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Sample records for pickering ngs model

  1. Commissioning quality assurance at Pickering NGS

    International Nuclear Information System (INIS)

    Wieckowski, J.T.

    1983-05-01

    Ontario Hydro decided in 1978 to implement a formal quality assurance program applicable to commissioning and operation of nuclear generating stations. Pickering NGS is the first station to have the commissioning quality assurance (CQA) program applied to it. This paper outlines the scope, implementation, and evaluation of the CQA program as applied to Pickering Unit 5

  2. Pickering NGS-A versus Pickering NGS-B: changes in commissioning techniques and their impact

    International Nuclear Information System (INIS)

    Talbot, K.H.

    1983-05-01

    Modernization of equipment, changes in design codes and standards, and tightening of regulatory requirements have combined to make Pickering NGS-B in many ways different from its predecessor, Pickering 'A'. This paper briefly describes how a few selected commissioning techniques used to place Pickering 'A' into service were further developed to cope with the new requirements for Pickering 'B'. The relative performance of the commissioning programmes between the two stations is also compared

  3. Comparison of Pickering NGS performance with world power reactors, 1977

    International Nuclear Information System (INIS)

    Buhay, S.

    Pickering NGS performance is compared, in highly graphic form, with the perfomance of other nuclear power plants around the world. The four Pickering reactors score in the top six, rated by gross capacity factor. Major system suppliers for world power reactors above 500 MW are cataloged. (E.C.B.)

  4. AECB staff review of Pickering NGS operations for the year 1988

    International Nuclear Information System (INIS)

    1989-05-01

    The operation of Pickering NGS-A Units 1-4 and Pickering NGS-B Units 5-8 are monitored to ensure compliance with licensing requirements by the AECB Pickering project office staff. This report presents AECB staff's review of major licensing issues and of the operational performance of Pickering NGS during 1988. The report is limited to those aspects that AECB staff considers to have particular safety significance. More detailed information on routine performance is contained in Ontario Hydro's 1988 Quarterly Technical Reports for Pickering NGS-A and Pickering NGS-B

  5. Pickering NGS end of commercial operations

    Energy Technology Data Exchange (ETDEWEB)

    Swami, L. [Ontario Power Generation, Pickering, ON (Canada)

    2015-07-01

    Pickering continues as a valued asset for the Province • OPG's current business plan is to continue to operate Pickering to the end of 2020 • Planning its shutdown is underway and includes the following activities to: • Place the units into safe store • Manage the wastes arising • Repurpose the Pickering lands and facilities • Decommissioning will take place in the future and will include appropriate waste management activities. © Copyright 2015 by the Canadian Nuclear Society. All rights reserved.

  6. Evolution of CANDU vacuum building and pressure relief structures from Pickering NGS A to Darlington NGS A

    International Nuclear Information System (INIS)

    Beg, Z.M.; Ghosh, R.S.

    1987-01-01

    The vacuum building (VB) and pressure relief structures (PRS) are the unique features of multiple unit CANDU containments. In case of loss-of-coolant accident, the released radionuclides are drawn through the PRS into the subatmospheric VB, doused and contained without being released to the environment. This paper describes the differences in design, configuration and layout of the VB and PRS from Pickering NGS A to Darlington NGS A due to new developments in design concepts and to requirements which have proceeded from the experience gained in both the design and operation of the nuclear stations. (orig.)

  7. AECB staff annual report of Pickering NGS for the year 1991

    International Nuclear Information System (INIS)

    1992-11-01

    The AECB Pickering project staff, in cooperation with AECB staff in Ottawa, monitor the operation of Pickering NGS-A units 1-4 and Pickering NGS-B units 5-8 to ensure that Ontario Hydro operates the station in compliance with the licensing and safety requirements of the Atomic Energy Control Board. This report presents the review of licensing issues and station performance during 1991. Improvement over 1990 station operation occurred in the following areas: availability of special safety systems; reduction of the station external dose; reorganization of station management to improve focus; station chemistry; housekeeping and material condition; fuel handling capability; training of operators and maintenance staff. However, little change occurred and improvement is still needed in the following: compliance with operating licence; system surveillance program; station maintenance; environmental qualification; radiation emergency response; fire and rescue emergency response; limited capability to predict and prevent equipment failures such as the boiler tube failure on unit 5. (L.L.)

  8. The 1994 loss of coolant incident at Pickering NGS

    Energy Technology Data Exchange (ETDEWEB)

    Charlebois, P R; Clarke, T R; Goodman, R M; McEwan, W F [Ontario Hydro, Pickering, ON (Canada). Pickering Generating Station; Cuttler, J M [Atomic Energy of Canada Ltd., Mississauga, ON (Canada)

    1996-12-31

    Fracture of the rubber diaphragm in a liquid relief valve initiated events leading to a loss of coolant in Unit 2, on December 10. The valve failed open, filling the bleed condenser. The reactor shut itself down. When pressure recovered, two spring-loaded safety relief valves opened and one of them chattered. The shock and pulsations cracked the inlet pipe to the chattering valve, and the subsequent loss of coolant triggered the emergency core cooling system. The incident was terminated by operator action. No abnormal radioactivity was released. The four reactor units of Pickering A remained shut down until the corrective actions were completed in April/May 1995. (author). 4 figs.

  9. Seismic analysis of mechanical systems at Pickering NGS

    International Nuclear Information System (INIS)

    Ghobarah, A.

    1995-11-01

    The objective of this study is to assess the seismic withstand capacity of selected safety-related mechanical systems associated with the Pressure Relief Duct (PRD) at the Pickering A Nuclear Generating Station. These systems are attached to the PRD and include the Emergency Coolant Injection System piping, the Vacuum Ducts, the Emergency Water Storage System, the PRD expansion joint seals and the PRD to Reactor Building joint seals. The input support motion to the mechanical systems is taken to be the seismic response of the PRD determined in an earlier study using various levels of predetermined ground response spectrum envelope. (author). 12 refs., 13 tabs., 48 figs

  10. Pressure tube replacement in Pickering NGS A units 1 and 2

    International Nuclear Information System (INIS)

    Irvine, H.S.; Bennett, E.J.; Talbot, K.H.

    1986-10-01

    Being able to technically and economically replace the most radioactive components (excluding the nuclear fuel) in operating reactors will help to ensure the ongoing acceptance of nuclear power as a viable energy source for the future. Ontario Hydro is well along the path to meeting the above objective for its CANDU-PHW reactors. Following the failure of a Zircaloy-II pressure tube in unit 2 of Pickering NGS A in August, 1983, Ontario Hydro has embarked on a program to replace all Zircaloy-II pressure tubes in units 1 and 2 at Pickering. This program integrates the in-house research, design, construction, and operating skills of a large utility (Ontario Hydro) with the skills of a national nuclear organization (Atomic Energy of Canada Limited) and the private engineering sector of the Canadian nuclear industry. The paper describes the background to the pressure tube failure in Pickering unit 2 and to the efforts incurred in understanding the failure mechanism and how similar failures are not expected for the zirconium-niobium pressure tube material used in all other large CANDU-PHW units after units 1 and 2 of Pickering NGS A. The tooling developed for the pressure tube replacement program is described as well as the organization to undertake the program in an operating nuclear station. The retubing of units 1 and 2 at Pickering NGS A is nearing a successful completion and shows the benefits of being able to integrate the various skills required for this success. Pressure tube replacement in a CANDU-PHW reactor is equivalent to replacement of the reactor vessel in a LWR. The fact that this replacement can be done economically and with acceptable radiation dose to workers augurs well for the continued viability of the use of nuclear energy for the benefit of mankind. (author)

  11. Assessment of ichthyoplankton entrainment at Pickering 'A' NGS using a pump/net in lake system

    International Nuclear Information System (INIS)

    McKinley, R.S.

    1985-03-01

    Annual entrainment at Pickering 'A' NGS was estimated for alewife as 13.6 X 10 6 larvae and 409 X 10 6 eggs. A substantial portion of eggs and larvae entering the intake were dead due to natural mortality (41%-81%) prior to entrainment. Viable eggs and larvae, immediately following entrainment showed mortalities of 54% and 44% respectively. The latent mortality of entrained eggs was 100% (48 h)

  12. Investigation of tritium in groundwater at Pickering NGS

    International Nuclear Information System (INIS)

    DeWilde, J.; Yu, L.; Belanger, D.; Wootton, R.; Hansen, K.; McGurk, E.; Teare, A.

    2001-01-01

    Ontario Power Generation Inc. (OPG) investigated tritium in groundwater at the Pickering Nuclear Generating Station (PNGS). The objectives of the study were to evaluate and define the extent of radio-nuclides, primarily tritium, in groundwater, investigate the causes or sources of contamination, determine impacts on the natural environment, and provide recommendations to prevent future discharges. This paper provides an overview of the investigations conducted in 1999 and 2000 to identify the extent of the tritium beneath the site and the potential sources of tritium released to the groundwater. The investigation and findings are summarized with a focus on unique aspects of the investigation, on lessons learned and benefits. Some of the investigative techniques discussed include process assessments, video inspections, hydrostatic and tracer tests, Helium 3 analysis for tritium age dating, deuterium and tritium in soil analysis. The investigative techniques have widespread applications to other nuclear generating stations. (author)

  13. AECB staff annual report on Pickering NGS for the year 1989

    International Nuclear Information System (INIS)

    1990-06-01

    This report presents a review of major licensing issues and the operational performance of Pickering NGS-A (Units 1-4) and Pickering NGS-B (Units 5-8) by the staff of the Atomic Energy Control Board (AECB) during 1989. Operations are monitored to ensure compliance with licensing requirements. This report is limited to those aspects that AECB staff consider to have particular safety significance. The number of infractions of the operating licence and the AECB Regulations doubled in 1989 compared to 1988. Three workers were exposed to radiation doses in excess of the regulatory limits. The AECB also found inadequate procedural compliance and an unacceptable level of housekeeping. Performance also requires improvement in response to AECB Health Physics appraisals; surveillance of systems by the Technical Section; chemical control performance; response to outstanding AECB action items; availability of special safety systems; operating memos, jumper records, call-ups and deficiency reports in effect; and fire fighting capability. Ontario Hydro has initiated a number of programs that are expected to result in improvements in these areas: an in-service station quality improvement plan; a program to improve and give assurance of compliance with the AECB Regulations, the operating licenses and the Operating Policies and Principles; a housekeeping and material condition improvement plan; and an action plan undertaken following radiation over-exposures. Given adequate resources and management support these programs should result in a noticeable improvement in station performance in 1990

  14. Leakage rate from LOCA-aged inflatable airlock seals Pickering NGS 'B' personnel doors

    International Nuclear Information System (INIS)

    Fayle, G.W.; Cordingley, D.C.

    1985-01-01

    In order to demonstrate to the Atomic Energy Control Board that an air-lock inflatable seal will function after a LOCA exposure, an inflatable seal intended for personnel doors at the Pickering NGS 'B' was exposed to the thermal/moisture conditions of the LOCA requirement. While attending to determine the post-LOCA leakage rate it was found that additional leaks developed during each post-LOCA inflation/deflation cycle. The seal had been significantly and irreparably deteriorated by the LOCA exposure. The test has demonstrated that this type of LOCA exposed seal should not be expected to withstand either additional pressure above 207 kPa or additional inflation/deflation cycling. A higher inflation pressure and/or cycling will reduce the likelihood of a post-LOCA seal retaining an inflation pressure sufficient to prevent leakage across the seal

  15. Calculation of homogenized Pickering NGS stainless steel adjuster rod neutron cross-sections using conservation of reaction rates

    Energy Technology Data Exchange (ETDEWEB)

    Robinson, R C [Atlantic Nuclear Services Ltd. (Canada); Tran, F [Ontario Hydro, Pickering, ON (Canada). Pickering Generating Station

    1996-12-31

    A homogenization methodology for calculation of reactivity device incremental cross-sections has been developed using reaction rate conservation (RRC). A heterogeneous transport calculation of flux was utilised to produce the homogenized cross-sections for a finite difference two group diffusion code. The RRC cross-sections have been shown to improve significantly the prediction of reactivity worth for stainless steel adjuster rods installed in Pickering NGS reactors. (author). 10 refs., 3 tabs., 6 figs.

