song-Qi; LA, Lei; An, Hai-Yan; Pang, Jie

2016-02-01

To explore the molecular mechanism by which Biejiajian pills inhibit hepatocellular carcinoma in a nude mouse model bearing HepG2 cell xenograft. The inhibitory effect of Biejiajian pills on the growth of HepG2 cell xenograft in nude mice was observed. Immunohistochemical method was used to examine proliferating cell nuclear antigen (PCNA) expression in HepG2 cell xenograft, and TUNEL method was employed to detect the cell apoptosis; the expression levels of β-catenin and Tbx3 were measured by Western blotting. Biejiajian pills significantly suppressed the growth of HepG2 cell xenograft in nude mice. The tumor-bearing mice treated with a high and a moderate dose of Biejiajian pills showed significantly increased apoptosis rate of the tumor cells [(22.9±1.220)% and (14.7±0.50)%, respectively] compared with the control group [(5.5±0.90)%, P<0.05]. Treatment with Biejiajian pills significantly decreased the expressions of PNCA, β-catenin, and Tbx3 in the cell xenograft (P<0.05). Biejiajian pills can inhibit the growth of HepG2 cell xenograft in nude mice and promote tumor cell apoptosis possibly by inhibiting PNCA expression and the Wnt/β-catenin signaling pathway.

[6]-Shogaol, a dietary phenolic compound, induces oxidative stress mediated mitochondrial dependant apoptosis through activation of proapoptotic factors in Hep-2 cells.

PubMed

Annamalai, Govindhan; Kathiresan, Suresh; Kannappan, Nagappan

2016-08-01

Ginger (Zingiber officinale) is a well-known herb used in ethnomedicine. [6]-shogaol, a phenolic nature is a major constituent of ginger. In this study, we investigated the anticancer activity of [6]-shogaol in Laryngeal cancer (Hep-2) cells. We demonstrated the effects of [6]-shogaol on the cell growth and apoptosis in Hep-2 cells were analyzed by the generation of reactive oxygen species (ROS), the level of mitochondrial membrane potential (ΔYm), DNA damage and apoptotic morphological changes were analyzed by AO/EtBr, AO and Hoechst staining. Further, apoptotic protein expressions were analyzed by western blot analysis. Our results indicated that [6]-shogaol induces apoptosis as evidenced by loss of cell viability, enhanced ROS, lipid peroxidation results in altered mitochondrial membrane potential, increased DNA damage in Hep-2 cells. Further, the prooxidant role of [6]-shogaol inhibit Bcl-2 expression with the simultaneous up-regulation of Bax, Cytochrome c, Caspase-9 and -3 protein expressions were observed in Hep-2 cells. Thus, [6]-shogaol induces apoptosis in Hep-2 cells through inducing oxidative damage and modulate apoptotic marker expressions. Therefore, [6]-shogaol might be used as a therapeutic agent for the treatment of laryngeal cancer. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

People's perception on impacts of hydro-power projects in Bhagirathi river valley, India.

PubMed

Negi, G C S; Punetha, Disha

2017-04-01

The people's perception on environmental and socio-economic impacts due to three hydro-electric projects (HEPs; commissioned and under construction) were studied in the north-west Indian Himalaya. Surveys among 140 project-affected people (PAPs) using a checklist of impacts indicate that among the negative impacts, decrease in flora/fauna, agriculture, flow of river, aesthetic beauty; and increase in water pollution, river bed quarrying for sand/stone, human settlement on river banks and social evils; and among the positive impacts, increase in standard of living, road connectivity, means of transport, public amenities, tourism and environmental awareness were related with HEPs. The PAPs tend to forget the negative impacts with the age of the HEPs after it becomes functional, and the positive impacts seem to outweigh the negative impacts. Study concludes that it is difficult to separate the compounding impacts due to HEP construction and other anthropogenic and natural factors, and in the absence of cause-and-effect analyses, it is hard to dispel the prevailing notion that HEPs are undesirable in the study area that led to agitations by the environmentalists and stopped construction of one of these HEPs. To overcome the situation, multi-disciplinary scientific studies involving the PAPs need to be carried out in planning and decision-making to make HEPs environment friendly and sustainable in this region. There is also a need to adopt low carbon electric power technologies and promote a decentralized energy strategy through joint ventures between public and private companies utilizing locally available renewable energy resources.

Habitat Evaluation Procedures (HEP) Report Wanaket Wildlife Area, Techical Report 2005-2006.

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

Ashley, Paul

2006-02-01

The Regional HEP Team (RHT) and Confederated Tribes of the Umatilla Indian Reservation (CTUIR) Wildlife Program staff conducted a follow-up habitat evaluation procedures (HEP) analysis on the Wanaket Wildlife Management Area in June 2005. The 2005 HEP investigation generated 3,084.48 habitat units (HUs) for a net increase of 752.18 HUs above 1990/1995 baseline survey results. The HU to acre ratio also increased from 0.84:1.0 to 1.16:1.0. The largest increase in habitat units occurred in the shrubsteppe/grassland cover type (California quail and western meadowlark models), which increased from 1,544 HUs to 2,777 HUs (+43%), while agriculture cover type HUs were eliminatedmore » because agricultural lands (managed pasture) were converted to shrubsteppe/grassland. In addition to the agriculture cover type, major changes in habitat structure occurred in the shrubsteppe/grassland cover type due to the 2001 wildfire which removed the shrub component from well over 95% of its former range. The number of acres of all other cover types remained relatively stable; however, habitat quality improved in the riparian herb and riparian shrub cover types. The number and type of HEP species models used during the 2005 HEP analysis were identical to those used in the 1990/1995 baseline HEP surveys. The number of species models employed to evaluate the shrubsteppe/grassland, sand/gravel/mud/cobble, and riparian herb cover types, however, were fewer than reported in the McNary Dam Loss Assessment (Rassmussen and Wright 1989) for the same cover types.« less

Performance evaluation of the HepB Typer-Entecavir kit for detection of entecavir resistance mutations in chronic hepatitis B.

PubMed

Ahn, Sang Hoon; Chun, Ji-Yong; Shin, Soo-Kyung; Park, Jun Yong; Yoo, Wangdon; Hong, Sun Pyo; Kim, Soo-Ok; Han, Kwang-Hyub

2013-12-01

Molecular diagnostic methods have enabled the rapid diagnosis of drug-resistant mutations in hepatitis B virus (HBV) and have reduced both unnecessary therapeutic interventions and medical costs. In this study we evaluated the analytical and clinical performances of the HepB Typer-Entecavir kit (GeneMatrix, Korea) in detecting entecavir-resistance-associated mutations. The HepB Typer-Entecavir kit was evaluated for its limit of detection, interference, cross-reactivity, and precision using HBV reference standards made by diluting high-titer viral stocks in HBV-negative human serum. The performance of the HepB Typer-Entecavir kit for detecting mutations related to entecavir resistance was compared with direct sequencing for 396 clinical samples from 108 patients. Using the reference standards, the detection limit of the HepB Typer-Entecavir kit was found to be as low as 500 copies/mL. No cross-reactivity was observed, and elevated levels of various interfering substances did not adversely affect its analytical performance. The precision test conducted by repetitive analysis of 2,400 replicates with reference standards at various concentrations showed 99.9% agreement (2398/2400). The overall concordance rate between the HepB Typer-Entecavir kit and direct sequencing assays in 396 clinical samples was 99.5%. The HepB Typer-Entecavir kit showed high reliability and precision, and comparable sensitivity and specificity for detecting mutant virus populations in reference and clinical samples in comparison with direct sequencing. Therefore, this assay would be clinically useful in the diagnosis of entecavir-resistance-associated mutations in chronic hepatitis B.

Improving birth dose coverage of hepatitis B vaccine.

PubMed Central

Hipgrave, David B.; Maynard, James E.; Biggs, Beverley-Ann

2006-01-01

Administration of a birth dose of hepatitis B vaccine (HepB vaccine) to neonates is recommended to prevent mother-to-infant transmission and chronic infection with the hepatitis B virus (HBV). Although manufacturers recommend HepB vaccine distribution and storage at 2-8 degrees C, recognition of the heat stability of hepatitis B surface antigen stimulated research into its use after storage at, or exposure to, ambient or high temperatures. Storage of HepB vaccine at ambient temperatures would enable birth dosing for neonates delivered at home in remote areas or at health posts lacking refrigeration. This article reviews the current evidence on the thermostability of HepB vaccine when stored outside the cold chain (OCC). The reports reviewed show that the vaccines studied were safe and effective whether stored cold or OCC. Field and laboratory data also verifies the retained potency of the vaccine after exposure to heat. The attachment of a highly stable variety of a vaccine vial monitor (measuring cumulative exposure to heat) on many HepB vaccines strongly supports policies allowing their storage OCC, when this will benefit birth dose coverage. We recommend that this strategy be introduced to improve birth dose coverage, especially in rural and remote areas. Concurrent monitoring and evaluation should be undertaken to affirm the safe implementation of this strategy, and assess its cost, feasibility and effect on reducing HBV infection rates. Meanwhile, release of manufacturer data verifying the potency of currently available HepB vaccines after exposure to heat will increase confidence in the use of vaccine vial monitors as a managerial tool during storage of HepB vaccine OCC. PMID:16501717

MicroRNA expression in the vildagliptin-treated two- and three-dimensional HepG2 cells.

PubMed

Yamashita, Yasunari; Asakura, Mitsutoshi; Mitsugi, Ryo; Fujii, Hideaki; Nagai, Kenichiro; Atsuda, Koichiro; Itoh, Tomoo; Fujiwara, Ryoichi

2016-06-01

Vildagliptin is an inhibitor of dipeptidyl peptidase-4 that is used for the treatment of type 2 diabetes mellitus. While vildagliptin can induce hepatic dysfunction in humans, the molecular mechanism has not been determined yet. Recent studies indicated that certain types of microRNA (miRNA) were linking to the development of drug-induced hepatotoxicity. In the present study, therefore, we identified hepatic miRNAs that were highly induced or reduced by the vildagliptin treatment in mice. MiR-222 and miR-877, toxicity-associated miRNAs, were induced 31- and 53-fold, respectively, by vildagliptin in the liver. While a number of miRNAs were significantly regulated by the orally treated vildagliptin in vivo, such regulation was not observed in the vildagliptin-treated HepG2 cells. In addition to the regular two-dimensional (2D) culture, we carried out the three-dimensional (3D) culturing of HepG2 cells. In the 3D-HepG2 cells, a significant reduction of miR-222 was observed compared to the expression level in 2D-HepG2 cells. A slight induction of miR-222 by vildagliptin was observed in the 3D-HepG2 cells, although miR-877 was not induced by vildagliptin even in the 3D-HepG2 cells. Further investigations are needed to overcome the discrepancy in the responsiveness of the miRNA expressions to vildagliptin between in vivo and in vitro. Copyright © 2016 The Japanese Society for the Study of Xenobiotics. Published by Elsevier Ltd. All rights reserved.

