The Pathogen-Host Interactions database (PHI-base): additions and future developments.

PubMed

Urban, Martin; Pant, Rashmi; Raghunath, Arathi; Irvine, Alistair G; Pedro, Helder; Hammond-Kosack, Kim E

2015-01-01

Rapidly evolving pathogens cause a diverse array of diseases and epidemics that threaten crop yield, food security as well as human, animal and ecosystem health. To combat infection greater comparative knowledge is required on the pathogenic process in multiple species. The Pathogen-Host Interactions database (PHI-base) catalogues experimentally verified pathogenicity, virulence and effector genes from bacterial, fungal and protist pathogens. Mutant phenotypes are associated with gene information. The included pathogens infect a wide range of hosts including humans, animals, plants, insects, fish and other fungi. The current version, PHI-base 3.6, available at http://www.phi-base.org, stores information on 2875 genes, 4102 interactions, 110 host species, 160 pathogenic species (103 plant, 3 fungal and 54 animal infecting species) and 181 diseases drawn from 1243 references. Phenotypic and gene function information has been obtained by manual curation of the peer-reviewed literature. A controlled vocabulary consisting of nine high-level phenotype terms permits comparisons and data analysis across the taxonomic space. PHI-base phenotypes were mapped via their associated gene information to reference genomes available in Ensembl Genomes. Virulence genes and hotspots can be visualized directly in genome browsers. Future plans for PHI-base include development of tools facilitating community-led curation and inclusion of the corresponding host target(s). © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Nicotine can skew the characterization of the macrophage type-1 (M{Phi}1) phenotype differentiated with granulocyte-macrophage colony-stimulating factor to the M{Phi}2 phenotype

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

Yanagita, Manabu; Kobayashi, Ryohei; Murakami, Shinya, E-mail: ipshinya@dent.osaka-u.ac.jp

Macrophages (M{Phi}s) exhibit functional heterogeneity and plasticity in the local microenvironment. Recently, it was reported that M{Phi}s can be divided into proinflammatory M{Phi}s (M{Phi}1) and anti-inflammatory M{Phi}s (M{Phi}2) based on their polarized functional properties. Here, we report that nicotine, the major ingredient of cigarette smoke, can modulate the characteristics of M{Phi}1. Granulocyte-macrophage colony-stimulating factor-driven M{Phi}1 with nicotine (Ni-M{Phi}1) showed the phenotypic characteristics of M{Phi}2. Like M{Phi}2, Ni-M{Phi}1 exhibited antigen-uptake activities. Ni-M{Phi}1 suppressed IL-12, but maintained IL-10 and produced high amounts of MCP-1 upon lipopolysaccharide stimulation compared with M{Phi}1. Moreover, we observed strong proliferative responses of T cells to lipopolysaccharide-stimulated M{Phi}1,more » whereas Ni-M{Phi}1 reduced T cell proliferation and inhibited IFN-{gamma} production by T cells. These results suggest that nicotine can change the functional characteristics of M{Phi} and skew the M{Phi}1 phenotype to M{Phi}2. We propose that nicotine is a potent regulator that modulates immune responses in microenvironments.« less

Vectorization for Molecular Dynamics on Intel Xeon Phi Corpocessors

NASA Astrophysics Data System (ADS)

Yi, Hongsuk

2014-03-01

Many modern processors are capable of exploiting data-level parallelism through the use of single instruction multiple data (SIMD) execution. The new Intel Xeon Phi coprocessor supports 512 bit vector registers for the high performance computing. In this paper, we have developed a hierarchical parallelization scheme for accelerated molecular dynamics simulations with the Terfoff potentials for covalent bond solid crystals on Intel Xeon Phi coprocessor systems. The scheme exploits multi-level parallelism computing. We combine thread-level parallelism using a tightly coupled thread-level and task-level parallelism with 512-bit vector register. The simulation results show that the parallel performance of SIMD implementations on Xeon Phi is apparently superior to their x86 CPU architecture.

Bidirectional and simultaneous FTTX/Ethernet services using RSOA based remodulation and polarization multiplexing technique

NASA Astrophysics Data System (ADS)

Das, Anindya S.; Patra, Ardhendu S.

2015-08-01

A bidirectional and simultaneous transmission of Ethernet, FTTX services through single optical carrier wavelength employing polarization multiplexing technique in the transmitter end and the user end. 10 Gbps and 2.5 Gbps datarates are transmitted over 50 km single mode fiber employing POLMUX technique at OLT and ONU to provide Ethernet and FTTX services concurrently to the user. Reflective semiconductor optical amplifier is used to reuse and remodulate the downlink signal to uplink transmission. The upstream and the downstream transmission performances are observed by the bit error rate values and the eye diagrams obtained by the BER analyzer.

A Realization of Theoretical Maximum Performance in IPSec on Gigabit Ethernet

NASA Astrophysics Data System (ADS)

Onuki, Atsushi; Takeuchi, Kiyofumi; Inada, Toru; Tokiniwa, Yasuhisa; Ushirozawa, Shinobu

This paper describes “IPSec(IP Security) VPN system" and how it attains a theoretical maximum performance on Gigabit Ethernet. The Conventional System is implemented by software. However, the system has several bottlenecks which must be overcome to realize a theoretical maximum performance on Gigabit Ethernet. Thus, we newly propose IPSec VPN System with the FPGA(Field Programmable Gate Array) based hardware architecture, which transmits a packet by the pipe-lined flow processing and has 6 parallel structure of encryption and authentication engines. We show that our system attains the theoretical maximum performance in the short packet which is difficult to realize until now.

Summing up the Euler [phi] Function

ERIC Educational Resources Information Center

Loomis, Paul; Plytage, Michael; Polhill, John

2008-01-01

The Euler [phi] function counts the number of positive integers less than and relatively prime to a positive integer n. Here we look at perfect totient numbers, number for which [phi](n) + [phi]([phi](n)) + [phi]([phi]([phi](n))) + ... + 1 = n.

Tsunami survivors' perspectives on vulnerability and vulnerability reduction: evidence from Koh Phi Phi Don and Khao Lak, Thailand.

PubMed

Steckley, Marylynn; Doberstein, Brent

2011-07-01

This paper presents the results of primary research with 40 survivors of the 2004 Indian Ocean tsunami in two communities: Khao Lak (n=20) and Koh Phi Phi Don (n=20), Thailand. It traces tsunami survivors' perceptions of vulnerability, determines whether residents felt that the tsunami affected different communities differently, identifies the populations and sub-community groups that survivors distinguished as being more vulnerable than others, highlights community-generated ideas about vulnerability reduction, and pinpoints a range of additional vulnerability reduction actions. Tsunami survivors most consistently identified the 'most vulnerable' community sub-populations as women, children, the elderly, foreigners, and the poor. In Khao Lak, however, respondents added 'Burmese migrants' to this list, whereas in Koh Phi Phi Don, they added 'Thai Muslims'. Results suggest that the two case study communities, both small, coastal, tourism-dominated communities no more than 100 kilometres apart, have differing vulnerable sub-groups and environmental vulnerabilities, requiring different post-disaster vulnerability reduction efforts. © 2011 The Author(s). Disasters © Overseas Development Institute, 2011.

Release and bioactivity of bone morphogenetic protein-2 are affected by scaffold binding techniques in vitro and in vivo.

PubMed

Suliman, Salwa; Xing, Zhe; Wu, Xujun; Xue, Ying; Pedersen, Torbjorn O; Sun, Yang; Døskeland, Anne P; Nickel, Joachim; Waag, Thilo; Lygre, Henning; Finne-Wistrand, Anna; Steinmüller-Nethl, Doris; Krueger, Anke; Mustafa, Kamal

2015-01-10

A low dose of 1μg rhBMP-2 was immobilised by four different functionalising techniques on recently developed poly(l-lactide)-co-(ε-caprolactone) [(poly(LLA-co-CL)] scaffolds. It was either (i) physisorbed on unmodified scaffolds [PHY], (ii) physisorbed onto scaffolds modified with nanodiamond particles [nDP-PHY], (iii) covalently linked onto nDPs that were used to modify the scaffolds [nDP-COV] or (iv) encapsulated in microspheres distributed on the scaffolds [MICS]. Release kinetics of BMP-2 from the different scaffolds was quantified using targeted mass spectrometry for up to 70days. PHY scaffolds had an initial burst of release while MICS showed a gradual and sustained increase in release. In contrast, NDP-PHY and nDP-COV scaffolds showed no significant release, although nDP-PHY scaffolds maintained bioactivity of BMP-2. Human mesenchymal stem cells cultured in vitro showed upregulated BMP-2 and osteocalcin gene expression at both week 1 and week 3 in the MICS and nDP-PHY scaffold groups. These groups also demonstrated the highest BMP-2 extracellular protein levels as assessed by ELISA, and mineralization confirmed by Alizarin red. Cells grown on the PHY scaffolds in vitro expressed collagen type 1 alpha 2 early but the scaffold could not sustain rhBMP-2 release to express mineralization. After 4weeks post-implantation using a rat mandible critical-sized defect model, micro-CT and Masson trichrome results showed accelerated bone regeneration in the PHY, nDP-PHY and MICS groups. The results demonstrate that PHY scaffolds may not be desirable for clinical use, since similar osteogenic potential was not seen under both in vitro and in vivo conditions, in contrast to nDP-PHY and MICS groups, where continuous low doses of BMP-2 induced satisfactory bone regeneration in both conditions. The nDP-PHY scaffolds used here in critical-sized bone defects for the first time appear to have promise compared to growth factors adsorbed onto a polymer alone and the short distance effect prevents adverse systemic side effects. Copyright © 2014. Published by Elsevier B.V.

Temperature dependence of emission measure in solar X-ray plasmas. 1: Non-flaring active regions

NASA Technical Reports Server (NTRS)

Phillips, K. J. H.

1974-01-01

X-ray and ultraviolet line emission from hot, optically thin material forming coronal active regions on the sun may be described in terms of an emission measure distribution function, Phi (T). A relationship is developed between line flux and Phi (T), a theory which assumes that the electron density is a single-valued function of temperature. The sources of error involved in deriving Phi (T) from a set of line fluxes are examined in some detail. These include errors in atomic data (collisional excitation rates, assessment of other mechanisms for populating excited states of transitions, element abundances, ion concentrations, oscillator strengths) and errors in observed line fluxes arising from poorly - known instrumental responses. Two previous analyses are discussed in which Phi (T) for a non-flaring active region is derived. A least squares method of Batstone uses X-ray data of low statistical significance, a fact which appears to influence the results considerably. Two methods for finding Phi (T) ab initio are developed. The coefficients are evaluated by least squares. These two methods should have application not only to active-region plasmas, but also to hot, flare-produced plasmas.

Human umbilical cord blood-derived f-macrophages retain pluripotentiality after thrombopoietin expansion

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

Zhao Yong; Mazzone, Theodore

2005-11-01

We have previously characterized a new type of stem cell from human peripheral blood, termed fibroblast-like macrophage (f-M{phi}). Here, using umbilical cord blood as a source, we identified cells with similar characteristics including expression of surface markers (CD14, CD34, CD45, CD117, and CD163), phagocytosis, and proliferative capacity. Further, thrombopoietin (TPO) significantly stimulated the proliferation of cord blood-derived f-M{phi} (CB f-M{phi}) at low dosage without inducing a megakaryocytic phenotype. Additional experiments demonstrated that TPO-expanded cord blood-derived f-M{phi} (TCB f-M{phi}) retained their surface markers and differentiation ability. Treatment with vascular endothelial cell growth factor (VEGF) gave rise to endothelial-like cells, expressing Flt-1,more » Flk-1, von Willebrand Factor (vWF), CD31, acetylated low density lipoprotein internalization, and the ability to form endothelial-like cell chains. In the presence of lipopolyssacharide (LPS) and 25 mM glucose, the TCB f-M{phi} differentiated to express insulin mRNA, C-peptide, and insulin. In vitro functional analysis demonstrated that these insulin-positive cells could release insulin in response to glucose and other secretagogues. These findings demonstrate a potential use of CB f-M{phi} and may lead to develop new therapeutic strategy for treating dominant disease.« less

Radiated emissions comparison of seven-stage modal filter constructions for Ethernet 100Base-T network protection

NASA Astrophysics Data System (ADS)

Khazhibekov, R. R.; Zabolotsky, A. M.

2018-05-01

The authors consider Ethernet protection devices based on modal filtering. Radiated emission measurement results for three modal filter constructions are presented. It is shown that the improved construction of a non-resistive filter has lower emission levels than the original one.

A Single-Domain Response Regulator Functions as an Integrating Hub To Coordinate General Stress Response and Development in Alphaproteobacteria

PubMed Central

2018-01-01

ABSTRACT The alphaproteobacterial general stress response is governed by a conserved partner-switching mechanism that is triggered by phosphorylation of the response regulator PhyR. In the model organism Caulobacter crescentus, PhyR was proposed to be phosphorylated by the histidine kinase PhyK, but biochemical evidence in support of such a role of PhyK is missing. Here, we identify a single-domain response regulator, MrrA, that is essential for general stress response activation in C. crescentus. We demonstrate that PhyK does not function as a kinase but accepts phosphoryl groups from MrrA and passes them on to PhyR, adopting the role of a histidine phosphotransferase. MrrA is phosphorylated by at least six histidine kinases that likely serve as stress sensors. MrrA also transfers phosphate to LovK, a histidine kinase involved in C. crescentus holdfast production and attachment, which also negatively regulates the general stress response. We show that LovK together with the response regulator LovR acts as a phosphate sink to redirect phosphate flux away from the PhyKR branch. In agreement with the biochemical data, an mrrA mutant is unable to activate the general stress response and shows a hyperattachment phenotype, which is linked to decreased expression of the major holdfast inhibitory protein HfiA. We propose that MrrA serves as a central phosphorylation hub that coordinates the general stress response with C. crescentus development and other adaptive behaviors. The characteristic bow-tie architecture of this phosphorylation network with MrrA as the central knot may expedite the evolvability and species-specific niche adaptation of this group of bacteria. PMID:29789370

Understanding the branching ratios of {chi}{sub c1{yields}{phi}{phi}}, {omega}{omega}, {omega}{phi} observed at BES-III

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

Chen Dianyong; He Jun; Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000

In this work, we discuss the contribution of the mesonic loops to the decay rates of {chi}{sub c1{yields}{phi}{phi}}, {omega}{omega}, which are suppressed by the helicity selection rules and {chi}{sub c1{yields}{phi}{omega}}, which is a double-Okubo-Zweig-Iizuka forbidden process. We find that the mesonic loop effects naturally explain the clear signals of {chi}{sub c1{yields}{phi}{phi}}, {omega}{omega} decay modes observed by the BES Collaboration. Moreover, we investigate the effects of the {omega}-{phi} mixing, which may result in the order of magnitude of the branching ratio BR({chi}{sub c1{yields}{omega}{phi}}) being 10{sup -7}. Thus, we are waiting for the accurate measurements of the BR({chi}{sub c1{yields}{omega}{omega}}), BR({chi}{sub c1{yields}{phi}{phi}}), andmore » BR({chi}{sub c1{yields}{omega}{phi}}), which may be very helpful for testing the long-distant contribution and the {omega}-{phi} mixing in {chi}{sub c1{yields}{phi}{phi}}, {omega}{omega}, {omega}{phi} decays.« less

Optimal future liver remnant in patients treated with extensive preoperative chemotherapy for colorectal liver metastases.

PubMed

Shindoh, Junichi; Tzeng, Ching-Wei D; Aloia, Thomas A; Curley, Steven A; Zimmitti, Giuseppe; Wei, Steven H; Huang, Steven Y; Mahvash, Armeen; Gupta, Sanjay; Wallace, Michael J; Vauthey, Jean-Nicolas

2013-08-01

Patients with colorectal liver metastases (CLM) are increasingly treated with preoperative chemotherapy. Chemotherapy associated liver injury is associated with postoperative hepatic insufficiency (PHI) and mortality. The adequate minimum future liver remnant (FLR) volume in patients treated with extensive chemotherapy remains unknown. All patients with standardized FLR > 20 %, who underwent extended right hepatectomy for CLM from 1993-2011, were divided into three cohorts by chemotherapy duration: no chemotherapy (NC, n = 30), short duration (SD, ≤12 weeks, n = 78), long duration (LD, >12 weeks, n = 86). PHI and mortality were compared by using uni-/multivariate analyses. Optimal FLR for LD chemotherapy was determined using a minimum p-value approach. A total of 194 patients met inclusion criteria. LD chemotherapy was significantly associated with PHI (NC + SD 3.7 vs. LD 16.3%, p = 0.006). Ninety-day mortality rates were 0 % in NC, 1.3 % in SD, and 2.3% in LD patients, respectively (p = 0.95). In patients with FLR > 30 %, PHI occurred in only two patients (both LD, 2/20, 10 %), but all patients with FLR > 30 % survived. The best cutoff of FLR for preventing PHI after chemotherapy >12 weeks was estimated as >30 %. Both LD chemotherapy (odds ratio [OR] 5.4, p = 0.004) and FLR ≤ 30 % (OR 6.3, p = 0.019) were independent predictors of PHI. Preoperative chemotherapy >12 weeks increases the risk of PHI after extended right hepatectomy. In patients treated with long-duration chemotherapy, FLR > 30 % reduces the rate of PHI and may provide enough functional reserve for clinical rescue if PHI develops.

The Design of Passive Optical Networking+Ethernet over Coaxial Cable Access Networking and Video-on-Demand Services Carrying

NASA Astrophysics Data System (ADS)

Ji, Wei

2013-07-01

Video on demand is a very attractive service used for entertainment, education, and other purposes. The design of passive optical networking+Ethernet over coaxial cable accessing and a home gateway system is proposed. The network integrates the passive optical networking and Ethernet over coaxial cable to provide high dedicated bandwidth for the metropolitan video-on-demand services. Using digital video broadcasting, IP television protocol, unicasting, and broadcasting mechanisms maximizes the system throughput. The home gateway finishes radio frequency signal receiving and provides three kinds of interfaces for high-definition video, voice, and data, which achieves triple-play and wire/wireless access synchronously.

Private expenditure and the role of private health insurance in Greece: status quo and future trends.

PubMed

Siskou, Olga; Kaitelidou, Daphne; Economou, Charalampos; Kostagiolas, Peter; Liaropoulos, Lycourgos

2009-10-01

The health care system in Greece is financed in almost equal proportions by public and private sources. Private expenditure, consists mostly of out-of-pocket and under-the-table payments. Such payments strongly suggest dissatisfaction with the public system, due to under financing during the last 25 years. This gap has been filled rapidly by the private sector. From this point of view, one might suggest that the flourishing development of private provision may lead in turn to a corresponding growth in private health insurance (PHI). This paper aims to examine the role of PHI in Greece, to identify the factors influencing its development, and to make some suggestions about future policies and trends. In the decade of 1985-1995 PHI show increasing activity, reflecting the intention of some citizens to seek health insurance solutions in the form of supplementary cover in order to ensure faster access, better quality of services, and increased consumer choice. The benefits include programs covering hospital expenses, cash benefits, outpatient care expenses, disability income insurance, as well as limited managed care programs. However, despite recent interest, PHI coverage remains low in Greece compared to other EU countries. Economic, social and cultural factors such as low average household income, high unemployment, obligatory and full coverage by social insurance, lead to reluctance to pay for second-tier insurance. Instead, there is a preference to pay a doctor or hospital directly even in the form of under-the-table payments (which are remarkably high in Greece), when the need arises. There are also factors endogenous to the PHI industry, related to market policies, low organisational capacity, cream skimming, and the absence of insurance products meeting consumer requirements, which explain the relatively low state of development of PHI in Greece.

A Study of the Ethernet Troughput Performance of the Embedded System

NASA Astrophysics Data System (ADS)

Duan, Zhi-Yu; Zhao, Zhao-Wang

2007-09-01

An ethernet acceleration solution developed for the NIOS II Embedded System in astronomical applications - Mason Express is introduced in this paper. By manually constructing the proper network protocol headers and directly driving the hardware, Mason Express goes around the performance bottleneck of the Light Weighted IP stack (LWIP), and achieves up to 90Mb/s unidirectional data troughput rate from the embedded system board to the data collecting computer. With the LWIP stack, the maximum data rate is about 10.57Mb/s. Mason Express is a total software solution and no hardware changes required, neither does it affect the uCOS II operating system nor the LWIP stack, and can be implemented with or without any embedded operating system. It maximally protects the intelligence investment of the users.

Impact of the Shodan Computer Search Engine on Internet-facing Industrial Control System Devices

DTIC Science & Technology

2014-03-27

bridge implementation. The transparent bridge is designed using a Raspberry Pi configured with Linux IPtables and bridge-utils to bridge the on board...Ethernet card and a second USB Ethernet adapter. A Raspberry Pi is a credit-card-sized single-board computer running a version of Debian Linux. There

76 FR 62431 - Notice of Issuance of Final Determination Concerning Certain Ethernet Switches

Federal Register 2010, 2011, 2012, 2013, 2014

2011-10-07

... importing 7 Series Ethernet switches assembled in China. The switches are designed to interconnect servers... country of origin of Arista's 7048, 7050, 7100, 7124, and 7500 series (``7 Series'') local area network..., packaged, and prepared for shipping. Arista's EOS TM (Extensible Operating System) software is designed to...

Far side Helioseismology with Solar Orbiter

NASA Astrophysics Data System (ADS)

Appourchaux, T.; Birch, A.; Gizon, L. C.; Löptien, B.; Schou, J.; Solanki, S. K.; del Toro Iniesta, J. C.; Gandorfer, A.; Hirzberger, J.; Alvarez-Herrero, A.; Woch, J. G.; Schmidt, W.

2016-12-01

The Solar Orbiter mission, to be launched in October 2018, will carry a suite of remote sensing and in-situ instruments, including the Polarimetric and Helioseismic Imager (PHI). PHI will deliver high-cadence images of the Sun in intensity and Doppler velocity suitable for carrying out novel helioseismic studies. The orbit of the Solar Orbiter spacecraft will reach a solar latitude up to 34 degrees by the end of the extended mission and thus will enable the first local helioseismology studies of the polar regions. The full range of Earth-Sun-spacecraft angles provided by the orbit will enable helioseismology from two vantage points by combining PHI with another instrument: stereoscopic helioseismology will allow the study of the deep solar interior and a better understanding of the physics of solar oscillations in both quiet Sun and sunspots. In this paper we will review the helioseismic objectives achievable with PHI, and will also give a short status report of the development of the Flight Model of PHI.

Multimedia Networks: Mission Impossible?

ERIC Educational Resources Information Center

Weiss, Andrew M.

1996-01-01

Running multimedia on a network, often difficult because of the memory and processing power required, is becoming easier thanks to new protocols and products. Those developing network design criteria may wish to consider making use of Fast Ethernet, Asynchronous Transfer Method (ATM), switches, "fat pipes", additional network…

SPIDR, a general-purpose readout system for pixel ASICs

NASA Astrophysics Data System (ADS)

van der Heijden, B.; Visser, J.; van Beuzekom, M.; Boterenbrood, H.; Kulis, S.; Munneke, B.; Schreuder, F.

2017-02-01

The SPIDR (Speedy PIxel Detector Readout) system is a flexible general-purpose readout platform that can be easily adapted to test and characterize new and existing detector readout ASICs. It is originally designed for the readout of pixel ASICs from the Medipix/Timepix family, but other types of ASICs or front-end circuits can be read out as well. The SPIDR system consists of an FPGA board with memory and various communication interfaces, FPGA firmware, CPU subsystem and an API library on the PC . The FPGA firmware can be adapted to read out other ASICs by re-using IP blocks. The available IP blocks include a UDP packet builder, 1 and 10 Gigabit Ethernet MAC's and a "soft core" CPU . Currently the firmware is targeted at the Xilinx VC707 development board and at a custom board called Compact-SPIDR . The firmware can easily be ported to other Xilinx 7 series and ultra scale FPGAs. The gap between an ASIC and the data acquisition back-end is bridged by the SPIDR system. Using the high pin count VITA 57 FPGA Mezzanine Card (FMC) connector only a simple chip carrier PCB is required. A 1 and a 10 Gigabit Ethernet interface handle the connection to the back-end. These can be used simultaneously for high-speed data and configuration over separate channels. In addition to the FMC connector, configurable inputs and outputs are available for synchronization with other detectors. A high resolution (≈ 27 ps bin size) Time to Digital converter is provided for time stamping events in the detector. The SPIDR system is frequently used as readout for the Medipix3 and Timepix3 ASICs. Using the 10 Gigabit Ethernet interface it is possible to read out a single chip at full bandwidth or up to 12 chips at a reduced rate. Another recent application is the test-bed for the VeloPix ASIC, which is developed for the Vertex Detector of the LHCb experiment. In this case the SPIDR system processes the 20 Gbps scrambled data stream from the VeloPix and distributes it over four 10 Gigabit Ethernet links, and in addition provides the slow and fast control for the chip.

Physical Layer Ethernet Clock Synchronization

DTIC Science & Technology

2010-11-01

42 nd Annual Precise Time and Time Interval (PTTI) Meeting 77 PHYSICAL LAYER ETHERNET CLOCK SYNCHRONIZATION Reinhard Exel, Georg...oeaw.ac.at Nikolaus Kerö Oregano Systems, Mohsgasse 1, 1030 Wien, Austria E-mail: nikolaus.keroe@oregano.at Abstract Clock synchronization ...is a service widely used in distributed networks to coordinate data acquisition and actions. As the requirement to achieve tighter synchronization

Integrated Formal Analysis of Timed-Triggered Ethernet

NASA Technical Reports Server (NTRS)

Dutertre, Bruno; Shankar, Nstarajan; Owre, Sam

2012-01-01

We present new results related to the verification of the Timed-Triggered Ethernet (TTE) clock synchronization protocol. This work extends previous verification of TTE based on model checking. We identify a suboptimal design choice in a compression function used in clock synchronization, and propose an improvement. We compare the original design and the improved definition using the SAL model checker.

Hopkins installs wire harnesses

NASA Image and Video Library

2013-11-24

ISS038-E-008291 (24 Nov. 2013) --- NASA astronaut Michael Hopkins, Expedition 38 flight engineer, installs wire harnesses in the International Space Station?s Harmony node to support the installation of Ethernet video cables for the station?s local area network. These new cables will provide Ethernet connectivity to the visiting vehicles that dock to Harmony?s Earth-facing port.

An Assessment of Gigabit Ethernet Technology and Its Applications at the NASA Glenn Research Center

NASA Technical Reports Server (NTRS)

Bakes, Catherine Murphy; Kim, Chan M.; Ramos, Calvin T.

2000-01-01

This paper describes Gigabit Ethernet and its role in supporting R&D programs at NASA Glenn. These programs require an advanced high-speed network capable of transporting multimedia traffic, including real-time visualization, high- resolution graphics, and scientific data. GigE is a 1 Gbps extension to 10 and 100 Mbps Ethernet. The IEEE 802.3z and 802.3ab standards define the MAC layer and 1000BASE-X and 1000BASE-T physical layer specifications for GigE. GigE switches and buffered distributors support IEEE 802.3x flow control. The paper also compares GigE with ATM in terms of quality of service, data rate, throughput, scalability, interoperability, network management, and cost of ownership.

Measuring Ionospheric Irregularities Globally by the Rate of TEC Index and GNSS Networks

NASA Technical Reports Server (NTRS)

Pi, Xiaoqing

2012-01-01

Outline of presentation: Why do we use the rate of TEC index (ROTI) instead of the standard s4 and sigma-phi indices? What are the differences between S4, sigma-phi and ROTI? Examples of ROTI measurements and Development status and plan.

NASA Tech Briefs, January 2014

NASA Technical Reports Server (NTRS)

2014-01-01

Topics include: Multi-Source Autonomous Response for Targeting and Monitoring of Volcanic Activity; Software Suite to Support In-Flight Characterization of Remote Sensing Systems; Visual Image Sensor Organ Replacement; Ultra-Wideband, Dual-Polarized, Beam-Steering P-Band Array Antenna; Centering a DDR Strobe in the Middle of a Data Packet; Using a Commercial Ethernet PHY Device in a Radiation Environment; Submerged AUV Charging Station; Habitat Demonstration Unit (HDU) Vertical Cylinder Habitat; Origami-Inspired Folding of Thick, Rigid Panels; A Novel Protocol for Decoating and Permeabilizing Bacterial Spores for Epifluorescent Microscopy; Method and Apparatus for Automated Isolation of Nucleic Acids from Small Cell Samples; Enabling Microliquid Chromatography by Microbead Packing of Microchannels; On-Command Force and Torque Impeding Devices (OC-FTID) Using ERF; Deployable Fresnel Rings; Transition-Edge Hot-Electron Microbolometers for Millimeter and Submillimeter Astrophysics; Spacecraft Trajectory Analysis and Mission Planning Simulation (STAMPS) Software; Cross Support Transfer Service (CSTS) Framework Library; Arbitrary Shape Deformation in CFD Design; Range Safety Flight Elevation Limit Calculation Software; Frequency-Modulated, Continuous-Wave Laser Ranging Using Photon-Counting Detectors; Calculation of Operations Efficiency Factors for Mars Surface Missions; GPU Lossless Hyperspectral Data Compression System; Robust, Optimal Subsonic Airfoil Shapes; Protograph-Based Raptor-Like Codes; Fuzzy Neuron: Method and Hardware Realization; Kalman Filter Input Processor for Boresight Calibration; Organizing Compression of Hyperspectral Imagery to Allow Efficient Parallel Decompression; and Temperature Dependences of Mechanisms Responsible for the Water-Vapor Continuum Absorption.

Scalable SCPPM Decoder

NASA Technical Reports Server (NTRS)

Quir, Kevin J.; Gin, Jonathan W.; Nguyen, Danh H.; Nguyen, Huy; Nakashima, Michael A.; Moision, Bruce E.

2012-01-01

A decoder was developed that decodes a serial concatenated pulse position modulation (SCPPM) encoded information sequence. The decoder takes as input a sequence of four bit log-likelihood ratios (LLR) for each PPM slot in a codeword via a XAUI 10-Gb/s quad optical fiber interface. If the decoder is unavailable, it passes the LLRs on to the next decoder via a XAUI 10-Gb/s quad optical fiber interface. Otherwise, it decodes the sequence and outputs information bits through a 1-GB/s Ethernet UDP/IP (User Datagram Protocol/Internet Protocol) interface. The throughput for a single decoder unit is 150-Mb/s at an average of four decoding iterations; by connecting a number of decoder units in series, a decoding rate equal to that of the aggregate rate is achieved. The unit is controlled through a 1-GB/s Ethernet UDP/IP interface. This ground station decoder was developed to demonstrate a deep space optical communication link capability, and is unique in the scalable design to achieve real-time SCPP decoding at the aggregate data rate.

Experience with PACS in an ATM/Ethernet switched network environment.

PubMed

Pelikan, E; Ganser, A; Kotter, E; Schrader, U; Timmermann, U

1998-03-01

Legacy local area network (LAN) technologies based on shared media concepts are not adequate for the growth of a large-scale picture archiving and communication system (PACS) in a client-server architecture. First, an asymmetric network load, due to the requests of a large number of PACS clients for only a few main servers, should be compensated by communication links to the servers with a higher bandwidth compared to the clients. Secondly, as the number of PACS nodes increases, the network throughout should not measurably cut production. These requirements can easily be fulfilled using switching technologies. Here asynchronous transfer mode (ATM) is clearly one of the hottest topics in networking because the ATM architecture provides integrated support for a variety of communication services, and it supports virtual networking. On the other hand, most of the imaging modalities are not yet ready for integration into a native ATM network. For a lot of nodes already joining an Ethernet, a cost-effective and pragmatic way to benefit from the switching concept would be a combined ATM/Ethernet switching environment. This incorporates an incremental migration strategy with the immediate benefits of high-speed, high-capacity ATM (for servers and high-sophisticated display workstations), while preserving elements of the existing network technologies. In addition, Ethernet switching instead of shared media Ethernet improves the performance considerably. The LAN emulation (LANE) specification by the ATM forum defines mechanisms that allow ATM networks to coexist with legacy systems using any data networking protocol. This paper points out the suitability of this network architecture in accordance with an appropriate system design.

Impact Analysis of Flow Shaping in Ethernet-AVB/TSN and AFDX from Network Calculus and Simulation Perspective

PubMed Central

He, Feng; Zhao, Lin; Li, Ershuai

2017-01-01

Ethernet-AVB/TSN (Audio Video Bridging/Time-Sensitive Networking) and AFDX (Avionics Full DupleX switched Ethernet) are switched Ethernet technologies, which are both candidates for real-time communication in the context of transportation systems. AFDX implements a fixed priority scheduling strategy with two priority levels. Ethernet-AVB/TSN supports a similar fixed priority scheduling with an additional Credit-Based Shaper (CBS) mechanism. Besides, TSN can support time-triggered scheduling strategy. One direct effect of CBS mechanism is to increase the delay of its flows while decreasing the delay of other priority ones. The former effect can be seen as the shaping restriction and the latter effect can be seen as the shaping benefit from CBS. The goal of this paper is to investigate the impact of CBS on different priority flows, especially on the intermediate priority ones, as well as the effect of CBS bandwidth allocation. It is based on a performance comparison of AVB/TSN and AFDX by simulation in an automotive case study. Furthermore, the shaping benefit is modeled based on integral operation from network calculus perspective. Combing with the analysis of shaping restriction and shaping benefit, some configuration suggestions on the setting of CBS bandwidth are given. Results show that the effect of CBS depends on flow loads and CBS configurations. A larger load of high priority flows in AVB tends to a better performance for the intermediate priority flows when compared with AFDX. Shaping benefit can be explained and calculated according to the changing from the permitted maximum burst. PMID:28531158

Katherine: Ethernet Embedded Readout Interface for Timepix3

NASA Astrophysics Data System (ADS)

Burian, P.; Broulím, P.; Jára, M.; Georgiev, V.; Bergmann, B.

2017-11-01

The Timepix3—the latest generation of hybrid particle pixel detectors of Medipix family—yields a lot of new possibilities, i.e. a high hit-rate, a time resolution of 1.56 ns, event data-driven readout mode, and the capability of measuring the Time-over-Threshold (ToT - energy) and the Time-of-Arrival (ToA) simultaneously. This paper introduces a newly developed readout device for the Timepix3, called "Katherine", featuring a Gigabit Ethernet interface. The primary benefit of the Katherine is the operation of Timepix3 at long distance (up to 100 m) from computer or server, which is advantageous for the installation at beam lines, where the access is difficult or where radiation levels are too high for human interventions. The maximal hit-rate is limited by the bandwidth of the Ethernet connection (peer-to-peer connection; up to 16 Mhit/s). Since the Katherine interface is equipped with a processor of high computational power (ARM Cortex-A9 dual-core processor), it permits the use as a stand-alone (autonomous) radiation detector. The key features of the device are described in detail. These are the implemented high voltage power supply offering both polarities of bias voltage (up to ± 300 V), the automatic data sending to a sever via SSH, the automatic compensation of ToA values from columns with shifted matrix clock, etc. A dedicated control software was developed, which can be used for the detector preparation (sensor equalization, the DACs dependency scan, and the THL scan) and measurement control. Measured energy spectra from photon fields are shown.

(Quasi)-convexification of Barta's (multi-extrema) bounding theorem: Inf_x\\big(\\ssty\\frac{H\\Phi(x)}{\\Phi(x)} \\big) \\le E_gr \\le Sup_x \\big(\\ssty\\frac{H\\Phi(x)}{\\Phi(x)} \\big)

NASA Astrophysics Data System (ADS)

Handy, C. R.

2006-03-01

There has been renewed interest in the exploitation of Barta's configuration space theorem (BCST) (Barta 1937 C. R. Acad. Sci. Paris 204 472) which bounds the ground-state energy, Inf_x\\big({{H\\Phi(x)}\\over {\\Phi(x)}} \\big ) \\leq E_gr \\leq Sup_x \\big({{H\\Phi(x)}\\over {\\Phi(x)}}\\big) , by using any Φ lying within the space of positive, bounded, and sufficiently smooth functions, {\\cal C} . Mouchet's (Mouchet 2005 J. Phys. A: Math. Gen. 38 1039) BCST analysis is based on gradient optimization (GO). However, it overlooks significant difficulties: (i) appearance of multi-extrema; (ii) inefficiency of GO for stiff (singular perturbation/strong coupling) problems; (iii) the nonexistence of a systematic procedure for arbitrarily improving the bounds within {\\cal C} . These deficiencies can be corrected by transforming BCST into a moments' representation equivalent, and exploiting a generalization of the eigenvalue moment method (EMM), within the context of the well-known generalized eigenvalue problem (GEP), as developed here. EMM is an alternative eigenenergy bounding, variational procedure, overlooked by Mouchet, which also exploits the positivity of the desired physical solution. Furthermore, it is applicable to Hermitian and non-Hermitian systems with complex-number quantization parameters (Handy and Bessis 1985 Phys. Rev. Lett. 55 931, Handy et al 1988 Phys. Rev. Lett. 60 253, Handy 2001 J. Phys. A: Math. Gen. 34 5065, Handy et al 2002 J. Phys. A: Math. Gen. 35 6359). Our analysis exploits various quasi-convexity/concavity theorems common to the GEP representation. We outline the general theory, and present some illustrative examples.

Intracellular pH imaging in cancer cells in vitro and tumors in vivo using the new genetically encoded sensor SypHer2.

PubMed

Shirmanova, Marina V; Druzhkova, Irina N; Lukina, Maria M; Matlashov, Mikhail E; Belousov, Vsevolod V; Snopova, Ludmila B; Prodanetz, Natalia N; Dudenkova, Varvara V; Lukyanov, Sergey A; Zagaynova, Elena V

2015-09-01

Measuring intracellular pH (pHi) in tumors is essential for the monitoring of cancer progression and the response of cancer cells to various treatments. The purpose of the study was to develop a method for pHi mapping in living cancer cells in vitro and in tumors in vivo, using the novel genetically encoded indicator, SypHer2. A HeLa Kyoto cell line stably expressing SypHer2 in the cytoplasm was used, to perform ratiometric (dual excitation) imaging of the probe in cell culture, in 3D tumor spheroids and in tumor xenografts in living mice. Using SypHer2, pHi was demonstrated to be 7.34±0.11 in monolayer HeLa cells in vitro under standard cultivation conditions. An increasing pHi gradient from the center to the periphery of the spheroids was displayed. We obtained fluorescence ratio maps for HeLa tumors in vivo and ex vivo. Comparison of the map with the pathomorphology and with hypoxia staining of the tumors revealed a correspondence of the zones with higher pHi to the necrotic and hypoxic areas. Our results demonstrate that pHi imaging with the genetically encoded pHi indicator, SypHer2, can be a valuable tool for evaluating tumor progression in xenograft models. We have demonstrated, for the first time, the possibility of using the genetically encoded sensor SypHer2 for ratiometric pH imaging in cancer cells in vitro and in tumors in vivo. SypHer2 shows great promise as an instrument for pHi monitoring able to provide high accuracy and spatiotemporal resolution. Copyright © 2015 Elsevier B.V. All rights reserved.

PKS1 plays a role in red-light-based positive phototropism in roots.

PubMed

Molas, Maria Lia; Kiss, John Z

2008-06-01

Aerial parts of plants curve towards the light (i.e. positive phototropism), and roots typically grow away from the light (i.e. negative phototropism). In addition, Arabidopsis roots exhibit positive phototropism relative to red light (RL), and this response is mediated by phytochromes A and B (phyA and phyB). Upon light stimulation, phyA and phyB interact with the phytochrome kinase substrate (PKS1) in the cytoplasm. In this study, we investigated the role of PKS1, along with phyA and phyB, in the positive phototropic responses to RL in roots. Using a high-resolution feedback system, we studied the phenotypic responses of roots of phyA, phyB, pks1, phyA pks1 and phyB pks1 null mutants as well as the PKS1-overexpressing line in response to RL. PKS1 emerged as an intermediary in the signalling pathways and appears to promote a negative curvature to RL in roots. In addition, phyA and phyB were both essential for a positive response to RL and act in a complementary fashion. However, either photoreceptor acting without the other results in negative curvature in response to red illumination so that the mode of action differs depending on whether phyA and phyB act independently or together. Our results suggest that PKS1 is part of a signalling pathway independent of phyA and phyB and that PKS1 modulates RL-based root phototropism.

78 FR 14152 - Notice of Intent To Grant Buy America Waiver to Illinois Department of Transportation To Use...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-03-04

... included in IDOT's waiver request are: (1) An ethernet cable; (2) an omni directional antenna; and (3) a... cables, routers, air filtration system, power supplies, radios, antennae, displays, and sensors, which... from INET-II Radio to Ethernet Switch; (2) a 900 MHz Omni- directional antenna; and (3) a RuggedComm RX...

The Skp1 Protein from Toxoplasma Is Modified by a Cytoplasmic Prolyl 4-Hydroxylase Associated with Oxygen Sensing in the Social Amoeba Dictyostelium*

PubMed Central

Xu, Yuechi; Brown, Kevin M.; Wang, Zhuo A.; van der Wel, Hanke; Teygong, Crystal; Zhang, Dongmei; Blader, Ira J.; West, Christopher M.

2012-01-01

In diverse types of organisms, cellular hypoxic responses are mediated by prolyl 4-hydroxylases that use O2 and α-ketoglutarate as substrates to hydroxylate conserved proline residues in target proteins. Whereas in metazoans these enzymes control the stability of the HIFα family of transcription factor subunits, the Dictyostelium enzyme (DdPhyA) contributes to O2 regulation of development by a divergent mechanism involving hydroxylation and subsequent glycosylation of DdSkp1, an adaptor subunit in E3SCF ubiquitin ligases. Sequences related to DdPhyA, DdSkp1, and the glycosyltransferases that cap Skp1 hydroxyproline occur also in the genomes of Toxoplasma and other protists, suggesting that this O2 sensing mechanism may be widespread. Here we show by disruption of the TgphyA locus that this enzyme is required for Skp1 glycosylation in Toxoplasma and that disrupted parasites grow slowly at physiological O2 levels. Conservation of cellular function was tested by expression of TgPhyA in DdphyA-null cells. Simple gene replacement did not rescue Skp1 glycosylation, whereas overexpression not only corrected Skp1 modification but also restored the O2 requirement to a level comparable to that of overexpressed DdPhyA. Bacterially expressed TgPhyA protein can prolyl hydroxylate both Toxoplasma and Dictyostelium Skp1s. Kinetic analyses showed that TgPhyA has similar properties to DdPhyA, including a superimposable dependence on the concentration of its co-substrate α-ketoglutarate. Remarkably, however, TgPhyA had a significantly higher apparent affinity for O2. The findings suggest that Skp1 hydroxylation by PhyA is a conserved process among protists and that this biochemical pathway may indirectly sense O2 by detecting the levels of O2-regulated metabolites such as α-ketoglutarate. PMID:22648409

Analysis and solutions of security issues in Ethernet PON

NASA Astrophysics Data System (ADS)

Meng, Yu; Jiang, Tao; Xiao, Dingzhong

2005-02-01

Ethernet Passive Optical Network (EPON), which combines the low cost Ethernet equipment and economic fiber infrastructure, is being considered as a promising solution for Fiber-To-The-Home (FTTH). However, since EPON is an optical shared medium network, some unique features make it more vulnerable to security attacks. In this paper, the key security threats of EPON are firstly analyzed. And then, considering some specific properties which might be utilized for security, such as the safety of transmissions in upstream direction, some novel methods are presented to solve security problems. Firstly, based on some modification about registration, the mechanism of access control is achieved. Secondly, we implement an AES-128 symmetrical encryption and decryption in the EPON system. The AES-128 algorithm can process data blocks of 128 bits, but the length of Ethernet frame is variable. How to deal with the last block, which is not up to 128 bits, is discussed in detail. Finally, key update is accomplished through a vendor specific OAM frame in order to enhance the level of security. The proposed mechanism will remain in conformance with P2MP specification defined by 802.3ah TF, and can supply a complete security solution for EPON.

Cosmic Ray Flux in the Presence of a Neutral Background

NASA Technical Reports Server (NTRS)

Wilson, Thomas L.; Lodhi, Arfin; Diaz, Abel

2007-01-01

The study of cosmic rays (CRs) is a very mature subject developed around the concept of radiative particle flux phi as a mono-variant function of energy E, that is phi = phi(E). This is based on the notion of the cosmos as being filled with cosmic radiation in the form of a collisionless exosphere of plasma. Neutrals, however, are likewise ubiquitous in space and planetary trapped-radiation belts. It will be shown that in the presence of a neutral background of density rho, flux phi is actually bivariant in energy E and rho, creating a surface phi(E,rho). This is an intrinsic property of charged-particle flux, that flux is not merely a function of E but is dependent upon density rho when a background of neutrals is present. The effect is produced by multiple scattering of charged particles off neutral and ionized atoms along with ionization loss where charged and neutral populations interact. For the harder portion of CR spectra, flux is mono-variant but at nonrelativistic energies (below approx, 350 MeV) it becomes sensitive to the presence of neutral backgrounds. The dependence of phi(E,rho) upon background neutrals is helpful in discussing the anomalous CR (ACR) flux made up of ionized components of the heliospheric neutral atmosphere.

PhyLIS: a simple GNU/Linux distribution for phylogenetics and phyloinformatics.

PubMed

Thomson, Robert C

2009-07-30

PhyLIS is a free GNU/Linux distribution that is designed to provide a simple, standardized platform for phylogenetic and phyloinformatic analysis. The operating system incorporates most commonly used phylogenetic software, which has been pre-compiled and pre-configured, allowing for straightforward application of phylogenetic methods and development of phyloinformatic pipelines in a stable Linux environment. The software is distributed as a live CD and can be installed directly or run from the CD without making changes to the computer. PhyLIS is available for free at http://www.eve.ucdavis.edu/rcthomson/phylis/.

PhyLIS: A Simple GNU/Linux Distribution for Phylogenetics and Phyloinformatics

PubMed Central

Thomson, Robert C.

2009-01-01

PhyLIS is a free GNU/Linux distribution that is designed to provide a simple, standardized platform for phylogenetic and phyloinformatic analysis. The operating system incorporates most commonly used phylogenetic software, which has been pre-compiled and pre-configured, allowing for straightforward application of phylogenetic methods and development of phyloinformatic pipelines in a stable Linux environment. The software is distributed as a live CD and can be installed directly or run from the CD without making changes to the computer. PhyLIS is available for free at http://www.eve.ucdavis.edu/rcthomson/phylis/. PMID:19812729

[Use of [-2] pro PSA and phi index for early detection of prostate cancer: a prospective of 452 patients].

PubMed

Houlgatte, A; Vincendeau, S; Desfemmes, F; Ramirez, J; Benoist, N; Bensalah, K; Durand, X

2012-05-01

Early detection of prostate cancer (Pca) is a real challenge to reduce morbidity and mortality while avoiding over-diagnosis and over-treatment. The prostate specific antigen (PSA) is characterized by its imperfections justifying the evaluation of new serum or urinary specific markers allowing a better selection of patients at risk of developing aggressive Pca. To compare the value of -2pro PSA and phi index to total and free PSA. Serum sampled from 452 patients from two university centers were used to determine levels of PSA before performing biopsies. The patients were included in this study based on the PSA serum concentration between 1.6 ng/mL and 8 ng/mL according to the WHO international standard. All biopsies were performed according to a standardized protocol consisting of 12 cores or more. Sera were analyzed centrally in one of the two institutions with on a single analyzer. Sera from 243 prostate cancer and 208 negative biopsies patients have been taken into account. Sera were analyzed blinded for total PSA, free PSA and [-2] proPSA using Access(®) immunoassay method from Beckman Coulter. The Prostate Health Index (phi) was calculated using the formula phi=([-2] proPSA/fPSA)×sqrt (PSA). The median value of the phi index is significantly (P>0.0001) higher for patients with cancer (phi=65.8) compared to patients with negative biopsies (phi=40.6). At a given sensitivity, the phi index significantly increases the specificity of detection of prostate cancer compared to other markers. The phi index currently appears as the best predictor of prostate cancer for patients with a total PSA between 1.6 and 8 ng/mL according to the WHO standard. The improvement in specificity of the phi index over tPSA could reduce significantly the numbers of unnecessary biopsies. Whether this new biomarker could be an indicator of aggressive prostate cancer remains to be confirmed. Copyright © 2011 Elsevier Masson SAS. All rights reserved.

PPKs mediate direct signal transfer from phytochrome photoreceptors to transcription factor PIF3

DOE PAGES

Ni, Weimin; Xu, Shou-Ling; González-Grandío, Eduardo; ...

2017-05-11

Upon light-induced nuclear translocation, phytochrome (phy) sensory photoreceptors interact with, and induce rapid phosphorylation and consequent ubiquitin-mediated degradation of, transcription factors, called PIFs, thereby regulating target gene expression and plant development. Nevertheless, the biochemical mechanism of phy-induced PIF phosphorylation has remained ill-defined. Here in this paper we identify a family of nuclear protein kinases, designated Photoregulatory Protein Kinases (PPK1–4; formerly called MUT9-Like Kinases (MLKs)), that interact with PIF3 and phyB in a light-induced manner in vivo. Genetic analyses demonstrate that the PPKs are collectively necessary for the normal light-induced phosphorylation and degradation of PIF3. PPK1 directly phosphorylates PIF3 in vitro,more » with a phosphosite pattern that strongly mimics the light-induced pattern in vivo. These data establish that the PPKs are directly involved in catalysing the photoactivated-phy-induced phosphorylation of PIF3 in vivo, and thereby are critical components of a transcriptionally centred signalling hub that pleiotropically regulates plant growth and development in response to multiple signalling pathways.« less

The Caulobacter crescentus phage phiCbK: genomics of a canonical phage

PubMed Central

2012-01-01

Background The bacterium Caulobacter crescentus is a popular model for the study of cell cycle regulation and senescence. The large prolate siphophage phiCbK has been an important tool in C. crescentus biology, and has been studied in its own right as a model for viral morphogenesis. Although a system of some interest, to date little genomic information is available on phiCbK or its relatives. Results Five novel phiCbK-like C. crescentus bacteriophages, CcrMagneto, CcrSwift, CcrKarma, CcrRogue and CcrColossus, were isolated from the environment. The genomes of phage phiCbK and these five environmental phage isolates were obtained by 454 pyrosequencing. The phiCbK-like phage genomes range in size from 205 kb encoding 318 proteins (phiCbK) to 280 kb encoding 448 proteins (CcrColossus), and were found to contain nonpermuted terminal redundancies of 10 to 17 kb. A novel method of terminal ligation was developed to map genomic termini, which confirmed termini predicted by coverage analysis. This suggests that sequence coverage discontinuities may be useable as predictors of genomic termini in phage genomes. Genomic modules encoding virion morphogenesis, lysis and DNA replication proteins were identified. The phiCbK-like phages were also found to encode a number of intriguing proteins; all contain a clearly T7-like DNA polymerase, and five of the six encode a possible homolog of the C. crescentus cell cycle regulator GcrA, which may allow the phage to alter the host cell’s replicative state. The structural proteome of phage phiCbK was determined, identifying the portal, major and minor capsid proteins, the tail tape measure and possible tail fiber proteins. All six phage genomes are clearly related; phiCbK, CcrMagneto, CcrSwift, CcrKarma and CcrRogue form a group related at the DNA level, while CcrColossus is more diverged but retains significant similarity at the protein level. Conclusions Due to their lack of any apparent relationship to other described phages, this group is proposed as the founding cohort of a new phage type, the phiCbK-like phages. This work will serve as a foundation for future studies on morphogenesis, infection and phage-host interactions in C. crescentus. PMID:23050599

Genomics of Three New Bacteriophages Useful in the Biocontrol of Salmonella

PubMed Central

Bardina, Carlota; Colom, Joan; Spricigo, Denis A.; Otero, Jennifer; Sánchez-Osuna, Miquel; Cortés, Pilar; Llagostera, Montserrat

2016-01-01

Non-typhoid Salmonella is the principal pathogen related to food-borne diseases throughout the world. Widespread antibiotic resistance has adversely affected human health and has encouraged the search for alternative antimicrobial agents. The advances in bacteriophage therapy highlight their use in controlling a broad spectrum of food-borne pathogens. One requirement for the use of bacteriophages as antibacterials is the characterization of their genomes. In this work, complete genome sequencing and molecular analyses were carried out for three new virulent Salmonella-specific bacteriophages (UAB_Phi20, UAB_Phi78, and UAB_Phi87) able to infect a broad range of Salmonella strains. Sequence analysis of the genomes of UAB_Phi20, UAB_Phi78, and UAB_Phi87 bacteriophages did not evidence the presence of known virulence-associated and antibiotic resistance genes, and potential immunoreactive food allergens. The UAB_Phi20 genome comprised 41,809 base pairs with 80 open reading frames (ORFs); 24 of them with assigned function. Genome sequence showed a high homology of UAB_Phi20 with Salmonella bacteriophage P22 and other P22likeviruses genus of the Podoviridae family, including ST64T and ST104. The DNA of UAB_Phi78 contained 44,110 bp including direct terminal repeats (DTR) of 179 bp and 58 putative ORFs were predicted and 20 were assigned function. This bacteriophage was assigned to the SP6likeviruses genus of the Podoviridae family based on its high similarity not only with SP6 but also with the K1-5, K1E, and K1F bacteriophages, all of which infect Escherichia coli. The UAB_Phi87 genome sequence consisted of 87,669 bp with terminal direct repeats of 608 bp; although 148 ORFs were identified, putative functions could be assigned to only 29 of them. Sequence comparisons revealed the mosaic structure of UAB_Phi87 and its high similarity with bacteriophages Felix O1 and wV8 of E. coli with respect to genetic content and functional organization. Phylogenetic analysis of large terminase subunits confirms their packaging strategies and grouping to the different phage genus type. All these studies are necessary for the development and the use of an efficient cocktail with commercial applications in bacteriophage therapy against Salmonella. PMID:27148229

Optical Network Virtualisation Using Multitechnology Monitoring and SDN-Enabled Optical Transceiver

NASA Astrophysics Data System (ADS)

Ou, Yanni; Davis, Matthew; Aguado, Alejandro; Meng, Fanchao; Nejabati, Reza; Simeonidou, Dimitra

2018-05-01

We introduce the real-time multi-technology transport layer monitoring to facilitate the coordinated virtualisation of optical and Ethernet networks supported by optical virtualise-able transceivers (V-BVT). A monitoring and network resource configuration scheme is proposed to include the hardware monitoring in both Ethernet and Optical layers. The scheme depicts the data and control interactions among multiple network layers under the software defined network (SDN) background, as well as the application that analyses the monitored data obtained from the database. We also present a re-configuration algorithm to adaptively modify the composition of virtual optical networks based on two criteria. The proposed monitoring scheme is experimentally demonstrated with OpenFlow (OF) extensions for a holistic (re-)configuration across both layers in Ethernet switches and V-BVTs.

General dynamical properties of cosmological models with nonminimal kinetic coupling

NASA Astrophysics Data System (ADS)

Matsumoto, Jiro; Sushkov, Sergey V.

2018-01-01

We consider cosmological dynamics in the theory of gravity with the scalar field possessing the nonminimal kinetic coupling to curvature given as η Gμνphi,μphi,ν, where η is an arbitrary coupling parameter, and the scalar potential V(phi) which assumed to be as general as possible. With an appropriate dimensionless parametrization we represent the field equations as an autonomous dynamical system which contains ultimately only one arbitrary function χ (x)= 8 π | η | V(x/√8 π) with x=√8 πphi. Then, assuming the rather general properties of χ(x), we analyze stationary points and their stability, as well as all possible asymptotical regimes of the dynamical system. It has been shown that for a broad class of χ(x) there exist attractors representing three accelerated regimes of the Universe evolution, including de Sitter expansion (or late-time inflation), the Little Rip scenario, and the Big Rip scenario. As the specific examples, we consider a power-law potential V(phi)=M4(phi/phi0)σ, Higgs-like potential V(phi)=λ/4(phi2‑phi02)2, and exponential potential V(phi)=M4 e‑phi/phi0.

Public health intelligence and the detection of potential pandemics.

PubMed

French, Martin; Mykhalovskiy, Eric

2013-02-01

This article considers contemporary developments in public health intelligence (PHI), especially their focus on health events of pandemic potential. It argues that the sociological study of PHI can yield important insights for the sociology of pandemics. PHI aims to detect health events as (or even before) they unfold. Whilst its apparatuses envelope traditional public health activities, such as epidemiological surveillance, they increasingly extend to non-traditional public health activities such as data-mining in electronically mediated social networks. With a focus on non-traditional PHI activities, the article first situates the study of PHI in relation to the sociology of public health. It then discusses the conceptualisation and actualisation of pandemics, reflecting on how public health professionals and organisations must equip themselves with diverse allies in order to realise the claims they make about pandemic phenomena. Finally, using the analytic tools of actor-network theory, sites for future empirical research that can contribute to the sociology of pandemics are suggested. © 2012 The Authors. Sociology of Health & Illness © 2012 Foundation for the Sociology of Health & Illness/Blackwell Publishing Ltd.

The Prototype HyspIRI Thermal Infrared Radiometer (PHyTIR): A High Speed, Multispectral, Thermal Instrument Development in Support of HyspIRI-TIR

NASA Technical Reports Server (NTRS)

Hook, Simon

2011-01-01

The Prototype HyspIRI Thermal Infrared Radiometer (PHyTIR) is being developed as part of the risk reduction activities associated with the Hyperspectral Infrared Imager (HyspIRI). The HyspIRI mission was recommended by the National Research Council Decadal Survey and includes a visible shortwave infrared (SWIR) pushboom spectrometer and a multispectral whiskbroom thermal infrared (TIR) imager. Data from the HyspIRI mission will be used to address key science questions related to the Solid Earth and Carbon Cycle and Ecosystems focus areas of the NASA Science Mission Directorate. The HyspIRI TIR system will have 60m ground resolution, better than 200mK noise equivalent delta temperature (NEDT), 0.5C absolute temperature resolution with a 5-day repeat from LEO orbit. PHyTIR addresses the technology readiness level (TRL) of certain key subsystems of the TIR imager, primarily the detector assembly and scanning mechanism. PHyTIR will use Mercury Cadmium Telluride (MCT) technology at the focal plane and operate in time delay integration mode. A custom read out integrated circuit (ROIC) will provide the high speed readout hence allowing the high data rates needed for the 5 day repeat. PHyTIR will also demonstrate a newly developed interferometeric metrology system. This system will provide an absolute measurement of the scanning mirror to an order of magnitude better than conventional optical encoders. This will minimize the reliance on ground control points hence minimizing post-processing (e.g. geo-rectification computations).

Mathematical modeling of acid-base physiology

PubMed Central

Occhipinti, Rossana; Boron, Walter F.

2015-01-01

pH is one of the most important parameters in life, influencing virtually every biological process at the cellular, tissue, and whole-body level. Thus, for cells, it is critical to regulate intracellular pH (pHi) and, for multicellular organisms, to regulate extracellular pH (pHo). pHi regulation depends on the opposing actions of plasma-membrane transporters that tend to increase pHi, and others that tend to decrease pHi. In addition, passive fluxes of uncharged species (e.g., CO2, NH3) and charged species (e.g., HCO3− , NH4+) perturb pHi. These movements not only influence one another, but also perturb the equilibria of a multitude of intracellular and extracellular buffers. Thus, even at the level of a single cell, perturbations in acid-base reactions, diffusion, and transport are so complex that it is impossible to understand them without a quantitative model. Here we summarize some mathematical models developed to shed light onto the complex interconnected events triggered by acids-base movements. We then describe a mathematical model of a spherical cell–which to our knowledge is the first one capable of handling a multitude of buffer reaction–that our team has recently developed to simulate changes in pHi and pHo caused by movements of acid-base equivalents across the plasma membrane of a Xenopus oocyte. Finally, we extend our work to a consideration of the effects of simultaneous CO2 and HCO3− influx into a cell, and envision how future models might extend to other cell types (e.g., erythrocytes) or tissues (e.g., renal proximal-tubule epithelium) important for whole-body pH homeostasis. PMID:25617697

Noninvasive NIR measurement of tissue pH to assess hemorrhagic shock in swine

NASA Astrophysics Data System (ADS)

Soller, Babs R.; Zhang, Songbiao; Micheels, Ronald H.; Puyana, Juan C.

1999-07-01

Body-worn noninvasive physilogical sensors are needed to continuously monitor soldiers for hemorrhage and to provide real-time information for minimally skilled medics to treat the injured. In the hospital intramucosal pHi of the gut is used to monitor shock and its treatment. We hypothesize that abdominal wall muscle (AWM) pH can be measured noninvasively using near infrared (NIR) spectroscopy and partial least squares analysis (PLS) and will correlate with pHi. METHODS: AWM pH was measured with microelectrodes and gastric pHi was measured with a tonometric catheter simultaneously while NIR spectra were collected using prototype LED spectrometers placed on the pig's flanks. Animals were subject to hemorrhagic shock at 45 mm Hg for 45 minutes, then resuscitated with blood and lactated ringers. Relationships between electrode pH, pHi and NIR spectra were developed using PLS with cross validation. RESULTS: NIR spectral changes noninvasively acquired through the skin were shown to be from the muscle, not from changes in skin blood flow. Trending ability (R2) model accuracy (RMSD), and relative error were calculated for individual pigs. Using electrode pH as the reference, average R2 was 0.88 with a predicted accuracy of 0.17 pH units, a 9.3% relative error. Slightly degraded results were observed when pHi was used as a reference. CONCLUSIONS: NIR measurement of tissue pH can be used to noninvasively monitor for shock and guide its treatment in a swine model. These measurements correlate with gastric pHi, a clinically accepted measure of shock, providing an approach to develop similar methodology for humans.

ZEUS hardware control system

NASA Astrophysics Data System (ADS)

Loveless, R.; Erhard, P.; Ficenec, J.; Gather, K.; Heath, G.; Iacovacci, M.; Kehres, J.; Mobayyen, M.; Notz, D.; Orr, R.; Orr, R.; Sephton, A.; Stroili, R.; Tokushuku, K.; Vogel, W.; Whitmore, J.; Wiggers, L.

1989-12-01

The ZEUS collaboration is building a system to monitor, control and document the hardware of the ZEUS detector. This system is based on a network of VAX computers and microprocessors connected via ethernet. The database for the hardware values will be ADAMO tables; the ethernet connection will be DECNET, TCP/IP, or RPC. Most of the documentation will also be kept in ADAMO tables for easy access by users.

Real-time flight test data distribution and display

NASA Technical Reports Server (NTRS)

Nesel, Michael C.; Hammons, Kevin R.

1988-01-01

Enhancements to the real-time processing and display systems of the NASA Western Aeronautical Test Range are described. Display processing has been moved out of the telemetry and radar acquisition processing systems super-minicomputers into user/client interactive graphic workstations. Real-time data is provided to the workstations by way of Ethernet. Future enhancement plans include use of fiber optic cable to replace the Ethernet.

Bacteriophage phi11 lysin: physicochemical characterization and comparison with phage phi80a lysin

USDA-ARS?s Scientific Manuscript database

Phage lytic enzymes are promising antimicrobial agents. Lysins of phage phi11 (LysPhi11) and phi80a (LysPhi80a) can lyse (destroy) biofilms and cells of antibiotic-resistant strains of Staphylococcus aureus. Stability of enzymes is one of the parameters making their practical use possible. The obj...

Interactions of phytochromes A, B1 and B2 in light-induced competence for adventitious shoot formation in hypocotyl of tomato (Solanum lycopersicum L.).

PubMed

Lercari, B; Bertram, L

2004-02-01

The interactions of phytochrome A (phyA), phytochrome B1 (phyB1) and phytochrome B2 (phyB2) in light-dependent shoot regeneration from the hypocotyl of tomato was analysed using all eight possible homozygous allelic combinations of the null mutants. The donor plants were pre-grown either in the dark or under red or far-red light for 8 days after sowing; thereafter hypocotyl segments (apical, middle and basal portions) were transferred onto hormone-free medium for culture under different light qualities. Etiolated apical segments cultured in vitro under white light showed a very high frequency of regeneration for all of the genotypes tested besides phyB1phyB2, phyAphyB1 and phyAphyB1phyB2 mutants. Evidence is provided of a specific interference of phyB2 with phyA-mediated HIR to far-red and blue light in etiolated explants. Pre-treatment of donor plants by growth under red light enhanced the competence of phyB1phyB2, phyAphyB1 and phyAphyB1phyB2 mutants for shoot regeneration, whereas pre-irradiation with far-red light enhanced the frequency of regeneration only in the phyAphyB1 mutant. Multiple phytochromes are involved in red light- and far-red light-dependent acquisition of competence for shoot regeneration. The position of the segments along the hypocotyl influenced the role of the various phytochromes and the interactions between them. The culture of competent hypocotyl segments under red, far-red or blue light reduced the frequency of explants forming shoots compared to those cultured under white light, with different genotypes having different response patterns.

BioAir: Bio-Inspired Airborne Infrastructure Reconfiguration

DTIC Science & Technology

2016-01-01

PI minicomputer powered by a different supply. The ODROID and Raspberry PI communicate via an Ethernet connection through a software interface named...HardKernel, an Atheros Wi-Fi card connected to it, and a dedicated power pack developed by RavPower. The hexarotor’s autopilot runs on a separate Raspberry

DelPhiForce web server: electrostatic forces and energy calculations and visualization.

PubMed

Li, Lin; Jia, Zhe; Peng, Yunhui; Chakravorty, Arghya; Sun, Lexuan; Alexov, Emil

2017-11-15

Electrostatic force is an essential component of the total force acting between atoms and macromolecules. Therefore, accurate calculations of electrostatic forces are crucial for revealing the mechanisms of many biological processes. We developed a DelPhiForce web server to calculate and visualize the electrostatic forces at molecular level. DelPhiForce web server enables modeling of electrostatic forces on individual atoms, residues, domains and molecules, and generates an output that can be visualized by VMD software. Here we demonstrate the usage of the server for various biological problems including protein-cofactor, domain-domain, protein-protein, protein-DNA and protein-RNA interactions. The DelPhiForce web server is available at: http://compbio.clemson.edu/delphi-force. delphi@clemson.edu. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Optimizing the updated Goddard shortwave radiation Weather Research and Forecasting (WRF) scheme for Intel Many Integrated Core (MIC) architecture

NASA Astrophysics Data System (ADS)

Mielikainen, Jarno; Huang, Bormin; Huang, Allen H.-L.

2015-05-01

Intel Many Integrated Core (MIC) ushers in a new era of supercomputing speed, performance, and compatibility. It allows the developers to run code at trillions of calculations per second using the familiar programming model. In this paper, we present our results of optimizing the updated Goddard shortwave radiation Weather Research and Forecasting (WRF) scheme on Intel Many Integrated Core Architecture (MIC) hardware. The Intel Xeon Phi coprocessor is the first product based on Intel MIC architecture, and it consists of up to 61 cores connected by a high performance on-die bidirectional interconnect. The co-processor supports all important Intel development tools. Thus, the development environment is familiar one to a vast number of CPU developers. Although, getting a maximum performance out of Xeon Phi will require using some novel optimization techniques. Those optimization techniques are discusses in this paper. The results show that the optimizations improved performance of the original code on Xeon Phi 7120P by a factor of 1.3x.