  16. The examination of the ruptured Zircaloy-2 pressure tube from Pickering NGS Unit 2

    International Nuclear Information System (INIS)

    Cheadle, B.A.; Smith, A.D.; Baskin, C.C.

    1985-07-01

    On 1983 August 01 a Zircaloy-2 pressure tube in Pickering NGS Unit 2 ruptured. All the fuel channel components, the fuel bundles, pressure tube, end fittings, garter springs and calandria tubes were shipped to Chalk River Nuclear Laboratories for examination to determine the cause of the rupture. The examination showed that the rupture initiated at a series of hydride blisters on the outside surface of the pressure tube. The blisters formed because of the garter spring spacers between the pressure tube and calandria tube was about one metre out of position. This allowed the horizontal pressure tube to sag by creep and touch the cool calandria tube. The resulting thermal gradients in the pressure tube concentrated the hydrogen and deuterium at the cool zones and blisters of solid hydride formed. Cracks initiated at several of the blisters and linked together to form a partial through wall critical crack which initiated the final rupture. The video presentation shows how the examination of the fuel channel components was conducted in underwater bays and shielded cells and explains the sequence of events that caused the rupture

  17. Pickering NGS A reactor building 1 dome refurbishment long-term monitoring of coating

    International Nuclear Information System (INIS)

    Deans, J.J.; Chan, P.; Gomme, R.

    2006-01-01

    'Full text:' To reduce air leakage through the dome of Pickering NGS A Reactor Building 1, in August 1993 a portion of the exterior concrete surface was coated with a single component elastomeric polyurethane material. An internal positive pressure test of the building, conducted between November 5 and 7, 1993, found that the air leakage rates were significantly lower in this test than leakage rates which had been measured during a pressure test conducted in 1992. This reduction in leakage was attributed to the successful performance of the coating. The need for a high-performance, elastomeric surface coating was identified for reduction of air leakage levels through the dome of Reactor Building l of Ontario Power Generation's (formerly Ontario Hydro's) Pickering 'A' Nuclear Generating Station near Toronto. A number of candidate coatings were extensively tested to assess the performance characteristics and identify a material that could withstand the elements and perform effectively for around 20 years. Under normal operating conditions, a licensing limit of 2.7% of contained mass/hour is set for permissible containment leakage whilst the operational working target is less than 1%. The facility's engineers determined that any leakages were pressure-dependent, so in an effort to remain well within their working target, they sought a system that would bridge and seal any hairline cracks in the concrete dome and thereby prevent the passage of gas or vapour through the substrate. On the basis of scheduling and cost, they concluded that a high performance coating was most appropriate for the project, and hired Kinectrics (formerly Ontario Hydro Technologies (OHT)) to select, test, assess and arrange for the application to the RB 1 Dome. In all, nearly 70 separate manufacturers were approached by Kinectrics with a view to obtaining recommendations for treatment. The respective performance data of the respondents' products were compared with a set of specific design

  18. Pickering NGS emergency water supply system emergency start flow simulation and experiment

    Energy Technology Data Exchange (ETDEWEB)

    Davidge, E.; Misra, A. [Ontario Power Generation Inc., Nuclear Safety Analysis & Technology Department, Toronto, Ontario (Canada)

    2012-07-01

    A proposed modification to the OPG Pickering Nuclear Generation Station Emergency Water Supply (EWS) system was analyzed using the Industry Standard Toolset code GOTHIC to determine the acceptability of the proposed system configuration during pump start-up. The new configuration of the system included a vertical dead-ended pipe, initially filled with air. The simulation demonstrated that no significant water hammer effects were predicted and tests performed with the new configuration confirmed the analysis results. (author)

  19. Remote tooling for inspection and repair in Pickering NGS-A calandria vault

    International Nuclear Information System (INIS)

    Hadji-Mirzai, M.; Tokarz, A.; Vandenberg, J.P.

    1993-01-01

    In recent years it has been necessary to develop capabilities for the inspection and repair of carbon steel components located within calandria vaults at Ontario Hydro's Pickering Nuclear Generating Station 'A'. Concerns about corrosion of piping and some of the structural components have made necessary the development of remote manipulators to inspect and repair carbon steel components within the vaults to ensure continued reliable operation of the units. Remote manipulators for this program have been designed to perform a number of inspection and repair tasks, and several versions have been developed to specialise in detailed inspection techniques and precision tooling module manipulation. (author)

  20. Evaluation of organic coatings to reduce air leakage through cracks in the Pickering NGS 'A' reactor building 1

    International Nuclear Information System (INIS)

    Deans, J.J.; Sato, J.A.; Hampton, J.H.D.; Cullen, R.; Paterson, G.; Chan, P.; Rajagopalan, R.

    1994-01-01

    Pressure tests conducted in 1992 on the Pickering NGS 'A' Reactor Building 1 showed that the containment leakage rate of the building was close to the licensing limit. The leakage was found to be pressure dependent and was attributed to cracks in the concrete dome. A number of solutions were studied by a task group, and the application of an organic coating to the exterior surface of the dome was identified as the most viable solution under the constraints of schedule and cost. In addition to reducing the air leakage rate, the coating material must be flexible to bridge existing moving cracks, it must have excellent adhesion to the concrete substrate to sustain the design pressure of 41.4 kPa(g) during pressure tests, and it must be durable for an exterior application and service conditions. Five candidate organic coating materials were selected for laboratory testing. As a result of the testing, a single-component elastomeric polyurethane coating was selected to be used on the dome. This paper discusses the selection process, laboratory tests and results, and the application of the polyurethane coating system to the exterior concrete dome surface. However, the main emphasis of the paper is on the laboratory evaluation of the five candidate materials. (author). 2 refs., 3 tabs., 1 fig

  1. Fitness for service after a LOCA: A process applied to Pickering NGS Unit 2

    International Nuclear Information System (INIS)

    McLean, J.A.; Beaton, D.L.

    1996-01-01

    The fitness for service process provides a unique proven methodology for assessing and correcting post-LOCA damage, essential to plant restart. The process uses the as-built plant configuration for modelling input and features self correcting feedback from inspection to validate assessment models. This paper focuses on the process steps and the infrastructure necessary to execute the process

  2. Life extension, power upgrade, and return to service work for Pickering NGS and other PWR and CANDU plants

    International Nuclear Information System (INIS)

    Millman, J.; Idvorian, N.; Schneider, W.

    2002-01-01

    Work on life extension, power upgrade and return to service has been performed and is in progress for a number of PWR and CANDU plants. For PWR plants, power upgrade work has been done for the new replacement steam generators in several cases. This work consists of redoing the formal equipment qualification analysis and reports for the uprated operating conditions to support the application for license adjustment. Life extension assessments have been performed for several CANDU plants. These are highly detailed assessments in which the particular steam generator is reassessed part by part as to the ability of each to sustain full life operation and also extended life operation. Return to service work for Pickering NGSA specifically has included this type of assessment and also specific repair, cleaning and retrofit activities including secondary side inspection, waterlancing, divider plate repair, eddy current inspection, etc. Steam generator modifications and retrofit work have been performed in a number of cases. The paper discusses various life extension, power upgrade, equipment modification and return to service activities all of which are part of the renewed drive in the industry to realise the full potential of nuclear plants by getting more and better performance from the extended service of existing plants. (author)

  3. Thermalhydraulic assessment of the Pickering NGS 'B' feed and bleed system for the hot boiler chemical clean (Siemens Process)

    International Nuclear Information System (INIS)

    Lorencez, Carlos M.

    2000-01-01

    The Hot Boiler Chemical Clean (HBCC) process from Siemens, to be used in PNGS, requires that the Heat Transport System (HTS) temperature be maintained in the range 160 to 170 o C for several days. To achieve these thermalhydraulic condition, the core decay power and the pump power of the main circulating pumps in a 3-3 configuration are employed to warm up the HTS from approximately 38 o C to 170 o C. At this point, high Bleed bias is applied to the signal of the HTS pressure controller to provide high Feed and Bleed flows, which are used to control the HTS temperature by means of the Bleed Cooler. To address any concern posed by these infrequently used HTS thermalhydraulic conditions, a detailed thermalhydraulic model of the Feed and Bleed System, that also includes the Gland Supply, Gland Return and Purification systems, was developed for the TUF code to determine the suitability of the Feed and Bleed System to conduct the HBCC. The model was then used to estimate the parameters such as Feed and Bleed flows, valve openings, pressure and temperature distributions throughout the Feed and Bleed System required for the application of HBCC. (author)

  4. Statistical modelling of spatio-temporal dependencies in NGS data

    NARCIS (Netherlands)

    Ranciati, Saverio

    2016-01-01

    Next-generation sequencing (NGS) heeft zich snel gevestigd als de huidige standaard in de genetische analyse. Deze omschakeling van microarray naar NGS vereist nieuwe statistische strategieën om de onderzoeksvragen aan te pakken. Ten eerste, NGS data bestaat uit discrete waarnemingen, meestal

  5. Development of upgraded full-core 3D diffusion models for the Pickering stations

    Energy Technology Data Exchange (ETDEWEB)

    Arsenault, B., E-mail: benoit.arsenault@amecfw.com [AMEC Foster Wheeler, Toronto, ON (Canada); Catovic, Z., E-mail: zlatko.catovic@opg.com [Ontario Power Generation, Pickering, ON (Canada); Shaula, S., E-mail: sergiy.shaula@amecfw.com [AMEC Foster Wheeler, Toronto, ON (Canada); Buchan, P.D., E-mail: david.buchan@opg.com [Ontario Power Generation, Pickering, ON (Canada)

    2015-07-01

    This paper describes a methodology used to model Pickering reactors with the Reactor Physics toolset currently in use at OPG stations, which includes the Reactor Physics Industry Standard Toolset (RFSP-IST/WIMS-IST/DRAGON-IST) and the fuel management code SORO. Detailed geometries were modeled in DRAGON-IST with devices and structures that extended into the reflector region and incremental properties were calculated for reactivity devices, guide tubes and structural materials based on the engineering drawings. Simulations and comparisons with measurements performed showed improved predictive capabilities of the new reactor physics models. (author)

  6. Development of upgraded full-core 3D diffusion models for the Pickering stations

    International Nuclear Information System (INIS)

    Arsenault, B.; Catovic, Z.; Shaula, S.; Buchan, P.D.

    2015-01-01

    This paper describes a methodology used to model Pickering reactors with the Reactor Physics toolset currently in use at OPG stations, which includes the Reactor Physics Industry Standard Toolset (RFSP-IST/WIMS-IST/DRAGON-IST) and the fuel management code SORO. Detailed geometries were modeled in DRAGON-IST with devices and structures that extended into the reflector region and incremental properties were calculated for reactivity devices, guide tubes and structural materials based on the engineering drawings. Simulations and comparisons with measurements performed showed improved predictive capabilities of the new reactor physics models. (author)

  7. Pickering seismic safety margin

    International Nuclear Information System (INIS)

    Ghobarah, A.; Heidebrecht, A.C.; Tso, W.K.