Kupffer cells facilitate the acute effects of leptin on hepatic lipid metabolism.

PubMed

Metlakunta, Anantha; Huang, Wan; Stefanovic-Racic, Maja; Dedousis, Nikolaos; Sipula, Ian; O'Doherty, Robert M

2017-01-01

Leptin has potent effects on lipid metabolism in a number of peripheral tissues. In liver, an acute leptin infusion (~120 min) stimulates hepatic fatty acid oxidation (~30%) and reduces triglycerides (TG, ~40%), effects that are dependent on phosphoinositol-3-kinase (PI3K) activity. In the current study we addressed the hypothesis that leptin actions on liver-resident immune cells are required for these metabolic effects. Myeloid cell-specific deletion of the leptin receptor (ObR) in mice or depletion of liver Kupffer cells (KC) in rats in vivo prevented the acute effects of leptin on liver lipid metabolism, while the metabolic effects of leptin were maintained in mice lacking ObR in hepatocytes. Notably, liver TG were elevated in both lean and obese myeloid cell ObR, but the degree of obesity and insulin resistance induced by a high-fat diet was similar to control mice. In isolated primary hepatocytes (HEP), leptin had no effects on HEP lipid metabolism and only weakly stimulated PI3K. However, the coculture of KC with HEP restored leptin action on HEP fatty acid metabolism and stimulation of HEP PI3K. Notably, leptin stimulated the release from KC of a number of cytokines. However, the exposure of HEP to these cytokines individually [granulocyte macrophage colony-stimulating factor, IL-1α, IL-1β, IL-6, IL-10, and IL-18] or in combination had no effects on HEP lipid metabolism. Together, these data demonstrate a role for liver mononuclear cells in the regulation of liver lipid metabolism by leptin. Copyright © 2017 the American Physiological Society.

Resveratrol Differentially Regulates NAMPT and SIRT1 in Hepatocarcinoma Cells and Primary Human Hepatocytes

PubMed Central

Schuster, Susanne; Penke, Melanie; Gorski, Theresa; Petzold-Quinque, Stefanie; Damm, Georg; Gebhardt, Rolf; Kiess, Wieland; Garten, Antje

2014-01-01

Resveratrol is reported to possess chemotherapeutic properties in several cancers. In this study, we wanted to investigate the molecular mechanisms of resveratrol-induced cell cycle arrest and apoptosis as well as the impact of resveratrol on NAMPT and SIRT1 protein function and asked whether there are differences in hepatocarcinoma cells (HepG2, Hep3B cells) and non-cancerous primary human hepatocytes. We found a lower basal NAMPT mRNA and protein expression in hepatocarcinoma cells compared to primary hepatocytes. In contrast, SIRT1 was significantly higher expressed in hepatocarcinoma cells than in primary hepatocytes. Resveratrol induced cell cycle arrest in the S- and G2/M- phase and apoptosis was mediated by activation of p53 and caspase-3 in HepG2 cells. In contrast to primary hepatocytes, resveratrol treated HepG2 cells showed a reduction of NAMPT enzymatic activity and increased p53 acetylation (K382). Resveratrol induced NAMPT release from HepG2 cells which was associated with increased NAMPT mRNA expression. This effect was absent in primary hepatocytes where resveratrol was shown to function as NAMPT and SIRT1 activator. SIRT1 inhibition by EX527 resembled resveratrol effects on HepG2 cells. Furthermore, a SIRT1 overexpression significantly decreased both p53 hyperacetylation and resveratrol-induced NAMPT release as well as S-phase arrest in HepG2 cells. We could show that NAMPT and SIRT1 are differentially regulated by resveratrol in hepatocarcinoma cells and primary hepatocytes and that resveratrol did not act as a SIRT1 activator in hepatocarcinoma cells. PMID:24603648

Fungal 7-epi-10-deacetyltaxol produced by an endophytic Pestalotiopsis microspora induces apoptosis in human hepatocellular carcinoma cell line (HepG2).

PubMed

Subban, Kamalraj; Singh, Satpal; Subramani, Ramesh; Johnpaul, Muthumary; Chelliah, Jayabaskaran

2017-11-28

Paclitaxel (taxol) is a potent anticancer drug that is used in the treatment of a wide variety of cancerous. In the present study, we identified a taxol derivative named 7-epi-10-deacetyltaxol (EDT) from the culture of an endophytic fungus Pestalotiopsis microspora isolated from the bark of Taxodium mucronatum. This study was carried out to investigate the effects of fungal EDT on cell proliferation, the induction of apoptosis and the molecular mechanisms of apoptosis in human hepatoma HepG2 cells in vitro. The endophytic fungus was identified by traditional and molecular taxonomical characterization and the fungal EDT was purified using column chromatography and confirmed by various spectroscopic and chromatographic comparisons with authentic paclitaxel. We studied the in vitro effects of EDT on HepG2 cells for parameters such as cell cycle distribution, DNA fragmentation, reactive oxygen species (ROS) generation and nuclear morphology. Further, western blot analysis was used to evaluate Bcl-2-associated X protein (Bax), B-cell lymphoma 2 (Bcl-2), p38-mitogen activated protein kinase (MAPK) and poly [ADP-ribose] polymerase (PARP) expression. We demonstrate that the fungal EDT exhibited significant in vitro cytotoxicity in HepG2 cells. We investigated cytotoxicity mechanism of EDT in HepG2 cells. The results showed nuclear condensation and DNA fragmentation were observed in cells treated with fungal EDT. Besides, the fungal EDT arrested HepG2 cells at G2/M phase of cell cycle. Furthermore, fungal EDT induced apoptosis in HepG2 cells in a dose-dependent manner associated with ROS generation and increased Bax/Bcl-2 ratio, p38 MAPKs and PARP cleavage. Our data show that EDT induced apoptotic cell death in HepG2 cells occurs through intrinsic pathway by generation of ROS mediated and activation of MAPK pathway. This is the first report for 7-epi-10-deacetyltaxol (EDT) isolated from a microbial source.

Leg extensor muscle strength, postural stability, and fear of falling after a 2-month home exercise program in women with severe knee joint osteoarthritis.

PubMed

Rätsepsoo, Monika; Gapeyeva, Helena; Sokk, Jelena; Ereline, Jaan; Haviko, Tiit; Pääsuke, Mati

2013-01-01

BACKGROUND AND OBJECTIVE. The aim of this study was to compare the leg extensor muscle strength, the postural stability, and the fear of falling in the women with severe knee joint osteoarthritis (OA) before and after a 2-month home exercise program (HEP). MATERIAL AND METHODS. In total, 17 women aged 46-72 years with late-stage knee joint OA scheduled for total knee arthroplasty participated in this study before and after the 2-month HEP with strengthening, stretching, balance, and step exercises. The isometric peak torque (PT) of the leg extensors and postural stability characteristics when standing on a firm or a foam surface for 30 seconds were recorded. The fear of falling and the pain intensity (VAS) were estimated. RESULTS. A significant increase in the PT and the PT-to-body weight (PT-to-BW) ratio of the involved leg as well as the bilateral PT and the PT-to-BW ratio was found after the 2-month HEP compared with the data before the HEP (P<0.05). The PT and the PT-to-BW ratio of the involved leg were significantly lower compared with the uninvolved leg before the HEP (P<0.05). The center of the pressure sway length (foam surface) decreased significantly after the HEP (P<0.05). Significant correlations were found between the PT of the involved leg and the bilateral PT and the fear of falling and between the PT of the involved leg and the postural sway (foam surface) before the HEP. CONCLUSIONS. After the 2-month HEP, the leg extensor muscle strength increased and the postural sway length on a foam surface decreased. The results indicate that the increased leg extensor muscle strength improves postural stability and diminishes the fear of falling in women with late-stage knee joint OA.

Engaging youth in food activism in New York City: lessons learned from a youth organization, health department, and university partnership.

PubMed

Tsui, Emma; Bylander, Kim; Cho, Milyoung; Maybank, Aletha; Freudenberg, Nicholas

2012-10-01

Research indicates that insufficient emphasis on community collaboration and partnership can thwart innovative community-driven work on the social determinants of health by local health departments. Appreciating the importance of enhancing community participation, the New York City Department of Health and Mental Hygiene (DOHMH) helped lead the development of the Health Equity Project (HEP), an intervention aimed at increasing the capacity of urban youth to identify and take action to reduce food-related health disparities. DOHMH partnered with the City University of New York School of Public Health and several local youth organizations to design and implement the intervention. HEP was conducted with 373 young people in 17 cohorts at 14 unique sites: six in Brooklyn, six in the Bronx, and two in Harlem. Partnered youth organizations hosted three stages of work: interactive workshops on neighborhood health disparities, food environments, and health outcomes; food-focused research projects conducted by youth; and small-scale action projects designed to change local food environments. Through these activities, HEP appears to have been successful in introducing youth to the social, economic, and political factors that shape food environments and to the influence of food on health outcomes. The intervention was also somewhat successful in providing youth with community-based participatory research skills and engaging them in documenting and then acting to change their neighborhood food environments. In the short term, we are unable to assess how successful HEP has been in building young leaders who will continue to engage in this kind of activism, but we suspect that more extended interactions would be needed to achieve this more ambitious goal. Experiences at these sites suggest that youth organizations with a demonstrated capacity to engage youth in community service or activism and a commitment to improving food or other health-promoting community resources make the most suitable and successful partners for this kind of effort.

The Escherichia coli Subtilase Cytotoxin A Subunit Specifically Cleaves Cell-surface GRP78 Protein and Abolishes COOH-terminal-dependent Signaling

PubMed Central

Ray, Rupa; de Ridder, Gustaaf G.; Eu, Jerry P.; Paton, Adrienne W.; Paton, James C.; Pizzo, Salvatore V.