Alternatives to Greek-Letter Organizations Warrant a Second Look

ERIC Educational Resources Information Center

David, Marc C.

2004-01-01

Because of the discriminatory practices and lack of appeal of many predominantly White Greek-letter organizations, students of color sought the development of their own. Alpha Phi Alpha, Rho Psi, MALIK Sigma Psi, Lambda Theta Phi, and Alpha Pi Omega set the stage for later African American, Asian, African, Latino and American Indian Greek-letter…

Warm inflationary model in loop quantum cosmology

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

Herrera, Ramon

A warm inflationary universe model in loop quantum cosmology is studied. In general we discuss the condition of inflation in this framework. By using a chaotic potential, V({phi}){proportional_to}{phi}{sup 2}, we develop a model where the dissipation coefficient {Gamma}={Gamma}{sub 0}=constant. We use recent astronomical observations for constraining the parameters appearing in our model.

Phi ({Phi}) and psi ({Psi}) angles involved in malarial peptide bonds determine sterile protective immunity

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

Patarroyo, Manuel E., E-mail: mepatarr@gmail.com; Universidad Nacional de Colombia, Bogota; Moreno-Vranich, Armando

Highlights: Black-Right-Pointing-Pointer Phi ({Phi}) and psi ({Psi}) angles determine sterile protective immunity. Black-Right-Pointing-Pointer Modified peptide's tendency to assume a regular conformation related to a PPII{sub L}. Black-Right-Pointing-Pointer Structural modifications in mHABPs induce Ab and protective immunity. Black-Right-Pointing-Pointer mHABP backbone atom's interaction with HLA-DR{beta}1{sup Asterisk-Operator} is stabilised by H-bonds. -- Abstract: Modified HABP (mHABP) regions interacting with HLA-DR{beta}1{sup Asterisk-Operator} molecules have a more restricted conformation and/or sequence than other mHABPs which do not fit perfectly into their peptide binding regions (PBR) and do not induce an acceptable immune response due to the critical role of their {Phi} and {Psi} torsion angles.more » These angle's critical role was determined in such highly immunogenic, protection-inducing response against experimental malaria using the conformers (mHABPs) obtained by {sup 1}H-NMR and superimposed into HLA-DR{beta}1{sup Asterisk-Operator }-like Aotus monkey molecules; their phi ({Phi}) and psi ({Psi}) angles were measured and the H-bond formation between these molecules was evaluated. The aforementioned mHABP propensity to assume a regular conformation similar to a left-handed polyproline type II helix (PPII{sub L}) led to suggesting that favouring these conformations according to their amino acid sequence would lead to high antibody titre production and sterile protective immunity induction against malaria, thereby adding new principles or rules for vaccine development, malaria being one of them.« less

Incentive Spirometry after Lung Resection: A Randomized Controlled Trial.

PubMed

Malik, Peter Ra; Fahim, Christine; Vernon, Jordyn; Thomas, Priya; Schieman, Colin; Finley, Christian J; Agzarian, John; Shargall, Yaron; Farrokhyar, Forough; Hanna, Wael C

2018-04-24

Incentive spirometry (IS) is thought to reduce the incidence of postoperative pulmonary complications (PPC) after lung resection. We sought to determine whether the addition of IS to routine physiotherapy following lung resection results in a lower rate of PPC, as compared to physiotherapy alone. A single-blind prospective randomized controlled trial was conducted in adults undergoing lung resection. Individuals with previous lung surgery or home oxygen were excluded. Participants randomized to the control arm (PHY) received routine physiotherapy alone (deep breathing, ambulation and shoulder exercises). Those randomized to the intervention arm (PHY/IS) received IS in addition to routine physiotherapy. The trial was powered to detect a 10% difference in the rate of PPC (beta=80%). Student's t-test and chi-square were utilized for continuous and categorical variables respectively, with a significance level of p=0.05. A total of 387 participants (n=195 PHY/IS; n=192 PHY) were randomized between 2014-2017. Baseline characteristics were comparable for both arms. The majority of patients underwent a pulmonary lobectomy (PHY/IS=59.5%, PHY=61.0%, p=0.84), with no difference in the rates of minimally invasive and open procedures. There were no differences in the incidence of PPC at 30 days postoperatively (PHY/IS=12.3%, PHY=13.0%, p=0.88). There were no differences in rates of pneumonia (PHY/IS=4.6%, PHY=7.8%, p=0.21), mechanical ventilation (PHY/IS=2.1%, PHY=1.0%, p=0.41), home-oxygen (PHY/IS=13.8%, PHY=14.6%, p=0.89), hospital length of stay (PHY/IS=4 days, PHY=4 days, p=0.34), or rate of readmission to hospital (PHY/IS=10.3%, PH=9.9%, p=1.00). The addition of IS to routine postoperative physiotherapy does not reduce the incidence of PPC after lung resection. Copyright © 2018. Published by Elsevier Inc.

Purification and characterization of two distinct acidic phytases with broad pH stability from Aspergillus niger NCIM 563.

PubMed

Soni, S K; Magdum, A; Khire, J M

2010-11-01

Aspergillus niger NCIM 563 produced two different extracellular phytases (Phy I and Phy II) under submerged fermentation conditions at 30°C in medium containing dextrin-glucose-sodium nitrate-salts. Both the enzymes were purified to homogeneity using Rotavapor concentration, Phenyl-Sepharose column chromatography and Sephacryl S-200 gel filtration. The molecular mass of Phy I and II as determined by SDS-PAGE and gel filtration were 66, 264, 150 and 148 kDa respectively, indicating that Phy I consists of four identical subunits and Phy II is a monomer. The pI values of Phy I and II were 3.55 and 3.91, respectively. Phy I was highly acidic with optimum pH of 2.5 and was stable over a broad pH range (1.5-9.0) while Phy II showed a pH optimum of 5.0 with stability in the range of pH 3.5-9.0. Phy I exhibited very broad substrate specificity while Phy II was more specific for sodium phytate. Similarly Phy II was strongly inhibited by Ag(+), Hg(2+) (1 mM) metal ions and Phy I was partially inhibited. Peptide analysis by Mass Spectrometry (MS) MALDI-TOF also indicated that both the proteins were totally different. The K(m) for Phy I and II for sodium phytate was 2.01 and 0.145 mM while V(max) was 5,018 and 1,671 μmol min(-1) mg(-1), respectively. The N-terminal amino acid sequences of Phy I and Phy II were FSYGAAIPQQ and GVDERFPYTG, respectively. Phy II showed no homology with Phy I and any other known phytases from the literature suggesting its unique nature. This, according to us, is the first report of two distinct novel phytases from Aspergillus niger.

A study of the relationship between the chemical structures and the fluorescence quantum yields of coumarins, quinoxalinones and benzoxazinones for the development of sensitive fluorescent derivatization reagents.

PubMed

Azuma, Kentaro; Suzuki, Sachiko; Uchiyama, Seiichi; Kajiro, Toshi; Santa, Tomofumi; Imai, Kazuhiro

2003-04-01

To develop new fluorescent derivatization reagents, we investigated the relationship between the chemical structures and the fluorescence quantum yields (phi(f)) of coumarins, quinoxalinones and benzoxadinones. Forty-six compounds were synthesized and their fluorescence spectra were measured in n-hexane, ethyl acetate, methanol and water. The energy levels of these compounds were calculated by combination of the semi-empirical AM1 and INDO/S (CI = all) methods. The deltaE(Tn(n,pi*), S1(pi,pi*)) (the energy gap between the Tn(n,pi*) and S1(pi,pi*) states) values were well correlated with the phi(f) values, which enables us to predict the phi(f) values from their chemical structures. Based on this relationship, 3-phenyl-7-N-piperazinoquinoxalin-2(1H)-one (PQ-Pz) and 7-(3-(S)-aminopyrrolidin-1-yl)-3-phenylquinoxalin-2-(1H)-one (PQ-APy) were developed as fluorescent derivatization reagents for carboxylic acids. The derivatives of the carboxylic acids with PQ-Pz and PQ-APy showed large phi(f) values even in polar solvents, suggesting that these reagents are suitable for the microanalysis of biologically important carboxylic acids by reversed phase HPLC.

Fruit-localized Phytochromes Regulate Plastid Biogenesis, Starch Synthesis and Carotenoid Metabolism in Tomato.

PubMed

Ernesto Bianchetti, Ricardo; Silvestre Lira, Bruno; Santos Monteiro, Scarlet; Demarco, Diego; Purgatto, Eduardo; Rothan, Christophe; Rossi, Magdalena; Freschi, Luciano

2018-04-18

Light signaling has long been reported to influence fruit biology, though the regulatory impact of fruit-localized photoreceptors on fruit development and metabolism remains elusive. Studies performed in phytochrome(PHY)-deficient tomato (Solanum lycopersicum) mutants suggest that SlPHYA, SlPHYB2 and to a lesser extent SlPHYB1 influence fruit development and ripening. By employing fruit-specific RNAi-mediated silencing of SlPHY genes, we demonstrated that fruit-localized SlPHYA and SlPHYB2 play contrasting roles in regulating plastid biogenesis and maturation in tomato. Data revealed that fruit-localized SlPHYA, rather than SlPHYB1 or SlPHYB2, positively influence tomato plastid differentiation and division machinery via changes in both light and cytokinin signaling-related gene expression. Fruit-localized SlPHYA and SlPHYB2 were also shown to modulate sugar metabolism in early developing fruits via overlapping, yet distinct, mechanisms involving the coordinated transcriptional regulation of sink- and starch biosynthesis-related genes. Fruit-specific SlPHY silencing also drastically altered the transcriptional profile of genes encoding light repressor proteins and carotenoid biosynthesis regulators, leading to reduced carotenoid biosynthesis during fruit ripening. Therefore, besides providing conclusive evidence on the regulation of tomato quality by fruit-localized phytochromes, our data also demonstrate the existence of an intricate PHY-hormonal interplay during fruit development and ripening.

Phytochrome B Requires PIF Degradation and Sequestration to Induce Light Responses Across a Wide Range of Light Conditions.

PubMed

Park, Eunae; Kim, Yeojae; Choi, Giltsu

2018-05-15

Phytochrome B (phyB) inhibits the function of phytochrome-interacting factors (PIFs) by inducing their degradation and sequestration, but the relative physiological importance of these two phyB activities is unclear. In an analysis of published Arabidopsis thaliana phyB mutations, we identified a point mutation in the N-terminal half of phyB (phyBG111D) that abolishes its PIF sequestration activity without affecting its PIF degradation activity. We also identified a point mutation in the phyB C-terminal domain, which, when combined with a deletion of the C-terminal end (phyB990G767R), does the opposite; it blocks PIF degradation without affecting PIF sequestration. The resulting phyB proteins, phyB990G767R and phyBG111D, are equally capable of inducing light responses under continuous red light. However, phyBG111D, which exhibits only the PIF degradation activity, induces stronger light responses than phyB990G767R under white light with prolonged dark periods (i.e., diurnal cycles). In contrast, phyB990G767R, which exhibits only the PIF sequestration activity, induces stronger light responses in flickering light (a condition that mimics sunflecks). Together, our results indicate that both of these separable phyB activities are required for light responses in varying light conditions. © 2018 American Society of Plant Biologists. All rights reserved.

Broadband Optical Access Technologies to Converge towards a Broadband Society in Europe

NASA Astrophysics Data System (ADS)

Coudreuse, Jean-Pierre; Pautonnier, Sophie; Lavillonnière, Eric; Didierjean, Sylvain; Hilt, Benoît; Kida, Toshimichi; Oshima, Kazuyoshi

This paper provides insights on the status of broadband optical access market and technologies in Europe and on the expected trends for the next generation optical access networks. The final target for most operators, cities or any other player is of course FTTH (Fibre To The Home) deployment although we can expect intermediate steps with copper or wireless technologies. Among the two candidate architectures for FTTH, PON (Passive Optical Network) is by far the most attractive and cost effective solution. We also demonstrate that Ethernet based optical access network is very adequate to all-IP networks without any incidence on the level of quality of service. Finally, we provide feedback from a FTTH pilot network in Colmar (France) based on Gigabit Ethernet PON technology. The interest of this pilot lies on the level of functionality required for broadband optical access networks but also on the development of new home network configurations.

Ethernet-based test stand for a CAN network

NASA Astrophysics Data System (ADS)

Ziebinski, Adam; Cupek, Rafal; Drewniak, Marek

2017-11-01

This paper presents a test stand for the CAN-based systems that are used in automotive systems. The authors propose applying an Ethernet-based test system that supports the virtualisation of a CAN network. The proposed solution has many advantages compared to classical test beds that are based on dedicated CAN-PC interfaces: it allows the physical constraints associated with the number of interfaces that can be simultaneously connected to a tested system to be avoided, which enables the test time for parallel tests to be shortened; the high speed of Ethernet transmission allows for more frequent sampling of the messages that are transmitted by a CAN network (as the authors show in the experiment results section) and the cost of the proposed solution is much lower than the traditional lab-based dedicated CAN interfaces for PCs.

[The relevance of multiple sclerosis drugs in private health insurance (PHI)].

PubMed

Wild, F

2015-06-01

The development of expenses and prescriptions in the pharmacotherapy for multiple sclerosis (MS) is examined on the basis of prescription data of 14 PHI firms. The drugs for the treatment of MS are among the most top-selling drugs in the PHI. From 2007 to 2012, the expenses increase 2.33-fold. The main cause is the increas of the prescription figures. In 2012, about 8,400 privately insured persons receive an MS drug. The prevalence of MS is 2.3 times higher in women than in men Impro ved diagnostic possibilities and expensive new drugs will lead to a dynamic cost de velopment in the next years.

Role of the N*(1535) in pp{yields}pp{phi} and {pi}{sup -}p{yields}n{phi} reactions

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

Xie Jujun; Graduate University of Chinese Academy of Sciences, Beijing 100049; Zou Bingsong

2008-01-15

The near-threshold {phi}-meson production in proton-proton and {pi}{sup -}p collisions is studied with the assumption that the production mechanism is due to the sub-N{phi}-threshold N*(1535) resonance. The {pi}{sup 0}-,{eta}-, and {rho}{sup 0}-meson exchanges for proton-proton collisions are considered. It is shown that the contribution to the pp{yields}pp{phi} reaction from the t-channel {pi}{sup 0}-meson exchange is dominant. With a significant N*(1535)N{phi} coupling [g{sub N*(1535)N{phi}}{sup 2}/4{pi}=0.13], both pp{yields}pp{phi} and {pi}{sup -}p{yields}n{phi} data are very well reproduced. The significant coupling of the N*(1535) resonance to N{phi} is compatible with previous indications of a large ss component in the quark wave function of themore » N*(1535) resonance and may be the real origin of the significant enhancement of the {phi} production over the naive OZI-rule predictions.« less

The differential production cross section of the $$\\phi $$ (1020) meson in $$\\sqrt{s}$$ TeV $pp$ collisions measured with the ATLAS detector

DOE PAGES

Aad, G.; Abajyan, T.; Abbott, B.; ...

2014-07-01

Ameasurement is presented of themore » $$\\phi $$×BR($$\\phi $$ →K < sup > + < /sup > K < sup > - < /sup > ) production cross section at √s = 7 TeV using pp collision data corresponding to an integrated luminosity of 383 μb -1, collected with the ATLAS experiment at the HC. Selection of $$\\phi $$(1020) mesons is based on the identification of charged kaons by their energy loss in the pixel detector. The differential cross section ismeasured as a function of the transverse momentum, pT,$$\\phi $$ , and rapidity, y$$\\phi $$, of the $$\\phi $$(1020) meson in the fiducial region 500 < pT,$$\\phi $$ < 1200MeV, |y$$\\phi $$ | < 0.8, kaon p T,K > 230 MeV and kaon momentum p K < 800 MeV. The integrated $$\\phi $$(1020)-meson production cross section in this fiducial range is measured to be sφ×BR($$\\phi $$ →K < sup > + < /sup > K < sup > - < /sup > ) = 570 ± 8 (stat) ± 66 (syst) ± 20 (lumi) μb.« less

CHEETAH: circuit-switched high-speed end-to-end transport architecture

NASA Astrophysics Data System (ADS)

Veeraraghavan, Malathi; Zheng, Xuan; Lee, Hyuk; Gardner, M.; Feng, Wuchun

2003-10-01

Leveraging the dominance of Ethernet in LANs and SONET/SDH in MANs and WANs, we propose a service called CHEETAH (Circuit-switched High-speed End-to-End Transport ArcHitecture). The service concept is to provide end hosts with high-speed, end-to-end circuit connectivity on a call-by-call shared basis, where a "circuit" consists of Ethernet segments at the ends that are mapped into Ethernet-over-SONET long-distance circuits. This paper focuses on the file-transfer application for such circuits. For this application, the CHEETAH service is proposed as an add-on to the primary Internet access service already in place for enterprise hosts. This allows an end host that is sending a file to first attempt setting up an end-to-end Ethernet/EoS circuit, and if rejected, fall back to the TCP/IP path. If the circuit setup is successful, the end host will enjoy a much shorter file-transfer delay than on the TCP/IP path. To determine the conditions under which an end host with access to the CHEETAH service should attempt circuit setup, we analyze mean file-transfer delays as a function of call blocking probability in the circuit-switched network, probability of packet loss in the IP network, round-trip times, link rates, and so on.

Root development and structure in seedlings of Ginkgo biloba.

PubMed

Bonacorsi, Nikole K; Seago, James L

2016-02-01

The popular, highly recognizable, well-known gymnosperm, Ginkgo biloba, was studied to document selected developmental features, which are little known in its primary root system from root tips to cotyledonary node following seed germination. Using seedlings grown in soil, vermiculite, or a mixture, we examined sections at various distances from the root cap to capture a developmental sequence of anatomical structures by using standard brightfield, epifluorescence, and confocal microscopic techniques. The vascular cylinder is usually a diarch stele, although modified diarchy and triarchy are found. Between exarch protoxylem poles, metaxylem usually develops into a complete disc, except near the transition region, which has irregularly arranged tracheary cells. The disc of primary xylem undergoes secondary growth on its metaxylem flanks with many tracheids added radially within a few weeks. Production of fibers in secondary phloem also accompanies secondary growth. In the cortex, endodermis produces Casparian bands early in development and continues into the upper transition region. Phi cells with phi-thickenings (bands of lignified walls) of a layer of inner cortex are often evident before endodermis, and then adjoining, additional layers of cortex develop phi cells; phi cells do not occur in the upper transition region or stem. An exodermis is produced early in root development and is continuous into the transition region and cotyledonary node. Seedling root axes of Ginkgo biloba are more complex than the literature suggests, and our findings contribute to our knowledge of root structure of this ancient gymnosperm. © 2016 Botanical Society of America.

Commensurability effects in one-dimensional Anderson localization: Anomalies in eigenfunction statistics

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

Kravtsov, V.E., E-mail: kravtsov@ictp.it; Landau Institute for Theoretical Physics, 2 Kosygina st., 117940 Moscow; Yudson, V.I., E-mail: yudson@isan.troitsk.ru

Highlights: > Statistics of normalized eigenfunctions in one-dimensional Anderson localization at E = 0 is studied. > Moments of inverse participation ratio are calculated. > Equation for generating function is derived at E = 0. > An exact solution for generating function at E = 0 is obtained. > Relation of the generating function to the phase distribution function is established. - Abstract: The one-dimensional (1d) Anderson model (AM), i.e. a tight-binding chain with random uncorrelated on-site energies, has statistical anomalies at any rational point f=(2a)/({lambda}{sub E}) , where a is the lattice constant and {lambda}{sub E} is the demore » Broglie wavelength. We develop a regular approach to anomalous statistics of normalized eigenfunctions {psi}(r) at such commensurability points. The approach is based on an exact integral transfer-matrix equation for a generating function {Phi}{sub r}(u, {phi}) (u and {phi} have a meaning of the squared amplitude and phase of eigenfunctions, r is the position of the observation point). This generating function can be used to compute local statistics of eigenfunctions of 1d AM at any disorder and to address the problem of higher-order anomalies at f=p/q with q > 2. The descender of the generating function P{sub r}({phi}){identical_to}{Phi}{sub r}(u=0,{phi}) is shown to be the distribution function of phase which determines the Lyapunov exponent and the local density of states. In the leading order in the small disorder we derived a second-order partial differential equation for the r-independent ('zero-mode') component {Phi}(u, {phi}) at the E = 0 (f=1/2 ) anomaly. This equation is nonseparable in variables u and {phi}. Yet, we show that due to a hidden symmetry, it is integrable and we construct an exact solution for {Phi}(u, {phi}) explicitly in quadratures. Using this solution we computed moments I{sub m} = N< vertical bar {psi} vertical bar {sup 2m}> (m {>=} 1) for a chain of the length N {yields} {infinity} and found an essential difference between their m-behavior in the center-of-band anomaly and for energies outside this anomaly. Outside the anomaly the 'extrinsic' localization length defined from the Lyapunov exponent coincides with that defined from the inverse participation ratio ('intrinsic' localization length). This is not the case at the E = 0 anomaly where the extrinsic localization length is smaller than the intrinsic one. At E = 0 one also observes an anomalous enhancement of large moments compatible with existence of yet another, much smaller characteristic length scale.« less

Comparative Study of Blood-Based Biomarkers, α2,3-Sialic Acid PSA and PHI, for High-Risk Prostate Cancer Detection.

PubMed

Ferrer-Batallé, Montserrat; Llop, Esther; Ramírez, Manel; Aleixandre, Rosa Núria; Saez, Marc; Comet, Josep; de Llorens, Rafael; Peracaula, Rosa

2017-04-17

Prostate Specific Antigen (PSA) is the most commonly used serum marker for prostate cancer (PCa), although it is not specific and sensitive enough to allow the differential diagnosis of the more aggressive tumors. For that, new diagnostic methods are being developed, such as PCA-3, PSA isoforms that have resulted in the 4K score or the Prostate Health Index (PHI), and PSA glycoforms. In the present study, we have compared the PHI with our recently developed PSA glycoform assay, based on the determination of the α2,3-sialic acid percentage of serum PSA (% α2,3-SA), in a cohort of 79 patients, which include 50 PCa of different grades and 29 benign prostate hyperplasia (BPH) patients. The % α2,3-SA could distinguish high-risk PCa patients from the rest of patients better than the PHI (area under the curve (AUC) of 0.971 vs. 0.840), although the PHI correlated better with the Gleason score than the % α2,3-SA. The combination of both markers increased the AUC up to 0.985 resulting in 100% sensitivity and 94.7% specificity to differentiate high-risk PCa from the other low and intermediate-risk PCa and BPH patients. These results suggest that both serum markers complement each other and offer an improved diagnostic tool to identify high-risk PCa, which is an important requirement for guiding treatment decisions.

Accelerating the Pace of Protein Functional Annotation With Intel Xeon Phi Coprocessors.

PubMed

Feinstein, Wei P; Moreno, Juana; Jarrell, Mark; Brylinski, Michal

2015-06-01

Intel Xeon Phi is a new addition to the family of powerful parallel accelerators. The range of its potential applications in computationally driven research is broad; however, at present, the repository of scientific codes is still relatively limited. In this study, we describe the development and benchmarking of a parallel version of eFindSite, a structural bioinformatics algorithm for the prediction of ligand-binding sites in proteins. Implemented for the Intel Xeon Phi platform, the parallelization of the structure alignment portion of eFindSite using pragma-based OpenMP brings about the desired performance improvements, which scale well with the number of computing cores. Compared to a serial version, the parallel code runs 11.8 and 10.1 times faster on the CPU and the coprocessor, respectively; when both resources are utilized simultaneously, the speedup is 17.6. For example, ligand-binding predictions for 501 benchmarking proteins are completed in 2.1 hours on a single Stampede node equipped with the Intel Xeon Phi card compared to 3.1 hours without the accelerator and 36.8 hours required by a serial version. In addition to the satisfactory parallel performance, porting existing scientific codes to the Intel Xeon Phi architecture is relatively straightforward with a short development time due to the support of common parallel programming models by the coprocessor. The parallel version of eFindSite is freely available to the academic community at www.brylinski.org/efindsite.

The Pemberton Happiness Index: Validation of the Universal Portuguese version in a large Brazilian sample.

PubMed

Paiva, Bianca Sakamoto Ribeiro; de Camargos, Mayara Goulart; Demarzo, Marcelo Marcos Piva; Hervás, Gonzalo; Vázquez, Carmelo; Paiva, Carlos Eduardo

2016-09-01

The Pemberton Happiness Index (PHI) is a recently developed integrative measure of well-being that includes components of hedonic, eudaimonic, social, and experienced well-being. The PHI has been validated in several languages, but not in Portuguese. Our aim was to cross-culturally adapt the Universal Portuguese version of the PHI and to assess its psychometric properties in a sample of the Brazilian population using online surveys.An expert committee evaluated 2 versions of the PHI previously translated into Portuguese by the original authors using a standardized form for assessment of semantic/idiomatic, cultural, and conceptual equivalence. A pretesting was conducted employing cognitive debriefing methods. In sequence, the expert committee evaluated all the documents and reached a final Universal Portuguese PHI version. For the evaluation of the psychometric properties, the data were collected using online surveys in a cross-sectional study. The study population included healthcare professionals and users of the social network site Facebook from several Brazilian geographic areas. In addition to the PHI, participants completed the Satisfaction with Life Scale (SWLS), Diener and Emmons' Positive and Negative Experience Scale (PNES), Psychological Well-being Scale (PWS), and the Subjective Happiness Scale (SHS). Internal consistency, convergent validity, known-group validity, and test-retest reliability were evaluated. Satisfaction with the previous day was correlated with the 10 items assessing experienced well-being using the Cramer V test. Additionally, a cut-off value of PHI to identify a "happy individual" was defined using receiver-operating characteristic (ROC) curve methodology.Data from 1035 Brazilian participants were analyzed (health professionals = 180; Facebook users = 855). Regarding reliability results, the internal consistency (Cronbach alpha = 0.890 and 0.914) and test-retest (intraclass correlation coefficient = 0.814) were both considered adequate. Most of the validity hypotheses formulated a priori (convergent and know-group) was further confirmed. The cut-off value of higher than 7 in remembered PHI was identified (AUC = 0.780, sensitivity = 69.2%, specificity = 78.2%) as the best one to identify a happy individual.We concluded that the Universal Portuguese version of the PHI is valid and reliable for use in the Brazilian population using online surveys.

Mucosal safety of PHI-443 and stampidine as a combination microbicide to prevent genital transmission of HIV-1.

PubMed

D'Cruz, Osmond J; Uckun, Fatih M

2007-10-01

To investigate the in vitro and in vivo mucosal safety of a nonnucleoside reverse transcriptase (RT) inhibitor (PHI-443) and a nucleoside analogue RT inhibitor (stampidine)-based anti-HIV microbicide either alone or in combination. In vitro and in vivo studies using three-dimensional vaginal epithelia integrating Langerhans cells and 16 New Zealand White rabbits, respectively. Research laboratory. Rabbits in groups of four were exposed intravaginally to a gel with and without 1% PHI-443, 1% stampidine, or 1% PHI-443 plus 1% stampidine for 14 days. Cytokine/chemokine release by three-dimensional co-cultures in the presence and absence of PHI-443 or stampidine. Histologic scoring of vaginal tissue for mucosal toxicity at 24 hours after dosing. Simultaneous evaluation of levels of 10 cytokines (granulocyte-macrophage colony-stimulating factor, interleukin-1 alpha, interleukin-13, macrophage inflammatory protein-1 beta, granulocyte colony-stimulating factor, interleukin-18, tumor necrosis factor-alpha, interleukin-6, interleukin-1 beta, and interferon-gamma) and 6 chemokines (epithelial neutrophil-activating peptide-78, interleukin-8, monocyte/macrophage chemoattractant protein-1, macrophage inflammatory protein-3 alpha, interferon-inducible protein-10, and regulated upon activation of normal T-cell expressed and secreted) in culture media by a multiplexed chemiluminescence-based immunoassay. In the rabbit model, repeated intravaginal administration of PHI-443 plus stampidine via a gel formulation at concentrations nearly 2,000 and 10,000 times higher than their respective in vitro anti-HIV IC(50) values did not result in vaginal irritation. The levels of proinflammatory cytokines/chemokines secreted by multilayered human genital epithelia integrating Langerhans cells were unaffected by prolonged exposure to PHI-443 or stampidine. The combination of PHI-443 and stampidine was noncytotoxic to vaginal epithelial cells, nonirritating to vaginal mucosa, and did not induce the secretion of proinflammatory cytokines and chemokines by co-cultures of human genital epithelia and Langerhans cells. These attributes are particularly useful for the clinical development of PHI-443 and stampidine as a combination microbicide and as a prophylactic anti-HIV agent to curb genital transmission of HIV-1 by semen.

List-mode PET image reconstruction for motion correction using the Intel XEON PHI co-processor

NASA Astrophysics Data System (ADS)

Ryder, W. J.; Angelis, G. I.; Bashar, R.; Gillam, J. E.; Fulton, R.; Meikle, S.

2014-03-01

List-mode image reconstruction with motion correction is computationally expensive, as it requires projection of hundreds of millions of rays through a 3D array. To decrease reconstruction time it is possible to use symmetric multiprocessing computers or graphics processing units. The former can have high financial costs, while the latter can require refactoring of algorithms. The Xeon Phi is a new co-processor card with a Many Integrated Core architecture that can run 4 multiple-instruction, multiple data threads per core with each thread having a 512-bit single instruction, multiple data vector register. Thus, it is possible to run in the region of 220 threads simultaneously. The aim of this study was to investigate whether the Xeon Phi co-processor card is a viable alternative to an x86 Linux server for accelerating List-mode PET image reconstruction for motion correction. An existing list-mode image reconstruction algorithm with motion correction was ported to run on the Xeon Phi coprocessor with the multi-threading implemented using pthreads. There were no differences between images reconstructed using the Phi co-processor card and images reconstructed using the same algorithm run on a Linux server. However, it was found that the reconstruction runtimes were 3 times greater for the Phi than the server. A new version of the image reconstruction algorithm was developed in C++ using OpenMP for mutli-threading and the Phi runtimes decreased to 1.67 times that of the host Linux server. Data transfer from the host to co-processor card was found to be a rate-limiting step; this needs to be carefully considered in order to maximize runtime speeds. When considering the purchase price of a Linux workstation with Xeon Phi co-processor card and top of the range Linux server, the former is a cost-effective computation resource for list-mode image reconstruction. A multi-Phi workstation could be a viable alternative to cluster computers at a lower cost for medical imaging applications.

The Pemberton Happiness Index

PubMed Central

Paiva, Bianca Sakamoto Ribeiro; de Camargos, Mayara Goulart; Demarzo, Marcelo Marcos Piva; Hervás, Gonzalo; Vázquez, Carmelo; Paiva, Carlos Eduardo

2016-01-01

Abstract The Pemberton Happiness Index (PHI) is a recently developed integrative measure of well-being that includes components of hedonic, eudaimonic, social, and experienced well-being. The PHI has been validated in several languages, but not in Portuguese. Our aim was to cross-culturally adapt the Universal Portuguese version of the PHI and to assess its psychometric properties in a sample of the Brazilian population using online surveys. An expert committee evaluated 2 versions of the PHI previously translated into Portuguese by the original authors using a standardized form for assessment of semantic/idiomatic, cultural, and conceptual equivalence. A pretesting was conducted employing cognitive debriefing methods. In sequence, the expert committee evaluated all the documents and reached a final Universal Portuguese PHI version. For the evaluation of the psychometric properties, the data were collected using online surveys in a cross-sectional study. The study population included healthcare professionals and users of the social network site Facebook from several Brazilian geographic areas. In addition to the PHI, participants completed the Satisfaction with Life Scale (SWLS), Diener and Emmons’ Positive and Negative Experience Scale (PNES), Psychological Well-being Scale (PWS), and the Subjective Happiness Scale (SHS). Internal consistency, convergent validity, known-group validity, and test–retest reliability were evaluated. Satisfaction with the previous day was correlated with the 10 items assessing experienced well-being using the Cramer V test. Additionally, a cut-off value of PHI to identify a “happy individual” was defined using receiver-operating characteristic (ROC) curve methodology. Data from 1035 Brazilian participants were analyzed (health professionals = 180; Facebook users = 855). Regarding reliability results, the internal consistency (Cronbach alpha = 0.890 and 0.914) and test–retest (intraclass correlation coefficient = 0.814) were both considered adequate. Most of the validity hypotheses formulated a priori (convergent and know-group) was further confirmed. The cut-off value of higher than 7 in remembered PHI was identified (AUC = 0.780, sensitivity = 69.2%, specificity = 78.2%) as the best one to identify a happy individual. We concluded that the Universal Portuguese version of the PHI is valid and reliable for use in the Brazilian population using online surveys. PMID:27661039

Managing protected health information in distributed research network environments: automated review to facilitate collaboration.

PubMed

Bredfeldt, Christine E; Butani, Amy; Padmanabhan, Sandhyasree; Hitz, Paul; Pardee, Roy

2013-03-22

Multi-site health sciences research is becoming more common, as it enables investigation of rare outcomes and diseases and new healthcare innovations. Multi-site research usually involves the transfer of large amounts of research data between collaborators, which increases the potential for accidental disclosures of protected health information (PHI). Standard protocols for preventing release of PHI are extremely vulnerable to human error, particularly when the shared data sets are large. To address this problem, we developed an automated program (SAS macro) to identify possible PHI in research data before it is transferred between research sites. The macro reviews all data in a designated directory to identify suspicious variable names and data patterns. The macro looks for variables that may contain personal identifiers such as medical record numbers and social security numbers. In addition, the macro identifies dates and numbers that may identify people who belong to small groups, who may be identifiable even in the absences of traditional identifiers. Evaluation of the macro on 100 sample research data sets indicated a recall of 0.98 and precision of 0.81. When implemented consistently, the macro has the potential to streamline the PHI review process and significantly reduce accidental PHI disclosures.

A Peptidomics Strategy to Elucidate the Proteolytic Pathways that Inactivate Peptide Hormones

PubMed Central

Tinoco, Arthur D.; Kim, Yun-Gon; Tagore, Debarati M.; Wiwczar, Jessica; Lane, William S.; Danial, Nika N.; Saghatelian, Alan

2011-01-01

Proteolysis plays a key role in regulating the levels and activity of peptide hormones. Characterization of the proteolytic pathways that cleave peptide hormones is of basic interest and can, in some cases, spur the development of novel therapeutics. The lack, however, of an efficient approach to identify endogenous fragments of peptide hormones has hindered the elucidation of these proteolytic pathways. Here, we apply a mass spectrometry (MS)-based peptidomics approach to characterize the intestinal fragments of peptide histidine isoleucine (PHI), a hormone that promotes glucose-stimulated insulin secretion (GSIS). Our approach reveals a proteolytic pathway in the intestine that truncates PHI at its C-terminus to produce a PHI fragment that is inactive in a GSIS assay—a result that provides a potential mechanism of PHI regulation in vivo. Differences between these in vivo peptidomics studies and in vitro lysate experiments, which showed N- and C-terminal processing of PHI, underscore the effectiveness of this approach to discover physiologically relevant proteolytic pathways. Moreover, integrating this peptidomics approach with bioassays (i.e. GSIS) provides a general strategy to reveal proteolytic pathways that may regulate the activity of peptide hormones. PMID:21299233

Optimization and evaluation of single-cell whole-genome multiple displacement amplification.

PubMed

Spits, C; Le Caignec, C; De Rycke, M; Van Haute, L; Van Steirteghem, A; Liebaers, I; Sermon, K

2006-05-01

The scarcity of genomic DNA can be a limiting factor in some fields of genetic research. One of the methods developed to overcome this difficulty is whole genome amplification (WGA). Recently, multiple displacement amplification (MDA) has proved very efficient in the WGA of small DNA samples and pools of cells, the reaction being catalyzed by the phi29 or the Bst DNA polymerases. The aim of the present study was to develop a reliable, efficient, and fast protocol for MDA at the single-cell level. We first compared the efficiency of phi29 and Bst polymerases on DNA samples and single cells. The phi29 polymerase generated accurately, in a short time and from a single cell, sufficient DNA for a large set of tests, whereas the Bst enzyme showed a low efficiency and a high error rate. A single-cell protocol was optimized using the phi29 polymerase and was evaluated on 60 single cells; the DNA obtained DNA was assessed by 22 locus-specific PCRs. This new protocol can be useful for many applications involving minute quantities of starting material, such as forensic DNA analysis, prenatal and preimplantation genetic diagnosis, or cancer research. (c) 2006 Wiley-Liss, Inc.

Measurement of the decays B--> phiK and B--> phiK*.

PubMed

Aubert, B; Boutigny, D; Gaillard, J M; Hicheur, A; Karyotakis, Y; Lees, J P; Robbe, P; Tisserand, V; Palano, A; Chen, G P; Chen, J C; Qi, N D; Rong, G; Wang, P; Zhu, Y S; Eigen, G; Reinertsen, P L; Stugu, B; Abbott, B; Abrams, G S; Borgland, A W; Breon, A B; Brown, D N; Button-Shafer, J; Cahn, R N; Clark, A R; Fan, Q; Gill, M S; Gowdy, S J; Gritsan, A; Groysman, Y; Jacobsen, R G; Kadel, R W; Kadyk, J; Kerth, L T; Kluth, S; Kolomensky, Y G; Kral, J F; LeClerc, C; Levi, M E; Liu, T; Lynch, G; Meyer, A B; Momayezi, M; Oddone, P J; Perazzo, A; Pripstein, M; Roe, N A; Romosan, A; Ronan, M T; Shelkov, V G; Telnov, A V; Wenzel, W A; Bright-Thomas, P G; Harrison, T J; Hawkes, C M; Kirk, A; Knowles, D J; O'Neale, S W; Penny, R C; Watson, A T; Watson, N K; Deppermann, T; Koch, H; Krug, J; Kunze, M; Lewandowski, B; Peters, K; Schmuecker, H; Steinke, M; Andress, J C; Barlow, N R; Bhimji, W; Chevalier, N; Clark, P J; Cottingham, W N; De Groot, N; Dyce, N; Foster, B; Mass, A; McFall, J D; Wallom, D; Wilson, F F; Abe, K; Hearty, C; Mattison, T S; McKenna, J A; Thiessen, D; Camanzi, B; Jolly, S; McKemey, A K; Tinslay, J; Blinov, V E; Bukin, A D; Bukin, D A; Buzykaev, A R; Dubrovin, M S; Golubev, V B; Ivanchenko, V N; Korol, A A; Kravchenko, E A; Onuchin, A P; Salnikov, A A; Serednyakov, S I; Skovpen, Y I; Telnov, V I; Yushkov, A N; Lankford, A J; Mandelkern, M; McMahon, S; Stoker, D P; Ahsan, A; Arisaka, K; Buchanan, C; Chun, S; Branson, J G; MacFarlane, D B; Prell, S; Rahatlou, S; Raven, G; Sharma, V; Campagnari, C; Dahmes, B; Hart, P A; Kuznetsova, N; Levy, S L; Long, O; Lu, A; Richman, J D; Verkerke, W; Witherell, M; Yellin, S; Beringer, J; Dorfan, D E; Eisner, A M; Frey, A; Grillo, A A; Grothe, M; Heusch, C A; Johnson, R P; Kroeger, W; Lockman, W S; Pulliam, T; Sadrozinski, H; Schalk, T; Schmitz, R E; Schumm, B A; Seiden, A; Turri, M; Walkowiak, W; Williams, D C; Wilson, M G; Chen, E; Dubois-Felsmann, G P; Dvoretskii, A; Hitlin, D G; Metzler, S; Oyang, J; Porter, F C; Ryd, A; Samuel, A; Weaver, M; Yang, S; Zhu, R Y; Devmal, S; Geld, T L; Jayatilleke, S; Mancinelli, G; Meadows, B T; Sokoloff, M D; Bloom, P; Fahey, S; Ford, W T; Gaede, F; Johnson, D R; Michael, A K; Nauenberg, U; Olivas, A; Park, H; Rankin, P; Roy, J; Sen, S; Smith, J G; van Hoek, W C; Wagner, D L; Blouw, J; Harton, J L; Krishnamurthy, M; Soffer, A; Toki, W H; Wilson, R J; Zhang, J; Brandt, T; Brose, J; Colberg, T; Dahlinger, G; Dickopp, M; Dubitzky, R S; Maly, E; Müller-Pfefferkorn, R; Otto, S; Schubert, K R; Schwierz, R; Spaan, B; Wilden, L; Behr, L; Bernard, D; Bonneaud, G R; Brochard, F; Cohen-Tanugi, J; Ferrag, S; Roussot, E; T'Jampens, S; Thiebaux, C; Vasileiadis, G; Verderi, M; Anjomshoaa, A; Bernet, R; Di Lodovico, F; Khan, A; Muheim, F; Playfer, S; Swain, J E; Falbo, M; Bozzi, C; Dittongo, S; Folegani, M; Piemontese, L; Treadwell, E; Anulli, F; Baldini-Ferroli, R; Calcaterra, A; de Sangro, R; Falciai, D; Finocchiaro, G; Patteri, P; Peruzzi, I M; Piccolo, M; Xie, Y; Zallo, A; Bagnasco, S; Buzzo, A; Contri, R; Crosetti, G; Fabbricatore, P; Farinon, S; Lo Vetere, M; Macri, M; Monge, M R; Musenich, R; Pallavicini, M; Parodi, R; Passaggio, S; Pastore, F C; Patrignani, C; Pia, M G; Priano, C; Robutti, E; Santroni, A; Morii, M; Bartoldus, R; Dignan, T; Hamilton, R; Mallik, U; Cochran, J; Crawley, H B; Fischer, P A; Lamsa, J; Meyer, W T; Rosenberg, E I; Benkebil, M; Grosdidier, G; Hast, C; Höcker, A; Lacker, H M; LePeltier, V; Lutz, A M; Plaszczynski, S; Schune, M H; Trincaz-Duvoid, S; Valassi, A; Wormser, G; Bionta, R M; Brigljevic, V; Fackler, O; Fujino, D; Lange, D J; Mugge, M; Shi, X; van Bibber, K; Wenaus, T J; Wright, D M; Wuest, C R; Carroll, M; Fry, J R; Gabathuler, E; Gamet, R; George, M; Kay, M; Payne, D J; Sloane, R J; Touramanis, C; Aspinwall, M L; Bowerman, D A; Dauncey, P D; Egede, U; Eschrich, I; Gunawardane, N J; Martin, R; Nash, J A; Sanders, P; Smith, D; Azzopardi, D E; Back, J J; Dixon, P; Harrison, P F; Potter, R J; Shorthouse, H W; Strother, P; Vidal, P B; Williams, M I; Cowan, G; George, S; Green, M G; Kurup, A; Marker, C E; McGrath, P; McMahon, T R; Ricciardi, S; Salvatore, F; Scott, I; Vaitsas, G; Brown, D; Davis, C L; Allison, J; Barlow, R J; Boyd, J T; Forti, A; Fullwood, J; Jackson, F; Lafferty, G D; Savvas, N; Simopoulos, E T; Weatherall, J H; Farbin, A; Jawahery, A; Lillard, V; Olsen, J; Roberts, D A; Schieck, J R; Blaylock, G; Dallapiccola, C; Flood, K T; Hertzbach, S S; Kofler, R; Lin, C S; Moore, T B; Staengle, H; Willocq, S; Wittlin, J; Brau, B; Cowan, R; Sciolla, G; Taylor, F; Yamamoto, R K; Britton, D I; Milek, M; Patel, P M; Trischuk, J; Lanni, F; Palombo, F; Bauer, J M; Booke, M; Cremaldi, L; Eschenburg, V; Kroeger, R; Reidy, J; Sanders, D A; Summers, D J; Martin, J P; Nief, J Y; Seitz, R; Taras, P; Zacek, V; Nicholson, H; Sutton, C S; Cartaro, C; Cavallo, N; De Nardo, G; Fabozzi, F; Gatto, C; Lista, L; Paolucci, P; Piccolo, D; Sciacca, C; LoSecco, J M; Alsmiller, J R; Gabriel, T A; Handler, T; Brau, J; Frey, R; Iwasaki, M; Sinev, N B; Strom, D; Colecchia, F; Dal Corso, F; Dorigo, A; Galeazzi, F; Margoni, M; Michelon, G; Morandin, M; Posocco, M; Rotondo, M; Simonetto, F; Stroili, R; Torassa, E; Voci, C; Benayoun, M; Briand, H; Chauveau, J; David, P; De La Vaissière, C; Del Buono, L; Hamon, O; Le Diberder, F; Leruste, P; Lory, J; Roos, L; Stark, J; Versillé, S; Manfredi, P F; Re, V; Speziali, V; Frank, E D; Gladney, L; Guo, Q H; Panetta, J H; Angelini, C; Batignani, G; Bettarini, S; Bondioli, M; Carpinelli, M; Forti, F; Giorgi, M A; Lusiani, A; Martinez-Vidal, F; Morganti, M; Neri, N; Paoloni, E; Rama, M; Rizzo, G; Sandrelli, F; Simi, G; Triggiani, G; Walsh, J; Haire, M; Judd, D; Paick, K; Turnbull, L; Wagoner, D E; Albert, J; Bula, C; Lu, C; McDonald, K T; Miftakov, V; Schaffner, S F; Smith, A J; Tumanov, A; Varnes, E W; Cavoto, G; del Re, D; Faccini, R; Ferrarotto, F; Ferroni, F; Fratini, K; Lamanna, E; Leonardi, E; Mazzoni, M A; Morganti, S; Piredda, G; Safai Tehrani, F; Serra, M; Voena, C; Christ, S; Waldi, R; Adye, T; Franek, B; Geddes, N I; Gopal, G P; Xella, S M; Aleksan, R; De Domenico, G; Emery, S; Gaidot, A; Ganzhur, S F; Giraud, P F; Hamel De Monchenault, G; Kozanecki, W; Langer, M; London, G W; Mayer, B; Serfass, B; Vasseur, G; Yeche, C; Zito, M; Copty, N; Purohit, M V; Singh, H; Yumiceva, F X; Adam, I; Anthony, P L; Aston, D; Baird, K; Bartelt, J; Bloom, E; Boyarski, A M; Bulos, F; Calderini, G; Claus, R; Convery, M R; Coupal, D P; Coward, D H; Dorfan, J; Doser, M; Dunwoodie, W; Field, R C; Glanzman, T; Godfrey, G L; Grosso, P; Himel, T; Huffer, M E; Innes, W R; Jessop, C P; Kelsey, M H; Kim, P; Kocian, M L; Langenegger, U; Leith, D W; Luitz, S; Luth, V; Lynch, H L; Manzin, G; Marsiske, H; Menke, S; Messner, R; Moffeit, K C; Mount, R; Muller, D R; O'Grady, C P; Petrak, S; Quinn, H; Ratcliff, B N; Robertson, S H; Rochester, L S; Roodman, A; Schietinger, T; Schindler, R H; Schwiening, J; Serbo, V V; Snyder, A; Soha, A; Spanier, S M; Stahl, A; Stelzer, J; Su, D; Sullivan, M K; Talby, M; Tanaka, H A; Trunov, A; Va'vra, J; Wagner, S R; Weinstein, A J; Wisniewski, W J; Young, C C; Burchat, P R; Cheng, C H; Kirkby, D; Meyer, T I; Roat, C; De Silva, A; Henderson, R; Bugg, W; Cohn, H; Hart, E; Weidemann, A W; Benninger, T; Izen, J M; Kitayama, I; Lou, X C; Turcotte, M; Bianchi, F; Bona, M; Di Girolamo, B; Gamba, D; Smol, A; Zanin, D; Bosisio, L; Della Ricca, G; Lanceri, L; Pompili, A; Poropat, P; Prest, M; Vallazza, E; Vuagnin, G; Panvini, R S; Brown, C M; Kowalewski, R; Roney, J M; Band, H R; Charles, E; Dasu, S; Elmer, P; Hu, H; Johnson, J R; Liu, R; Nielsen, J; Orejudos, W; Pan, Y; Prepost, R; Scott, I J; Sekula, S J; von Wimmersperg-Toeller, J H; Wu, S L; Yu, Z; Zobering, H; Kordich, T M; Neal, H

2001-10-08

We have observed the decays B--> phiK and phiK(*) in a sample of over 45 million B mesons collected with the BABAR detector at the PEP-II collider. The measured branching fractions are B(B+--> phiK+) = (7.7(+1.6)(-1.4)+/-0.8)x10(-6), B(B0--> phiK0) = (8.1(+3.1)(-2.5)+/-0.8)x10(-6), B(B+--> phiK(*+)) = (9.7(+4.2)(-3.4)+/-1.7)x10(-6), and B(B0--> phiK(*0)) = (8.7(+2.5)(-2.1)+/-1.1)x10(-6). We also report the upper limit B(B+--> phipi(+))<1.4x10(-6) ( 90% C.L.).

Virtual Laboratory for QoS Study in Next-Generation Networks with Metro Ethernet Access

ERIC Educational Resources Information Center

Gomez-Sacristan, Angel; Sempere-Paya, Victor M.; Rodriguez-Hernandez, Miguel A.

2016-01-01

Teaching in university engineering departments is currently facing a number of challenges, especially for those involved in the most innovative and dynamic areas of information and communication technology. Learning model developments that place greater weight on laboratory activities require investment in specific equipment that is often very…

ETHERNET BASED EMBEDDED SYSTEM FOR FEL DIAGNOSTICS AND CONTROLS

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

Jianxun Yan; Daniel Sexton; Steven Moore

2006-10-24

An Ethernet based embedded system has been developed to upgrade the Beam Viewer and Beam Position Monitor (BPM) systems within the free-electron laser (FEL) project at Jefferson Lab. The embedded microcontroller was mounted on the front-end I/O cards with software packages such as Experimental Physics and Industrial Control System (EPICS) and Real Time Executive for Multiprocessor System (RTEMS) running as an Input/Output Controller (IOC). By cross compiling with the EPICS, the RTEMS kernel, IOC device supports, and databases all of these can be downloaded into the microcontroller. The first version of the BPM electronics based on the embedded controller wasmore » built and is currently running in our FEL system. The new version of BPM that will use a Single Board IOC (SBIOC), which integrates with an Field Programming Gate Array (FPGA) and a ColdFire embedded microcontroller, is presently under development. The new system has the features of a low cost IOC, an open source real-time operating system, plug&play-like ease of installation and flexibility, and provides a much more localized solution.« less

Migration of optical core network to next generation networks - Carrier Grade Ethernet Optical Transport Network

NASA Astrophysics Data System (ADS)

Glamočanin, D.

2017-05-01

In order to maintain the continuity of the telecom operators’ network construction, while monitoring development needs, increasing customers’ demands and application of technological improvements, it is necessary to migrate optical transport core network to the next generation networks - Carrier Grade Ethernet Optical Transport Network (OTN CE). The primary objective of OTN CE is to realize an environment that is based solely on the switching in the optical domain, i.e. the realization of transparent optical networks and optical switching to the second layer of ISO / OSI model. The realization of such a network provides opportunities for further development of existing, but also technologically more demanding, new services. It is also a prerequisite to provide higher scalability, reliability, security and quality of QoS service, as well as prerequisites for the establishment of SLA (Service Level Agreement) for existing services, especially traffic in real time. This study aims to clarify the proposed model, which has the potential to be eventually adjusted in accordance with new scientific knowledge in this field as well as market requirements.

Effect of dietary phosphorus, phytase, and 25-hydroxycholecalciferol on broiler chicken bone mineralization, litter phosphorus, and processing yields.

PubMed

Angel, R; Saylor, W W; Mitchell, A D; Powers, W; Applegate, T J

2006-07-01

Three floor pen experiments (Exp) were conducted to evaluate low nonphytin P (NPP) concentrations and the NPP sparing effect of phytase (PHY) and 25-hydroxycholecalciferol (25D) on bone mineralization, bone breaking during commercial processing, litter P, and water-soluble P (WSP) concentrations. Tested treatments (TRT) were control, National Research Council NPP; University of Maryland (UMD) NPP; UMD + PHY, UMD NPP reduced by 0.064% NPP + 600 U of PHY/kg; UMD + PHY + 25D, UMD NPP reduced by 0.090% NPP + 600 U of PHY and 70 microg of 25D/kg; control + PHY mimicked the industry practice of diets by 0.1% when PHY is added; and negative control with 90% UMD NPP concentrations. UMD + PHY and control + PHY diets contained 600 U of PHY/kg, and UMD + PHY + 25D contained 600 U of PHY + 70 microg of 25D/kg. Performance results were presented separately. After each Exp, litter P and WSP were determined, and bone measurements were obtained on 8 or 10 broilers per pen. Tested TRT did not affect broiler BW. Femur ash weight of broilers fed the UMD and UMD + PHY + 25D was lower in all Exp compared with that of broilers fed the control diet. Femur ash was similar for control and UMD + PHY broilers, yet averaged over all Exp, UMD + PHY broilers consumed 39% less NPP and required less NPP per gram of femur ash than those on the control (4.87 and 7.77 g of NPP/g of ash, Exp 3). At the end of Exp 3, broilers were processed in a commercial facility. Despite reductions in NPP intake and bone mineralization, no differences were observed in measurements of economic importance (parts lost, carcass yield, and incidence of broken bones). The P excretion per bird was lowest for birds fed the UMD + PHY + 25D diet followed by those fed the UMD + PHY and negative control diets (10.44, 12.00, and 13.78 g of P/bird, respectively) and were highest for those fed the control diet (19.55 g of P/bird). These results suggest that feeding diets low in P together with PHY and 25D will not affect performance or increase losses at processing while resulting in improved P retention and reductions in P and WSP excreted.

What’s Past is Prologue: A Scoping Review of Recent Public Health and Global Health Informatics Literature

PubMed Central

Dixon, Brian E.; Pina, Jamie; Kharrazi, Hadi; Gharghabi, Fardad; Richards, Janise

2015-01-01

Objective: To categorize and describe the public health informatics (PHI) and global health informatics (GHI) literature between 2012 and 2014. Methods: We conducted a semi-systematic review of articles published between January 2012 and September 2014 where information and communications technologies (ICT) was a primary subject of the study or a main component of the study methodology. Additional inclusion and exclusion criteria were used to filter PHI and GHI articles from the larger biomedical informatics domain. Articles were identified using MEDLINE as well as personal bibliographies from members of the American Medical Informatics Association PHI and GHI working groups. Results: A total of 85 PHI articles and 282 GHI articles were identified. While systems in PHI continue to support surveillance activities, we identified a shift towards support for prevention, environmental health, and public health care services. Furthermore, articles from the U.S. reveal a shift towards PHI applications at state and local levels. GHI articles focused on telemedicine, mHealth and eHealth applications. The development of adequate infrastructure to support ICT remains a challenge, although we identified a small but growing set of articles that measure the impact of ICT on clinical outcomes. Discussion: There is evidence of growth with respect to both implementation of information systems within the public health enterprise as well as a widening of scope within each informatics discipline. Yet the articles also illuminate the need for more primary research studies on what works and what does not as both searches yielded small numbers of primary, empirical articles. Conclusion: While the body of knowledge around PHI and GHI continues to mature, additional studies of higher quality are needed to generate the robust evidence base needed to support continued investment in ICT by governmental health agencies. PMID:26392846

Muscle fatigue in frog semitendinosus: role of intracellular pH

NASA Technical Reports Server (NTRS)

Thompson, L. V.; Balog, E. M.; Fitts, R. H.

1992-01-01

The purpose of this study was to utilize glass microelectrodes to characterize the intracellular pH (pHi) before and during recovery from fatigue in the frog semitendinosus (ST) muscle. A second objective was to evaluate the relationship between pHi and contractile function. The frog ST muscle (22 degrees C) was fatigued by direct electrical stimulation with 100-ms 150-Hz trains at 1/s for 5 min. Peak tetanic force (Po) was reduced to 8.5% of initial force and recovered in a biphasic manner, returning to the resting value by 40 min. Resting pHi was 7.00 +/- 0.02 (n = 37) and declined with fatigue to an average value of 6.42 at 3 min of recovery. During recovery pHi significantly increased and by 25 min had returned to the prefatigue value. The pHi recovery was highly correlated to the slow phase of Po recovery (r = 0.98, P less than 0.001). The mean resting membrane potential was -78 +/- 1.0 mV (n = 42) and at 3 min of recovery was depolarized to -67 +/- 4 mV. Both the peak rate of twitch force development (+dP/dt) (r = 0.99, P less than 0.001) and decline (-dP/dt) (r = 0.94, P less than 0.014) were highly correlated to pHi during the slow phase of recovery. Contraction time (CT) and one-half relaxation time (1/2RT) increased significantly and recovered exponentially. The recovery of CT and 1/2RT were both significantly correlated to pHi (r = -0.93, P less than 0.001 and r = -0.86, P less than 0.001 for CT and 1/2RT, respectively).(ABSTRACT TRUNCATED AT 250 WORDS).

Management Requirements of the 3COM Ethernet Local Area Network

DTIC Science & Technology

1988-09-01

Management Information System . With the introduction of new technology comes the requirement to administer the network. This paper describes LAN services available on the network, management philosophies for the LAN services, and areas of LAN administration considered important to the successful operation and maintenance of a LAN. LAN administration problems identified by users are also addressed. Keywords included; Local area network (LAN); Lan management; Lan administration; 3COM ETHERNET LAN.

Observation of {chi}{sub c1} Decays into Vector Meson Pairs {phi}{phi}, {omega}{omega}, and {omega}{phi}

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

Ablikim, M.; An, Z. H.; Bai, J. Z.

Using (106{+-}4)x10{sup 6} {psi}(3686) events accumulated with the BESIII detector at the BEPCII e{sup +}e{sup -} collider, we present the first measurement of decays of {chi}{sub c1} to vector meson pairs {phi}{phi}, {omega}{omega}, and {omega}{phi}. The branching fractions are measured to be (4.4{+-}0.3{+-}0.5)x10{sup -4}, (6.0{+-}0.3{+-}0.7)x10{sup -4}, and (2.2{+-}0.6{+-}0.2)x10{sup -5}, for {chi}{sub c1}{yields}{phi}{phi}, {omega}{omega}, and {omega}{phi}, respectively, which indicates that the hadron helicity selection rule is significantly violated in {chi}{sub cJ} decays. In addition, the measurement of {chi}{sub cJ}{yields}{omega}{phi} provides the first indication of the rate of doubly OZI-suppressed {chi}{sub cJ} decay. Finally, we present improved measurements for the branching fractionsmore » of {chi}{sub c0} and {chi}{sub c2} to vector meson pairs.« less

A real-time control system for the control of suspended interferometers based on hybrid computing techniques

NASA Astrophysics Data System (ADS)

Acernese, Fausto; Barone, Fabrizio; De Rosa, Rosario; Eleuteri, Antonio; Milano, Leopoldo; Pardi, Silvio; Ricciardi, Iolanda; Russo, Guido

2004-09-01

One of the main requirements of a digital system for the control of interferometric detectors of gravitational waves is the computing power, that is a direct consequence of the increasing complexity of the digital algorithms necessary for the control signals generation. For this specific task many specialized non standard real-time architectures have been developed, often very expensive and difficult to upgrade. On the other hand, such computing power is generally fully available for off-line applications on standard Pc based systems. Therefore, a possible and obvious solution may be provided by the integration of both the real-time and off-line architecture resulting in a hybrid control system architecture based on standards available components, trying to get both the advantages of the perfect data synchronization provided by the real-time systems and by the large computing power available on Pc based systems. Such integration may be provided by the implementation of the link between the two different architectures through the standard Ethernet network, whose data transfer speed is largely increasing in these years, using the TCP/IP, UDP and raw Ethernet protocols. In this paper we describe the architecture of an hybrid Ethernet based real-time control system prototype we implemented in Napoli, discussing its characteristics and performances. Finally we discuss a possible application to the real-time control of a suspended mass of the mode cleaner of the 3m prototype optical interferometer for gravitational wave detection (IDGW-3P) operational in Napoli.

Phosphite, an analog of phosphate, suppresses the coordinated expression of genes under phosphate starvation.

PubMed

Varadarajan, Deepa K; Karthikeyan, Athikkattuvalasu S; Matilda, Paino Durzo; Raghothama, Kashchandra G

2002-07-01

Phosphate (Pi) and its analog phosphite (Phi) are acquired by plants via Pi transporters. Although the uptake and mobility of Phi and Pi are similar, there is no evidence suggesting that plants can utilize Phi as a sole source of phosphorus. Phi is also known to interfere with many of the Pi starvation responses in plants and yeast (Saccharomyces cerevisiae). In this study, effects of Phi on plant growth and coordinated expression of genes induced by Pi starvation were analyzed. Phi suppressed many of the Pi starvation responses that are commonly observed in plants. Enhanced root growth and root to shoot ratio, a hallmark of Pi stress response, was strongly inhibited by Phi. The negative effects of Phi were not obvious in plants supplemented with Pi. The expression of Pi starvation-induced genes such as LePT1, LePT2, AtPT1, and AtPT2 (high-affinity Pi transporters); LePS2 (a novel acid phosphatase); LePS3 and TPSI1 (novel genes); and PAP1 (purple acid phosphatase) was suppressed by Phi in plants and cell cultures. Expression of luciferase reporter gene driven by the Pi starvation-induced AtPT2 promoter was also suppressed by Phi. These analyses showed that suppression of Pi starvation-induced genes is an early response to addition of Phi. These data also provide evidence that Phi interferes with gene expression at the level of transcription. Synchronized suppression of multiple Pi starvation-induced genes by Phi points to its action on the early molecular events, probably signal transduction, in Pi starvation response.

PubMed Central

GALLUS, R.; DE CARLINI, M.; PICCIOTTI, P.M.; MUZZI, E.; CICIRIELLO, E.; ORZAN, E.; CONTI, G.

2016-01-01

SUMMARY Diagnosis of child permanent hearing impairment (PHI) can be made with extreme timeliness compared to the past thanks to improvements in PHI identification through newborn hearing screening programmes. It now becomes essential to provide an effective amplification as quickly as possible in order to restore auditory function and favour speech and language development. The early fitting of hearing aids and possible later cochlear implantation indeed prompts the development of central auditory pathways, connections with secondary sensory brain areas, as well as with motor and articulatory cortex. The aim of this paper is to report the results of a strategic analysis that involves identification of strengths, weaknesses, opportunities and threats regarding the process of achieving early amplification in all cases of significant childhood PHI. The analysis is focused on the Italian situation and is part of the Italian Ministry of Health project CCM 2013 "Preventing Communication Disorders: a Regional Program for Early Identification, Intervention and Care of Hearing Impaired Children". PMID:27054389

USE OF THE PROSTATE HEALTH INDEX FOR DETECTION OF PROSTATE CANCER: RESULTS FROM A LARGE ACADEMIC PRACTICE

PubMed Central

Tosoian, Jeffrey J.; Druskin, Sasha C.; Andreas, Darian; Mullane, Patrick; Chappidi, Meera; Joo, Sarah; Ghabili, Kamyar; Agostino, Joseph; Macura, Katarzyna J.; Carter, H. Ballentine; Schaeffer, Edward M.; Partin, Alan W.; Sokoll, Lori J.; Ross, Ashley E.

2016-01-01

BACKGROUND The Prostate Health Index (phi) outperforms PSA and other PSA derivatives for the diagnosis of prostate cancer (PCa). The impact of phi testing in the real-world clinical setting has not been previously assessed. METHODS In a single, large, academic center, phi was tested in 345 patients presenting for diagnostic evaluation for PCa. Findings on prostate biopsy (including Grade Group [GG], defined as GG1: Gleason score [GS] 6, GG2: GS 3+4=7, GG3: GS 4+3=7, GG4: GS 8, and GG5: GS 9-10), magnetic resonance imaging (MRI), and radical prostatectomy (RP) were prospectively recorded. Biopsy rates and outcomes were compared to a contemporary cohort that did not undergo phi testing (n=1318). RESULTS Overall, 39% of men with phi testing underwent prostate biopsy. No men with phi<19.6 were diagnosed with PCa, and only 3 men with phi<27 had cancer of GG≥2. Phi was superior to PSA for the prediction of any PCa (AUC 0.72 vs. 0.47) and GG≥2 PCa (AUC 0.77 vs. 0.53) on prostate biopsy. Among men undergoing MRI and phi, no men with phi<27 and PI-RADS≤3 had GG≥2 cancer. For those men proceeding to RP, increasing phi was associated with higher pathologic GG (p=0.002) and stage (p=0.001). Compared to patients who did not undergo phi testing, the use of phi was associated with a 9% reduction in the rate of prostate biopsy (39% vs. 48%; p<0.001). Importantly, the reduction in biopsy among the phi population was secondary to decreased incidence of negative (8%) and GG1 (1%) biopsies, while the proportion of biopsies detecting GG≥2 cancers remained unchanged. CONCLUSIONS In this large, real-time clinical experience, phi outperformed PSA alone, was associated with high-grade PCa, and provided complementary information to MRI. Incorporation of phi into clinical practice reduced the rate of unnecessary biopsies without changing the frequency of detection of higher grade cancers. PMID:28117387

Transepithelial SCFA fluxes link intracellular and extracellular pH regulation of mouse colonocytes.

PubMed

Chu, S; Montrose, M H

1997-10-01

We have studied pH regulation in both intracellular and extracellular compartments of mouse colonic crypts, using distal colonic mucosa with intact epithelial architecture. In this work, we question how transepithelial SCFA gradients affect intracellular pH (pHi) and examine interactions between extracellular pH (pHo) and pHi regulation in crypts of distal colonic epithelium from mouse. We studied pH regulation in three adjacent compartments of distal colonic epithelium (crypt lumen, crypt epithelial cell cytosol, and lamina propria) with SNARF-1 (a pH sensitive fluorescent dye), digital imaging microscopy (for pHi), and confocal microscopy (for pHo). Combining results from the three compartments allows us to find how pHi and pHo are regulated and related under the influence of physiological transepithelial SCFA gradients, and develop a better understanding of pH regulation mechanisms in colonic crypts. Results suggest a complex interdependency between SCFA fluxes and pHo values, which can directly affect how strongly SCFAs acidify colonocytes.

Multiple phytochromes are involved in red-light-induced enhancement of first-positive phototropism in arabidopsis thaliana

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

Janoudi, A.K.; Gordon, W.R.; Poff, K.L.