    1992-06-01

    A study was conducted to recommend a methodology for the seismic safety margin review of existing Canadian CANDU nuclear generating stations such as Pickering A. The purpose of the seismic safety margin review is to determine whether the nuclear plant has sufficient seismic safety margin over its design basis to assure plant safety. In this review process, it is possible to identify the weak links which might limit the seismic performance of critical structures, systems and components. The proposed methodology is a modification the EPRI (Electric Power Research Institute) approach. The methodology includes: the characterization of the site margin earthquake, the definition of the performance criteria for the elements of a success path, and the determination of the seismic withstand capacity. It is proposed that the margin earthquake be established on the basis of using historical records and the regional seismo-tectonic and site specific evaluations. The ability of the components and systems to withstand the margin earthquake is determined by database comparisons, inspection, analysis or testing. An implementation plan for the application of the methodology to the Pickering A NGS is prepared

  8. Statistical model based gender prediction for targeted NGS clinical panels

    Directory of Open Access Journals (Sweden)

    Palani Kannan Kandavel

    2017-12-01

    The reference test dataset are being used to test the model. The sensitivity on predicting the gender has been increased from the current “genotype composition in ChrX” based approach. In addition, the prediction score given by the model can be used to evaluate the quality of clinical dataset. The higher prediction score towards its respective gender indicates the higher quality of sequenced data.

  9. Interfacial rheology of model particles at liquid interfaces and its relation to (bicontinuous) Pickering emulsions

    Science.gov (United States)

    Thijssen, J. H. J.; Vermant, J.

    2018-01-01

    Interface-dominated materials are commonly encountered in both science and technology, and typical examples include foams and emulsions. Conventionally stabilised by surfactants, emulsions can also be stabilised by micron-sized particles. These so-called Pickering-Ramsden (PR) emulsions have received substantial interest, as they are model arrested systems, rather ubiquitous in industry and promising templates for advanced materials. The mechanical properties of the particle-laden liquid-liquid interface, probed via interfacial rheology, have been shown to play an important role in the formation and stability of PR emulsions. However, the morphological processes which control the formation of emulsions and foams in mixing devices, such as deformation, break-up, and coalescence, are complex and diverse, making it difficult to identify the precise role of the interfacial rheological properties. Interestingly, the role of interfacial rheology in the stability of bicontinuous PR emulsions (bijels) has been virtually unexplored, even though the phase separation process which leads to the formation of these systems is relatively simple and the interfacial deformation processes can be better conceptualised. Hence, the aims of this topical review are twofold. First, we review the existing literature on the interfacial rheology of particle-laden liquid interfaces in rheometrical flows, focussing mainly on model latex suspensions consisting of polystyrene particles carrying sulfate groups, which have been most extensively studied to date. The goal of this part of the review is to identify the generic features of the rheology of such systems. Secondly, we will discuss the relevance of these results to the formation and stability of PR emulsions and bijels.

  10. SEBIM pilot operated tandems. A new solution for Darlington NGS bleed condenser relief valves

    International Nuclear Information System (INIS)

    Paetzold, H.; Hera, V.; Schaumburg, G.

    1996-01-01

    Following incidents at Pickering, Wolsung and Bruce NGS, involving instability of bleed condenser relief valves, Darlington station decided to replace the spring loaded RV's by new pilot operated SEBIM tandem valves. This paper is presenting the approach taken, the design and the testing of the new solution, as well as some of the computer modeling work performed in connection with this project. The SEBIM tandems, following successful testing in France, will be installed in Darlington Unit 2, this spring. The new valves can perform with absence of instability and prevent a LOCA incident due to their design, which includes a protection and a redundant valve in series. (author)

  11. NgsRelate

    DEFF Research Database (Denmark)

    Korneliussen, Thorfinn Sand; Moltke, Ida

    2015-01-01

    . Using both simulated and real data, we show that NgsRelate provides markedly better estimates for low-depth NGS data than two state-of-the-art genotype-based methods. AVAILABILITY: NgsRelate is implemented in C++ and is available under the GNU license at www.pop gen.dk/software. CONTACT: ida...... be called with high certainty. RESULTS: We present a software tool, NgsRelate, for estimating pairwise relatedness from NGS data. It provides maximum likelihood estimates that are based on genotype likelihoods instead of genotypes and thereby takes the inherent uncertainty of the genotypes into account...

  12. Pickering nuclear fish diversion net

    Energy Technology Data Exchange (ETDEWEB)

    Xiao, J.; Lew, A. [Ontario Power Generation, Toronto, Ontario (Canada)

    2013-07-01

    Pickering Fish Diversion Net - An Engineered Environmental Solution that has significantly reduced fish impingement at the Pickering Nuclear Facility. Note: As a recent urgent request/discussed by Mark Elliot, CNE-OPG and Jacques Plourde, CNS.

  13. Pickering tool management system

    International Nuclear Information System (INIS)

    Wong, E.H.; Green, A.H.

    1997-01-01

    Tools were being deployed in the station with no process in effect to ensure that they are maintained in good repair so as to effectively support the performance of Maintenance activities. Today's legal requirements require that all employers have a process in place to ensure that tools are maintained in a safe condition. This is specified in the Ontario Health and Safety Act. The Pickering Tool Management System has been chosen as the process at Pickering N.D to manage tools. Tools are identified by number etching and bar codes. The system is a Windows application installed on several file servers

  14. Pickering irradiated fuel transfer conveyor isolation

    Energy Technology Data Exchange (ETDEWEB)

    Koivisto, D J; Eijsermans, L J [Atomic Energy of Canada Ltd., Mississauga, ON (Canada)

    1997-12-31

    Pickering A NGS has been in operation for 25 years and is one of the longest in service CANDU stations. Some underwater fuel handling equipment, notably the conveyor stops, have been without maintenance throughout that time. This paper describes the concept of a conveyor isolation system that permits draining of a single or multiple elevator columns and also the early stages of a development program for the elastomeric sealing element. The prototype seal element has been proven in lab tests to be capable of limiting leakage to 0.5 IGPM (imperial gallons per minute) at the design pressure of 6.5 psi. The design of a sealing element is particularly interesting because the conveyor tube is a square cross-section which contains an additional obstruction , a conveyor drive cable. A seal delivery, actuating and positioning system has been conceptually laid out and the design is proceeding, with projected implementation in 1998. (author). 8 figs.

  15. Pickering irradiated fuel transfer conveyor isolation

    International Nuclear Information System (INIS)

    Koivisto, D.J.; Eijsermans, L.J.

    1996-01-01

    Pickering A NGS has been in operation for 25 years and is one of the longest in service CANDU stations. Some underwater fuel handling equipment, notably the conveyor stops, have been without maintenance throughout that time. This paper describes the concept of a conveyor isolation system that permits draining of a single or multiple elevator columns and also the early stages of a development program for the elastomeric sealing element. The prototype seal element has been proven in lab tests to be capable of limiting leakage to 0.5 IGPM (imperial gallons per minute) at the design pressure of 6.5 psi. The design of a sealing element is particularly interesting because the conveyor tube is a square cross-section which contains an additional obstruction , a conveyor drive cable. A seal delivery, actuating and positioning system has been conceptually laid out and the design is proceeding, with projected implementation in 1998. (author). 8 figs

  16. Pickering education centre aids nuclear acceptance

    International Nuclear Information System (INIS)

    Anon.

    1979-01-01

    Activities at the new education centre at Pickering are described. The opening of the Nuclear Communications Centre, in 1978, resulting from a search for an effective means of maintaining public acceptance of Ontario Hydro's extensive nuclear power programme. Activities include participation in the interactive computer games, guided tours of educational exhibits including a model of Pickering A generating station, and displays depicting the Candu fuel cycle, outdoor exhibits of renewable energy sources, and tours of the plant. Outside activities include lectures to schools and citizen, business, or professional groups. (U.K.)

  17. NGS Absolute Gravity Data

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The NGS Absolute Gravity data (78 stations) was received in July 1993. Principal gravity parameters include Gravity Value, Uncertainty, and Vertical Gradient. The...

  18. NGS Survey Control Map

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The NGS Survey Control Map provides a map of the US which allows you to find and display geodetic survey control points stored in the database of the National...

  19. Moderator inlet line hanger replacement for Pickering nuclear power station

    International Nuclear Information System (INIS)

    Kirkpatrick, R.A.; Bowman, J.M.; Symmons, W.R.; El-Nesr, S.

    1988-01-01

    Ontario Hydro's Pickering Nuclear Generating Station (PNGS), Units 1 and 2 were shutdown for large scale fuel channel replacement. Other nonroutine inspection and maintenance activities were performed to determine the overall condition of the units and it was seen that a moderator inlet line hanger (identified as HR-29) had failed in both units. Subsequent inspections during planned maintenance outages of Pickering NGS Units 3 and 4 revealed that hanger HR-29 had failed and required replacement. A research program was conducted to find a suitable technique. These problems included accessing tooling through small inspection ports, manipulating tooling from a significant distance and the high radiation fields within the vault. This paper describes the program undertaken to replace hanger HR-29. (author)

  20. The attached algae community near Pickering GS: III

    International Nuclear Information System (INIS)

    McKinley, S.R.

    1982-01-01

    The relationship between attached algae and macro-invertebrates in the nearshore zone of Lake Ontario was investigated in the vicinity of the Pickering 'A' NGS. Measures of faunal density, richness, evenness, and biomass were generally higher from areas which supported attached algae. Gammarus fasciatus, Cricotopus bicinctus, Dicrotendipes spp., Orthocladius obumbratus, Cladotanytarsus spp., Orthocladius spp., and Parakiefferiella spp., were significantly correlated with algal standing crop. All of the above dominant invertebrates ingested epiphytes associated with Cladophora glomerata. Attempts to explain the distribution of the zoobenthic assemblages using the physical/biological characteristics of the study area indicated algal cover, substrate size, wind velocity and water temperature were most important

  1. Pickering safeguards: a preliminary analysis

    International Nuclear Information System (INIS)

    Todd, J.L.; Hodgkinson, J.G.

    1977-05-01

    A summary is presented of thoughts relative to a systems approach for implementing international safeguards. Included is a preliminary analysis of the Pickering Generating Station followed by a suggested safeguards system for the facility

  2. A randomized and blinded comparison of qPCR and NGS-based detection of aneuploidy in a cell line mixture model of blastocyst biopsy mosaicism.

    Science.gov (United States)

    Goodrich, David; Tao, Xin; Bohrer, Chelsea; Lonczak, Agnieszka; Xing, Tongji; Zimmerman, Rebekah; Zhan, Yiping; Scott, Richard T; Treff, Nathan R

    2016-11-01

    A subset of preimplantation stage embryos may possess mosaicism of chromosomal constitution, representing a possible limitation to the clinical predictive value of comprehensive chromosome screening (CCS) from a single biopsy. However, contemporary methods of CCS may be capable of predicting mosaicism in the blastocyst by detecting intermediate levels of aneuploidy within a trophectoderm biopsy. This study evaluates the sensitivity and specificity of aneuploidy detection by two CCS platforms using a cell line mixture model of a mosaic trophectoderm biopsy. Four cell lines with known karyotypes were obtained and mixed together at specific ratios of six total cells (0:6, 1:5, 2:4, 3:3, 4:2, 5:1, and 6:0). A female euploid and a male trisomy 18 cell line were used for one set, and a male trisomy 13 and a male trisomy 15 cell line were used for another. Replicates of each mixture were prepared, randomized, and blinded for analysis by one of two CCS platforms (quantitative polymerase chain reaction (qPCR) or VeriSeq next-generation sequencing (NGS)). Sensitivity and specificity of aneuploidy detection at each level of mosaicism was determined and compared between platforms. With the default settings for each platform, the sensitivity of qPCR and NGS were not statistically different, and 100 % specificity was observed (no false positives) at all levels of mosaicism. However, the use of previously published custom criteria for NGS increased sensitivity but also significantly decreased specificity (33 % false-positive prediction of aneuploidy). By demonstrating increased false-positive diagnoses when reducing the stringency of predicting an abnormality, these data illustrate the importance of preclinical evaluation of new testing paradigms before clinical implementation.