2012-01-01

GRP78, a molecular chaperone with critical endoplasmic reticulum functions, is aberrantly expressed on the surface of cancer cells, including prostate and melanoma. Here it functions as a pro-proliferative and anti-apoptotic signaling receptor via NH2-terminal domain ligation. Auto-antibodies to this domain may appear in cancer patient serum where they are a poor prognostic indicator. Conversely, GRP78 COOH-terminal domain ligation is pro-apoptotic and anti-proliferative. There is no method to disrupt cell-surface GRP78 without compromising the total GRP78 pool, making it difficult to study cell-surface GRP78 function. We studied six cell lines representing three cancer types. One cell line per group expresses high levels of cell-surface GRP78, and the other expresses low levels (human hepatoma: Hep3B and HepG2; human prostate cancer: PC3 and 1-LN; murine melanoma: B16F0 and B16F1). We investigated the effect of Escherichia coli subtilase cytoxin catalytic subunit (SubA) on GRP78. We report that SubA specifically cleaves cell-surface GRP78 on HepG2, 1-LN, and B16F1 cells without affecting intracellular GRP78. B16F0 cells (GRP78low) have lower amounts of cleaved cell-surface GRP78. SubA has no effect on Hep3B and PC3 cells. The predicted 28-kDa GRP78 COOH-terminal fragment is released into the culture medium by SubA treatment, and COOH-terminal domain signal transduction is abrogated, whereas pro-proliferative signaling mediated through NH2-terminal domain ligation is unaffected. These experiments clarify cell-surface GRP78 topology and demonstrate that the COOH-terminal domain is necessary for pro-apoptotic signal transduction occurring upon COOH-terminal antibody ligation. SubA is a powerful tool to specifically probe the functions of cell-surface GRP78. PMID:22851173

The Escherichia coli subtilase cytotoxin A subunit specifically cleaves cell-surface GRP78 protein and abolishes COOH-terminal-dependent signaling.

PubMed

Ray, Rupa; de Ridder, Gustaaf G; Eu, Jerry P; Paton, Adrienne W; Paton, James C; Pizzo, Salvatore V

2012-09-21

GRP78, a molecular chaperone with critical endoplasmic reticulum functions, is aberrantly expressed on the surface of cancer cells, including prostate and melanoma. Here it functions as a pro-proliferative and anti-apoptotic signaling receptor via NH(2)-terminal domain ligation. Auto-antibodies to this domain may appear in cancer patient serum where they are a poor prognostic indicator. Conversely, GRP78 COOH-terminal domain ligation is pro-apoptotic and anti-proliferative. There is no method to disrupt cell-surface GRP78 without compromising the total GRP78 pool, making it difficult to study cell-surface GRP78 function. We studied six cell lines representing three cancer types. One cell line per group expresses high levels of cell-surface GRP78, and the other expresses low levels (human hepatoma: Hep3B and HepG2; human prostate cancer: PC3 and 1-LN; murine melanoma: B16F0 and B16F1). We investigated the effect of Escherichia coli subtilase cytoxin catalytic subunit (SubA) on GRP78. We report that SubA specifically cleaves cell-surface GRP78 on HepG2, 1-LN, and B16F1 cells without affecting intracellular GRP78. B16F0 cells (GRP78(low)) have lower amounts of cleaved cell-surface GRP78. SubA has no effect on Hep3B and PC3 cells. The predicted 28-kDa GRP78 COOH-terminal fragment is released into the culture medium by SubA treatment, and COOH-terminal domain signal transduction is abrogated, whereas pro-proliferative signaling mediated through NH(2)-terminal domain ligation is unaffected. These experiments clarify cell-surface GRP78 topology and demonstrate that the COOH-terminal domain is necessary for pro-apoptotic signal transduction occurring upon COOH-terminal antibody ligation. SubA is a powerful tool to specifically probe the functions of cell-surface GRP78.

Predictors of parents' adherence to home exercise programs for children with developmental disabilities, regarding both exercise frequency and duration: a survey design.

PubMed

Medina-Mirapeix, Francesc; Lillo-Navarro, Carmen; Montilla-Herrador, Joaquina; Gacto-Sánchez, Mariano; Franco-Sierra, María Á; Escolar-Reina, Pilar

2017-08-01

Many families have problems adhering to home exercise programs (HEP) for children with developmental disabilities. However, parental participation in HEP is known to have a positive effect on child-related outcome variables, as well as on parental functioning. This study examined whether the different behaviours of health professionals, and the behaviour and social characteristics of parents determine rates of parental adherence to both the frequency per week, and duration per session, of HEP for children with developmental disabilities attending paediatric services in early intervention centres. In this study, developmental disabilities include those caused by developmental delay or specific health conditions such as cerebral palsy, congenital illness, or others. Survey. Eighteen early intervention centers. Parents of children with developmental disabilities receiving HEP. A self-reported questionnaire was used to examine: whether frequency and duration of weekly exercise sessions was prescribed by physiotherapists; whether the child had received the HEP according to what was prescribed; and items related to the individual, social support, illnesses and the involvement of the health professional. Multiple logistic regression analyses examined their relative relevance. In this study 219 parents participated. The rate of adherence to the prescribed frequency and duration of the HEP was similar (61.4-57.2%). The probability of adherence to both components increased for parents who had a low perception of the existence of barriers for integrating the exercises into their daily routine (OR=2.62 and 4.83). Furthermore, other cognitive factors of parents had a variable influence. The involvement of the professional had a significant impact regarding the frequency of the HEP. Professional involvement increased the probability of exercises being followed accurately by adopting strategies such as: providing information about the progress and evolution of the exercises (OR=3.75); justifying their usefulness (OR=2.17); giving advice on how to include them into the daily routine (OR=2.54); checking skills during follow-up (OR=2.21) and asking about home adherence (OR=2.20). Providing information during clinical encounters, advising how to include exercises into the daily routine, and checking skills and adherence during follow-up represent practical targets for clinicians aiming to improve the frequency of HEP for children with developmental disabilities. This study contributes to the knowledge of physicians and therapists regarding how their interventions (in particular, information, instructions for HEP and follow-up) influence parents regarding their adherence to HEP.

Characterizing the Role of Hep27 in Liver and Colorectal Cancer Stress Tolerance

DTIC Science & Technology

2018-01-01

hepatocellular carcinoma, and its high expression correlates with decreased survival in colon cancers. It was hypothesized that Hep27 overexpression is a...Hep27, is overexpressed in hepatocellular carcinoma, and its high expression correlates with decreased survival in colon cancers. I hypothesize that...text. Examples include original copies of journal articles, reprints of manuscripts and abstracts, a curriculum vitae, patent applications, study questionnaires, and surveys , etc. 15 Nothing to report.

Silencing of cytosolic NADP+-dependent isocitrate dehydrogenase gene enhances ethanol-induced toxicity in HepG2 cells.

PubMed

Yang, Eun Sun; Lee, Su-Min; Park, Jeen-Woo

2010-07-01

It has been shown that acute and chronic alcohol administrations increase the production of reactive oxygen species, lower cellular antioxidant levels and enhance oxidative stress in many tissues. We recently reported that cytosolic NADP(+)-dependent isocitrate dehydrogenase (IDPc) functions as an antioxidant enzyme by supplying NADPH to the cytosol. Upon exposure to ethanol, IDPc was susceptible to the loss of its enzyme activity in HepG2 cells. Transfection of HepG2 cells with an IDPc small interfering RNA noticeably downregulated IDPc and enhanced the cells' vulnerability to ethanol-induced cytotoxicity. Our results suggest that suppressing the expression of IDPc enhances ethanol-induced toxicity in HepG2 cells by further disruption of the cellular redox status.

Simulation of LHC events on a millions threads

NASA Astrophysics Data System (ADS)

Childers, J. T.; Uram, T. D.; LeCompte, T. J.; Papka, M. E.; Benjamin, D. P.

2015-12-01

Demand for Grid resources is expected to double during LHC Run II as compared to Run I; the capacity of the Grid, however, will not double. The HEP community must consider how to bridge this computing gap by targeting larger compute resources and using the available compute resources as efficiently as possible. Argonne's Mira, the fifth fastest supercomputer in the world, can run roughly five times the number of parallel processes that the ATLAS experiment typically uses on the Grid. We ported Alpgen, a serial x86 code, to run as a parallel application under MPI on the Blue Gene/Q architecture. By analysis of the Alpgen code, we reduced the memory footprint to allow running 64 threads per node, utilizing the four hardware threads available per core on the PowerPC A2 processor. Event generation and unweighting, typically run as independent serial phases, are coupled together in a single job in this scenario, reducing intermediate writes to the filesystem. By these optimizations, we have successfully run LHC proton-proton physics event generation at the scale of a million threads, filling two-thirds of Mira.

Intrusion Prevention and Detection in Grid Computing - The ALICE Case

NASA Astrophysics Data System (ADS)

Gomez, Andres; Lara, Camilo; Kebschull, Udo

2015-12-01

Grids allow users flexible on-demand usage of computing resources through remote communication networks. A remarkable example of a Grid in High Energy Physics (HEP) research is used in the ALICE experiment at European Organization for Nuclear Research CERN. Physicists can submit jobs used to process the huge amount of particle collision data produced by the Large Hadron Collider (LHC). Grids face complex security challenges. They are interesting targets for attackers seeking for huge computational resources. Since users can execute arbitrary code in the worker nodes on the Grid sites, special care should be put in this environment. Automatic tools to harden and monitor this scenario are required. Currently, there is no integrated solution for such requirement. This paper describes a new security framework to allow execution of job payloads in a sandboxed context. It also allows process behavior monitoring to detect intrusions, even when new attack methods or zero day vulnerabilities are exploited, by a Machine Learning approach. We plan to implement the proposed framework as a software prototype that will be tested as a component of the ALICE Grid middleware.

Habitat Evaluation Procedure (HEP) Report for the Pend Oreille Wetlands Wildlife II Project, Technical Report 2002.

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

Holmes, Darren

The Habitat Evaluation Procedure (HEP), developed in 1980 by the U.S. Fish and Wildlife Service (USFWS 1980a, USFWS 1980b), uses a habitat/species based approach to assessing project impacts, and is a convenient tool to document the predicted effects of proposed management actions. The Northwest Power Planning Council (NPPC) endorsed the use of HEP in its Columbia River Basin Fish and Wildlife Program to evaluate wildlife benefits and impacts associated with the development and operation of the federal Columbia River Basin hydroelectric system (NPPC 1994). The Albeni Falls Interagency Work Group (AFIWG) used HEP in 1987 to evaluate wildlife habitat lossesmore » attributed to the Albeni Falls hydroelectric facility (Martin et al. 1988). In 1992, the AFIWG (Idaho Department of Fish and Game; Kalispel, Coeur d'Alene, and Kootenai Tribes) began implementing activities to mitigate these losses. Implementation activities include protecting, restoring and enhancing wildlife habitat. HEPs are used extensively within the NPPC's Columbia River Basin Fish and Wildlife Program. Wildlife managers use HEP to determine habitat lost from the construction of the federal hydroelectric projects and habitat gained through NPPC mitigation program. Habitat Suitability Index (HSI) models for each of the seven target species are used to determine habitat quality and quantity losses for representative habitat cover types for this project. Target species include Bald Eagle, black-capped chickadee, Canada goose, mallard, muskrat, white-tailed deer and yellow warbler. In 2002, a HEP team determined the habitat condition of the 164-acre Pend Oreille Wetlands Wildlife II Project (Figure 1). The HEP team consisted of the following members and agencies: Roy Finley, Kalispel Natural Resource Department (KNRD); Neil Lockwood, KNRD; Brian Merson, KNRD; Sonny Finley, KNRD; Darren Holmes, KNRD; Anna, Washington Dept. of Fish and Game (WDFW); and Scott, WDFW. Baseline Habitat Units (HU) will be credited to Bonneville Power Administration (BPA) for protection of habitats within the project area. The HSI models used were identical to those modified for use in 1991 (Appendix 2). The objective of using HEP as an assessment tool is two-fold. First, it provides an unbiased and measured assessment of wildlife habitats within the mitigation parcel. This data is used to offset the Albeni Falls Dam HU loss ledger. That ledger accounts for the loss of wildlife habitat that resulted from the construction and inundation of Albeni Falls hydroelectric project and the extent to which those losses have been mitigated. Additionally, the baseline HEP evaluation describes existing habitat conditions on the property and will be used, along with other tools, to determine initial management, restoration, and enhancement activities. HEP analyses will be completed every five years to quantitatively evaluate the effectiveness of management strategies in improving and maintaining habitat conditions while providing additional HU crediting to BPA for enhanced habitat values.« less

Habitat Evaluation Procedure (HEP) Report for the Pend Oreille Wetlands Wildlife Project, Technical Report 2002.