1997-03-01

The amplitude of phototropic curvature to blue light is enhanced by a prior exposure of seedlings to red light. This enhancement is mediated by phytochrome. Fluence-response relationships have been constructed for red-light-induced enhancement in the phytochrome A (phyA) null mutant, the phytochrome B- (phyB) deficient mutant, and in two transgenic lines of Arabidopsis thaliana that overexpress either phyA or phyB. These fluence-response relationships demonstrate the existence of two responses in enhancement, a response in the very-low-to-low-fluence range, and a response in the high-fluence range. Only the response in the high-fluence range is present in the phyA null mutant. In contrast,more » the phyB-deficient mutant is indistinguishable from the wild-type parent in red-light responsiveness. These data indicate that phyA is necessary for the very-low-to-low but not the high-fluence response, and that phyB is not necessary for either response range. Based on these results, the high-fluence response, if controlled by a single phytochrome, must be controlled by a phytochrome other than phyA or phyB. Overexpression of phyA has a negative effect and overexpression of phyB has an enhancing effect in the high fluence range. These results suggest that overexpression of either phytochrome perturbs the function of the endogenous photoreceptor system in unpreditable fashion. 25 refs., 3 figs.« less

SUMOylation of phytochrome-B negatively regulates light-induced signaling in Arabidopsis thaliana

PubMed Central

Sadanandom, Ari; Ádám, Éva; Orosa, Beatriz; Viczián, András; Klose, Cornelia; Zhang, Cunjin; Josse, Eve-Marie; Kozma-Bognár, László; Nagy, Ferenc

2015-01-01

The red/far red light absorbing photoreceptor phytochrome-B (phyB) cycles between the biologically inactive (Pr, λmax, 660 nm) and active (Pfr; λmax, 730 nm) forms and functions as a light quality and quantity controlled switch to regulate photomorphogenesis in Arabidopsis. At the molecular level, phyB interacts in a conformation-dependent fashion with a battery of downstream regulatory proteins, including PHYTOCHROME INTERACTING FACTOR transcription factors, and by modulating their activity/abundance, it alters expression patterns of genes underlying photomorphogenesis. Here we report that the small ubiquitin-like modifier (SUMO) is conjugated (SUMOylation) to the C terminus of phyB; the accumulation of SUMOylated phyB is enhanced by red light and displays a diurnal pattern in plants grown under light/dark cycles. Our data demonstrate that (i) transgenic plants expressing the mutant phyBLys996Arg-YFP photoreceptor are hypersensitive to red light, (ii) light-induced SUMOylation of the mutant phyB is drastically decreased compared with phyB-YFP, and (iii) SUMOylation of phyB inhibits binding of PHYTOCHROME INTERACTING FACTOR 5 to phyB Pfr. In addition, we show that OVERLY TOLERANT TO SALT 1 (OTS1) de-SUMOylates phyB in vitro, it interacts with phyB in vivo, and the ots1/ots2 mutant is hyposensitive to red light. Taken together, we conclude that SUMOylation of phyB negatively regulates light signaling and it is mediated, at least partly, by the action of OTS SUMO proteases. PMID:26283376

Smart Microgrid Energy Management Controls for Improved Energy Efficiency and Renewables Integration at DoD Installations

DTIC Science & Technology

2013-05-01

flare gas, wind , solar) and can reduce overall energy price volatility; • Renewable DER such as wind and solar PV cells provide emissions-free energy...infrastructure which uses both Ethernet and Wireless media. Ethernet is easily extendable and supports multiple protocols, accommodating a broad range of...by faults or switching events. Remote resources are also integrated into the microgrid network using wireless network currently existing in the Base

Real-time ground motions monitoring system developed by Raspberry Pi 3

NASA Astrophysics Data System (ADS)

Chen, P.; Jang, J. P.; Chang, H.; Lin, C. R.; Lin, P. P.; Wang, C. C.

2016-12-01

Ground-motions seismic stations are usually installed in the special geological area, like high possibility landslide area, active volcanoes, or nearby faults, to real-time monitor the possible geo-hazards. Base on the demands, three main issues needs to be considered: size, low-power consumption and real-time data transmission. Raspberry Pi 3 has the suitable characteristics to fit our requests. Thus, we develop a real-time ground motions monitoring system by Raspberry Pi 3. The Raspberry Pi has the credit-card-sized with single-board computers. The operating system is based on the programmable Linux system.The volume is only 85.6 by 53.98 by 17 mm with USB and Ethernet interfaces. The power supply is only needed 5 Volts and 2.1 A. It is easy to get power by using solar power and transmit the real-time data through Ethernet or by the mobile signal through USB adapter. As Raspberry Pi still a kind of small computer, the service, software or GUI can be very flexibly developed, such as the basic web server, ftp server, SSH connection, and real-time visualization interface tool etc. Until now, we have developed ten instruments with on-line/ real-time data transmission and have installed in the Taiping Mountain in Taiwan to motor the geohazard like mudslide.

[Genetic study of bacteriophage phi81. I. Isolation, study of complementation and preliminary mapping of amber-mutants of bacteriophage phi81].

PubMed

Sineokiĭ, S P; Pogosov, V Z; Iankovskiĭ, N K; Krylov, V N

1976-01-01

123 Amber mutants of lambdoid bacteriophage phi81 are isolated and distributed into 19 complementation groups. Deletion mapping made possible to locate 5 gene groups on the genetic map of bacteriophage phi81 and to determine a region of possible location of mm' sticky ends on the prophage genetic map. A gene of phage phi81 is localized, which controls the adsorption specificity, and which functional similarity to a respective gene of phage phi80 is demonstrated.

Clinical utility of the Prostate Health Index (phi) for biopsy decision management in a large group urology practice setting.

PubMed

White, Jay; Shenoy, B Vittal; Tutrone, Ronald F; Karsh, Lawrence I; Saltzstein, Daniel R; Harmon, William J; Broyles, Dennis L; Roddy, Tamra E; Lofaro, Lori R; Paoli, Carly J; Denham, Dwight; Reynolds, Mark A

2018-04-01

Deciding when to biopsy a man with non-suspicious DRE findings and tPSA in the 4-10 ng/ml range can be challenging, because two-thirds of such biopsies are typically found to be benign. The Prostate Health Index (phi) exhibits significantly improved diagnostic accuracy for prostate cancer detection when compared to tPSA and %fPSA, however only one published study to date has investigated its impact on biopsy decisions in clinical practice. An IRB approved observational study was conducted at four large urology group practices using a physician reported two-part questionnaire. Physician recommendations were recorded before and after receiving the phi test result. A historical control group was queried from each site's electronic medical records for eligible men who were seen by the same participating urologists prior to the implementation of the phi test in their practice. 506 men receiving a phi test were prospectively enrolled and 683 men were identified for the historical control group (without phi). Biopsy and pathological findings were also recorded for both groups. Men receiving a phi test showed a significant reduction in biopsy procedures performed when compared to the historical control group (36.4% vs. 60.3%, respectively, P < 0.0001). Based on questionnaire responses, the phi score impacted the physician's patient management plan in 73% of cases, including biopsy deferrals when the phi score was low, and decisions to perform biopsies when the phi score indicated an intermediate or high probability of prostate cancer (phi ≥36). phi testing significantly impacted the physician's biopsy decision for men with tPSA in the 4-10 ng/ml range and non-suspicious DRE findings. Appropriate utilization of phi resulted in a significant reduction in biopsy procedures performed compared to historical patients seen by the same participating urologists who would have met enrollment eligibility but did not receive a phi test.

Nuclear phytochrome A signaling promotes phototropism in Arabidopsis.

PubMed

Kami, Chitose; Hersch, Micha; Trevisan, Martine; Genoud, Thierry; Hiltbrunner, Andreas; Bergmann, Sven; Fankhauser, Christian

2012-02-01

Phototropin photoreceptors (phot1 and phot2 in Arabidopsis thaliana) enable responses to directional light cues (e.g., positive phototropism in the hypocotyl). In Arabidopsis, phot1 is essential for phototropism in response to low light, a response that is also modulated by phytochrome A (phyA), representing a classical example of photoreceptor coaction. The molecular mechanisms underlying promotion of phototropism by phyA remain unclear. Most phyA responses require nuclear accumulation of the photoreceptor, but interestingly, it has been proposed that cytosolic phyA promotes phototropism. By comparing the kinetics of phototropism in seedlings with different subcellular localizations of phyA, we show that nuclear phyA accelerates the phototropic response, whereas in the fhy1 fhl mutant, in which phyA remains in the cytosol, phototropic bending is slower than in the wild type. Consistent with this data, we find that transcription factors needed for full phyA responses are needed for normal phototropism. Moreover, we show that phyA is the primary photoreceptor promoting the expression of phototropism regulators in low light (e.g., PHYTOCHROME KINASE SUBSTRATE1 [PKS1] and ROOT PHOTO TROPISM2 [RPT2]). Although phyA remains cytosolic in fhy1 fhl, induction of PKS1 and RPT2 expression still occurs in fhy1 fhl, indicating that a low level of nuclear phyA signaling is still present in fhy1 fhl.

Nuclear Phytochrome A Signaling Promotes Phototropism in Arabidopsis[W][OA

PubMed Central

Kami, Chitose; Hersch, Micha; Trevisan, Martine; Genoud, Thierry; Hiltbrunner, Andreas; Bergmann, Sven; Fankhauser, Christian

2012-01-01

Phototropin photoreceptors (phot1 and phot2 in Arabidopsis thaliana) enable responses to directional light cues (e.g., positive phototropism in the hypocotyl). In Arabidopsis, phot1 is essential for phototropism in response to low light, a response that is also modulated by phytochrome A (phyA), representing a classical example of photoreceptor coaction. The molecular mechanisms underlying promotion of phototropism by phyA remain unclear. Most phyA responses require nuclear accumulation of the photoreceptor, but interestingly, it has been proposed that cytosolic phyA promotes phototropism. By comparing the kinetics of phototropism in seedlings with different subcellular localizations of phyA, we show that nuclear phyA accelerates the phototropic response, whereas in the fhy1 fhl mutant, in which phyA remains in the cytosol, phototropic bending is slower than in the wild type. Consistent with this data, we find that transcription factors needed for full phyA responses are needed for normal phototropism. Moreover, we show that phyA is the primary photoreceptor promoting the expression of phototropism regulators in low light (e.g., PHYTOCHROME KINASE SUBSTRATE1 [PKS1] and ROOT PHOTO TROPISM2 [RPT2]). Although phyA remains cytosolic in fhy1 fhl, induction of PKS1 and RPT2 expression still occurs in fhy1 fhl, indicating that a low level of nuclear phyA signaling is still present in fhy1 fhl. PMID:22374392

How does gravity save or kill Q-balls?

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

Tamaki, Takashi; Sakai, Nobuyuki; Department of Education, Yamagata University, Yamagata 990-8560

2011-02-15

We explore stability of gravitating Q-balls with potential V{sub 4}({phi})=(m{sup 2}/2){phi}{sup 2}-{lambda}{phi}{sup 4}+({phi}{sup 6}/M{sup 2}) via catastrophe theory, as an extension of our previous work on Q-balls with potential V{sub 3}({phi})=(m{sup 2}/2){phi}{sup 2}-{mu}{phi}{sup 3}+{lambda}{phi}{sup 4}. In flat spacetime Q-balls with V{sub 4} in the thick-wall limit are unstable and there is a minimum charge Q{sub min}, where Q-balls with Q

Managing protected health information in distributed research network environments: automated review to facilitate collaboration

PubMed Central

2013-01-01

Background Multi-site health sciences research is becoming more common, as it enables investigation of rare outcomes and diseases and new healthcare innovations. Multi-site research usually involves the transfer of large amounts of research data between collaborators, which increases the potential for accidental disclosures of protected health information (PHI). Standard protocols for preventing release of PHI are extremely vulnerable to human error, particularly when the shared data sets are large. Methods To address this problem, we developed an automated program (SAS macro) to identify possible PHI in research data before it is transferred between research sites. The macro reviews all data in a designated directory to identify suspicious variable names and data patterns. The macro looks for variables that may contain personal identifiers such as medical record numbers and social security numbers. In addition, the macro identifies dates and numbers that may identify people who belong to small groups, who may be identifiable even in the absences of traditional identifiers. Results Evaluation of the macro on 100 sample research data sets indicated a recall of 0.98 and precision of 0.81. Conclusions When implemented consistently, the macro has the potential to streamline the PHI review process and significantly reduce accidental PHI disclosures. PMID:23521861

Interaction between physostigmine and soman on brain regional cholinesterase activity and /sup 3/H-physostigmine distribution

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

Hallak, M.E.; Woodruff, E.; Giacobini, E.

1986-03-05

Physostigmine (Phy) concentrations (as radioactivity) were studied in various brain areas after /sup 3/H-Phy administration as a function of time. Five min after 500 ..mu..g/kg i.m., cortex (CX) and total brain showed similar concentrations (370 ng/g) which were 50-90% higher than those of other brain regions (striatum, hippocampus, and medulla oblongata). Soman did not affect Phy levels in whole brain after pretreatment with Phy (100 or 500 ..mu..g/kg), however, the regional distribution of Phy was altered by soman as was ChE inhibition. A significant increase in Phy concentration was seen in HC (22 and 45% at 5 and 30 min,more » respectively) and CX (21% at 30 min). ChE activity in total brain was 12, 30, and 24% (5, 15 and 30 min after soman administration) lower than after Phy alone. If the pretreatment dose of Phy was increased to 500 ..mu..g/kg /sup 3/H-Phy, ChE activity was further reduced to 4, 13 and 19%. This might indicate that higher doses of Phy provide more protection of the enzyme from soman than lower doses. The protective role of Phy seen in total brain was not consistent for all brain regions. Soman alone produced a 95% ChE inhibition and there were no differences in its effect between total brain or brain areas. Pretreatment of the rat with Phy produced a protective effect upon ChE activity up to 30 min. However, no protective effect on survival was observed.« less

A novel dominant selectable system for the selection of transgenic plants under in vitro and greenhouse conditions based on phosphite metabolism.

PubMed

López-Arredondo, Damar L; Herrera-Estrella, Luis

2013-05-01

Antibiotic and herbicide resistance genes are currently the most frequently used selectable marker genes for plant research and crop development. However, the use of antibiotics and herbicides must be carefully controlled because the degree of susceptibility to these compounds varies widely among plant species and because they can also affect plant regeneration. Therefore, new selectable marker systems that are effective for a broad range of plant species are still needed. Here, we report a simple and inexpensive system based on providing transgenic plant cells the capacity to convert a nonmetabolizable compound (phosphite, Phi) into an essential nutrient for cell growth (phosphate) trough the expression of a bacterial gene encoding a phosphite oxidoreductase (PTXD). This system is effective for the selection of Arabidopsis transgenic plants by germinating T0 seeds directly on media supplemented with Phi and to select transgenic tobacco shoots from cocultivated leaf disc explants using nutrient media supplemented with Phi as both a source of phosphorus and selective agent. Because the ptxD/Phi system also allows the establishment of large-scale screening systems under greenhouse conditions completely eliminating false transformation events, it should facilitate the development of novel plant transformation methods. © 2013 Society for Experimental Biology, Association of Applied Biologists and Blackwell Publishing Ltd.

Intracellular pH Regulation in Cultured Astrocytes from Rat Hippocampus

PubMed Central

Bevensee, Mark O.; Weed, Regina A.; Boron, Walter F.

1997-01-01

We studied the regulation of intracellular pH (pHi) in single cultured astrocytes passaged once from the hippocampus of the rat, using the dye 2′,7′-biscarboxyethyl-5,6-carboxyfluorescein (BCECF) to monitor pHi. Intrinsic buffering power (βI) was 10.5 mM (pH unit)−1 at pHi 7.0, and decreased linearly with pHi; the best-fit line to the data had a slope of −10.0 mM (pH unit)−2. In the absence of HCO3 −, pHi recovery from an acid load was mediated predominantly by a Na-H exchanger because the recovery was inhibited 88% by amiloride and 79% by ethylisopropylamiloride (EIPA) at pHi 6.05. The ethylisopropylamiloride-sensitive component of acid extrusion fell linearly with pHi. Acid extrusion was inhibited 68% (pHi 6.23) by substituting Li+ for Na+ in the bath solution. Switching from a CO2/HCO3 −-free to a CO2/HCO3 −-containing bath solution caused mean steady state pHi to increase from 6.82 to 6.90, due to a Na+-driven HCO3 − transporter. The HCO3 −-induced pHi increase was unaffected by amiloride, but was inhibited 75% (pHi 6.85) by 400 μM 4,4′-diisothiocyanatostilbene-2,2′-disulfonic acid (DIDS), and 65% (pHi 6.55–6.75) by pretreating astrocytes for up to ∼6.3 h with 400 μM 4-acetamide-4′-isothiocyanatostilbene-2,2′-disulfonic acid (SITS). The CO2/HCO3 −-induced pHi increase was blocked when external Na+ was replaced with N-methyl-d-glucammonium (NMDG+). In the presence of HCO3 −, the Na+-driven HCO3 − transporter contributed to the pHi recovery from an acid load. For example, HCO3 − shifted the plot of acid-extrusion rate vs. pHi by 0.15–0.3 pH units in the alkaline direction. Also, with Na-H exchange inhibited by amiloride, HCO3 − increased acid extrusion 3.8-fold (pHi 6.20). When astrocytes were acid loaded in amiloride, with Li+ as the major cation, HCO3 − failed to elicit a substantial increase in pHi. Thus, Li+ does not appear to substitute well for Na+ on the HCO3 − transporter. We conclude that an amiloride-sensitive Na-H exchanger and a Na+-driven HCO3 − transporter are the predominant acid extruders in astrocytes. PMID:9379175

Enhancing Network Communication in NPSNET-V Virtual Environments Using XML-Described Dynamic Behavior (DBP) Protocols

DTIC Science & Technology

2001-09-01

testing is performed between two machines connected by either a 100 Mbps Ethernet connection or a 56K modem connection. This testing is performed...and defined as follows: • The available bandwidth is set at two different levels (Ethernet 100 Mbps and 56K modem ). 32 • The packet size is set... modem connection. These two connections represent the target 100 Mbps high end and 56k bps low end of anticipated client connections in web-based

Interfacing the VAX 11/780 Using Berkeley Unix 4.2.BSD and Ethernet Based Xerox Network Systems. Volume 1.

DTIC Science & Technology

1984-12-01

3Com Corporation ....... A-18 Ethernet Controller Support . . . . . . A-19 Host Systems Support . . . . . . . . . A-20 Personal Computers Support...A-23 VAX EtherSeries Software 0 * A-23 Network Research Corporation . o o o . o A-24 File Transfer Service . . . . o A-25 Virtual Terminal Service 0...Control office is planning to acquire a Digital Equipment Corporation VAX 11/780 mainframe computer with the Unix Berkeley 4.2BSD operating system. They

76 FR 63342 - Petition for Exemption; Summary of Petition Received

Federal Register 2010, 2011, 2012, 2013, 2014

2011-10-12

...-1039. Petitioner: PHI, Inc. Section of 14 CFR Affected: Sec. 91.9(a). Description of Relief Sought: PHI, Inc. (PHI), requests an exemption from 91.9(a) to allow PHI to operate S-92A helicopters in accordance...

Intracellular pH change does not accompany egg activation in the mouse.

PubMed

Phillips, K P; Baltz, J M

1996-09-01

In the sea urchin, some other marine invertebrates, and the frog, Xenopus, egg activation at fertilization is accompanied by an increase in intracellular pH (pHi). We measured pHi in germinal vesicle (GV)-intact mouse oocytes, ovulated eggs, and in vivo fertilized zygotes using the pH indicator dye, SNARF-1. The mean pH, was 6.96 +/- 0.004 (+/- SEM) in GV-intact oocytes, 7.00 +/- 0.01 in ovulated, unfertilized eggs, and 7.02 +/- 0.01 in fertilized zygotes, indicating no sustained changes in pHi after germinal vesicle breakdown (GVBD) or fertilization. To examine whether transient changes in pHi occur shortly after egg activation, mouse eggs were parthenogenetically activated by 7% ethanol in phosphate buffered saline (PBS); no significant change in pHi followed ethanol activation. Since increased Na+/H+ antiporter activity is responsible for pHi increase in the sea urchin, pHi was measured in the absence of added bicarbonate or CO2 (a condition under which the antiporter would be the only major pHi regulatory mechanism able to operate, since the others were bicarbonate-dependent) in GV-intact oocytes, ovulated eggs, and in vivo fertilized zygotes to determine whether a Na+/H+ antiporter was activated. There was no physiologically significant difference in pHi after GVBD or fertilization, when pHi was measured in bicarbonate-free medium, nor any change upon parthenogenetic activation. Thus, a change in pHi is not a feature of egg activation in the mouse.

A review on computational systems biology of pathogen–host interactions

PubMed Central

Durmuş, Saliha; Çakır, Tunahan; Özgür, Arzucan; Guthke, Reinhard

2015-01-01

Pathogens manipulate the cellular mechanisms of host organisms via pathogen–host interactions (PHIs) in order to take advantage of the capabilities of host cells, leading to infections. The crucial role of these interspecies molecular interactions in initiating and sustaining infections necessitates a thorough understanding of the corresponding mechanisms. Unlike the traditional approach of considering the host or pathogen separately, a systems-level approach, considering the PHI system as a whole is indispensable to elucidate the mechanisms of infection. Following the technological advances in the post-genomic era, PHI data have been produced in large-scale within the last decade. Systems biology-based methods for the inference and analysis of PHI regulatory, metabolic, and protein–protein networks to shed light on infection mechanisms are gaining increasing demand thanks to the availability of omics data. The knowledge derived from the PHIs may largely contribute to the identification of new and more efficient therapeutics to prevent or cure infections. There are recent efforts for the detailed documentation of these experimentally verified PHI data through Web-based databases. Despite these advances in data archiving, there are still large amounts of PHI data in the biomedical literature yet to be discovered, and novel text mining methods are in development to unearth such hidden data. Here, we review a collection of recent studies on computational systems biology of PHIs with a special focus on the methods for the inference and analysis of PHI networks, covering also the Web-based databases and text-mining efforts to unravel the data hidden in the literature. PMID:25914674

Many-integrated core (MIC) technology for accelerating Monte Carlo simulation of radiation transport: A study based on the code DPM

NASA Astrophysics Data System (ADS)

Rodriguez, M.; Brualla, L.

2018-04-01

Monte Carlo simulation of radiation transport is computationally demanding to obtain reasonably low statistical uncertainties of the estimated quantities. Therefore, it can benefit in a large extent from high-performance computing. This work is aimed at assessing the performance of the first generation of the many-integrated core architecture (MIC) Xeon Phi coprocessor with respect to that of a CPU consisting of a double 12-core Xeon processor in Monte Carlo simulation of coupled electron-photonshowers. The comparison was made twofold, first, through a suite of basic tests including parallel versions of the random number generators Mersenne Twister and a modified implementation of RANECU. These tests were addressed to establish a baseline comparison between both devices. Secondly, through the p DPM code developed in this work. p DPM is a parallel version of the Dose Planning Method (DPM) program for fast Monte Carlo simulation of radiation transport in voxelized geometries. A variety of techniques addressed to obtain a large scalability on the Xeon Phi were implemented in p DPM. Maximum scalabilities of 84 . 2 × and 107 . 5 × were obtained in the Xeon Phi for simulations of electron and photon beams, respectively. Nevertheless, in none of the tests involving radiation transport the Xeon Phi performed better than the CPU. The disadvantage of the Xeon Phi with respect to the CPU owes to the low performance of the single core of the former. A single core of the Xeon Phi was more than 10 times less efficient than a single core of the CPU for all radiation transport simulations.

[Application study on PHI and 16PF and SCL-90 for freshman's psychology inspection].

PubMed

Niu, Peng

2009-07-01

To explore the effect of application of the measurement table of PHI and 16PF and SCL-90 for freshmen psychology inspection. The measurement tables of PHI and 16PF for psychology inspection of freshmen of 2004-2007 years were used to sift crisis intervention objects. Continuous four years test showed certain stability, in addition to excited factors,the scores of Freshmen's PHI factors were more lower than normal. The incidence rates of mental problems screened by PHI table were very low and 3-5 serious-mental-problem students weren't detected. The problem can be resolved by the application of PHI combined with 16PF through remesuring the suspected cases by SCL-90. The combinative application of PHI, 16PF and SCL-90 would be better.

Molecular characterization of a genomic region in a Lactococcus bacteriophage that is involved in its sensitivity to the phage defense mechanism AbiA.

PubMed

Dinsmore, P K; Klaenhammer, T R

1997-05-01

A spontaneous mutant of the lactococcal phage phi31 that is insensitive to the phage defense mechanism AbiA was characterized in an effort to identify the phage factor(s) involved in sensitivity of phi31 to AbiA. A point mutation was localized in the genome of the AbiA-insensitive phage (phi31A) by heteroduplex analysis of a 9-kb region. The mutation (G to T) was within a 738-bp open reading frame (ORF245) and resulted in an arginine-to-leucine change in the predicted amino acid sequence of the protein. The mutant phi31A-ORF245 reduced the sensitivity of phi31 to AbiA when present in trans, indicating that the mutation in ORF245 is responsible for the AbiA insensitivity of phi31A. Transcription of ORF245 occurs early in the phage infection cycles of phi31 and phi31A and is unaffected by AbiA. Expansion of the phi31 sequence revealed ORF169 (immediately upstream of ORF245) and ORF71 (which ends 84 bp upstream of ORF169). Two inverted repeats lie within the 84-bp region between ORF71 and ORF169. Sequence analysis of an independently isolated AbiA-insensitive phage, phi31B, identified a mutation (G to A) in one of the inverted repeats. A 118-bp fragment from phi31, encompassing the 84-bp region between ORF71 and ORF169, eliminates AbiA activity against phi31 when present in trans, establishing a relationship between AbiA and this fragment. The study of this region of phage phi31 has identified an open reading frame (ORF245) and a 118-bp DNA fragment that interact with AbiA and are likely to be involved in the sensitivity of this phage to AbiA.

[Improvement of Phi bodies stain and its clinical significance].

PubMed

Gong, Xu-Bo; Lu, Xing-Guo; Yan, Li-Juan; Xiao, Xi-Bin; Wu, Dong; Xu, Gen-Bo; Zhang, Xiao-Hong; Zhao, Xiao-Ying

2009-02-01

The aim of this study was to improve the dyeing method of hydroperoxidase (HPO), to analyze the morphologic features of Phi bodies and to evaluate the clinical application of this method. 128 bone marrow or peripheral blood smears from patients with myeloid and lymphoid malignancies were stained by improved HPO staining. The Phi bodies were observed with detection rate of Phi bodies in different leukemias. 69 acute myeloid leukemia (AML) specimens were chosen randomly, the positive rate and the number of Phi bodies between the improved HPO and POX stain based on the same substrate of 3, 3'diaminobenzidine were compared. The results showed that the shape of bundle-like Phi bodies was variable, long or short. while the nubbly Phi bodies often presented oval and smooth. Club-like Phi bodies were found in M(3). The detection rates of bundle-like Phi bodies in AML M(1)-M(5) were 42.9% (6/14), 83.3% (15/18), 92.0% (23/25), 52.3% (11/21), 33.3% (5/15) respectively, and those of nubbly Phi bodies were 28.6% (4/14), 66.7% (12/18), 11.1% (3/25), 33.3% (7/21), 20.0% (3/15) respectively. The detection rate of bundle-like Phi bodies in M(3) was significantly higher than that in (M(1) + M(2)) or (M(4) + M(5)) groups. The detection rate of nubbly Phi bodies in (M(1) + M(2)) group was higher than that in M(3) group. In conclusion, after improvement of staining method, the HPO stain becomes simple, the detection rate of Phi bodies is higher than that by the previous method, the positive granules are more obvious, and the results become stable. This improved method plays an important role in differentiating AML from ALL, subtyping AML, and evaluating the therapeutic results.

Density perturbations in general modified gravitational theories

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

De Felice, Antonio; Tsujikawa, Shinji; Mukohyama, Shinji

2010-07-15

We derive the equations of linear cosmological perturbations for the general Lagrangian density f(R,{phi},X)/2+L{sub c}, where R is a Ricci scalar, {phi} is a scalar field, and X=-{partial_derivative}{sup {mu}{phi}{partial_derivative}}{sub {mu}{phi}/}2 is a field kinetic energy. We take into account a nonlinear self-interaction term L{sub c}={xi}({phi}) {open_square}{phi}({partial_derivative}{sup {mu}{phi}{partial_derivative}}{sub {mu}{phi}}) recently studied in the context of ''Galileon'' cosmology, which keeps the field equations at second order. Taking into account a scalar-field mass explicitly, the equations of matter density perturbations and gravitational potentials are obtained under a quasistatic approximation on subhorizon scales. We also derive conditions for the avoidance of ghosts and Laplacianmore » instabilities associated with propagation speeds. Our analysis includes most of modified gravity models of dark energy proposed in literature; and thus it is convenient to test the viability of such models from both theoretical and observational points of view.« less

Reliable Wide-Area Wavelength Division Multiplexing Passive Optical Network Accommodating Gigabit Ethernet and 10-Gb Ethernet Services

NASA Astrophysics Data System (ADS)

Nakamura, Hirotaka; Suzuki, Hiro; Kani, Jun-Ichi; Iwatsuki, Katsumi

2006-05-01

This paper proposes and demonstrates a reliable wide-area wavelength-division-multiplexing passive optical network (WDM-PON) with a wavelength-shifted protection scheme. This protection scheme utilizes the cyclic property of 2 × N athermal arrayed-waveguide grating and two kinds of wavelength allocations, each of which is assigned for working and protection, respectively. Compared with conventional protection schemes, this scheme does not need a 3-dB optical coupler, thus leading to ensure the large loss budget that is suited for wide-area WDM-PONs. It also features a passive access node and does not have a protection function in the optical network unit (ONU). The feasibility of the proposed scheme is experimentally confirmed by the carrier-distributed WDM-PON with gigabit Ethernet interface (GbE-IF) and 10-GbE-IF, in which the ONU does not employ a light source, and all wavelengths for upstream signals are centralized and distributed from the central office.

Systems and technologies for high-speed inter-office/datacenter interface

NASA Astrophysics Data System (ADS)

Sone, Y.; Nishizawa, H.; Yamamoto, S.; Fukutoku, M.; Yoshimatsu, T.

2017-01-01

Emerging requirements for inter-office/inter-datacenter short reach links for data center interconnects (DCI) and metro transport networks have led to various inter-office and inter-datacenter optical interface technologies. These technologies are bringing significant changes to systems and network architectures. In this paper, we present a system and ZR optical interface technologies for DCI and metro transport networks, then introduce the latest challenges facing the system framework. There are two trends in reach extension; one is to use Ethernet and the other is to use digital coherent technologies. The first approach achieves reach extension while using as many existing Ethernet components as possible. It offers low costs as reuses the cost-effective components created for the large Ethernet market. The second approach adopts low-cost and low power coherent DSPs that implement the minimal set long haul transmission functions. This paper introduces an architecture that integrates both trends. The architecture satisfies both datacom and telecom needs with a common control and management interface and automated configuration.

On TTEthernet for Integrated Fault-Tolerant Spacecraft Networks

NASA Technical Reports Server (NTRS)

Loveless, Andrew

2015-01-01

There has recently been a push for adopting integrated modular avionics (IMA) principles in designing spacecraft architectures. This consolidation of multiple vehicle functions to shared computing platforms can significantly reduce spacecraft cost, weight, and de- sign complexity. Ethernet technology is attractive for inclusion in more integrated avionic systems due to its high speed, flexibility, and the availability of inexpensive commercial off-the-shelf (COTS) components. Furthermore, Ethernet can be augmented with a variety of quality of service (QoS) enhancements that enable its use for transmitting critical data. TTEthernet introduces a decentralized clock synchronization paradigm enabling the use of time-triggered Ethernet messaging appropriate for hard real-time applications. TTEthernet can also provide two forms of event-driven communication, therefore accommodating the full spectrum of traffic criticality levels required in IMA architectures. This paper explores the application of TTEthernet technology to future IMA spacecraft architectures as part of the Avionics and Software (A&S) project chartered by NASA's Advanced Exploration Systems (AES) program.

Tonometry revisited: perfusion-related, metabolic, and respiratory components of gastric mucosal acidosis in acute cardiorespiratory failure.

PubMed

Jakob, Stephan M; Parviainen, Ilkka; Ruokonen, Esko; Kogan, Alexander; Takala, Jukka

2008-05-01

Mucosal pH (pHi) is influenced by local perfusion and metabolism (mucosal-arterial pCO2 gradient, DeltapCO2), systemic metabolic acidosis (arterial bicarbonate), and respiration (arterial pCO2). We determined these components of pHi and their relation to outcome during the first 24 h of intensive care. We studied 103 patients with acute respiratory or circulatory failure (age, 63+/-2 [mean+/-SEM]; Acute Physiology and Chronic Health Evaluation II score, 20+/-1; Sequential Organ Failure Assessment score, 8+/-0). pHi, and the effects of bicarbonate and arterial and mucosal pCO2 on pHi, were assessed at admission, 6, and 24 h. pHi was reduced (at admission, 7.27+/-0.01) due to low arterial bicarbonate and increased DeltapCO2. Low pHi (<7.32) at admission (n=58; mortality, 29% vs. 13% in those with pHi>or=7.32 at admission; P=0.061) was associated with an increased DeltapCO2 in 59% of patients (mortality, 47% vs. 4% for patients with low pHi and normal DeltapCO2; P=0.0003). An increased versus normal DeltapCO2, regardless of pHi, was associated with increased mortality at admission (51% vs. 5%; P<0.0001; n=39) and at 6 h (34% vs. 13%; P=0.016; n=45). A delayed normalization or persistently low pHi (n=47) or high DeltapCO2 (n=25) was associated with high mortality (low pHi [34%] vs. high DeltapCO2 [60%]; P=0.046). In nonsurvivors, hypocapnia increased pHi at baseline, 6, and 24 h (all P

Some demographic issues affecting private health insurance.

PubMed

Hanning, Brian

2004-01-01

There will be significant changes in the demography of persons with Private Health Insurance (PHI). Two methods of projecting PHI coverage are discussed in this paper. The first assumes the only factors affecting PHI coverage are demographic change and mortality and facilitates comparisons between actual and projected PHI coverage. The second projects the percentage of the population insured in each five year age cohort, and makes allowance for changes in PHI coverage due to all factors. Demographic change will increase Registered Health Benefit Organization (RHBO) premiums by 1.7% per annum. The role of these projections in analysing the effect of future premium increases on PHI retention rates is also discussed.

Independent regulation of reovirus membrane penetration and apoptosis by the mu1 phi domain.

PubMed

Danthi, Pranav; Coffey, Caroline M; Parker, John S L; Abel, Ty W; Dermody, Terence S

2008-12-01

Apoptosis plays an important role in the pathogenesis of reovirus encephalitis. Reovirus outer-capsid protein mu1, which functions to penetrate host cell membranes during viral entry, is the primary regulator of apoptosis following reovirus infection. Ectopic expression of full-length and truncated forms of mu1 indicates that the mu1 phi domain is sufficient to elicit a cell death response. To evaluate the contribution of the mu1 phi domain to the induction of apoptosis following reovirus infection, phi mutant viruses were generated by reverse genetics and analyzed for the capacity to penetrate cell membranes and elicit apoptosis. We found that mutations in phi diminish reovirus membrane penetration efficiency by preventing conformational changes that lead to generation of key reovirus entry intermediates. Independent of effects on membrane penetration, amino acid substitutions in phi affect the apoptotic potential of reovirus, suggesting that phi initiates apoptosis subsequent to cytosolic delivery. In comparison to wild-type virus, apoptosis-defective phi mutant viruses display diminished neurovirulence following intracranial inoculation of newborn mice. These results indicate that the phi domain of mu1 plays an important regulatory role in reovirus-induced apoptosis and disease.

Phi is not beta, and why Wertheimer's discovery launched the Gestalt revolution.

PubMed

Steinman, R M; Pizlo, Z; Pizlo, F J

2000-01-01

Max Wertheimer (1880-1943), the founder of the Gestalt School of Psychology, published a monograph on the perception of apparent motion in 1912, which initiated a new direction for a great deal of subsequent perceptual theory and research. Wertheimer's research was inspired by a serendipitous observation of a pure apparent movement, which he called the phi-phenomenon to distinguish it from optimal apparent movement (beta), which resembles real movement. Wertheimer called his novel observation 'pure' because it was perceived in the absence of any object being seen to change its position in space. The phi-phenomenon, as well as the best conditions for seeing it, were not described clearly in this monograph, leading to considerable subsequent confusion about its appearance and occurrence. We review the history leading to the discovery of the phi-phenomenon, and then describe: (i) a likely source for the confusion evident in most contemporary research on the phi-phenomenon; (ii) the best conditions for seeing the phi-phenomenon; (iii) new conditions that provide a particularly vivid phi-phenomenon; and (iv) two lines of thought that may provide explanations of the phi-phenomenon and also distinguish phi from beta.

Na+, HCO3--cotransporter NBCn1 increases pHi gradients, filopodia, and migration of smooth muscle cells and promotes arterial remodelling.

PubMed

Boedtkjer, Ebbe; Bentzon, Jacob F; Dam, Vibeke S; Aalkjaer, Christian

2016-08-01

Arterial remodelling can cause luminal narrowing and obstruct blood flow. We tested the hypothesis that cellular acid-base transport facilitates proliferation and migration of vascular smooth muscle cells (VSMCs) and enhances remodelling of conduit arteries. [Formula: see text]-cotransport via NBCn1 (Slc4a7) mediates net acid extrusion and controls steady-state intracellular pH (pHi) in VSMCs of mouse carotid arteries and primary aortic explants. Carotid arteries undergo hypertrophic inward remodelling in response to partial or complete ligation in vivo, but the increase in media area and thickness and reduction in lumen diameter are attenuated in arteries from NBCn1 knock-out compared with wild-type mice. With [Formula: see text] present, gradients for pHi (∼0.2 units magnitude) exist along the axis of VSMC migration in primary explants from wild-type but not NBCn1 knock-out mice. Knock-out or pharmacological inhibition of NBCn1 also reduces filopodia and lowers initial rates of VSMC migration after scratch-wound infliction. Interventions to reduce H(+)-buffer mobility (omission of [Formula: see text] or inhibition of carbonic anhydrases) re-establish axial pHi gradients, filopodia, and migration rates in explants from NBCn1 knock-out mice. The omission of [Formula: see text] also lowers global pHi and inhibits proliferation in primary explants. Under physiological conditions (i.e. with [Formula: see text] present), NBCn1-mediated [Formula: see text] uptake raises VSMC pHi and promotes filopodia, VSMC migration, and hypertrophic inward remodelling. We propose that axial pHi gradients enhance VSMC migration whereas global acidification inhibits VSMC proliferation and media hypertrophy after carotid artery ligation. These findings support a key role of acid-base transport, particularly via NBCn1, for development of occlusive artery disease. Published on behalf of the European Society of Cardiology. All rights reserved. © The Author 2016. For permissions please email: journals.permissions@oup.com.

PHI-base: a new interface and further additions for the multi-species pathogen–host interactions database

PubMed Central

Urban, Martin; Cuzick, Alayne; Rutherford, Kim; Irvine, Alistair; Pedro, Helder; Pant, Rashmi; Sadanadan, Vidyendra; Khamari, Lokanath; Billal, Santoshkumar; Mohanty, Sagar; Hammond-Kosack, Kim E.

2017-01-01

The pathogen–host interactions database (PHI-base) is available at www.phi-base.org. PHI-base contains expertly curated molecular and biological information on genes proven to affect the outcome of pathogen–host interactions reported in peer reviewed research articles. In addition, literature that indicates specific gene alterations that did not affect the disease interaction phenotype are curated to provide complete datasets for comparative purposes. Viruses are not included. Here we describe a revised PHI-base Version 4 data platform with improved search, filtering and extended data display functions. A PHIB-BLAST search function is provided and a link to PHI-Canto, a tool for authors to directly curate their own published data into PHI-base. The new release of PHI-base Version 4.2 (October 2016) has an increased data content containing information from 2219 manually curated references. The data provide information on 4460 genes from 264 pathogens tested on 176 hosts in 8046 interactions. Prokaryotic and eukaryotic pathogens are represented in almost equal numbers. Host species belong ∼70% to plants and 30% to other species of medical and/or environmental importance. Additional data types included into PHI-base 4 are the direct targets of pathogen effector proteins in experimental and natural host organisms. The curation problems encountered and the future directions of the PHI-base project are briefly discussed. PMID:27915230

Use of the cytosensor microphysiometer to predict results of a 21-day cumulative irritation patch test in humans.

PubMed

Landin, Wendell E; Mun, Greg C; Nims, Raymond W; Harbell, John W

2007-09-01

The cytosensor microphysiometer (mu phi) was investigated as a rapid, relatively inexpensive test to predict performance of skin cleansing wipes on the human 21-day cumulative irritation patch test (21CIPT). It indirectly measures metabolic rate changes in L929 cells as a function of test article dose, by measuring the acidification rate in a low-buffer medium. The dose producing a 50% reduction in metabolic rate (MRD50), relative to the baseline rate, is used as a measure of toxicity. The acute toxicity of the mu phi assay can be compared to the chronic toxicity of the 21CIPT, which is based largely on the exposure of test agents to the epidermal cells, resulting in damage and penetration of the stratum corneum leading to cell toxicity. Two series of surfactant-based cleansing wipe products were tested via the mu phi assay and 21CIPT. The first series, consisting of 20 products, was used to determine a prediction model. The second series of 38 products consisted of routine product development formulas or marketed products. Comparing the results from both tests, samples with an MRD50 greater than 50 mg/ml provided a 21CIPT score consistent with a product that performs satisfactorily in the market. When the MRD50 was greater than 78 mg/ml, the 21CIPT score was usually zero. The mu phi may be more sensitive than the 21CIPT for ranking minimally irritating materials. The mu phi assay is useful as a screen for predicting the performance of a wet wipes formula on the 21CIPT, and concurrently reduces the use of animals for safety testing in a product development program for cleansing wipes.

Development Status of the Rad-Tolerant TTEthernet Controller

NASA Astrophysics Data System (ADS)

Fidi, Christian; van Masar, Ivan

2016-08-01

The use of switched networking technologies for aerospace and more recently automotive brings additional advantages for space applications like the increase in performance of the overall avionics of a spacecraft. These networks are characterized by a central device (switch) and a point-to-point structure between switch and terminal devices that eases electrical and logical insulation.However, for a use in highly-reliable or highly-available applications as in launchers or satellites systems, these network technologies need to provide built-in determinism and redundancy to fulfill the tight latency and jitter requirements of the avionics control loops and the respective hardware redundancy. Therefore a state of the art networking technology already provides these features and allows the modularity and scalability to be used for the different space applications and would allow combining the deterministic avionics with the high speed payload network in a spacecraft [1].Introducing the time-triggered principle to Ethernet allows combining the open industry standard IEE802.3 Ethernet currently use in almost all GSE platforms, with full control of latency and jitter of the time-triggered approach. To allow the time-triggered data flow over Ethernet, a network- wide synchronization time-base has to be established to allow deriving all network events on a globally known time which is typically done in software in almost all spacecrafts. The additional synchronization service of Time-triggered Ethernet has been implemented as additional quality of service (QoS) on layer 2 of the ISO/OSI network model and been standardized in the SAE AS6802 [3].Within a launcher, the communication system ensured the data exchanges between avionic functions during all phases of the launcher lifecycle which is composed of three areas: AIT operations, ground phase and flight phase. To ensure the use of a single network for the different phases, the network needs to support features like the handling of different traffic classes (critical traffic and non-critical traffic, i.e. TT, RC and BE [2]). Also the compatibility to the IEEE1588 synchronization protocol can be used to connect legacy IEEE1588 equipment for GSE equipment.However this commercially available technology currently used in the aviation-, the industrial- and the automotive market needs to be matured for the use in space applications. Therefore a development of the necessary space-grade components, mainly the switch and the end system is needed.This paper presents the current development status of a radiation tolerant integrated circuit for the use in different space applications. It outlines the different steps needed to be performed to ensure the usability of this digital chip in highly reliable as well as in highly available space applications.

Deformation Monitoring of Waste-Rock-Backfilled Mining Gob for Ground Control

PubMed Central

Zhao, Tongbin; Zhang, Yubao; Zhang, Zhenyu; Li, Zhanhai; Ma, Shuqi

2017-01-01

Backfill mining is an effective option to mitigate ground subsidence, especially for mining under surface infrastructure, such as buildings, dams, rivers and railways. To evaluate its performance, continual long-term field monitoring of the deformation of backfilled gob is important to satisfy strict public scrutiny. Based on industrial Ethernet, a real-time monitoring system was established to monitor the deformation of waste-rock-backfilled gob at −700 m depth in the Tangshan coal mine, Hebei Province, China. The designed deformation sensors, based on a resistance transducer mechanism, were placed vertically between the roof and floor. Stress sensors were installed above square steel plates that were anchored to the floor strata. Meanwhile, data cables were protected by steel tubes in case of damage. The developed system continually harvested field data for three months. The results show that industrial Ethernet technology can be reliably used for long-term data transmission in complicated underground mining conditions. The monitoring reveals that the roof subsidence of the backfilled gob area can be categorized into four phases. The bearing load of the backfill developed gradually and simultaneously with the deformation of the roof strata, and started to be almost invariable when the mining face passed 97 m. PMID:28475168

Deformation Monitoring of Waste-Rock-Backfilled Mining Gob for Ground Control.

PubMed

Zhao, Tongbin; Zhang, Yubao; Zhang, Zhenyu; Li, Zhanhai; Ma, Shuqi

2017-05-05

Backfill mining is an effective option to mitigate ground subsidence, especially for mining under surface infrastructure, such as buildings, dams, rivers and railways. To evaluate its performance, continual long-term field monitoring of the deformation of backfilled gob is important to satisfy strict public scrutiny. Based on industrial Ethernet, a real-time monitoring system was established to monitor the deformation of waste-rock-backfilled gob at -700 m depth in the Tangshan coal mine, Hebei Province, China. The designed deformation sensors, based on a resistance transducer mechanism, were placed vertically between the roof and floor. Stress sensors were installed above square steel plates that were anchored to the floor strata. Meanwhile, data cables were protected by steel tubes in case of damage. The developed system continually harvested field data for three months. The results show that industrial Ethernet technology can be reliably used for long-term data transmission in complicated underground mining conditions. The monitoring reveals that the roof subsidence of the backfilled gob area can be categorized into four phases. The bearing load of the backfill developed gradually and simultaneously with the deformation of the roof strata, and started to be almost invariable when the mining face passed 97 m.

Handheld hyperspectral imager system for chemical/biological and environmental applications

NASA Astrophysics Data System (ADS)

Hinnrichs, Michele; Piatek, Bob

2004-08-01

A small, hand held, battery operated imaging infrared spectrometer, Sherlock, has been developed by Pacific Advanced Technology and was field tested in early 2003. The Sherlock spectral imaging camera has been designed for remote gas leak detection, however, the architecture of the camera is versatile enough that it can be applied to numerous other applications such as homeland security, chemical/biological agent detection, medical and pharmaceutical applications as well as standard research and development. This paper describes the Sherlock camera, theory of operations, shows current applications and touches on potential future applications for the camera. The Sherlock has an embedded Power PC and performs real-time-image processing function in an embedded FPGA. The camera has a built in LCD display as well as output to a standard monitor, or NTSC display. It has several I/O ports, ethernet, firewire, RS232 and thus can be easily controlled from a remote location. In addition, software upgrades can be performed over the ethernet eliminating the need to send the camera back to the factory for a retrofit. Using the USB port a mouse and key board can be connected and the camera can be used in a laboratory environment as a stand alone imaging spectrometer.

Hand-held hyperspectral imager for chemical/biological and environmental applications

NASA Astrophysics Data System (ADS)

Hinnrichs, Michele; Piatek, Bob

2004-03-01

A small, hand held, battery operated imaging infrared spectrometer, Sherlock, has been developed by Pacific Advanced Technology and was field tested in early 2003. The Sherlock spectral imaging camera has been designed for remote gas leak detection, however, the architecture of the camera is versatile enough that it can be applied to numerous other applications such as homeland security, chemical/biological agent detection, medical and pharmaceutical applications as well as standard research and development. This paper describes the Sherlock camera, theory of operations, shows current applications and touches on potential future applications for the camera. The Sherlock has an embedded Power PC and performs real-time-image processing function in an embedded FPGA. The camera has a built in LCD display as well as output to a standard monitor, or NTSC display. It has several I/O ports, ethernet, firewire, RS232 and thus can be easily controlled from a remote location. In addition, software upgrades can be performed over the ethernet eliminating the need to send the camera back to the factory for a retrofit. Using the USB port a mouse and key board can be connected and the camera can be used in a laboratory environment as a stand alone imaging spectrometer.

PCH1 integrates circadian and light-signaling pathways to control photoperiod-responsive growth in Arabidopsis

PubMed Central

Huang, He; Yoo, Chan Yul; Bindbeutel, Rebecca; Goldsworthy, Jessica; Tielking, Allison; Alvarez, Sophie; Naldrett, Michael J; Evans, Bradley S; Chen, Meng; Nusinow, Dmitri A

2016-01-01

Plants react to seasonal change in day length through altering physiology and development. Factors that function to harmonize growth with photoperiod are poorly understood. Here we characterize a new protein that associates with both circadian clock and photoreceptor components, named PHOTOPERIODIC CONTROL OF HYPOCOTYL1 (PCH1). pch1 seedlings have overly elongated hypocotyls specifically under short days while constitutive expression of PCH1 shortens hypocotyls independent of day length. PCH1 peaks at dusk, binds phytochrome B (phyB) in a red light-dependent manner, and co-localizes with phyB into photobodies. PCH1 is necessary and sufficient to promote the biogenesis of large photobodies to maintain an active phyB pool after light exposure, potentiating red-light signaling and prolonging memory of prior illumination. Manipulating PCH1 alters PHYTOCHROME INTERACTING FACTOR 4 levels and regulates light-responsive gene expression. Thus, PCH1 is a new factor that regulates photoperiod-responsive growth by integrating the clock with light perception pathways through modulating daily phyB-signaling. DOI: http://dx.doi.org/10.7554/eLife.13292.001 PMID:26839287

Wedding Rigorous Scientific Methodology and Ancient Herbal Wisdom to Benefit Cancer Patients: The Development of PHY906.

PubMed

Chu, Edward

2018-02-15

Our research group has extensively characterized the preclinical and clinical activities of PHY906, a traditional Chinese herbal medicine, as a modulator of irinotecan-based chemotherapy for the treatment of colorectal cancer. This article reviews the critical issues of quality control and standardization of PHY906 and highlights the importance of high-quality material for the conduct of preclinical and clinical studies. Studies to investigate the potential biological mechanisms of action using a systems biology approach play a pivotal role in providing the preclinical rationale to move forward with clinical studies. For early-phase clinical studies, translational biomarkers should be incorporated to characterize the biological effects of the herbal medicine. These biomarkers include tumor mutational load, cytokine/chemokine expression, metabolomic profiling, and the presence of key herbal metabolites. Sophisticated bioinformatic approaches are critical for mining the data and identifying those biomarkers that can define the subset of patients who will benefit from PHY906 or any other herbal medicine, in terms of reduced treatment toxicity, improved quality of life, and/or enhanced clinical activity of treatment.

Colocalization of numerous immunoreactivities in endocrine cells of the chicken proventriculus at hatching.

PubMed

Martínez, A; Buchan, A M; López, J; Sesma, P

2000-05-01

The colocalization of regulatory peptide immunoreactivities in endocrine cells of the chicken proventriculus at hatching has been investigated using the avidin-biotin technique in serial sections and double immunofluorescence in the same section for light microscopy, and double immunogold staining for electron microscopy. In addition to the eight immunoreactivities previously described in this organ, cells immunoreactive for peptide histidine isoleucine (PHI), peptide gene product 9.5 (PGP), and the amidating enzyme, peptidylglycine alpha-amidating monooxygenase (PAM) were observed. All the cells immunoreactive to glucagon were also immunostained by the PHI antiserum. In addition, all the glucagon-like peptide 1, avian pancreatic polypeptide, and some of the neurotensin-like cells costored also glucagon- and PHI-immunoreactive substances. PGP- and PAM-immunoreactivities were also found in the glucagon-positive cells. A small proportion of the somatostatin-containing cells were positive for PHI but not for other regulatory peptides. These results could suggest either the existence of a very complex regulatory system or that the endocrine system of the newborn chickens is not yet fully developed.

SAS and SPSS macros to calculate standardized Cronbach's alpha using the upper bound of the phi coefficient for dichotomous items.

PubMed

Sun, Wei; Chou, Chih-Ping; Stacy, Alan W; Ma, Huiyan; Unger, Jennifer; Gallaher, Peggy

2007-02-01

Cronbach's a is widely used in social science research to estimate the internal consistency of reliability of a measurement scale. However, when items are not strictly parallel, the Cronbach's a coefficient provides a lower-bound estimate of true reliability, and this estimate may be further biased downward when items are dichotomous. The estimation of standardized Cronbach's a for a scale with dichotomous items can be improved by using the upper bound of coefficient phi. SAS and SPSS macros have been developed in this article to obtain standardized Cronbach's a via this method. The simulation analysis showed that Cronbach's a from upper-bound phi might be appropriate for estimating the real reliability when standardized Cronbach's a is problematic.

Studies with infections fragments of phage DNA. Final report, January 1, 1970--June 30, 1976

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

Schachtele, C. F.

The minute, virulent and structurally intricate Bacillus subtilis bacteriophage phi 29 was utilized to study in vivo viral development. Purified strands of phi 29 DNA were used to analyze transcription of the viral genome. Early mRNA hybridizes to the light DNA strand which controls DNA replication and other early functions. Late mRNA hybridizes to the heavy DNA strand which codes for phage structural proteins. The temporal sequence of specific viral protein synthesis was analyzed by gel electrophoresis and was shown to directly correlate with the RNA transcription pattern. The genes carried by phi 29 have been marked with ts andmore » sus mutations and mapped by appropriate crosses yielding a linear map of 17 cistrons. Fragments of the phi 29 DNA were shown to retain their biological activity and marker rescue studies indicated that gene transfer could be performed with pieces having a molecular weight of less than 1 million daltons. Mutant infection under nonpermissive conditions and the analysis of precursor structures has allowed the formation of a tentative morphogenetic pathway leading to the formation of infectious particles. Work with phi 29 has established this virus as an advantageous model system for studying a variety of problems in molecular biology and approximately a dozen laboratories in the country and abroad are working with this phage.« less

X-Phi and Carnapian Explication.

PubMed

Shepherd, Joshua; Justus, James

2015-04-01

The rise of experimental philosophy (x-phi) has placed metaphilosophical questions, particularly those concerning concepts, at the center of philosophical attention. X-phi offers empirically rigorous methods for identifying conceptual content, but what exactly it contributes towards evaluating conceptual content remains unclear. We show how x-phi complements Rudolf Carnap's underappreciated methodology for concept determination, explication. This clarifies and extends x-phi's positive philosophical import, and also exhibits explication's broad appeal. But there is a potential problem: Carnap's account of explication was limited to empirical and logical concepts, but many concepts of interest to philosophers (experimental and otherwise) are essentially normative. With formal epistemology as a case study, we show how x-phi assisted explication can apply to normative domains.

phiGENOME: an integrative navigation throughout bacteriophage genomes.

PubMed

Stano, Matej; Klucar, Lubos

2011-11-01

phiGENOME is a web-based genome browser generating dynamic and interactive graphical representation of phage genomes stored in the phiSITE, database of gene regulation in bacteriophages. phiGENOME is an integral part of the phiSITE web portal (http://www.phisite.org/phigenome) and it was optimised for visualisation of phage genomes with the emphasis on the gene regulatory elements. phiGENOME consists of three components: (i) genome map viewer built using Adobe Flash technology, providing dynamic and interactive graphical display of phage genomes; (ii) sequence browser based on precisely formatted HTML tags, providing detailed exploration of genome features on the sequence level and (iii) regulation illustrator, based on Scalable Vector Graphics (SVG) and designed for graphical representation of gene regulations. Bringing 542 complete genome sequences accompanied with their rich annotations and references, makes phiGENOME a unique information resource in the field of phage genomics. Copyright © 2011 Elsevier Inc. All rights reserved.

DNA conformational change induced by the bacteriophage phi 29 connector.

PubMed Central

Valpuesta, J M; Serrano, M; Donate, L E; Herranz, L; Carrascosa, J L

1992-01-01

Translocation of viral DNA inwards and outwards of the capsid of double-stranded DNA bacteriophages occurs through the connector, a key viral structure that is known to interact with DNA. It is shown here that phage phi 29 connector binds both linear and circular double-stranded DNA. However, DNA-mediated protection of phi 29 connectors against Staphylococcus aureus endoprotease V8 digestion suggests that binding to linear DNA is more stable than to circular DNA. Endoprotease V8-protection assays also suggest that the length of the linear DNA required to produce a stable phi 29 connector-DNA interaction is, at least, twice longer than the phi 29 connector channel. This result is confirmed by experiments of phi 29 connector-protection of DNA against DNase I digestion. Furthermore, DNA circularization assays indicate that phi 29 connectors restrain negative supercoiling when bound to linear DNA. This DNA conformational change is not observed upon binding to circular DNA and it could reflect the existence of some left-handed DNA coiling or DNA untwisting inside of the phi 29 connector channel. Images PMID:1454519

Scaling of ion expansion energy with laser flux in moderate-Z plasmas produced by lasers

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

Gupta, P.D.; Goel, S.K.; Uppal, J.S.

1982-09-01

Ion expansion energy measurements in plasmas created by focusing 1-GW, 5-nsec Nd:glass laser on plane solid targets of polythene, carbon, and aluminum are reported. It is observed that the scaling of ion expansion energy with laser flux Phi varies between Phi/sup 0.28/ and Phi/sup 0.66/ for polythene, Phi/sup 0.28/ and Phi/sup 0.70/ for carbon, and Phi/sup 0.51/ and Phi/sup 0.44/ for aluminum in the flux range 5 x 10/sup 10/--5 x 10/sup 12/ W/cm/sup 2/ of our experiment. The scaling is either much slower or faster than a scaling of Phi/sup 4/9/ expected from a self-regulating model for plasmas createdmore » in the low flux range. It is shown that this behavior, as well as results of experiments on similar plasmas reported by other authors, can be explained when radiation losses and the energy spent in ionization are also considered in the self-regulating model.« less

Defining, Describing, and Categorizing Public Health Infrastructure Priorities for Tropical Cyclone, Flood, Storm, Tornado, and Tsunami-Related Disasters.

PubMed

Ryan, Benjamin J; Franklin, Richard C; Burkle, Frederick M; Watt, Kerrianne; Aitken, Peter; Smith, Erin C; Leggat, Peter

2016-08-01

The study aim was to undertake a qualitative research literature review to analyze available databases to define, describe, and categorize public health infrastructure (PHI) priorities for tropical cyclone, flood, storm, tornado, and tsunami-related disasters. Five electronic publication databases were searched to define, describe, or categorize PHI and discuss tropical cyclone, flood, storm, tornado, and tsunami-related disasters and their impact on PHI. The data were analyzed through aggregation of individual articles to create an overall data description. The data were grouped into PHI themes, which were then prioritized on the basis of degree of interdependency. Sixty-seven relevant articles were identified. PHI was categorized into 13 themes with a total of 158 descriptors. The highest priority PHI identified was workforce. This was followed by water, sanitation, equipment, communication, physical structure, power, governance, prevention, supplies, service, transport, and surveillance. This review identified workforce as the most important of the 13 thematic areas related to PHI and disasters. If its functionality fails, workforce has the greatest impact on the performance of health services. If addressed post-disaster, the remaining forms of PHI will then be progressively addressed. These findings are a step toward providing an evidence base to inform PHI priorities in the disaster setting. (Disaster Med Public Health Preparedness. 2016;10:598-610).

The occurrence of phi in dento-facial beauty of fine art from antiquity through the Renaissance.

PubMed

Wiener, R Constance; Wiener Pla, Regina M

2012-01-01

External beauty is a complex construct that influences lives and may be impacted by dentists. Beauty is not easily quantified, but one cited anthropometric of beauty is the ratio phi, the number 1.618033(...). This study examined phi as a measure of female frontal facial beauty in classic Western art, using pre- Renaissance (N = 30), and Renaissance (N = 30) artwork. Four horizontal and five vertical ratios were determined in the works of art, which were then compared with the phi ratio. All horizontal ratios for both pre-Renaissance and Renaissance artwork were similar to each other, but did not contain the phi ratio (P < 0.001). Nevertheless, all vertical ratios for pre-Renaissance and Renaissance art-work did contain the phi ratio within their confidence intervals with the exception of the vertical ratio, "intereye point to soft tissue menton/ intereye point to stomion", that was found to be less than phi in the Renaissance group. The study provides evidence of the presence of the phi ratio in vertical aspect of females in artwork from pre-Renaissance through the Renaissance demonstrating consistent temporal preferences. Therefore, the phi ratio seems to be an important consideration in altering vertical facial dimensions in full mouth rehabilitation and reconstructive orthognathic surgery involving females.

Cytoplasmic pH influences cytoplasmic calcium in MC3T3-E1 osteoblast cells

NASA Technical Reports Server (NTRS)

Lin, H. S.; Hughes-Fulford, M.; Kumegawa, M.; Pitts, A. C.; Snowdowne, K. W.

1993-01-01

We found that the cytoplasmic concentration of calcium (Cai) of MC3T3-E1 osteoblasts was influenced by the type of pH buffer we used in the perfusing medium, suggesting that intracellular pH (pHi) might influence Cai. To study this effect, the Cai and pHi were monitored as we applied various experimental conditions known to change pHi. Exposure to NH4Cl caused a transient increase in both pHi and Cai without a change in extracellular pH (pHo). Decreasing pHo and pHi by lowering the bicarbonate concentration of the medium decreased Cai, and increasing pHi by the removal of 5% CO2 increased Cai. Clamping pHi to known values with 10 microM nigericin, a potassium proton ionophore, also influenced Cai: acid pHi lowered Cai, whereas alkaline pHi increased it. The rise in Cai appears to be very sensitive to the extracellular concentration of calcium, suggesting the existence of a pH-sensitive calcium influx mechanism. We conclude that physiologic changes in pH could modulate Cai by controlling the influx of calcium ions and could change the time course of the Cai transient associated with hormonal activation.

RNA packaging device of double-stranded RNA bacteriophages, possibly as simple as hexamer of P4 protein.

PubMed

Kainov, Denis E; Pirttimaa, Markus; Tuma, Roman; Butcher, Sarah J; Thomas, George J; Bamford, Dennis H; Makeyev, Eugene V

2003-11-28

Genomes of complex viruses have been demonstrated, in many cases, to be packaged into preformed empty capsids (procapsids). This reaction is performed by molecular motors translocating nucleic acid against the concentration gradient at the expense of NTP hydrolysis. At present, the molecular mechanisms of packaging remain elusive due to the complex nature of packaging motors. In the case of the double-stranded RNA bacteriophage phi 6 from the Cystoviridae family, packaging of single-stranded genomic precursors requires a hexameric NTPase, P4. In the present study, the purified P4 proteins from two other cystoviruses, phi 8 and phi 13, were characterized and compared with phi 6 P4. All three proteins are hexameric, single-stranded RNA-stimulated NTPases with alpha/beta folds. Using a direct motor assay, we found that phi 8 and phi 13 P4 hexamers translocate 5' to 3' along ssRNA, whereas the analogous activity of phi 6 P4 requires association with the procapsid. This difference is explained by the intrinsically high affinity of phi 8 and phi 13 P4s for nucleic acids. The unidirectional translocation results in RNA helicase activity. Thus, P4 proteins of Cystoviridae exhibit extensive similarity to hexameric helicases and are simple models for studying viral packaging motor mechanisms.

Measurements of CP Asymmetries in the Decay B --> {phi}K

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

Aubert, B

The authors present a preliminary measurement of the time-dependent CP asymmetry for the neutral B-meson decay B{sup 0} --> {phi}K{sup 0}. They use a sample of approximately 227 million B-meson pairs recorded at the {Upsilon}(4S) resonance with the BABAR detector at the PEP-II B-meson Factory at SLAC. They reconstruct the CP eigenstates {phi}K{sub s}{sup 0} and {phi}K{sub L}{sup 0} where {phi} --> K{sup +}K{sup -}, K{sub s}{sup 0} --> {pi}{sup +}{pi}{sup -}, and K{sub L}{sup 0} is observed via its hadronic interactions. The other B meson in the event is tagged as either a B{sup 0} or {bar B}{sup 0}more » from its decay products. The values of the CP-violation parameters deived from the combined {phi}K{sup 0} dataset are S{sub {phi}K} = +0.50 {+-} 0.25(stat.){sub -0.04}{sup +0.07}(syst.) and C{sub {phi}K} = 0.00 {+-} 0.23(stat.) {+-}0.05(syst.). In addition, the authors measure the CP-violating charge asymmetry A{sub CP}(B{sup +} --> {phi}K{sup +}) = 0.054 {+-} 0.056(stat.) {+-} 0.012(syst.). All results are preliminary.« less

Kinetics and metabolism of physostigmine in rat in the presence of soman

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

Khalique, A.; Somani, S.M.

1986-03-01

The effect of soman (105 ..mu..g/kg; 1.5 LD/sub 50/ s.c.) administration on pharmacokinetics and metabolism of /sup 3/H-physostigmine (Phy) was studied in rats. The rats were pretreated with either Phy 100 ..mu..g/kg i.v. or 500 ..mu..g/kg i.m., 5 or 15 min prior to soman administration. Phy and metabolites were determined in plasma and brain by HPLC. The half-life of Phy in plasma after i.v. administration was 15.5 min both in the presence and absence of soman, however the t/sub 1/2/ in brain was 11 min and 13 min, respectively. Clearance was 71.4 ml/min/kg in the Phy treated rat and 90more » ml/min/kg in the presence of soman. The half-life of Phy in plasma was 18 min and 17 min, and in brain 17 min and 15 min, respectively in the absence and presence of soman after i.m. dose of Phy. Clearance after Phy treatment was 85.2 mlmin/kg however in the presence of soman, it was 66.7 ml/min/kg. Phy was slightly less metabolized to eseroline and two other metabolites, M/sub 1/ and M/sub 2/, in the presence of soman after i.v. as well as after i.m. administration in plasma and brain. The soman administration does not change the pharmacokinetics of Phy by the two different dosages and routes of administration.« less

PHI-base: a new interface and further additions for the multi-species pathogen-host interactions database.

PubMed

Urban, Martin; Cuzick, Alayne; Rutherford, Kim; Irvine, Alistair; Pedro, Helder; Pant, Rashmi; Sadanadan, Vidyendra; Khamari, Lokanath; Billal, Santoshkumar; Mohanty, Sagar; Hammond-Kosack, Kim E

2017-01-04

The pathogen-host interactions database (PHI-base) is available at www.phi-base.org PHI-base contains expertly curated molecular and biological information on genes proven to affect the outcome of pathogen-host interactions reported in peer reviewed research articles. In addition, literature that indicates specific gene alterations that did not affect the disease interaction phenotype are curated to provide complete datasets for comparative purposes. Viruses are not included. Here we describe a revised PHI-base Version 4 data platform with improved search, filtering and extended data display functions. A PHIB-BLAST search function is provided and a link to PHI-Canto, a tool for authors to directly curate their own published data into PHI-base. The new release of PHI-base Version 4.2 (October 2016) has an increased data content containing information from 2219 manually curated references. The data provide information on 4460 genes from 264 pathogens tested on 176 hosts in 8046 interactions. Prokaryotic and eukaryotic pathogens are represented in almost equal numbers. Host species belong ∼70% to plants and 30% to other species of medical and/or environmental importance. Additional data types included into PHI-base 4 are the direct targets of pathogen effector proteins in experimental and natural host organisms. The curation problems encountered and the future directions of the PHI-base project are briefly discussed. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Sri Lanka's national assessment on innovation and intellectual property for access to medical products.