  3. Waste Pickers: Why are they there?

    CSIR Research Space (South Africa)

    Oelofse, Suzanna HH

    2011-07-01

    Full Text Available of pickers ? Increase job stability and earnings of pickers ? Enhance the effectiveness of their contribution to waste management ? Entrepreneural activities as observed require a level of organisation in the informal sector ? Research are required... about 4 400 pickers operational in Johannesburg 15/07/2011 3 ? CSIR 2011 www.csir.co.za Informal sector waste pickers and entrepreneurs ? Do not pay taxes ? No trading license ? No social welfare or government insurance scheme...

  4. PROFILE OF PLASTIC WATER BOTTLES WASTES PROCESSING BUSINESS UNIT FOR WASTE PICKERS

    Directory of Open Access Journals (Sweden)

    Herijanto P.

    2017-09-01

    Full Text Available Used plastic water bottles waste pickers can be categorized as one of the informal sector’s component. They work for themselves by picking up used water bottles and selling them to the waste collectors. The problem to be solved in this research is How the Most Appropriate Used Plastic Water Bottles Business Model for Waste Pickers Is that enables them to be categorized as formal sector. From the result of the interview with 120 waste pickers, 96 results were qualified to be analyzed. The interview was located in several waste collectors, which were visited by waste pickers at certain hours. The data were analyzed descriptively based on six business aspects. Specifically for production facilities, Quality Function Deployment (QFD and Value Engineering (VE analysis were performed. The results of the analysis indicate that the business is practicable for waste pickers and has the potential to enable them run a formal business sector.

  5. Field testing of behavioral barriers for cooling water intake structures -test site 1 - Pickering Nuclear Generating Station

    International Nuclear Information System (INIS)

    Patrick, P.H.; McKinley, R.S.; Micheletti, W.C.

    1988-01-01

    A multi-year research program was developed by the Electric Power Research Institute to evaluate the effectiveness of selected behavioral systems for fish exclusion at sites representative of different aquatic environments. The first test site was the Pickering Nuclear Generating Station (NGS) located on Lake Ontario which represented the Great Lakes environment. A single pneumatic popper, a low frequency, high amplitude sound deterrent, was found to effectively exclude adult alewife, the principal species impinged at Pickering NGS. An air bubble curtain, used either alone or combined with strobe lights, was not a consistent deterrent. Effectiveness of air bubbles was only enhanced when used in association with a popper. Strobe lights were the least effective of the three devices tested. Operation of all three devices together did not surpass the effectiveness of the popper when used alone. Sound deterrents show promise for fish exclusion at generating stations located on the Great Lakes

  6. Climate change web picker. A tool bridging daily climate needs in process based modelling in forestry and agriculture

    International Nuclear Information System (INIS)

    Palma, J.H.N.

    2017-01-01

    Aim of study: Climate data is a need for different types of modeling assessments, especially those involving process based modeling focusing on climate change impacts. However, there is a scarcity of tools delivering easy access to climate datasets to use in biological related modeling. This study aimed at the development of a tool that could provide an user-friendly interface to facilitate access to climate datasets, that are used to supply climate scenarios for the International Panel on Climate Change. Area of study: The tool provides daily datasets across Europe, and also parts of northern Africa Material and Methods: The tool uses climatic datasets generated from third party sources (IPCC related) while a web based interface was developed in JavaScript to ease the access to the datasets Main Results: The interface delivers daily (or monthly) climate data from a user-defined location in Europe for 7 climate variables: minimum and maximum temperature, precipitation, radiation, minimum and maximum relative humidity and wind speed). The time frame ranges from 1951 to 2100, providing the basis to use the data for climate change impact assessments. The tool is free and publicly available at http://www.isa.ulisboa.pt/proj/clipick/. Research Highlights: A new and easy-to-use tool is suggested that will promote the use of climate change scenarios across Europe, especially when daily time steps are needed. CliPick eases the communication between climatic and modelling communities such as agriculture and forestry.

  7. Climate change web picker. A tool bridging daily climate needs in process based modelling in forestry and agriculture

    Energy Technology Data Exchange (ETDEWEB)

    Palma, J.H.N.

    2017-11-01

    Aim of study: Climate data is a need for different types of modeling assessments, especially those involving process based modeling focusing on climate change impacts. However, there is a scarcity of tools delivering easy access to climate datasets to use in biological related modeling. This study aimed at the development of a tool that could provide an user-friendly interface to facilitate access to climate datasets, that are used to supply climate scenarios for the International Panel on Climate Change. Area of study: The tool provides daily datasets across Europe, and also parts of northern Africa Material and Methods: The tool uses climatic datasets generated from third party sources (IPCC related) while a web based interface was developed in JavaScript to ease the access to the datasets Main Results: The interface delivers daily (or monthly) climate data from a user-defined location in Europe for 7 climate variables: minimum and maximum temperature, precipitation, radiation, minimum and maximum relative humidity and wind speed). The time frame ranges from 1951 to 2100, providing the basis to use the data for climate change impact assessments. The tool is free and publicly available at http://www.isa.ulisboa.pt/proj/clipick/. Research Highlights: A new and easy-to-use tool is suggested that will promote the use of climate change scenarios across Europe, especially when daily time steps are needed. CliPick eases the communication between climatic and modelling communities such as agriculture and forestry.

  8. Pickering Unit 1 chemical cleaning

    International Nuclear Information System (INIS)

    Smee, J.L.; Fiola, R.J.; Brennenstuhl, K.R.; Zerkee, D.D.; Daniel, C.M.

    1995-01-01

    The secondary sides of all 12 boilers at Pickering Unit 1 were chemically cleaned in 1994 by the team of Ontario Hydro, B and W International (Cambridge, Ontario) and B and W Nuclear Technologies (Lynchburg, Virginia). A multi-step EPRI/SGOG process was employed in a similar manner to previous clearings at Units 5 and 6 in 1992 and 1993, respectively. A major innovation with the Unit 1 cleaning was the incorporation of a crevice cleaning step, the first time this had been done on Ontario Hydro plants. In addition, six boilers were cleaned in parallel compared to three at a time in previous Pickering cleanings. This significantly reduced cleaning time. A total of 6,770 kg of sludge was removed through direct chemical dissolution. It consisted of 66% iron/nickel oxides and 28% copper metal. A total of 1,600,000 L (420,000 US gallons) of liquid waste was produced. It was processed through the spent solvent treatment facility located at the Bruce Nuclear Power Development site. Visual inspection performed after the cleaning indicated that the crevices between the boiler tubes and the tube support structure were completely clear of deposit and the general condition of the tubing and lattice bars appeared to be in 'as new' condition. (author)

  9. Pickering emulsions for skin decontamination.

    Science.gov (United States)

    Salerno, Alicia; Bolzinger, Marie-Alexandrine; Rolland, Pauline; Chevalier, Yves; Josse, Denis; Briançon, Stéphanie

    2016-08-01

    This study aimed at developing innovative systems for skin decontamination. Pickering emulsions, i.e. solid-stabilized emulsions, containing silica (S-PE) or Fuller's earth (FE-PE) were formulated. Their efficiency for skin decontamination was evaluated, in vitro, 45min after an exposure to VX, one of the most highly toxic chemical warfare agents. Pickering emulsions were compared to FE (FE-W) and silica (S-W) aqueous suspensions. PE containing an oil with a similar hydrophobicity to VX should promote its extraction. All the formulations reduced significantly the amount of VX quantified on and into the skin compared to the control. Wiping the skin surface with a pad already allowed removing more than half of VX. FE-W was the less efficient (85% of VX removed). The other formulations (FE-PE, S-PE and S-W) resulted in more than 90% of the quantity of VX removed. The charge of particles was the most influential factor. The low pH of formulations containing silica favored electrostatic interactions of VX with particles explaining the better elimination from the skin surface. Formulations containing FE had basic pH, and weak interactions with VX did not improve the skin decontamination. However, these low interactions between VX and FE promote the transfer of VX into the oil droplets in the FE-PE. Copyright © 2016 Elsevier B.V. All rights reserved.

  10. Pipe support program at Pickering

    International Nuclear Information System (INIS)

    Sahazizian, L.A.; Jazic, Z.

    1997-01-01

    This paper describes the pipe support program at Pickering. The program addresses the highest priority in operating nuclear generating stations, safety. We present the need: safety, the process: managed and strategic, and the result: assurance of critical piping integrity. In the past, surveillance programs periodically inspected some systems, equipment, and individual components. This comprehensive program is based on a managed process that assesses risk to identify critical piping systems and supports and to develop a strategy for surveillance and maintenance. The strategy addresses all critical piping supports. Successful implementation of the program has provided assurance of critical piping and support integrity and has contributed to decreasing probability of pipe failure, reducing risk to worker and public safety, improving configuration management, and reducing probability of production losses. (author)

  11. Safe "cloudification" of large images through picker APIs.

    Science.gov (United States)

    Bremer, Erich; Kurc, Tahsin; Gao, Yi; Saltz, Joel; Almeida, Jonas S

    2016-01-01

    The "Box model" allows users with no particular training in informatics, or access to specialized infrastructure, operate generic cloud computing resources through a temporary URI dereferencing mechanism known as "drop-file-picker API" ("picker API" for sort). This application programming interface (API) was popularized in the web app development community by DropBox, and is now a consumer-facing feature of all major cloud computing platforms such as Box.com, Google Drive and Amazon S3. This reports describes a prototype web service application that uses picker APIs to expose a new, "cloudified", API tailored for image analysis, without compromising the private governance of the data exposed. In order to better understand this cross-platform cloud computing landscape, we first measured the time for both transfer and traversing of large image files generated by whole slide imaging (WSI) in Digital Pathology. The verification that there is extensive interconnectivity between cloud resources let to the development of a prototype software application that exposes an image-traversing REST API to image files stored in any of the consumer-facing "boxes". In summary, an image file can be upload/synchronized into a any cloud resource with a file picker API and the prototype service described here will expose an HTTP REST API that remains within the safety of the user's own governance. The open source prototype is publicly available at sbu-bmi.github.io/imagebox. Availability The accompanying prototype application is made publicly available, fully functional, with open source, at http://sbu-bmi.github.io/imagebox://sbu-bmi.github.io/imagebox. An illustrative webcasted use of this Web App is included with the project codebase at https://github.com/SBU-BMI/imageboxs://github.com/SBU-BMI/imagebox.

  12. Arresting relaxation in Pickering Emulsions

    Science.gov (United States)

    Atherton, Tim; Burke, Chris

    2015-03-01

    Pickering emulsions consist of droplets of one fluid dispersed in a host fluid and stabilized by colloidal particles absorbed at the fluid-fluid interface. Everyday materials such as crude oil and food products like salad dressing are examples of these materials. Particles can stabilize non spherical droplet shapes in these emulsions through the following sequence: first, an isolated droplet is deformed, e.g. by an electric field, increasing the surface area above the equilibrium value; additional particles are then adsorbed to the interface reducing the surface tension. The droplet is then allowed to relax toward a sphere. If more particles were adsorbed than can be accommodated by the surface area of the spherical ground state, relaxation of the droplet is arrested at some non-spherical shape. Because the energetic cost of removing adsorbed colloids exceeds the interfacial driving force, these configurations can remain stable over long timescales. In this presentation, we present a computational study of the ordering present in anisotropic droplets produced through the mechanism of arrested relaxation and discuss the interplay between the geometry of the droplet, the dynamical process that produced it, and the structure of the defects observed.