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

Holmes, Darren

The Habitat Evaluation Procedure (HEP), developed in 1980 by the U.S. Fish and Wildlife Service (USFWS 1980a, USFWS 1980b), uses a habitat/species based approach to assessing project impacts, and is a convenient tool to document the predicted effects of proposed management actions. The Northwest Power Planning Council (NPPC) endorsed the use of HEP in its Columbia River Basin Fish and Wildlife Program to evaluate wildlife benefits and impacts associated with the development and operation of the federal Columbia River Basin hydroelectric system (NPPC 1994). The Albeni Falls Interagency Work Group (AFIWG) used HEP in 1987 to evaluate wildlife habitat lossesmore » attributed to the Albeni Falls hydroelectric facility (Martin et al. 1988). In 1992, the AFIWG (Idaho Department of Fish and Game; Kalispel, Coeur d'Alene, and Kootenai Tribes) began implementing activities to mitigate these losses. Implementation activities include protecting, restoring and enhancing wildlife habitat. HEPs are used extensively within the NPPC's Columbia River Basin Fish and Wildlife Program. Wildlife managers use HEP to determine habitat lost from the construction of the federal hydroelectric projects and habitat gained through NPPC mitigation program. Habitat Suitability Index (HSI) models for each of the seven target species are used to determine habitat quality and quantity losses for representative habitat cover types for this project. Target species include Bald Eagle, black-capped chickadee, Canada goose, mallard, muskrat, white-tailed deer and yellow warbler. In 2002, a HEP team determined the habitat condition of the 436-acre Pend Oreille Wetlands Wildlife Project (Figure 1). The HEP team consisted of the following members and agencies: Roy Finley, Kalispel Natural Resource Department (KNRD); Neil Lockwood, KNRD; Brian Merson, KNRD; Sonny Finley, KNRD; Darren Holmes, KNRD; Anna, Washington Dept. of Fish and Game (WDFW); and Scott, WDFW. Baseline Habitat Units (HU) will be credited to Bonneville Power Administration (BPA) for protection of habitats within the project area. The HSI models used were identical to those modified for use in 1991 (Attachment A). The objective of using HEP as an assessment tool is two-fold. First, it provides an unbiased and measured assessment of wildlife habitats within the mitigation parcel. This data is used to offset the Albeni Falls Dam HU loss ledger. That ledger accounts for the loss of wildlife habitat that resulted from the construction and inundation of Albeni Falls hydroelectric project and the extent to which those losses have been mitigated. Additionally, the baseline HEP evaluation describes existing habitat conditions on the property and will be used, along with other tools, to determine initial management, restoration, and enhancement activities. HEP analyses will be completed every five years to quantitatively evaluate the effectiveness of management strategies in improving and maintaining habitat conditions while providing additional HU crediting to BPA for enhanced habitat values.« less

Nicotinamide riboside attenuates alcohol induced liver injuries via activation of SirT1/PGC-1α/mitochondrial biosynthesis pathway.

PubMed

Wang, Sufan; Wan, Ting; Ye, Mingtong; Qiu, Yun; Pei, Lei; Jiang, Rui; Pang, Nengzhi; Huang, Yuanling; Liang, Baoxia; Ling, Wenhua; Lin, Xiaojun; Zhang, Zhenfeng; Yang, Lili

2018-07-01

Nicotinamide riboside (NR) is a nicotinamide adenine dinucleotide (NAD + ) precursor which is present in foods such as milk and beer. It was reported that NR can prevent obesity, increase longevity, and promote liver regeneration. However, whether NR can prevent ethanol-induced liver injuries is not known. This study aimed to explore the effect of NR on ethanol induced liver injuries and the underlying mechanisms. We fed C57BL/6 J mice with Lieber-DeCarli ethanol liquid diet with or without 400 mg/kg·bw NR for 16 days. Liver injuries and SirT1-PGC-1α-mitochondrial function were analyzed. In in vitro experiments, HepG2 cells (CYP2E1 over-expressing cells) were incubated with ethanol ± 0.5 mmol/L NR. Lipid accumulation and mitochondrial function were compared. SirT1 knockdown in HepG2 cells were further applied to confirm the role of SirT1 in the protection of NR on lipid accumulation. We found that ethanol significantly decreased the expression and activity of hepatic SirT1 and induced abnormal expression of enzymes of lipid metabolism in mice. Both in vivo and in vitro experiments showed that NR activated SirT1 through increasing NAD + levels, decreased oxidative stress, increased deacetylation of PGC-1α and mitochondrial function. In SirT1 knockdown HepG2 cells, NR lost its ability in enhancing mitochondrial function, and its protection against lipid accumulation induced by ethanol. NR can protect against ethanol induced liver injuries via replenishing NAD + , reducing oxidative stress, and activating SirT1-PGC-1α-mitochondrial biosynthesis. Our data indicate that SirT1 plays an important role in the protection of NR against lipid accumulation and mitochondrial dysfunctions induced by ethanol. Copyright © 2018 The Authors. Published by Elsevier B.V. All rights reserved.

Total alkaloids of Rubus aleaefolius Poir inhibit hepatocellular carcinoma growth in vivo and in vitro via activation of mitochondrial-dependent apoptosis.

PubMed

Zhao, Jinyan; Chen, Xuzheng; Lin, Wei; Wu, Guangwen; Zhuang, Qunchuan; Zhong, Xiaoyong; Hong, Zhenfeng; Peng, Jun

2013-03-01

The aim of this study was to evaluate the therapeutic efficacy of Rubus aleaefolius Poir total alkaloids (TARAP) against hepatocellular carcinoma growth in vivo and in vitro, and to investigate the possible molecular mechanisms mediating its biological activity. Nude mice were implanted with HepG2 human hepatocellular carcinoma cells and fed with vehicle (physiological saline) or 3 g/kg/d dose of TARAP, 5 days per week, for 21 days. The in vivo efficacy of TARAP against tumor growth was investigated by evaluating its effect on tumor volume and tumor weight in mice with HCC xenografts and its adverse effect was determined by measuring the body weight gain. The in vitro effect of TARAP on the viability of HepG2 cells was determined by MTT assay. HepG2 cell morphology was observed via phase-contrast microscopy. Apoptosis in tumor tissues or in HepG2 cells was analyzed by TUNEL assay or FACS analysis with Annexin V/PI, respectively. The loss of mitochondrial membrane potential in HepG2 cells was determined via JC-1 staining followed by FACS analysis. Activation of caspase-9 and -3 in HepG2 cells was examined by a colorimetric assay. The mRNA and protein expression of Bcl-2 and Bax in tumor tissues were measured by RT-PCR and immunohistochemistry. TARAP reduced tumor volume and tumor weight, but had no effect on the body weight gain in HCC mice. TARAP decreased the viability of HepG2 cells and induced cell morphological changes in vitro in a dose- and time-dependent manner. In addition, TARAP induced apoptosis both in tumor tissues and in HepG2 cells. Moreover, TARAP treatment resulted in the collapse of mitochondrial membrane potential in HepG2 cells, as well as the activation of caspase-9 and -3. Furthermore, administration of TARAP increased the pro-apoptotic Bax/Bcl-2 ratio in HCC mouse tumors, at both transcriptional and translational levels. TARAP inhibits hepatocellular carcinoma growth both in vivo and in vitro probably through the activation of mitochondrial-dependent apoptosis, which may, in part, explain its anticancer activity. These results suggest that total alkaloids in Rubus aleaefolius Poir may be a potential novel therapeutic agent for the treatment of hepatocellular carcinoma and other cancers.

[Puerariae Lobatae Radix elevated expression levels of OB-R, IRS2, GLUT1 and GLUT2 to regulate glucose metabolism in insulin-resistance HepG2 cells].

PubMed

Li, Yu; Luo, Xin-Xin; Yan, Feng-Dong; Wei, Zhang-Bin; Tu, Jun

2017-05-01

To observe the anti-hyperglycemic effect of Puerariae Lobatae Radix in hepatocyte insulin resistance(IR) models, and investigate its preliminary molecular mechanism. IR-HepG2 cell model was stably established with 1×10-9 mol•L⁻¹ insulin plus 3.75×10-6 mol•L-1 dexamethasone treatment for 48 h according to optimized protocol in our research group. After IR-HepG2 cells were treated with different concentrations(5%,10% and 15%) of Puerariae Lobatae Radix-containing serum, cell viability was detected by CCK-8 assay; the glucose consumptions in IR-HepG2 cells were separately detected at different time points (12, 15, 18, 21, 24, 30, 36 h) by using glucose oxidase method; intracellular glycogen content was detected by anthrone method; and the protein expression levels of leptin receptor (Ob-R), insulin receptor substrate-2 (IRS2), glucose transporter 1(GLUT1) and GLUT2 were detected by Western blot assay. The results showed that Puerariae Lobatae Radix-containing serum (5%, 10% and 15%) had no significant effect on IR-HepG2 cell viability; 5% and 10% Puerariae Lobatae Radix-containing serum significantly increased glucose consumption of IR-HepG2 cells (P<0.01) at 18, 21 and 24 h; 15% Puerariae Lobatae Radix-containing serum elevated the glucose consumption of IR-HepG2 cells at 15 h (P<0.05), and significantly elevated the glucose consumption at 18, 21, 24 and 30 h (P<0.01) in a dose-dependent manner. The optimized time of anti-hyperglycemic effect was defined as 24 h, and further study showed that Puerariae Lobatae Radix-containing serum could increase intracellular glycogen content after 24 h treatment (P<0.01), and up-regulate IRS2, Ob-R, GLUT1 and GLUT2 protein expression levels. Our results indicated that Puerariae Lobatae Radix-containing serum could achieve the anti-hyperglycemic effect through important PI3K/PDK signaling pathway partially by up-regulating the expression levels of Ob-R and IRS2, GLUT1 and GLUT2 in IR-HepG2 cells, accelerating the glucose transport into hepatocytes and increasing hepatic glycogen synthesis to enhance the anti-hyperglycemic effect of IR-HepG2 cells. Copyright© by the Chinese Pharmaceutical Association.