PubMed

Beneragama, Hemantha; Shridhar, Manisha; Ranasinghe, Thushara; Dissanayake, Vajira Hw

2016-09-01

In 2008, the Global strategy and plan of action on public health, innovation and intellectual property (GSPA-PHI) was launched by the World Health Organization, to stimulate fresh thinking on innovation in, and access to, medicines and to build sustainable research on diseases disproportionately affecting low- and middle-income countries. As part of the activities of the GSPA-PHI, Sri Lanka has been the first country to date to assess the national environment for medical technology and innovation. This year-long, multistakeholder, participative analysis facilitated identification of clear and implementable policy recommendations, for the government to increase its effectiveness in promoting innovation in health products through institutional development, investment and coordination among all areas relevant to public health. The assessment also highlighted areas for priority action, including closing the technology gap in development of health products, facilitating technology transfer, and building the health-research and allied workforces. The Sri Lankan experience will inform the ongoing independent external evaluation of the GSPA-PHI worldwide. The assessment process coincided with the passing of the National Medicines Regulatory Authority Act in 2015. In addition, there is growing recognition that regional cooperation will be critical to improving access to medical products in the future. Sri Lanka is therefore actively promoting cooperation to establish a regional regulatory affairs network. Lessons learnt from the Sri Lankan assessment may also benefit other countries embarking on a national GSPA-PHI assessment.

Novel phytochrome sequences in Arabidopsis thaliana: Structure, evolution, and differential expression of a plant regulatory photoreceptor family

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

Sharrock, R.A.; Quail, P.H.

1989-01-01

Phytochrome is a plant regulatory photoreceptor that mediates red light effects on a wide variety of physiological and molecular responses. DNA blot analysis indicates that the Arabidopsis thaliana genome contains four to five phytochrome-related gene sequences. The authors have isolated and sequenced cDNA clones corresponding to three of these genes and have deduced the amino acid sequence of the full-length polypeptide encoded in each case. One of these proteins (phyA) shows 65-80% amino acid sequence identity with the major, etiolated-tissue phytochrome apoproteins described previously in other plant species. The other two polypeptides (phyB and phyC) are unique in that theymore » have low sequence identity with each other, with phyA, and with all previously described phytochromes. The phyA, phyB, and phyC proteins are of similar molecular mass, have related hydropathic profiles, and contain a conserved chromophore attachment region. However, the sequence comparison data indicate that the three phy genes diverged early in plant evolution, well before the divergence of the two major groups of angiosperms, the monocots and dicots. The steady-state level of the phyA transcript is high in dark-grown A. thaliana seedlings and is down-regulated by light. In contrast, the phyB and phyC transcripts are present at lower levels and are not strongly light-regulated. These findings indicate that the red/far red light-responsive phytochrome photoreceptor system in A. thaliana, and perhaps in all higher plants, consists of a family of chromoproteins that are heterogeneous in structure and regulation.« less

Time course of cholinesterase activity in plasma, brain and muscle of rat pretreated with physostigmine, and then soman

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

Giacobini, E.; Boyer, A.; Somani, S.M.

1986-03-05

Time course of /sup 3/H-physostigmine (Phy) concentration and cholinesterase (ChE) activity in plasma and tissues was studied in rats pretreated with Phy and then soman. Rats were dosed with Phy (100 ..mu..g/kg, i.v.), 5 or 15 min prior to soman (105 ..mu..g/kg, 1.5 LD/sub 50/, s.c.) treatment and were sacrificed at various times; Phys conc. and ChE activity were determined. BuChE activity in plasma was 5% of control from 7-30 min after Phy i.v. pretreatment and soman or soman alone treatment. Plasma Phy conc. steadily declined (32.6 ng/ml at 7 min) to 15 ng/ml at 30 min. ChE activity inmore » muscle was 60-50% of control for Phy pretreated but soman alone gave 85-72% activity from 2-30 min. Brain ChE activity was about 5% of control within 2 min after soman treatment; however, with Phy pretreatment, the activity was about 52% at 7 min, 40% at 22 min, which recovered to 45% of control at 35 min, indicating that Phy protected brain ChE. Brain Phy conc. steadily declined (58.6 ng/g at 7 min) to 11.7 ng/g at 30 min. However, pretreatment of rat with a higher dose of Phy and then soman showed BuChE in plasma and ChE in brain and muscle to be about 25, 35 and 51%, in comparison to about 5% in plasma and brain with soman alone treatment, indicating higher protection of ChE enzyme with higher conc. of Phy in plasma and brain.« less

A phytochrome/phototropin chimeric photoreceptor of fern functions as a blue/far-red light-dependent photoreceptor for phototropism in Arabidopsis.

PubMed

Kanegae, Takeshi; Kimura, Izumi

2015-08-01

In the fern Adiantum capillus-veneris, the phototropic response of the protonemal cells is induced by blue light and partially inhibited by subsequent irradiation with far-red light. This observation strongly suggests the existence of a phytochrome that mediates this blue/far-red reversible response; however, the phytochrome responsible for this response has not been identified. PHY3/NEO1, one of the three phytochrome genes identified in Adiantum, encodes a chimeric photoreceptor composed of both a phytochrome and a phototropin domain. It was demonstrated that phy3 mediates the red light-dependent phototropic response of Adiantum, and that phy3 potentially functions as a phototropin. These findings suggest that phy3 is the phytochrome that mediates the blue/far-red response in Adiantum protonemata. In the present study, we expressed Adiantum phy3 in a phot1 phot2 phototropin-deficient Arabidopsis line, and investigated the ability of phy3 to induce phototropic responses under various light conditions. Blue light irradiation clearly induced a phototropic response in the phy3-expressing transgenic seedlings, and this effect was fully inhibited by simultaneous irradiation with far-red light. In addition, experiments using amino acid-substituted phy3 indicated that FMN-cysteinyl adduct formation in the light, oxygen, voltage (LOV) domain was not necessary for the induction of blue light-dependent phototropism by phy3. We thus demonstrate that phy3 is the phytochrome that mediates the blue/far-red reversible phototropic response in Adiantum. Furthermore, our results imply that phy3 can function as a phototropin, but that it acts principally as a phytochrome that mediates both the red/far-red and blue/far-red light responses. © 2015 The Authors The Plant Journal © 2015 John Wiley & Sons Ltd.

Expression of Aspergillus nidulans phy Gene in Nicotiana benthamiana Produces Active Phytase with Broad Specificities

PubMed Central

Oh, Tae-Kyun; Oh, Sung; Kim, Seongdae; Park, Jae Sung; Vinod, Nagarajan; Jang, Kyung Min; Kim, Sei Chang; Choi, Chang Won; Ko, Suk-Min; Jeong, Dong Kee; Udayakumar, Rajangam

2014-01-01

A full-length phytase gene (phy) of Aspergillus nidulans was amplified from the cDNA library by polymerase chain reaction (PCR), and it was introduced into a bacterial expression vector, pET-28a. The recombinant protein (rPhy-E, 56 kDa) was overexpressed in the insoluble fraction of Escherichia coli culture, purified by Ni-NTA resin under denaturing conditions and injected into rats as an immunogen. To express A. nidulans phytase in a plant, the full-length of phy was cloned into a plant expression binary vector, pPZP212. The resultant construct was tested for its transient expression by Agrobacterium-infiltration into Nicotiana benthamiana leaves. Compared with a control, the agro-infiltrated leaf tissues showed the presence of phy mRNA and its high expression level in N. benthamiana. The recombinant phytase (rPhy-P, 62 kDa) was strongly reacted with the polyclonal antibody against the nonglycosylated rPhy-E. The rPhy-P showed glycosylation, two pH optima (pH 4.5 and pH 5.5), an optimum temperature at 45~55 °C, thermostability and broad substrate specificities. After deglycosylation by peptide-N-glycosidase F (PNGase-F), the rPhy-P significantly lost the phytase activity and retained 1/9 of the original activity after 10 min of incubation at 45 °C. Therefore, the deglycosylation caused a significant reduction in enzyme thermostability. In animal experiments, oral administration of the rPhy-P at 1500 U/kg body weight/day for seven days caused a significant reduction of phosphorus excretion by 16% in rat feces. Besides, the rPhy-P did not result in any toxicological changes and clinical signs. PMID:25192284

Genome of Enterobacteriophage Lula/phi80 and Insights into Its Ability To Spread in the Laboratory Environment

PubMed Central

Rotman, Ella; Kouzminova, Elena; Plunkett, Guy

2012-01-01

The novel temperate bacteriophage Lula, contaminating laboratory Escherichia coli strains, turned out to be the well-known lambdoid phage phi80. Our previous studies revealed that two characteristics of Lula/phi80 facilitate its spread in the laboratory environment: cryptic lysogen productivity and stealthy infectivity. To understand the genetics/genomics behind these traits, we sequenced and annotated the Lula/phi80 genome, encountering an E. coli-toxic gene revealed as a gap in the sequencing contig and analyzing a few genes in more detail. Lula/phi80's genome layout copies that of lambda, yet homology with other lambdoid phages is mostly limited to the capsid genes. Lula/phi80's DNA is resistant to cutting with several restriction enzymes, suggesting DNA modification, but deletion of the phage's damL gene, coding for DNA adenine methylase, did not make DNA cuttable. The damL mutation of Lula/phi80 also did not change the phage titer in lysogen cultures, whereas the host dam mutation did increase it almost 100-fold. Since the high phage titer in cultures of Lula/phi80 lysogens is apparently in response to endogenous DNA damage, we deleted the only Lula/phi80 SOS-controlled gene, dinL. We found that dinL mutant lysogens release fewer phage in response to endogenous DNA damage but are unchanged in their response to external DNA damage. The toxic gene of Lula/phi80, gamL, encodes an inhibitor of the host ATP-dependent exonucleases, RecBCD and SbcCD. Its own antidote, agt, apparently encoding a modifier protein, was found nearby. Interestingly, Lula/phi80 lysogens are recD and sbcCD phenocopies, so GamL and Agt are part of lysogenic conversion. PMID:23042999

Relationship between intracellular pH and proton mobility in rat and guinea-pig ventricular myocytes.

PubMed

Swietach, Pawel; Vaughan-Jones, Richard D

2005-08-01

Intracellular H+ ion mobility in eukaryotic cells is low because of intracellular buffering. We have investigated whether Hi+ mobility varies with pHi. A dual microperfusion apparatus was used to expose guinea-pig or rat myocytes to small localized doses (3-5 mm) of ammonium chloride (applied in Hepes-buffered solution). Intracellular pH (pHi) was monitored confocally using the fluorescent dye, carboxy-SNARF-1. Local ammonium exposure produced a stable, longitudinal pHi gradient. Its size was fed into a look-up table (LUT) to give an estimate of the apparent intracellular proton diffusion coefficient (D(app)H). LUTs were generated using a diffusion-reaction model of Hi+ mobility based on intracellular buffer diffusion. To examine the pHi sensitivity of D(app)H, whole-cell pHi was initially displaced using a whole-cell ammonium or acetate prepulse, before locally applying the low dose of ammonium. In both rat and guinea-pig, D(app)H decreased with pHi over the range 7.5-6.5. In separate pipette-loading experiments, the intracellular diffusion coefficient for carboxy-SNARF-1 (a mobile-buffer analogue) exhibited no significant pHi dependence. The pHi sensitivity of D(app)H is thus likely to be governed by the mobile fraction of intrinsic buffering capacity. These results reinforce the buffer hypothesis of Hi+ mobility. The pHi dependence of D(app)H was used to characterize the mobile and fixed buffer components, and to estimate D(mob) (the average diffusion coefficient for intracellular mobile buffer). One consequence of a decline in Hi+ mobility at low pHi is that it will predispose the myocardium to pHi nonuniformity. The physiological relevance of this is discussed.

Comparison of High Performance Network Options: EDR InfiniBand vs.100Gb RDMA Capable Ethernet

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

Kachelmeier, Luke Anthony; Van Wig, Faith Virginia; Erickson, Kari Natania

These are the slides for a presentation at the HPC Mini Showcase. This is a comparison of two different high performance network options: EDR InfiniBand and 100Gb RDMA capable ethernet. The conclusion of this comparison is the following: there is good potential, as shown with the direct results; 100Gb technology is too new and not standardized, thus deployment effort is complex for both options; different companies are not necessarily compatible; if you want 100Gb/s, you must get it all from one place.

Hydrogen ion dynamics in human red blood cells

PubMed Central

Swietach, Pawel; Tiffert, Teresa; Mauritz, Jakob M A; Seear, Rachel; Esposito, Alessandro; Kaminski, Clemens F; Lew, Virgilio L; Vaughan-Jones, Richard D

2010-01-01

Our understanding of pH regulation within red blood cells (RBCs) has been inferred mainly from indirect experiments rather than from in situ measurements of intracellular pH (pHi). The present work shows that carboxy-SNARF-1, a pH fluorophore, when used with confocal imaging or flow cytometry, reliably reports pHi in individual, human RBCs, provided intracellular fluorescence is calibrated using a ‘null-point’ procedure. Mean pHi was 7.25 in CO2/HCO3−-buffered medium and 7.15 in Hepes-buffered medium, and varied linearly with extracellular pH (slope of 0.77). Intrinsic (non-CO2/HCO3−-dependent) buffering power, estimated in the intact cell (85 mmol (l cell)−1 (pH unit)−1 at resting pHi), was somewhat higher than previous estimates from cell lysates (50–70 mmol (l cell)−1 (pH unit)−1). Acute displacement of pHi (superfusion of weak acids/bases) triggered rapid pHi recovery. This was mediated via membrane Cl−/HCO3− exchange (the AE1 gene product), irrespective of whether recovery was from an intracellular acid or base load, and with no evident contribution from other transporters such as Na+/H+ exchange. H+-equivalent flux through AE1 was a linear function of [H+]i and reversed at resting pHi, indicating that its activity is not allosterically regulated by pHi, in contrast to other AE isoforms. By simultaneously monitoring pHi and markers of cell volume, a functional link between membrane ion transport, volume and pHi was demonstrated. RBC pHi is therefore tightly regulated via AE1 activity, but modulated during changes of cell volume. A comparable volume–pHi link may also be important in other cell types expressing anion exchangers. Direct measurement of pHi should be useful in future investigations of RBC physiology and pathology. PMID:20962000

Prostate Health Index (Phi) and Prostate Cancer Antigen 3 (PCA3) Significantly Improve Prostate Cancer Detection at Initial Biopsy in a Total PSA Range of 2–10 ng/ml

PubMed Central

Perdonà, Sisto; Marino, Ada; Mazzarella, Claudia; Perruolo, Giuseppe; D’Esposito, Vittoria; Cosimato, Vincenzo; Buonerba, Carlo; Di Lorenzo, Giuseppe; Musi, Gennaro; De Cobelli, Ottavio; Chun, Felix K.; Terracciano, Daniela

2013-01-01

Many efforts to reduce prostate specific antigen (PSA) overdiagnosis and overtreatment have been made. To this aim, Prostate Health Index (Phi) and Prostate Cancer Antigen 3 (PCA3) have been proposed as new more specific biomarkers. We evaluated the ability of phi and PCA3 to identify prostate cancer (PCa) at initial prostate biopsy in men with total PSA range of 2–10 ng/ml. The performance of phi and PCA3 were evaluated in 300 patients undergoing first prostate biopsy. ROC curve analyses tested the accuracy (AUC) of phi and PCA3 in predicting PCa. Decision curve analyses (DCA) were used to compare the clinical benefit of the two biomarkers. We found that the AUC value of phi (0.77) was comparable to those of %p2PSA (0.76) and PCA3 (0.73) with no significant differences in pairwise comparison (%p2PSA vs phi p = 0.673, %p2PSA vs. PCA3 p = 0.417 and phi vs. PCA3 p = 0.247). These three biomarkers significantly outperformed fPSA (AUC = 0.60), % fPSA (AUC = 0.62) and p2PSA (AUC = 0.63). At DCA, phi and PCA3 exhibited a very close net benefit profile until the threshold probability of 25%, then phi index showed higher net benefit than PCA3. Multivariable analysis showed that the addition of phi and PCA3 to the base multivariable model (age, PSA, %fPSA, DRE, prostate volume) increased predictive accuracy, whereas no model improved single biomarker performance. Finally we showed that subjects with active surveillance (AS) compatible cancer had significantly lower phi and PCA3 values (p<0.001 and p = 0.01, respectively). In conclusion, both phi and PCA3 comparably increase the accuracy in predicting the presence of PCa in total PSA range 2–10 ng/ml at initial biopsy, outperforming currently used %fPSA. PMID:23861782

Prostate Health Index (Phi) and Prostate Cancer Antigen 3 (PCA3) significantly improve prostate cancer detection at initial biopsy in a total PSA range of 2-10 ng/ml.

PubMed

Ferro, Matteo; Bruzzese, Dario; Perdonà, Sisto; Marino, Ada; Mazzarella, Claudia; Perruolo, Giuseppe; D'Esposito, Vittoria; Cosimato, Vincenzo; Buonerba, Carlo; Di Lorenzo, Giuseppe; Musi, Gennaro; De Cobelli, Ottavio; Chun, Felix K; Terracciano, Daniela

2013-01-01

Many efforts to reduce prostate specific antigen (PSA) overdiagnosis and overtreatment have been made. To this aim, Prostate Health Index (Phi) and Prostate Cancer Antigen 3 (PCA3) have been proposed as new more specific biomarkers. We evaluated the ability of phi and PCA3 to identify prostate cancer (PCa) at initial prostate biopsy in men with total PSA range of 2-10 ng/ml. The performance of phi and PCA3 were evaluated in 300 patients undergoing first prostate biopsy. ROC curve analyses tested the accuracy (AUC) of phi and PCA3 in predicting PCa. Decision curve analyses (DCA) were used to compare the clinical benefit of the two biomarkers. We found that the AUC value of phi (0.77) was comparable to those of %p2PSA (0.76) and PCA3 (0.73) with no significant differences in pairwise comparison (%p2PSA vs phi p = 0.673, %p2PSA vs. PCA3 p = 0.417 and phi vs. PCA3 p = 0.247). These three biomarkers significantly outperformed fPSA (AUC = 0.60), % fPSA (AUC = 0.62) and p2PSA (AUC = 0.63). At DCA, phi and PCA3 exhibited a very close net benefit profile until the threshold probability of 25%, then phi index showed higher net benefit than PCA3. Multivariable analysis showed that the addition of phi and PCA3 to the base multivariable model (age, PSA, %fPSA, DRE, prostate volume) increased predictive accuracy, whereas no model improved single biomarker performance. Finally we showed that subjects with active surveillance (AS) compatible cancer had significantly lower phi and PCA3 values (p<0.001 and p = 0.01, respectively). In conclusion, both phi and PCA3 comparably increase the accuracy in predicting the presence of PCa in total PSA range 2-10 ng/ml at initial biopsy, outperforming currently used %fPSA.

Evaluating current automatic de-identification methods with Veteran's health administration clinical documents.

PubMed

Ferrández, Oscar; South, Brett R; Shen, Shuying; Friedlin, F Jeffrey; Samore, Matthew H; Meystre, Stéphane M

2012-07-27

The increased use and adoption of Electronic Health Records (EHR) causes a tremendous growth in digital information useful for clinicians, researchers and many other operational purposes. However, this information is rich in Protected Health Information (PHI), which severely restricts its access and possible uses. A number of investigators have developed methods for automatically de-identifying EHR documents by removing PHI, as specified in the Health Insurance Portability and Accountability Act "Safe Harbor" method.This study focuses on the evaluation of existing automated text de-identification methods and tools, as applied to Veterans Health Administration (VHA) clinical documents, to assess which methods perform better with each category of PHI found in our clinical notes; and when new methods are needed to improve performance. We installed and evaluated five text de-identification systems "out-of-the-box" using a corpus of VHA clinical documents. The systems based on machine learning methods were trained with the 2006 i2b2 de-identification corpora and evaluated with our VHA corpus, and also evaluated with a ten-fold cross-validation experiment using our VHA corpus. We counted exact, partial, and fully contained matches with reference annotations, considering each PHI type separately, or only one unique 'PHI' category. Performance of the systems was assessed using recall (equivalent to sensitivity) and precision (equivalent to positive predictive value) metrics, as well as the F(2)-measure. Overall, systems based on rules and pattern matching achieved better recall, and precision was always better with systems based on machine learning approaches. The highest "out-of-the-box" F(2)-measure was 67% for partial matches; the best precision and recall were 95% and 78%, respectively. Finally, the ten-fold cross validation experiment allowed for an increase of the F(2)-measure to 79% with partial matches. The "out-of-the-box" evaluation of text de-identification systems provided us with compelling insight about the best methods for de-identification of VHA clinical documents. The errors analysis demonstrated an important need for customization to PHI formats specific to VHA documents. This study informed the planning and development of a "best-of-breed" automatic de-identification application for VHA clinical text.

Beam Instrument Development System

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

DOOLITTLE, LAWRENCE; HUANG, GANG; DU, QIANG

Beam Instrumentation Development System (BIDS) is a collection of common support libraries and modules developed during a series of Low-Level Radio Frequency (LLRF) control and timing/synchronization projects. BIDS includes a collection of Hardware Description Language (HDL) libraries and software libraries. The BIDS can be used for the development of any FPGA-based system, such as LLRF controllers. HDL code in this library is generic and supports common Digital Signal Processing (DSP) functions, FPGA-specific drivers (high-speed serial link wrappers, clock generation, etc.), ADC/DAC drivers, Ethernet MAC implementation, etc.

The phi-meson and Chiral-mass-meson production in heavy-ion collisions as potential probes of quark-gluon-plasma and Chiral symmetry transitions

NASA Technical Reports Server (NTRS)

Takahashi, Y.; Eby, P. B.

1985-01-01

Possibilities of observing abundances of phi mesons and narrow hadronic pairs, as results of QGP and Chiral transitions, are considered for nucleus-nucleus interactions. Kinematical requirements in forming close pairs are satisfied in K+K decays of S(975) and delta (980) mesons with small phi, and phi (91020) mesons with large PT, and in pi-pi decays of familiar resonance mesons only in a partially restored chiral symmetry. Gluon-gluon dominance in QGP can enhance phi meson production. High hadronization rates of primordial resonance mesons which form narrow hadronic pairs are not implausible. Past cosmic ray evidences of anomalous phi production and narrow pair abundances are considered.

Datamonkey 2.0: a modern web application for characterizing selective and other evolutionary processes.

PubMed

Weaver, Steven; Shank, Stephen D; Spielman, Stephanie J; Li, Michael; Muse, Spencer V; Kosakovsky Pond, Sergei L

2018-01-02

Inference of how evolutionary forces have shaped extant genetic diversity is a cornerstone of modern comparative sequence analysis. Advances in sequence generation and increased statistical sophistication of relevant methods now allow researchers to extract ever more evolutionary signal from the data, albeit at an increased computational cost. Here, we announce the release of Datamonkey 2.0, a completely re-engineered version of the Datamonkey web-server for analyzing evolutionary signatures in sequence data. For this endeavor, we leveraged recent developments in open-source libraries that facilitate interactive, robust, and scalable web application development. Datamonkey 2.0 provides a carefully curated collection of methods for interrogating coding-sequence alignments for imprints of natural selection, packaged as a responsive (i.e. can be viewed on tablet and mobile devices), fully interactive, and API-enabled web application. To complement Datamonkey 2.0, we additionally release HyPhy Vision, an accompanying JavaScript application for visualizing analysis results. HyPhy Vision can also be used separately from Datamonkey 2.0 to visualize locally-executed HyPhy analyses. Together, Datamonkey 2.0 and HyPhy Vision showcase how scientific software development can benefit from general-purpose open-source frameworks. Datamonkey 2.0 is freely and publicly available at http://www.datamonkey. org, and the underlying codebase is available from https://github.com/veg/datamonkey-js. © The Author 2018. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Risk factors for ventilator-associated pneumonia in trauma patients: A descriptive analysis.

PubMed

Arumugam, Suresh Kumar; Mudali, Insolvisagan; Strandvik, Gustav; El-Menyar, Ayman; Al-Hassani, Ammar; Al-Thani, Hassan

2018-01-01

We sought to evaluate the risk factors for developing ventilator-associated pneumonia (VAP) and whether the location of intubation posed a risk in trauma patients. Data were retrospectively reviewed for adult trauma patients requiring intubation for > 48 hours, admitted between 2010 and 2013. Patients' demographics, clinical presentations and outcomes were compared according to intubation location (prehospital intubation [PHI] vs. trauma room [TRI]) and presence vs. absence of VAP. Multivariate regression analysis was performed to identify predictors of VAP. Of 471 intubated patients, 332 patients met the inclusion criteria (124 had PHI and 208 had TRI) with a mean age of 30.7±14.8 years. PHI group had lower GCS ( P =0.001), respiratory rate ( P =0.001), and higher frequency of head ( P =0.02) and chest injuries ( P =0.04). The rate of VAP in PHI group was comparable to the TRI group ( P =0.60). Patients who developed VAP were 6 years older, had significantly lower GCS and higher ISS, head AIS, and higher rates of polytrauma. The overall mortality was 7.5%, and was not associated with intubation location or pneumonia rates. In the early-VAP group, gram-positive pathogens were more common, while gram-negative microorganisms were more frequently encountered in the late VAP group. Logistic regression analysis and modeling showed that the impact of the location of intubation in predicting the risk of VAP appeared only when chest injury was included in the models. In trauma, the risk of developing VAP is multifactorial. However, the location of intubation and presence of chest injury could play an important role.

IRBIT plays an important role in NHE3-mediated pHi regulation in HSG cells.

PubMed

Tran, Tien Manh; Park, Moon-Yong; Lee, Jiyeon; Bae, Jun-Seok; Hwang, Sung-Min; Choi, Se-Young; Mikoshiba, Katsuhiko; Park, Kyungpyo

2013-07-19

Expression of inositol-1,4,5-trisphosphate (IP3) receptor-binding protein (IRBIT) has been reported in epithelial cells. However, its role in pHi regulation is not well understood. In this study, we investigated the role of IRBIT in pHi regulation, mediated by Na(+)/H(+) exchangers (NHEs), in salivary glands. We measured pHi recovery from cell acidification in BCECF-loaded salivary HSG cells. Western blot and co-immunoprecipitation (CO-IP) assays were also performed, showing that NHE1, 2 and 3 are expressed, and IRBIT binds to NHE3. HOE642, a specific NHE1 blocker, inhibited pHi recovery, but 40% pH(i) recovery was still observed even at the highest concentration of HOE642. Furthermore, pretreatment of the cells with siIRBIT significantly inhibited pHi recovery, indicating that NHE3 potentially plays a role in pHi recovery as well. The amount of membrane-localized NHE3 and its interaction with IRBIT are also significantly increased by cell acidification. In addition, we found that Ste20p-related proline alanine-rich kinase (SPAK) reverses the effect of IRBIT on membrane NHE3 translocation. Taken together, we conclude that IRBIT plays an important role in pHi regulation, mediated by NHE3, and further regulated by SPAK. Copyright © 2013 Elsevier Inc. All rights reserved.

Characterisation of transition state structures for protein folding using 'high', 'medium' and 'low' {Phi}-values.

PubMed

Geierhaas, Christian D; Salvatella, Xavier; Clarke, Jane; Vendruscolo, Michele

2008-03-01

It has been suggested that Phi-values, which allow structural information about transition states (TSs) for protein folding to be obtained, are most reliably interpreted when divided into three classes (high, medium and low). High Phi-values indicate almost completely folded regions in the TS, intermediate Phi-values regions with a detectable amount of structure and low Phi-values indicate mostly unstructured regions. To explore the extent to which this classification can be used to characterise in detail the structure of TSs for protein folding, we used Phi-values divided into these classes as restraints in molecular dynamics simulations. This type of procedure is related to that used in NMR spectroscopy to define the structure of native proteins from the measurement of inter-proton distances derived from nuclear Overhauser effects. We illustrate this approach by determining the TS ensembles of five proteins and by showing that the results are similar to those obtained by using as restraints the actual numerical Phi-values measured experimentally. Our results indicate that the simultaneous consideration of a set of low-resolution Phi-values can provide sufficient information for characterising the architecture of a TS for folding of a protein.

A novel protein tyrosine phosphatase like phytase from Lactobacillus fermentum NKN51: Cloning, characterization and application in mineral release for food technology applications.

PubMed

Sharma, Rekha; Kumar, Piyush; Kaushal, Vandana; Das, Rahul; Kumar Navani, Naveen

2018-02-01

A novel protein tyrosine phosphatase like phytase (PTPLP), designated as PhyLf from probiotic bacterium Lactobacillus fermentum NKN51 was identified, cloned, expressed and characterized. The recombinant PhyLf showed specific activity of 174.5 U/mg. PhyLf exhibited strict specificity towards phytate and optimum temperature at 60 °C, pH 5.0 and ionic strength of 100 mM. K m and K cat of PhyLf for phytate were 0.773 mM and 84.31 s -1 , respectively. PhyLf exhibited high resistance against oxidative inactivation. PhyLf shares no homology, sans the active site with reported PTLPs, warranting classification as a new subclass. Dephytinization of durum wheat and finger millet under in vitro gastrointestinal conditions using PhyLf enhanced the bioaccessibility of mineral ions. Probiotic origin, phytate specificity, resistance to oxidative environment and gastric milieu coupled with ability to release micronutrients are unique properties of PhyLf which present a strong case for its use in ameliorating nutritional value of cereals and animal feed. Copyright © 2017 Elsevier Ltd. All rights reserved.

Evaluating and optimizing the NERSC workload on Knights Landing

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

Barnes, T; Cook, B; Deslippe, J

2017-01-30

NERSC has partnered with 20 representative application teams to evaluate performance on the Xeon-Phi Knights Landing architecture and develop an application-optimization strategy for the greater NERSC workload on the recently installed Cori system. In this article, we present early case studies and summarized results from a subset of the 20 applications highlighting the impact of important architecture differences between the Xeon-Phi and traditional Xeon processors. We summarize the status of the applications and describe the greater optimization strategy that has formed.

Evaluating and Optimizing the NERSC Workload on Knights Landing

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

Barnes, Taylor; Cook, Brandon; Doerfler, Douglas

2016-01-01

NERSC has partnered with 20 representative application teams to evaluate performance on the Xeon-Phi Knights Landing architecture and develop an application-optimization strategy for the greater NERSC workload on the recently installed Cori system. In this article, we present early case studies and summarized results from a subset of the 20 applications highlighting the impact of important architecture differences between the Xeon-Phi and traditional Xeon processors. We summarize the status of the applications and describe the greater optimization strategy that has formed.

Ordovician and Silurian Phi Kappa and Trail Creek formations, Pioneer Mountains, central Idaho; stratigraphic and structural revisions, and new data on graptolite faunas

USGS Publications Warehouse

Dover, James H.; Berry, William B.N.; Ross, Reuben James

1980-01-01

Recent geologic mapping in the northern Pioneer Mountains combined with the identification of graptolites from 116 new collections indicate that the Ordovician and Silurian Phi Kappa and Trail Creek Formations occur in a series of thrust-bounded slices within a broad zone of imbricate thrust faulting. Though confirming a deformational style first reported in a 1963 study by Michael Churkin, our data suggest that the complexity and regional extent of the thrust zone were not previously recognized. Most previously published sections of the Phi Kappa and Trail Creek Formations were measured across unrecognized thrust faults and therefore include not only structural repetitions of graptolitic Ordovician and Silurian rocks but also other tectonically juxtaposed lithostratigraphic units of diverse ages as well. Because of this discovery, the need to reconsider the stratigraphic validity of these formations and their lithology, nomenclature, structural distribution, facies relations, and graptolite faunas has arisen. The Phi Kappa Formation in most thrust slices has internal stratigraphic continuity despite the intensity of deformation to which it was subjected. As revised herein, the Phi Kappa Formation is restricted to a structurally repeated succession of predominantly black, carbonaceous, graptolitic argillite and shale. Some limy, light-gray-weathering shale occurs in the middle part of the section, and fine-grained locally pebbly quartzite is present at the base. The basal quartzite is here named the Basin Gulch Quartzite Member of the Phi Kappa. The Phi Kappa redefined on a lithologic basis represents the span of Ordovician time from W. B. N. Berry's graptolite zones 2-4 through 15 and also includes approximately 17 m of lithologically identical shale of Early and Middle Silurian age at the top. The lower contact of the formation as revised is tectonic. The Phi Kappa is gradationally overlain by the Trail Creek Formation as restricted herein. Most of the coarser clastic rocks reported in previously measured sections of the Phi Kappa, as well as the sequence along Phi Kappa Creek from which the name originates, are excluded from the Phi Kappa as revised and are reassigned to two structural plates of Mississippian Copper Basin Formation; other strata now excluded from the formation are reassigned to the Trail Creek Formation and to an unnamed Silurian and Devonian unit. As redefined, the Phi Kappa Formation is only about 240 m thick, compared with the 3,860 m originally estimated, and it occupies only about 25 percent of the outcrop area previously mapped in 1930 by H. G. Westgate and C. P. Ross. Despite this drastic reduction in thickness and the exclusion of the rocks along Phi Kappa Creek, the name Phi Kappa is retained because of widely accepted prior usage to denote the Ordovician graptolitic shale facies of central Idaho, and because the Phi Kappa Formation as revised is present in thrust slices on Phi Kappa Mountain, at the head of Phi Kappa Creek. The lithic and faunal consistency of this unit throughout the area precludes the necessity for major facies telescoping along individual faults within the outcrop belt. However, tens of kilometers of tectonic shortening seems required to juxtapose the imbricated Phi Kappa shale facies with the Middle Ordovician part of the carbonate and quartzite shale sequence of east central Idaho. The shelf rocks are exposed in the Wildhorse structural window of the northeastern Pioneer Mountains, and attain a thickness of at least 1,500 m throughout the region north and east of the Pioneer Mountains. The Phi Kappa is in direct thrust contact on intensely deformed medium- to high-grade metamorphic equivalents of the same shelf sequence in the Pioneer window at the south end of the Phi Kappa-Trail Creek outcrop belt. Along East Pass, Big Lake, and Pine Creeks, north of the Pioneer Mountains, some rocks previously mapped as Ramshorn Slate are lithologically and faunally equivalent to the P

The extraction of Φ – N total cross section from d ( γ , p K + K - ) n

DOE PAGES

Qian, X.; Chen, W.; Gao, H.; ...

2009-10-01

We report on the first measurement of the differential cross section ofmore » $$\\phi$$-meson photoproduction for the $$d(\\gamma,pK^{+}K^{-})n$$ exclusive reaction channel. The experiment was performed using a \\textcolor{black}{tagged-photon} beam and the CEBAF Large Acceptance Spectrometer (CLAS) at Jefferson Lab. A combined analysis using data from the $$d(\\gamma,pK^{+}K^{-})n$$ channel and those from a previous publication on coherent $$\\phi$$ production on the deuteron has been carried out to extract the $$\\phi-N$$ total cross section, $$\\sigma_{\\phi N}$$. The extracted $$\\phi-N$$ total cross section favors a value above 20 mb. This value is larger than the value extracted using vector-meson dominance models for $$\\phi$$ photoproduction on the proton.« less

Analyzing the impact of severe tropical cyclone Yasi on public health infrastructure and the management of noncommunicable diseases.

PubMed

Ryan, Benjamin J; Franklin, Richard C; Burkle, Frederick M; Watt, Kerrianne; Aitken, Peter; Smith, Erin C; Leggat, Peter

2015-02-01

Traditionally, post disaster response activities have focused on immediate trauma and communicable diseases. In developed countries such as Australia, the post disaster risk for communicable disease is low. However, a "disease transition" is now recognized at the population level where noncommunicable diseases (NCDs) are increasingly documented as a post disaster issue. This potentially places an extra burden on health care resources and may have implications for disaster-management systems. With increasing likelihood of major disasters for all sectors of global society, there is a need to ensure that health systems, including public health infrastructure (PHI), can respond properly. Problem There is limited peer-reviewed literature on the impact of disasters on NCDs. Research is required to better determine both the impact of NCDs post disaster and their impact on PHI and disaster-management systems. A literature review was used to collect and analyze data on the impact of the index case event, Australia's Severe Tropical Cyclone Yasi (STC Yasi), on PHI and the management of NCDs. The findings were compared with data from other world cyclone events. The databases searched were MEDLINE, CINAHL, Google Scholar, and Google. The date range for the STC Yasi search was January 26, 2011 through May 2, 2013. No time limits were applied to the search from other cyclone events. The variables compared were tropical cyclones and their impacts on PHI and NCDs. The outcome of interest was to identify if there were trends across similar world events and to determine if this could be extrapolated for future crises. This research showed a tropical cyclone (including a hurricane and typhoon) can impact PHI, for instance, equipment (oxygen, syringes, and medications), services (treatment and care), and clean water availability/access that would impact both the treatment and management of NCDs. The comparison between STC Yasi and worldwide tropical cyclones found the challenges faced were linked closely. These relate to communication, equipment and services, evacuation, medication, planning, and water supplies. This research demonstrated that a negative trend pattern existed between the impact of STC Yasi and other similar world cyclone events on PHI and the management of NCDs. This research provides an insight for disaster planners to address concerns of people with NCDs. While further research is needed, this study provides an understanding of areas for improvement, specifically enhancing protective PHI and the development of strategies for maintaining treatment and alternative care options, such as maintaining safe water for dialysis patients.

The Novel Phages phiCD5763 and phiCD2955 Represent Two Groups of Big Plasmidial Siphoviridae Phages of Clostridium difficile.

PubMed

Ramírez-Vargas, Gabriel; Goh, Shan; Rodríguez, César

2018-01-01

Until recently, Clostridium difficile phages were limited to Myoviruses and Siphoviruses of medium genome length (32-57 kb). Here we report the finding of phiCD5763, a Siphovirus with a large extrachromosomal circular genome (132.5 kb, 172 ORFs) and a large capsid (205.6 ± 25.6 nm in diameter) infecting MLST Clade 1 strains of C. difficile . Two subgroups of big phage genomes similar to phiCD5763 were identified in 32 NAP CR1 /RT012/ST-54 C. difficile isolates from Costa Rica and in whole genome sequences (WGS) of 41 C. difficile isolates of Clades 1, 2, 3, and 4 from Canada, USA, UK, Belgium, Iraq, and China. Through comparative genomics we discovered another putative big phage genome in a non-NAP CR1 isolate from Costa Rica, phiCD2955, which represents other big phage genomes found in 130 WGS of MLST Clade 1 and 2 isolates from Canada, USA, Hungary, France, Austria, and UK. phiCD2955 (131.6 kb, 172 ORFs) is related to a previously reported C. difficile phage genome, phiCD211/phiCDIF1296T. Detailed genome analyses of phiCD5763, phiCD2955, phiCD211/phiCDIF1296T, and seven other putative C. difficile big phage genome sequences of 131-136 kb reconstructed from publicly available WGS revealed a modular gene organization and high levels of sequence heterogeneity at several hotspots, suggesting that these genomes correspond to biological entities undergoing recombination. Compared to other C. difficile phages, these big phages have unique predicted terminase, capsid, portal, neck and tail proteins, receptor binding proteins (RBPs), recombinases, resolvases, primases, helicases, ligases, and hypothetical proteins. Moreover, their predicted gene load suggests a complex regulation of both phage and host functions. Overall, our results indicate that the prevalence of C. difficile big bacteriophages is more widespread than realized and open new avenues of research aiming to decipher how these viral elements influence the biology of this emerging pathogen.

The Presence of Phage Orthologous Genes in Helicobacter pylori Correlates with the Presence of the Virulence Factors CagA and VacA.

PubMed

Kyrillos, Alexandra; Arora, Gaurav; Murray, Bradley; Rosenwald, Anne G

2016-06-01

The bacterium Helicobacter pylori is associated with ulcers and the development of gastric cancer. Several genes, including cytotoxin-associated gene A (CagA) and vacuolating cytotoxin A (VacA), are associated with increased gastric cancer risk. Some strains of H. pylori also contain sequences related to bacteriophage phiHP33; however, the significance of these phage-related sequences remains unknown. We assessed the extent to which phiHP33-related sequences are present in 335 H. pylori strains using homology searches then mapped shared genes between phiHP33 and H. pylori strains onto an existing phylogeny. One hundred and twenty-one H. pylori strains contain phage orthologous sequences, and the presence of the phage-related sequences correlates with the presence of CagA and VacA. Mapping of the phage orthologs onto a phylogeny of H. pylori is consistent with the hypothesis that these genes were acquired by horizontal gene transfer. phiHP33 phage orthologous sequences might be of significance in understanding virulence of different H. pylori strains. © 2015 John Wiley & Sons Ltd.

Hypocotyl growth orientation in blue light is determined by phytochrome A inhibition of gravitropism and phototropin promotion of phototropism.

PubMed

Lariguet, Patricia; Fankhauser, Christian

2004-12-01

How developing seedlings integrate gravitropic and phototropic stimuli to determine their direction of growth is poorly understood. In this study we tested whether blue light influences hypocotyl gravitropism in Arabidopsis. Phototropin1 (phot1) triggers phototropism under low fluence rates of blue light but, at least in the dark, has no effect on gravitropism. By analyzing the growth orientation of phototropism-deficient seedlings in response to gravitropic and phototropic stimulations we show that blue light not only triggers phototropism but also represses hypocotyl gravitropism. At low fluence rates of blue light phot1 mutants were agravitropic. In contrast, phyAphot1 double mutants grew exclusively according to gravity demonstrating that phytochrome A (phyA) is necessary to inhibit gravitropism. Analyses of phot1cry1cry2 triple mutants indicate that cryptochromes play a minor role in this response. Thus the optimal growth orientation of hypocotyls is determined by the action of phyA-suppressing gravitropism and the phototropin-triggering phototropism. It has long been known that phytochromes promote phototropism but the mechanism involved is still unknown. Our data show that by inhibiting gravitropism phyA acts as a positive regulator of phototropism.

Signal-off Electrochemiluminescence Biosensor Based on Phi29 DNA Polymerase Mediated Strand Displacement Amplification for MicroRNA Detection.

PubMed

Chen, Anyi; Gui, Guo-Feng; Zhuo, Ying; Chai, Ya-Qin; Xiang, Yun; Yuan, Ruo

2015-06-16

A target induced cycling strand displacement amplification (SDA) mediated by phi29 DNA polymerase (phi29) was first investigated and applied in a signal-off electrochemiluminescence (ECL) biosensor for microRNA (miRNA) detection. Herein, the target miRNA triggered the phi29-mediated SDA which could produce amounts of single-stranded DNA (assistant probe) with accurate and comprehensive nucleotide sequence. Then, the assistant probe hybridized with the capture probe and the ferrocene-labeled probe (Fc-probe) to form a ternary "Y" structure for ECL signal quenching by ferrocene. Therefore, the ECL intensity would decrease with increasing concentration of the target miRNA, and the sensitivity of biosensor would be promoted on account of the efficient signal amplification of the target induced cycling reaction. Besides, a self-enhanced Ru(II) ECL system was designed to obtain a stable and strong initial signal to further improve the sensitivity. The ECL assay for miRNA-21 detection is developed with excellent sensitivity of a concentration variation from 10 aM to 1.0 pM and limit of detection down to 3.3 aM.

Highly efficient and exact method for parallelization of grid-based algorithms and its implementation in DelPhi

PubMed Central

Li, Chuan; Li, Lin; Zhang, Jie; Alexov, Emil

2012-01-01

The Gauss-Seidel method is a standard iterative numerical method widely used to solve a system of equations and, in general, is more efficient comparing to other iterative methods, such as the Jacobi method. However, standard implementation of the Gauss-Seidel method restricts its utilization in parallel computing due to its requirement of using updated neighboring values (i.e., in current iteration) as soon as they are available. Here we report an efficient and exact (not requiring assumptions) method to parallelize iterations and to reduce the computational time as a linear/nearly linear function of the number of CPUs. In contrast to other existing solutions, our method does not require any assumptions and is equally applicable for solving linear and nonlinear equations. This approach is implemented in the DelPhi program, which is a finite difference Poisson-Boltzmann equation solver to model electrostatics in molecular biology. This development makes the iterative procedure on obtaining the electrostatic potential distribution in the parallelized DelPhi several folds faster than that in the serial code. Further we demonstrate the advantages of the new parallelized DelPhi by computing the electrostatic potential and the corresponding energies of large supramolecular structures. PMID:22674480

Model of transient drug diffusion across cornea.

PubMed

Zhang, Wensheng; Prausnitz, Mark R; Edwards, Aurélie

2004-09-30

A mathematical model of solute transient diffusion across the cornea to the anterior chamber of the eye was developed for topical drug delivery. Solute bioavailability was predicted given solute molecular radius and octanol-to-water distribution coefficient (Phi), ocular membrane ultrastructural parameters, tear fluid hydrodynamics, as well as solute distribution volume (Vd) and clearance rate (Cla) in the anterior chamber. The results suggest that drug bioavailability is primarily determined by solute lipophilicity. In human eyes, bioavailability is predicted to range between 1% and 5% for lipophilic molecules (Phi>1), and to be less than 0.5% for hydrophilic molecules (Phi<0.01). The simulations indicate that the distribution coefficient that maximizes bioavailability is on the order of 10. It was also found that the maximum solute concentration in the anterior chamber (Cmax) and the time needed to reach Cmax significantly depend on Phi, Vd, and Cla. Consistent with experimental findings, model predictions suggest that drug bioavailability can be increased by lowering the conjunctival-to-corneal permeability ratio and reducing precorneal solute drainage. Because of its mechanistic basis, this model will be useful to predict drug transport kinetics and bioavailability for new compounds and in diseased eyes.

Simultaneous two-photon imaging of intracellular chloride concentration and pH in mouse pyramidal neurons in vivo

PubMed Central

Sulis Sato, Sebastian; Artoni, Pietro; Landi, Silvia; Cozzolino, Olga; Parra, Riccardo; Pracucci, Enrico; Trovato, Francesco; Szczurkowska, Joanna; Arosio, Daniele; Beltram, Fabio; Cancedda, Laura; Kaila, Kai

2017-01-01

Intracellular chloride ([Cl−]i) and pH (pHi) are fundamental regulators of neuronal excitability. They exert wide-ranging effects on synaptic signaling and plasticity and on development and disorders of the brain. The ideal technique to elucidate the underlying ionic mechanisms is quantitative and combined two-photon imaging of [Cl−]i and pHi, but this has never been performed at the cellular level in vivo. Here, by using a genetically encoded fluorescent sensor that includes a spectroscopic reference (an element insensitive to Cl− and pH), we show that ratiometric imaging is strongly affected by the optical properties of the brain. We have designed a method that fully corrects for this source of error. Parallel measurements of [Cl−]i and pHi at the single-cell level in the mouse cortex showed the in vivo presence of the widely discussed developmental fall in [Cl−]i and the role of the K-Cl cotransporter KCC2 in this process. Then, we introduce a dynamic two-photon excitation protocol to simultaneously determine the changes of pHi and [Cl−]i in response to hypercapnia and seizure activity. PMID:28973889

Intracellular pH in mammalian stages of Trypanosoma cruzi is K+-dependent and regulated by H+-ATPases.

PubMed

Van Der Heyden, N; Docampo, R

2000-02-05

Regulation of intracellular pH (pHi) was investigated in Trypanosoma cruzi amastigotes and trypomastigotes using 2',7'-bis-(carboxyethyl)-5(and-6)-carboxyfluorescein (BCECF). pHi was determined to be 7.33 +/- 0.08 and 7.35 +/- 0.07 in amastigotes and trypomastigotes, respectively, and there were no significant differences in the regulation of pH, between the two stages. Steady-state pHi, recovery of pHi from acidification, and H+-efflux were all decreased markedly by the H+-ATPase inhibitors N,N'-dicyclohexylcarbodi-imide (DCCD), diethylstilbestrol (DES) and N-ethylmaleimide (NEM) supporting a significant role for a plasma membrane H+-ATPase in the regulation of pHi. pHi was maintained at neutrality over a range of external pH (pHe) from 5-8 in parasites suspended in a buffer containing Na+ and K+ (standard buffer) but was acidified at low pHe in the absence of these cations (choline buffer). The pHi of trypomastigotes decreased significantly when they transformed into amastigotes. The rate of recovery of pHi by acidified parasites was similar in Na+-free buffer and standard buffer but was slower in the absence of K+ (K+-free or choline buffer) and parasites suspended in choline buffer were acidic by 0.25 pH units as compared with controls. Ba2+ and Cs+ decreased the pHi of parasites suspended in standard but not choline buffer suggesting the presence of an inward directed K+ channel. The pHi of amastigotes and trypomastigotes suspended in Cl(-)-free buffer was decreased by 0.13 and 0.2 pH units, respectively, supporting the presence of a chloride conductive channel. No evidence of pH regulation via a Na+/H+ or Cl-/HCO3- exchanger was found. These results are consistent with the presence of a plasma membrane H+-ATPase that regulates pHi and is supported by K+ and Cl- channels.

Medically Unexplained and Explained Physical Symptoms in the General Population: Association with Prevalent and Incident Mental Disorders

PubMed Central

van Eck van der Sluijs, Jonna; ten Have, Margreet; Rijnders, Cees; van Marwijk, Harm; de Graaf, Ron; van der Feltz-Cornelis, Christina

2015-01-01

Background Clinical studies have shown that Medically Unexplained Symptoms (MUS) are related to common mental disorders. It is unknown how often common mental disorders occur in subjects who have explained physical symptoms (PHY), MUS or both, in the general population, what the incidence rates are, and whether there is a difference between PHY and MUS in this respect. Aim To study the prevalence and incidence rates of mood, anxiety and substance use disorders in groups with PHY, MUS and combined MUS and PHY compared to a no-symptoms reference group in the general population. Method Data were derived from the Netherlands Mental Health Survey and Incidence Study-2 (NEMESIS-2), a nationally representative face-to-face survey of the general population aged 18-64 years. We selected subjects with explained physical symptoms only (n=1952), with MUS only (n=177), with both MUS and PHY (n=209), and a reference group with no physical symptoms (n=4168). The assessment of common mental disorders was through the Composite International Diagnostic Interview 3.0. Multivariate logistic regression analyses were used to examine the association between group membership and the prevalence and first-incidence rates of comorbid mental disorders, adjusted for socio-demographic characteristics. Results MUS were associated with the highest prevalence rates of mood and anxiety disorders, and combined MUS and PHY with the highest prevalence rates of substance disorder. Combined MUS and PHY were associated with a higher incidence rate of mood disorder only (OR 2.9 (95%CI:1.27,6.74)). Conclusion In the general population, PHY, MUS and the combination of both are related to mood and anxiety disorder, but odds are highest for combined MUS and PHY in relation to substance use disorder. Combined MUS and PHY are related to a greater incidence of mood disorder. These findings warrant further research into possibilities to improve recognition and early intervention in subjects with combined MUS and PHY. PMID:25853676

Specific binding of (/sup 3/H-Tyr8)physalaemin to rat submaxillary gland substance P receptor

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

Bahouth, S.W.; Lazaro, D.M.; Brundish, D.E.

1985-01-01

(/sup 3/H)Physalaemin ((/sup 3/H)PHY) binds to a single class of noninteracting sites on rat submaxillary gland membranes suspended in high ionic strength media with a KD of 2.7 nM, a Bmax of 240 fmol/mg of protein, and low nonspecific binding. The relative potencies of substance P (SP) and its fragments in competing with (/sup 3/H)PHY correlate with their relative salivation potencies. This indicates that (/sup 3/H)PHY interacts with a physiologically relevant SP receptor. In low ionic strength media, the KD of (/sup 3/H)PHY does not change, but SP and some of its fragments are more potent than PHY in competingmore » with (/sup 3/H) PHY. Computer-assisted analysis of (/sup 3/H)PHY and (/sup 3/H)SP binding in high and low ionic strength media demonstrated that both peptides are equipotent in high ionic strength but that the affinity of SP increases by 70-fold in low ionic strength. The SP fragments that contain a basic residue in positions 1 and/or 3 also display an increased affinity in low ionic strength. These findings document that (/sup 3/H)PHY binding in high ionic strength (mu . 0.6) accurately reflects the pharmacological potencies of agonists on the SP-P receptor. The binding of (/sup 3/H)PHY, like that of (/sup 3/H)SP, increases by the addition of divalent cations (Mg2+ greater than Ca2+ greater than Mn2+). Guanine nucleotides decrease (/sup 3/H)PHY binding by decreasing the Bmax to the same level (160 fmol/mg of protein), in the presence or absence of Mg2+.« less

Evolutionary divergence of phytochrome protein function in Zea mays PIF3 signaling.

PubMed

Kumar, Indrajit; Swaminathan, Kankshita; Hudson, Karen; Hudson, Matthew E

2016-07-01

Two maize phytochrome-interacting factor (PIF) basic helix-loop-helix (bHLH) family members, ZmPIF3.1 and ZmPIF3.2, were identified, cloned and expressed in vitro to investigate light-signaling interactions. A phylogenetic analysis of sequences of the maize bHLH transcription factor gene family revealed the extent of the PIF family, and a total of seven predicted PIF-encoding genes were identified from genes encoding bHLH family VIIa/b proteins in the maize genome. To investigate the role of maize PIFs in phytochrome signaling, full-length cDNAs for phytochromes PhyA2, PhyB1, PhyB2 and PhyC1 from maize were cloned and expressed in vitro as chromophorylated holophytochromes. We showed that ZmPIF3.1 and ZmPIF3.2 interact specifically with the Pfr form of maize holophytochrome B1 (ZmphyB1), showing no detectable affinity for the Pr form. Maize holophytochrome B2 (ZmphyB2) showed no detectable binding affinity for PIFs in either Pr or Pfr forms, but phyB Pfr from Arabidopsis interacted with ZmPIF3.1 similarly to ZmphyB1 Pfr. We conclude that subfunctionalization at the protein-protein interaction level has altered the role of phyB2 relative to that of phyB1 in maize. Since the phyB2 mutant shows photomorphogenic defects, we conclude that maize phyB2 is an active photoreceptor, without the binding of PIF3 seen in other phyB family proteins. © The Author 2016. Published by Oxford University Press on behalf of the Society for Experimental Biology.

Plasma HIV viral rebound following protocol-indicated cessation of ART commenced in primary and chronic HIV infection.

PubMed

Hamlyn, Elizabeth; Ewings, Fiona M; Porter, Kholoud; Cooper, David A; Tambussi, Giuseppe; Schechter, Mauro; Pedersen, Court; Okulicz, Jason F; McClure, Myra; Babiker, Abdel; Weber, Jonathan; Fidler, Sarah

2012-01-01

The magnitude of HIV viral rebound following ART cessation has consequences for clinical outcome and onward transmission. We compared plasma viral load (pVL) rebound after stopping ART initiated in primary (PHI) and chronic HIV infection (CHI). Two populations with protocol-indicated ART cessation from SPARTAC (PHI, n = 182) and SMART (CHI, n = 1450) trials. Time for pVL to reach pre-ART levels after stopping ART was assessed in PHI using survival analysis. Differences in pVL between PHI and CHI populations 4 weeks after stopping ART were examined using linear and logistic regression. Differences in pVL slopes up to 48 weeks were examined using linear mixed models and viral burden was estimated through a time-averaged area-under-pVL curve. CHI participants were categorised by nadir CD4 at ART stop. Of 171 PHI participants, 71 (41.5%) rebounded to pre-ART pVL levels, at a median of 50 (95% CI 48-51) weeks after stopping ART. Four weeks after stopping treatment, although the proportion with pVL ≥ 400 copies/ml was similar (78% PHI versus 79% CHI), levels were 0.45 (95% CI 0.26-0.64) log(10) copies/ml lower for PHI versus CHI, and remained lower up to 48 weeks. Lower CD4 nadir in CHI was associated with higher pVL after ART stop. Rebound for CHI participants with CD4 nadir >500 cells/mm(3) was comparable to that experienced by PHI participants. Stopping ART initiated in PHI and CHI was associated with viral rebound to levels conferring increased transmission risk, although the level of rebound was significantly lower and sustained in PHI compared to CHI.

A Systematic Review and Meta-analysis of the Diagnostic Accuracy of Prostate Health Index and 4-Kallikrein Panel Score in Predicting Overall and High-grade Prostate Cancer.

PubMed

Russo, Giorgio Ivan; Regis, Federica; Castelli, Tommaso; Favilla, Vincenzo; Privitera, Salvatore; Giardina, Raimondo; Cimino, Sebastiano; Morgia, Giuseppe

2017-08-01

Markers for prostate cancer (PCa) have progressed over recent years. In particular, the prostate health index (PHI) and the 4-kallikrein (4K) panel have been demonstrated to improve the diagnosis of PCa. We aimed to review the diagnostic accuracy of PHI and the 4K panel for PCa detection. We performed a systematic literature search of PubMed, EMBASE, Cochrane, and Academic One File databases until July 2016. We included diagnostic accuracy studies that used PHI or 4K panel for the diagnosis of PCa or high-grade PCa. The methodological quality was assessed using the Quality Assessment of Diagnostic Accuracy Studies (QUADAS-2) tool. Twenty-eight studies including 16,762 patients have been included for the analysis. The pooled data showed a sensitivity of 0.89 and 0.74 for PHI and 4K panel, respectively, for PCa detection and a pooled specificity of 0.34 and 0.60 for PHI and 4K panel, respectively. The derived area under the curve (AUC) from the hierarchical summary receiver operating characteristic (HSROC) showed an accuracy of 0.76 and 0.72 for PHI and 4K panel respectively. For high-grade PCa detection, the pooled sensitivity was 0.93 and 0.87 for PHI and 4K panel, respectively, whereas the pooled specificity was 0.34 and 0.61 for PHI and 4K panel, respectively. The derived AUC from the HSROC showed an accuracy of 0.82 and 0.81 for PHI and 4K panel, respectively. Both PHI and the 4K panel provided good diagnostic accuracy in detecting overall and high-grade PCa. Copyright © 2016 Elsevier Inc. All rights reserved.

Vehicle fault diagnostics and management system

NASA Astrophysics Data System (ADS)

Gopal, Jagadeesh; Gowthamsachin

2017-11-01

This project is a kind of advanced automatic identification technology, and is more and more widely used in the fields of transportation and logistics. It looks over the main functions with like Vehicle management, Vehicle Speed limit and Control. This system starts with authentication process to keep itself secure. Here we connect sensors to the STM32 board which in turn is connected to the car through Ethernet cable, as Ethernet in capable of sending large amounts of data at high speeds. This technology involved clearly shows how a careful combination of software and hardware can produce an extremely cost-effective solution to a problem.

A search for a doubly-charged Higgs boson in pp collisions at $$\\sqrt{s} = 7 \\ \\mbox{TeV}$$

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

Chatrchyan, S.; Khachatryan, V.; Sirunyan, A. M.

A search for a doubly-charged Higgs boson in pp collisions atmore » $$ \\sqrt{s}=7 $$ TeV is presented. The data correspond to an integrated luminosity of 4.9 inverse femtobarns, collected by the CMS experiment at the LHC. The search is performed using events with three or more isolated charged leptons of any flavor, giving sensitivity to the decays of pair-produced triplet components Phi[++]Phi[--], and Phi[++]Phi[-] from associated production. No excess is observed compared to the background prediction, and upper limits at the 95% confidence level are set on the Phi[++] production cross section, under specific assumptions on its branching fractions. Lower bounds on the Phi[++] mass are reported, providing significantly more stringent constraints than previously published limits.« less

Effects of intracellular pH on the mitotic apparatus and mitotic stage in the sand dollar egg.

PubMed

Watanabe, K; Hamaguchi, M S; Hamaguchi, Y

1997-01-01

The effect of change in intracellular pH (pHi) on mitosis was investigated in the sand dollar egg. The pHi in the fertilized egg of Scaphechinus mirabilis and Clypeaster japonicus, which was 7.34 and 7.31, respectively, changed by means of treating the egg at nuclear envelope breakdown with sea water containing acetate and/or ammonia at various values of pH. The mitotic apparatus at pHi 6.70 became larger than that of normal fertilized eggs; that is, the mitotic spindle had the maximal size, especially in length at pHi 6.70. The spindle length linearly decreased when pHi increased from 6.70 to 7.84. By polarization microscopy, the increase in birefringence retardation was detected at slightly acidic pHi, suggesting that the increase in size of the spindle is caused by the increase in the amount of microtubules in the spindle. At pHi 6.30, the organization of the mitotic apparatus was inhibited. Furthermore, slightly acidic pHi caused cleavage retardation or inhibition. By counting the number of the eggs at various mitotic stages with time after treating them with the media, it is found that metaphase was persistent and most of the S. mirabilis eggs were arrested at metaphase under the condition of pHi 6.70. It is concluded that at slightly acidic pH, the microtubules in the spindle are stabilized and more microtubules assembled than those in the normal eggs.

Achieving effective hearing aid fitting within one month after identification of childhood permanent hearing impairment.

PubMed

Bastanza, G; Gallus, R; De Carlini, M; Picciotti, P M; Muzzi, E; Ciciriello, E; Orzan, E; Conti, G

2016-02-01

Diagnosis of child permanent hearing impairment (PHI) can be made with extreme timeliness compared to the past thanks to improvements in PHI identification through newborn hearing screening programmes. It now becomes essential to provide an effective amplification as quickly as possible in order to restore auditory function and favour speech and language development. The early fitting of hearing aids and possible later cochlear implantation indeed prompts the development of central auditory pathways, connections with secondary sensory brain areas, as well as with motor and articulatory cortex. The aim of this paper is to report the results of a strategic analysis that involves identification of strengths, weaknesses, opportunities and threats regarding the process of achieving early amplification in all cases of significant childhood PHI. The analysis is focused on the Italian situation and is part of the Italian Ministry of Health project CCM 2013 "Preventing Communication Disorders: a Regional Program for Early Identification, Intervention and Care of Hearing Impaired Children". © Copyright by Società Italiana di Otorinolaringologia e Chirurgia Cervico-Facciale.

Integrating clinical performance improvement across physician organizations: the PhyCor experience.

PubMed

Loeppke, R; Howell, J W

1999-02-01

There is a paucity of literature describing the implementation of clinical performance improvement (CPI) efforts across geographically dispersed multispecialty group practices and independent practice associations. PhyCor, a physician management company based in Nashville, Tennessee, has integrated CPI initiatives into its operating infrastructure. PhyCor CPI INITIATIVES: The strategic framework guiding PhyCor's CPI initiatives is built around a physician-driven, patient-centered model. Physician/administrator leadership teams develop and implement a clinical and financial strategic plan for performance improvement; adopt local clinical and operational performance indicators; and agree on and gain consensus with local physician champions to engage in CPI initiatives. The area/regional leadership councils integrate and coordinate regional medical management and CPI initiatives among local groups and independent practice associations. In addition to these councils and a national leadership council, condition-specific care management councils have also been established. These councils develop condition-specific protocols and outcome measures and lead the implementation of CPI initiatives at their own clinics. Key resources supporting CPI initiatives include information/knowledge management, education and training, and patient education and consumer decision support. Localized efforts in both the asthma care and diabetes management initiatives have led to some preliminary improvements in quality of care indicators. Physician leadership and strategic vision, CPI-oriented organizational infrastructure, broad-based physician involvement in CPI, providing access to performance data, parallel incentives, and creating a sense of urgency for accelerated change are all critical success factors to the implementation of CPI strategies at the local, regional, and national levels.

Elevated Prostate Health Index (phi) and Biopsy Reclassification During Active Surveillance of Prostate Cancer.

PubMed

Andreas, Darian; Tosoian, Jeffrey J; Landis, Patricia; Wolf, Sacha; Glavaris, Stephanie; Lotan, Tamara L; Schaeffer, Edward M; Sokoll, Lori J; Ross, Ashley E

2016-07-01

The Prostate Health Index (phi) has been FDA approved for decision-making regarding prostate biopsy. Phi has additionally been shown to positively correlate with tumor volume, extraprostatic disease and higher Gleason grade tumors. Here we describe a case in which an elevated phi encouraged biopsy of a gentleman undergoing active surveillance leading to reclassification of his disease as high risk prostate cancer.

Dye to use with virus challenge for testing barrier materials.

PubMed Central

Lytle, C D; Felten, R P; Truscott, W

1991-01-01

Can FD&C Blue no. 1 dye photoinactivate bacteriophages phi X174, T7, PRD1, and phi 6 under laboratory lighting conditions? At high levels of light, the dye (500 microM) photoinactivated only phi 6. Thus, this dye can be used at concentrations up to 500 microM with bacteriophages phi X174, T7, and PRD1 to test barrier material integrity. PMID:1872612

Tiny abortive initiation transcripts exert antitermination activity on an RNA hairpin-dependent intrinsic terminator.

PubMed

Lee, Sooncheol; Nguyen, Huong Minh; Kang, Changwon

2010-10-01

No biological function has been identified for tiny RNA transcripts that are abortively and repetitiously released from initiation complexes of RNA polymerase in vitro and in vivo to date. In this study, we show that abortive initiation affects termination in transcription of bacteriophage T7 gene 10. Specifically, abortive transcripts produced from promoter phi 10 exert trans-acting antitermination activity on terminator T phi both in vitro and in vivo. Following abortive initiation cycling of T7 RNA polymerase at phi 10, short G-rich and oligo(G) RNAs were produced and both specifically sequestered 5- and 6-nt C + U stretch sequences, consequently interfering with terminator hairpin formation. This antitermination activity depended on sequence-specific hybridization of abortive transcripts with the 5' but not 3' half of T phi RNA. Antitermination was abolished when T phi was mutated to lack a C + U stretch, but restored when abortive transcript sequence was additionally modified to complement the mutation in T phi, both in vitro and in vivo. Antitermination was enhanced in vivo when the abortive transcript concentration was increased via overproduction of RNA polymerase or ribonuclease deficiency. Accordingly, antitermination activity exerted on T phi by abortive transcripts should facilitate expression of T phi-downstream promoter-less genes 11 and 12 in T7 infection of Escherichia coli.

Estimation of Reconnection Flux Using Post-Eruption Arcades and Its Relevance to Magnetic Clouds at 1 AU

NASA Technical Reports Server (NTRS)

Gopalswamy, N.; Yashiro, S.; Akiyama, S.; Xie, H.

2017-01-01

We report on a new method to compute the flare reconnection (RC) flux from post-eruption arcades (PEAs) and the underlying photospheric magnetic fields. In previous works, the RC flux has been computed using the cumulative flare ribbon area. Here we obtain the RC flux as the flux in half of the area underlying the PEA in EUV imaged after the flare maximum. We apply this method to a set of 21 eruptions that originated near the solar disk center in Solar Cycle 23. We find that the RC flux from the arcade method ((Phi)rA) has excellent agreement with the flux from the flare-ribbon method ((Phi)rR) according to (Phi)rA = 1.24((Phi)rR)(sup 0.99). We also find (Phi)rA to be correlated with the poloidal flux ((Phi)P) of the associated magnetic cloud at 1 AU: (Phi)P = 1.20((Phi)rA)(sup 0.85). This relation is nearly identical to that obtained by Qiu et al. (Astrophys. J. 659, 758, 2007) using a set of only 9 eruptions. Our result supports the idea that flare reconnection results in the formation of the flux rope and PEA as a common process.