  13. Exploiting the pliability and lateral mobility of Pickering emulsion for enhanced vaccination

    Science.gov (United States)

    Xia, Yufei; Wu, Jie; Wei, Wei; Du, Yiqun; Wan, Tao; Ma, Xiaowei; An, Wenqi; Guo, Aiying; Miao, Chunyu; Yue, Hua; Li, Shuoguo; Cao, Xuetao; Su, Zhiguo; Ma, Guanghui

    2018-02-01

    A major challenge in vaccine formulations is the stimulation of both the humoral and cellular immune response for well-defined antigens with high efficacy and safety. Adjuvant research has focused on developing particulate carriers to model the sizes, shapes and compositions of microbes or diseased cells, but not antigen fluidity and pliability. Here, we develop Pickering emulsions--that is, particle-stabilized emulsions that retain the force-dependent deformability and lateral mobility of presented antigens while displaying high biosafety and antigen-loading capabilities. Compared with solid particles and conventional surfactant-stabilized emulsions, the optimized Pickering emulsions enhance the recruitment, antigen uptake and activation of antigen-presenting cells, potently stimulating both humoral and cellular adaptive responses, and thus increasing the survival of mice upon lethal challenge. The pliability and lateral mobility of antigen-loaded Pickering emulsions may provide a facile, effective, safe and broadly applicable strategy to enhance adaptive immunity against infections and diseases.

  14. The Pickering mesonet 1988 data report

    International Nuclear Information System (INIS)

    Salmon, J.R.; Taylor, P.A.

    1989-10-01

    This report describes the demonstration mesoscale meteorological monitoring network (mesonet) installed in the vicinity of the Pickering Nuclear Generating Station. It also summarizes the data collected by the network during 1988 and provides some examples of situations in which mesoscale effects dominate the local wind flow

  15. Analytical Diagnostics of Non-Optimal Use of Pesticides and Health Hazards for Vegetable Pickers

    International Nuclear Information System (INIS)

    Zafar, M.; Mehmood, T.; Baig, I. A.; Saboor, A.; Sadiq, S.; Mahmood, K.

    2016-01-01

    Economically pesticides are meant to control pests in the fields. Up to certain optimal use of a typical pesticide, it enhances the yield of crops and vegetables. But, eventually amplified use of pesticides results in contamination of environment (water, soil, and air) and increase the health cost of vegetable pickers. The purpose of this study is to estimate the excessive use of pesticides and economic cost of health hazards for the vegetable pickers in district Vehari. Data from 90 respondents were collected and analyzed. The most common health problems identified during the survey were headache, eye irritation, skin infection, cough and shortness of breath. Health cost consists of costs related to precautionary measure, medication, traveling, the opportunity cost of attended persons and productivity loss. The mean health cost of vegetable pickers in the study area was about Rs. 385 per picker per year. Health cost model was used to measure the health cost of vegetable pickers. The regression results showed that pesticides were being applied non-optimally in the study area i.e., number of pesticide applications for vegetables (7-31) were substantially higher than the recommended dose. Health cost function was significantly different from zero as indicated by F-stat (32.18) and it is also supported by R/sup 2/ that about 70 percent variation in health cost is explained by medication accompanied by productivity loss (Rs. 223), precautionary measure (Rs. 134), attended person cost (Rs. 14) and traveling expenditures (Rs. 16). Hence, strict legislation is required to overcome the availability of hazardous pesticides and to keep the vegetable pickers aware of the optimal use of pesticides through appropriate extension services. (author)

  16. Pickering unit 1 containment leakage characterization

    International Nuclear Information System (INIS)

    Zakaib, G.D.

    1994-01-01

    Results of the design pressure test carried out on Pickering Reactor Building number 1 during late 1992 showed that the leakage rate of the building was close to the safety analysis value of 2.7% contained mass per hour at the design pressure of 41.4 kPa(g) and was significantly higher than that reported after the previous test conducted in the spring of 1987. This unexpected finding initiated the longest and the most comprehensive containment leakage investigation ever undertaken by Ontario Hydro. A thorough investigation of leakage behaviour by repeated testing, inspections, leak search and analysis was launched. The extensive leak search effort included items such as: leak source detection by soap solution application, use of ultrasonic detectors, fogging and tracer gas techniques, systematic systems isolation, thermal imaging of the exterior, and quantification of leak sites by flowmeter and bagging. Using a specially designed volumetric technique, the root cause of the problem was finally confirmed as being due to 'pressure dependent laminar leakage' through the hairline cracks in the dome concrete. Structural analysis indicated that the thermal gradients and pressure loading combined to cause the cracking early in the structure's operating history and that overall structural integrity has not been compromised. Leakage rate analysis using a new fluid mechanics model augmented by the effect of thermal strains indicated that the leakage could be significantly less under certain transient temperature gradient conditions. Several options for repairing the dome were considered by a multidisciplinary team and it was finally decided to apply a specially engineered multilayer elastomeric coating to the exterior concrete surface. When the unit was re-tested in October 1993, a dramatic ten-fold improvement in leakage rate (down to 0.25%/h at design pressure) was observed. This is lower than even the commissioning results and comparable to the performance of newer units

  17. Condition based maintenance pilot projects at Pickering ND

    International Nuclear Information System (INIS)

    Zemdegs, R.T.

    1995-01-01

    Ontario Hydro has recognized that the approaches to maintenance have undergone significant changes to the past decades. The traditional break down maintenance approach has been replaced by preventative maintenance and more recently, by condition based maintenance. The nuclear plants of Ontario Hydro have evaluated on a number of alternative programs to improve their maintenance effectiveness and to reduce costs, including Reliability Centred Maintenance (RCM), call-up review, component-based PM programs, analysis of failure history and so on. Pickering ND (nuclear division) and Ontario Hydro's Nuclear Technologies Services Division, have embarked on a Condition Based Maintenance pilot project to address the above issues as a breakthrough solution for smarter maintenance. The Condition Based Maintenance pilot project will demonstrate an end-to-end process utilizing a Reliability Centred Maintenance structured approach to re-engineer and redefine the existing maintenance programs. The project emphasizes on-condition maintenance where justified, and utilizes an information management tool to provide the required records keeping and analysis infrastructure. This paper briefly describes the planned maintenance model at Pickering ND used to guide the CBM pilot, and an overview of the methodology used to develop on-condition equipment indicators as part of a re-engineered maintenance plan

  18. Altools: a user friendly NGS data analyser.

    Science.gov (United States)

    Camiolo, Salvatore; Sablok, Gaurav; Porceddu, Andrea

    2016-02-17

    Genotyping by re-sequencing has become a standard approach to estimate single nucleotide polymorphism (SNP) diversity, haplotype structure and the biodiversity and has been defined as an efficient approach to address geographical population genomics of several model species. To access core SNPs and insertion/deletion polymorphisms (indels), and to infer the phyletic patterns of speciation, most such approaches map short reads to the reference genome. Variant calling is important to establish patterns of genome-wide association studies (GWAS) for quantitative trait loci (QTLs), and to determine the population and haplotype structure based on SNPs, thus allowing content-dependent trait and evolutionary analysis. Several tools have been developed to investigate such polymorphisms as well as more complex genomic rearrangements such as copy number variations, presence/absence variations and large deletions. The programs available for this purpose have different strengths (e.g. accuracy, sensitivity and specificity) and weaknesses (e.g. low computation speed, complex installation procedure and absence of a user-friendly interface). Here we introduce Altools, a software package that is easy to install and use, which allows the precise detection of polymorphisms and structural variations. Altools uses the BWA/SAMtools/VarScan pipeline to call SNPs and indels, and the dnaCopy algorithm to achieve genome segmentation according to local coverage differences in order to identify copy number variations. It also uses insert size information from the alignment of paired-end reads and detects potential large deletions. A double mapping approach (BWA/BLASTn) identifies precise breakpoints while ensuring rapid elaboration. Finally, Altools implements several processes that yield deeper insight into the genes affected by the detected polymorphisms. Altools was used to analyse both simulated and real next-generation sequencing (NGS) data and performed satisfactorily in terms of

  19. Data-driven warehouse optimization : Deploying skills of order pickers

    NARCIS (Netherlands)

    M. Matusiak (Marek); M.B.M. de Koster (René); J. Saarinen (Jari)

    2015-01-01

    textabstractBatching orders and routing order pickers is a commonly studied problem in many picker-to-parts warehouses. The impact of individual differences in picking skills on performance has received little attention. In this paper, we show that taking into account differences in the skills of

  20. Fire fighting capability assessment program Darlington NGS

    International Nuclear Information System (INIS)

    1995-05-01

    This is a report on the completion of work relating to the assessment of the capability of Darlington NGS to cope with a large fire incident. This included an evaluation of an exercise scenario that would simulate a large fire incident and of their fire plans and procedures which became the subject of interim reports as part of the process of preparing for the fire fighting and rescue exercise. Finally the execution of fire plans by Darlington Nuclear Generating Station (NGS), as demonstrated by their application of human and material resources during a simulated large fire, was observed. 1 tab., 1 fig

  1. Pickering Nuclear site wide groundwater monitoring system

    International Nuclear Information System (INIS)

    DeWilde, J.; Chin-Cheong, D.; Lledo, C.; Wootton, R.; Belanger, D.; Hansen, K.

    2001-01-01

    Ontario Power Generation Inc. (OPG) is continuing its efforts to understand the chemical and physical characteristics of the groundwater flow systems beneath the Pickering Nuclear Generating Station (PNGS). To this end, OPG constructed a site-wide Groundwater Monitoring System (GMS) at the PNGS to provide support to other ongoing environmental investigations and to provide a means to monitor current and future groundwater environmental issues. This paper will present the results of this work, including the development of a state-of-the-art data management system for storage and retrieval of environmental data for the site, which has applications for other power generation facilities. (author)

  2. Estimating inbreeding coefficients from NGS data

    DEFF Research Database (Denmark)

    Garrett Vieira, Filipe Jorge; Fumagalli, Matteo; Albrechtsen, Anders

    2013-01-01

    Most methods for Next-Generation Sequencing (NGS) data analyses incorporate information regarding allele frequencies using the assumption of Hardy-Weinberg Equilibrium (HWE) as a prior. However, many organisms including domesticated, partially selfing or with asexual life cycles show strong...

  3. Tuning Amphiphilicity of Particles for Controllable Pickering Emulsion

    Directory of Open Access Journals (Sweden)

    Zhen Wang

    2016-11-01

    Full Text Available Pickering emulsions with the use of particles as emulsifiers have been extensively used in scientific research and industrial production due to their edge in biocompatibility and stability compared with traditional emulsions. The control over Pickering emulsion stability and type plays a significant role in these applications. Among the present methods to build controllable Pickering emulsions, tuning the amphiphilicity of particles is comparatively effective and has attracted enormous attention. In this review, we highlight some recent advances in tuning the amphiphilicity of particles for controlling the stability and type of Pickering emulsions. The amphiphilicity of three types of particles including rigid particles, soft particles, and Janus particles are tailored by means of different mechanisms and discussed here in detail. The stabilization-destabilization interconversion and phase inversion of Pickering emulsions have been successfully achieved by changing the surface properties of these particles. This article provides a comprehensive review of controllable Pickering emulsions, which is expected to stimulate inspiration for designing and preparing novel Pickering emulsions, and ultimately directing the preparation of functional materials.