The anti-tumour activity of rLj-RGD4, an RGD toxin protein from Lampetra japonica, on human laryngeal squamous carcinoma Hep-2 cells in nude mice.

PubMed

Shao, Fangyu; Lv, Mei; Zheng, Yuanyuan; Jiang, Junshu; Wang, Yue; Lv, Li; Wang, Jihong

2015-12-01

The objective of this study is to investigate the antiproliferative activity and mechanism of integrin-binding rLj-RGD4 in a Hep-2 human laryngeal carcinoma-bearing nude mouse model. Human laryngeal squamous carcinoma cells (Hep-2) were inoculated subcutaneously into the axilla of nude mice to generate a Hep-2 human laryngeal carcinoma-bearing nude mouse model. When the Hep-2 xenograft model was successfully established, the animals were randomly separated into five groups. Three groups were treated with different dosages of rLj-RGD4. Cisplatin was administered to the positive control group, and normal saline (NaCl) was administered to the negative control group for 3 weeks. The body weights and the survival of the nude mice were evaluated, and the volumes and weights of the solid tumours were measured. The mechanism underlying rLj-RGD4 inhibition of tumour growth in transplanted Hep-2 human laryngeal carcinoma-bearing nude mice was evaluated by haematoxylin-eosin (HE) staining, terminal deoxynucleotidyl transferase-mediated dUTP-biotin nick end labelling (TUNEL), measurement of intratumoural microvessel density (MVD), Western blotting, and quantitative reverse transcription-polymerase chain reaction (qRT-PCR). The tumour volumes and weights of the treatment groups were reduced compared with the model group, and survival times were improved by rLj-RGD4 treatment in Hep-2 human laryngeal carcinoma-bearing nude mice. The number of apoptotic Hep-2 human cells and intratumoural MVD significantly decreased after the administration of rLj-RGD4. In the xenograft tissue of animals treated with rLj-RGD4, FAK, PI3K, and Akt expression was unaltered, whereas P-FAK, P-PI3K, Bcl-2, P-Akt, and VEGF levels were down-regulated. In addition, activated caspase-3, activated caspase-9, and Bax levels were up-regulated. rLj-RGD4 exhibits potent in vivo activity and inhibits the growth of transplanted Hep-2 human laryngeal carcinoma cells in a nude mouse model. Thus, these results indicate that the recombinant RGD toxin protein rLj-RGD4 may serve as a potent clinical therapy for human laryngeal squamous carcinoma. Copyright © 2015 Elsevier B.V. and Société Française de Biochimie et Biologie Moléculaire (SFBBM). All rights reserved.

Modeling techniques and fluorescence imaging investigation of the interactions of an anthraquinone derivative with HSA and ctDNA

NASA Astrophysics Data System (ADS)

Fu, Zheng; Cui, Yanrui; Cui, Fengling; Zhang, Guisheng

2016-01-01

A new anthraquinone derivative (AORha) was synthesized. Its interactions with human serum albumin (HSA) and calf thymus DNA (ctDNA) were investigated by fluorescence spectroscopy, UV-visible absorption spectroscopy and molecular modeling. Cell viability assay and cell imaging experiment were performed using cervical cancer cells (HepG2 cells). The fluorescence results revealed that the quenching mechanism was static quenching. At different temperatures (290, 300, 310 K), the binding constants (K) and the number of binding sites (n) were determined, respectively. The positive ΔH and ΔS values showed that the binding of AORha with HSA was hydrophobic force, which was identical with the molecular docking result. Studying the fluorescence spectra, UV spectra and molecular modeling also verified that the binding mode of AORha and ctDNA might be intercalative. When HepG2 cells were treated with AORha, the fluorescence became brighter and turned green, which could be used for bioimaging.

Modeling techniques and fluorescence imaging investigation of the interactions of an anthraquinone derivative with HSA and ctDNA.

PubMed

Fu, Zheng; Cui, Yanrui; Cui, Fengling; Zhang, Guisheng

2016-01-15

A new anthraquinone derivative (AORha) was synthesized. Its interactions with human serum albumin (HSA) and calf thymus DNA (ctDNA) were investigated by fluorescence spectroscopy, UV-visible absorption spectroscopy and molecular modeling. Cell viability assay and cell imaging experiment were performed using cervical cancer cells (HepG2 cells). The fluorescence results revealed that the quenching mechanism was static quenching. At different temperatures (290, 300, 310 K), the binding constants (K) and the number of binding sites (n) were determined, respectively. The positive ΔH and ΔS values showed that the binding of AORha with HSA was hydrophobic force, which was identical with the molecular docking result. Studying the fluorescence spectra, UV spectra and molecular modeling also verified that the binding mode of AORha and ctDNA might be intercalative. When HepG2 cells were treated with AORha, the fluorescence became brighter and turned green, which could be used for bioimaging. Copyright © 2015 Elsevier B.V. All rights reserved.

On the Relevancy of Efficient, Integrated Computer and Network Monitoring in HEP Distributed Online Environment

NASA Astrophysics Data System (ADS)

Carvalho, D.; Gavillet, Ph.; Delgado, V.; Albert, J. N.; Bellas, N.; Javello, J.; Miere, Y.; Ruffinoni, D.; Smith, G.

Large Scientific Equipments are controlled by Computer Systems whose complexity is growing driven, on the one hand by the volume and variety of the information, its distributed nature, the sophistication of its treatment and, on the other hand by the fast evolution of the computer and network market. Some people call them genetically Large-Scale Distributed Data Intensive Information Systems or Distributed Computer Control Systems (DCCS) for those systems dealing more with real time control. Taking advantage of (or forced by) the distributed architecture, the tasks are more and more often implemented as Client-Server applications. In this framework the monitoring of the computer nodes, the communications network and the applications becomes of primary importance for ensuring the safe running and guaranteed performance of the system. With the future generation of HEP experiments, such as those at the LHC in view, it is proposed to integrate the various functions of DCCS monitoring into one general purpose Multi-layer System.

Analysis and comparison of oxygen consumption of HepG2 cells in a monolayer and three-dimensional high density cell culture by use of a matrigrid®.

PubMed

Weise, Frank; Fernekorn, Uta; Hampl, Jörg; Klett, Maren; Schober, Andreas

2013-09-01

By the use of a MatriGrid® we have established a three-dimensional high density cell culture. The MatriGrid® is a culture medium permeable, polymeric scaffold with 187 microcavities. In these cavities (300 μm diameter and 207 μm deep) the cells can growth three-dimensionally. For these experiments we measured the oxygen consumption of HepG2 cell cultures in order to optimize cultivation conditions. We measured and compared the oxygen consumption, growth rate and vitality under three different cultivation conditions: monolayer, three-dimensional static and three-dimensional actively perfused. The results show that the cells in a three-dimensional cell culture consume less oxygen as in a monolayer cell culture and that the actively perfused three-dimensional cell culture in the MatriGrid® has a similar growth rate and vitality as the monolayer culture. Copyright © 2013 Wiley Periodicals, Inc.

Optimization of enzyme-assisted extraction and characterization of polysaccharides from Hericium erinaceus.

PubMed

Zhu, Yang; Li, Qian; Mao, Guanghua; Zou, Ye; Feng, Weiwei; Zheng, Daheng; Wang, Wei; Zhou, Lulu; Zhang, Tianxiu; Yang, Jun; Yang, Liuqing; Wu, Xiangyang

2014-01-30

The enzyme-assisted extraction (EAE) of polysaccharides from the fruits of Hericium erinaceus was studied. In this study, response surface methodology and the Box-Behnken design based on single-factor and orthogonal experiments were applied to optimize the EAE conditions. The optimal extraction conditions were as follows: a pH of 5.71, a temperature of 52.03°C and a time of 33.79 min. The optimal extraction conditions resulted in the highest H. erinaceus polysaccharides (HEP) yield, with a value 13.46 ± 0.37%, which represented an increase of 67.72% compared to hot water extraction (HWE). The polysaccharides were characterized by FT-IR, SEM, CD, AFM, and GC. The results showed that HEP was composed of mannose, glucose, xylose, and galactose in a molar ratio of 15.16:5.55:4.21:1. The functional groups of the H. erinaceus polysaccharides extracted by HWE and EAE were fundamentally identical but had apparent conformational changes. Copyright © 2013 Elsevier Ltd. All rights reserved.

HEP Computing

Science.gov Websites

Argonne National Laboratory HEP Laptop Computing Problem Report Service Request Password Help New on ANL Exchange: See section for your OS Printing Available Software for Download VPN: Virtual

Melatonin-induced increase in sensitivity of human hepatocellular carcinoma cells to sorafenib is associated with reactive oxygen species production and mitophagy

PubMed Central

Prieto-Domínguez, Néstor; Ordóñez, Raquel; Fernández, Anna; Méndez-Blanco, Carolina; Baulies, Anna; Garcia-Ruiz, Carmen; Fernández-Checa, José C.; Mauriz, José L.; González-Gallego, Javier

2016-01-01

Effects of sorafenib in hepatocellular carcinoma (HCC) are frequently transient due to tumor-acquired resistance, a phenotype that could be targeted by other molecules to reduce this adaptive response. Because melatonin is known to exert antitumor effects in HCC cells, this study investigated whether and how melatonin reduces resistance to sorafenib. Susceptibility to sorafenib (10 nM to 50 μM) in the presence of melatonin (1 and 2 mM) was assessed in HCC cell lines HepG2, HuH7 and Hep3B. Cell viability was reduced by sorafenib from 1 μM in HepG2 or HuH7 cells, and 2.5 μM in Hep3B cells. Co-administration of melatonin and sorafenib exhibited a synergistic cytotoxic effect on HepG2 and HuH7 cells, while Hep3B cells displayed susceptibility to doses of sorafenib that had no effect when administrated alone. Co-administration of 2.5 μM sorafenib and 1 mM melatonin induced apoptosis in Hep3B cells, increasing PARP hydrolysis and BAX expression. We also observed an early colocalization of mitochondria with lysosomes, correlating with the expression of mitophagy markers PINK1 and Parkin and a reduction of mitofusin-2 and mtDNA compared with sorafenib administration alone. Moreover, increased reactive oxygen species production and mitochondrial membrane depolarization were elicited by drug combination, suggesting their contribution to mitophagy induction. Interestingly, Parkin silencing by siRNA to impair mitophagy significantly reduced cell killing, PARP cleavage and BAX expression. These results demonstrate that the pro-oxidant capacity of melatonin and its impact on mitochondria stability and turnover via mitophagy increase sensitivity to the cytotoxic effect of sorafenib. PMID:27484637