Role of phi cells and the endodermis under salt stress in Brassica oleracea.

PubMed

Fernandez-Garcia, N; Lopez-Perez, L; Hernandez, M; Olmos, E

2009-01-01

Phi cell layers were discovered in the 19th century in a small number of species, including members of the Brassicaceae family. A mechanical role was first suggested for this structure; however, this has never been demonstrated. The main objective of the present work was to analyse the ultrastructure of phi cells, their influence on ion movement from the cortex to the stele, and their contribution to salt stress tolerance in Brassica oleracea. Transmission electron microscopy and X-ray microanalysis studies were used to analyse the subcellular structure and distribution of ions in phi cells and the endodermis under salt stress. Ion movement was analysed using lanthanum as an apoplastic tracer. The ultrastructural results confirm that phi cells are specialized cells showing cell wall ingrowths in the inner tangential cell walls. X-ray microanalysis confirmed a build-up of sodium. Phi thickenings were lignified and lanthanum moved periplasmically at this level. To the best of our knowledge, this is the first study reporting the possible role of the phi cells as a barrier controlling the movement of ions from the cortex to the stele. Therefore, the phi cell layer and endodermis seem to be regulating ion transport in Brassica oleracea under salt stress.

Intracellular pH in sperm physiology.

PubMed

Nishigaki, Takuya; José, Omar; González-Cota, Ana Laura; Romero, Francisco; Treviño, Claudia L; Darszon, Alberto

2014-08-01

Intracellular pH (pHi) regulation is essential for cell function. Notably, several unique sperm ion transporters and enzymes whose elimination causes infertility are either pHi dependent or somehow related to pHi regulation. Amongst them are: CatSper, a Ca(2+) channel; Slo3, a K(+) channel; the sperm-specific Na(+)/H(+) exchanger and the soluble adenylyl cyclase. It is thus clear that pHi regulation is of the utmost importance for sperm physiology. This review briefly summarizes the key components involved in pHi regulation, their characteristics and participation in fundamental sperm functions such as motility, maturation and the acrosome reaction. Copyright © 2014 Elsevier Inc. All rights reserved.

On character amenability of Banach algebras

NASA Astrophysics Data System (ADS)

Kaniuth, E.; Lau, A. T.; Pym, J.

2008-08-01

We continue our work [E. Kaniuth, A.T. Lau, J. Pym, On [phi]-amenability of Banach algebras, Math. Proc. Cambridge Philos. Soc. 144 (2008) 85-96] in the study of amenability of a Banach algebra A defined with respect to a character [phi] of A. Various necessary and sufficient conditions of a global and a pointwise nature are found for a Banach algebra to possess a [phi]-mean of norm 1. We also completely determine the size of the set of [phi]-means for a separable weakly sequentially complete Banach algebra A with no [phi]-mean in A itself. A number of illustrative examples are discussed.

Design and Deployment of a General Purpose, Open Source LoRa to Wi-Fi Hub and Data Logger

NASA Astrophysics Data System (ADS)

DeBell, T. C.; Udell, C.; Kwon, M.; Selker, J. S.; Lopez Alcala, J. M.

2017-12-01

Methods and technologies facilitating internet connectivity and near-real-time status updates for in site environmental sensor data are of increasing interest in Earth Science. However, Open Source, Do-It-Yourself technologies that enable plug and play functionality for web-connected sensors and devices remain largely inaccessible for typical researchers in our community. The Openly Published Environmental Sensing Lab at Oregon State University (OPEnS Lab) constructed an Open Source 900 MHz Long Range Radio (LoRa) receiver hub with SD card data logger, Ethernet and Wi-Fi shield, and 3D printed enclosure that dynamically uploads transmissions from multiple wirelessly-connected environmental sensing devices. Data transmissions may be received from devices up to 20km away. The hub time-stamps, saves to SD card, and uploads all transmissions to a Google Drive spreadsheet to be accessed in near-real-time by researchers and GeoVisualization applications (such as Arc GIS) for access, visualization, and analysis. This research expands the possibilities of scientific observation of our Earth, transforming the technology, methods, and culture by combining open-source development and cutting edge technology. This poster details our methods and evaluates the application of using 3D printing, Arduino Integrated Development Environment (IDE), Adafruit's Open-Hardware Feather development boards, and the WIZNET5500 Ethernet shield for designing this open-source, general purpose LoRa to Wi-Fi data logger.

[PHI regulates histone methylation and acetylation in Burkitt lymphoma Daudi cell line].

PubMed

Hong, Ling-Ling; Ma, Xu-Dong; Huang, Yi-Qun

2011-02-01

This study was purposed to investigate the effects of phenylhexyl isothiocyanate (PHI) on Burkitt lymphoma Daudi cell line and regulation of histone acetylation and methylation in Daudi cells, and to explore the potential mechanism. The apoptotic rate of Daudi cells treated with PHI was measured by flow cytometry, the changes of histone H3 and H4 acetylation, histone H3K9 and H3K4 methylation in Daudi cells treated with PHI were detected by Western blot. The results showed that PHI could induce apoptosis of Daudi cells, increased the acetylation level of H3 and H4, enhanced the methylation of H3K4, but reduced the methylation of H3K9. It is concluded that the PHI can up-regulate the acetylation level of histone H3 associated with transcription stimulation and the methylation of histone H3K4, down-regulate the methylation on histone H3K9 associated with transcription inhibition, promotes the apoptosis of Daudi cells. PHI may be a potential agent for target therapy of lymphoma.

Genome packaging in EL and Lin68, two giant phiKZ-like bacteriophages of P. aeruginosa.

PubMed

Sokolova, O S; Shaburova, O V; Pechnikova, E V; Shaytan, A K; Krylov, S V; Kiselev, N A; Krylov, V N

2014-11-01

A unique feature of the Pseudomonas aeruginosa giant phage phiKZ is its way of genome packaging onto a spool-like protein structure, the inner body. Until recently, no similar structures have been detected in other phages. We have studied DNA packaging in P. aeruginosa phages EL and Lin68 using cryo-electron microscopy and revealed the presence of inner bodies. The shape and positioning of the inner body and the density of the DNA packaging in EL are different from those found in phiKZ and Lin68. This internal organization explains how the shorter EL genome is packed into a large EL capsid, which has the same external dimensions as the capsids of phiKZ and Lin68. The similarity in the structural organization in EL and other phiKZ-like phages indicates that EL is phylogenetically related to other phiKZ-like phages, and, despite the lack of detectable DNA homology, EL, phiKZ, and Lin68 descend from a common ancestor. Copyright © 2014 Elsevier Inc. All rights reserved.

Shape Phase Transition from Octupole Deformation to Octupole Vibrations: The Analytic Quadrupole Octupole Axially Symmetric Model

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

Bonatsos, Dennis; Lenis, D.; Petrellis, D.

An analytic collective model in which the relative presence of the quadrupole and octupole deformations is determined by a parameter ({phi}0), while axial symmetry is obeyed, is developed. The model [to be called the Analytic Quadrupole Octupole Axially symmetric model (AQOA)] involves an infinite well potential, provides predictions for energy and B(EL) ratios which depend only on {phi}0, draws the border between the regions of octupole deformation and octupole vibrations in an essentially parameter-independent way, and in the actinide region describes well 226Th and 226Ra, for which experimental energy data are shown to suggest that they lie close to thismore » border. The similarity of the AQOA results with {phi}0 = 45 deg. for ground state band spectra and B(E2) transition rates to the predictions of the X(5) model is pointed out.« less

Vigil: Providing Trust for Enhanced Security in Pervasive Systems

DTIC Science & Technology

2005-01-01

environment consisting of Bluetooth, Infrared, 802.11b and Ethernet. Vigil is the extension and culmination of our two previous projects: Centaurus [22] and...Centau- rus2 [36]. The main design goal of the Centaurus project was the development of a framework for building portals to services using various...types of mobile devices. Centaurus provides a uniform infrastructure for access to heterogeneous hardware and software components. It uses a language

System and method for constructing filters for detecting signals whose frequency content varies with time

DOEpatents

Qian, S.; Dunham, M.E.

1996-11-12

A system and method are disclosed for constructing a bank of filters which detect the presence of signals whose frequency content varies with time. The present invention includes a novel system and method for developing one or more time templates designed to match the received signals of interest and the bank of matched filters use the one or more time templates to detect the received signals. Each matched filter compares the received signal x(t) with a respective, unique time template that has been designed to approximate a form of the signals of interest. The robust time domain template is assumed to be of the order of w(t)=A(t)cos(2{pi}{phi}(t)) and the present invention uses the trajectory of a joint time-frequency representation of x(t) as an approximation of the instantaneous frequency function {phi}{prime}(t). First, numerous data samples of the received signal x(t) are collected. A joint time frequency representation is then applied to represent the signal, preferably using the time frequency distribution series. The joint time-frequency transformation represents the analyzed signal energy at time t and frequency f, P(t,f), which is a three-dimensional plot of time vs. frequency vs. signal energy. Then P(t,f) is reduced to a multivalued function f(t), a two dimensional plot of time vs. frequency, using a thresholding process. Curve fitting steps are then performed on the time/frequency plot, preferably using Levenberg-Marquardt curve fitting techniques, to derive a general instantaneous frequency function {phi}{prime}(t) which best fits the multivalued function f(t). Integrating {phi}{prime}(t) along t yields {phi}{prime}(t), which is then inserted into the form of the time template equation. A suitable amplitude A(t) is also preferably determined. Once the time template has been determined, one or more filters are developed which each use a version or form of the time template. 7 figs.

Intracellular pH of symbiotic dinoflagellates

NASA Astrophysics Data System (ADS)

Gibbin, E. M.; Davy, S. K.

2013-09-01

Intracellular pH (pHi) is likely to play a key role in maintaining the functional success of cnidarian-dinoflagellate symbiosis, yet until now the pHi of the symbiotic dinoflagellates (genus Symbiodinium) has never been quantified. Flow cytometry was used in conjunction with the ratiometric fluorescent dye BCECF to monitor changes in pHi over a daily light/dark cycle. The pHi of Symbiodinium type B1 freshly isolated from the model sea anemone Aiptasia pulchella was 7.25 ± 0.01 (mean ± SE) in the light and 7.10 ± 0.02 in the dark. A comparable effect of irradiance was seen across a variety of cultured Symbiodinium genotypes (types A1, B1, E1, E2, F1, and F5) which varied between pHi 7.21-7.39 in the light and 7.06-7.14 in the dark. Of note, there was a significant genotypic difference in pHi, irrespective of irradiance.

Analog quadrature signal to phase angle data conversion by a quadrature digitizer and quadrature counter

DOEpatents

Buchenauer, C.J.

1981-09-23

The quadrature phase angle phi (t) of a pair of quadrature signals S/sub 1/(t) and S/sub 2/(t) is digitally encoded on a real time basis by a quadrature digitizer for fractional phi (t) rotational excursions and by a quadrature up/down counter for full phi (t) rotations. The pair of quadrature signals are of the form S/sub 1/(t) = k(t) sin phi (t) and S/sub 2/(t) = k(t) cos phi (t) where k(t) is a signal common to both. The quadrature digitizer and the quadrature up/down counter may be used together or singularly as desired or required. Optionally, a digital-to-analog converter may follow the outputs of the quadrature digitizer and the quadrature up/down counter to provide an analog signal output of the quadrature phase angle phi (t).

Analog quadrature signal to phase angle data conversion by a quadrature digitizer and quadrature counter

DOEpatents

Buchenauer, C. Jerald

1984-01-01

The quadrature phase angle .phi.(t) of a pair of quadrature signals S.sub.1 (t) and S.sub.2 (t) is digitally encoded on a real time basis by a quadrature digitizer for fractional .phi.(t) rotational excursions and by a quadrature up/down counter for full .phi.(t) rotations. The pair of quadrature signals are of the form S.sub.1 (t)=k(t) sin .phi.(t) and S.sub.2 (t)=k(t) cos .phi.(t) where k(t) is a signal common to both. The quadrature digitizer and the quadrature up/down counter may be used together or singularly as desired or required. Optionally, a digital-to-analog converter may follow the outputs of the quadrature digitizer and the quadrature up/down counter to provide an analog signal output of the quadrature phase angle .phi.(t).

Macrophage tumoricidal mechanisms are selectively altered by prenatal chlordane exposure.

PubMed

Theus, S A; Tabor, D R; Soderberg, L S; Barnett, J B

1992-09-01

Macrophages (m phi) derived from mice treated in utero with chlordane show a significant delay of tumoricidal induction activity. In this study, m phi from chlordane-treated animals required a 48 h in vitro period of induction with interferon-gamma and lipopolysaccharide (IFN/LPS) before they could kill P815 targets. Similarly, m phi from chlordane-treated animals also failed to produce an immediate H2O2 burst upon perturbation. Conversely, their stimulated control m phi counterparts were tumoricidal by 2 h and exhibited a respiratory burst without any delay. Moreover, levels of the second messenger, inositol triphosphate (IP3), were significantly delayed in chlordane-treated animals following interaction with IFN/LPS. When nitrate/nitrite production was analyzed as an alternate mechanism for killing tumors, stimulated m phi from both normal and chlordane-treated animals responded equally. The data show that chlordane differentially introduces defects in m phi biochemical mechanisms associated with tumor killing.

Order and disorder in crystals of hexameric NTPases from dsRNA bacteriophages.

PubMed

Mancini, Erika J; Grimes, Jonathan M; Malby, Robyn; Sutton, Geoffrey C; Kainov, Denis E; Juuti, Jarmo T; Makeyev, Eugene V; Tuma, Roman; Bamford, Dennis H; Stuart, David I

2003-12-01

The packaging of genomic RNA in members of the Cystoviridae is performed by P4, a hexameric protein with NTPase activity. Across family members such as Phi6, Phi8 and Phi13, the P4 proteins show low levels of sequence identity, but presumably have similar atomic structures. Initial structure-determination efforts for P4 from Phi6 and Phi8 were hampered by difficulties in obtaining crystals that gave ordered diffraction. Diffraction from crystals of full-length P4 showed a variety of disorder and anisotropy. Subsequently, crystals of Phi13 P4 were obtained which yielded well ordered diffraction to 1.7 A. Comparison of the packing arrangements of P4 hexamers in different crystal forms and analysis of the disorder provides insights into the flexibility of this family of proteins, which might be an integral part of their biological function.

Measurement of differential cross sections in the $$\\phi^*$$ variable for inclusive Z boson production in pp collisions at $$\\sqrt{s}=$$ 8 TeV

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

Sirunyan, Albert M; et al.

Measurements of differential cross sections dmore » $$\\sigma$$/d$$\\phi^*$$ and double-differential cross sections d$$^2\\sigma$$/d$$\\phi^*\\,$$d$|y|$ for inclusive Z boson production are presented using the dielectron and dimuon final states. The kinematic observable $$\\phi^*$$ correlates with the dilepton transverse momentum but has better resolution, and $y$ is the dilepton rapidity. The analysis is based on data collected with the CMS experiment at a centre-of-mass energy of 8 TeV corresponding to an integrated luminosity of 19.7 fb$$^{-1}$$. The normalised cross section (1/$$\\sigma$$)$$\\,$$d$$\\sigma$$/d$$\\phi^*$$, within the fiducial kinematic region, is measured with a precision of better than 0.5% for $$\\phi^*$$<1. The measurements are compared to theoretical predictions and they agree, typically, within few percent.« less

Risk factors for ventilator-associated pneumonia in trauma patients: A descriptive analysis

PubMed Central

Arumugam, Suresh Kumar; Mudali, Insolvisagan; Strandvik, Gustav; El-Menyar, Ayman; Al-Hassani, Ammar; Al-Thani, Hassan

2018-01-01

BACKGROUND: We sought to evaluate the risk factors for developing ventilator-associated pneumonia (VAP) and whether the location of intubation posed a risk in trauma patients. METHODS: Data were retrospectively reviewed for adult trauma patients requiring intubation for > 48 hours, admitted between 2010 and 2013. Patients’ demographics, clinical presentations and outcomes were compared according to intubation location (prehospital intubation [PHI] vs. trauma room [TRI]) and presence vs. absence of VAP. Multivariate regression analysis was performed to identify predictors of VAP. RESULTS: Of 471 intubated patients, 332 patients met the inclusion criteria (124 had PHI and 208 had TRI) with a mean age of 30.7±14.8 years. PHI group had lower GCS (P=0.001), respiratory rate (P=0.001), and higher frequency of head (P=0.02) and chest injuries (P=0.04). The rate of VAP in PHI group was comparable to the TRI group (P=0.60). Patients who developed VAP were 6 years older, had significantly lower GCS and higher ISS, head AIS, and higher rates of polytrauma. The overall mortality was 7.5%, and was not associated with intubation location or pneumonia rates. In the early-VAP group, gram-positive pathogens were more common, while gram-negative microorganisms were more frequently encountered in the late VAP group. Logistic regression analysis and modeling showed that the impact of the location of intubation in predicting the risk of VAP appeared only when chest injury was included in the models. CONCLUSION: In trauma, the risk of developing VAP is multifactorial. However, the location of intubation and presence of chest injury could play an important role. PMID:29796145

A new role for the Arabidopsis AP2 transcription factor, LEAFY PETIOLE, in gibberellin-induced germination is revealed by the misexpression of a homologous gene, SOB2/DRN-LIKE.

PubMed

Ward, Jason M; Smith, Alison M; Shah, Purvi K; Galanti, Sarah E; Yi, Hankuil; Demianski, Agnes J; van der Graaff, Eric; Keller, Beat; Neff, Michael M

2006-01-01

Gibberellic acid (GA) promotes germination, stem/hypocotyl elongation, and leaf expansion during seedling development. Using activation-tagging mutagenesis, we identified a mutation, sob2-D (for suppressor of phytochromeB-4 [phyB-4]#2 dominant), which suppresses the long-hypocotyl phenotype of a phyB missense allele, phyB-4. This mutant phenotype is caused by the overexpression of an APETALA2 transcription factor, SOB2, also called DRN-like. SOB2/DRN-like transcript is not detectable in wild-type seedling or adult tissues via RT-PCR analysis, suggesting that SOB2/DRN-like may not be involved in seedling development under normal conditions. Adult sob2-D phyB-4 plants have curled leaves and club-like siliques, resembling plants that overexpress a closely related gene, LEAFY PETIOLE (LEP). Hypocotyls of a LEP-null allele, lep-1, are shorter in the light and dark, suggesting LEP involvement in seedling development. This aberrant hypocotyl phenotype is due at least in part to a delay in germination. In addition, lep-1 is less responsive to GA and more sensitive to the GA biosynthesis inhibitor paclobutrazol, indicating that LEP is a positive regulator of GA-induced germination. RT-PCR shows that LEP transcript accumulates in wild-type seeds during imbibition and germination, and the transcript levels of REPRESSOR OF ga1-3-LIKE2 (RGL2), a negative regulator of GA signaling during germination, is unaffected in lep-1. These results suggest LEP is a positive regulator of GA-induced germination acting independently of RGL2. An alternative model places LEP downstream of RGL2 in the GA-signaling cascade.

Reusable design: A proposed approach to Public Health Informatics system design

PubMed Central

2011-01-01

Background Since it was first defined in 1995, Public Health Informatics (PHI) has become a recognized discipline, with a research agenda, defined domain-specific competencies and a specialized corpus of technical knowledge. Information systems form a cornerstone of PHI research and implementation, representing significant progress for the nascent field. However, PHI does not advocate or incorporate standard, domain-appropriate design methods for implementing public health information systems. Reusable design is generalized design advice that can be reused in a range of similar contexts. We propose that PHI create and reuse information design knowledge by taking a systems approach that incorporates design methods from the disciplines of Human-Computer Interaction, Interaction Design and other related disciplines. Discussion Although PHI operates in a domain with unique characteristics, many design problems in public health correspond to classic design problems, suggesting that existing design methods and solution approaches are applicable to the design of public health information systems. Among the numerous methodological frameworks used in other disciplines, we identify scenario-based design and participatory design as two widely-employed methodologies that are appropriate for adoption as PHI standards. We make the case that these methods show promise to create reusable design knowledge in PHI. Summary We propose the formalization of a set of standard design methods within PHI that can be used to pursue a strategy of design knowledge creation and reuse for cost-effective, interoperable public health information systems. We suggest that all public health informaticians should be able to use these design methods and the methods should be incorporated into PHI training. PMID:21333000

Integration Of An MR Image Network Into A Clinical PACS

NASA Astrophysics Data System (ADS)

Ratib, Osman M.; Mankovich, Nicholas J.; Taira, Ricky K.; Cho, Paul S.; Huang, H. K.

1988-06-01

A direct link between a clinical pediatric PACS module and a FONAR MRI image network was implemented. The original MR network combines together the MR scanner, a remote viewing station and a central archiving station. The pediatric PACS directly connects to the archiving unit through an Ethernet TCP-IP network adhering to FONAR's protocol. The PACS communication software developed supports the transfer of patient studies and the patient information directly from the MR archive database to the pediatric PACS. In the first phase of our project we developed a package to transfer data between a VAX-111750 and the IBM PC I AT-based MR archive database through the Ethernet network. This system served as a model for PACS-to-modality network communication. Once testing was complete on this research network, the software and network hardware was moved to the clinical pediatric VAX for full PACS integration. In parallel to the direct transmission of digital images to the Pediatric PACS, a broadband communication system in video format was developed for real-time broadcasting of images originating from the MR console to 8 remote viewing stations distributed in the radiology department. These analog viewing stations allow the radiologists to directly monitor patient positioning and to select the scan levels during a patient examination from remote locations in the radiology department. This paper reports (1) the technical details of this implementation, (2) the merits of this network development scheme, and (3) the performance statistics of the network-to-PACS interface.

Direct CP Violation in Charmless Hadronic B-Meson Decays at the PEP-II Asymmetric B-Meson Factory

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

Telnov, Alexandre Valerievich; /UC, Berkeley

2005-05-06

The study of the quark transition b {yields} s{bar s}s, which is a pure loop-level (''penguin'') process leading to several B-meson-decay final states, most notably {phi}K, is arguably the hottest topic in B-meson physics today. The reason is the sensitivity of the amplitudes and the CP-violating asymmetries in such processes to physics beyond the Standard Model. By performing these measurements, we improve our understanding of the phenomenon of combined-parity (CP) violation, which is believed to be responsible for the dominance of matter over antimatter in our Universe. Here, we present measurements of branching fractions and charge asymmetries in the decaysmore » B{sup +} {yields} {phi}K{sup +} and B{sup 0} {yields} {phi}K{sup 0} in a sample of approximately 89 million B{bar B} pairs collected by the BABAR detector at the PEP-II asymmetric-energy B-meson Factory at SLAC. We determine {Beta}(B{sup +} {yields} {phi}K{sup +}) = (10.0{sub -0.8}{sup +0.9} {+-} 0.5) x 10{sup -6} and {Beta}(B{sup 0} {yields} {phi}K{sup 0}) = (8.4{sub -1.3}{sup +1.5} {+-} 0.5) x 10{sup -6}, where the first error is statistical and the second is systematic. Additionally, we measure the CP-violating charge asymmetry {Alpha}{sub CP}(B{sup {+-}} {yields} {phi}K{sup {+-}}) = 0.04 {+-} 0.09 {+-} 0.01, with a 90% confidence-level interval of [-0.10, 0.18], and set an upper limit on the CKM- and color-suppressed decay B{sup +} {yields} {phi}{pi}{sup +}, {Beta}(B{sup +} {yields} {phi}{pi}{sup +}) < 0.41 x 10{sup -6} (at the 90% confidence level). Our results are consistent with the Standard Model, which predicts {Alpha}{sub CP}(B{sup {+-}} {yields} {phi}K{sup {+-}}) {approx}< 1% and {Beta}(B {yields} {phi}{tau}) << 10{sup -7}. Since many models of physics beyond the Standard Model introduce additional loop diagrams with new heavy particles and new CP-violating phases that would contribute to these decays, potentially making {Alpha}{sub CP} (B{sup {+-}} {yields} {phi}K{sup {+-}}) and {Beta}(B {yields} {phi}{pi}) quite large, our results can be used to substantially constrain the parameter spaces of such models.« less

Evaluating the transport layer of the ALFA framework for the Intel® Xeon Phi™ Coprocessor

NASA Astrophysics Data System (ADS)

Santogidis, Aram; Hirstius, Andreas; Lalis, Spyros

2015-12-01

The ALFA framework supports the software development of major High Energy Physics experiments. As part of our research effort to optimize the transport layer of ALFA, we focus on profiling its data transfer performance for inter-node communication on the Intel Xeon Phi Coprocessor. In this article we present the collected performance measurements with the related analysis of the results. The optimization opportunities that are discovered, help us to formulate the future plans of enabling high performance data transfer for ALFA on the Intel Xeon Phi architecture.

Is there a field-theoretic explanation for precursor biopolymers?

PubMed

Rosen, Gerald

2002-08-01

A Hu-Barkana-Gruzinov cold dark matter scalar field phi may enter a weak isospin invariant derivative interaction that causes the flow of right-handed electrons to align parallel to (inverted delta phi). Hence, in the outer regions of galaxies where (inverted delta phi) is large, as in galactic halos, the derivative interaction may induce a chirality-imbued quantum chemistry. Such a chirality-imbued chemistry would in turn be conducive to the formation of abundant precursor biopolymers on interstellar dust grains, comets and meteors in galactic halo regions, with subsequent delivery to planets in the inner galactic regions where phi and (inverted delta phi) are concomitantly near zero and left-right symmetric terrestrial quantum chemistry prevails.

Development of a Deterministic Ethernet Building blocks for Space Applications

NASA Astrophysics Data System (ADS)

Fidi, C.; Jakovljevic, Mirko

2015-09-01

The benefits of using commercially based networking standards and protocols have been widely discussed and are expected to include reduction in overall mission cost, shortened integration and test (I&T) schedules, increased operations flexibility, and hardware and software upgradeability/scalability with developments ongoing in the commercial world. The deterministic Ethernet technology TTEthernet [1] diploid on the NASA Orion spacecraft has demonstrated the use of the TTEthernet technology for a safety critical human space flight application during the Exploration Flight Test 1 (EFT-1). The TTEthernet technology used within the NASA Orion program has been matured for the use within this mission but did not lead to a broader use in space applications or an international space standard. Therefore TTTech has developed a new version which allows to scale the technology for different applications not only the high end missions allowing to decrease the size of the building blocks leading to a reduction of size weight and power enabling the use in smaller applications. TTTech is currently developing a full space products offering for its TTEthernet technology to allow the use in different space applications not restricted to launchers and human spaceflight. A broad space market assessment and the current ESA TRP7594 lead to the development of a space grade TTEthernet controller ASIC based on the ESA qualified Atmel AT1C8RHA95 process [2]. In this paper we will describe our current TTEthernet controller development towards a space qualified network component allowing future spacecrafts to operate in significant radiation environments while using a single onboard network for reliable commanding and data transfer.

Hypophosphataemia after major hepatectomy and the risk of post-operative hepatic insufficiency and mortality: an analysis of 719 patients

PubMed Central

Squires, Malcolm H; Dann, Gregory C; Lad, Neha L; Fisher, Sarah B; Martin, Benjamin M; Kooby, David A; Sarmiento, Juan M; Russell, Maria C; Cardona, Kenneth; Staley, Charles A; Maithel, Shishir K

2014-01-01

Background Hypophosphataemia after a hepatectomy suggests hepatic regeneration. It was hypothesized that the absence of hypophosphataemia is associated with post-operative hepatic insufficiency (PHI) and complications. Methods Patients who underwent a major hepatectomy from 2000–2012 at a single institution were identified. Post-operative serum phosphorus levels were assessed. Primary outcomes were PHI (peak bilirubin >7 mg/dl), major complications, and 30- and 90-day mortality. Results Seven hundred and nineteen out of 749 patients had post-operative phosphorus levels available. PHI and major complications occurred in 63 (8.8%) and 169 (23.5%) patients, respectively. Thirty- and 90-day mortality were 4.0% and 5.4%, respectively. The median phosphorus level on post-operative-day (POD) 2 was 2.2 mg/dl; 231 patients (32.1%) had phosphorus >2.4 on POD2. Patients with POD2 phosphorus >2.4 had a significantly higher incidence of PHI, major complications and mortality. On multivariate analysis, POD2 phosphorus >2.4 remained a significant risk factor for PHI [(hazard ratio HR):1.78; 95% confidence interval (CI):1.02–3.17; P = 0.048], major complications (HR:1.57; 95%CI:1.02–2.47; P = 0.049), 30-day mortality (HR:2.70; 95%CI:1.08–6.76; P = 0.034) and 90-day mortality (HR:2.51; 95%CI:1.03–6.15; P = 0.044). Similarly, patients whose phosphorus level reached nadir after POD3 had higher PHI, major complications and mortality. Conclusion Elevated POD2 phosphorus levels >2.4 mg/dl and a delayed nadir in phosphorus beyond POD3 are associated with increased post-operative hepatic insufficiency, major complications and early mortality. Failure to develop hypophosphataemia within 72 h after a major hepatectomy may reflect insufficient liver remnant regeneration. PMID:24830898

Hypophosphataemia after major hepatectomy and the risk of post-operative hepatic insufficiency and mortality: an analysis of 719 patients.

PubMed

Squires, Malcolm H; Dann, Gregory C; Lad, Neha L; Fisher, Sarah B; Martin, Benjamin M; Kooby, David A; Sarmiento, Juan M; Russell, Maria C; Cardona, Kenneth; Staley, Charles A; Maithel, Shishir K

2014-10-01

Hypophosphataemia after a hepatectomy suggests hepatic regeneration. It was hypothesized that the absence of hypophosphataemia is associated with post-operative hepatic insufficiency (PHI) and complications. Patients who underwent a major hepatectomy from 2000-2012 at a single institution were identified. Post-operative serum phosphorus levels were assessed. Primary outcomes were PHI (peak bilirubin >7 mg/dl), major complications, and 30- and 90-day mortality. Seven hundred and nineteen out of 749 patients had post-operative phosphorus levels available. PHI and major complications occurred in 63 (8.8%) and 169 (23.5%) patients, respectively. Thirty- and 90-day mortality were 4.0% and 5.4%, respectively. The median phosphorus level on post-operative-day (POD) 2 was 2.2 mg/dl; 231 patients (32.1%) had phosphorus >2.4 on POD2. Patients with POD2 phosphorus >2.4 had a significantly higher incidence of PHI, major complications and mortality. On multivariate analysis, POD2 phosphorus >2.4 remained a significant risk factor for PHI [(hazard ratio HR):1.78; 95% confidence interval (CI):1.02-3.17; P = 0.048], major complications (HR:1.57; 95%CI:1.02-2.47; P = 0.049), 30-day mortality (HR:2.70; 95%CI:1.08-6.76; P = 0.034) and 90-day mortality (HR:2.51; 95%CI:1.03-6.15; P = 0.044). Similarly, patients whose phosphorus level reached nadir after POD3 had higher PHI, major complications and mortality. Elevated POD2 phosphorus levels >2.4 mg/dl and a delayed nadir in phosphorus beyond POD3 are associated with increased post-operative hepatic insufficiency, major complications and early mortality. Failure to develop hypophosphataemia within 72 h after a major hepatectomy may reflect insufficient liver remnant regeneration. © 2014 International Hepato-Pancreato-Biliary Association.

Effects of neuropeptides and capsaicin on the canine tracheal vasculature in vivo.

PubMed

Salonen, R O; Webber, S E; Widdicombe, J G

1988-12-01

1. The nonadrenergic, noncholinergic nervous system may control the airway vasculature via various neuropeptides. We have perfused the cranial tracheal arteries of the anaesthetized dog and investigated the effects of neuropeptides and capsaicin (which is supposed to release neuropeptides from sensory nerve endings) on the tracheal vasculature by injecting them locally into the perfusion system. 2. Neurokinin A (NKA, 0.02-20 pmol), calcitonin gene-related peptide (CGRP, 2-200 pmol) and peptide histidine isoleucine (PHI, 0.02-2 nmol) dose-dependently decreased tracheal vascular resistance (Rtv). NKA was 10 and 100 times more potent than CGRP and PHI, respectively. The duration of the response to CGRP was greatly prolonged with larger doses. Galanin (0.2-2 nmol) had no appreciable effect on Rtv. 3. Neuropeptide Y (NPY 0.02-2 nmol) and bombesin (0.02-10 nmol) dose-dependently increased Rtv. However, the dose-response curve for bombesin was bell-shaped suggesting the development of tachyphylaxis with larger doses. In smaller doses, bombesin was twice as potent as NPY. The duration of the response to NPY was prolonged with larger doses. 4. With the exception of PHI no neuropeptide altered tracheal smooth muscle tone; PHI (1 and 2 nmol) caused small dilatations of the trachea. 5. The effects of capsaicin (2-100 nmol) were complex. Usually, the vascular response had two dose-dependent phases: a rapid vasoconstriction followed by a small, longer-lasting vasodilatation. The tracheal smooth muscle response was usually biphasic, a contraction followed by a relaxation. 6. According to previous and present data, the order of potency of the neuropeptides on the canine tracheal vasculature is for the vasodilators : NKA > vasoactive intestinal peptide (VIP) > CGRP > substance P > PHI, and for the vasoconstrictors: bombesin > NPY. The longer-acting neuropeptides (VIP, CGRP and NPY) may be more important than the shorter-acting neuropeptides (substance P, NKA, PHI and bombesin) as regulators of the airway wall blood flow.

Thermal performance testing of two Thales 9310 pulse-tube cryocoolers for PHyTIR

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

Paine, Christopher G.

2014-01-29

PHyTIR is a NASA-funded technology demonstration for a near-term earth-observing instrument in the thermal infrared spectrum, intended for use in the HyspIRI mission. PHyTIR will use two Thales 9310 single-stage pulse tube cryocoolers, one to directly cool the FPA, the other to simulate a passive radiator. We report performance measurements for the two Thales 9310 cryocoolers intended for inclusion in the PHyTIR demonstrator.

Genomic characterization of Ralstonia solanacearum phage phiRSB1, a T7-like wide-host-range phage.

PubMed

Kawasaki, Takeru; Shimizu, Mio; Satsuma, Hideki; Fujiwara, Akiko; Fujie, Makoto; Usami, Shoji; Yamada, Takashi

2009-01-01

PhiRSB1 is a wide-host-range, T7-like bacteriophage that infects and efficiently lyses the phytopathogenic bacterium Ralstonia solanacearum. The phiRSB1 genome comprises 43,079 bp of double-stranded DNA (61.7% G+C) with 325-bp terminal repeats and contains 47 open reading frames. Strong activity of tandem early promoters and wide specificity of phage promoters of phiRSB1 were demonstrated.

[The value of PHI/PCA3 in the early diagnosis of prostate cancer].

PubMed

Tan, S J; Xu, L W; Xu, Z; Wu, J P; Liang, K; Jia, R P

2016-01-12

To investigate the value of prostate health index (PHI) and prostate cancer gene 3 (PCA3) in the early diagnosis of prostate cancer (PCa). A total of 190 patients with abnormal serum prostate specific antigen (PSA) or abnormal digital rectal examination were enrolled. They were all underwent initial biopsy and 11 of them were also underwent repeated biopsy. In addition, 25 healthy cases (with normal digital rectal examination and PSA<4 ng/ml) were the control group.The PHI and PCA3 were detected by using immunofluorescence and Loop-Mediated Isothermal Amplification (LAMP). The sensitivity and specificity of diagnosis were determined by ROC curve.In addition, the relationship between PHI/PSA and the Gleason score and clinical stage were analyzed. A total of 89 patients were confirmed PCa by Pathological diagnosis. The other 101 patients were diagnosed as benign prostatic hyperplasia (BPH). The sensitivity and specificity of PCA3 test were 85.4% was 92.1%. Area under curve (AUC) of PHI is higher than AUC of PSA (0.727>0.699). The PHI in peripheral blood was positively correlated with Gleason score and clinical stage. The detection of PCA3 and PHI shows excellent detecting effectiveness. Compared with single PSA, the combined detection of PHI and PCA3 improved the diagnostic specificity. It can provide a new method for the early diagnosis in prostate cancer and avoid unnecessary biopsies.

Genome packaging in EL and Lin68, two giant phiKZ-like bacteriophages of P. aeruginosa

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

Sokolova, O.S., E-mail: sokolova@mail.bio.msu.ru; A.V. Shoubnikov Institute of Crystallography RAS, Moscow; Shaburova, O.V.

A unique feature of the Pseudomonas aeruginosa giant phage phiKZ is its way of genome packaging onto a spool-like protein structure, the inner body. Until recently, no similar structures have been detected in other phages. We have studied DNA packaging in P. aeruginosa phages EL and Lin68 using cryo-electron microscopy and revealed the presence of inner bodies. The shape and positioning of the inner body and the density of the DNA packaging in EL are different from those found in phiKZ and Lin68. This internal organization explains how the shorter EL genome is packed into a large EL capsid, whichmore » has the same external dimensions as the capsids of phiKZ and Lin68. The similarity in the structural organization in EL and other phiKZ-like phages indicates that EL is phylogenetically related to other phiKZ-like phages, and, despite the lack of detectable DNA homology, EL, phiKZ, and Lin68 descend from a common ancestor. - Highlights: • We performed a comparative structural study of giant P. aeruginosa phages: EL, Lin68 and phiKZ. • We revealed that the inner body is a common feature in giant phages. • The phage genome size correlates with the overall dimensions of the inner body.« less

Expression, purification and characterization of a phyAm-phyCs fusion phytase*

PubMed Central

Zou, Li-kou; Wang, Hong-ning; Pan, Xin; Tian, Guo-bao; Xie, Zi-wen; Wu, Qi; Chen, Hui; Xie, Tao; Yang, Zhi-rong

2008-01-01

The phyAm gene encoding acid phytase and optimized neutral phytase phyCs gene were inserted into expression vector pPIC9K in correct orientation and transformed into Pichia pastoris in order to expand the pH profile of phytase and decrease the cost of production. The fusion phytase phyAm-phyCs gene was successfully overexpressed in P. pastoris as an active and extracellular phytase. The yield of total extracellular fusion phytase activity is (25.4±0.53) U/ml at the flask scale and (159.1±2.92) U/ml for high cell-density fermentation, respectively. Purified fusion phytase exhibits an optimal temperature at 55 °C and an optimal pH at 5.5~6.0 and its relative activity remains at a relatively high level of above 70% in the range of pH 2.0 to 7.0. About 51% to 63% of its original activity remains after incubation at 75 °C to 95 °C for 10 min. Due to heavy glycosylation, the expressed fusion phytase shows a broad and diffuse band in SDS-PAGE (sodium dodecyl sulfate-polyacrylamide gel electrophoresis). After deglycosylation by endoglycosidase H (EndoHf), the enzyme has an apparent molecular size of 95 kDa. The characterization of the fusion phytase was compared with those of phyCs and phyAm. PMID:18600783

PhiC31 recombination system demonstrates heritable germinal transmission of site-specific excision from the Arabidopsis genome

PubMed Central

2010-01-01

Background The large serine recombinase phiC31 from broad host range Streptomyces temperate phage, catalyzes the site-specific recombination of two recognition sites that differ in sequence, typically known as attachment sites attB and attP. Previously, we characterized the phiC31 catalytic activity and modes of action in the fission yeast Schizosaccharomyces pombe. Results In this work, the phiC31 recombinase gene was placed under the control of the Arabidopsis OXS3 promoter and introduced into Arabidopsis harboring a chromosomally integrated attB and attP-flanked target sequence. The phiC31 recombinase excised the attB and attP-flanked DNA, and the excision event was detected in subsequent generations in the absence of the phiC31 gene, indicating germinal transmission was possible. We further verified that the genomic excision was conservative and that introduction of a functional recombinase can be achieved through secondary transformation as well as manual crossing. Conclusion The phiC31 system performs site-specific recombination in germinal tissue, a prerequisite for generating stable lines with unwanted DNA removed. The precise site-specific deletion by phiC31 in planta demonstrates that the recombinase can be used to remove selectable markers or other introduced transgenes that are no longer desired and therefore can be a useful tool for genome engineering in plants. PMID:20178628

SuperPhy: predictive genomics for the bacterial pathogen Escherichia coli.

PubMed

Whiteside, Matthew D; Laing, Chad R; Manji, Akiff; Kruczkiewicz, Peter; Taboada, Eduardo N; Gannon, Victor P J

2016-04-12

Predictive genomics is the translation of raw genome sequence data into a phenotypic assessment of the organism. For bacterial pathogens, these phenotypes can range from environmental survivability, to the severity of human disease. Significant progress has been made in the development of generic tools for genomic analyses that are broadly applicable to all microorganisms; however, a fundamental missing component is the ability to analyze genomic data in the context of organism-specific phenotypic knowledge, which has been accumulated from decades of research and can provide a meaningful interpretation of genome sequence data. In this study, we present SuperPhy, an online predictive genomics platform ( http://lfz.corefacility.ca/superphy/ ) for Escherichia coli. The platform integrates the analytical tools and genome sequence data for all publicly available E. coli genomes and facilitates the upload of new genome sequences from users under public or private settings. SuperPhy provides real-time analyses of thousands of genome sequences with results that are understandable and useful to a wide community, including those in the fields of clinical medicine, epidemiology, ecology, and evolution. SuperPhy includes identification of: 1) virulence and antimicrobial resistance determinants 2) statistical associations between genotypes, biomarkers, geospatial distribution, host, source, and phylogenetic clade; 3) the identification of biomarkers for groups of genomes on the based presence/absence of specific genomic regions and single-nucleotide polymorphisms and 4) in silico Shiga-toxin subtype. SuperPhy is a predictive genomics platform that attempts to provide an essential link between the vast amounts of genome information currently being generated and phenotypic knowledge in an organism-specific context.

The Effect of Curcumin on Intracellular pH (pHi), Membrane Hyperpolarization and Sperm Motility.

PubMed

Naz, Rajesh K

2014-04-01

Curcumin has shown to affect sperm motility and function in vitro and fertility in vivo. The molecular mechanism(s) by which curcumin affects sperm motility has not been delineated. Since modulation of intracellular pH (pHi) and plasma membrane polarization is involved in sperm motility, the present study was conducted to investigate the effect of curcumin on these sperm (human and murine) parameters. The effect of curcumin on sperm forward motility was examined by counting percentages of forward moving sperm. The effect of curcumin on intracellular pH (pHi) was measured by the fluorescent pH indicator 2,7-bicarboxyethyl-5,6-carboxyfluorescein-acetoxymethyl ester (BCECF-AM). The effect of curcumin on plasma membrane polarization was examined using the fluorescence sensitive dye bis (1,3-dibarbituric acid)-trimethine oxanol [DiBAC4(3)]. Curcumin caused a concentration-dependent (p<0.05) decrease in forward motility of both human and mouse sperm. It also caused a concentration-dependent decrease in intracellular pH (pHi) in both human and mouse sperm. Curcumin induced significant (p<0.05) hyperpolarization of the plasma membrane in both human and mouse sperm. These findings indicate that curcumin inhibits sperm forward motility by intracellular acidification and hyperpolarization of sperm plasma membrane. This is the first study to our knowledge which examined the effect of curcumin on sperm pHi and membrane polarization that affect sperm forward motility. These exciting findings will have application in deciphering the signal transduction pathway involved in sperm motility and function and in development of a novel non-steroidal contraceptive for infertility.

PhiSiGns: an online tool to identify signature genes in phages and design PCR primers for examining phage diversity.

PubMed

Dwivedi, Bhakti; Schmieder, Robert; Goldsmith, Dawn B; Edwards, Robert A; Breitbart, Mya

2012-03-04

Phages (viruses that infect bacteria) have gained significant attention because of their abundance, diversity and important ecological roles. However, the lack of a universal gene shared by all phages presents a challenge for phage identification and characterization, especially in environmental samples where it is difficult to culture phage-host systems. Homologous conserved genes (or "signature genes") present in groups of closely-related phages can be used to explore phage diversity and define evolutionary relationships amongst these phages. Bioinformatic approaches are needed to identify candidate signature genes and design PCR primers to amplify those genes from environmental samples; however, there is currently no existing computational tool that biologists can use for this purpose. Here we present PhiSiGns, a web-based and standalone application that performs a pairwise comparison of each gene present in user-selected phage genomes, identifies signature genes, generates alignments of these genes, and designs potential PCR primer pairs. PhiSiGns is available at (http://www.phantome.org/phisigns/; http://phisigns.sourceforge.net/) with a link to the source code. Here we describe the specifications of PhiSiGns and demonstrate its application with a case study. PhiSiGns provides phage biologists with a user-friendly tool to identify signature genes and design PCR primers to amplify related genes from uncultured phages in environmental samples. This bioinformatics tool will facilitate the development of novel signature genes for use as molecular markers in studies of phage diversity, phylogeny, and evolution.

PhiSiGns: an online tool to identify signature genes in phages and design PCR primers for examining phage diversity

PubMed Central

2012-01-01

Background Phages (viruses that infect bacteria) have gained significant attention because of their abundance, diversity and important ecological roles. However, the lack of a universal gene shared by all phages presents a challenge for phage identification and characterization, especially in environmental samples where it is difficult to culture phage-host systems. Homologous conserved genes (or "signature genes") present in groups of closely-related phages can be used to explore phage diversity and define evolutionary relationships amongst these phages. Bioinformatic approaches are needed to identify candidate signature genes and design PCR primers to amplify those genes from environmental samples; however, there is currently no existing computational tool that biologists can use for this purpose. Results Here we present PhiSiGns, a web-based and standalone application that performs a pairwise comparison of each gene present in user-selected phage genomes, identifies signature genes, generates alignments of these genes, and designs potential PCR primer pairs. PhiSiGns is available at (http://www.phantome.org/phisigns/; http://phisigns.sourceforge.net/) with a link to the source code. Here we describe the specifications of PhiSiGns and demonstrate its application with a case study. Conclusions PhiSiGns provides phage biologists with a user-friendly tool to identify signature genes and design PCR primers to amplify related genes from uncultured phages in environmental samples. This bioinformatics tool will facilitate the development of novel signature genes for use as molecular markers in studies of phage diversity, phylogeny, and evolution. PMID:22385976

Evaluating the Applicability of Phi Coefficient in Indicating Habitat Preferences of Forest Soil Fauna Based on a Single Field Study in Subtropical China.

PubMed

Cui, Yang; Wang, Silong; Yan, Shaokui

2016-01-01

Phi coefficient directly depends on the frequencies of occurrence of organisms and has been widely used in vegetation ecology to analyse the associations of organisms with site groups, providing a characterization of ecological preference, but its application in soil ecology remains rare. Based on a single field experiment, this study assessed the applicability of phi coefficient in indicating the habitat preferences of soil fauna, through comparing phi coefficient-induced results with those of ordination methods in charactering soil fauna-habitat(factors) relationships. Eight different habitats of soil fauna were implemented by reciprocal transfer of defaunated soil cores between two types of subtropical forests. Canonical correlation analysis (CCorA) showed that ecological patterns of fauna-habitat relationships and inter-fauna taxa relationships expressed, respectively, by phi coefficients and predicted abundances calculated from partial redundancy analysis (RDA), were extremely similar, and a highly significant relationship between the two datasets was observed (Pillai's trace statistic = 1.998, P = 0.007). In addition, highly positive correlations between phi coefficients and predicted abundances for Acari, Collembola, Nematode and Hemiptera were observed using linear regression analysis. Quantitative relationships between habitat preferences and soil chemical variables were also obtained by linear regression, which were analogous to the results displayed in a partial RDA biplot. Our results suggest that phi coefficient could be applicable on a local scale in evaluating habitat preferences of soil fauna at coarse taxonomic levels, and that the phi coefficient-induced information, such as ecological preferences and the associated quantitative relationships with habitat factors, will be largely complementary to the results of ordination methods. The application of phi coefficient in soil ecology may extend our knowledge about habitat preferences and distribution-abundance relationships, which will benefit the understanding of biodistributions and variations in community compositions in the soil. Similar studies in other places and scales apart from our local site will be need for further evaluation of phi coefficient.

Evaluating the Applicability of Phi Coefficient in Indicating Habitat Preferences of Forest Soil Fauna Based on a Single Field Study in Subtropical China

PubMed Central

Cui, Yang; Wang, Silong; Yan, Shaokui

2016-01-01

Phi coefficient directly depends on the frequencies of occurrence of organisms and has been widely used in vegetation ecology to analyse the associations of organisms with site groups, providing a characterization of ecological preference, but its application in soil ecology remains rare. Based on a single field experiment, this study assessed the applicability of phi coefficient in indicating the habitat preferences of soil fauna, through comparing phi coefficient-induced results with those of ordination methods in charactering soil fauna-habitat(factors) relationships. Eight different habitats of soil fauna were implemented by reciprocal transfer of defaunated soil cores between two types of subtropical forests. Canonical correlation analysis (CCorA) showed that ecological patterns of fauna-habitat relationships and inter-fauna taxa relationships expressed, respectively, by phi coefficients and predicted abundances calculated from partial redundancy analysis (RDA), were extremely similar, and a highly significant relationship between the two datasets was observed (Pillai's trace statistic = 1.998, P = 0.007). In addition, highly positive correlations between phi coefficients and predicted abundances for Acari, Collembola, Nematode and Hemiptera were observed using linear regression analysis. Quantitative relationships between habitat preferences and soil chemical variables were also obtained by linear regression, which were analogous to the results displayed in a partial RDA biplot. Our results suggest that phi coefficient could be applicable on a local scale in evaluating habitat preferences of soil fauna at coarse taxonomic levels, and that the phi coefficient-induced information, such as ecological preferences and the associated quantitative relationships with habitat factors, will be largely complementary to the results of ordination methods. The application of phi coefficient in soil ecology may extend our knowledge about habitat preferences and distribution-abundance relationships, which will benefit the understanding of biodistributions and variations in community compositions in the soil. Similar studies in other places and scales apart from our local site will be need for further evaluation of phi coefficient. PMID:26930593

Evidence for the role of a Na(+)/HCO(3)(-) cotransporter in trout hepatocyte pHi regulation.

PubMed

Furimsky, M; Moon, T W; Perry, S F

2000-07-01

The mechanisms of intracellular pH (pHi) regulation were examined in hepatocytes of the rainbow trout Oncorhynchus mykiss. pHi was monitored using the pH-sensitive fluorescent dye BCECF, and the effects of various media and pharmacological agents were examined for their influence on baseline pHi and recovery rates from acid and base loading. Rates of Na(+) uptake were measured using (22)Na, and changes in membrane potential were examined using the potentiometric fluorescent dye Oxonol VI. The rate of proton extrusion following acid loading was diminished by the blockade of either Na(+)/H(+) exchange (using amiloride) or anion transport (using DIDS). The removal of external HCO(3)(-) and the abolition of outward K(+) diffusion by the channel blocker Ba(2+) also decreased the rate of proton extrusion following acid load. Depolarization of the cell membrane with 50 mmol l(-)(1) K(+), however, did not affect pHi. The rate of recovery from base loading was significantly diminished by the blockade of anion transport, removal of external HCO(3)(-) and, to a lesser extent, by blocking Na(+)/H(+) exchange. The blockade of K(+) conductance had no effect. The decrease in Na(+) uptake rate observed in the presence of the anion transport blocker DIDS and the DIDS-sensitive hyperpolarization of membrane potential during recovery from acid loading suggest that a Na(+)-dependent electrogenic transport system is involved in the restoration of pHi after intracellular acidification. The effects on baseline pHi indicate that the different membrane exchangers are tonically active in the maintenance of steady-state pHi. This study confirms the roles of a Na(+)/H(+) exchanger and a Cl(-)/HCO(3)(-) exchanger in the regulation of trout hepatocyte pHi and provides new evidence that a Na(+)/HCO(3)(-) cotransporter contributes to pHi regulation.

Intracellular pH regulation by acid-base transporters in mammalian neurons

PubMed Central

Ruffin, Vernon A.; Salameh, Ahlam I.; Boron, Walter F.; Parker, Mark D.

2014-01-01

Intracellular pH (pHi) regulation in the brain is important in both physiological and physiopathological conditions because changes in pHi generally result in altered neuronal excitability. In this review, we will cover 4 major areas: (1) The effect of pHi on cellular processes in the brain, including channel activity and neuronal excitability. (2) pHi homeostasis and how it is determined by the balance between rates of acid loading (JL) and extrusion (JE). The balance between JE and JL determine steady-state pHi, as well as the ability of the cell to defend pHi in the face of extracellular acid-base disturbances (e.g., metabolic acidosis). (3) The properties and importance of members of the SLC4 and SLC9 families of acid-base transporters expressed in the brain that contribute to JL (namely the Cl-HCO3 exchanger AE3) and JE (the Na-H exchangers NHE1, NHE3, and NHE5 as well as the Na+- coupled HCO3− transporters NBCe1, NBCn1, NDCBE, and NBCn2). (4) The effect of acid-base disturbances on neuronal function and the roles of acid-base transporters in defending neuronal pHi under physiopathologic conditions. PMID:24592239

Comparative evaluation of urinary PCA3 and TMPRSS2: ERG scores and serum PHI in predicting prostate cancer aggressiveness.

PubMed

Tallon, Lucile; Luangphakdy, Devillier; Ruffion, Alain; Colombel, Marc; Devonec, Marian; Champetier, Denis; Paparel, Philippe; Decaussin-Petrucci, Myriam; Perrin, Paul; Vlaeminck-Guillem, Virginie

2014-07-30

It has been suggested that urinary PCA3 and TMPRSS2:ERG fusion tests and serum PHI correlate to cancer aggressiveness-related pathological criteria at prostatectomy. To evaluate and compare their ability in predicting prostate cancer aggressiveness, PHI and urinary PCA3 and TMPRSS2:ERG (T2) scores were assessed in 154 patients who underwent radical prostatectomy for biopsy-proven prostate cancer. Univariate and multivariate analyses using logistic regression and decision curve analyses were performed. All three markers were predictors of a tumor volume≥0.5 mL. Only PHI predicted Gleason score≥7. T2 score and PHI were both independent predictors of extracapsular extension(≥pT3), while multifocality was only predicted by PCA3 score. Moreover, when compared to a base model (age, digital rectal examination, serum PSA, and Gleason sum at biopsy), the addition of both PCA3 score and PHI to the base model induced a significant increase (+12%) when predicting tumor volume>0.5 mL. PHI and urinary PCA3 and T2 scores can be considered as complementary predictors of cancer aggressiveness at prostatectomy.

Bacteriophage phi 6 RNA-dependent RNA polymerase: molecular details of initiating nucleic acid synthesis without primer.

PubMed

Laurila, Minni R L; Makeyev, Eugene V; Bamford, Dennis H

2002-05-10

Like most RNA polymerases, the polymerase of double-strand RNA bacteriophage phi6 (phi6pol) is capable of primer-independent initiation. Based on the recently solved phi6pol initiation complex structure, a four-amino acid-long loop (amino acids 630-633) has been suggested to stabilize the first two incoming NTPs through stacking interactions with tyrosine, Tyr(630). A similar loop is also present in the hepatitis C virus polymerase, another enzyme capable of de novo initiation. Here, we use a series of phi6pol mutants to address the role of this element. As predicted, mutants at the Tyr(630) position are inefficient in initiation de novo. Unexpectedly, when the loop is disordered by changing Tyr(630)-Lys(631)-Trp(632) to GSG, phi6pol becomes a primer-dependent enzyme, either extending complementary oligonucleotide or, when the template 3' terminus can adopt a hairpin-like conformation, utilizing a "copy-back" initiation mechanism. In contrast to the wild-type phi6pol, the GSG mutant does not require high GTP concentration for its optimal activity. These findings suggest a general model for the initiation of de novo RNA synthesis.

77 FR 71172 - Proposed Collection; Comment Request

Federal Register 2010, 2011, 2012, 2013, 2014

2012-11-29

... beneficiaries on their TRICARE benefits. Personal health information (PHI) and personally identifiable.../PHI to obtain and verify TRICARE eligibility, treatment, payment, and other healthcare operations... during the case resolution process, individuals may object to the collection of PHI and PII via verbal or...

Spectral observations of Be stars in the visible range. I - Phi Per, Psi Per, 11 Cam, and Phi And

NASA Astrophysics Data System (ADS)

Krugov, V. D.

1986-02-01

Phi Per was found to display considerable variations of emission in H-alpha and H-beta. The H-alpha and H-beta emission profiles of Psi Per appeared to vary with a period of several years. A complete disappearance of H-alpha emission was observed for 11 Cam. Finally, the H-alpha emission for Phi And did not display intensity variations during the entire period of observations in 1983.

The Effects of Exercise on Pharmacokinetics and Pharmacodynamics of Physostigmine in Rats

DTIC Science & Technology

1989-02-15

Phy ( cholinesterase activity ) are likely to be altered by exercise due to altered blood flow rates to liver and pH of muscle. During exercise...concurrent acute exercise on the ChE activity in RBC aad tissues and in blood biochemical parameters in rats. Phy has been reported to reduce the...Springfield, Illinois. Also, we have studied the effect of exercise training, Phy and training + Phy on ChE activity in RBC and tissues and on blood biochemi

Implementation of the beamline controls at the Florence accelerator laboratory

NASA Astrophysics Data System (ADS)

Carraresi, L.; Mirto, F. A.

2008-05-01

The new Tandetron accelerator in Florence, with many different beamlines, has required a new organization of all the control signals of the used equipment (slow control). We present our solution, which allows us the control of all the employed instruments simultaneously from a number of different workplaces. All of our equipment has been designed to be Ethernet based and this is the key to accomplish two very important requirements: simultaneous remote control from many computers and electrical isolation to achieve a lower noise level. The control of the instruments requires only one Ethernet network and no particular interfaces or drivers on the computers.

A Systematic Scheme for Multiple Access in Ethernet Passive Optical Access Networks

NASA Astrophysics Data System (ADS)

Ma, Maode; Zhu, Yongqing; Hiang Cheng, Tee

2005-11-01

While backbone networks have experienced substantial changes in the last decade, access networks have not changed much. Recently, passive optical networks (PONs) seem to be ready for commercial deployment as access networks, due to the maturity of a number of enabling technologies. Among the PON technologies, Ethernet PON (EPON) standardized by the IEEE 802.3ah Ethernet in the First Mile (EFM) Task Force is the most attractive one because of its high speed, low cost, familiarity, interoperability, and low overhead. In this paper, we consider the issue of upstream channel sharing in the EPONs. We propose a novel multiple-access control scheme to provide bandwidth-guaranteed service for high-demand customers, while providing best effort service to low-demand customers according to the service level agreement (SLA). The analytical and simulation results prove that the proposed scheme performs best in what it is designed to do compared to another well-known scheme that has not considered providing differentiated services. With business customers preferring premium services with guaranteed bandwidth and residential users preferring low-cost best effort services, our scheme could benefit both groups of subscribers, as well as the operators.

PHI and PCA3 improve the prognostic performance of PRIAS and Epstein criteria in predicting insignificant prostate cancer in men eligible for active surveillance.

PubMed

Cantiello, Francesco; Russo, Giorgio Ivan; Cicione, Antonio; Ferro, Matteo; Cimino, Sebastiano; Favilla, Vincenzo; Perdonà, Sisto; De Cobelli, Ottavio; Magno, Carlo; Morgia, Giuseppe; Damiano, Rocco

2016-04-01

To assess the performance of prostate health index (PHI) and prostate cancer antigen 3 (PCA3) when added to the PRIAS or Epstein criteria in predicting the presence of pathologically insignificant prostate cancer (IPCa) in patients who underwent radical prostatectomy (RP) but eligible for active surveillance (AS). An observational retrospective study was performed in 188 PCa patients treated with laparoscopic or robot-assisted RP but eligible for AS according to Epstein or PRIAS criteria. Blood and urinary specimens were collected before initial prostate biopsy for PHI and PCA3 measurements. Multivariate logistic regression analyses and decision curve analysis were carried out to identify predictors of IPCa using the updated ERSPC definition. At the multivariate analyses, the inclusion of both PCA3 and PHI significantly increased the accuracy of the Epstein multivariate model in predicting IPCa with an increase of 17 % (AUC = 0.77) and of 32 % (AUC = 0.92), respectively. The inclusion of both PCA3 and PHI also increased the predictive accuracy of the PRIAS multivariate model with an increase of 29 % (AUC = 0.87) and of 39 % (AUC = 0.97), respectively. DCA revealed that the multivariable models with the addition of PHI or PCA3 showed a greater net benefit and performed better than the reference models. In a direct comparison, PHI outperformed PCA3 performance resulting in higher net benefit. In a same cohort of patients eligible for AS, the addition of PHI and PCA3 to Epstein or PRIAS models improved their prognostic performance. PHI resulted in greater net benefit in predicting IPCa compared to PCA3.

Distinct moieties underlie biphasic H+ gating of connexin43 channels, producing a pH optimum for intercellular communication

PubMed Central

Garciarena, Carolina D.; Malik, Akif; Swietach, Pawel; Moreno, Alonso P.; Vaughan-Jones, Richard D.

2018-01-01

Most mammalian cells can intercommunicate via connexin-assembled, gap-junctional channels. To regulate signal transmission, connexin (Cx) channel permeability must respond dynamically to physiological and pathophysiological stimuli. One key stimulus is intracellular pH (pHi), which is modulated by a tissue’s metabolic and perfusion status. Our understanding of the molecular mechanism of H+ gating of Cx43 channels—the major isoform in the heart and brain—is incomplete. To interrogate the effects of acidic and alkaline pHi on Cx43 channels, we combined voltage-clamp electrophysiology with pHi imaging and photolytic H+ uncaging, performed over a range of pHi values. We demonstrate that Cx43 channels expressed in HeLa or N2a cell pairs are gated biphasically by pHi via a process that consists of activation by H+ ions at alkaline pHi and inhibition at more acidic pHi. For Cx43 channel–mediated solute/ion transmission, the ensemble of these effects produces a pHi optimum, near resting pHi. By using Cx43 mutants, we demonstrate that alkaline gating involves cysteine residues of the C terminus and is independent of motifs previously implicated in acidic gating. Thus, we present a molecular mechanism by which cytoplasmic acid–base chemistry fine tunes intercellular communication and establishes conditions for the optimal transmission of solutes and signals in tissues, such as the heart and brain.—Garciarena, C. D., Malik, A., Swietach, P., Moreno, A. P., Vaughan-Jones, R. D. Distinct moieties underlie biphasic H+ gating of connexin43 channels, producing a pH optimum for intercellular communication. PMID:29183963

Prostate health index (phi) and prostate cancer antigen 3 (PCA3) significantly improve diagnostic accuracy in patients undergoing prostate biopsy.

PubMed

Perdonà, Sisto; Bruzzese, Dario; Ferro, Matteo; Autorino, Riccardo; Marino, Ada; Mazzarella, Claudia; Perruolo, Giuseppe; Longo, Michele; Spinelli, Rosa; Di Lorenzo, Giuseppe; Oliva, Andrea; De Sio, Marco; Damiano, Rocco; Altieri, Vincenzo; Terracciano, Daniela

2013-02-15

Prostate health index (phi) and prostate cancer antigen 3 (PCA3) have been recently proposed as novel biomarkers for prostate cancer (PCa). We assessed the diagnostic performance of these biomarkers, alone or in combination, in men undergoing first prostate biopsy for suspicion of PCa. One hundred sixty male subjects were enrolled in this prospective observational study. PSA molecular forms, phi index (Beckman coulter immunoassay), PCA3 score (Progensa PCA3 assay), and other established biomarkers (tPSA, fPSA, and %fPSA) were assessed before patients underwent a 18-core first prostate biopsy. The discriminating ability between PCa-negative and PCa-positive biopsies of Beckman coulter phi and PCA3 score and other used biomarkers were determined. One hundred sixty patients met inclusion criteria. %p2PSA (p2PSA/fPSA × 100), phi and PCA3 were significantly higher in patients with PCa compared to PCa-negative group (median values: 1.92 vs. 1.55, 49.97 vs. 36.84, and 50 vs. 32, respectively, P ≤ 0.001). ROC curve analysis showed that %p2PSA, phi, and PCA3 are good indicator of malignancy (AUCs = 0.68, 0.71, and 0.66, respectively). A multivariable logistic regression model consisting of both the phi index and PCA3 score allowed to reach an overall diagnostic accuracy of 0.77. Decision curve analysis revealed that this "combined" marker achieved the highest net benefit over the examined range of the threshold probability. phi and PCA3 showed no significant difference in the ability to predict PCa diagnosis in men undergoing first prostate biopsy. However, diagnostic performance is significantly improved by combining phi and PCA3. Copyright © 2012 Wiley Periodicals, Inc.

Effects of plasmalemmal V-ATPase activity on plasma membrane potential of resident alveolar macrophages.

PubMed

Heming, T A; Bidani, A

2003-01-01

The acid-base status and functional responses of alveolar macrophages (mphi) are influenced by the activity of plasmalemmal V-type H+-pump (V-ATPase), an electrogenic H+ extruder that provides a possible link between intracellular pH (pHi) and plasma membrane potential (Em). This study examined the relationships among Em, pHi, and plasmalemmal V-ATPase activity in resident alveolar mphi from rabbits. Em and pHi were measured using fluorescent probes. Em was -46 mV and pHi was 7.14 at an extracellular pH (pHo) of 7.4. The pHi declined progressively at lower pHo values. Decrements in pHo, also caused depolarization of the plasma membrane, independent of V-ATPase activity. The pH effects on Em were sensitive to external K+, and hence, probably involved pH-sensitive K+ conductance. H+ were not distributed at equilibrium across the plasma membrane. V-ATPase activity was a major determinant of the transmembrane H+ disequilibrium. Pump inhibition with bafilomycin A1 caused cytosolic acidification, due most likely to the retention of metabolically generated H+. V-ATPase inhibition also caused depolarization of the plasma membrane, but the effects were mediated indirectly via the accompanying pHi changes. V-ATPase activity was sensitive to Em. Em hyperpolarization (valinomycin-clamp) reduced V-ATPase activity, causing an acidic shift in baseline pHi under steady-state conditions and slowing pHi recovery from NH4Cl prepulse acid-loads. The findings indicate that a complex relationship exists among Em, pHi, and pHo that was partially mediated by plasmalemmal V-ATPase activity. This relationship could have important consequences for the expression of pH- and/or voltage-sensitive functions in alveolar mphi.

User perception and interpretation of tornado probabilistic hazard information: Comparison of four graphical designs.