  4. The number of pickers and stock-keeping unit arrangement on a uni-directional picking line

    Directory of Open Access Journals (Sweden)

    Hagspihl, Robert

    2014-10-01

    Full Text Available The order picking process is often the single largest expense in a distribution centre (DC. The DC considered in this paper uses a picking line configuration to perform order picking. The number of pickers in a picking line, and the initial arrangement of stock-keeping units (SKUs, are two important factors that affect the total completion time of the picking lines. In this paper, the picking line configuration is simulated with an agent-based approach to describe the behaviour of an individual picker. The simulation is then used to analyse the effect of the number of pickers and the SKU arrangement. Verification and validation of this model shows that the model represents the real-world picking line to a satisfactory degree. Marginal analysis (MA was chosen to determine a ‘good’ number of pickers by means of the simulation model. A look-up table is presented to provide decision support for the choice of a ‘good’ number of pickers to improve completion times of the picking line, for the properties of a specific picking line. The initial SKU arrangement on a picking line is shown to be a factor that can affect the level of picker congestion and the total completion time. The greedy ranking and partitioning (GRP and organ pipe arrangement (OPA techniques from the literature, as well as the historical SKU arrangements used by the retailer under consideration, were compared with the proposed classroom discipline heuristic (CDH for SKU arrangement. It was found that the CDH provides an more even spread of SKUs that are picked most frequently, thus decreasing congestion and total completion time.

  5. Toxocariasis in waste pickers: a case control seroprevalence study.

    Directory of Open Access Journals (Sweden)

    Cosme Alvarado-Esquivel

    Full Text Available BACKGROUND: The epidemiology of Toxocara infection in humans in Mexico has been poorly explored. There is a lack of information about Toxocara infection in waste pickers. AIMS: Determine the seroepidemiology of Toxocara infection in waste pickers. METHODS: Through a case control study design, the presence of anti-Toxocara IgG antibodies was determined in 90 waste pickers and 90 age- and gender-matched controls using an enzyme-linked immunoassay. Associations of Toxocara exposure with socio-demographic, work, clinical, and behavioral data of the waste pickers were also evaluated. RESULTS: The seroprevalence of anti-Toxocara IgG antibodies was significantly higher in waste pickers (12/90: 13% than in control subjects (1/90: 1% (OR = 14; 95% CI: 2-288. The seroprevalence was not influenced by socio-demographic or work characteristics. In contrast, increased seroprevalence was found in waste pickers suffering from gastritis, and reflex and visual impairments. Multivariate analysis showed that Toxocara exposure was associated with a low frequency of eating out of home (OR = 26; 95% CI: 2-363 and negatively associated with consumption of chicken meat (OR = 0.03; 95% CI: 0.003-0.59. Other behavioral characteristics such as animal contacts or exposure to soil were not associated with Toxocara seropositivity. CONCLUSIONS: 1 Waste pickers are a risk group for Toxocara infection. 2 Toxocara is impacting the health of waste pickers. This is the first report of Toxocara exposure in waste pickers and of associations of gastritis and reflex impairment with Toxocara seropositivity. Results warrant for further research.

  6. Nanocellulose-stabilized Pickering emulsions and their applications.

    Science.gov (United States)

    Fujisawa, Shuji; Togawa, Eiji; Kuroda, Katsushi

    2017-01-01

    Pickering emulsion, which is an emulsion stabilized by solid particles, offers a wide range of potential applications because it generally provides a more stable system than surfactant-stabilized emulsion. Among various solid stabilizers, nanocellulose may open up new opportunities for future Pickering emulsions owing to its unique nanosizes, amphiphilicity, and other favorable properties (e.g. chemical stability, biodegradability, biocompatibility, and renewability). In this review, the preparation and properties of nanocellulose-stabilized Pickering emulsions are summarized. We also provide future perspectives on their applications, such as drug delivery, food, and composite materials.

  7. Automatic pickers performances in the case of the Emilia sequence of May-June 2012.

    Science.gov (United States)

    Tiberi, Lara; Spallarossa, Daniele; Costa, Giovanni

    2013-04-01

    The automatic processing of seismic data, whether for real-time seismic warning system or to reprocessing large amount of seismic recordings, is increasingly being demanded by seismologists especially in case of emergency as for the Emilia sequence in may-june 2012. In this study is presented a comparison between the AutoPicker (DipTeRiS, University of Genova) a new method used for automatic accurate onset phase picking for both P and S wave arrival based on the Akaike's information criterion (AIC), a solid and tested picker as the STA/LTA in Antelope software and the manual pickings. In order to construct the database used for the relocation of Emilia sequence, the RAN strong motion database has been merged with the available velocity and acceleration data extracted from the EIDA database (European Integrated Data Archive) and velocity data recorded by the Southeastern Alps Integrated Network (DMG, OGS, ARSO and ZAMG). The fault system of the Emilia earthquake area is complex and it is not easy to assess which fault has moved. A precise localization of the sequence is essential. The manual pickings, the equivalent locations and the choice of the most appropriate velocity model ("Iside") used in this study are the results of a work done in collaboration with Università di Chieti and DPC, not described here. The main problem of the AutoPicker and Antelope software is to discriminate events that occur very close to each other in time. The best way to solve that issue is choosing the best setup of both techniques to minimize the problem. Then we would like to implement the AutoPicker technique developed by Prof. Spallarossa on the Antelope system routinely used by UTS-DMG for the real-time data analysis.

  8. Remotely controlled repairs at Douglas Point NGS

    International Nuclear Information System (INIS)

    Broad, Les

    In September, 1977, leakage of heavy water at a rate of 125 kg/hr was detected in an area of the Douglas Point NGS reactor vault below the calandria known as the lower labyrinth. Radiation in the area ranges up to 5000 R/hr and the only ready access was through four 75 mm inspection ports that open into the moderator room. Remote-controlled equipment was designed and built to diagnose the problems and carry out repairs. All damaged piping was fixed, supports were replaced as needed, and system vibration was reduced. The work was done with no injuries and little radiation dose

  9. Estimating cancer risk in relation to tritium exposure from routine operation of a nuclear-generating station in Pickering, Ontario.

    Science.gov (United States)

    Wanigaratne, S; Holowaty, E; Jiang, H; Norwood, T A; Pietrusiak, M A; Brown, P

    2013-09-01

    Evidence suggests that current levels of tritium emissions from CANDU reactors in Canada are not related to adverse health effects. However, these studies lack tritium-specific dose data and have small numbers of cases. The purpose of our study was to determine whether tritium emitted from a nuclear-generating station during routine operation is associated with risk of cancer in Pickering, Ontario. A retrospective cohort was formed through linkage of Pickering and north Oshawa residents (1985) to incident cancer cases (1985-2005). We examined all sites combined, leukemia, lung, thyroid and childhood cancers (6-19 years) for males and females as well as female breast cancer. Tritium estimates were based on an atmospheric dispersion model, incorporating characteristics of annual tritium emissions and meteorology. Tritium concentration estimates were assigned to each cohort member based on exact location of residence. Person-years analysis was used to determine whether observed cancer cases were higher than expected. Cox proportional hazards regression was used to determine whether tritium was associated with radiation-sensitive cancers in Pickering. Person-years analysis showed female childhood cancer cases to be significantly higher than expected (standardized incidence ratio [SIR] = 1.99, 95% confidence interval [CI]: 1.08-3.38). The issue of multiple comparisons is the most likely explanation for this finding. Cox models revealed that female lung cancer was significantly higher in Pickering versus north Oshawa (HR = 2.34, 95% CI: 1.23-4.46) and that tritium was not associated with increased risk. The improved methodology used in this study adds to our understanding of cancer risks associated with low-dose tritium exposure. Tritium estimates were not associated with increased risk of radiationsensitive cancers in Pickering.

  10. Fragger: a protein fragment picker for structural queries.

    Science.gov (United States)

    Berenger, Francois; Simoncini, David; Voet, Arnout; Shrestha, Rojan; Zhang, Kam Y J

    2017-01-01

    Protein modeling and design activities often require querying the Protein Data Bank (PDB) with a structural fragment, possibly containing gaps. For some applications, it is preferable to work on a specific subset of the PDB or with unpublished structures. These requirements, along with specific user needs, motivated the creation of a new software to manage and query 3D protein fragments. Fragger is a protein fragment picker that allows protein fragment databases to be created and queried. All fragment lengths are supported and any set of PDB files can be used to create a database. Fragger can efficiently search a fragment database with a query fragment and a distance threshold. Matching fragments are ranked by distance to the query. The query fragment can have structural gaps and the allowed amino acid sequences matching a query can be constrained via a regular expression of one-letter amino acid codes. Fragger also incorporates a tool to compute the backbone RMSD of one versus many fragments in high throughput. Fragger should be useful for protein design, loop grafting and related structural bioinformatics tasks.

  11. Superhydrophobic cellulose-based bionanocomposite films from Pickering emulsions

    Science.gov (United States)

    Bayer, Ilker S.; Steele, Adam; Martorana, Philip J.; Loth, Eric; Miller, Lance

    2009-04-01

    Inherently superhydrophobic and flexible cellulose-based bionanocomposites were fabricated from solid stabilized (Pickering) emulsions. Emulsions were formed by dispersing cyclosiloxanes in water stabilized by layered silicate particles and were subsequently modified by blending into a zinc oxide nanofluid. The polymer matrix was a blend of cellulose nitrate and fluoroacrylic polymer (Zonyl 8740) precompatibilized in solution. Coatings were spray cast onto aluminum substrates from polymer blends dispersed in modified Pickering emulsions. No postsurface treatment was required to induce superhydrophobicity. Effect of antiseptic additives on bionanocomposite superhydrophobicity is also discussed. Replacing cellulose nitrate with commercial liquid bandage solutions produced identical superhydrophobic coatings.

  12. System dynamics applied to closed loop supply chains of desktops and laptops in Brazil: A perspective for social inclusion of waste pickers.

    Science.gov (United States)

    Ghisolfi, Verônica; Diniz Chaves, Gisele de Lorena; Ribeiro Siman, Renato; Xavier, Lúcia Helena

    2017-02-01

    The structure of reverse logistics for waste electrical and electronic equipment (WEEE) is essential to minimize the impacts of their improper disposal. In this context, the Brazilian Solid Waste Policy (BSWP) was a regulatory milestone in Brazil, submitting WEEE to the mandatory implementation of reverse logistics systems, involving the integration of waste pickers on the shared responsibility for the life cycle of products. This article aims to measure the impact of such legal incentives and the bargaining power obtained by the volume of collected waste on the effective formalization of waste pickers. The proposed model evaluates the sustainability of supply chains in terms of the use of raw materials due to disposal fees, collection, recycling and return of some materials from desktops and laptops using system dynamics methodology. The results show that even in the absence of bargaining power, the formalization of waste pickers occurs due to legal incentives. It is important to ensure the waste pickers cooperatives access to a minimum amount, which requires a level of protection against unfair competition with companies. Regarding the optimal level of environmental policies, even though the formalization time is long, it is still not enough to guarantee the formalization of waste picker cooperatives, which is dependent on their bargaining power. Steel is the material with the largest decrease in acquisition rate of raw material. Copyright © 2016 Elsevier Ltd. All rights reserved.

  13. From pioneering to implementing automated blood pressure measurement in clinical practice: Thomas Pickering's legacy

    DEFF Research Database (Denmark)

    Stolarz-Skrzypek, Katarzyna; Thijs, Lutgarde; Wizner, Barbara

    2010-01-01

    Thomas G. Pickering spent most of his scientific career in carrying out research on clinical hypertension and blood pressure (BP) measurement. In our review of Pickering's seminal work, we first focused on white-coat hypertension and masked hypertension, two terms that he had introduced. Next, we...... highlighted the early publications of Pickering on diurnal BP variability and on the clinical application of self-measured BP. Pickering's work inspired many investigators worldwide and constituted a solid basis for further research. Pickering's original ideas led to algorithms for risk stratification...