Performance evaluation of the HepB Typer-Entecavir kit for detection of entecavir resistance mutations in chronic hepatitis B

PubMed Central

Ahn, Sang Hoon; Chun, Ji-Yong; Shin, Soo-Kyung; Park, Jun Yong; Yoo, Wangdon; Hong, Sun Pyo; Han, Kwang-Hyub

2013-01-01

Background/Aims Molecular diagnostic methods have enabled the rapid diagnosis of drug-resistant mutations in hepatitis B virus (HBV) and have reduced both unnecessary therapeutic interventions and medical costs. In this study we evaluated the analytical and clinical performances of the HepB Typer-Entecavir kit (GeneMatrix, Korea) in detecting entecavir-resistance-associated mutations. Methods The HepB Typer-Entecavir kit was evaluated for its limit of detection, interference, cross-reactivity, and precision using HBV reference standards made by diluting high-titer viral stocks in HBV-negative human serum. The performance of the HepB Typer-Entecavir kit for detecting mutations related to entecavir resistance was compared with direct sequencing for 396 clinical samples from 108 patients. Results Using the reference standards, the detection limit of the HepB Typer-Entecavir kit was found to be as low as 500 copies/mL. No cross-reactivity was observed, and elevated levels of various interfering substances did not adversely affect its analytical performance. The precision test conducted by repetitive analysis of 2,400 replicates with reference standards at various concentrations showed 99.9% agreement (2398/2400). The overall concordance rate between the HepB Typer-Entecavir kit and direct sequencing assays in 396 clinical samples was 99.5%. Conclusions The HepB Typer-Entecavir kit showed high reliability and precision, and comparable sensitivity and specificity for detecting mutant virus populations in reference and clinical samples in comparison with direct sequencing. Therefore, this assay would be clinically useful in the diagnosis of entecavir-resistance-associated mutations in chronic hepatitis B. PMID:24459645

20(S)-Protopanaxadiol induces apoptosis in human hepatoblastoma HepG2 cells by downregulating the protein kinase B signaling pathway.

PubMed

Lu, Zeyuan; Xu, Huali; Yu, Xiaofeng; Wang, Yuchen; Huang, Long; Jin, Xin; Sui, Dayun

2018-02-01

Hepatoblastoma is the most common primary liver tumor for children aged <5 years old. 20(S)-Protopanaxadiol (PPD) is a ginsenoside extracted from Pananx quinquefolium L ., which inhibits tumor growth in several cancer cell lines. The purpose of the present study was to assess the anticancer activities of 20(S)-PPD in human hepatoblastoma HepG2 cells. The cytotoxicity of 20(S)-PPD on HepG2 cells was evaluated using an MTT assay. Apoptosis was detected using DAPI staining and flow cytometry. The expression of apoptosis-associated proteins was identified by western blotting. The results demonstrated that 20(S)-PPD inhibited the viability of HepG2 cell in a dose and time-dependent manner. The IC 50 values were 81.35, 73.5, 48.79 µM at 24, 48 and 72 h, respectively. Topical morphological changes of apoptotic body formation following 20(S)-PPD treatment were detected by DAPI staining. The percentage of Annexin V-fluoroscein isothyiocyanate positive cells were 3.73, 17.61, 23.44 and 65.43% in HepG2 cells treated with 0, 40, 50 and 60 µM of 20(S)-PPD, respectively. Furthermore, 20(S)-PPD upregulated the expression of Bax and downregulated the expression of Bcl-2 and also activated caspases-3 and -9, and Poly [ADP-ribose] polymerase cleavage. In addition, 20(S)-PPD inhibited the phosphorylation of protein kinase B (Akt; Ser473). The results indicate that 20(S)-PPD inhibits the viability of HepG2 cells and induces apoptosis in HepG2 cells by inhibiting the phosphoinositide-3-kinase/Akt pathway.

[Using the stable HSPA1A promoter-driven luciferase reporter HepG2 cells to assess the overall toxicity of coke oven emissions].

PubMed

Xin, Li-li; Li, Xiao-hai; Deng, Hua-xin; Kuang, Dan; Dai, Xia-yun; Huang, Su-Li; Wang, Feng; He, Mei-an; Currie, R William; Wu, Tang-chun

2012-12-01

Using the stable HSPA1A (HSP70-1) promoter-driven luciferase reporter HepG2 cells (HepG2/HSPA1A cells) to assess the overall toxicity of coke oven emissions. The stable HepG2/HSPA1A cells were treated with different concentrations of coke oven emissions (COEs) collected from the top, side, and bottom of a coke oven battery for 24 h. After the treatments, luciferase activity, cell viability, malondialdehyde (MDA) concentration, Olive tail moment, and micronuclei frequency were determined, respectively. The bottom COEs induced significant increases (P < 0.01) in relative luciferase activity up to 1.4 times the control level at 0.15 µg/L. The low dose of side COEs (0.02 µg/L) led to a significant increase (P < 0.01) in relative luciferase activity that progressively increased to 2.1 times the control level at 65.4 µg/L. The top COEs produced a strong dose-dependent induction of relative luciferase activity up to over 5 times the control level at the highest concentration tested (202 µg/L). In HepG2/HSPA1A cells treated with the bottom COEs, relative luciferase activity was positively correlated with MDA concentration (r = 0.404, P < 0.05). For the three COEs samples, positive correlations were observed between relative luciferase activity and Olive tail moment and micronuclei frequency. The relative luciferase activity in HepG2/HSPA1A cells can sensitively reflect the overall toxicity of COEs. The stable HepG2/HSPA1A cells can be used for rapid screening of the overall toxicity of complex air pollutants in the workplace.

Simultaneous Distinction of Monospecific and Mixed DFS70 Patterns During ANA Screening with a Novel HEp-2 ELITE/DFS70 Knockout Substrate

PubMed Central

Malyavantham, Kishore S.; Suresh, Lakshmanan

2018-01-01

Systemic autoimmune connective tissue disorders are characterized by circulating antinuclear antibodies (ANA). Although there are several technologies available for ANA screening, indirect immunofluorescence (IIF) using Human epithelial cells-2 (HEp-2) substrate remains the primary and recommended method because of its superior sensitivity. HEp-2 substrates can detect a multitude of patterns resulting from autoantibody binding to various protein and nucleic acid autoantigens distributed throughout the nucleus and cytoplasm of the cells. The great diversity of monospecific and mixed patterns resulting from positive reactions on HEp-2 substrate also complicate the interpretation and accuracy of reporting. One specific example which received utmost attention recently is the dense fine speckled 70 (DFS70) pattern resulting from autoantibodies that specifically bind to a protein called lens epithelium derived growth factor (LEDGF). Lack of clear association with a specific systemic autoimmune disease and high prevalence in healthy populations have made accurate interpretation of DFS70 pattern important. Accurate distinction of DFS70 pattern from disease-associated patterns using conventional HEp-2 substrate is challenging. Moreover, frequent co-occurrence of DFS70 pattern along with disease-associated patterns such as homogeneous, speckled, and mixed homogeneous-speckled patterns complicate the IIF interpretation. The goal of this paper is to demonstrate the utility of a novel engineered HEp-2 IIF substrate that retains all advantages of conventional HEp-2 substrate while simultaneously providing the ability to distinguish DFS70 pattern with high confidence in both monospecific and mixed ANA positive examples. The new substrate is further able to unmask disease-associated ANA patterns previously concealed by DFS70 pattern. PMID:29364249

Comparative analysis of 3D culture methods on human HepG2 cells.

PubMed

Luckert, Claudia; Schulz, Christina; Lehmann, Nadja; Thomas, Maria; Hofmann, Ute; Hammad, Seddik; Hengstler, Jan G; Braeuning, Albert; Lampen, Alfonso; Hessel, Stefanie

2017-01-01

Human primary hepatocytes represent a gold standard in in vitro liver research. Due to their low availability and high costs alternative liver cell models with comparable morphological and biochemical characteristics have come into focus. The human hepatocarcinoma cell line HepG2 is often used as a liver model for toxicity studies. However, under two-dimensional (2D) cultivation conditions the expression of xenobiotic-metabolizing enzymes and typical liver markers such as albumin is very low. Cultivation for 21 days in a three-dimensional (3D) Matrigel culture system has been reported to strongly increase the metabolic competence of HepG2 cells. In our present study we further compared HepG2 cell cultivation in three different 3D systems: collagen, Matrigel and Alvetex culture. Cell morphology, albumin secretion, cytochrome P450 monooxygenase enzyme activities, as well as gene expression of xenobiotic-metabolizing and liver-specific enzymes were analyzed after 3, 7, 14, and 21 days of cultivation. Our results show that the previously reported increase of metabolic competence of HepG2 cells is not primarily the result of 3D culture but a consequence of the duration of cultivation. HepG2 cells grown for 21 days in 2D monolayer exhibit comparable biochemical characteristics, CYP activities and gene expression patterns as all 3D culture systems used in our study. However, CYP activities did not reach the level of HepaRG cells. In conclusion, the increase of metabolic competence of the hepatocarcinoma cell line HepG2 is not due to 3D cultivation but rather a result of prolonged cultivation time.

CXC195 suppresses proliferation and inflammatory response in LPS-induced human hepatocellular carcinoma cells via regulating TLR4-MyD88-TAK1-mediated NF-κB and MAPK pathway

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

Wang, Yiting; Tu, Qunfei; Yan, Wei

Highlights: • CXC195 exhibited significant anti-proliferative effect and induced cell cycle arrest in LPS-induced HepG2 cells. • CXC195 suppressed the release of pro-inflammatory mediators in LPS-induced HepG2 cells. • CXC195 regulated TLR4-MyD88-TAK1-mediated NF-κB and MAPK pathway in LPS-induced HepG2 cells. - Abstract: CXC195 showed strong protective effects in neuronal apoptosis by exerting its antioxidant activity. However, the anti-cancer effects of CXC195 is still with limited acquaintance. Here, we investigated the role of CXC195 in lipopolysaccharide (LPS)-induced human hepatocellular carcinoma (HCC) cells lines (HepG2) and the possible signaling pathways. CXC195 exhibited significant anti-proliferative effect and induced cell cycle arrest in LPS-inducedmore » HepG2 cells. In addition, CXC195 suppressed the release of pro-inflammatory mediators in LPS-induced HepG2 cells, including TNF-α, iNOS, IL-1β, IL-6, CC chemokine ligand (CCL)-2, CCL-22 and epidermal growth factor receptor (EGFR). Moreover, CXC195 inhibited the expressions and interactions of TLR4, MyD88 and TAK1, NF-κB translocation to nucleus and its DNA binding activity, phosphorylation of ERK1/2, p38 and JNK. Our results suggested that treatment with CXC195 could attenuate the TLR4-mediated proliferation and inflammatory response in LPS-induced HepG2 cells, thus might be beneficial for the treatment of HCC.« less

Ornithine transcarbamylase and arginase I deficiency are responsible for diminished urea cycle function in the human hepatoblastoma cell line HepG2.