PubMed

Miran, Seyed M; Ling, Chen; James, Joseph J; Gerard, Alan; Rothfusz, Lans

2017-11-01

Effective design for presenting severe weather information is important to reduce devastating consequences of severe weather. The Probabilistic Hazard Information (PHI) system for severe weather is being developed by NOAA National Severe Storms Laboratory (NSSL) to communicate probabilistic hazardous weather information. This study investigates the effects of four PHI graphical designs for tornado threat, namely, "four-color"," red-scale", "grayscale" and "contour", on users' perception, interpretation, and reaction to threat information. PHI is presented on either a map background or a radar background. Analysis showed that the accuracy was significantly higher and response time faster when PHI was displayed on map background as compared to radar background due to better contrast. When displayed on a radar background, "grayscale" design resulted in a higher accuracy of responses. Possibly due to familiarity, participants reported four-color design as their favorite design, which also resulted in the fastest recognition of probability levels on both backgrounds. Our study shows the importance of using intuitive color-coding and sufficient contrast in conveying probabilistic threat information via graphical design. We also found that users follows a rational perceiving-judging-feeling-and acting approach in processing probabilistic hazard information for tornado. Copyright © 2017 Elsevier Ltd. All rights reserved.

Computational prediction of virus-human protein-protein interactions using embedding kernelized heterogeneous data.

PubMed

Nourani, Esmaeil; Khunjush, Farshad; Durmuş, Saliha

2016-05-24

Pathogenic microorganisms exploit host cellular mechanisms and evade host defense mechanisms through molecular pathogen-host interactions (PHIs). Therefore, comprehensive analysis of these PHI networks should be an initial step for developing effective therapeutics against infectious diseases. Computational prediction of PHI data is gaining increasing demand because of scarcity of experimental data. Prediction of protein-protein interactions (PPIs) within PHI systems can be formulated as a classification problem, which requires the knowledge of non-interacting protein pairs. This is a restricting requirement since we lack datasets that report non-interacting protein pairs. In this study, we formulated the "computational prediction of PHI data" problem using kernel embedding of heterogeneous data. This eliminates the abovementioned requirement and enables us to predict new interactions without randomly labeling protein pairs as non-interacting. Domain-domain associations are used to filter the predicted results leading to 175 novel PHIs between 170 human proteins and 105 viral proteins. To compare our results with the state-of-the-art studies that use a binary classification formulation, we modified our settings to consider the same formulation. Detailed evaluations are conducted and our results provide more than 10 percent improvements for accuracy and AUC (area under the receiving operating curve) results in comparison with state-of-the-art methods.

Fast CPU-based Monte Carlo simulation for radiotherapy dose calculation.

PubMed

Ziegenhein, Peter; Pirner, Sven; Ph Kamerling, Cornelis; Oelfke, Uwe

2015-08-07

Monte-Carlo (MC) simulations are considered to be the most accurate method for calculating dose distributions in radiotherapy. Its clinical application, however, still is limited by the long runtimes conventional implementations of MC algorithms require to deliver sufficiently accurate results on high resolution imaging data. In order to overcome this obstacle we developed the software-package PhiMC, which is capable of computing precise dose distributions in a sub-minute time-frame by leveraging the potential of modern many- and multi-core CPU-based computers. PhiMC is based on the well verified dose planning method (DPM). We could demonstrate that PhiMC delivers dose distributions which are in excellent agreement to DPM. The multi-core implementation of PhiMC scales well between different computer architectures and achieves a speed-up of up to 37[Formula: see text] compared to the original DPM code executed on a modern system. Furthermore, we could show that our CPU-based implementation on a modern workstation is between 1.25[Formula: see text] and 1.95[Formula: see text] faster than a well-known GPU implementation of the same simulation method on a NVIDIA Tesla C2050. Since CPUs work on several hundreds of GB RAM the typical GPU memory limitation does not apply for our implementation and high resolution clinical plans can be calculated.

X-Phi and Carnapian Explication

PubMed Central

Shepherd, Joshua; Justus, James

2015-01-01

The rise of experimental philosophy (x-phi) has placed metaphilosophical questions, particularly those concerning concepts, at the center of philosophical attention. X-phi offers empirically rigorous methods for identifying conceptual content, but what exactly it contributes towards evaluating conceptual content remains unclear. We show how x-phi complements Rudolf Carnap’s underappreciated methodology for concept determination, explication. This clarifies and extends x-phi’s positive philosophical import, and also exhibits explication’s broad appeal. But there is a potential problem: Carnap’s account of explication was limited to empirical and logical concepts, but many concepts of interest to philosophers (experimental and otherwise) are essentially normative. With formal epistemology as a case study, we show how x-phi assisted explication can apply to normative domains. PMID:26345713

The Johns Hopkins Medical Institutions' Premise Distribution Plan

PubMed Central

Barta, Wendy; Buckholtz, Howard; Johnston, Mark; Lenhard, Raymond; Tolchin, Stephen; Vienne, Donald

1987-01-01

A Premise Distribution Plan is being developed to address the growing voice and data communications needs at Johns Hopkins Medical Institutions. More specifically, the use of a rapidly expanding Ethernet computer network and a new Integrated Services Digital Network (ISDN) Digital Centrex system must be planned to provide easy, reliable and cost-effective data and voice communications services. Existing Premise Distribution Systems are compared along with voice and data technologies which would use them.

Advanced On-the-Job Training System: System Specification

DTIC Science & Technology

1990-05-01

3.1.5.2.10 Evaluation Subsystem spotfor the Traking Devopment and Deliery Subsystem ..... 22 3.1.5.2.11 TrIning Development=dDelivery Subsystem sL...e. Alsys Ada compiler f. Ethernet Local Area Network reference manual(s) g. Infotron 992 network reference manual(s) h. Computer Program Source...1989 a. Daily check of mainframe components, including all elements critical to support the terminal network . b. Restoration of mainframe equipment

Computer code for scattering from impedance bodies of revolution. Part 3: Surface impedance with s and phi variation. Analytical and numerical results

NASA Technical Reports Server (NTRS)

Uslenghi, Piergiorgio L. E.; Laxpati, Sharad R.; Kawalko, Stephen F.

1993-01-01

The third phase of the development of the computer codes for scattering by coated bodies that has been part of an ongoing effort in the Electromagnetics Laboratory of the Electrical Engineering and Computer Science Department at the University of Illinois at Chicago is described. The work reported discusses the analytical and numerical results for the scattering of an obliquely incident plane wave by impedance bodies of revolution with phi variation of the surface impedance. Integral equation formulation of the problem is considered. All three types of integral equations, electric field, magnetic field, and combined field, are considered. These equations are solved numerically via the method of moments with parametric elements. Both TE and TM polarization of the incident plane wave are considered. The surface impedance is allowed to vary along both the profile of the scatterer and in the phi direction. Computer code developed for this purpose determines the electric surface current as well as the bistatic radar cross section. The results obtained with this code were validated by comparing the results with available results for specific scatterers such as the perfectly conducting sphere. Results for the cone-sphere and cone-cylinder-sphere for the case of an axially incident plane were validated by comparing the results with the results with those obtained in the first phase of this project. Results for body of revolution scatterers with an abrupt change in the surface impedance along both the profile of the scatterer and the phi direction are presented.

Cellular reflectarray antenna and method of making same

NASA Technical Reports Server (NTRS)

Romanofsky, Robert R (Inventor)

2011-01-01

A method of manufacturing a cellular reflectarray antenna arranged in an m by n matrix of radiating elements for communication with a satellite includes steps of determining a delay .phi.m,n for each of said m by n matrix of elements of said cellular reflectarray antenna using sub-steps of: determining the longitude and latitude of operation, determining elevation and azimuth angles of the reflectarray with respect to the satellite and converting theta.sub.0 (.theta..sub.0) and phi.sub.0 (.phi..sub.0), determining .DELTA..beta..sub.m,n, the pointing vector correction, for a given inter-element spacing and wavelength, determining .DELTA..phi..sub.m,n, the spherical wave front correction factor, for a given radius from the central element and/or from measured data from the feed horn; and, determining a delay .phi.m,n for each of said m by n matrix of elements as a function of .DELTA..beta..sub.m,n and .DELTA..phi..sub.m,n.

Cellular reflectarray antenna and method of making same

NASA Technical Reports Server (NTRS)

Romanofsky, Robert R (Inventor)

2010-01-01

A method of manufacturing a cellular reflectarray antenna arranged in an m by n matrix of radiating elements for communication with a satellite includes steps of determining a delay .phi.m,n for each of said m by n matrix of elements of said cellular reflectarray antenna using sub-steps of: determining the longitude and latitude of operation, determining elevation and azimuth angles of the reflectarray with respect to the satellite and converting theta.sub.0 (.theta..sub.0) and phi.sub.0 (.phi..sub.0), determining .DELTA..beta..sub.m,n, the pointing vector correction, for a given inter-element spacing and wavelength, determining .DELTA..phi..sub.m,n, the spherical wave front correction factor, for a given radius from the central element and/or from measured data from the feed horn; and, determining a delay .phi.m,n for each of said m by n matrix of elements as a function of .DELTA..beta..sub.m,n and .DELTA..phi..sub.m,n..

An RR Lyrae period shift in terms of the Fourier parameter Phi sub 31

NASA Technical Reports Server (NTRS)

Clement, Christine M.; Jankulak, Michael; Simon, Norman R.

1992-01-01

The Fourier phase parameter Phi sub 31 has been determined for RRc stars in five globular clusters, NGC 6171, M5, M3, M53, and M15. The results indicate that the RRc stars in a given cluster show a sequence of Phi sub 31 increasing with period, and that the higher the cluster metallicity, the higher the sequence lies in a plot of Phi sub 31 with period. The Phi sub 31 values for the stars in NGC 6171 and M5 presented here are based on observations made with the University of Toronto 0.61 m telescope at Las Campanas, Chile, while those for M3, M53, and M15 are based on published data. A bootstrap procedure has been used to establish the uncertainties in the Fourier parameters. The physical significance of the relationship among Phi sub 31, period, and metallicity is not yet understood. It will need to be tested with hydrodynamic pulsation models computed with new opacities.

The complete genome sequence and proteomics of Yersinia pestis phage Yep-phi.

PubMed

Zhao, Xiangna; Wu, Weili; Qi, Zhizhen; Cui, Yujun; Yan, Yanfeng; Guo, Zhaobiao; Wang, Zuyun; Wang, Hu; Deng, Haijun; Xue, Yan; Chen, Weijun; Wang, Xiaoyi; Yang, Ruifu

2011-01-01

Yep-phi, a lytic phage of Yersinia pestis, was isolated in China and is routinely used as a diagnostic phage for the identification of the plague pathogen. Yep-phi has an isometric hexagonal head containing dsDNA and a short non-contractile conical tail. In this study, we sequenced the Yep-phi genome (GenBank accession no. HQ333270) and performed proteomics analysis. The genome consists of 38 ,616 bp of DNA, including direct terminal repeats of 222 bp, and is predicted to contain 45 ORFs. Most structural proteins were identified by proteomics analysis. Compared with the three available genome sequences of lytic phages for Y. pestis, the phages could be divided into two subgroups. Yep-phi displays marked homology to the bacteriophages Berlin (GenBank accession no. AM183667) and Yepe2 (GenBank accession no. EU734170), and these comprise one subgroup. The other subgroup is represented by bacteriophage ΦA1122 (GenBank accession no. AY247822). Potential recombination was detected among the Yep-phi subgroup.

[Prevalence of HIV treatment in PHI].

PubMed

Wild, F; Finkenstädt, V

2013-12-01

The importance of HIV in PHI is examined on the basis of the "AIDS statistics" of the Association of PHI and pharmaceutical data from PHI. The observation period is from 2007 to 2011. We define a HIV case if a private insured person has submitted at least one HIV-related invoice (e.g., an antiretroviral drug) for reimbursement during the observation period. In 2011, 7,624 people in PHI received HIV therapy, that is 32% (+1888) more than in 2007. The number of new HIV cases in 2011 was 673, and thus 12% (-92) lower than in 2007. The proportion of people receiving antiretroviral therapy in PHI is higher than in the general population in Germany. HIV infections occur in all age groups, but peaks in the age group 41 to 50 years old. Men are affected more than women. In contrast, the number of HIV cases among 11- to 15-year-old girls is higher compared to boys of the same age.

Partonic Flow and phi-Meson production in Au+Au collisions at sqrt radical sNN = 200 GeV.

PubMed

Abelev, B I; Aggarwal, M M; Ahammed, Z; Anderson, B D; Arkhipkin, D; Averichev, G S; Bai, Y; Balewski, J; Barannikova, O; Barnby, L S; Baudot, J; Baumgart, S; Belaga, V V; Bellingeri-Laurikainen, A; Bellwied, R; Benedosso, F; Betts, R R; Bhardwaj, S; Bhasin, A; Bhati, A K; Bichsel, H; Bielcik, J; Bielcikova, J; Bland, L C; Blyth, S-L; Bombara, M; Bonner, B E; Botje, M; Bouchet, J; Brandin, A V; Bravar, A; Burton, T P; Bystersky, M; Cadman, R V; Cai, X Z; Caines, H; Calderón de la Barca Sánchez, M; Callner, J; Catu, O; Cebra, D; Chajecki, Z; Chaloupka, P; Chattopadhyay, S; Chen, H F; Chen, J H; Chen, J Y; Cheng, J; Cherney, M; Chikanian, A; Christie, W; Chung, S U; Coffin, J P; Cormier, T M; Cosentino, M R; Cramer, J G; Crawford, H J; Das, D; Dash, S; Daugherity, M; de Moura, M M; Dedovich, T G; DePhillips, M; Derevschikov, A A; Didenko, L; Dietel, T; Djawotho, P; Dogra, S M; Dong, X; Drachenberg, J L; Draper, J E; Du, F; Dunin, V B; Dunlop, J C; Dutta Mazumdar, M R; Eckardt, V; Edwards, W R; Efimov, L G; Emelianov, V; Engelage, J; Eppley, G; Erazmus, B; Estienne, M; Fachini, P; Fatemi, R; Fedorisin, J; Feng, A; Filip, P; Finch, E; Fine, V; Fisyak, Y; Fu, J; Gagliardi, C A; Gaillard, L; Ganti, M S; Garcia-Solis, E; Ghazikhanian, V; Ghosh, P; Gorbunov, Y G; Gos, H; Grebenyuk, O; Grosnick, D; Grube, B; Guertin, S M; Guimaraes, K S F F; Gupta, N; Haag, B; Hallman, T J; Hamed, A; Harris, J W; He, W; Heinz, M; Henry, T W; Heppelmann, S; Hippolyte, B; Hirsch, A; Hjort, E; Hoffman, A M; Hoffmann, G W; Hofman, D J; Hollis, R S; Horner, M J; Huang, H Z; Hughes, E W; Humanic, T J; Igo, G; Iordanova, A; Jacobs, P; Jacobs, W W; Jakl, P; Jia, F; Jones, P G; Judd, E G; Kabana, S; Kang, K; Kapitan, J; Kaplan, M; Keane, D; Kechechyan, A; Kettler, D; Khodyrev, V Yu; Kim, B C; Kiryluk, J; Kisiel, A; Kislov, E M; Klein, S R; Knospe, A G; Kocoloski, A; Koetke, D D; Kollegger, T; Kopytine, M; Kotchenda, L; Kouchpil, V; Kowalik, K L; Kravtsov, P; Kravtsov, V I; Krueger, K; Kuhn, C; Kulikov, A I; Kumar, A; Kurnadi, P; Kuznetsov, A A; Lamont, M A C; Landgraf, J M; Lange, S; LaPointe, S; Laue, F; Lauret, J; Lebedev, A; Lednicky, R; Lee, C-H; Lehocka, S; LeVine, M J; Li, C; Li, Q; Li, Y; Lin, G; Lin, X; Lindenbaum, S J; Lisa, M A; Liu, F; Liu, H; Liu, J; Liu, L; Ljubicic, T; Llope, W J; Longacre, R S; Love, W A; Lu, Y; Ludlam, T; Lynn, D; Ma, G L; Ma, J G; Ma, Y G; Mahapatra, D P; Majka, R; Mangotra, L K; Manweiler, R; Margetis, S; Markert, C; Martin, L; Matis, H S; Matulenko, Yu A; McClain, C J; McShane, T S; Melnick, Yu; Meschanin, A; Millane, J; Miller, M L; Minaev, N G; Mioduszewski, S; Mironov, C; Mischke, A; Mitchell, J; Mohanty, B; Morozov, D A; Munhoz, M G; Nandi, B K; Nattrass, C; Nayak, T K; Nelson, J M; Nepali, C; Netrakanti, P K; Nogach, L V; Nurushev, S B; Odyniec, G; Ogawa, A; Okorokov, V; Oldenburg, M; Olson, D; Pachr, M; Pal, S K; Panebratsev, Y; Pavlinov, A I; Pawlak, T; Peitzmann, T; Perevoztchikov, V; Perkins, C; Peryt, W; Phatak, S C; Planinic, M; Pluta, J; Poljak, N; Porile, N; Poskanzer, A M; Potekhin, M; Potrebenikova, E; Potukuchi, B V K S; Prindle, D; Pruneau, C; Putschke, J; Qattan, I A; Raniwala, R; Raniwala, S; Ray, R L; Relyea, D; Ridiger, A; Ritter, H G; Roberts, J B; Rogachevskiy, O V; Romero, J L; Rose, A; Roy, C; Ruan, L; Russcher, M J; Sahoo, R; Sakrejda, I; Sakuma, T; Salur, S; Sandweiss, J; Sarsour, M; Sazhin, P S; Schambach, J; Scharenberg, R P; Schmitz, N; Seger, J; Selyuzhenkov, I; Seyboth, P; Shabetai, A; Shahaliev, E; Shao, M; Sharma, M; Shen, W Q; Shimanskiy, S S; Sichtermann, E P; Simon, F; Singaraju, R N; Smirnov, N; Snellings, R; Sorensen, P; Sowinski, J; Speltz, J; Spinka, H M; Srivastava, B; Stadnik, A; Stanislaus, T D S; Staszak, D; Stock, R; Strikhanov, M; Stringfellow, B; Suaide, A A P; Suarez, M C; Subba, N L; Sumbera, M; Sun, X M; Sun, Z; Surrow, B; Symons, T J M; Szanto de Toledo, A; Takahashi, J; Tang, A H; Tarnowsky, T; Thomas, J H; Timmins, A R; Timoshenko, S; Tokarev, M; Trainor, T A; Trentalange, S; Tribble, R E; Tsai, O D; Ulery, J; Ullrich, T; Underwood, D G; Van Buren, G; van der Kolk, N; van Leeuwen, M; Vander Molen, A M; Varma, R; Vasilevski, I M; Vasiliev, A N; Vernet, R; Vigdor, S E; Viyogi, Y P; Vokal, S; Voloshin, S A; Waggoner, W T; Wang, F; Wang, G; Wang, J S; Wang, X L; Wang, Y; Watson, J W; Webb, J C; Westfall, G D; Wetzler, A; Whitten, C; Wieman, H; Wissink, S W; Witt, R; Wu, J; Wu, Y; Xu, N; Xu, Q H; Xu, Z; Yepes, P; Yoo, I-K; Yue, Q; Yurevich, V I; Zhan, W; Zhang, H; Zhang, W M; Zhang, Y; Zhang, Z P; Zhao, Y; Zhong, C; Zhou, J; Zoulkarneev, R; Zoulkarneeva, Y; Zubarev, A N; Zuo, J X

2007-09-14

We present first measurements of the phi-meson elliptic flow (v2(pT)) and high-statistics pT distributions for different centralities from radical sNN=200 GeV Au+Au collisions at RHIC. In minimum bias collisions the v2 of the phi meson is consistent with the trend observed for mesons. The ratio of the yields of the Omega to those of the phi as a function of transverse momentum is consistent with a model based on the recombination of thermal s quarks up to pT approximately 4 GeV/c, but disagrees at higher momenta. The nuclear modification factor (R CP) of phi follows the trend observed in the K S 0 mesons rather than in Lambda baryons, supporting baryon-meson scaling. These data are consistent with phi mesons in central Au+Au collisions being created via coalescence of thermalized s quarks and the formation of a hot and dense matter with partonic collectivity at RHIC.

The Effects of Flocculation on the Propagation of Ultrasound in Dilute Kaolin Slurries.

PubMed

Austin; Challis

1998-10-01

A broadband ultrasonic spectrometer has been used to measure ultrasonic attenuation and phase velocity dispersion as functions of frequency in kaolin suspensions over a range of solid volume fractions from phi = 0.01 to phi = 0.08 and over a pH range from 3 to 9. The Harker and Temple theory was used to simulate ultrasound propagation in the suspension, using measured slope viscosity, particle size, and size distribution. Simulated results for ultrasonic attenuation and phase velocity agree well with measured values. Both sets of results agree well and show that for volume fractions above phi approximately 0.05 attenuation and velocity dispersion increase for increasing floc size, whereas for volume fractions below phi approximately 0.05 attenuation and velocity dispersion both decrease. It is proposed that the mechanism for this change in behavior around phi approximately 0.05 involves changes in floc density and floc size distribution with phi and pH. Copyright 1998 Academic Press.

Two types of phytases (histidine acid phytase and β-propeller phytase) in Serratia sp. TN49 from the gut of Batocera horsfieldi (coleoptera) larvae.

PubMed

Zhang, Rui; Yang, Peilong; Huang, Huoqing; Shi, Pengjun; Yuan, Tiezheng; Yao, Bin

2011-11-01

Microbial phytases play a major role in the mineralization of organic phosphorous, especially in symbiotic plants and animals. In this study, we identified two types of phytases in Serratia sp. TN49 that was harbored in the gut of Batocera horsfieldi (Coleoptera) larvae. The two phytases, an acidic histidine acid phosphatase (PhyH49) and an alkaline β-propeller phytase (PhyB49), shared low identities with known phytases (61% at most). PhyH49 and PhyB49 produced in Escherichia coli exhibited maximal activities at pH 5.0 (60°C) and pH 7.5-8.0 (45°C), respectively, and are complementary in phytate degradation over the pH range 2.0-9.0. Serratia sp. TN49 harboring both PhyH49 and PhyB49 might make it more adaptive to environment change, corresponding to the evolution trend of microorganism.

Demand for private health insurance: how important is the quality gap?

PubMed

Costa, Joan; García, Jaume

2003-07-01

Perceived quality of private and public health care, income and insurance premium are among the determinants of demand for private health insurance (PHI). In the context of a model in which individuals are expected utility maximizers, the non purchasing choice can result in consuming either public health care or private health care with full cost paid out-of-pocket. This paper empirically analyses the effect of the determinants of the demand for PHI on the probability of purchasing PHI by estimating a pseudo-structural model to deal with missing data and endogeneity issues. Our findings support the hypothesis that the demand for PHI is indeed driven by the quality gap between private and public health care. As expected, PHI is a normal good and a rise in the insurance premium reduces the probability of purchasing PHI albeit displaying price elasticities smaller than one in absolute value for different groups of individuals. Copyright 2002 John Wiley & Sons, Ltd.

Role of the N*(1535) resonance and the {pi}{sup -}p{yields}KY amplitudes in the OZI forbidden {pi}N{yields}{phi}N reaction

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

Doering, M.; Oset, E.; Zou, B. S.

2008-08-15

We study the {pi}N{yields}{phi}N reaction close to the {phi}N threshold within the chiral unitary approach, by combining the {pi}{sup -}p{yields}K{sup +}{sigma}{sup -},{pi}{sup -}p{yields}K{sup 0}{sigma}{sup 0}, and {pi}{sup -}p{yields}K{sup 0}{lambda} amplitudes with the coupling of {phi} to the K components of the final states of these reactions via quantum loops. We obtain good agreement with experiment when the dominant {pi}{sup -}p{yields}K{sup 0}{lambda} amplitude is constrained with its experimental cross section. We also evaluate the coupling of N*(1535) to {phi}N and find a moderate coupling as a consequence of partial cancellation of the large KY components of N*(1535). We also show thatmore » the N*(1535) pole approximation is too small to reproduce the measured cross section for the {pi}{sup -}N{yields}{phi}N reaction.« less

Modulatory effects of neuropsychopharmaca on intracellular pH of hippocampal neurones in vitro

PubMed Central

Bonnet, Udo; Bingmann, Dieter; Wiltfang, Jens; Scherbaum, Norbert; Wiemann, Martin

2010-01-01

Background and purpose: The intracellular pH (pHi) of neurones is tightly regulated by, for example, membrane-bound acid-exchangers and loaders. Nevertheless, excessive bioelectric activity lowers steady-state pHi. In turn, even a moderate acidification can inhibit neuronal activity, a process believed to be part of a negative feedback loop controlling neuronal excitation. As moclobemide, an antidepressant, and also some antiepileptic drugs can reduce neuronal pHi in hippocampus slices in vitro, we screened a panel of currently used neuropsychopharmaca for comparable effects. Experimental approach: BCECF-AM loaded hippocampal slices were superfused with 16 different neuroleptics, antidepressants and antiepileptics under bicarbonate-buffered conditions. Changes in steady-state pHi of CA3 neurones were measured fluorometrically. Key results: The antipsychotics haloperidol, clozapine, ziprasidone, and the antidepressants amitriptyline, doxepin, trimipramine, citalopram, mirtazapine, as well as the anticonvulsive drug tiagabine reversibly reduced the steady-state pHi by up to 0.35 pH-units in concentrations of 5–50 µM. In contrast, venlafaxine, the anticonvulsants carbamazepine, clonazepam, gabapentin, lamotrigine, zonisamide, and the mood stabilizer lithium had no effect on neuronal pHi. Conclusion and implications: These data substantiate the view that clinically relevant concentrations of neuroleptics and antidepressants can mediate changes in neuronal pHi, which may contribute to their pharmacological mode of action. Effects on pHi should be taken into account when therapeutic or even harmful effects of these drugs are evaluated. PMID:20015293

Remote Advanced Payload Test Rig (RAPTR) Portable Payload Test System for the International Space Station

NASA Technical Reports Server (NTRS)

De La Cruz, Melinda; Henderson, Steve

2016-01-01

The RAPTR was developed to test ISS payloads for NASA. RAPTR is a simulation of the Command and Data Handling (C&DH) interfaces of the ISS (MIL-STD1553B, Ethernet and TAXI) and is designed for rapid testing and deployment of payload experiments to the ISS. The ISS's goal is to reduce the amount of time it takes for a payload developer to build, test and fly a payload, including payload software. The RAPTR meets this need with its user oriented, visually rich interface.

A multitasking, multisinked, multiprocessor data acquisition front end

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

Fox, R.; Au, R.; Molen, A.V.

1989-10-01

The authors have developed a generalized data acquisition front end system which is based on MC68020 processors running a commercial real time kernel (rhoSOS), and implemented primarily in a high level language (C). This system has been attached to the back end on-line computing system at NSCL via our high performance ETHERNET protocol. Data may be simultaneously sent to any number of back end systems. Fixed fraction sampling along links to back end computing is also supported. A nonprocedural program generator simplifies the development of experiment specific code.

Multiplexing the Ethernet Interface Among VAX/VMS Users.

DTIC Science & Technology

1983-12-01

Microcomputer Development Systems (MDS) and VAX/VPS sy’stemn were used for the implementation and testing of the project. The software is designed in such a...detailed design and .splesenta- toa of tie project. Is realLty chape: I constitutes the doee-.at os of the developed software. In soms instances, thisgs that...changes. 460i9n4t 4 provides a high level design of a virtual x $44 aletwock. alcag with some hints which may be useful So 44e W". who will work in this

The iPhyClassifier, an interactive online tool for phytoplasma classification and taxonomic assignment

USDA-ARS?s Scientific Manuscript database

The iPhyClassifier is an Internet-based research tool for quick identification and classification of diverse phytoplasmas. The iPhyClassifier simulates laboratory restriction enzyme digestions and subsequent gel electrophoresis and generates virtual restriction fragment length polymorphism (RFLP) p...

Intracellular pH Response to Weak Acid Stress in Individual Vegetative Bacillus subtilis Cells

PubMed Central

Pandey, Rachna; Vischer, Norbert O. E.; Smelt, Jan P. P. M.; van Beilen, Johan W. A.; Ter Beek, Alexander; De Vos, Winnok H.; Manders, Erik M. M.

2016-01-01

ABSTRACT Intracellular pH (pHi) critically affects bacterial cell physiology. Hence, a variety of food preservation strategies are aimed at perturbing pHi homeostasis. Unfortunately, accurate pHi quantification with existing methods is suboptimal, since measurements are averages across populations of cells, not taking into account interindividual heterogeneity. Yet, physiological heterogeneity in isogenic populations is well known to be responsible for differences in growth and division kinetics of cells in response to external stressors. To assess in this context the behavior of intracellular acidity, we have developed a robust method to quantify pHi at single-cell levels in Bacillus subtilis. Bacilli spoil food, cause disease, and are well known for their ability to form highly stress-resistant spores. Using an improved version of the genetically encoded ratiometric pHluorin (IpHluorin), we have quantified pHi in individual B. subtilis cells, cultured at an external pH of 6.4, in the absence or presence of weak acid stresses. In the presence of 3 mM potassium sorbate, a decrease in pHi and an increase in the generation time of growing cells were observed. Similar effects were observed when cells were stressed with 25 mM potassium acetate. Time-resolved analysis of individual bacteria in growing colonies shows that after a transient pH decrease, long-term pH evolution is highly cell dependent. The heterogeneity at the single-cell level shows the existence of subpopulations that might be more resistant and contribute to population survival. Our approach contributes to an understanding of pHi regulation in individual bacteria and may help scrutinizing effects of existing and novel food preservation strategies. IMPORTANCE This study shows how the physiological response to commonly used weak organic acid food preservatives, such as sorbic and acetic acids, can be measured at the single-cell level. These data are key to coupling often-observed single-cell heterogeneous growth behavior upon the addition of weak organic acid food preservatives. Generally, these data are gathered in the form of plate counting of samples incubated with the acids. Here, we visualize the underlying heterogeneity in cellular pH homeostasis, opening up avenues for mechanistic analyses of the heterogeneity in the weak acid stress response. Thus, microbial risk assessment can become more robust, widening the scope of use of these well-known weak organic acid food preservatives. PMID:27565617

Capture and alignment of phi29 viral particles in sub-40 nanometer porous alumina membranes.

PubMed

Moon, Jeong-Mi; Akin, Demir; Xuan, Yi; Ye, Peide D; Guo, Peixuan; Bashir, Rashid

2009-02-01

Bacteriophage phi29 virus nanoparticles and its associated DNA packaging nanomotor can provide for novel possibilities towards the development of hybrid bio-nano structures. Towards the goal of interfacing the phi29 viruses and nanomotors with artificial micro and nanostructures, we fabricated nanoporous Anodic Aluminum Oxide (AAO) membranes with pore size of 70 nm and shrunk the pores to sub 40 nm diameter using atomic layer deposition (ALD) of Aluminum Oxide. We were able to capture and align particles in the anodized nanopores using two methods. Firstly, a functionalization and polishing process to chemically attach the particles in the inner surface of the pores was developed. Secondly, centrifugation of the particles was utilized to align them in the pores of the nanoporous membranes. In addition, when a mixture of empty capsids and packaged particles was centrifuged at specific speeds, it was found that the empty capsids deform and pass through 40 nm diameter pores whereas the particles packaged with DNA were mainly retained at the top surface of the nanoporous membranes. Fluorescence microscopy was used to verify the selective filtration of empty capsids through the nanoporous membranes.

Towards a Unified Quark-Hadron-Matter Equation of State for Applications in Astrophysics and Heavy-Ion Collisions

NASA Astrophysics Data System (ADS)

Bastian, Niels-Uwe; Blaschke, David; Fischer, Tobias; Röpke, Gerd

2018-05-01

We outline an approach to a unified equation of state for quark-hadron matter on the basis of a $\\Phi-$derivable approach to the generalized Beth-Uhlenbeck equation of state for a cluster decomposition of thermodynamic quantities like the density. To this end we summarize the cluster virial expansion for nuclear matter and demonstrate the equivalence of the Green's function approach and the $\\Phi-$derivable formulation. For an example, the formation and dissociation of deuterons in nuclear matter is discussed. We formulate the cluster $\\Phi-$derivable approach to quark-hadron matter which allows to take into account the specifics of chiral symmetry restoration and deconfinement in triggering the Mott-dissociation of hadrons. This approach unifies the description of a strongly coupled quark-gluon plasma with that of a medium-modified hadron resonance gas description which are contained as limiting cases. The developed formalism shall replace the common two-phase approach to the description of the deconfinement and chiral phase transition that requires a phase transition construction between separately developed equations of state for hadronic and quark matter phases. Applications to the phenomenology of heavy-ion collisions and astrophysics are outlined.

Design of a framework for modeling, integration and simulation of physiological models.

PubMed

Erson, E Zeynep; Cavuşoğlu, M Cenk

2012-09-01

Multiscale modeling and integration of physiological models carry challenges due to the complex nature of physiological processes. High coupling within and among scales present a significant challenge in constructing and integrating multiscale physiological models. In order to deal with such challenges in a systematic way, there is a significant need for an information technology framework together with related analytical and computational tools that will facilitate integration of models and simulations of complex biological systems. Physiological Model Simulation, Integration and Modeling Framework (Phy-SIM) is an information technology framework providing the tools to facilitate development, integration and simulation of integrated models of human physiology. Phy-SIM brings software level solutions to the challenges raised by the complex nature of physiological systems. The aim of Phy-SIM, and this paper is to lay some foundation with the new approaches such as information flow and modular representation of the physiological models. The ultimate goal is to enhance the development of both the models and the integration approaches of multiscale physiological processes and thus this paper focuses on the design approaches that would achieve such a goal. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

Study of {chi}{sub cj} Decays at BES III

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

Zhong, J.

2010-08-05

In spring 2009 BES III has taken its first large data sample on the {psi}(2S) resonance. More than 1{center_dot}10{sup 8} {psi}(2S) decays have been recorded. First results on the analyses {chi}{sub cJ{yields}{pi}}{sup 0{pi}0}, {chi}{sub cj{yields}{eta}{eta}} and {chi}{sub cj{yields}{phi}{phi}} are presented. The decay mode {chi}{sub c1{yields}{phi}{phi}} has been observed for the first time. The results presented in this document are preliminary.

Anisotropic singularities in modified gravity models

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

Figueiro, Michele Ferraz; Saa, Alberto; Departamento de Matematica Aplicada, IMECC-UNICAMP, C.P. 6065, 13083-859 Campinas, SP

2009-09-15

We show that the common singularities present in generic modified gravity models governed by actions of the type S={integral}d{sup 4}x{radical}(-g)f(R,{phi},X), with X=-(1/2)g{sup ab}{partial_derivative}{sub a}{phi}{partial_derivative}{sub b}{phi}, are essentially the same anisotropic instabilities associated to the hypersurface F({phi})=0 in the case of a nonminimal coupling of the type F({phi})R, enlightening the physical origin of such singularities that typically arise in rather complex and cumbersome inhomogeneous perturbation analyses. We show, moreover, that such anisotropic instabilities typically give rise to dynamically unavoidable singularities, precluding completely the possibility of having physically viable models for which the hypersurface ({partial_derivative}f/{partial_derivative}R)=0 is attained. Some examples are explicitly discussed.

The Contradiction Between the Measurement Theory of Quantum Mechanics and the Theory that the Velocity of Any Particle Can Not be Larger than the Velocity of Light

NASA Technical Reports Server (NTRS)

Shen, Y.; Shen, Z. J.; Shen, G. T.; Yang, B. C.

1996-01-01

By the measurement theory of quantum mechanics and the method of Fourier transform,we proved that the wave function psi(x,y,z,t)= (8/((2(pi)(2L(exp (1/2)))(exp 3))(Phi(L,t,x)Phi(L,t,y)Phi(L,t,z)). According to the theory that the velocity of any particle can not be larger than the velocity of light and the Born interpretation, when absolute value of delta greater than (ct+ L),Phi(L,t,delta) = 0. But according to the calculation, we proved that for some delta, even if absolute value of delta is greater than (ct+L), Phi(L,t,delta) is not equal to 0.

Do radiology and other health care presentations posted on the Internet contain accessible protected health information?

PubMed

Weadock, William J; Londy, Frank J; Ellis, James H; Goldman, Edward B

2008-10-01

To determine the prevalence of protected health information (PHI) in PowerPoint presentations available for downloading from the Internet. No institutional review board approval was needed for this project, which involved no patient subjects. Two Google searches, each limited to PowerPoint files, were performed by using the criteria "Cardiac CT" and "Magnetic Resonance Imaging." The first 100 hits of each search were downloaded from the source Web site. The presentations were examined for the PHI contained on any images, links, or notes pages. Two hundred presentations were evaluated. There were 143 presentations with images, image links, or notes, and 52 (36%) of these contained PHI. There were 129 presentations containing radiologic images; 51 (40%) of these contained PHI, and 31 (24%) showed the patient's name. At least 132 (66%) of the 200 presentations originated from the United States. Thirty-five (37%) of 94 presentations with images, image links, or notes contained PHI. Eighty-six U.S. presentations contained radiologic images; 34 (40%) of these contained PHI, and 19 (22%) showed the patient's name. Online or other distributions of PowerPoint presentations that contain radiologic images often contain PHI, and this may violate laws, including the U.S. Health Insurance Portability and Accountability Act. (c) RSNA, 2008.

Unimodular Gravity and General Relativity UV divergent contributions to the scattering of massive scalar particles

NASA Astrophysics Data System (ADS)

Gonzalez-Martin, S.; Martin, C. P.

2018-01-01

We work out the one-loop and order κ2 mphi2 UV divergent contributions, coming from Unimodular Gravity and General Relativity, to the S matrix element of the scattering process phi + phi→ phi + phi in a λ phi4 theory with mass mphi. We show that both Unimodular Gravity and General Relativity give rise to the same UV divergent contributions in Dimensional Regularization. This seems to be at odds with the known result that in a multiplicative MS dimensional regularization scheme the General Relativity corrections, in the de Donder gauge, to the beta function, βλ, of the λ coupling do not vanish, whereas the Unimodular Gravity corrections, in a certain gauge, do vanish. Actually, by comparing the UV divergent contributions calculated in this paper with those which give rise to the non-vanishing gravitational corrections to βλ, one readily concludes that the UV divergent contributions that yield the just mentioned non-vanishing gravitational corrections to βλ do not contribute to the UV divergent behaviour of the S matrix element of phi + phi→ phi + phi. This shows that any physical consequence—such as the existence of asymptotic freedom due to gravitational interactions—drawn from the value of βλ is not physically meaningful.

Attractor scenarios and superluminal signals in k-essence cosmology

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

Kang, Jin U; Arnold Sommerfeld Center, Department of Physics, Ludwig-Maximilians University, Theresienstrasse 37, 80333 Munich; Vanchurin, Vitaly

Cosmological scenarios with k-essence are invoked in order to explain the observed late-time acceleration of the Universe. These scenarios avoid the need for fine-tuned initial conditions (the 'coincidence problem') because of the attractorlike dynamics of the k-essence field {phi}. It was recently shown that all k-essence scenarios with Lagrangians p=L(X){phi}{sup -2}, where X{identical_to}(1/2){phi}{sub ,{mu}}{phi}{sup ,{mu}}, necessarily involve an epoch where perturbations of {phi} propagate faster than light (the 'no-go theorem'). We carry out a comprehensive study of attractorlike cosmological solutions ('trackers') involving a k-essence scalar field {phi} and another matter component. The result of this study is a complete classificationmore » of k-essence Lagrangians that admit asymptotically stable tracking solutions, among all Lagrangians of the form p=K({phi})L(X). Using this classification, we select the class of models that describe the late-time acceleration and avoid the coincidence problem through the tracking mechanism. An analogous 'no-go theorem' still holds for this class of models, indicating the existence of a superluminal epoch. In the context of k-essence cosmology, the superluminal epoch does not lead to causality violations. We discuss the implications of superluminal signal propagation for possible causality violations in Lorentz-invariant field theories.« less

The structure of premixed particle-cloud flames

NASA Technical Reports Server (NTRS)

Seshadri, K.; Berlad, A. L.; Tangirala, V.

1992-01-01

The structure of premixed flames propagating in combustible systems, containing uniformly distributed volatile fuel particles, in an oxidizing gas mixture, is analyzed. It is presumed that the fuel particles vaporize first to yield a gaseous fuel of known chemical structure, which is subsequently oxidized in the gas phase. The analysis is performed in the asymptotic limit, where the value of the characteristic Zeldovich number, based on the gas-phase oxidation of the gaseous fuel is large, and for values of phi(u) greater than or equal to 1.0, where phi(u) is the equivalence ratio based on the fuel available in the fuel particles. The structure of the flame is presumed to consist of a preheat vaporization zone where the rate of the gas-phase chemical reaction is small, a reaction zone where convection and the rate of vaporization of the fuel particles are small and a convection zone where diffusive terms in the conservation equations are small. For given values phi(u) the analysis yields results for the burning velocity and phi(g) where phi(g) is the effective equivalence ratio in the reaction zone. The analysis shows that even though phi(u) greater than or equal to 1.0, for certain cases the calculated value of phi(g) is less than unity. This prediction is in agreement with experimental observations.

Field line twist and field-aligned currents in an axially symmetric equilibrium magnetosphere. [of Uranus

NASA Technical Reports Server (NTRS)

Voigt, Gerd-Hannes

1986-01-01

Field-aligned Birkeland currents and the angle of the magnetic line twist were calculated for an axially symmetric pole-on magnetosphere (assumed to be in MHD equilibrium). The angle of the field line twist was shown to have a strong radial dependence on the axisymmetric magnetotail as well as on the ionospheric conductivity and the amount of thermal plasma contained in closed magnetotail flux tubes. The field line twist results from the planetary rotation, which leads to the development of a toroidal magnetic B-sub-phi component and to differentially rotating magnetic field lines. It was shown that the time development of the toroidal magnetic B-sub-phi component and the rotation frequency are related through an induction equation.

Testing and reference model analysis of FTTH system

NASA Astrophysics Data System (ADS)

Feng, Xiancheng; Cui, Wanlong; Chen, Ying

2009-08-01

With rapid development of Internet and broadband access network, the technologies of xDSL, FTTx+LAN , WLAN have more applications, new network service emerges in endless stream, especially the increase of network game, meeting TV, video on demand, etc. FTTH supports all present and future service with enormous bandwidth, including traditional telecommunication service, traditional data service and traditional TV service, and the future digital TV and VOD. With huge bandwidth of FTTH, it wins the final solution of broadband network, becomes the final goal of development of optical access network.. Fiber to the Home (FTTH) will be the goal of telecommunications cable broadband access. In accordance with the development trend of telecommunication services, to enhance the capacity of integrated access network, to achieve triple-play (voice, data, image), based on the existing optical Fiber to the curb (FTTC), Fiber To The Zone (FTTZ), Fiber to the Building (FTTB) user optical cable network, the optical fiber can extend to the FTTH system of end-user by using EPON technology. The article first introduced the basic components of FTTH system; and then explain the reference model and reference point for testing of the FTTH system; Finally, by testing connection diagram, the testing process, expected results, primarily analyze SNI Interface Testing, PON interface testing, Ethernet performance testing, UNI interface testing, Ethernet functional testing, PON functional testing, equipment functional testing, telephone functional testing, operational support capability testing and so on testing of FTTH system. ...

Selective fertilization with phosphite allows unhindered growth of cotton plants expressing the ptxD gene while suppressing weeds.

PubMed

Pandeya, Devendra; López-Arredondo, Damar L; Janga, Madhusudhana R; Campbell, LeAnne M; Estrella-Hernández, Priscila; Bagavathiannan, Muthukumar V; Herrera-Estrella, Luis; Rathore, Keerti S

2018-06-04

Weeds, which have been the bane of agriculture since the beginning of civilization, are managed manually, mechanically, and, more recently, by chemicals. However, chemical control options are rapidly shrinking due to the recent rise in the number of herbicide-resistant weeds in crop fields, with few alternatives on the horizon. Therefore, there is an urgent need for alternative weed suppression systems to sustain crop productivity while reducing our dependence on herbicides and tillage. Such a development will also allay some of the negative perceptions associated with the use of herbicide-resistance genes and heavy dependence on herbicides. Transgenic plants expressing the bacterial phosphite dehydrogenase ( ptxD ) gene gain an ability to convert phosphite (Phi) into orthophosphate [Pi, the metabolizable form of phosphorus (P)]. Such plants allow for a selective fertilization scheme, based on Phi as the sole source of P for the crop, while offering an effective alternative for suppressing weed growth. Here, we show that, when P is supplied in the form of Phi, ptxD -expressing cotton ( Gossypium hirsutum L.) plants outcompete, in both artificial substrates and natural soils from agricultural fields, three different monocot and dicot weed species intentionally introduced in the experiments, as well as weeds naturally present in the tested soils. Importantly, the ptxD /Phi system proved highly efficacious in inhibiting the growth of glyphosate-resistant Palmer amaranth. With over 250 weed species resistant to currently available herbicides, ptxD -transgenic plants fertilized with Phi could provide an effective alternative to suppressing the growth of these weeds while providing adequate nutrition to the crop. Copyright © 2018 the Author(s). Published by PNAS.

Gaps in the existing public health informatics training programs: a challenge to the development of a skilled global workforce.

PubMed

Joshi, Ashish; Perin, Douglas Marcel Puricelli

2012-01-01

The objective of this study was to explore public health informatics (PHI) training programs that currently exist to meet the growing demand for a trained global workforce. We used several search engines, scientific databases, and the websites of informatics organizations; sources included PubMed, Google, the American Medical Informatics Organization, and the International Medical Informatics Organization. The search was conducted from May to July 2011 and from January to February 2012 using key words such as informatics, public health informatics, or biomedical informatics along with academic programs, training, certificate, graduate programs, or postgraduate programs. Course titles and catalog descriptions were gathered from the program or institution websites. Variables included PHI program categories, location and mode of delivery, program credits, and costs. Each course was then categorized based on its title and description as available on the Internet. Finally, we matched course titles and descriptions with the competencies for PHIs determined by Centers for Disease Control and Prevention (CDC). Descriptive analysis was performed to report means and frequency distributions for continuous and categorical variables. Stratified analysis was performed to explore average credits and cost per credit among both the public and private institutions. Fifteen PHI programs were identified across 13 different institutions, the majority of which were US-based. The average number of credits and the associated costs required to obtain PHI training were much higher in private as compared to public institutions. The study results suggest that a need for online contextual and cost-effective PHI training programs exists to address the growing needs of professionals worldwide who are using technology to improve public health in their respective countries.

The Physician Recommendation Coding System (PhyReCS): A Reliable and Valid Method to Quantify the Strength of Physician Recommendations During Clinical Encounters

PubMed Central

Scherr, Karen A.; Fagerlin, Angela; Williamson, Lillie D.; Davis, J. Kelly; Fridman, Ilona; Atyeo, Natalie; Ubel, Peter A.

2016-01-01

Background Physicians’ recommendations affect patients’ treatment choices. However, most research relies on physicians’ or patients’ retrospective reports of recommendations, which offer a limited perspective and have limitations such as recall bias. Objective To develop a reliable and valid method to measure the strength of physician recommendations using direct observation of clinical encounters. Methods Clinical encounters (n = 257) were recorded as part of a larger study of prostate cancer decision making. We used an iterative process to create the 5-point Physician Recommendation Coding System (PhyReCS). To determine reliability, research assistants double-coded 50 transcripts. To establish content validity, we used one-way ANOVAs to determine whether relative treatment recommendation scores differed as a function of which treatment patients received. To establish concurrent validity, we examined whether patients’ perceived treatment recommendations matched our coded recommendations. Results The PhyReCS was highly reliable (Krippendorf’s alpha =. 89, 95% CI [.86, .91]). The average relative treatment recommendation score for each treatment was higher for individuals who received that particular treatment. For example, the average relative surgery recommendation score was higher for individuals who received surgery versus radiation (mean difference = .98, SE = .18, p < .001) or active surveillance (mean difference = 1.10, SE = .14, p < .001). Patients’ perceived recommendations matched coded recommendations 81% of the time. Conclusion The PhyReCS is a reliable and valid way to capture the strength of physician recommendations. We believe that the PhyReCS would be helpful for other researchers who wish to study physician recommendations, an important part of patient decision making. PMID:27343015

The Physician Recommendation Coding System (PhyReCS): A Reliable and Valid Method to Quantify the Strength of Physician Recommendations During Clinical Encounters.

PubMed

Scherr, Karen A; Fagerlin, Angela; Williamson, Lillie D; Davis, J Kelly; Fridman, Ilona; Atyeo, Natalie; Ubel, Peter A

2017-01-01

Physicians' recommendations affect patients' treatment choices. However, most research relies on physicians' or patients' retrospective reports of recommendations, which offer a limited perspective and have limitations such as recall bias. To develop a reliable and valid method to measure the strength of physician recommendations using direct observation of clinical encounters. Clinical encounters (n = 257) were recorded as part of a larger study of prostate cancer decision making. We used an iterative process to create the 5-point Physician Recommendation Coding System (PhyReCS). To determine reliability, research assistants double-coded 50 transcripts. To establish content validity, we used 1-way analyses of variance to determine whether relative treatment recommendation scores differed as a function of which treatment patients received. To establish concurrent validity, we examined whether patients' perceived treatment recommendations matched our coded recommendations. The PhyReCS was highly reliable (Krippendorf's alpha = 0.89, 95% CI [0.86, 0.91]). The average relative treatment recommendation score for each treatment was higher for individuals who received that particular treatment. For example, the average relative surgery recommendation score was higher for individuals who received surgery versus radiation (mean difference = 0.98, SE = 0.18, P < 0.001) or active surveillance (mean difference = 1.10, SE = 0.14, P < 0.001). Patients' perceived recommendations matched coded recommendations 81% of the time. The PhyReCS is a reliable and valid way to capture the strength of physician recommendations. We believe that the PhyReCS would be helpful for other researchers who wish to study physician recommendations, an important part of patient decision making. © The Author(s) 2016.

Integrated information in discrete dynamical systems: motivation and theoretical framework.

PubMed

Balduzzi, David; Tononi, Giulio

2008-06-13

This paper introduces a time- and state-dependent measure of integrated information, phi, which captures the repertoire of causal states available to a system as a whole. Specifically, phi quantifies how much information is generated (uncertainty is reduced) when a system enters a particular state through causal interactions among its elements, above and beyond the information generated independently by its parts. Such mathematical characterization is motivated by the observation that integrated information captures two key phenomenological properties of consciousness: (i) there is a large repertoire of conscious experiences so that, when one particular experience occurs, it generates a large amount of information by ruling out all the others; and (ii) this information is integrated, in that each experience appears as a whole that cannot be decomposed into independent parts. This paper extends previous work on stationary systems and applies integrated information to discrete networks as a function of their dynamics and causal architecture. An analysis of basic examples indicates the following: (i) phi varies depending on the state entered by a network, being higher if active and inactive elements are balanced and lower if the network is inactive or hyperactive. (ii) phi varies for systems with identical or similar surface dynamics depending on the underlying causal architecture, being low for systems that merely copy or replay activity states. (iii) phi varies as a function of network architecture. High phi values can be obtained by architectures that conjoin functional specialization with functional integration. Strictly modular and homogeneous systems cannot generate high phi because the former lack integration, whereas the latter lack information. Feedforward and lattice architectures are capable of generating high phi but are inefficient. (iv) In Hopfield networks, phi is low for attractor states and neutral states, but increases if the networks are optimized to achieve tension between local and global interactions. These basic examples appear to match well against neurobiological evidence concerning the neural substrates of consciousness. More generally, phi appears to be a useful metric to characterize the capacity of any physical system to integrate information.

Characterization of tail sheath protein of giant bacteriophage phiKZ Pseudomonas aeruginosa

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

Kurochkina, Lidia P., E-mail: lpk@ibch.r; Aksyuk, Anastasia A.; Sachkova, Maria Yu.

2009-12-20

The tail sheath protein of giant bacteriophage phiKZ Pseudomonas aeruginosa encoded by gene 29 was identified and its expression system was developed. Localization of the protein on the virion was confirmed by immunoelectron microscopy. Properties of gene product (gp) 29 were studied by electron microscopy, immunoblotting and limited trypsinolysis. Recombinant gp29 assembles into the regular tubular structures (polysheaths) of variable length. Trypsin digestion of gp29 within polysheaths or extended sheath of virion results in specific cleavage of the peptide bond between Arg135 and Asp136. However, this cleavage does not affect polymeric structure of polysheaths, sheaths and viral infectivity. Digestion bymore » trypsin of the C-truncated gp29 mutant, lacking the ability to self-assemble, results in formation of a stable protease-resistant fragment. Although there is no sequence homology of phiKZ proteins to proteins of other bacteriophages, some characteristic biochemical properties of gp29 revealed similarities to the tail sheath protein of bacteriophage T4.« less

Genome-wide identification and expression profiling of the cystatin gene family in apple (Malus × domestica Borkh.).

PubMed

Tan, Yanxiao; Wang, Suncai; Liang, Dong; Li, Mingjun; Ma, Fengwang

2014-06-01

Cystatins or phytocystatins (PhyCys) comprise a family of plant-specific inhibitors of cysteine proteinases. Such inhibitors are thought to be involved in the regulation of several endogenous processes as well as defense against biotic or abiotic stresses. However, information about this family is limited in apple. We identified 26 PhyCys genes within the entire apple genome. They were clustered into three distinct groups distributed across several chromosomes. All of their putative proteins contained one or two typical cystatin domains, which shared the characteristic motifs of PhyCys. Eight selected genes displayed differential expression patterns in various tissues. Moreover, their transcript levels were also up-regulated significantly in leaves during maturation, senescence or in response to treatment with one or more abiotic stresses. Our results indicated that members of this family may function in tissue development, leaf senescence, and adaptation to adverse environments in apple. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

PubMed Central

CICIRIELLO, E.

2016-01-01

SUMMARY Non-uniform, late, or inappropriate care of childhood with permanent hearing impairment (PHI) predisposes many children to develop communicative- behaviour problems and impaired psychosocial adjustment that can persist in adolescence and adulthood.In March 2014, the CCM (Centro Controllo Malattie or Disease Control Centre) of the Italian Ministry of Health funded a project entitled " Preventing Communication Disorders: a Regional Program for Early Identification, Intervention and Care of Hearing Impaired Children". The project involved 5 tertiary centres with UNHS programs formally approved by the Region. The main purpose of the project is to define and launch an integrated regionally-based public health model for identification, diagnosis and intervention of childhood PHI. The first phase of the project investigated the state of art and produced recommendations for positive changes in identification, diagnosis, therapy and care of childhood PHI in Italy, taking into account diagnostic and treatment innovations, family empowerment, treatment alliance and an interdisciplinary approach. Recommendations drawn from this initial phase will represent the basis for a regional system for early intervention that is validated, integrated and shared between the five regions. PMID:27054384

Improved site-specific recombinase-based method to produce selectable marker- and vector-backbone-free transgenic cells

NASA Astrophysics Data System (ADS)

Yu, Yuan; Tong, Qi; Li, Zhongxia; Tian, Jinhai; Wang, Yizhi; Su, Feng; Wang, Yongsheng; Liu, Jun; Zhang, Yong

2014-02-01

PhiC31 integrase-mediated gene delivery has been extensively used in gene therapy and animal transgenesis. However, random integration events are observed in phiC31-mediated integration in different types of mammalian cells; as a result, the efficiencies of pseudo attP site integration and evaluation of site-specific integration are compromised. To improve this system, we used an attB-TK fusion gene as a negative selection marker, thereby eliminating random integration during phiC31-mediated transfection. We also excised the selection system and plasmid bacterial backbone by using two other site-specific recombinases, Cre and Dre. Thus, we generated clean transgenic bovine fetal fibroblast cells free of selectable marker and plasmid bacterial backbone. These clean cells were used as donor nuclei for somatic cell nuclear transfer (SCNT), indicating a similar developmental competence of SCNT embryos to that of non-transgenic cells. Therefore, the present gene delivery system facilitated the development of gene therapy and agricultural biotechnology.

Trust Model for Protection of Personal Health Data in a Global Environment.

PubMed

Ruotsalainen, Pekka; Blobel, Bernd

2017-01-01

Successful health care, eHealth, digital health, and personal health systems increasingly take place in cross-jurisdictional, dynamic and risk-encumbered information space. They require rich amount of personal health information (PHI). Trust is and will be the cornerstone and prerequisite for successful health services. In global environments, trust cannot be expected as granted. In this paper, health service in the global environment is perceived as a meta-system, and a trust management model is developed to support it. The predefined trusting belief currently used in health care is not transferable to global environments. In the authors' model, the level of trust is dynamically calculated from measurable attributes. These attributes describe trust features of the service provider and its environment. The calculated trust value or profile can be used in defining the risk service user has to accept when disclosing PHI, and in definition of additional privacy and security safeguards before disclosing PHI and/or using services.

Real-time hierarchically distributed processing network interaction simulation

NASA Technical Reports Server (NTRS)

Zimmerman, W. F.; Wu, C.

1987-01-01

The Telerobot Testbed is a hierarchically distributed processing system which is linked together through a standard, commercial Ethernet. Standard Ethernet systems are primarily designed to manage non-real-time information transfer. Therefore, collisions on the net (i.e., two or more sources attempting to send data at the same time) are managed by randomly rescheduling one of the sources to retransmit at a later time interval. Although acceptable for transmitting noncritical data such as mail, this particular feature is unacceptable for real-time hierarchical command and control systems such as the Telerobot. Data transfer and scheduling simulations, such as token ring, offer solutions to collision management, but do not appropriately characterize real-time data transfer/interactions for robotic systems. Therefore, models like these do not provide a viable simulation environment for understanding real-time network loading. A real-time network loading model is being developed which allows processor-to-processor interactions to be simulated, collisions (and respective probabilities) to be logged, collision-prone areas to be identified, and network control variable adjustments to be reentered as a means of examining and reducing collision-prone regimes that occur in the process of simulating a complete task sequence.

Disease registries on the nationwide health information network.

PubMed

Russler, Daniel

2011-05-01

Donation by individuals of their protected health information (PHI) for evidence-based research potentially benefits all individuals with disease through improved understandings of disease patterns. In the future, a better understanding of how disease features combine into unique patterns of disease will generate new disease classifications, supporting greater specificity in health management techniques. However, without large numbers of people who donate their PHI to disease registries designed for research, it is difficult for researchers to discover the existence of complex patterns or to create more specific evidence-based management techniques. In order to identify new opportunities in disease registry design, an analysis of the current stage of maturity of the newly created U.S. Nationwide Health Information Network (NwHIN) related to large-scale consumer donation of PHI is presented. Utilizing a use-case analysis methodology, the consumer-centric designs of the policies and technologies created for the NwHIN were examined for the potential to support consumer donations of PHI to research. The NwHIN design has placed the enforcement point for the policy-based release of PHI over the Internet into a specialized gateway accessible to consumer authorization. However, current NwHIN policies leave the final decision regarding release of PHI for research to the health care providers rather than to the consumers themselves. Should disease registries designed for research be established on the NwHIN, consumers might then directly authorize the donation of their PHI to these disease registries. However, under current NwHIN policies, consumer authorization does not guarantee release of PHI by health providers. © 2011 Diabetes Technology Society.

Viral dynamics in primary HIV-1 infection. Karolinska Institutet Primary HIV Infection Study Group.

PubMed

Lindbäck, S; Karlsson, A C; Mittler, J; Blaxhult, A; Carlsson, M; Briheim, G; Sönnerborg, A; Gaines, H

2000-10-20

To study the natural course of viremia during primary HIV infection (PHI). Eight patients were followed from a median of 5 days from the onset of PHI illness. Plasma HIV-1 RNA levels were measured frequently and the results were fitted to mathematical models. HIV-1 RNA levels were also monitored in nine patients given two reverse transcriptase inhibitors and a protease inhibitor after a median of 7 days from the onset of PHI illness. HIV-1 RNA appeared in the blood during the week preceding onset of PHI illness and increased rapidly during the first viremic phase, reaching a peak at a mean of 7 days after onset of illness. This was followed by a phase of rapidly decreasing levels of HIV-1 RNA to an average of 21 days after onset. Viral density continued to decline thereafter but at a 5- to 50-fold lower rate; a steady-state level was reached at a median of 2 months after onset of PHI. Peak viral density levels correlated significantly with levels measured between days 50 and 600. Initiation of antiretroviral treatment during PHI resulted in rapidly declining levels to below 50 copies/mL. This study demonstrates the kinetic phases of viremia during PHI and indicates two new contributions to the natural history of HIV-1 infection: PHI peak levels correlate with steady-state levels and HIV-1 RNA declines biphasically; an initial rapid decay is usually followed by a slow decay, which is similar to the initial changes seen with antiviral treatment.

Evaluation of [-2] proPSA and Prostate Health Index (phi) for the detection of prostate cancer: a systematic review and meta-analysis.

PubMed

Filella, Xavier; Giménez, Nuria

2013-04-01

The usefulness of %[-2] proPSA and Prostate Health Index (phi) in the detection of prostate cancer are currently unknown. It has been suggested that these tests can distinguish prostate cancer from benign prostatic diseases better than PSA or %fPSA. We performed a systematic review and meta-analysis of the available scientific evidence to evaluate the clinical usefulness of %[-2] proPSA and phi. Relevant published papers were identified by searching computerized bibliographic systems. Data on sensitivity and specificity were extracted from 12 studies: 10 studies about %[-2] proPSA (3928 patients in total, including 1762 with confirmed prostate cancer) and eight studies about phi (2919 patients in total, including 1515 with confirmed prostate cancer). The sensitivity for the detection of prostate cancer was 90% for %[-2] proPSA and phi, while the pooled specificity was 32.5% (95% CI 30.6-34.5) and 31.6% (95% CI 29.2-34.0) for %[-2] proPSA and phi, respectively. The measurement of %[-2] proPSA improves the accuracy of prostate cancer detection in comparison with PSA or %fPSA, particularly in the group of patients with PSA between 2 μg/L and 10 μg/L. Similar results were obtained measuring phi. Using these tests, it is possible to reduce the number of unnecessary biopsies, maintaining a high cancer detection rate. Published results also showed that %[-2] proPSA and phi are related to the aggressiveness of the tumor.

Observation of phiK. pi. decay of the K/sup 0/(2060)

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

Torres, S.; Ficenec, J.R.; Mikocki, S.

We have studied inclusive pN..-->..K-/sup +/K/sup -/K/sup +/K/sup -/X final states at 400 GeV/c and present here evidence for K/sup *//sup 0/(2060)..-->..phiK/sup +-/..pi../sup minus-or-plus/ and phiK-italic/sup *//sup 0/(890). .AE

The special radiation-hardened processors for new highly informative experiments in space

NASA Astrophysics Data System (ADS)

Serdin, O. V.; Antonov, A. A.; Dubrovsky, A. G.; Novogilov, E. A.; Zuev, A. L.

2017-01-01

The article provides a detailed description of the series of special radiation-hardened microprocessor developed by SRISA for use in space technology. The microprocessors have 32-bit and 64-bit KOMDIV architecture with embedded SpaceWire, RapidIO, Ethernet and MIL-STD-1553B interfaces. These devices are used in space telescope GAMMA-400 data acquisition system, and may also be applied to other experiments in space (such as observatory “Millimetron” etc.).

The Measurement of Spectral Characteristics and Composition of Radiation in Atlas with MEDIPIX2-USB Devices

NASA Astrophysics Data System (ADS)

Campbell, M.; Doležal, Z.; Greiffenberg, D.; Heijne, E.; Holy, T.; Idárraga, J.; Jakůbek, J.; Král, V.; Králík, M.; Lebel, C.; Leroy, C.; Llopart, X.; Lord, G.; Maneuski, D.; Ouellette, O.; Sochor, V.; Pospíšil, S.; Suk, M.; Tlustos, L.; Vykydal, Z.; Wilhelm, I.

2008-06-01

A network of devices to perform real-time measurements of the spectral characteristics and composition of radiation in the ATLAS detector and cavern during its operation is being built. This system of detectors will be a stand alone system fully capable of delivering real-time images of fluxes and spectral composition of different particle species including slow and fast neutrons. The devices are based on MEDIPIX2 pixel silicon detectors that will be operated via active USB cables and USB-Ethernet extenders through an Ethernet network by a PC located in the USA15 ATLAS control room. The installation of 14 devices inside ATLAS (detector and cavern) is in progress.

Characterization of a new ViI-like Erwinia amylovora bacteriophage phiEa2809.

PubMed

Lagonenko, Alexander L; Sadovskaya, Olga; Valentovich, Leonid N; Evtushenkov, Anatoly N

2015-04-01

Erwinia amylovora is a Gram-negative plant pathogenic bacteria causing fire blight disease in many Rosaceae species. A novel E. amylovora bacteriophage, phiEa2809, was isolated from symptomless apple leaf sample collected in Belarus. This phage was also able to infect Pantoea agglomerans strains. The genome of phiEa2809 is a double-stranded linear DNA 162,160 bp in length, including 145 ORFs and one tRNA gene. The phiEa2809 genomic sequence is similar to the genomes of the Serratia plymutica phage MAM1, Shigella phage AG-3, Dickeya phage vB DsoM LIMEstone1 and Salmonella phage ViI and lacks similarity to described E. amylovora phage genomes. Based on virion morphology (an icosahedral head, long contractile tail) and genome structure, phiEa2809 was classified as a member of Myoviridae, ViI-like bacteriophages group. PhiEa2809 is the firstly characterized ViI-like bacteriophage able to lyse E. amylovora. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Increased intracellular pH is necessary for adult epithelial and embryonic stem cell differentiation

PubMed Central

Azimova, Dinara R.

2016-01-01

Despite extensive knowledge about the transcriptional regulation of stem cell differentiation, less is known about the role of dynamic cytosolic cues. We report that an increase in intracellular pH (pHi) is necessary for the efficient differentiation of Drosophila adult follicle stem cells (FSCs) and mouse embryonic stem cells (mESCs). We show that pHi increases with differentiation from FSCs to prefollicle cells (pFCs) and follicle cells. Loss of the Drosophila Na+–H+ exchanger DNhe2 lowers pHi in differentiating cells, impairs pFC differentiation, disrupts germarium morphology, and decreases fecundity. In contrast, increasing pHi promotes excess pFC cell differentiation toward a polar/stalk cell fate through suppressing Hedgehog pathway activity. Increased pHi also occurs with mESC differentiation and, when prevented, attenuates spontaneous differentiation of naive cells, as determined by expression of microRNA clusters and stage-specific markers. Our findings reveal a previously unrecognized role of pHi dynamics for the differentiation of two distinct types of stem cell lineages, which opens new directions for understanding conserved regulatory mechanisms. PMID:27821494

High Performance Parallel Architectures

NASA Technical Reports Server (NTRS)

El-Ghazawi, Tarek; Kaewpijit, Sinthop

1998-01-01

Traditional remote sensing instruments are multispectral, where observations are collected at a few different spectral bands. Recently, many hyperspectral instruments, that can collect observations at hundreds of bands, have been operational. Furthermore, there have been ongoing research efforts on ultraspectral instruments that can produce observations at thousands of spectral bands. While these remote sensing technology developments hold great promise for new findings in the area of Earth and space science, they present many challenges. These include the need for faster processing of such increased data volumes, and methods for data reduction. Dimension Reduction is a spectral transformation, aimed at concentrating the vital information and discarding redundant data. One such transformation, which is widely used in remote sensing, is the Principal Components Analysis (PCA). This report summarizes our progress on the development of a parallel PCA and its implementation on two Beowulf cluster configuration; one with fast Ethernet switch and the other with a Myrinet interconnection. Details of the implementation and performance results, for typical sets of multispectral and hyperspectral NASA remote sensing data, are presented and analyzed based on the algorithm requirements and the underlying machine configuration. It will be shown that the PCA application is quite challenging and hard to scale on Ethernet-based clusters. However, the measurements also show that a high- performance interconnection network, such as Myrinet, better matches the high communication demand of PCA and can lead to a more efficient PCA execution.