  14. Particle Shape Anisotropy in Pickering Emulsions: Cubes and Peanuts

    NARCIS (Netherlands)

    de Folter, J.W.J.; Hutter, E.M.; Castillo, S.I.R.; Klop, K.E.; Philipse, A.P.; Kegel, W.K.

    2014-01-01

    We have investigated the effect of particle shape in Pickering emulsions by employing, for the first time, cubic and peanut-shaped particles. The interfacial packing and orientation of anisotropic microparticles are revealed at the single-particle level by direct microscopy observations. The uniform

  15. Pickering Emulsions for Food Applications: Background, Trends, and Challenges

    NARCIS (Netherlands)

    Berton-Carabin, C.C.; Schroën, C.G.P.H.

    2015-01-01

    Particle-stabilized emulsions, also referred to as Pickering emulsions, have garnered exponentially increasing interest in recent years. This has also led to the first food applications, although the number of related publications is still rather low. The involved stabilization mechanisms are

  16. Picker versus stripper harvesters on the High Plains of Texas

    Science.gov (United States)

    A break even analysis based on NPV was conducted to compare picker-based and stripper-based harvest systems with and without field cleaners. Under no conditions analyzed was the NPV of a stripper system without a field cleaner greater than a stripper system with a field cleaner. Break even curves re...

  17. Seismic assessment of the Pickering pressure relief duct

    International Nuclear Information System (INIS)

    Ghobarah, A.

    1995-05-01

    The objectives of the study are to examine the structural response of the Pickering pressure relief duct when subjected to earthquake ground motion and to estimate the seismic withstand capacity of various components of the structural system on the basis of performance criteria consistent with the safety function of the duct. (author). 24 refs., 16 tabs., 31 figs

  18. Improving diagnosis for congenital cataract by introducing NGS genetic testing.

    Science.gov (United States)

    Musleh, Mohammud; Ashworth, Jane; Black, Graeme; Hall, Georgina

    2016-01-01

    Childhood cataract (CC) has an incidence of 3.5 per 10,000 by age 15 years. Diagnosis of any underlying cause is important to ensure effective and prompt management of multisystem complications, to facilitate accurate genetic counselling and to streamline multidisciplinary care. Next generation sequencing (NGS) has been shown to be effective in providing an underlying diagnosis in 70% of patients with CC in a research setting. This project aimed to integrate NGS testing in CC within six months of presentation and increase the rate of diagnosis. A retrospective case note review was undertaken to define the baseline efficacy of current care in providing a precise diagnosis. Quality improvement methods were used to integrate and optimize NGS testing in clinical care and measure the improvements made. The percentage of children receiving an NGS result within six months increased from 26% to 71% during the project period. The mean time to NGS testing and receiving a report decreased and there was a reduction in variation over the study period. Several patients and families had a change in management or genetic counselling as a direct result of the diagnosis given by the NGS test. The current recommended investigation of patients with bilateral CC is ineffective in identifying a diagnosis. Quality Improvement methods have facilitated successful integration of NGS testing into clinical care, improving time to diagnosis and leading to development of a new care pathway.

  19. jviz webcomponents: a foundation js framework for clinical NGS bioinformatics

    OpenAIRE

    Juanes, Jose; Fuentes, Azahara; Arnau, Vicente; Chaves, Felipe Javier; Garcia-Garcia, Ana Barbara; Marin-Garcia, Pablo

    2017-01-01

    IntroductionMGviz is a fully integrated NGS QC and data análisis suite that creates automatic NGS clinical reports for clinicians to review. Summarized quality control measures with threshold based from all the previous runs are computed to warm about any kind of bias and check also for sample swap. These are Intuitive and interactive tools that help prioritize and select the variants of interest related to the patients phenotype from our NGS gene panels and commercial exome panels.Materials ...

  20. Preparation of Small RNA NGS Libraries from Biofluids.

    Science.gov (United States)

    Etheridge, Alton; Wang, Kai; Baxter, David; Galas, David

    2018-01-01

    Next generation sequencing (NGS) is a powerful method for transcriptome analysis. Unlike other gene expression profiling methods, such as microarrays, NGS provides additional information such as splicing variants, sequence polymorphisms, and novel transcripts. For this reason, NGS is well suited for comprehensive profiling of the wide range of extracellular RNAs (exRNAs) in biofluids. ExRNAs are of great interest because of their possible biological role in cell-to-cell communication and for their potential use as biomarkers or for therapeutic purposes. Here, we describe a modified protocol for preparation of small RNA libraries for NGS analysis. This protocol has been optimized for use with low-input exRNA-containing samples, such as plasma or serum, and has modifications designed to reduce the sequence-specific bias typically encountered with commercial small RNA library construction kits.

  1. Next generation sequencing (NGS)technologies and applications

    Energy Technology Data Exchange (ETDEWEB)

    Vuyisich, Momchilo [Los Alamos National Laboratory

    2012-09-11

    NGS technology overview: (1) NGS library preparation - Nucleic acids extraction, Sample quality control, RNA conversion to cDNA, Addition of sequencing adapters, Quality control of library; (2) Sequencing - Clonal amplification of library fragments, (except PacBio), Sequencing by synthesis, Data output (reads and quality); and (3) Data analysis - Read mapping, Genome assembly, Gene expression, Operon structure, sRNA discovery, and Epigenetic analyses.

  2. Selective removal of erythromycin by magnetic imprinted polymers synthesized from chitosan-stabilized Pickering emulsion.

    Science.gov (United States)

    Ou, Hongxiang; Chen, Qunhui; Pan, Jianming; Zhang, Yunlei; Huang, Yong; Qi, Xueyong

    2015-05-30

    Magnetic imprinted polymers (MIPs) were synthesized by Pickering emulsion polymerization and used to adsorb erythromycin (ERY) from aqueous solution. The oil-in-water Pickering emulsion was stabilized by chitosan nanoparticles with hydrophobic Fe3O4 nanoparticles as magnetic carrier. The imprinting system was fabricated by radical polymerization with functional and crosslinked monomer in the oil phase. Batches of static and dynamic adsorption experiments were conducted to analyze the adsorption performance on ERY. Isotherm data of MIPs well fitted the Freundlich model (from 15 °C to 35 °C), which indicated heterogeneous adsorption for ERY. The ERY adsorption capacity of MIPs was about 52.32 μmol/g at 15 °C. The adsorption kinetics was well described by the pseudo-first-order model, which suggested that physical interactions were primarily responsible for ERY adsorption. The Thomas model used in the fixed-bed adsorption design provided a better fit to the experimental data. Meanwhile, ERY exhibited higher affinity during adsorption on the MIPs compared with the adsorption capacity of azithromycin and chloramphenicol. The MIPs also exhibited excellent regeneration capacity with only about 5.04% adsorption efficiency loss in at least three repeated adsorption-desorption cycles. Copyright © 2015 Elsevier B.V. All rights reserved.

  3. Genetic Architecture of Milk, Fat, Protein, Mastitis and Fertility Studied using NGS Data in Holstein Cattle

    DEFF Research Database (Denmark)

    Sahana, Goutam; Janss, Luc; Guldbrandtsen, Bernt

    The use of genomic information in genetic evaluation has revolutionized dairy cattle breeding. It remains a major challenge to understand the genetic basis of variation for quantitative traits. Here, we study the genetic architecture for milk, fat, protein, mastitis and fertility indices in dairy...... cattle using NGS variants. The analysis was done using a linear mixed model (LMM) and a Bayesian mixture model (BMM). The top 10 QTL identified by LMM analyses explained 22.61, 23.86, 10.88, 18.58 and 14.83% of the total genetic variance for these traits respectively. Trait-specific sets of 4,964 SNPs...... from NGS variants (most ‘associated’ SNP for each 0.5 Mbp bin) explained 81.0, 81.6, 85.0, 60.4 and 70.9% of total genetic variance for milk, fat, protein, mastitis and fertility indices when analyzed simultaneously by BMM...

  4. Safe “cloudification” of large images through picker APIs

    Science.gov (United States)

    Bremer, Erich; Kurc, Tahsin; Gao, Yi; Saltz, Joel; Almeida, Jonas S

    2016-01-01

    The “Box model” allows users with no particular training in informatics, or access to specialized infrastructure, operate generic cloud computing resources through a temporary URI dereferencing mechanism known as “drop-file-picker API” (“picker API” for sort). This application programming interface (API) was popularized in the web app development community by DropBox, and is now a consumer-facing feature of all major cloud computing platforms such as Box.com, Google Drive and Amazon S3. This reports describes a prototype web service application that uses picker APIs to expose a new, “cloudified”, API tailored for image analysis, without compromising the private governance of the data exposed. In order to better understand this cross-platform cloud computing landscape, we first measured the time for both transfer and traversing of large image files generated by whole slide imaging (WSI) in Digital Pathology. The verification that there is extensive interconnectivity between cloud resources let to the development of a prototype software application that exposes an image-traversing REST API to image files stored in any of the consumer-facing “boxes”. In summary, an image file can be upload/synchronized into a any cloud resource with a file picker API and the prototype service described here will expose an HTTP REST API that remains within the safety of the user’s own governance. The open source prototype is publicly available at sbu-bmi.github.io/imagebox. Availability The accompanying prototype application is made publicly available, fully functional, with open source, at http://sbu-bmi.github.io/imagebox://sbu-bmi.github.io/imagebox. An illustrative webcasted use of this Web App is included with the project codebase at https://github.com/SBU-BMI/imageboxs://github.com/SBU-BMI/imagebox. PMID:28269829

  5. The cracking of pressure tubes in the Pickering reactor

    International Nuclear Information System (INIS)

    Ross-Ross, P.A.

    1978-01-01

    Small cracks in 17 of the 390 pressure tubes in Unit 3 of the 2056 MW (electrical) Pickering Generating Station and of 52 tubes in Unit 4, resulted in each of these units being out of service for many months. The cracks originated at areas of extremely high residual tensile stress produced by improper positioning of the rolling tool used during construction to join the pressure tube to its end-fitting. The mechanism of failure was delayed hydrogen cracking. (author)

  6. Ergonomic Evaluation of Battery Powered Portable Cotton Picker

    Science.gov (United States)

    Dixit, A.; Manes, G. S.; Singh, A.; Prakash, A.; Mahal, J. S.

    2012-09-01

    Ergonomic evaluation of battery powered portable manual cotton picker was carried out on two subjects for three cotton varieties and was compared against manual method of picking. It is a hand operated machine and has a pair of chain with small sharp edged teeth and sprockets and is operated by a light weight 12 V battery. Cotton gets entangled with the chain and is collected and guided into the collection bag. Average heart rate, oxygen consumption, workload, energy expenditure was more in case of cotton picking by manual cotton picker as compared to manual picking for both the subjects for all three cotton variety types. Oxygen consumption varied from 0.81 to 0.97 l/min, workload varied from 36.32 to 46.16 W and energy expenditure varied from 16.83 to 20.33 kJ/min for both the subject in case of machine picking for all three cotton varieties. The maximum discomfort experienced by the subjects during picking cotton by manual cotton picker was in right wrist palm, right forearm, upper and lower back, left shoulder and in lower legs and both feet.