PubMed

Mavri-Damelin, Demetra; Eaton, Simon; Damelin, Leonard H; Rees, Myrddin; Hodgson, Humphrey J F; Selden, Clare

2007-01-01

A possible cell source for a bio-artificial liver is the human hepatblastoma-derived cell line HepG2 as it confers many hepatocyte functions, however, the urea cycle is not maintained resulting in the lack of ammonia detoxification via this cycle. We investigated urea cycle activity in HepG2 cells at both a molecular and biochemical level to determine the causes for the lack of urea cycle expression, and subsequently addressed reinstatement of the cycle by gene transfer. Metabolic labelling studies showed that urea production from 15N-ammonium chloride was not detectable in HepG2 conditioned medium, nor could 14C-labelled urea cycle intermediates be detected. Gene expression data from HepG2 cells revealed that although expression of three urea cycle genes Carbamoyl Phosphate Synthase I, Arginosuccinate Synthetase and Arginosuccinate Lyase was evident, Ornithine Transcarbamylase and Arginase I expression were completely absent. These results were confirmed by Western blot for arginase I, where no protein was detected. Radiolabelled enzyme assays showed that Ornithine Transcarbamylase functional activity was missing but that Carbamoyl Phosphate Synthase I, Arginosuccinate Synthetase and Arginosuccinate Lyase were functionally expressed at levels comparable to cultured primary human hepatocytes. To restore the urea cycle, HepG2 cells were transfected with full length Ornithine Transcarbamylase and Arginase I cDNA constructs under a CMV promoter. Co-transfected HepG2 cells displayed complete urea cycle activity, producing both labelled urea and urea cycle intermediates. This strategy could provide a cell source capable of urea synthesis, and hence ammonia detoxificatory function, which would be useful in a bio-artificial liver.

Lipopolysaccharide stimulates HepG2 human hepatoma cells in the presence of lipopolysaccharide-binding protein via CD14.

PubMed

Nanbo, A; Nishimura, H; Muta, T; Nagasawa, S

1999-02-01

Lipopolysaccharide (LPS)-binding protein (LBP), an opsonin for activation of macrophages by bacterial LPS, is synthesized in hepatocytes and is known to be an acute phase protein. Recently, cytokine-induced production of LBP was reported to increase 10-fold in hepatocytes isolated from LPS-treated rats, compared with those from normal rats. However, the mechanism by which the LPS treatment enhances the effect of cytokines remains to be clarified. In the present study, we examined whether LPS alone or an LPS/LBP complex directly stimulates the hepatocytes, leading to acceleration of the cytokine-induced LBP production. HepG2 cells (a human hepatoma cell line) were shown to express CD14, a glycosylphosphatidylinositol-anchored LPS receptor, by both RT/PCR and flow cytometric analyses. An LPS/LBP complex was an effective stimulator for LBP and CD14 production in HepG2 cells, but stimulation of the cells with either LPS or LBP alone did not significantly accelerate the production of these proteins. The findings were confirmed by semiquantitative RT/PCR analysis of mRNA levels of LBP and CD14 in HepG2 cells after stimulation with LPS alone and an LPS/LBP complex. In addition, two monoclonal antibodies (mAbs) to CD14 (3C10 and MEM-18) inhibited LPS/LBP-induced cellular responses of HepG2 cells. Furthermore, prestimulation of HepG2 cells with LPS/LBP augmented cytokine-induced production and gene expression of LBP and CD14. All these findings suggest that an LPS/LBP complex, but not free LPS, stimulates HepG2 cells via CD14 leading to increased basal and cytokine-induced LBP and CD14 production.

Evaluation of NGAL TestTM on Cobas 6000.

PubMed

Hansen, Young B L; Damgaard, Anette; Poulsen, Jørgen H

2014-01-01

Neutrophil Gelatinase-Associated Lipocalin (NGAL) is a promising biomarker for acute kidney injury (AKI). Our objectives were to evaluate the NGAL Test(TM) from Bioporto for both urine NGAL and plasma NGAL on the Cobas 6000 c501 (Roche Diagnostics, Rotkreuz, Switzerland) with matched measurements run on Hitachi 917, the method's linearity on the Cobas 6000 in urine, EDTA and Lithium-Heparin (Li-Hep), the influence of using EDTA or Li-Hep tubes and, finally, the impact of freezing and thawing on the sample. Forty matched samples of Li-Hep and EDTA plasma and 40 urine samples were analyzed for method, anticoagulant, and freeze-thaw comparisons. Linearity was assessed using high NGAL samples diluted in urine, EDTA, and Li-Hep plasma. Commercial internal controls were used for the imprecision study. The Cobas 6000 measured identically with the Hitachi 917, however, not in EDTA plasma (Median Difference = 17.50 μg/L, p < 0.0001). Freeze-thaw process reduced NGAL ((EDTA: Mean Difference = = 15.13 μg/L, p = 0.0014)(Li-Hep: Median Difference = = 6.5 μg/L, p = 0.0129)). NGAL results were higher in Li-Hep plasma than in EDTA plasma ((Non-thawed: Median Difference = = 14.5 μg/L, p < 0.0001), (Thawed: Median Difference = = 21.5 μg/L, p = 0.0003)). Linearity agreements were observed in all three specimens. Imprecision (CV%) was below 3%. The NGAL Test(TM) can be applied on the Cobas 6000 with acceptable performance, although the Cobas 6000 measured higher than the Hitachi 917 in EDTA plasma. Though clinically insignificant, we found that the freeze-thaw process had a reduced effect. NGAL results were higher in Li-Hep tubes than in EDTA tubes. Thus, for blood samples we recommend use of EDTA tubes for NGAL measurements.

[3D evaluation model for drug hepatotoxicity testing on HepG2 cells and its application in drug safety evaluation].

PubMed

Li, Dan-Dan; Tang, Xiang-Lin; Tan, Hong-Ling; Liang, Qian-de; Wang, Yu-Guang; Ma, Zeng-Chun; Xiao, Cheng-Rong; Gao, Yue

2016-04-01

3D in vitro toxicity testing model was developed by magnetic levitation method for culture of the human hepatoma cell line HepG2 and applied to evaluate the drug hepatotoxicity. After formation of stable 3D structure for HepG2 cells, their glycogen storage capacity under 2D and 3D culture conditions were detected by immunohistochemistry technology, and the mRNA expression levels of phase Ⅰ and Ⅱ drug metabolism enzymes, drug transporters, nuclear receptors and liver-specific marker albumin(ALB) were compared between 2D and 3D culture conditions by using RT-PCR method. Immunohistochemistry results showed that HepG2 cells had abundant glycogen storage capacity under 3D culture conditions, which was similar to human liver tissues. The mRNA expression levels of major drug metabolism enzymes, drug transporters, nuclear receptors and ALB in HepG2 cells under 3D culture conditions were up-regulated as compared with 2D culture conditions. For drug hepatotoxicity evaluation, the typical hepatotoxic drug acetaminophen(APAP), and most reported drugs Polygonum multiflorum Thunb.(Chinese name He-shou-wu) and Psoraleae corylifolia L.(Chinese name Bu-gu-zhi) were selected for single dose and repeated dose(7 d) exposure. In the repeated dose exposure test, 3D HepG2 cells showed higher sensitivity. This established 3D HepG2 cells model with magnetic levitation 3D culture techniques was more close to the human liver tissues both in morphology and functions, so it was a better 3D hepatotoxicity evaluation model. Copyright© by the Chinese Pharmaceutical Association.

GABA stimulates human hepatocellular carcinoma growth through overexpressed GABAA receptor theta subunit

PubMed Central

Li, Yue-Hui; Liu, Yan; Li, Yan-Dong; Liu, Yan-Hong; Li, Feng; Ju, Qiang; Xie, Ping-Li; Li, Guan-Cheng

2012-01-01

AIM: To investigate the function of gamma-aminobutyric acid (GABA) and gamma-aminobutyric acid A receptor θ subunit (GABRQ) in hepatocellular carcinoma (HCC). METHODS: Semiquantitative polymerase chain reaction was used for detecting the expression of GABRQ receptor among HCC cell line HepG2, normal liver cell line L-02, non-malignant Chang’s liver cells, 8 samples of HCC tissues and paired non-cancerous tissues. HepG2 cells were treated with GABA at serial concentrations (0, 1, 10, 20, 40 and 60 μmol/L), and their proliferating abilities were analyzed with the methyl thiazolyl tetrazolium assay, cell cycle analysis and tumor implanted in nude mice. Small interfering RNA was used for knocking down the endogenous GABRQ in HepG2. Proliferating abilities of these cells treated with or without GABA were analyzed. RESULTS: We identified the overexpression of GABRQ in HCC cell lines and half of the tested HCC tissues. Knockdown of endogenous GABRQ expression in HepG2 attenuated HCC cell growth, suggesting its role in HCC cell viability. We studied the effect of GABA in the proliferation of GABRQ-positive cell lines in vitro and in vivo, and found that GABA increased HCC growth in a dose-dependent manner. Notably, the addition of GABA into the cell culture medium promoted the proliferation of GABRQ-expressing HepG2 cells, but not GABRQ-knockdown HepG2 cells, which means that GABA stimulates HepG2 cell growth through GABRQ. CONCLUSION: GABRQ play important roles in HCC development and progression and could be a promising molecular target for the development of new diagnostic and therapeutic strategies of HCC. PMID:22690081

Cisplatin combined with hyperthermia kills HepG2 cells in intraoperative blood salvage but preserves the function of erythrocytes.