Gravitino-overproduction problem in an inflationary universe

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

Kawasaki, Masahiro; Takahashi, Fuminobu; Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607 Hamburg

We show that the gravitino-overproduction problem is prevalent among inflation models in supergravity. An inflaton field {phi} generically acquires (effective) nonvanishing auxiliary field G{sub {phi}}{sup (eff)}, if the Kaehler potential is nonminimal. The inflaton field then decays into a pair of the gravitinos. We extensively study the cosmological constraints on G{sub {phi}}{sup (eff)} for a wide range of the gravitino mass. For many inflation models we explicitly estimate G{sub {phi}}{sup (eff)}, and show that the gravitino-overproduction problem severely constrains the inflation models, unless such an interaction as K={kappa}/2 vertical bar {phi}|{sup 2}z{sup 2}+H.c. is suppressed (here z is the fieldmore » responsible for the supersymmetry breaking). We find that many of them are already excluded or on the verge of, if {kappa}{approx}O(1)« less

A de-identifier for medical discharge summaries.

PubMed

Uzuner, Ozlem; Sibanda, Tawanda C; Luo, Yuan; Szolovits, Peter

2008-01-01

Clinical records contain significant medical information that can be useful to researchers in various disciplines. However, these records also contain personal health information (PHI) whose presence limits the use of the records outside of hospitals. The goal of de-identification is to remove all PHI from clinical records. This is a challenging task because many records contain foreign and misspelled PHI; they also contain PHI that are ambiguous with non-PHI. These complications are compounded by the linguistic characteristics of clinical records. For example, medical discharge summaries, which are studied in this paper, are characterized by fragmented, incomplete utterances and domain-specific language; they cannot be fully processed by tools designed for lay language. In this paper, we show that we can de-identify medical discharge summaries using a de-identifier, Stat De-id, based on support vector machines and local context (F-measure=97% on PHI). Our representation of local context aids de-identification even when PHI include out-of-vocabulary words and even when PHI are ambiguous with non-PHI within the same corpus. Comparison of Stat De-id with a rule-based approach shows that local context contributes more to de-identification than dictionaries combined with hand-tailored heuristics (F-measure=85%). Comparison with two well-known named entity recognition (NER) systems, SNoW (F-measure=94%) and IdentiFinder (F-measure=36%), on five representative corpora show that when the language of documents is fragmented, a system with a relatively thorough representation of local context can be a more effective de-identifier than systems that combine (relatively simpler) local context with global context. Comparison with a Conditional Random Field De-identifier (CRFD), which utilizes global context in addition to the local context of Stat De-id, confirms this finding (F-measure=88%) and establishes that strengthening the representation of local context may be more beneficial for de-identification than complementing local with global context.

The organization of human epidermis: functional epidermal units and phi proportionality.

PubMed

Hoath, Steven B; Leahy, D G

2003-12-01

The concept that mammalian epidermis is structurally organized into functional epidermal units has been proposed on the basis of stratum corneum (SC) architecture, proliferation kinetics, melanocyte:keratinocyte ratios (1:36), and, more recently, Langerhans cell: epidermal cell ratios (1:53). This article examines the concept of functional epidermal units in human skin in which the maintenance of phi (1.618034) proportionality provides a central organizing principle. The following empirical measurements were used: 75,346 nucleated epidermal cells per mm2, 1394 Langerhans cells per mm2, 1999 melanocytes per mm2, 16 (SC) layers, 900-microm2 corneocyte surface area, 17,778 corneocytes per mm2, 14-d (SC) turnover time, and 93,124 per mm2 total epidermal cells. Given these empirical data: (1) the number of corneocytes is a mean proportional between the sum of the Langerhans cell + melanocyte populations and the number of epidermal cells, 3393/17,778-17,778/93,124; (2) the ratio of nucleated epidermal cells over corneocytes is phi proportional, 75,346/17,778 approximately phi3; (3) assuming similar 14-d turnover times for the (SC) and Malpighian epidermis, the number of corneocytes results from subtraction of a cellular fraction equal to approximately 2/phi2 x the number of living cells, 75,436 - (2/phi2 x 75,346) approximately 17,778; and (4) if total epidermal turnover time equals (SC) turnover time x the ratio of living/dead cells, then compartmental turnover times are unequal (14 d for (SC) to 45.3 d for nucleated epidermis approximately 1/2phi) and cellular replacement rates are 52.9 corneocytes/69.3 keratinocytes per mm2 per h approximately 2/phi2. These empirically derived equivalences provide logicomathematical support for the presence of functional epidermal units in human skin. Validation of a phi proportional unit architecture in human epidermis will be important for tissue engineering of skin and the design of instruments for skin measurement.

Functional characterization of intracellular pH regulators responsible for acid extrusion in human radial artery smooth muscle cells.

PubMed

Lee, Chung-Yi; Tsai, Yi-Ting; Chang, Chung-Yi; Chang, Yi-Yu; Cheng, Tzu-Hurng; Tsai, Chien-Sung; Loh, Shih-Hurng

2014-10-31

Intracellular pH (pHi) is a critical factor influencing many important cellular functions. Acid extrusion carriers such as an Na⁺/H⁺ exchanger (NHE) Na⁺/HCO₃⁻ cotransporter (NBC) and monocarboxylate transporters (MCT) can be activated when cells are in an acidic condition (pHi < 7.1). Human radial artery smooth muscle cells (HRASMC) is an important conduit in coronary artery bypass graft surgery. However, such far, the pHi regulators have not been characterized in HRASMCs. We therefore investigated the mechanism of pHi recovery from intracellular acidosis and alkalosis, induced by NH₄Cl-prepulse and Na-acetate-prepulse, respectively, using intracellular 2',7'-bis(2-carboxethyl)-5(6)- carboxy-fluorescein (BCECF)-fluorescence in HRASMCs. Cultured HRASMCs were derived from the segments of human radial artery that were obtained from patients undergoing bypass grafting. The resting pHi is 7.22 ± 0.03 and 7.17 ± 0.02 for HEPES- (nominally HCO₃⁻-free) and CO₂/HCO₃⁻- buffered solution, respectively. In HEPES-buffered solution, a pHi recovery from induced intracellular acidosis could be blocked completely by 30 μM HOE 694 (3-methylsulfonyl-4-piperidinobenzoyl, guanidine hydrochloride) a specific NHE inhibitor, or by removing [Na⁺]₀. In 3% CO₂/HCO₃⁻-buffered solution, HOE 694 slowed the pHi recovery from the induced intracellular acidosis only, while adding together with DIDS (a specific NBC inhibitor) or removal of [Na⁺]₀ entirely inhibited the acid extrusion. Moreover, α-cyano-4-hydroxycinnamate (CHC; a specific blocker of MCT) blocked the lactate-induced pHi changes. In conclusion, we demonstrate, for the first time, that 3 different pHi regulators responsible for acid extruding, i.e. NHE and NBC, and MCT, are functionally co-existed in cultured HRASMCs.

A De-identifier for Medical Discharge Summaries1

PubMed Central

Uzuner, Özlem; Sibanda, Tawanda C.; Luo, Yuan; Szolovits, Peter

2008-01-01

Objective Clinical records contain significant medical information that can be useful to researchers in various disciplines. However, these records also contain personal health information (PHI) whose presence limits the use of the records outside of hospitals. The goal of de-identification is to remove all PHI from clinical records. This is a challenging task because many records contain foreign and misspelled PHI; they also contain PHI that are ambiguous with non-PHI. These complications are compounded by the linguistic characteristics of clinical records. For example, medical discharge summaries, which are studied in this paper, are characterized by fragmented, incomplete utterances and domain-specific language; they cannot be fully processed by tools designed for lay language. Methods and Results In this paper, we show that we can de-identify medical discharge summaries using a de-identifier, Stat De-id, based on support vector machines and local context (F-measure = 97% on PHI). Our representation of local context aids de-identification even when PHI include out-of-vocabulary words and even when PHI are ambiguous with non-PHI within the same corpus. Comparison of Stat De-id with a rule-based approach shows that local context contributes more to de-identification than dictionaries combined with hand-tailored heuristics (F-measure = 85%). Comparison with two well-known named entity recognition (NER) systems, SNoW (F-measure = 94%) and IdentiFinder (F-measure = 36%), on five representative corpora show that when the language of documents is fragmented, a system with a relatively thorough representation of local context can be a more effective de-identifier than systems that combine (relatively simpler) local context with global context. Comparison with a Conditional Random Field De-identifier (CRFD), which utilizes global context in addition to the local context of Stat De-id, confirms this finding (F-measure = 88%) and establishes that strengthening the representation of local context may be more beneficial for de-identification than complementing local with global context. PMID:18053696

Biogas Laminar Burning Velocity and Flammability Characteristics in Spark Ignited Premix Combustion

NASA Astrophysics Data System (ADS)

Anggono, Willyanto; Wardana, I. N. G.; Lawes, M.; Hughes, K. J.; Wahyudi, Slamet; Hamidi, Nurkholis; Hayakawa, Akihiro

2013-04-01

Spherically expanding flames propagating at constant pressure were employed to determine the laminar burning velocity and flammability characteristics of biogas-air mixtures in premixed combustion to uncover the fundamental flame propagation characteristics of a new alternative and renewable fuel. The results are compared with those from a methane-air flame. Biogas is a sustainable and renewable fuel that is produced in digestion facilities. The composition of biogas discussed in this paper consists of 66.4% methane, 30.6% carbon dioxide and 3% nitrogen. Burning velocity was measured at various equivalence ratios (phi) using a photographic technique in a high pressure fan-stirred bomb, the initial condition being at room temperature and atmospheric pressure. The flame for methane-air mixtures propagates from phi=0.6 till phi=1.3. The flame at phi >= 1.4 does not propagate because the combustion reaction is quenched by the larger mass of fuel. At phi<=0.5, it does not propagate as well since the heat of reaction is insufficient to burn the mixtures. The flame for biogas-air mixtures propagates in a narrower range, that is from phi=0.6 to phi=1.2. Different from the methane flame, the biogas flame does not propagate at phi>=1.3 because the heat absorbed by inhibitors strengthens the quenching effect by the larger mass of fuel. As in the methane flame, the biogas flame at phi<=0.5 does not propagate. This shows that the effect of inhibitors in extremely lean mixtures is small. Compared to a methane-air mixture, the flammability characteristic (flammable region) of biogas becomes narrower in the presence of inhibitors (carbon dioxide and nitrogen) and the presence of inhibitors causes a reduction in the laminar burning velocity. The inhibitor gases work more effectively at rich mixtures because the rich biogas-air mixtures have a higher fraction of carbon dioxide and nitrogen components compared to the lean biogas-air mixtures.

Comparison of prostate cancer gene 3 score, prostate health index and percentage free prostate-specific antigen for differentiating histological inflammation from prostate cancer and other non-neoplastic alterations of the prostate at initial biopsy.

PubMed

De Luca, Stefano; Passera, Roberto; Bollito, Enrico; Manfredi, Matteo; Scarpa, Roberto Mario; Sottile, Antonino; Randone, Donato Franco; Porpiglia, Francesco

2014-12-01

To determine if prostate cancer gene 3 (PCA3) score, Prostate Health Index (PHI), and percent free prostate-specific antigen (%fPSA) may be used to differentiate prostatitis from prostate cancer (PCa), benign prostatic hyperplasia (BPH) and high-grade prostate intraepithelial neoplasia (HG-PIN) in patients with elevated PSA and negative digital rectal examination (DRE). in the present prospective study, 274 patients, undergoing PCA3 score, PHI and %fPSA assessments before initial biopsy, were enrolled. Three multivariate logistic regression models were used to test PCA3 score, PHI and %fPSA as risk factors for prostatitis vs. PCa, vs. BPH, and vs. HG-PIN. All the analyses were performed for the whole patient cohort and for the 'gray zone' of PSA (4-10 ng/ml) cohort (188 individuals). The determinants for prostatitis vs. PCa were PCA3 score, PHI and %fPSA (Odds Ratio [OR]=0.97, 0.96 and 0.94, respectively). Unit increase of PHI was the only risk factor for prostatitis vs. BPH (OR=1.06), and unit increase of PCA3 score for HG-PIN vs. prostatitis (OR=0.98). In the 'gray zone' PSA cohort, the determinants for prostatitis vs. PCa were PCA3 score, PHI and %fPSA (OR=0.96, 0.94 and 0.92, respectively), PCA3 score and PHI for prostatitis vs. BPH (OR=0.96 and 1.08, respectively), and PCA3 score for prostatitis vs. HG-PIN (OR=0.97). The clinical benefit of using PCA3 score and PHI to estimate prostatitis vs. PCa was comparable; even %fPSA had good diagnostic performance, being a faster and cheaper marker. PHI was the only determinant for prostatitis vs. BPH, while PCA3 score for prostatitis vs. HG-PIN. Copyright© 2014 International Institute of Anticancer Research (Dr. John G. Delinassios), All rights reserved.

The anticholinergic and antiglutamatergic drug caramiphen reduces seizure duration in soman-exposed rats: Synergism with the benzodiazepine diazepam

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

Schultz, M.K.; Wright, L.K.M.; Stone, M.F.

2012-03-15

Therapy of seizure activity following exposure to the nerve agent soman (GD) includes treatment with the anticonvulsant diazepam (DZP), an allosteric modulator of γ-aminobutyric acid A (GABA{sub A}) receptors. However, seizure activity itself causes the endocytosis of GABA{sub A} receptors and diminishes the inhibitory effects of GABA, thereby reducing the efficacy of DZP. Treatment with an N-methyl-D-aspartic acid (NMDA) receptor antagonist prevents this reduction in GABAergic inhibition. We examined the efficacy of the NMDA receptor antagonist caramiphen edisylate (CED; 20 mg/kg, im) and DZP (10 mg/kg, sc), administered both separately and in combination, at 10, 20 or 30 min followingmore » seizure onset for attenuation of the deleterious effects associated with GD exposure (1.2 LD{sub 50}; 132 μg/kg, sc) in rats. Outcomes evaluated were seizure duration, neuropathology, acetylcholinesterase (AChE) activity, body weight, and temperature. We also examined the use of the reversible AChE inhibitor physostigmine (PHY; 0.2 mg/kg, im) as a therapy for GD exposure. We found that the combination of CED and DZP yielded a synergistic effect, shortening seizure durations and reducing neuropathology compared to DZP alone, when treatment was delayed 20–30 min after seizure onset. PHY reduced the number of animals that developed seizures, protected a fraction of AChE from GD inhibition, and attenuated post-exposure body weight and temperature loss independent of CED and/or DZP treatment. We conclude that: 1) CED and DZP treatment offers considerable protection against the effects of GD and 2) PHY is a potential therapeutic option following GD exposure, albeit with a limited window of opportunity. -- Highlights: ► Soman (GD) produced seizure activity resulting in neuropathology in rats. ► Tx: caramiphen (CED) and/or diazepam (DZP) @ 10, 20 or 30 min after seizure onset. ► CED/DZP showed superior anticonvulsant and neuroprotective capacity. ► Physostigmine (PHY) was examined as an adjunct post-exposure therapy. ► PHY attenuated GD-induced seizure development, but not seizure duration.« less

System and method for constructing filters for detecting signals whose frequency content varies with time

DOEpatents

Qian, Shie; Dunham, Mark E.

1996-01-01

A system and method for constructing a bank of filters which detect the presence of signals whose frequency content varies with time. The present invention includes a novel system and method for developing one or more time templates designed to match the received signals of interest and the bank of matched filters use the one or more time templates to detect the received signals. Each matched filter compares the received signal x(t) with a respective, unique time template that has been designed to approximate a form of the signals of interest. The robust time domain template is assumed to be of the order of w(t)=A(t)cos{2.pi..phi.(t)} and the present invention uses the trajectory of a joint time-frequency representation of x(t) as an approximation of the instantaneous frequency function {.phi.'(t). First, numerous data samples of the received signal x(t) are collected. A joint time frequency representation is then applied to represent the signal, preferably using the time frequency distribution series (also known as the Gabor spectrogram). The joint time-frequency transformation represents the analyzed signal energy at time t and frequency .function., P(t,f), which is a three-dimensional plot of time vs. frequency vs. signal energy. Then P(t,f) is reduced to a multivalued function f(t), a two dimensional plot of time vs. frequency, using a thresholding process. Curve fitting steps are then performed on the time/frequency plot, preferably using Levenberg-Marquardt curve fitting techniques, to derive a general instantaneous frequency function .phi.'(t) which best fits the multivalued function f(t), a trajectory of the joint time-frequency domain representation of x(t). Integrating .phi.'(t) along t yields .phi.(t), which is then inserted into the form of the time template equation. A suitable amplitude A(t) is also preferably determined. Once the time template has been determined, one or more filters are developed which each use a version or form of the time template.

Complete Genome Sequences of Two Novel Staphylococcus aureus Podoviruses of Potential Therapeutic Use, vB_SauP_phiAGO1.3 and vB_SauP_phiAGO1.9

PubMed Central

Gozdek, Agnieszka; Głowacka-Rutkowska, Aleksandra; Gawor, Jan; Empel, Joanna; Gromadka, Robert

2018-01-01

ABSTRACT Here, we report the genome sequences of two Staphylococcus aureus phages belonging to the family Podoviridae and subfamily Picovirinae, vB_SauP_phiAGO1.3 and vB_SauP_phiAGO1.9, which were isolated from Warsaw sewage. Analysis of their genomes provides valuable information about the diversity of phages belonging to the genus Rosenblumvirus and their genes that undergo evolutionary adaptation to cells of different host strains. PMID:29700131

Complete Genome Sequences of Two Novel Staphylococcus aureus Podoviruses of Potential Therapeutic Use, vB_SauP_phiAGO1.3 and vB_SauP_phiAGO1.9.

PubMed

Gozdek, Agnieszka; Głowacka-Rutkowska, Aleksandra; Gawor, Jan; Empel, Joanna; Gromadka, Robert; Łobocka, Małgorzata B

2018-04-26

Here, we report the genome sequences of two Staphylococcus aureus phages belonging to the family Podoviridae and subfamily Picovirinae , vB_SauP_phiAGO1.3 and vB_SauP_phiAGO1.9, which were isolated from Warsaw sewage. Analysis of their genomes provides valuable information about the diversity of phages belonging to the genus Rosenblumvirus and their genes that undergo evolutionary adaptation to cells of different host strains. Copyright © 2018 Gozdek et al.

Prospects for studying penguin decays in LHCb experiments

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

Barsuk, S. Ya.; Pakhlova, G. V., E-mail: Galina.Pakhlova@cern.ch; Belyaev, I. M.

2006-04-15

Investigation of loop penguin decays of beauty hadrons seems promising in testing the predictions of the Standard Model of electroweak and strong interactions and in seeking new phenomena beyond the Standard Model. The possibility of studying the radiative penguin decays B{sup 0} {sup {yields}} K*{sup 0}{gamma}, B{sup 0}{sub s} {sup {yields}} {phi}{gamma}, and B{sup 0} {sup {yields}} {omega}{gamma} and the gluonic penguin decays B{sup 0} {sup {yields}} {phi}K{sup 0}{sub S} and B{sup 0}{sub s} {sup {yields}} {phi}{phi} in LHCb experiments is discussed.

The effect of extracellular weak acids and bases on the intracellular buffering power of snail neurones.

PubMed Central

Szatkowski, M S

1989-01-01

1. Intracellular pH (pHi) was measured in snail neurones using pH-sensitive glass microelectrodes. The influence of externally applied weak acids and bases on the total intracellular buffering power (beta T) was investigated by monitoring the pHi changes caused by the intracellular ionophoretic injection of HCl. 2. In the absence of weak acids or bases a reduction in the extracellular HEPES concentration had no effect on pHi or on beta T. It did, however, reduce slightly the rate of pHi recovery following HCl injection. 3. The presence of CO2 greatly increased beta T. However, as predicted for an open buffer system, the contributions to intracellular buffering by CO2 (beta CO2) decreased as pHi decreased. 4. When added to the superfusate, procaine, 4-aminopyridine, trimethylamine and NH4Cl (1-10 mM) all increased steady-state pHi. Procaine was fastest at increasing pHi and 4-aminopyridine the slowest. All four of these weak bases increased beta T. 5. The intracellular buffering action by these weak bases varied. HCl injection in the presence of procaine usually resulted in steady-state pHi changes with no pHi transients. In the presence of the other three weak bases HCl injections resulted in intracellular acidifications which were followed by pHi recovery-like transients. However, these were not blocked by SITS (4-acetamido-4'-isothiocyanatostilbene-2,2'-disulphonic acid) or by CaCl2 and I thus conclude that these transients were as a result of slow or incomplete intracellular buffering by the weak bases. 6. In many cells there was a good correlation between the measured contributions to intracellular buffering by the weak bases (beta base) and those predicted assuming a simple two-compartment open system. In all cases, as predicted, beta base increased as pHi decreased. 7. I found a clear relationship between the concentration of external buffer (HEPES) and the rate at which weak bases, applied to the superfusate, were able to increase pHi. The greater the extracellular buffer concentration the greater was the speed of intracellular alkalinization. 8. Lowering the extracellular buffer concentration reduced the efficiency of intracellular buffering by weak bases in response to an intracellular acid load. HCl injection in the presence of weak base caused a larger initial intracellular acidification if the extracellular HEPES concentration was reduced. 9. In conclusion, both weak acids and weak bases can make very large, pHi-dependent contributions to intracellular buffering by way of open buffer systems.(ABSTRACT TRUNCATED AT 400 WORDS) PMID:2555474

A pyruvate-proton symport and an H+-ATPase regulate the intracellular pH of Trypanosoma brucei at different stages of its life cycle.

PubMed

Vanderheyden, N; Wong, J; Docampo, R

2000-02-15

Regulation of intracellular pH (pH(i)) and H(+) efflux were investigated in Trypanosoma brucei bloodstream and procyclic trypomastigotes using the fluorescent dyes 2', 7'-bis-(2-carboxyethyl)-5(6)-carboxyfluorescein (BCECF) acetoxymethyl ester and free BCECF respectively. pH(i) in bloodstream and procyclic trypomastigotes was 7.47+/-0.06 and 7. 53+/-0.07 respectively. Differences in the mechanisms for the regulation of pH(i) were noted between bloodstream and procyclic forms. Procyclic trypomastigotes maintained their pH(i) at neutral over a wide range of external pH values from 6 to 8, and in the absence of K(+) or Na(+). The H(+)-ATPase inhibitors N, N'-dicyclohexylcarbodi-imide (DCCD), diethylstilboestrol and N-ethylmaleimide substantially decreased the steady-state pH(i) and inhibited its recovery from acidification. The rate of H(+) efflux in these forms was determined to be 62+/-6.5 nmol/min per mg of protein, and was substantially decreased by H(+)-ATPase inhibitors. The data support the presence of an H(+)-ATPase as the major regulator of pH(i) in procyclic trypomastigotes. In contrast, bloodstream trypomastigotes were unable to maintain a neutral pH under acidic conditions, and their steady-state pH(i) and recovery from acidification were unaffected by H(+)-ATPase inhibitors, except for DCCD (100 microM). Their steady-state pH(i) was markedly decreased in glucose-free buffer or by >/=10 mM pyruvate, whereas procyclic trypomastigotes were unaffected by similar treatments. The rate of H(+) efflux in bloodstream trypomastigotes was 534+/-38 nmol/min per mg of protein, and was decreased in the absence of glucose and by the addition of pyruvate or DCCD. Pyruvate efflux in these forms was calculated to be 499+/-34 nmol/min per mg of protein, and was significantly inhibited by DCCD, 4, 4'-di-isothiocyanatodihydrostilbene-2,2'-disulphonic acid and alpha-cyanohydroxycinnamic acid. The pyruvate analogues beta-hydroxypyruvate, 3-bromopyruvate, 3-oxoglutarate, oxaloacetate, 3-oxoisovalerate and 3-oxoisohexanoate significantly decreased pH(i), as well as proton and pyruvate efflux, whereas lactate had only a small effect, and no effect was observed with citrate or fumarate. The inhibition by pyruvate analogues of pyruvate efflux, proton efflux and acidification of pH(i) supports the hypothesis that pyruvate efflux is accompanied by proton efflux and that this is the major pH(i) control mechanism in bloodstream forms. Inhibition by H(+)-ATPase inhibitors of residual H(+) efflux in the absence of glucose or in the presence of high extracellular pyruvate indicates a minor role for H(+)-ATPase(s) in control of pH(i) in bloodstream forms.

A survey of reimbursement practices of private health insurance companies for pharmaceuticals not covered under the Pharmaceutical Benefits Scheme 2008.

PubMed

Lingaratnam, Senthil M; Kirsa, Sue W; Mellor, James D; Jackson, John; Crellin, Wallace; Fitzsimons, Michael; Zalcberg, John R

2011-05-01

To describe the current practices and policy of Australian private health insurance (PHI) companies with respect to cover for pharmaceuticals not subsidised under the Pharmaceutical Benefits Scheme (PBS). A 2008 review of web-published policy statements for top-level hospital and comprehensive general treatment insurance, and survey of reimbursement practices by way of questionnaire, of 31 Australian-registered, open-membership PHI companies. Description of the level of pharmaceutical cover and important considerations identified by PHI companies for funding non-PBS pharmaceuticals through benefit entitlements or ex-gratia payments. Nine of thirty-one PHI companies (29%) provided responses accounting for ~60% market share of PHI. The majority of smaller PHI firms either declined participation or did not respond. The maximum limits offered for non-PBS pharmaceuticals, under comprehensive general treatment insurance, varied significantly and typically did not adequately cover high-cost pharmaceuticals. Some companies occasionally offered ex-gratia payments (or discretionary payments in excess of the policyholder's entitlement benefits) for high cost-pharmaceuticals. Factors considered important in their decision to approve or reject ex-gratia requests were provided. All results were de-identified. There is little consistency across PHI companies in the manner in which they handle requests for high-cost pharmaceuticals in excess of the defined benefit limits. Such information and processes are not transparent to consumers.

Electroweak vacuum instability and renormalized Higgs field vacuum fluctuations in the inflationary universe

NASA Astrophysics Data System (ADS)

Kohri, Kazunori; Matsui, Hiroki

2017-08-01

In this work, we investigated the electroweak vacuum instability during or after inflation. In the inflationary Universe, i.e., de Sitter space, the vacuum field fluctuations < δ phi 2 > enlarge in proportion to the Hubble scale H2. Therefore, the large inflationary vacuum fluctuations of the Higgs field < δ phi 2 > are potentially catastrophic to trigger the vacuum transition to the negative-energy Planck-scale vacuum state and cause an immediate collapse of the Universe. However, the vacuum field fluctuations < δ phi 2 >, i.e., the vacuum expectation values have an ultraviolet divergence, and therefore a renormalization is necessary to estimate the physical effects of the vacuum transition. Thus, in this paper, we revisit the electroweak vacuum instability from the perspective of quantum field theory (QFT) in curved space-time, and discuss the dynamical behavior of the homogeneous Higgs field phi determined by the effective potential V eff( phi ) in curved space-time and the renormalized vacuum fluctuations < δ phi 2 >ren via adiabatic regularization and point-splitting regularization. We simply suppose that the Higgs field only couples the gravity via the non-minimal Higgs-gravity coupling ξ(μ). In this scenario, the electroweak vacuum stability is inevitably threatened by the dynamical behavior of the homogeneous Higgs field phi, or the formations of AdS domains or bubbles unless the Hubble scale is small enough H< ΛI .

The impact of financial incentives on physician empathy: a study from the perspective of patients with private and statutory health insurance.

PubMed

Neumann, Melanie; Bensing, Jozien; Wirtz, Markus; Wübker, Ansgar; Scheffer, Christian; Tauschel, Diethard; Edelhäuser, Friedrich; Ernstmann, Nicole; Pfaff, Holger

2011-08-01

We hypothesized that patients' ratings of physician empathy (PE) would be higher among those with private health insurance (PHI, referring to financial incentive) than among patients with statutory health insurance (SHI). A postal survey was administered to 710 cancer patients. PE was assessed using the Consultation-and-Relational-Empathy measure. T-tests were conducted to analyse whether PHI and SHI-patients differ in their ratings of PE and variables relating to contact time with the physician. Structural-equation-modelling (SEM) verified mediating effects. PHI-patients rated physician empathy higher. SEM revealed that PHI-status has a strong significant effect on frequency of talking with the physician, which has a strong significant effect (1) on PE and (2) has a moderate effect on patients' perception of medical staff stress, thereby also affecting patients' ratings of PE. Our findings suggest that PHI-status is one necessary precondition for physicians spending more time with the patient. Spending more time with the PHI-patient has two major effects: it results in a more positive perception of PE and positively impacts PHI-patients' perception of medical staff stress, which in turn, again influences PE. Health policy should discuss these findings in terms of equality in receiving high-quality care. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

Intracellular pH gradients in migrating cells.

PubMed

Martin, Christine; Pedersen, Stine F; Schwab, Albrecht; Stock, Christian

2011-03-01

Cell polarization along the axis of movement is required for migration. The localization of proteins and regulators of the migratory machinery to either the cell front or its rear results in a spatial asymmetry enabling cells to simultaneously coordinate cell protrusion and retraction. Protons might function as such unevenly distributed regulators as they modulate the interaction of focal adhesion proteins and components of the cytoskeleton in vitro. However, an intracellular pH (pH(i)) gradient reflecting a spatial asymmetry of protons has not been shown so far. One major regulator of pH(i), the Na(+)/H(+) exchanger NHE1, is essential for cell migration and accumulates at the cell front. Here, we test the hypothesis that the uneven distribution of NHE1 activity creates a pH(i) gradient in migrating cells. Using the pH-sensitive fluorescent dye BCECF, pH(i) was measured in five cell lines (MV3, B16V, NIH3T3, MDCK-F1, EA.hy926) along the axis of movement. Differences in pH(i) between the front and the rear end (ΔpH(i) front-rear) were present in all cell lines, and inhibition of NHE1 either with HOE642 or by absence of extracellular Na(+) caused the pH(i) gradient to flatten or disappear. In conclusion, pH(i) gradients established by NHE1 activity exist along the axis of movement.

Elevated intracellular pH appears in aged oocytes and causes oocyte aneuploidy associated with the loss of cohesion in mice

PubMed Central

Cheng, Jin-Mei; Li, Jian; Tang, Ji-Xin; Chen, Su-Ren; Deng, Shou-Long; Jin, Cheng; Zhang, Yan; Wang, Xiu-Xia; Zhou, Chen-Xi; Liu, Yi-Xun

2016-01-01

ABSTRACT Increases in the aneuploidy rate caused by the deterioration of cohesion with increasing maternal age have been well documented. However, the molecular mechanism for the loss of cohesion in aged oocytes remains unknown. In this study, we found that intracellular pH (pHi) was elevated in aged oocytes, which might disturb the structure of the cohesin ring to induce aneuploidy. We observed for the first time that full-grown germinal vesicle (GV) oocytes displayed an increase in pHi with advancing age in CD1 mice. Furthermore, during the in vitro oocyte maturation process, the pHi was maintained at a high level, up to ∼7.6, in 12-month-old mice. Normal pHi is necessary to maintain protein localization and function. Thus, we put forward a hypothesis that the elevated oocyte pHi might be related to the loss of cohesion and the increased aneuploidy in aged mice. Through the in vitro alkalinization treatment of young oocytes, we observed that the increased pHi caused an increase in the aneuploidy rate and the sister inter-kinetochore (iKT) distance associated with the strength of cohesion and caused a decline in the cohesin subunit SMC3 protein level. Young oocytes with elevated pHi exhibited substantially the increase in chromosome misalignment. PMID:27472084

Characterization of Natronobacterium magadii phage phi Ch1, a unique archaeal phage containing DNA and RNA.

PubMed

Witte, A; Baranyi, U; Klein, R; Sulzner, M; Luo, C; Wanner, G; Krüger, D H; Lubitz, W

1997-02-01

A novel archaeal bacteriophage, phi Ch1, was isolated from a haloalkalophilic archaeon Natronobacterium magadii upon spontaneous lysis. The phage-cured strain N. magadii(L13) was used to demonstrate infectivity of phage phi Ch1. The turbid-plaque morphology and the fact that N. magadii cells isolated from plaques were able to produce phage indicated that phi Ch1 is a temperate phage. The phage morphology resembles other members of Myoviridae-infecting Halobacterium species. In solution below 2M NaCl, the phage lost its morphological stability and infectivity. One- and two-dimensional SDS-PAGE of phage particles revealed at least four major and five minor proteins with molecular masses ranging from 15 to 80 kDa and acidic isoelectric points. Southern blot analysis of chromosomal DNA of a lysogenic N. magadii strain showed that phi Ch1 exists as a chromosomally integrated prophage. The phage particles contain both double-stranded, linear DNA (approx. 55 kbp) as well as several RNA species (80-700 nucleotides). Hybridization of labelled RNA fragments to total DNA from N. magadii and phi Ch1 showed that the virion-associated RNA is host encoded. Part of the phage DNA population is modified and restriction analysis revealed evidence for adenine methylation. Phage phi Ch1 is the first virus described for the genus natronobacterium, and the first phage containing DNA and RNA in mature phage particles.

SimPhy: Phylogenomic Simulation of Gene, Locus, and Species Trees

PubMed Central

Mallo, Diego; De Oliveira Martins, Leonardo; Posada, David

2016-01-01

We present a fast and flexible software package—SimPhy—for the simulation of multiple gene families evolving under incomplete lineage sorting, gene duplication and loss, horizontal gene transfer—all three potentially leading to species tree/gene tree discordance—and gene conversion. SimPhy implements a hierarchical phylogenetic model in which the evolution of species, locus, and gene trees is governed by global and local parameters (e.g., genome-wide, species-specific, locus-specific), that can be fixed or be sampled from a priori statistical distributions. SimPhy also incorporates comprehensive models of substitution rate variation among lineages (uncorrelated relaxed clocks) and the capability of simulating partitioned nucleotide, codon, and protein multilocus sequence alignments under a plethora of substitution models using the program INDELible. We validate SimPhy's output using theoretical expectations and other programs, and show that it scales extremely well with complex models and/or large trees, being an order of magnitude faster than the most similar program (DLCoal-Sim). In addition, we demonstrate how SimPhy can be useful to understand interactions among different evolutionary processes, conducting a simulation study to characterize the systematic overestimation of the duplication time when using standard reconciliation methods. SimPhy is available at https://github.com/adamallo/SimPhy, where users can find the source code, precompiled executables, a detailed manual and example cases. PMID:26526427

Calculated X-ray Intensities Using Monte Carlo Algorithms: A Comparison to Experimental EPMA Data

NASA Technical Reports Server (NTRS)

Carpenter, P. K.

2005-01-01

Monte Carlo (MC) modeling has been used extensively to simulate electron scattering and x-ray emission from complex geometries. Here are presented comparisons between MC results and experimental electron-probe microanalysis (EPMA) measurements as well as phi(rhoz) correction algorithms. Experimental EPMA measurements made on NIST SRM 481 (AgAu) and 482 (CuAu) alloys, at a range of accelerating potential and instrument take-off angles, represent a formal microanalysis data set that has been widely used to develop phi(rhoz) correction algorithms. X-ray intensity data produced by MC simulations represents an independent test of both experimental and phi(rhoz) correction algorithms. The alpha-factor method has previously been used to evaluate systematic errors in the analysis of semiconductor and silicate minerals, and is used here to compare the accuracy of experimental and MC-calculated x-ray data. X-ray intensities calculated by MC are used to generate a-factors using the certificated compositions in the CuAu binary relative to pure Cu and Au standards. MC simulations are obtained using the NIST, WinCasino, and WinXray algorithms; derived x-ray intensities have a built-in atomic number correction, and are further corrected for absorption and characteristic fluorescence using the PAP phi(rhoz) correction algorithm. The Penelope code additionally simulates both characteristic and continuum x-ray fluorescence and thus requires no further correction for use in calculating alpha-factors.

[Surface display of phytase on Saccharomyces cerevisiae for efficient bioethanol production from corn starch].

PubMed

Xiao, Yan; Chen, Xianzhong; Shen, Wei; Yang, Haiquan; Fan, You

2015-12-01

Production of bioethanol using starch as raw material has become a very prominent technology. However, phytate in the raw material not only decreases ethanol production efficiency, but also increases phosphorus discharge. In this study, to decrease phytate content in an ethanol fermentationprocess, Saccharomyces cerevisiae was engineered forheterologous expression of phytase on the cell surface. The phy gene encoding phytase gene was fused with the C-terminal-half region of α-agglutinin and then inserted downstream of the secretion signal gene, to produce a yeast surface-display expression vector pMGK-AG-phy, which was then transformed into S. cerevisiae. The recombinant yeast strain, PHY, successfully displayed phytase on the surface of cells producing 6.4 U/g wet cells and its properties were further characterized. The growthrate and ethanol production of the PHY strain were faster than the parent S. cerevisiae strain in the fermentation medium by simultaneous saccharification and fermentation. Moreover, the phytate concentration decreased by 91% in dry vinasse compared to the control. In summary, we constructed recombinant S. cerevisiae strain displaying phytase on the cell surface, which could effectively reduce the content of phytate, improve the utilization value of vinasse and reduce the discharge of phosphorus. The strain reported here represents a useful novel engineering platform for developing an environment-friendly system for bioethanol production from a corn substrate.

Large-scale contamination of microbial isolate genomes by Illumina PhiX control.

PubMed

Mukherjee, Supratim; Huntemann, Marcel; Ivanova, Natalia; Kyrpides, Nikos C; Pati, Amrita

2015-01-01

With the rapid growth and development of sequencing technologies, genomes have become the new go-to for exploring solutions to some of the world's biggest challenges such as searching for alternative energy sources and exploration of genomic dark matter. However, progress in sequencing has been accompanied by its share of errors that can occur during template or library preparation, sequencing, imaging or data analysis. In this study we screened over 18,000 publicly available microbial isolate genome sequences in the Integrated Microbial Genomes database and identified more than 1000 genomes that are contaminated with PhiX, a control frequently used during Illumina sequencing runs. Approximately 10% of these genomes have been published in literature and 129 contaminated genomes were sequenced under the Human Microbiome Project. Raw sequence reads are prone to contamination from various sources and are usually eliminated during downstream quality control steps. Detection of PhiX contaminated genomes indicates a lapse in either the application or effectiveness of proper quality control measures. The presence of PhiX contamination in several publicly available isolate genomes can result in additional errors when such data are used in comparative genomics analyses. Such contamination of public databases have far-reaching consequences in the form of erroneous data interpretation and analyses, and necessitates better measures to proofread raw sequences before releasing them to the broader scientific community.

Nanobody-based chimeric receptor gene integration in Jurkat cells mediated by PhiC31 integrase

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

Iri-Sofla, Farnoush Jafari; Rahbarizadeh, Fatemeh, E-mail: rahbarif@modares.ac.ir; Ahmadvand, Davoud

2011-11-01

The crucial role of T lymphocytes in anti-tumor immunity has led to the development of novel strategies that can target and activate T cells against tumor cells. Recombinant DNA technology has been used to generate non-MHC-restricted chimeric antigen receptors (CARs). Here, we constructed a panel of recombinant CAR that harbors the anti-MUC1 nanobody and the signaling and co-signaling moieties (CD3{zeta}/CD28) with different spacer regions derived from human IgG3 with one or two repeats of the hinge sequence or the hinge region of Fc{gamma}RII. The PhiC31 integrase system was employed to investigate if the recombination efficiency could be recruited for highmore » and stable expression of T cell chimeric receptor genes. The effect of nuclear localization signal (NLS) and two different promoters (CMV and CAG) on efficacy of PhiC31 integrase in human T cell lines was evaluated. The presence of integrase in combination with NLS, mediated up to 7.6 and 8.5 fold increases in CAR expression in ZCHN-attB and ZCHHN-attB cassette integrated T cells, respectively. Our results showed that highly efficient and stable transduction of the Jurkat cell line by PhiC31 integrase is a feasible modality for generating anti-cancer chimeric T cells for use in cancer immunotherapy.« less

Real Time Sensing and Discrimination of Single Chemicals Using Channel of Phi29 DNA Packaging Nanomotor

PubMed Central

Haque, Farzin; Lunn, Jennifer; Fang, Huaming; Smithrud, David; Guo, Peixuan

2012-01-01

A highly sensitive and reliable method to sense and identify a single chemical at extremely low concentrations and high contamination is important for environmental surveillance, homeland security, athlete drug monitoring, toxin/drug screening, and earlier disease diagnosis. This manuscript reports a method for precise detection of single chemicals. The hub of the bacteriophage phi29 DNA packaging motor is a connector consisting of twelve protein subunits encircled into a 3.6-nm channel as a path for dsDNA to enter during packaging and to exit during infection. The connector has previously been inserted into a lipid bilayer to serve as a membrane-embedded channel. Herein we report the modification of the phi29 channel to develop a class of sensors to detect single chemicals. The Lysine-234 of each protein subunit was mutated to cysteine, generating 12-SH ring lining the channel wall. Chemicals passing through this robust channel and interactions with the SH-group generated extremely reliable, precise, and sensitive current signatures as revealed by single channel conductance assays. Ethane (57 Daltons), thymine (167 Daltons), and benzene (105 Daltons) with reactive thioester moieties were clearly discriminated upon interaction with the available set of cysteine residues. The covalent attachment of each analyte induced discrete step-wise blockage in current signature with a corresponding decrease in conductance due to the physical blocking of the channel. Transient binding of the chemicals also produced characteristic fingerprints that were deduced from the unique blockage amplitude and pattern of the signals. This study shows that the phi29 connector can be used to sense chemicals with reactive thioesters or maleimide using single channel conduction assays based on their distinct fingerprints. The results demonstrated that this channel system could be further developed into very sensitive sensing devices. PMID:22458779

Real-time sensing and discrimination of single chemicals using the channel of phi29 DNA packaging nanomotor.

PubMed

Haque, Farzin; Lunn, Jennifer; Fang, Huaming; Smithrud, David; Guo, Peixuan

2012-04-24

A highly sensitive and reliable method to sense and identify a single chemical at extremely low concentrations and high contamination is important for environmental surveillance, homeland security, athlete drug monitoring, toxin/drug screening, and earlier disease diagnosis. This article reports a method for precise detection of single chemicals. The hub of the bacteriophage phi29 DNA packaging motor is a connector consisting of 12 protein subunits encircled into a 3.6 nm channel as a path for dsDNA to enter during packaging and to exit during infection. The connector has previously been inserted into a lipid bilayer to serve as a membrane-embedded channel. Herein we report the modification of the phi29 channel to develop a class of sensors to detect single chemicals. The lysine-234 of each protein subunit was mutated to cysteine, generating 12-SH ring lining the channel wall. Chemicals passing through this robust channel and interactions with the SH group generated extremely reliable, precise, and sensitive current signatures as revealed by single channel conductance assays. Ethane (57 Da), thymine (167 Da), and benzene (105 Da) with reactive thioester moieties were clearly discriminated upon interaction with the available set of cysteine residues. The covalent attachment of each analyte induced discrete stepwise blockage in current signature with a corresponding decrease in conductance due to the physical blocking of the channel. Transient binding of the chemicals also produced characteristic fingerprints that were deduced from the unique blockage amplitude and pattern of the signals. This study shows that the phi29 connector can be used to sense chemicals with reactive thioesters or maleimide using single channel conduction assays based on their distinct fingerprints. The results demonstrated that this channel system could be further developed into very sensitive sensing devices.

Adenovirus, MS2 and PhiX174 interactions with drinking water biofilms developed on PVC, cement and cast iron.

PubMed

Helmi, K; Menard-Szczebara, F; Lénès, D; Jacob, P; Jossent, J; Barbot, C; Delabre, K; Arnal, C

2010-01-01

Biofilms colonizing pipe surfaces of drinking water distribution systems could provide habitat and shelter for pathogenic viruses present in the water phase. This study aims (i) to develop a method to detect viral particles present in a drinking water biofilm and (ii) to study viral interactions with drinking water biofilms. A pilot scale system was used to develop drinking water biofilms on 3 materials (7 cm(2) discs): PVC, cast iron and cement. Biofilms were inoculated with viral model including MS2, PhiX174 or adenovirus. Five techniques were tested to recover virus from biofilms. The most efficient uses beef extract and glycine at pH = 9. After sonication and centrifugation, the pH of the supernatant is neutralized prior to viral analysis. The calculated recovery rates varied from 29.3 to 74.6% depending on the virus (MS2 or PhiX174) and the material. Applying this protocol, the interactions of virus models (MS2 and adenovirus) with drinking water biofilms were compared. Our results show that adsorption of viruses to biofilms depends on their isoelectric points, the disc material and the hydrodynamic conditions. Applying hydrodynamic conditions similar to those existing in drinking water networks resulted in a viral adsorption corresponding to less than 1% of the initial viral load.

Readout electronics for CBM-TOF super module quality evaluation based on 10 Gbps ethernet

NASA Astrophysics Data System (ADS)

Jiang, D.; Cao, P.; Huang, X.; Zheng, J.; Wang, Q.; Li, B.; Li, J.; Liu, S.; An, Q.

2017-07-01

The Compressed Baryonic Matter-Time of Flight (CBM-TOF) wall uses high performance of Multi-gap Resistive Plate Chambers (MRPC) assembled in super modules to identify charged particles with high channel density and high measurement precision at high event rate. Electronics meet the challenge for reading data out from a super module at high speed of about 6 Gbps in real time. In this paper, the readout electronics for CBM-TOF super module quality evaluation is proposed based on 10 Gigabit Ethernet. The digitized TOF data from one super module will be concentrated at the front-end electronics residing on the side of the super module and transmitted to an extreme speed readout module (XSRM) housed in the backend crate through the PCI Express (PCIe) protocol via optic channels. Eventually, the XSRM transmits data to the data acquisition (DAQ) system through four 10 Gbps Ethernet ports in real time. This readout structure has advantages of high performance and expansibility. Furthermore, it is easy to operate. Test results on the prototype show that the overall data readout performance for each XSRM can reach up to 28.8 Gbps, which means XSRM can meet the requirement of reading data out from 4 super modules with 1280 channels in real time.

A new control system hardware architecture for the Hobby-Eberly Telescope prime focus instrument package

NASA Astrophysics Data System (ADS)

Ramiller, Chuck; Taylor, Trey; Rafferty, Tom H.; Cornell, Mark E.; Rafal, Marc; Savage, Richard

2010-07-01

The Hobby-Eberly Telescope (HET) will be undergoing a major upgrade as a precursor to the HET Dark Energy Experiment (HETDEX‡). As part of this upgrade, the Prime Focus Instrument Package (PFIP) will be replaced with a new design that supports the HETDEX requirements along with the existing suite of instruments and anticipated future additions. This paper describes the new PFIP control system hardware plus the physical constraints and other considerations driving its design. Because of its location at the top end of the telescope, the new PFIP is essentially a stand-alone remote automation island containing over a dozen subsystems. Within the PFIP, motion controllers and modular IO systems are interconnected using a local Controller Area Network (CAN) bus and the CANOpen messaging protocol. CCD cameras that are equipped only with USB 2.0 interfaces are connected to a local Ethernet network via small microcontroller boards running embedded Linux. Links to ground-level systems pass through a 100 m cable bundle and use Ethernet over fiber optic cable exclusively; communications are either direct or through Ethernet/CAN gateways that pass CANOpen messages transparently. All of the control system hardware components are commercially available, designed for rugged industrial applications, and rated for extended temperature operation down to -10 °C.

25 Gbps 850 nm photodiode for emerging 100 Gb ethernet applications

NASA Astrophysics Data System (ADS)

Joshi, Abhay; Rue, Jim; Becker, Don; Datta, Shubhashish; McFaul, Will

2011-06-01

The IEEE Std 802.3ba-2010 for 40 Gb and 100 Gb Ethernet was released in July, 2010. This standard will continue to evolve over the next several years. Two of the challenging transmit/receive architectures contained in this standard are the 100GBASE-LR4 (<10 km range) and 100GBASE-ER4 (<40 km range). Although presently envisioned for 1310 nm optical wavelengths, both of these 4 lane, 25.78 GBaud formats may be adopted for the impending 850 nm short reach optical backplane market, whose range is below 150 m. Driven by major computer server companies, such as IBM, HP and Oracle, the 850 nm Active Optical Cable (AOC) market is presently undergoing an increase of serial rates up to 25 Gbaud to enhance backplane interconnectivity. With AOCs up to 16 channels, the potential for up to 400 Gbps backhaul composite data rates will soon be possible. We report a 25 Gbps photodiode with quantum efficiency ~ 0.6 at 850 nm. This InGaAs/InP device was optimized for high quantum efficiency at 850 nm. When pigtailed with multimode fiber and integrated with an application-specific RF amplifier, the resultant photoreceiver will provide multiple functionalities for these 100 Gb Ethernet markets.

77 FR 5087 - Petition for Exemption; Summary of Petition Received

Federal Register 2010, 2011, 2012, 2013, 2014

2012-02-01

....: FAA-2011-1233 Petitioner: PHI Air Medical, LLC Section of 14 CFR Affected: 14 CFR Sec. Sec. 135.293, 135.297, 135.299, and 135.343 Description of Relief Sought: PHI Air Medical, LLC requests an exemption to permit Air Medical to use pilots previously qualified under PHI, Inc.'s part 119 air carrier...

Mutant Screen Distinguishes between Residues Necessary for Light-Signal Perception and Signal Transfer by Phytochrome B

USDA-ARS?s Scientific Manuscript database

The phytochromes (phyA to phyE) are a major plant photoreceptor family that regulate a diversity of developmental processes in response to light. The N-terminal 651–amino acid domain of phyB (N651), which binds an open tetrapyrrole chromophore, acts to perceive and transduce regulatory light signals...

Prostate health index (PHI) and prostate-specific antigen (PSA) predictive models for prostate cancer in the Chinese population and the role of digital rectal examination-estimated prostate volume.

PubMed

Chiu, Peter K F; Roobol, Monique J; Teoh, Jeremy Y; Lee, Wai-Man; Yip, Siu-Ying; Hou, See-Ming; Bangma, Chris H; Ng, Chi-Fai

2016-10-01

To investigate PSA- and PHI (prostate health index)-based models for prediction of prostate cancer (PCa) and the feasibility of using DRE-estimated prostate volume (DRE-PV) in the models. This study included 569 Chinese men with PSA 4-10 ng/mL and non-suspicious DRE with transrectal ultrasound (TRUS) 10-core prostate biopsies performed between April 2008 and July 2015. DRE-PV was estimated using 3 pre-defined classes: 25, 40, or 60 ml. The performance of PSA-based and PHI-based predictive models including age, DRE-PV, and TRUS prostate volume (TRUS-PV) was analyzed using logistic regression and area under the receiver operating curves (AUC), in both the whole cohort and the screening age group of 55-75. PCa and high-grade PCa (HGPCa) was diagnosed in 10.9 % (62/569) and 2.8 % (16/569) men, respectively. The performance of DRE-PV-based models was similar to TRUS-PV-based models. In the age group 55-75, the AUCs for PCa of PSA alone, PSA with DRE-PV and age, PHI alone, PHI with DRE-PV and age, and PHI with TRUS-PV and age were 0.54, 0.71, 0.76, 0.78, and 0.78, respectively. The corresponding AUCs for HGPCa were higher (0.60, 0.70, 0.85, 0.83, and 0.83). At 10 and 20 % risk threshold for PCa, 38.4 and 55.4 % biopsies could be avoided in the PHI-based model, respectively. PHI had better performance over PSA-based models and could reduce unnecessary biopsies. A DRE-assessed PV can replace TRUS-assessed PV in multivariate prediction models to facilitate clinical use.

Electron cryo-tomographic structure of cystovirus phi 12.

PubMed

Hu, Guo-Bin; Wei, Hui; Rice, William J; Stokes, David L; Gottlieb, Paul

2008-03-01

Bacteriophage phi 12 is a member of the Cystoviridae virus family and contains a genome consisting of three segments of double-stranded RNA (dsRNA). This virus family contains eight identified members, of which four have been classified in regard to their complete genomic sequence and encoded viral proteins. A phospholipid envelope that contains the integral proteins P6, P9, P10, and P13 surrounds the viral particles. In species phi 6, host infection requires binding of a multimeric P3 complex to type IV pili. In species varphi8, phi 12, and phi 13, the attachment apparatus is a heteromeric protein assembly that utilizes the rough lipopolysaccharide (rlps) as a receptor. In phi 8 the protein components are designated P3a and P3b while in species phi 12 proteins P3a and P3c have been identified in the complex. The phospholipid envelope of the cystoviruses surrounds a nucleocapsid (NC) composed of two shells. The outer shell is composed of protein P8 with a T=13 icosahedral lattice while the primary component of the inner shell is a dodecahedral frame composed of dimeric protein P1. For the current study, the 3D architecture of the intact phi 12 virus was obtained by electron cryo-tomography. The nucleocapsid appears to be centered within the membrane envelope and possibly attached to it by bridging structures. Two types of densities were observed protruding from the membrane envelope. The densities of the first type were elongated, running parallel, and closely associated to the envelope outer surface. In contrast, the second density was positioned about 12 nm above the envelope connected to it by a flexible low-density stem. This second structure formed a torroidal structure termed "the donut" and appears to inhibit BHT-induced viral envelope fusion.

Restoration of prostaglandin E2-producing splenic macrophages in sup 89 Sr-treated mice with bone marrow from Corynebacterium parvum primed donors

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

Shibata, Y.

1989-05-01

Administration of Corynebacterium parvum (CP), 56 mg/kg ip to CBA/J mice effected the induction of prostaglandin E2 (PGE2) producing macrophages (M phi) in the bone marrow and the spleen. Maximal release of PGE2 from M phi cultured in vitro with calcium ionophore A23187 for 2 h was reached by marrow M phi removed on 5 days after CP (450 ng/mg cell protein), and by splenic M phi 9 days after CP (400 ng/mg). Neither M phi population, however, yielded more than 6.0 ng/mg leukotriene C4. To assess ontogenic relationships mice were depleted of bone marrow and blood monocytes by ivmore » injection of the bone-seeking isotope, 89Sr. CP was given at several points before or after bone marrow cell depletion. PGE2 production by splenic M phi harvested on day 9 after CP was profoundly impaired when CP was administered either concurrently with or 3 days after 89Sr. When CP was administered 1, 3, 5, and 7 days before 89Sr, however, the induction of PGE2-producing M phi in the spleen was unaffected. To determine whether bone marrow cells from CP-injected donors can restore PGE2-producing splenic M phi (PGSM) in 89Sr-mice, recipient mice which had and had not received CP 3 days after 89Sr were transfused with 5 x 10(6) syngeneic bone marrow cells from donor mice prepared at varying intervals after CP administration. The results clearly indicate the capacity of bone marrow cells harvested on either day 1 or 2 following CP to restore PGSM in CP-primed, but not unprimed, recipients.« less

Dissecting Phosphite-Induced Priming in Arabidopsis Infected with Hyaloperonospora arabidopsidis1[W

PubMed Central

Massoud, Kamal; Barchietto, Thierry; Le Rudulier, Thomas; Pallandre, Laurane; Didierlaurent, Laure; Garmier, Marie; Ambard-Bretteville, Françoise; Seng, Jean-Marc; Saindrenan, Patrick

2012-01-01

Phosphite (Phi), a phloem-mobile oxyanion of phosphorous acid (H3PO3), protects plants against diseases caused by oomycetes. Its mode of action is unclear, as evidence indicates both direct antibiotic effects on pathogens as well as inhibition through enhanced plant defense responses, and its target(s) in the plants is unknown. Here, we demonstrate that the biotrophic oomycete Hyaloperonospora arabidopsidis (Hpa) exhibits an unusual biphasic dose-dependent response to Phi after inoculation of Arabidopsis (Arabidopsis thaliana), with characteristics of indirect activity at low doses (10 mm or less) and direct inhibition at high doses (50 mm or greater). The effect of low doses of Phi on Hpa infection was nullified in salicylic acid (SA)-defective plants (sid2-1, NahG) and in a mutant impaired in SA signaling (npr1-1). Compromised jasmonate (jar1-1) and ethylene (ein2-1) signaling or abscisic acid (aba1-5) biosynthesis, reactive oxygen generation (atrbohD), or accumulation of the phytoalexins camalexin (pad3-1) and scopoletin (f6′h1-1) did not affect Phi activity. Low doses of Phi primed the accumulation of SA and Pathogenesis-Related protein1 transcripts and mobilized two essential components of basal resistance, Enhanced Disease Susceptibility1 and Phytoalexin Deficient4, following pathogen challenge. Compared with inoculated, Phi-untreated plants, the gene expression, accumulation, and phosphorylation of the mitogen-activated protein kinase MPK4, a negative regulator of SA-dependent defenses, were reduced in plants treated with low doses of Phi. We propose that Phi negatively regulates MPK4, thus priming SA-dependent defense responses following Hpa infection. PMID:22408091

Safety, reactogenicity and immunogenicity of a booster dose of the 10-valent pneumococcal non-typeable Haemophilus influenzae protein D conjugate vaccine (PHiD-CV) in Malian children.

PubMed

Dicko, Alassane; Santara, Gaoussou; Mahamar, Almahamoudou; Sidibe, Youssoufa; Barry, Amadou; Dicko, Yahia; Diallo, Aminata; Dolo, Amagana; Doumbo, Ogobara; Shafi, Fakrudeen; François, Nancy; Strezova, Ana; Borys, Dorota; Schuerman, Lode

2013-02-01

Primary vaccination with the 10-valent pneumococcal non-typeable Haemophilus influenzae protein D conjugate vaccine (PHiD-CV) was previously shown to be immunogenic and well tolerated in Malian children. Data on booster vaccination with a fourth consecutive dose of PHiD-CV are available for Europe, Asia and Latin America but are lacking for Africa. The present study evaluated further the safety, reactogenicity and immunogenicity of a fourth consecutive (booster) dose of PHiD-CV. Low incidences of AEs with grade 3 intensity (2.1% of subjects) were observed. There were no reports of large swelling reactions and serious adverse events. One month post-booster vaccination, for each vaccine pneumococcal serotype, at least 97.8% of subjects had antibody concentrations ≥ 0.2 μg/ml, and at least 97.1% of subjects had opsonophagocytic activity ≥ 8. From pre- to post-booster, a 12.3-fold increase in anti-protein D geometric mean concentration was observed. This phase III, open-label study was conducted in Ouelessebougou, Mali, between November 2009 and June 2010. The study population consisted of Malian children previously primed (3 doses) with PHiD-CV in study NCT00678301 receiving a fourth consecutive (booster) dose of PHiD-CV in the second year of life. The incidences of adverse events (AEs) with grade 3 intensity (primary objective) or of any intensity (secondary objective), and the immunogenicity (secondary objective) of the PHiD-CV booster dose were assessed. A booster dose of PHiD-CV was well tolerated when administered to Malian children in the second year of life and was highly immunogenic for all 10 vaccine pneumococcal serotypes and NTHi protein D. (ClinicalTrials.gov identifier: NCT00985465).

Flow cytometric kinetic assay of the activity of Na+/H+ antiporter in mammalian cells.

PubMed

Dolz, María; O'Connor, José-Enrique; Lequerica, Juan L

2004-10-01

The Na(+)/H(+) exchanger (NHE) of mammalian cells is an integral membrane protein that extrudes H(+) ion in exchange for extracellular Na(+) and plays a crucial role in the regulation of intracellular pH (pHi). Thus, when pHi is lowered, NHE extrudes protons at a rate depending of pHi that can be expressed as pH units/s. To abolish the activity of other cellular pH-restoring systems, cells were incubated in bicarbonate-free Dulbecco's modified Eagle's medium buffered with HEPES. Flow cytometry was used to determine pHi with 2',7'-bis-(2-carboxyethyl)-5-(and-6)-carboxyfluorescein acetoxymethyl ester or 5-(and-6)-carboxy SNARF-1 acetoxymethyl ester acetate, and the appropriate fluorescence ratios were measured. The calibration of fluorescence ratios versus pHi was established by using ionophore nigericin. The activity of NHE was calculated by a kinetic flow cytometric assay as the slope at time 0 of the best-fit curve of pHi recovery versus time after intracellular acidification with a pulse of exogenous sodium propionate. The kinetic method allowed determination of the pHi-dependent activity of NHE in cell lines and primary cell cultures. NHE activity values were demonstrated to be up to 0.016 pH units/s within the pHi range of 7.3 to 6.3. The inhibition of NHE activity by the specific inhibitor ethyl isopropyl amiloride was easily detected by this method. The assay conditions can be used to relate variations in pHi with the activity of NHE and provide a standardized method to compare between different cells, inhibitors, models of ischemia by acidification, and other relevant experimental or clinical situations.

The extent to which the public health 'war on obesity' reflects the ethical values and principles of critical health promotion: a multimedia critical discourse analysis.

PubMed

O'Hara, Lily; Taylor, Jane; Barnes, Margaret

2015-12-01

The discipline of health promotion is responsible for implementing strategies within weight-related public health initiatives (WR-PHI). It is imperative that such initiatives be subjected to critical analysis through a health promotion ethics lens to help ensure ethical health promotion practice. Multimedia critical discourse analysis was used to examine the claims, values, assumptions, power relationships and ideologies within Australian WR-PHI. The Health Promotion Values and Principles Continuum was used as a heuristic to evaluate the extent to which the WR-PHI reflected the ethical values of critical health promotion: active participation of people in the initiative; respect for personal autonomy; beneficence; non-maleficence; and strong evidential and theoretical basis for practice. Ten initiatives were analysed. There was some discourse about the need for participation of people in the WR-PHI, but people were routinely labelled as 'target groups' requiring 'intervention'. Strong evidence of a coercive and paternalistic discourse about choice was identified, with minimal attention to respect for personal autonomy. There was significant emphasis on the beneficiaries of the WR-PHI but minimal attention to the health benefits, and nothing about the potential for harm. Discourse about the evidence of need was objectivist, and there was no discussion about the theoretical foundations of the WR-PHI. The WR-PHI were not reflective of the ethical values and principles of critical health promotion. So what? Health promotion researchers and practitioners engaged in WR-PHI should critically reflect on the extent to which they are consistent with the ethical aspects of critical health promotion practice.

An Evaluation of Personal Health Information Remnants in Second-Hand Personal Computer Disk Drives

PubMed Central

Neri, Emilio; Jonker, Elizabeth

2007-01-01

Background The public is concerned about the privacy of their health information, especially as more of it is collected, stored, and exchanged electronically. But we do not know the extent of leakage of personal health information (PHI) from data custodians. One form of data leakage is through computer equipment that is sold, donated, lost, or stolen from health care facilities or individuals who work at these facilities. Previous studies have shown that it is possible to get sensitive personal information (PI) from second-hand disk drives. However, there have been no studies investigating the leakage of PHI in this way. Objectives The aim of the study was to determine the extent to which PHI can be obtained from second-hand computer disk drives. Methods A list of Canadian vendors selling second-hand computer equipment was constructed, and we systematically went through the shuffled list and attempted to purchase used disk drives from the vendors. Sixty functional disk drives were purchased and analyzed for data remnants containing PHI using computer forensic tools. Results It was possible to recover PI from 65% (95% CI: 52%-76%) of the drives. In total, 10% (95% CI: 5%-20%) had PHI on people other than the owner(s) of the drive, and 8% (95% CI: 7%-24%) had PHI on the owner(s) of the drive. Some of the PHI included very sensitive mental health information on a large number of people. Conclusions There is a strong need for health care data custodians to either encrypt all computers that can hold PHI on their clients or patients, including those used by employees and subcontractors in their homes, or to ensure that their computers are destroyed rather than finding a second life in the used computer market. PMID:17942386

Effects of supplementary private health insurance on physician visits in Korea.

PubMed

Kang, Sungwook; You, Chang Hoon; Kwon, Young Dae; Oh, Eun-Hwan

2009-12-01

The coverage of social health insurance has remained limited, despite it being compulsory in Korea. Accordingly, Koreans have come to rely upon supplementary private health insurance (PHI) to cover their medical costs. We examined the effects of supplementary PHI on physician visits in Korea. This study used individual data from 11,043 respondents who participated in the Korean Labor and Income Panel Survey in 2001. We conducted a single probit model to identify the relationship between PHI and physician visits, with adjustment for the following covariates: demographic characteristics, socioeconomic status, health status, and health-related behavior. Finally, we performed a bivariate probit model to examine the true effect of PHI on physician visits, with adjustment for the above covariates plus unobservable covariates that might affect not only physician visit, but also the purchase of PHI. We found that about 38% of all respondents had one or more private health plans. Forty-five percent of all respondents visited one or more physicians, and 49% of those who were privately insured had physician visits compared with 42% of the uninsured. The single probit model showed that those with PHI were about 14 percentage points more likely to visit physicians than those who do not have PHI. However, this distinction disappears in the bivariate probit model. This result might have been a consequence of the nature of private health plans in Korea. Private insurance companies pay a fixed amount directly to their enrollees in case of illness/injury, and the individuals are responsible subsequently for purchasing their own healthcare services. This study demonstrated the potential of Korean PHI to address the problem of moral hazard. These results serve as a reference for policy makers when considering how to finance healthcare services, as well as to contain healthcare expenditure.

Gigabit Ethernet Asynchronous Clock Compensation FIFO

NASA Technical Reports Server (NTRS)

Duhachek, Jeff

2012-01-01

Clock compensation for Gigabit Ethernet is necessary because the clock recovered from the 1.25 Gb/s serial data stream has the potential to be 200 ppm slower or faster than the system clock. The serial data is converted to 10-bit parallel data at a 125 MHz rate on a clock recovered from the serial data stream. This recovered data needs to be processed by a system clock that is also running at a nominal rate of 125 MHz, but not synchronous to the recovered clock. To cross clock domains, an asynchronous FIFO (first-in-first-out) is used, with the write pointer (wprt) in the recovered clock domain and the read pointer (rptr) in the system clock domain. Because the clocks are generated from separate sources, there is potential for FIFO overflow or underflow. Clock compensation in Gigabit Ethernet is possible by taking advantage of the protocol data stream features. There are two distinct data streams that occur in Gigabit Ethernet where identical data is transmitted for a period of time. The first is configuration, which happens during auto-negotiation. The second is idle, which occurs at the end of auto-negotiation and between every packet. The identical data in the FIFO can be repeated by decrementing the read pointer, thus compensating for a FIFO that is draining too fast. The identical data in the FIFO can also be skipped by incrementing the read pointer, which compensates for a FIFO draining too slowly. The unique and novel features of this FIFO are that it works in both the idle stream and the configuration streams. The increment or decrement of the read pointer is different in the idle and compensation streams to preserve disparity. Another unique feature is that the read pointer to write pointer difference range changes between compensation and idle to minimize FIFO latency during packet transmission.