PubMed

Yang, Jin-ting; Tang, Li-hui; Liu, Yun-qing; Wang, Yin; Wang, Lie-ju; Zhang, Feng-jiang; Yan, Min

2015-05-01

The safe use of intraoperative blood salvage (IBS) in cancer surgery remains controversial. Here, we investigated the killing effect of cisplatin combined with hyperthermia on human hepatocarcinoma (HepG2) cells and erythrocytes from IBS in vitro. HepG2 cells were mixed with concentrated erythrocytes and pretreated with cisplatin (50, 100, and 200 μg/ml) alone at 37 °C for 60 min and cisplatin (25, 50, 100, and 200 μg/ml) combined with hyperthermia at 42 °C for 60 min. After pretreatment, the cell viability, colony formation and DNA metabolism in HepG2 and the Na(+)-K(+)-ATPase activity, 2,3-diphosphoglycerate (2,3-DPG) concentration, free hemoglobin (Hb) level, osmotic fragility, membrane phosphatidylserine externalization, and blood gas variables in erythrocytes were determined. Pretreatment with cisplatin (50, 100, and 200 μg/ml) combined with hyperthermia (42 °C) for 60 min significantly decreased HepG2 cell viability, and completely inhibited colony formation and DNA metabolism when the HepG2 cell concentration was 5×10(4) ml(-1) in the erythrocyte (P<0.01). Erythrocytic Na(+)-K(+)-ATPase activity, 2,3-DPG level, phosphatidylserine externalization, and extra-erythrocytic free Hb were significantly altered by hyperthermia plus high concentrations of cisplatin (100 and 200 μg/ml) (P<0.05), but not by hyperthermia plus 50 μg/ml cisplatin (P>0.05). In conclusion, pretreatment with cisplatin (50 μg/ml) combined with hyperthermia (42 °C) for 60 min effectively eliminated HepG2 cells from IBS but did not significantly affect erythrocytes in vitro.

A sensitive and accurate quantification method for the detection of hepatitis B virus covalently closed circular DNA by the application of a droplet digital polymerase chain reaction amplification system.

PubMed

Mu, Di; Yan, Liang; Tang, Hui; Liao, Yong

2015-10-01

To develop a sensitive and accurate assay system for the quantification of covalently closed circular HBV DNA (cccDNA) for future clinical monitoring of cccDNA fluctuation during antiviral therapy in the liver of infected patients. A droplet digital PCR (ddPCR)-based assay system detected template DNA input at the single copy level (or ~10(-5) pg of plasmid HBV DNA) by using serially diluted plasmid HBV DNA samples. Compared with the conventional quantitative PCR assay in the detection of cccDNA, which required at least 50 ng of template DNA input, a parallel experiment applying a ddPCR system demonstrates that the lowest detection limit of cccDNA from HepG2.215 cellular DNA samples is around 1 ng, which is equivalent to 0.54 ± 0.94 copies of cccDNA. In addition, we demonstrated that the addition of cccDNA-safe exonuclease and utilization of cccDNA-specific primers in the ddPCR assay system significantly improved the detection accuracy of HBV cccDNA from HepG2.215 cellular DNA samples. The ddPCR-based cccDNA detection system is a sensitive and accurate assay for the quantification of cccDNA in HBV-transfected HepG2.215 cellular DNA samples and may represent an important method for future application in monitoring cccDNA fluctuation during antiviral therapy.

Isolation and characterization of antiproliferative peptides from Chinese three-striped box turtle (Cuora trifasciata).

PubMed

Mao, Xinliang; He, Shengjie; Zhang, Ting; Guo, Xiaolei; Ge, Yazhong; Ma, Chungwah; Zhang, Xuewu

2017-11-01

In this study, the whole proteins from a Chinese three-striped box turtle (Cuora trifasciata) were extracted and hydrolyzed using three proteases (alcalase, papain, and protamex). By orthogonal experiments, the optimal hydrolysis conditions for producing peptides with the highest cancer cells growth inhibition activity were determined. Such as, the maximum inhibition on MCF-7 cancer cells (92.37% at 1 mg/mL) was achieved by papain hydrolysis (pH 8, 37 °C, enzyme-to-substrate ratio (E/S) 1.5%), and the maximum inhibition on HepG2 cancer cells (94.16% at 1 mg/mL) was reached by protamex hydrolysis (pH 8, 40 °C, E/S 2%). Using ultrafiltration and Sephadex G-15 column chromatography, two polypeptides M2 and F4 were isolated. At 500 μg/mL, M2 exhibited 74.7% and 62.9% of antiproliferation activities on MCF-7 and HepG2 cancer cells, respectively; and F4 displayed good inhibitory effects on MCF-7 (70.59%) and HepG2 (78.6%) cancer cells. M2 and F4 had lower inhibition (<20%) than drug 5-FU (>60%) on normal liver cells L-O2. Moreover, three peptides, EMLQPPL, PGKPLFL, and SCCSCDED, were identified; their inhibitory effects on cancer cells were confirmed after synthesis. These data, for the first time, demonstrated that Cuora trifasciata-derived proteins could be used for preparing antiproliferation peptides. © 2016 International Union of Biochemistry and Molecular Biology, Inc.

Blazeispirol A from Agaricus blazei fermentation product induces cell death in human hepatoma Hep 3B cells through caspase-dependent and caspase-independent pathways.

PubMed

Su, Zheng-Yuan; Tung, Yen-Chen; Hwang, Lucy Sun; Sheen, Lee-Yan

2011-05-11

Currently, liver cancer is a leading cause of cancer-related death in the world. Hepatocellular carcinoma is the most common type of liver cancer. Previously, it was reported that blazeispirol A (BA) is the most active antihepatoma compound in an ethanolic extract of Agaricus blazei fermentation product. The aim of this study was to understand the antihepatoma mechanism of BA in human liver cancer Hep 3B cells. The results showed that BA inhibited the growth of Hep 3B cells and increased the percentage of cells in sub-G1 phase in a concentration- and time-dependent manner. In addition, BA treatment resulted in DNA fragmentation, caspase-9 and caspase-3 activations, poly(ADP-ribose)polymerase (PARP) degradation, down-regulation of Bcl-2 and Bcl-xL expressions, up-regulation of Bax expression, and disruption of the mitochondrial membrane potential (MMP) in Hep 3B cells. Furthermore, z-VAD-fmk, a caspase inhibitor, did not enhance the viability of BA-treated Hep 3B cells, and BA induced the release of HtrA2/Omi and apoptosis-inducing factor (AIF) from mitochondria into the cytosol. These findings suggested that BA with novel chemopreventive and chemotherapeutic potentials causes both caspase-dependent and caspase-independent cell death in Hep 3B cells.

ATPase domain and interdomain linker play a key role in aggregation of mitochondrial Hsp70 chaperone Ssc1.

PubMed

Blamowska, Marta; Sichting, Martin; Mapa, Koyeli; Mokranjac, Dejana; Neupert, Walter; Hell, Kai

2010-02-12

The co-chaperone Hep1 is required to prevent the aggregation of mitochondrial Hsp70 proteins. We have analyzed the interaction of Hep1 with mitochondrial Hsp70 (Ssc1) and the determinants in Ssc1 that make it prone to aggregation. The ATPase and peptide binding domain (PBD) of Hsp70 proteins are connected by a linker segment that mediates interdomain communication between the domains. We show here that the minimal Hep1 binding entity of Ssc1 consists of the ATPase domain and the interdomain linker. In the absence of Hep1, the ATPase domain with the interdomain linker had the tendency to aggregate, in contrast to the ATPase domain with the mutated linker segment or without linker, and in contrast to the PBD. The closest homolog of Ssc1, bacterial DnaK, and a Ssc1 chimera, in which a segment of the ATPase domain of Ssc1 was replaced by the corresponding segment from DnaK, did not aggregate in Delta hep1 mitochondria. The propensity to aggregate appears to be a specific property of the mitochondrial Hsp70 proteins. The ATPase domain in combination with the interdomain linker is crucial for aggregation of Ssc1. In conclusion, our results suggest that interdomain communication makes Ssc1 prone to aggregation. Hep1 counteracts aggregation by binding to this aggregation-prone conformer.

ATPase Domain and Interdomain Linker Play a Key Role in Aggregation of Mitochondrial Hsp70 Chaperone Ssc1*

PubMed Central

Blamowska, Marta; Sichting, Martin; Mapa, Koyeli; Mokranjac, Dejana; Neupert, Walter; Hell, Kai

2010-01-01

The co-chaperone Hep1 is required to prevent the aggregation of mitochondrial Hsp70 proteins. We have analyzed the interaction of Hep1 with mitochondrial Hsp70 (Ssc1) and the determinants in Ssc1 that make it prone to aggregation. The ATPase and peptide binding domain (PBD) of Hsp70 proteins are connected by a linker segment that mediates interdomain communication between the domains. We show here that the minimal Hep1 binding entity of Ssc1 consists of the ATPase domain and the interdomain linker. In the absence of Hep1, the ATPase domain with the interdomain linker had the tendency to aggregate, in contrast to the ATPase domain with the mutated linker segment or without linker, and in contrast to the PBD. The closest homolog of Ssc1, bacterial DnaK, and a Ssc1 chimera, in which a segment of the ATPase domain of Ssc1 was replaced by the corresponding segment from DnaK, did not aggregate in Δhep1 mitochondria. The propensity to aggregate appears to be a specific property of the mitochondrial Hsp70 proteins. The ATPase domain in combination with the interdomain linker is crucial for aggregation of Ssc1. In conclusion, our results suggest that interdomain communication makes Ssc1 prone to aggregation. Hep1 counteracts aggregation by binding to this aggregation-prone conformer. PMID:20007714

Hyperglycemia and Anthocyanin Inhibit Quercetin Metabolism in HepG2 Cells.

PubMed

Hashimoto, Naoto; Blumberg, Jeffrey B; Chen, C-Y Oliver

2016-02-01

A high glucose (Glu) milieu promotes generation of reactive oxygen species, which may not only cause cellular damage, but also modulate phase II enzymes that are responsible for the metabolism of flavonoids. Thus, we examined the effect of a high Glu milieu on quercetin (Q) metabolism in HepG2 cells. HepG2 cells were grown for 3 days in Glu ranging from 5.5 to 50 mmol/L and/or cyanidin-3-glucoside (C3G) ranging from 0 to 25 μmol/L. Subsequently, the capacity of HepG2 cells to metabolize Q was assessed for up to 16 h. Q metabolites were analyzed by high-performance liquid chromatography. Four major Q metabolites were observed in the culture medium and inside the HepG2 cells. Three of these metabolites appear to be sulfated forms of Q or methylated Q, and one was a methylated Q. These metabolites and Q itself were reduced or tended to be reduced in cells grown in a high Glu compared to a normal Glu medium. Addition of C3G or superoxide dismutase plus catalase did not prevent or enhance reduction of Q metabolites. In vitro, a hyperglycemic milieu decreases the production of the principal Q metabolites in HepG2 cells, mediated through mechanisms independent of oxidative stress.