Observation of a peaking structure in the $$J/\\psi \\phi$$ mass spectrum from $$B^{\\pm} \\to J/\\psi \\phi K^{\\pm}$$ decays

DOE PAGES

Chatrchyan, Serguei

2014-05-22

A peaking structure in the J/psi phi mass spectrum near threshold is observed in B(+/-) to J/psi phi K(+/-) decays, produced in pp collisions at sqrt(s) = 7 TeV collected with the CMS detector at the LHC. The data sample, selected on the basis of the dimuon decay mode of the J/psi, corresponds to an integrated luminosity of 5.2 inverse femtobarns. Fitting the structure to an S-wave relativistic Breit-Wigner lineshape above a three-body phase-space nonresonant component gives a signal statistical significance exceeding five standard deviations. The fitted mass and width values are m = 4148.0 +- 2.4 (stat.) +- 6.3more » (syst.) MeV and Gamma = 28 +15 -11 (stat.) +- 19 (syst.) MeV, respectively. Evidence for an additional peaking structure at higher J/psi phi mass is also reported.« less

Modular assembly of chimeric phi29 packaging RNAs that support DNA packaging.

PubMed

Fang, Yun; Shu, Dan; Xiao, Feng; Guo, Peixuan; Qin, Peter Z

2008-08-08

The bacteriophage phi29 DNA packaging motor is a protein/RNA complex that can produce strong force to condense the linear-double-stranded DNA genome into a pre-formed protein capsid. The RNA component, called the packaging RNA (pRNA), utilizes magnesium-dependent inter-molecular base-pairing interactions to form ring-shaped complexes. The pRNA is a class of non-coding RNA, interacting with phi29 motor proteins to enable DNA packaging. Here, we report a two-piece chimeric pRNA construct that is fully competent in interacting with partner pRNA to form ring-shaped complexes, in packaging DNA via the motor, and in assembling infectious phi29 virions in vitro. This is the first example of a fully functional pRNA assembled using two non-covalently interacting fragments. The results support the notion of modular pRNA architecture in the phi29 packaging motor.

PhySortR: a fast, flexible tool for sorting phylogenetic trees in R.

PubMed

Stephens, Timothy G; Bhattacharya, Debashish; Ragan, Mark A; Chan, Cheong Xin

2016-01-01

A frequent bottleneck in interpreting phylogenomic output is the need to screen often thousands of trees for features of interest, particularly robust clades of specific taxa, as evidence of monophyletic relationship and/or reticulated evolution. Here we present PhySortR, a fast, flexible R package for classifying phylogenetic trees. Unlike existing utilities, PhySortR allows for identification of both exclusive and non-exclusive clades uniting the target taxa based on tip labels (i.e., leaves) on a tree, with customisable options to assess clades within the context of the whole tree. Using simulated and empirical datasets, we demonstrate the potential and scalability of PhySortR in analysis of thousands of phylogenetic trees without a priori assumption of tree-rooting, and in yielding readily interpretable trees that unambiguously satisfy the query. PhySortR is a command-line tool that is freely available and easily automatable.

Modular assembly of chimeric phi29 packaging RNAs that support DNA packaging

PubMed Central

Fang, Yun; Shu, Dan; Xiao, Feng; Guo, Peixuan; Qin, Peter Z.

2008-01-01

The bacteriophage phi29 DNA packaging motor is a protein/RNA complex that can produce strong force to condense the linear-double stranded DNA genome into a pre-formed protein capsid. The RNA component, called the packaging RNA (pRNA), utilizes magnesium-dependent intermolecular base-pairing interactions to form ring-shaped complexes. The pRNA is a class of non-coding RNA, interacting with phi29 motor proteins to enable DNA packaging. Here, we report a 2-piece chimeric pRNA construct that is fully competent in interacting with partner pRNA to form ring-shaped complexes, in packaging DNA via the motor, and in assembling infectious phi29 virions in vitro. This is the first example of a fully functional pRNA assembled using two non-covalently interacting fragments. The results support the notion of modular pRNA architecture in the phi29 packaging motor. PMID:18514064

DelPhi web server v2: incorporating atomic-style geometrical figures into the computational protocol.

PubMed

Smith, Nicholas; Witham, Shawn; Sarkar, Subhra; Zhang, Jie; Li, Lin; Li, Chuan; Alexov, Emil

2012-06-15

A new edition of the DelPhi web server, DelPhi web server v2, is released to include atomic presentation of geometrical figures. These geometrical objects can be used to model nano-size objects together with real biological macromolecules. The position and size of the object can be manipulated by the user in real time until desired results are achieved. The server fixes structural defects, adds hydrogen atoms and calculates electrostatic energies and the corresponding electrostatic potential and ionic distributions. The web server follows a client-server architecture built on PHP and HTML and utilizes DelPhi software. The computation is carried out on supercomputer cluster and results are given back to the user via http protocol, including the ability to visualize the structure and corresponding electrostatic potential via Jmol implementation. The DelPhi web server is available from http://compbio.clemson.edu/delphi_webserver.

Phytochrome from Green Plants: Properties and biological Function

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

Quail, Peter H.

2014-07-25

Plants constantly monitor the light environment for informational light signals used to direct adaptational responses to the prevailing conditions. One major such response, the Shade-Avaoidance Response (SAR), triggered when plants sense the presence of competing neighbors, results in enhanced channeling of photosynthetically-fixed carbon into stem elongation at the expense of deposition in reproductive tissues. This response has been selected against in many modern food crops to ensure maximum edible yield (e.g. seeds). Converse enhancement of the SAR, with consequent increased carbon channeling into vegetative cellulose, could contribute to the generation of crops with improved yield of tissues suitable for cellulosicmore » biofuel production. The signal for this response is light enriched in far-red wavelengths. This signal is produced by sunlight filtered through, or reflected from, neighboring vegetation, as a result of preferential depletion of red photons through chlorophyll absorption. The plant phytochrome (phy) photoreceptor system (predominantly phyB) senses this signal through its capacity to switch reversibly, in milliseconds, between two molecular states: the biologically inactive Pr (red-light-absorbing) and biologically active Pfr (far-red-light-absorbing) conformers. The photoequilibrium established between these two conformers in light-grown plants is determined by the ratio of red-to-far-red wavelengths in the incoming signal. The levels of Pfr then dictate the recipient plant’s growth response: high levels suppress elongation growth; low levels promote elongation growth. Studies on seedling deetiolation have advanced our understanding considerably in recent years, of the mechanism by which the photoactivated phy molecule transduces its signal into cellular growth responses. The data show that a subfamily of phy-interacting bHLH transcription factors (PIFs) promote skotomorphogenic seedling development in post-germinative darkness, but that the phy Pfr conformer reverses this activity upon initial light exposure, inducing the switch to photomorphogenic development. This reversal involves light-triggered translocation of the photoactivated phy molecule into the nucleus where it interacts with PIF-family members, inducing rapid phosphorylation and degradation of the PIFs via the ubiquitin-proteasome system. This degradation in turn elicits rapid alterations in gene expression that drive the deetiolation transition. This project has made considerable progress in defining phy-PIF signaling activity in controlling the SAR. The biological functions of the multiple PIF-family members in controlling the SAR, including dissection of the relative contributions of the individual PIFs to this process, as well as to diurnal growth-control oscillations, have been investigated using higher-order pif-mutant combinations. Using microarray analysis of a quadruple pif mutant we have defined the shade-induced, PIF-regulated transcriptional network genome-wide. This has revealed that a dynamic antagonism between the phys and PIFs generates selective reciprocal responses during deetiolation and the SAR in a rapidly light-responsive transcriptional network. Using integrated RNA-seq and ChIP-seq analysis of higher order pif-mutant combinations, we have defined the direct gene-targets of PIF transcriptional regulation, and have obtained evidence that this regulation involves differential direct targeting of rapidly light-responsive genes by the individual PIF-family members. This project has provided significant advances in our understanding of the molecular mechanisms by which the phy-PIF photosensory signaling pathway regulates an important bioenergy-related plant response to the light environment. The identification of molecular targets in the primary transcriptional-regulatory circuitry of this pathway has the potential to enable genetic or reverse-genetic manipulation of the partitioning of carbon between reproductive and vegetative (cellulose-accumulating) tissue, toward enhanced bioenergy yield.« less

XMOS XC-2 Development Board for Mechanical Control and Data Collection

NASA Technical Reports Server (NTRS)

Jarnot, Robert F.; Bowden, William J.

2011-01-01

The scanning microwave limb sounder (SMLS) will use technological improvements in low-noise mixers to provide precise data on the Earth s atmospheric composition with high spatial resolution. This project focuses on the design and implementation of a realtime control system needed for airborne engineering tests of the SMLS. The system must coordinate the actuation of optical components using four motors with encoder readback, while collecting synchronized telemetric data from a GPS receiver and 3-axis gyrometric system. A graphical user interface for testing the control system was also designed using Python. Although the system could have been implemented with an FPGA(fieldprogrammable gate array)-based setup, a processor development kit manufactured by XMOS was chosen. The XMOS architecture allows parallel execution of multiple tasks on separate threads, making it ideal for this application. It is easily programmed using XC (a subset of C). The necessary communication interfaces were implemented in software, including Ethernet, with significant cost and time reduction compared to an FPGA-based approach. A simple approach to control the chopper, calibration mirror, and gimbal for the airborne SMLS was needed. The XMOS board allows for multiple threads and real-time data acquisition. The XC-2 development kit is an attractive choice for synchronized, real-time, event-driven applications. The XMOS is based on the transputer microprocessor architecture developed for parallel computing, which is being revamped in this new platform. The XMOS device has multiple cores capable of running parallel applications on separate threads. The threads communicate with each other via user-defined channels capable of transmitting data within the device. XMOS provides a C-based development environment using XC, which eliminates the need for custom tool kits associated with FPGA programming. The XC-2 has four cores and necessary hardware for Ethernet I/O.

ADC interface for data server with data preselection for luminosity detector in AIDA-2020 project

NASA Astrophysics Data System (ADS)

Daniluk, W.; Dziedzic, B.; Korcyl, G.; Wojtoń, T.; Zawiejski, L.

2017-08-01

Main aim of the AIDA-2020 project is development of detectors for future accelerators. In FCAL Colaboration we are working on forward subdetectors for ILC and CLIC accelerators. My team is developing prototype module which receives data from ADC, provides the data preselection, and transmits them as packages to the data server for further their analysis. Common prototype is based on AC701 evaluation board which contains Artix-7 FPGA and is equipped with SMA connectors for gigabit transceivers and ethernet connector. In my talk I will describe architecture of the device and current state of module development.

Lytic activity of the virion-associated peptidoglycan hydrolase HydH5 of staphylococcus aureus bacteriophage vB_SauS-phiIPLA88

USDA-ARS?s Scientific Manuscript database

Staphylococcus aureus bacteriophage vB_SauS-phiIPLA88 (phiIPLA88) contains a virion-associated muralytic enzyme (HydH5) encoded by orf58, which is located in the morphogenetic module. Comparative bioinformatic analysis revealed that HydH5 significantly resembled other peptidoglycan hydrolases encode...

Enzymatic Comparisons of Aspergillus niger PhyA and Escherichia coli AppA2 Phytases

USDA-ARS?s Scientific Manuscript database

This study was to compare three phytase activity assays and kinetics of Aspergillus niger PhyA and Escherichia coli AppA2 phytases expressed in Pichia pastoris at the observed stomach pH of 3.5. In Experiment 1, equivalent phytase activities in the crude preparations of PhyA and AppA2 were tested ...

Expression and GTP sensitivity of peptide histidine isoleucine high-affinity-binding sites in rat.

PubMed

Debaigt, Colin; Meunier, Annie-Claire; Goursaud, Stephanie; Montoni, Alicia; Pineau, Nicolas; Couvineau, Alain; Laburthe, Marc; Muller, Jean-Marc; Janet, Thierry

2006-07-01

High-affinity-binding sites for the vasoactive intestinal peptide (VIP) analogs peptide histidine/isoleucine-amide (PHI)/carboxyterminal methionine instead of isoleucine (PHM) are expressed in numerous tissues in the body but the nature of their receptors remains to be elucidated. The data presented indicate that PHI discriminated a high-affinity guanosine 5'-triphosphate (GTP)-insensitive-binding subtype that represented the totality of the PHI-binding sites in newborn rat tissues but was differentially expressed in adult animals. The GTP-insensitive PHI/PHM-binding sites were also observed in CHO cells over expressing the VPAC2 but not the VPAC1 VIP receptor.

Chameleon scalar fields in relativistic gravitational backgrounds

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

Tsujikawa, Shinji; Tamaki, Takashi; Tavakol, Reza, E-mail: shinji@rs.kagu.tus.ac.jp, E-mail: tamaki@gravity.phys.waseda.ac.jp, E-mail: r.tavakol@qmul.ac.uk

2009-05-15

We study the field profile of a scalar field {phi} that couples to a matter fluid (dubbed a chameleon field) in the relativistic gravitational background of a spherically symmetric spacetime. Employing a linear expansion in terms of the gravitational potential {Phi}{sub c} at the surface of a compact object with a constant density, we derive the thin-shell field profile both inside and outside the object, as well as the resulting effective coupling with matter, analytically. We also carry out numerical simulations for the class of inverse power-law potentials V({phi}) = M{sup 4+n}{phi}{sup -n} by employing the information provided by ourmore » analytical solutions to set the boundary conditions around the centre of the object and show that thin-shell solutions in fact exist if the gravitational potential {Phi}{sub c} is smaller than 0.3, which marginally covers the case of neutron stars. Thus the chameleon mechanism is present in the relativistic gravitational backgrounds, capable of reducing the effective coupling. Since thin-shell solutions are sensitive to the choice of boundary conditions, our analytic field profile is very helpful to provide appropriate boundary conditions for {Phi}{sub c}{approx}« less

Amelioration of Ethanol-Induced Gastric Ulcers in Rats Pretreated with Phycobiliproteins of Arthrospira (Spirulina) Maxima.

PubMed

Guzmán-Gómez, Oscar; García-Rodríguez, Rosa Virginia; Quevedo-Corona, Lucía; Pérez-Pastén-Borja, Ricardo; Rivero-Ramírez, Nora Lilia; Ríos-Castro, Emmanuel; Pérez-Gutiérrez, Salud; Pérez-Ramos, Julia; Chamorro-Cevallos, Germán Alberto

2018-06-13

Phycobiliproteins of Arthrospira ( Spirulina ) maxima have attracted attention because of their potential therapeutic antioxidant properties. The aim of this study was to assess the possible antiulcerogenic activity of these phycobiliproteins (ExPhy) against ethanol-induced gastric ulcers in rats. To explore the possible mechanisms of action, we examined antioxidant defense enzymes (e.g., catalase, superoxide dismutase, and glutathione peroxidase), as well as the level of lipid peroxidation (MDA) and the histopathological changes in the gastric mucosa. Intragastric administration of ExPhy (100, 200, and 400 mg/kg body weight) significantly lowered the ulcer index value compared to the ulcer control group ( p < 0.05). The greatest protection was provided by the concentration of 400 mg/kg. The histological study supported the observed gastroprotective activity of ExPhy, showing a reduced inflammatory response. Moreover, the alcohol-induced decrease in stomach antioxidant enzyme activity found in the ulcer control group was prevented by ExPhy pretreatment. Furthermore, ExPhy reversed the ethanol-induced increase in lipid peroxidation. In summary, the antiulcerogenic potential of ExPhy may be due, at least in part, to its anti-oxidant and anti-inflammatory effects.

Mechanisms of inactivation of bacteriophage phiX174 and its DNA in aerosols by ozone and ozonized cyclohexene.

PubMed Central

de Mik, G.; de Groot, I.

1977-01-01

The mechanisms of inactivation of aerosolized bacteriophage phiX174 in atmospheres containing ozone, cyclohexene, or ozonized cyclohexene were studied by using 32P-labelled phage. The inactivation of the aerosolized phage in clear air or in air containing cyclohexene is due to damage of the protein coat since the deoxyribonucleic acid (DNA) extracted from the inactivated phage retains its biological activity. Inactivation of the phage in air containing ozonized cyclohexene is due both to protein and DNA damage. Sucrose gradient analysis shows that aerosolized inactivated phiX174 releases unbroken DNA. In contrast, the DNA from phage phiX174 inactivated by ozonized cyclohexene is broken. The inactivation of aerosolized phage phiX174-DNA was studied in the same atmospheres using 32P-labelled DNA. phiX174-DNA aerosolized in clear air or air containing cyclohexene at 75% r.h. is inactivated by a factor of 2 in 30 min. The inactivated DNA is broken. Ozone as well as ozonized cyclohexene inactivates KNA very fast causing breaks in the molecule. This is in contrast with the intact bacteriophage in which ozone does not produce breaks in the DNA. PMID:265342

On absolutely continuous weakly mixing cocycles over irrational rotations

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

Rozhdestvenskii, A V

2003-06-30

A weakly mixing cocycle over a rotation {alpha} is a measurable function {phi}:S{sup 1}{yields}S{sup 1}, where S{sup 1}={l_brace}z element of C:|z|=1{r_brace}, such that the equation {phi}{sup n}(z)=c (h(exp(2{pi}i{alpha})z))/(h(z))for almost all z; (*) has no measurable solutions h( {center_dot} ):S{sup 1}{yields}S{sup 1} for any n element of Z{l_brace}0{r_brace} and c element of C, |c|=1. If the irrational number {alpha} has bounded convergents in its continued fraction expansion and a function M(y) increases more slowly than y ln{sup 1/2}y, then it is proved that there exists a weakly mixing cocycle of the form {phi}(exp(2{pi}ix))=exp(2{pi}i{phi}-tilde(x)), where {phi}-tilde:T{yields}R belongs to the class W{sup 1}(M(L)(T)).more » In addition, it is shown that equation (*) (and also the corresponding additive cohomological equation) is soluble for {phi}-tilde element of W{sup 1}(L log{sub +}{sup 1/2}L(T))« less

Public-private sector interactions and the demand for supplementary health insurance in the United Kingdom.

PubMed

Bíró, Anikó; Hellowell, Mark

2016-07-01

We examine the demand for private health insurance (PHI) in the United Kingdom and relate this to changes in the supply of public and private healthcare. Using a novel collection of administrative, private sector and survey data, we re-assess the relationships between the quality and availability of public and private sector inpatient care, and the demand for PHI. We find that PHI coverage in the United Kingdom is positively related to the median of the region- and year-specific public sector waiting times. We find that PHI prevalence ceteris paribus increases with being self-employed and employed, while it decreases with having financial difficulties. In addition, we highlight the complexities of inter-sectoral relations and their impact on PHI demand. Within a region, we find that an increase in private healthcare supply is associated with a decrease in public sector waiting times, implying lower PHI demand. This may be explained by the usage of private facilities by NHS commissioners. These results have important implications for policymakers interested in the role of private healthcare supply in enhancing the availability of and equitable access to acute inpatient care. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Model-Dependent Constraint on Quark Total Angular Momentum Based on the Transverse Target-spin Asymmetry Measured in Deeply Virtual Compton Scattering at HERMES

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

Nowak, Wolf-Dieter

Results are reported on the transverse target-spin asymmetry (TTSA) associated with deeply virtual Compton scattering on the proton. The data have been accumulated in the years 2002-2004 by the HERMES experiment at DESY, in which the HERA 27.6 GeV e+ beam scattered on a transversely polarized hydrogen target. Two azimuthal amplitudes of the TTSA appearing to LO in 1/Q and {alpha}s, A{sub UT}{sup sin({phi}-{phi}{sub S})cos{phi}} and A{sub UT}{sup cos({phi} -{phi}{sub S})sin{phi}}, are given as a function of -t,xB,Q2 in the kinematic range |t| < 0.7 GeV2, 0.03 < xB < 0.35 and 1 < Q2 < 10 GeV2. The firstmore » amplitude is found to be sensitive to the generalized parton distribution (GPD) E of the proton, which can be parameterized in a GPD model through quark total angular momentum Jq(q = u, d). Within the context of this model, a constraint in the (Ju,Jd) plane is obtained from HERMES TTSA data.« less

Biological Control of Phytophthora palmivora Causing Root Rot of Pomelo Using Chaetomium spp.

PubMed Central

Wattanachai, Pongnak; Kasem, Soytong; Poaim, Supatta

2015-01-01

Phytophthora diseases have become a major impediment in the citrus production in Thailand. In this study, an isolate of Phytophthora denominated as PHY02 was proven to be causal pathogen of root rot of Pomelo (Citrus maxima) in Thailand. The isolate PHY02 was morphologically characterized and identified as Phytophthora palmivora based on molecular analysis of an internal transcribed spacer rDNA sequence. This work also presents in vitro evaluations of the capacities of Chaetomium spp. to control the P. palmivora PHY02. As antagonists, Chaetomium globosum CG05, Chaetomium cupreum CC3003, Chaetomium lucknowense CL01 inhibited 50~61% mycelial growth, degraded mycelia and reduced 92~99% sporangial production of P. palmivora PHY02 in bi-culture test after 30 days. Fungal metabolites from Chaetomium spp. were tested against PHY02. Results showed that, methanol extract of C. globosum CG05 expressed strongest inhibitory effects on mycelial growth and sporangium formation of P. palmivora PHY02 with effective dose ED50 values of 26.5 µg/mL and 2.3 µg/mL, respectively. It is interesting that C. lucknowense is reported for the first time as an effective antagonist against a species of Phytophthora. PMID:25892917

Evaluating the Use of Monocytes with a Degradable Polyurethane for Vascular Tissue Regeneration

NASA Astrophysics Data System (ADS)

Battiston, Kyle Giovanni

Monocytes are one of the first cell types present following the implantation of a biomaterial or tissue engineered construct. Depending on the monocyte activation state supported by the biomaterial, monocytes and their derived macrophages (MDMs) can act as positive contributors to tissue regeneration and wound healing, or conversely promote a chronic inflammatory response that leads to fibrous encapsulation and implant rejection. A degradable polar hydrophobic iconic polyurethane (D-PHI) has been shown to reduce pro-inflammatory monocyte/macrophage response compared to tissue culture polystyrene (TCPS), a substrate routinely used for in vitro culture of cells, as well as poly(lactide- co-glycolide) (PLGA), a standard synthetic biodegradable biomaterial in the tissue engineering field. D-PHI has also shown properties suitable for use in a vascular tissue engineering context. In order to understand the mechanism through which D-PHI attenuates pro-inflammatory monocyte response, this thesis investigated the ability of D-PHI to modulate interactions with adsorbed serum proteins and the properties of D-PHI that were important for this activity. D-PHI was shown to regulate protein adsorption in a manner that produced divergent monocyte responses compared to TCPS and PLGA when coated with the serum proteins alpha2-macroglobulin or immunoglobulin G (IgG). In the case of IgG, D-PHI was shown to reduce pro-inflammatory binding site exposure as a function of the material's polar, hydrophobic, and ionic character. Due to the favourable monocyte activation state supported by D-PHI, and the importance of monocytes/macrophages in regulating the response of tissue-specific cell types in vivo, the ability of a D-PHI-stimulated monocyte/macrophage activation state to contribute to modulating the response of vascular smooth muscle cells (VSMCs) in a vascular tissue engineering context was investigated. D-PHI- stimulated monocytes promoted VSMC growth and migration through biomolecule release. Coupling monocyte-VSMC co-culture with biomechanical strain further enhanced these effects, while also promoting extracellular matrix deposition (collagen I, collagen III, and elastin) and enhancing the mechanical properties of VSMC-monocyte seeded tissue constructs. This thesis identifies the use of biomaterials with immunomodulatory capacity to harness the stimulatory potential of MDMs and contribute to tissue engineering strategies in vitro. This latter work in turn has contributed to identifying aspects of biomaterial design that can contribute to supporting desirable monocyte-biomaterial interactions that can facilitate this process.

Evaluation of the Intel Xeon Phi Co-processor to accelerate the sensitivity map calculation for PET imaging

NASA Astrophysics Data System (ADS)

Dey, T.; Rodrigue, P.

2015-07-01

We aim to evaluate the Intel Xeon Phi coprocessor for acceleration of 3D Positron Emission Tomography (PET) image reconstruction. We focus on the sensitivity map calculation as one computational intensive part of PET image reconstruction, since it is a promising candidate for acceleration with the Many Integrated Core (MIC) architecture of the Xeon Phi. The computation of the voxels in the field of view (FoV) can be done in parallel and the 103 to 104 samples needed to calculate the detection probability of each voxel can take advantage of vectorization. We use the ray tracing kernels of the Embree project to calculate the hit points of the sample rays with the detector and in a second step the sum of the radiological path taking into account attenuation is determined. The core components are implemented using the Intel single instruction multiple data compiler (ISPC) to enable a portable implementation showing efficient vectorization either on the Xeon Phi and the Host platform. On the Xeon Phi, the calculation of the radiological path is also implemented in hardware specific intrinsic instructions (so-called `intrinsics') to allow manually-optimized vectorization. For parallelization either OpenMP and ISPC tasking (based on pthreads) are evaluated.Our implementation achieved a scalability factor of 0.90 on the Xeon Phi coprocessor (model 5110P) with 60 cores at 1 GHz. Only minor differences were found between parallelization with OpenMP and the ISPC tasking feature. The implementation using intrinsics was found to be about 12% faster than the portable ISPC version. With this version, a speedup of 1.43 was achieved on the Xeon Phi coprocessor compared to the host system (HP SL250s Gen8) equipped with two Xeon (E5-2670) CPUs, with 8 cores at 2.6 to 3.3 GHz each. Using a second Xeon Phi card the speedup could be further increased to 2.77. No significant differences were found between the results of the different Xeon Phi and the Host implementations. The examination showed that a reasonable speedup of sensitivity map calculation could be achieved on the Xeon Phi either by a portable or a hardware specific implementation.

A Low-Cost Part-Task Flight Training System: An Application of a Head Mounted Display

DTIC Science & Technology

1990-12-01

architecture. The task at hand was to develop a software emulation libary that would emulate the function calls used within the Flight and Dog programs. This...represented in two hexadecimal digits for each color. The format of the packed long integer looks like aaggbbrr with each color value representing a...Western Digital ethernet card as the cheapest compatible card available. Good fortune arrived, as I was calling to order the card, I saw an unused card

HPC Programming on Intel Many-Integrated-Core Hardware with MAGMA Port to Xeon Phi

DOE PAGES

Dongarra, Jack; Gates, Mark; Haidar, Azzam; ...

2015-01-01

This paper presents the design and implementation of several fundamental dense linear algebra (DLA) algorithms for multicore with Intel Xeon Phi coprocessors. In particular, we consider algorithms for solving linear systems. Further, we give an overview of the MAGMA MIC library, an open source, high performance library, that incorporates the developments presented here and, more broadly, provides the DLA functionality equivalent to that of the popular LAPACK library while targeting heterogeneous architectures that feature a mix of multicore CPUs and coprocessors. The LAPACK-compliance simplifies the use of the MAGMA MIC library in applications, while providing them with portably performant DLA.more » High performance is obtained through the use of the high-performance BLAS, hardware-specific tuning, and a hybridization methodology whereby we split the algorithm into computational tasks of various granularities. Execution of those tasks is properly scheduled over the heterogeneous hardware by minimizing data movements and mapping algorithmic requirements to the architectural strengths of the various heterogeneous hardware components. Our methodology and programming techniques are incorporated into the MAGMA MIC API, which abstracts the application developer from the specifics of the Xeon Phi architecture and is therefore applicable to algorithms beyond the scope of DLA.« less

Modeling spatial variation in avian survival and residency probabilities

USGS Publications Warehouse

Saracco, James F.; Royle, J. Andrew; DeSante, David F.; Gardner, Beth

2010-01-01

The importance of understanding spatial variation in processes driving animal population dynamics is widely recognized. Yet little attention has been paid to spatial modeling of vital rates. Here we describe a hierarchical spatial autoregressive model to provide spatially explicit year-specific estimates of apparent survival (phi) and residency (pi) probabilities from capture-recapture data. We apply the model to data collected on a declining bird species, Wood Thrush (Hylocichla mustelina), as part of a broad-scale bird-banding network, the Monitoring Avian Productivity and Survivorship (MAPS) program. The Wood Thrush analysis showed variability in both phi and pi among years and across space. Spatial heterogeneity in residency probability was particularly striking, suggesting the importance of understanding the role of transients in local populations. We found broad-scale spatial patterning in Wood Thrush phi and pi that lend insight into population trends and can direct conservation and research. The spatial model developed here represents a significant advance over approaches to investigating spatial pattern in vital rates that aggregate data at coarse spatial scales and do not explicitly incorporate spatial information in the model. Further development and application of hierarchical capture-recapture models offers the opportunity to more fully investigate spatiotemporal variation in the processes that drive population changes.

Macrophage function in murine allogeneic bone marrow radiation chimeras in the early phase after transplantation

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

Roesler, J.; Baccarini, M.; Vogt, B.

1989-08-01

We tested several of the functions of macrophages (M phi) in the early phase after allogeneic bone marrow transfer to get information about this important aspect of the nonspecific immune system in the T-cell-deficient recipient. On days 3-5 after transfer, the number of M phi was reduced in the spleen, liver, lungs, and peritoneal cavity (Pe). The phagocytosis of sheep red blood cells (SRBC) by these M phi was normal or even enhanced, as in the case of Pe-M phi. Already on days 8-12 after transfer, the number of M phi in spleen and liver exceeded that of controls, whereasmore » the number was still reduced in lungs and Pe. We examined their ability to kill P815 tumor cells, to produce tumor necrosis factor-alpha (TNF alpha), to phagocytose SRBC, to produce reactive oxygen intermediates (ROI) in vitro and to kill Listeria monocytogenes in vivo. Most functions were normal and often even enhanced, depending on the organ origin, but the ability of Pe-M phi to produce ROI was reduced. Proliferative response to macrophage colony-stimulating factor (M-CSF) and killing of YAC-1 tumor cells revealed a high frequency of macrophage precursor cells in the spleen and liver and a high natural killer (NK) activity in the liver. Altogether, enhanced nonspecific immune function, especially preactivated M phi, may enable chimeras to survive attacks by opportunistic pathogens.« less

Characterization of a T7-like lytic bacteriophage (phiSG-JL2) of Salmonella enterica serovar gallinarum biovar gallinarum.

PubMed

Kwon, Hyuk-Joon; Cho, Sun-Hee; Kim, Tae-Eun; Won, Yong-Jin; Jeong, Jihye; Park, Se Chang; Kim, Jae-Hong; Yoo, Han-Sang; Park, Yong-Ho; Kim, Sun-Joong

2008-11-01

PhiSG-JL2 is a newly discovered lytic bacteriophage infecting Salmonella enterica serovar Gallinarum biovar Gallinarum but is nonlytic to a rough vaccine strain of serovar Gallinarum biovar Gallinarum (SG-9R), S. enterica serovar Enteritidis, S. enterica serovar Typhimurium, and S. enterica serovar Gallinarum biovar Pullorum. The phiSG-JL2 genome is 38,815 bp in length (GC content, 50.9%; 230-bp-long direct terminal repeats), and 55 putative genes may be transcribed from the same strand. Functions were assigned to 30 genes based on high amino acid similarity to known proteins. Most of the expected proteins except tail fiber (31.9%) and the overall organization of the genomes were similar to those of yersiniophage phiYeO3-12. phiSG-JL2 could be classified as a new T7-like virus and represents the first serovar Gallinarum biovar Gallinarum phage genome to be sequenced. On the basis of intraspecific ratios of nonsynonymous to synonymous nucleotide changes (Pi[a]/Pi[s]), gene 2 encoding the host RNA polymerase inhibitor displayed Darwinian positive selection. Pretreatment of chickens with phiSG-JL2 before intratracheal challenge with wild-type serovar Gallinarum biovar Gallinarum protected most birds from fowl typhoid. Therefore, phiSG-JL2 may be useful for the differentiation of serovar Gallinarum biovar Gallinarum from other Salmonella serotypes, prophylactic application in fowl typhoid control, and understanding of the vertical evolution of T7-like viruses.

Critical role for NHE1 in intracellular pH regulation in pancreatic acinar cells.

PubMed

Brown, David A; Melvin, James E; Yule, David I

2003-11-01

The primary function of pancreatic acinar cells is to secrete digestive enzymes together with a NaCl-rich primary fluid which is later greatly supplemented and modified by the pancreatic duct. A Na+/H+ exchanger(s) [NHE(s)] is proposed to be integral in the process of fluid secretion both in terms of the transcellular flux of Na+ and intracellular pH (pHi) regulation. Multiple NHE isoforms have been identified in pancreatic tissue, but little is known about their individual functions in acinar cells. The Na+/H+ exchange inhibitor 5-(N-ethyl-N-isopropyl) amiloride completely blocked pHi recovery after an NH4Cl-induced acid challenge, confirming a general role for NHE in pHi regulation. The targeted disruption of the Nhe1 gene also completely abolished pHi recovery from an acid load in pancreatic acini in both HCO3--containing and HCO3--free solutions. In contrast, the disruption of either Nhe2 or Nhe3 had no effect on pHi recovery. In addition, NHE1 activity was upregulated in response to muscarinic stimulation in wild-type mice but not in NHE1-deficient mice. Fluctuations in pHi could potentially have major effects on Ca2+ signaling following secretagogue stimulation; however, the targeted disruption of Nhe1 was found to have no significant effect on intracellular Ca2+ homeostasis. These data demonstrate that NHE1 is the major regulator of pHi in both resting and muscarinic agonist-stimulated pancreatic acinar cells.

Predicting prostate biopsy outcome: prostate health index (phi) and prostate cancer antigen 3 (PCA3) are useful biomarkers.

PubMed

Ferro, Matteo; Bruzzese, Dario; Perdonà, Sisto; Mazzarella, Claudia; Marino, Ada; Sorrentino, Alessandra; Di Carlo, Angelina; Autorino, Riccardo; Di Lorenzo, Giuseppe; Buonerba, Carlo; Altieri, Vincenzo; Mariano, Angela; Macchia, Vincenzo; Terracciano, Daniela

2012-08-16

Indication for prostate biopsy is presently mainly based on prostate-specific antigen (PSA) serum levels and digital-rectal examination (DRE). In view of the unsatisfactory accuracy of these two diagnostic exams, research has focused on novel markers to improve pre-biopsy prostate cancer detection, such as phi and PCA3. The purpose of this prospective study was to assess the diagnostic accuracy of phi and PCA3 for prostate cancer using biopsy as gold standard. Phi index (Beckman coulter immunoassay), PCA3 score (Progensa PCA3 assay) and other established biomarkers (tPSA, fPSA and %fPSA) were assessed before a 18-core prostate biopsy in a group of 251 subjects at their first biopsy. Values of %p2PSA and phi were significantly higher in patients with PCa compared with PCa-negative group (p<0.001) and also compared with high grade prostatic intraepithelial neoplasia (HGPIN) (p<0.001). PCA3 score values were significantly higher in PCa compared with PCa-negative subjects (p<0.001) and in HGPIN vs PCa-negative patients (p<0.001). ROC curve analysis showed that %p2PSA, phi and PCA3 are predictive of malignancy. In conclusion, %p2PSA, phi and PCA3 may predict a diagnosis of PCa in men undergoing their first prostate biopsy. PCA3 score is more useful in discriminating between HGPIN and non-cancer. Copyright © 2012 Elsevier B.V. All rights reserved.

A structural model of anti-anti-[sigma] inhibition by a two-component receiver domain: the PhyR stress response regulator

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

Herrou, Julien; Foreman, Robert; Fiebig, Aretha

2012-05-09

PhyR is a hybrid stress regulator conserved in {alpha}-proteobacteria that contains an N-terminal {sigma}-like (SL) domain and a C-terminal receiver domain. Phosphorylation of the receiver domain is known to promote binding of the SL domain to an anti-{sigma} factor. PhyR thus functions as an anti-anti-{sigma} factor in its phosphorylated state. We present genetic evidence that Caulobacter crescentus PhyR is a phosphorylation-dependent stress regulator that functions in the same pathway as {sigma}{sup T} and its anti-{sigma} factor, NepR. Additionally, we report the X-ray crystal structure of PhyR at 1.25 {angstrom} resolution, which provides insight into the mechanism of anti-anti-{sigma} regulation. Directmore » intramolecular contact between the PhyR receiver and SL domains spans regions {sigma}{sub 2} and {sigma}{sub 4}, likely serving to stabilize the SL domain in a closed conformation. The molecular surface of the receiver domain contacting the SL domain is the structural equivalent of {alpha}4-{beta}5-{alpha}5, which is known to undergo dynamic conformational change upon phosphorylation in a diverse range of receiver proteins. We propose a structural model of PhyR regulation in which receiver phosphorylation destabilizes the intramolecular interaction between SL and receiver domains, thereby permitting regions {sigma}{sub 2} and {sigma}{sub 4} in the SL domain to open about a flexible connector loop and bind anti-{sigma} factor.« less

A structural model of anti-anti-[sigma];#963; inhibition by a two-component receiver domain: the PhyR stress response regulator

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

Herrou, Julien; Foreman, Robert; Fiebig, Aretha

2012-03-30

PhyR is a hybrid stress regulator conserved in {alpha}-proteobacteria that contains an N-terminal {sigma}-like (SL) domain and a C-terminal receiver domain. Phosphorylation of the receiver domain is known to promote binding of the SL domain to an anti-{sigma} factor. PhyR thus functions as an anti-anti-{sigma} factor in its phosphorylated state. We present genetic evidence that Caulobacter crescentus PhyR is a phosphorylation-dependent stress regulator that functions in the same pathway as {sigma}{sup T} and its anti-{sigma} factor, NepR. Additionally, we report the X-ray crystal structure of PhyR at 1.25 {angstrom} resolution, which provides insight into the mechanism of anti-anti-{sigma} regulation. Directmore » intramolecular contact between the PhyR receiver and SL domains spans regions {sigma}{sub 2} and {sigma}{sub 4}, likely serving to stabilize the SL domain in a closed conformation. The molecular surface of the receiver domain contacting the SL domain is the structural equivalent of {alpha}4-{beta}5-{alpha}5, which is known to undergo dynamic conformational change upon phosphorylation in a diverse range of receiver proteins. We propose a structural model of PhyR regulation in which receiver phosphorylation destabilizes the intramolecular interaction between SL and receiver domains, thereby permitting regions {sigma}{sub 2} and {sigma}{sub 4} in the SL domain to open about a flexible connector loop and bind anti-{sigma} factor.« less

phiC31 Integrase-Mediated Site-Specific Recombination in Barley

PubMed Central

Rubtsova, Myroslava; Kumlehn, Jochen; Gils, Mario

2012-01-01

The Streptomyces phage phiC31 integrase was tested for its feasibility in excising transgenes from the barley genome through site-specific recombination. We produced transgenic barley plants expressing an active phiC31 integrase and crossed them with transgenic barley plants carrying a target locus for recombination. The target sequence involves a reporter gene encoding green fluorescent protein (GFP), which is flanked by the attB and attP recognition sites for the phiC31 integrase. This sequence disruptively separates a gusA coding sequence from an upstream rice actin promoter. We succeeded in producing site-specific recombination events in the hybrid progeny of 11 independent barley plants carrying the above target sequence after crossing with plants carrying a phiC31 expression cassette. Some of the hybrids displayed fully executed recombination. Excision of the GFP gene fostered activation of the gusA gene, as visualized in tissue of hybrid plants by histochemical staining. The recombinant loci were detected in progeny of selfed F1, even in individuals lacking the phiC31 transgene, which provides evidence of stability and generative transmission of the recombination events. In several plants that displayed incomplete recombination, extrachromosomal excision circles were identified. Besides the technical advance achieved in this study, the generated phiC31 integrase-expressing barley plants provide foundational stock material for use in future approaches to barley genetic improvement, such as the production of marker-free transgenic plants or switching transgene activity. PMID:23024817

OFDM and PAM comparison using a high baudrate low resolution IM/DD interface for 400G Ethernet access.

PubMed

André, Nuno Sequeira; Louchet, Hadrien; Filsinger, Volker; Hansen, Erik; Richter, André

2016-05-30

We compare OFDM and PAM for 400G Ethernet based on a 3-bit high baudrate IM/DD interface at 1550nm. We demonstrate 27Gb/s and 32Gb/s transmission over 10km SSMF using OFDM and PAM respectively. We show that capacity can be improved through adaptation/equalization to achieve 42Gb/s and 64Gb/s for OFDM and PAM respectively. Experimental results are used to create realistic simulations to extrapolate the performance of both modulation formats under varied conditions. For the considered interface we found that PAM has the best performance, OFDM is impaired by quantization noise. When the resolution limitation is relaxed, OFDM shows better performance.

Ethernet based data logger for gaseous detectors

NASA Astrophysics Data System (ADS)

Swain, S.; Sahu, P. K.; Sahu, S. K.

2018-05-01

A data logger is designed to monitor and record ambient parameters such as temperature, pressure and relative humidity along with gas flow rate as a function of time. These parameters are required for understanding the characteristics of gas-filled detectors such as Gas Electron Multiplier (GEM) and Multi-Wire Proportional Counter (MWPC). The data logger has different microcontrollers and has been interfaced to an ethernet port with a local LCD unit for displaying all measured parameters. In this article, the explanation of the data logger design, hardware, and software description of the master microcontroller and the DAQ system along with LabVIEW interface client program have been presented. We have implemented this device with GEM detector and displayed few preliminary results as a function of above parameters.

Environmental Acoustic Considerations for Passive Detection of Maritime Targets by Hydrophones in a Deep Ocean Trench

DTIC Science & Technology

2010-06-01

Science and Technology. Available: http://cmst.curtin.edu.au/local/docs/ products / actup_v2_2l_installation_user_guide.pdf (accessed 2 June 2010...noisecurve112(:,6)); %% Intergrating Noise Level Trench A n2=0; Itot=0; phi_t=atan(D1/L1); m=1; while (phi(m,1)>phi_t) m=m+1; end

Development of a translation stage for in situ noninvasive analysis and high-resolution imaging

NASA Astrophysics Data System (ADS)

Strivay, David; Clar, Mathieu; Rakkaa, Said; Hocquet, Francois-Philippe; Defeyt, Catherine

2016-11-01

Noninvasive imaging techniques and analytical instrumentation for cultural heritage object studies have undergone a tremendous development over the last years. Many new miniature and/or handheld systems have been developed and optimized. Nonetheless, these instruments are usually used with a tripod or a manual position system. This is very time consuming when performing point analysis or 2D scanning of a surface. The Centre Européen d'Archéométrie has built a translation system made of pluggable rails of 1 m long with a maximum length and height of 3 m. Three motors embedded in the system allow the platform to be moved along these axis, toward and backward from the sample. The rails hold a displacement system, providing a continuous movement. Any position can be reached with a reproducibility of 0.1 mm. The displacements are controlled by an Ethernet connection through a laptop computer running a multiplatform custom-made software written in JAVA. This software allows a complete control over the positioning using a simple, unique, and concise interface. Automatic scanning can be performed over a large surface of 3 m on 3 m. The Ethernet wires provide also the power for the different motors and, if necessary, the detection head. The platform has been originally designed for a XRF detection head (with its full power alimentation) but now can accommodate many different systems like IR reflectography, digital camera, hyperspectral camera, and Raman probes. The positioning system can be modified to combine the acquisition software of the imaging or analytical techniques and the positioning software.

Berry phase and entanglement of three qubits in a new Yang-Baxter system

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

Hu Taotao; Xue Kang; Wu Chunfeng

2009-08-15

In this paper we construct a new 8x8M matrix from the 4x4M matrix, where M/M is the image of the braid group representation. The 8x8M matrix and the 4x4M matrix both satisfy extraspecial 2-group algebra relations. By Yang-Baxteration approach, we derive a unitary R({theta},{phi}) matrix from the M matrix with parameters {phi} and {theta}. Three-qubit entangled states can be generated by using the R({theta},{phi}) matrix. A Hamiltonian for three qubits is constructed from the unitary R({theta},{phi}) matrix. We then study the entanglement and Berry phase of the Yang-Baxter system.

Energetic distributions of interface states Dit(phi sub s) of MOS transistors in extension of Kuhn's quasistatic C(V)-method

NASA Astrophysics Data System (ADS)

Krautschneider, W.; Wagemann, H. G.

1983-10-01

Kuhn's quasi-static C(V)-method has been extended to MOS transistors by considering the capacitances of the source and drain p-n junctions additionally to the MOS varactor circuit model. The width of the space charge layers w(phi sub s) is calculated as a function of the surface potential phi sub s and applied to the MOS capacitance as a function of the gate voltage. Capacitance behavior for different channel length is presented as a model and compared to measurement results and evaluations of energetic distributions of interface states Dit(phi sub s) for MOS transistor and MOS varactor on the same chip.

GST ( phi) gene from Macrophyte Lemna minor is involved in cadmium exposure responses

NASA Astrophysics Data System (ADS)

Chen, Shihua; Chen, Xin; Dou, Weihong; Wang, Liang; Yin, Haibo; Guo, Shanli

2016-03-01

Reactive oxygen species (ROS) scavengers, including ascorbate peroxidase, superoxide dismutase, catalase and peroxidase, are the most commonly used biomarkers in assessing an organisms' response to many biotic and abiotic stresses. In this study, we cloned an 866 bp GST ( phi) gene in Lemna minor and investigated its characteristics, expression and enzymatic activities under 75 μmol/L cadmium concentrations in comparison with other ROS scavengers. GST ( phi) gene expression patterns were similar to those of other scavengers of ROS. This suggests that GST ( phi) might be involved in responding to heavy metal (cadmium) stress and that its expression level could be used as a bio-indicator in monitoring cadmium pollution.

Ultra low thermal expansion, highly thermal shock resistant ceramic

DOEpatents

Limaye, Santosh Y.

1996-01-01

Three families of ceramic compositions having the given formula: .phi..sub.1+X Zr.sub.4 P.sub.6-2X Si.sub.2X O.sub.24, .phi..sub.1+X Zr.sub.4-2X Y.sub.2X P.sub.6 O.sub.24 and .phi..sub.1+X Zr.sub.4-X Y.sub.X P.sub.6-2X Si.sub.X O.sub.24 wherein .phi. is either Strontium or Barium and X has a value from about 0.2 to about 0.8 have been disclosed. Ceramics formed from these compositions exhibit very low, generally near neutral, thermal expansion over a wide range of elevated temperatures.

Deploying electromagnetic particle-in-cell (EM-PIC) codes on Xeon Phi accelerators boards

NASA Astrophysics Data System (ADS)

Fonseca, Ricardo

2014-10-01

The complexity of the phenomena involved in several relevant plasma physics scenarios, where highly nonlinear and kinetic processes dominate, makes purely theoretical descriptions impossible. Further understanding of these scenarios requires detailed numerical modeling, but fully relativistic particle-in-cell codes such as OSIRIS are computationally intensive. The quest towards Exaflop computer systems has lead to the development of HPC systems based on add-on accelerator cards, such as GPGPUs and more recently the Xeon Phi accelerators that power the current number 1 system in the world. These cards, also referred to as Intel Many Integrated Core Architecture (MIC) offer peak theoretical performances of >1 TFlop/s for general purpose calculations in a single board, and are receiving significant attention as an attractive alternative to CPUs for plasma modeling. In this work we report on our efforts towards the deployment of an EM-PIC code on a Xeon Phi architecture system. We will focus on the parallelization and vectorization strategies followed, and present a detailed performance evaluation of code performance in comparison with the CPU code.

Clinical performance of serum prostate-specific antigen isoform [-2]proPSA (p2PSA) and its derivatives, %p2PSA and the prostate health index (PHI), in men with a family history of prostate cancer: results from a multicentre European study, the PROMEtheuS project.

PubMed

Lazzeri, Massimo; Haese, Alexander; Abrate, Alberto; de la Taille, Alexandre; Redorta, Joan Palou; McNicholas, Thomas; Lughezzani, Giovanni; Lista, Giuliana; Larcher, Alessandro; Bini, Vittorio; Cestari, Andrea; Buffi, Nicolòmaria; Graefen, Markus; Bosset, Olivier; Le Corvoisier, Philippe; Breda, Alberto; de la Torre, Pablo; Fowler, Linda; Roux, Jacques; Guazzoni, Giorgio

2013-08-01

To test the sensitivity, specificity and accuracy of serum prostate-specific antigen isoform [-2]proPSA (p2PSA), %p2PSA and the prostate health index (PHI), in men with a family history of prostate cancer (PCa) undergoing prostate biopsy for suspected PCa. To evaluate the potential reduction in unnecessary biopsies and the characteristics of potentially missed cases of PCa that would result from using serum p2PSA, %p2PSA and PHI. The analysis consisted of a nested case-control study from the PRO-PSA Multicentric European Study, the PROMEtheuS project. All patients had a first-degree relative (father, brother, son) with PCa. Multivariable logistic regression models were complemented by predictive accuracy analysis and decision-curve analysis. Of the 1026 patients included in the PROMEtheuS cohort, 158 (15.4%) had a first-degree relative with PCa. p2PSA, %p2PSA and PHI values were significantly higher (P < 0.001), and free/total PSA (%fPSA) values significantly lower (P < 0.001) in the 71 patients with PCa (44.9%) than in patients without PCa. Univariable accuracy analysis showed %p2PSA (area under the receiver-operating characteristic curve [AUC]: 0.733) and PHI (AUC: 0.733) to be the most accurate predictors of PCa at biopsy, significantly outperforming total PSA ([tPSA] AUC: 0.549), free PSA ([fPSA] AUC: 0.489) and %fPSA (AUC: 0.600) (P ≤ 0.001). For %p2PSA a threshold of 1.66 was found to have the best balance between sensitivity and specificity (70.4 and 70.1%; 95% confidence interval [CI]: 58.4-80.7 and 59.4-79.5 respectively). A PHI threshold of 40 was found to have the best balance between sensitivity and specificity (64.8 and 71.3%, respectively; 95% CI 52.5-75.8 and 60.6-80.5). At 90% sensitivity, the thresholds for %p2PSA and PHI were 1.20 and 25.5, with a specificity of 37.9 and 25.5%, respectively. At a %p2PSA threshold of 1.20, a total of 39 (24.8%) biopsies could have been avoided, but two cancers with a Gleason score (GS) of 7 would have been missed. At a PHI threshold of 25.5 a total of 27 (17.2%) biopsies could have been avoided and two (3.8%) cancers with a GS of 7 would have been missed. In multivariable logistic regression models, %p2PSA and PHI achieved independent predictor status and significantly increased the accuracy of multivariable models including PSA and prostate volume by 8.7 and 10%, respectively (P ≤ 0.001). p2PSA, %p2PSA and PHI were directly correlated with Gleason score (ρ: 0.247, P = 0.038; ρ: 0.366, P = 0.002; ρ: 0.464, P < 0.001, respectively). %p2PSA and PHI are more accurate than tPSA, fPSA and %fPSA in predicting PCa in men with a family history of PCa. Consideration of %p2PSA and PHI results in the avoidance of several unnecessary biopsies. p2PSA, %p2PSA and PHI correlate with cancer aggressiveness. © 2013 BJU International.

HEALTH TECHNOLOGY ASSESSMENT OF PUBLIC HEALTH INTERVENTIONS: A SYNTHESIS OF METHODOLOGICAL GUIDANCE.

PubMed

Mathes, Tim; Antoine, Sunya-Lee; Prengel, Peggy; Bühn, Stefanie; Polus, Stephanie; Pieper, Dawid

2017-01-01

The evaluation of public health interventions poses some challenges. As a consequence, health technology assessment (HTA) methods for public health interventions (PHI) have to be adapted. This study aimed to summarize the available guidance on methods for HTA of PHI. We systematically searched for methodological guidance on HTA of PHIs. Our focus was on research synthesis methods to evaluate effectiveness. Relevant information was synthesized narratively in a standardized way. Only four guidance documents were identified specifically for HTAs of PHI. The approaches used for HTAs of PHIs are broader and more flexible than those for medical interventions. For this reason, there is a tendency to identify the intervention components and context factors that influence the effectiveness and transferability of an intervention rather than to assess its effectiveness in general. The details in the guidance vary without justification. Unjustified heterogeneity between the different guidance approaches is most pronounced for quality assessment, assessment of applicability, and methods to integrate qualitative and quantitative evidence. Descriptions for the assessment of integrity, heterogeneity, sustainability, context factors, and applicability are often vague. The heterogeneity in approaches indicates that there is currently no consensus on methods to deal with the challenges of the PHI evaluations. A possible explanation for this may be that the methods are not sufficiently developed, and advantages and disadvantages of a certain method in relation to the research question (e.g., broad/focused) have not yet been sufficiently evaluated.

Reducing adaptive optics latency using Xeon Phi many-core processors

NASA Astrophysics Data System (ADS)

Barr, David; Basden, Alastair; Dipper, Nigel; Schwartz, Noah

2015-11-01

The next generation of Extremely Large Telescopes (ELTs) for astronomy will rely heavily on the performance of their adaptive optics (AO) systems. Real-time control is at the heart of the critical technologies that will enable telescopes to deliver the best possible science and will require a very significant extrapolation from current AO hardware existing for 4-10 m telescopes. Investigating novel real-time computing architectures and testing their eligibility against anticipated challenges is one of the main priorities of technology development for the ELTs. This paper investigates the suitability of the Intel Xeon Phi, which is a commercial off-the-shelf hardware accelerator. We focus on wavefront reconstruction performance, implementing a straightforward matrix-vector multiplication (MVM) algorithm. We present benchmarking results of the Xeon Phi on a real-time Linux platform, both as a standalone processor and integrated into an existing real-time controller (RTC). Performance of single and multiple Xeon Phis are investigated. We show that this technology has the potential of greatly reducing the mean latency and variations in execution time (jitter) of large AO systems. We present both a detailed performance analysis of the Xeon Phi for a typical E-ELT first-light instrument along with a more general approach that enables us to extend to any AO system size. We show that systematic and detailed performance analysis is an essential part of testing novel real-time control hardware to guarantee optimal science results.

Impact of the introduction of the pneumococcal conjugate vaccine in the Brazilian routine childhood national immunization program.

PubMed

Moreira, Marta; Cintra, Otavio; Harriague, Julie; Hausdorff, William P; Hoet, Bernard

2016-05-27

Brazil introduced the 10-valent pneumococcal non-typeable Haemophilus influenzae protein D conjugate vaccine (PHiD-CV, Synflorix™, GSK Vaccines) in the routine childhood immunization program in 2010 with a 3+1 schedule (with catch-up for children <2 years-old). This review represents the first analysis of the overall impact of a second-generation pneumococcal conjugate vaccine on nasopharyngeal carriage and all the major pneumococcal disease manifestations in a single, pneumococcal conjugate vaccine-naïve, developing country. A total of 15 published articles and 13 congress abstracts were included in the analysis. In children <5 years-old, studies showed a positive impact of PHiD-CV on the incidence of vaccine-type and any-type invasive pneumococcal disease (including decreases in pneumococcal meningitis morbidity and mortality), on pneumonia incidence and mortality, and on otitis media. Nasopharyngeal carriage of vaccine-type and any-type pneumococci decreased after the primary doses, with no early signs of replacement with other pathogens. Finally, herd protection against vaccine-type invasive pneumococcal disease and pneumonia in unvaccinated subjects was shown in some studies for some age groups. In conclusion, pneumococcal disease decreased after the introduction of PHiD-CV into the Brazilian national immunization program. Further follow-up is needed to evaluate the long-term overall impact of PHiD-CV in the Brazilian population. Copyright © 2016 GlaxoSmithKline Biologicals SA. Published by Elsevier Ltd.. All rights reserved.

Temperate bacteriophage {phi}O18P from an Aeromonas media isolate: Characterization and complete genome sequence

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

Beilstein, Frauke; Dreiseikelmann, Brigitte

2008-03-30

A group of 74 Aeromonas isolates from surface water of three ponds in Bielefeld, Germany was screened for prophage induction after UV irradiation. The phage {phi}O18P was induced from the Aeromonas media isolate O18. {phi}O18P belongs to the Myoviridae phage family. The complete nucleotide sequence of the double stranded DNA genome of bacteriophage {phi}O18P consists of 33,985 bp. The genome has 5' protruding cohesive ends of 16 bases. On the {phi}O18P genome 46 open reading frames (orfs) were identified which are organized in the modules integration and regulation, replication, head, packaging, tail and lysis. Additionally the phage DNA includes amore » methylase gene. Comparison of the genome architecture with those of other bacteriophages revealed significant similarities to the P2 phage family and especially to the prophages of Aeromonas salmonicida and the Vibrio cholerae phage K139.« less

Structural Conservation of the Myoviridae Phage Tail Sheath Protein Fold

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

Aksyuk, Anastasia A.; Kurochkina, Lidia P.; Fokine, Andrei

2012-02-21

Bacteriophage phiKZ is a giant phage that infects Pseudomonas aeruginosa, a human pathogen. The phiKZ virion consists of a 1450 {angstrom} diameter icosahedral head and a 2000 {angstrom}-long contractile tail. The structure of the whole virus was previously reported, showing that its tail organization in the extended state is similar to the well-studied Myovirus bacteriophage T4 tail. The crystal structure of a tail sheath protein fragment of phiKZ was determined to 2.4 {angstrom} resolution. Furthermore, crystal structures of two prophage tail sheath proteins were determined to 1.9 and 3.3 {angstrom} resolution. Despite low sequence identity between these proteins, all ofmore » these structures have a similar fold. The crystal structure of the phiKZ tail sheath protein has been fitted into cryo-electron-microscopy reconstructions of the extended tail sheath and of a polysheath. The structural rearrangement of the phiKZ tail sheath contraction was found to be similar to that of phage T4.« less

Intramolecular co-action of two independent photosensory modules in the fern phytochrome 3.

PubMed

Kanegae, Takeshi

2015-01-01

Fern phytochrome3/neochrome1 (phy3/neo1) is a chimeric photoreceptor composed of a phytochrome-chromophore binding domain and an almost full-length phototropin. phy3 thus contains two different light-sensing modules; a red/far-red light receptor phytochrome and a blue light receptor phototropin. phy3 induces both red light- and blue light-dependent phototropism in phototropin-deficient Arabidopsis thaliana (phot1 phot2) seedlings. The red-light response is dependent on the phytochrome module of phy3, and the blue-light response is dependent on the phototropin module. We recently showed that both the phototropin-sensing module and the phytochrome-sensing module mediate the blue light-dependent phototropic response. Particularly under low-light conditions, these two light-sensing modules cooperate to induce the blue light-dependent phototropic response. This intramolecular co-action of two independent light-sensing modules in phy3 enhances light sensitivity, and perhaps allowed ferns to adapt to the low-light canopy conditions present in angiosperm forests.

Relative evolutionary rate inference in HyPhy with LEISR.

PubMed

Spielman, Stephanie J; Kosakovsky Pond, Sergei L

2018-01-01

We introduce LEISR (Likehood Estimation of Individual Site Rates, pronounced "laser"), a tool to infer relative evolutionary rates from protein and nucleotide data, implemented in HyPhy. LEISR is based on the popular Rate4Site (Pupko et al., 2002) approach for inferring relative site-wise evolutionary rates, primarily from protein data. We extend the original method for more general use in several key ways: (i) we increase the support for nucleotide data with additional models, (ii) we allow for datasets of arbitrary size, (iii) we support analysis of site-partitioned datasets to correct for the presence of recombination breakpoints, (iv) we produce rate estimates at all sites rather than at just a subset of sites, and (v) we implemented LEISR as MPI-enabled to support rapid, high-throughput analysis. LEISR is available in HyPhy starting with version 2.3.8, and it is accessible as an option in the HyPhy analysis menu ("Relative evolutionary rate inference"), which calls the HyPhy batchfile LEISR.bf.

[Isolation, idetification and anti-HIV-1 integrase activity of culturable endophytic fungi from Tibetan medicinal plant Phlomis younghusbandii Mukerjee].

PubMed

Zhang, Da-Wei; Zhao, Ming-Ming; Chen, Juan; Li, Chao; Guo, Shun-Xing

2013-05-01

A total of 52 endophytic fungi were isolated from roots and stems of Tibetan medicinal plant Phlomis younghusbandii Mukerjee. These fungal isolates were molecularly identified based on ITS sequnces and 28S sequences distributed to 12 genera, including Phoma, Chaetosphaeronema, Fusarium and Leptosphaeria, etc. Among them, the dominant genus was Phoma. Extracts of all strains were evaluated for anti-HIV-1 integrase activity by using soluable integrase expressed in E. coli BL21 (DE3). The results showed that seven samples from five fungal endophytes PHY-24, PHY-38, PHY-40, PHY-51, PHY-53, which belonged to genus Chaetosphaeronema, inhibited strand transfer reaction catalyzed by HIV-1 integrase with IC50 values, of 6.60, 5.20, 2.86, 7.86, 4.47, 4.56 and 3.23 microg x mL(-1) respectively. In conclusion, the endophytic fungi of Phlomis younghusbandii Mukerjee are valuable for further screening anti-HIV-1 integrase agents.

Statistical reporting inconsistencies in experimental philosophy

PubMed Central

Colombo, Matteo; Duev, Georgi; Nuijten, Michèle B.; Sprenger, Jan

2018-01-01

Experimental philosophy (x-phi) is a young field of research in the intersection of philosophy and psychology. It aims to make progress on philosophical questions by using experimental methods traditionally associated with the psychological and behavioral sciences, such as null hypothesis significance testing (NHST). Motivated by recent discussions about a methodological crisis in the behavioral sciences, questions have been raised about the methodological standards of x-phi. Here, we focus on one aspect of this question, namely the rate of inconsistencies in statistical reporting. Previous research has examined the extent to which published articles in psychology and other behavioral sciences present statistical inconsistencies in reporting the results of NHST. In this study, we used the R package statcheck to detect statistical inconsistencies in x-phi, and compared rates of inconsistencies in psychology and philosophy. We found that rates of inconsistencies in x-phi are lower than in the psychological and behavioral sciences. From the point of view of statistical reporting consistency, x-phi seems to do no worse, and perhaps even better, than psychological science. PMID:29649220

DelPhi Web Server: A comprehensive online suite for electrostatic calculations of biological macromolecules and their complexes

PubMed Central

Sarkar, Subhra; Witham, Shawn; Zhang, Jie; Zhenirovskyy, Maxim; Rocchia, Walter; Alexov, Emil

2011-01-01

Here we report a web server, the DelPhi web server, which utilizes DelPhi program to calculate electrostatic energies and the corresponding electrostatic potential and ionic distributions, and dielectric map. The server provides extra services to fix structural defects, as missing atoms in the structural file and allows for generation of missing hydrogen atoms. The hydrogen placement and the corresponding DelPhi calculations can be done with user selected force field parameters being either Charmm22, Amber98 or OPLS. Upon completion of the calculations, the user is given option to download fixed and protonated structural file, together with the parameter and Delphi output files for further analysis. Utilizing Jmol viewer, the user can see the corresponding structural file, to manipulate it and to change the presentation. In addition, if the potential map is requested to be calculated, the potential can be mapped onto the molecule surface. The DelPhi web server is available from http://compbio.clemson.edu/delphi_webserver. PMID:24683424

Photoassociation dynamics driven by a modulated two-color laser field

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

Zhang Wei; Zhao Zeyu; Xie Ting

2011-11-15

Photoassociation (PA) dynamics of ultracold cesium atoms steered by a modulated two-color laser field E(t)=E{sub 0}f(t)cos((2{pi}/T{sub p})-{phi})cos({omega}{sub L}t) is investigated theoretically by numerically solving the time-dependent Schroedinger equation. The PA dynamics is sensitive to the phase of envelope (POE) {phi} and the period of the envelope T{sub p}, which indicates that it can be controlled by varying POE {phi} and period T{sub p}. Moreover, we introduce the time- and frequency-resolved spectrum to illustrate how the POE {phi} and the period T{sub p} influence the intensity distribution of the modulated laser pulse and hence change the time-dependent population distribution of photoassociatedmore » molecules. When the Gaussian envelope contains a few oscillations, the PA efficiency is also dependent on POE {phi}. The modulated two-color laser field is available in the current experiment based on laser mode-lock technology.« less

Impact of Assay conditions on activity estimate and kinetics comparison of Aspergillus niger PhyA and Escherichia coli AppA2 phytases

USDA-ARS?s Scientific Manuscript database

This study was to compare three phytase activity assays and kinetics of Aspergillus niger PhyA and Escherichia coli AppA2 phytases expressed in Pichia pastoris at the observed stomach pH of 3.5. In Experiment 1, equivalent phytase activities in the crude preparations of PhyA and AppA2 were tested ...

Root phototropism: how light and gravity interact in shaping plant form

NASA Technical Reports Server (NTRS)

Kiss, John Z.; Correll, Melanie J.; Mullen, Jack L.; Hangarter, Roger P.; Edelmann, Richard E.

2003-01-01

The interactions among tropisms can be critical in determining the final growth form of plants and plant organs. We have studied tropistic responses in roots as an example of these type of interactions. While gravitropism is the predominant tropistic response in roots, phototropism also plays a role in the oriented growth in this organ in flowering plants. In blue or white light, roots exhibit negative phototropism, but red light induces positive phototropism. In the flowering plant Arabidopsis, the photosensitive pigments phytochrome A (phyA) and phytochrome B (phyB) mediate this positive red-light-based photoresponse in roots since single mutants (and the double phyAB mutant) were severely impaired in this response. While blue-light-based negative phototropism is primarily mediated by the phototropin family of photoreceptors, the phyA and phyAB mutants (but not phyB) were inhibited in this response relative to the WT. The differences observed in phototropic responses were not due to growth limitations since the growth rates among all the mutants tested were not significantly different from that of the WT. Thus, our study shows that the blue-light and red-light systems interact in plants and that phytochrome plays a key role in integrating multiple environmental stimuli.

Role of phytochromes A and B in the regulation of cell death and acclimatory responses to UV stress in Arabidopsis thaliana

PubMed Central

Rusaczonek, Anna; Czarnocka, Weronika; Kacprzak, Sylwia; Witoń, Damian; Ślesak, Ireneusz; Szechyńska-Hebda, Magdalena; Gawroński, Piotr; Karpiński, Stanisław

2015-01-01

Plants coordinate their responses to various biotic and abiotic stresses in order to optimize their developmental and acclimatory programmes. The ultimate response to an excessive amount of stress is local induction of cell death mechanisms. The death of certain cells can help to maintain tissue homeostasis and enable nutrient remobilization, thus increasing the survival chances of the whole organism in unfavourable environmental conditions. UV radiation is one of the environmental factors that negatively affects the photosynthetic process and triggers cell death. The aim of this work was to evaluate a possible role of the red/far-red light photoreceptors phytochrome A (phyA) and phytochrome B (phyB) and their interrelations during acclimatory responses to UV stress. We showed that UV-C treatment caused a disturbance in photosystem II and a deregulation of photosynthetic pigment content and antioxidant enzymes activities, followed by increased cell mortality rate in phyB and phyAB null mutants. We also propose a regulatory role of phyA and phyB in CO2 assimilation, non-photochemical quenching, reactive oxygen species accumulation and salicylic acid content. Taken together, our results suggest a novel role of phytochromes as putative regulators of cell death and acclimatory responses to UV. PMID:26385378