  7. Pickering emulsions stabilized by biodegradable block copolymer micelles for controlled topical drug delivery.

    Science.gov (United States)

    Laredj-Bourezg, Faiza; Bolzinger, Marie-Alexandrine; Pelletier, Jocelyne; Chevalier, Yves

    2017-10-05

    Surfactant-free biocompatible and biodegradable Pickering emulsions were investigated as vehicles for skin delivery of hydrophobic drugs. O/w emulsions of medium-chain triglyceride (MCT) oil droplets loaded with all-trans retinol as a model hydrophobic drug were stabilized by block copolymer nanoparticles: either poly(lactide)-block-poly(ethylene glycol) (PLA-b-PEG) or poly(caprolactone)-block-poly(ethylene glycol) (PCL-b-PEG). Those innovative emulsions were prepared using two different processes allowing drug loading either inside oil droplets or inside both oil droplets and non-adsorbed block copolymer nanoparticles. Skin absorption of retinol was investigated in vitro on pig skin biopsies using the Franz cell method. Supplementary experiments by confocal fluorescence microscopy allowed the visualization of skin absorption of the Nile Red dye on histological sections. Retinol and Nile Red absorption experiments showed the large accumulation of hydrophobic drugs in the stratum corneum for the Pickering emulsions compared to the surfactant-based emulsion and an oil solution. Loading drug inside both oil droplets and block copolymer nanoparticles enhanced again skin absorption of drugs, which was ascribed to the supplementary contribution of free block copolymer nanoparticles loaded with drug. Such effect allowed tuning drug delivery to skin over a wide range by means of a suitable selection of either the formulation or the drug loading process. Copyright © 2017 Elsevier B.V. All rights reserved.

  8. tropiTree: An NGS-Based EST-SSR Resource for 24 Tropical Tree Species

    Science.gov (United States)

    Russell, Joanne R.; Hedley, Peter E.; Cardle, Linda; Dancey, Siobhan; Morris, Jenny; Booth, Allan; Odee, David; Mwaura, Lucy; Omondi, William; Angaine, Peter; Machua, Joseph; Muchugi, Alice; Milne, Iain; Kindt, Roeland; Jamnadass, Ramni; Dawson, Ian K.

    2014-01-01

    The development of genetic tools for non-model organisms has been hampered by cost, but advances in next-generation sequencing (NGS) have created new opportunities. In ecological research, this raises the prospect for developing molecular markers to simultaneously study important genetic processes such as gene flow in multiple non-model plant species within complex natural and anthropogenic landscapes. Here, we report the use of bar-coded multiplexed paired-end Illumina NGS for the de novo development of expressed sequence tag-derived simple sequence repeat (EST-SSR) markers at low cost for a range of 24 tree species. Each chosen tree species is important in complex tropical agroforestry systems where little is currently known about many genetic processes. An average of more than 5,000 EST-SSRs was identified for each of the 24 sequenced species, whereas prior to analysis 20 of the species had fewer than 100 nucleotide sequence citations. To make results available to potential users in a suitable format, we have developed an open-access, interactive online database, tropiTree (http://bioinf.hutton.ac.uk/tropiTree), which has a range of visualisation and search facilities, and which is a model for the efficient presentation and application of NGS data. PMID:25025376

  9. Reconstruction of mitogenomes by NGS and phylogenetic implications for leaf beetles.

    Science.gov (United States)

    Song, Nan; Yin, Xinming; Zhao, Xincheng; Chen, Junhua; Yin, Jian

    2017-11-30

    Mitochondrial genome (mitogenome) sequences are frequently used to infer phylogenetic relationships of insects at different taxonomic levels. Next-generation sequencing (NGS) techniques are revolutionizing many fields of biology, and allow for acquisition of insect mitogenomes for large number of species simultaneously. In this study, 20 full or partial mitogenomes were sequenced from pooled genomic DNA samples by NGS for leaf beetles (Chrysomelidae). Combined with published mitogenome sequences, a higher level phylogeny of Chrysomelidae was reconstructed under maximum likelihood and Bayesian inference with different models and various data treatments. The results revealed support for a basal position of Bruchinae within Chrysomelidae. In addition, two major subfamily groupings were recovered: one including seven subfamilies, namely Donaciinae, Criocerinae, Spilopyrinae, Cassidinae, Cryptocephalinae, Chlamisinae and Eumolpinae, another containing a non-monophyletic Chrysomelinae and a monophyletic Galerucinae.

  10. Scalable and cost-effective NGS genotyping in the cloud.

    Science.gov (United States)

    Souilmi, Yassine; Lancaster, Alex K; Jung, Jae-Yoon; Rizzo, Ettore; Hawkins, Jared B; Powles, Ryan; Amzazi, Saaïd; Ghazal, Hassan; Tonellato, Peter J; Wall, Dennis P

    2015-10-15

    While next-generation sequencing (NGS) costs have plummeted in recent years, cost and complexity of computation remain substantial barriers to the use of NGS in routine clinical care. The clinical potential of NGS will not be realized until robust and routine whole genome sequencing data can be accurately rendered to medically actionable reports within a time window of hours and at scales of economy in the 10's of dollars. We take a step towards addressing this challenge, by using COSMOS, a cloud-enabled workflow management system, to develop GenomeKey, an NGS whole genome analysis workflow. COSMOS implements complex workflows making optimal use of high-performance compute clusters. Here we show that the Amazon Web Service (AWS) implementation of GenomeKey via COSMOS provides a fast, scalable, and cost-effective analysis of both public benchmarking and large-scale heterogeneous clinical NGS datasets. Our systematic benchmarking reveals important new insights and considerations to produce clinical turn-around of whole genome analysis optimization and workflow management including strategic batching of individual genomes and efficient cluster resource configuration.

  11. Estimating IBD tracts from low coverage NGS data

    DEFF Research Database (Denmark)

    Garrett Vieira, Filipe Jorge; Albrechtsen, Anders; Nielsen, Rasmus

    2016-01-01

    that the new method provides a marked increase in accuracy even at low coverage. AVAILABILITY AND IMPLEMENTATION: The methods presented in this work were implemented in C/C ++ and are freely available for non-commercial use from https://github.com/fgvieira/ngsF-HMM CONTACT: fgvieira@snm.ku.dk SUPPLEMENTARY...... method for estimating inbreeding IBD tracts from low coverage NGS data. Contrary to other methods that use genotype data, the one presented here uses genotype likelihoods to take the uncertainty of the data into account. We benchmark it under a wide range of biologically relevant conditions and show...

  12. From pioneering to implementing automated blood pressure measurement in clinical practice: Thomas Pickering's legacy

    DEFF Research Database (Denmark)

    Stolarz-Skrzypek, Katarzyna; Thijs, Lutgarde; Wizner, Barbara

    2010-01-01

    Thomas G. Pickering spent most of his scientific career in carrying out research on clinical hypertension and blood pressure (BP) measurement. In our review of Pickering's seminal work, we first focused on white-coat hypertension and masked hypertension, two terms that he had introduced. Next, we...

  13. Edible foam based on Pickering effect of probiotic bacteria and milk proteins

    DEFF Research Database (Denmark)

    Yücel, Cigdem; Geng, Xiaolu; Cárdenas, Marité

    2017-01-01

    We report the preparation and characterization of aqueous Pickering foams using bio-particles constituted by lactic acid bacteria surface modified by oppositely charged milk proteins. Cell surface modification was shown by zeta potential measurements. Foams stabilized by bacterial Pickering bio-p...

  14. Expanding worldwide urban solid waste recycling: The Brazilian social technology in waste pickers inclusion.

    Science.gov (United States)

    Rutkowski, Jacqueline E; Rutkowski, Emília W

    2015-12-01

    'If an integrated urban waste management system includes the informal recycling sector (IRS), there is a good chance that more solid waste is recycled' is common sense. However, informal integration brings additional social, environmental, and economic benefits, such as reduction of operational costs and environmental impacts of landfilling. Brazil is a global best practice example in terms of waste picker inclusion, and has received international recognition for its recycling levels. In addition to analysing the results of inclusive recycling approaches, this article evaluates a selection of the best Brazilian inclusive recycling practices and summaries and presents the resulting knowledge. The objective is to identify processes that enable the replication of the inclusion of the informal recycling sector model as part of municipal solid waste management. Qualitative and quantitative data have been collected in 25 Brazilian cities that have contracted waste pickers co-operatives for door-to-door selective collection of recyclables. Field data was collected in action research projects that worked with waste pickers co-operatives between 2006 and 2013. The Brazilian informal recycling sector integration model improves municipal solid waste recycling indicators: it shows an increase in the net tonness recycled, from 140 to 208 t month(-1), at a much lower cost per tonne than conventional selective collection systems. Inclusive systems show costs of US$35 per tonne of recyclables collected, well below the national average of US$195.26. This inclusive model improves the quality of collected material and the efficiency of municipal selective collection. It also diminishes the negative impacts of informal recycling, by reducing child labour, and by improving the conditions of work, occupational health and safety, and uncontrolled pollution. Although treating the Brazilian experience as a blueprint for transfer of experience in every case is unrealistic, the results

  15. Primary heat transport pump mechanical seal replacement strategy for Pickering B

    International Nuclear Information System (INIS)

    Chacinsi, V.

    1995-01-01

    Pickering Nuclear Generating Station is a CANDU PHWR eight unit station located on Lake Ontario. The station is divided into Pickering A (Units 1 to 4) and Pickering B (Units 5 to 8). Pickering B is the focus of this paper. Each unit is rated at 540 MWe. The Primary Heat Transport (PHT) system, which is used to cool the fuel, is divided into four quadrants. Each quadrant has four vertical Byron Jackson PHT main circulation pumps. Three pumps in each quadrant are required for normal operation, leaving one pump in each quadrant as a spare. Each Pickering PHT pump has a Byron Jackson Type SU two stage mechanical seal. The typical pressure breakdown across the seal is 8.7-4.5-1.0 MPa. Certain features of seal operation and the PHT system which influence seal replacement are discussed below. (author)

  16. Warehouse order-picking process. Order-picker routing problem

    Directory of Open Access Journals (Sweden)

    E. V. Korobkov

    2015-01-01

    Full Text Available This article continues “Warehouse order-picking process” cycle and describes order-picker routing sub-problem of a warehouse order-picking process. It draws analogies between the orderpickers’ routing problem and traveling salesman’s problem, shows differences between the standard problem statement of a traveling salesman and routing problem of warehouse orderpickers, and gives the particular Steiner’s problem statement of a traveling salesman.Warehouse layout with a typical order is represented by a graph, with some its vertices corresponding to mandatory order-picker’s visits and some other ones being noncompulsory. The paper describes an optimal Ratliff-Rosenthal algorithm to solve order-picker’s routing problem for the single-block warehouses, i.e. warehouses with only two crossing aisles, defines seven equivalent classes of partial routing sub-graphs and five transitions used to have an optimal routing sub-graph of a order-picker. An extension of optimal Ratliff-Rosenthal order-picker routing algorithm for multi-block warehouses is presented and also reasons for using the routing heuristics instead of exact optimal algorithms are given. The paper offers algorithmic description of the following seven routing heuristics: S-shaped, return, midpoint, largest gap, aisle-by-aisle, composite, and combined as well as modification of combined heuristics. The comparison of orderpicker routing heuristics for one- and two-block warehouses is to be described in the next article of the “Warehouse order-picking process” cycle.

  17. Ontario Hydro Pickering Generating Station fuel handling system performance

    International Nuclear Information System (INIS)

    Underhill, H.J.

    1986-01-01

    The report briefly describes the Pickering Nuclear Generating Station (PNGS) on-power fuel handling system and refuelling cycle. Lifetime performance parameters of the fuelling system are presented, including station incapability charged to the fuel handling system, cost of operating and maintenance, dose expenditure, events causing system unavailability, maintenance and refuelling strategy. It is concluded that the 'CANDU' on-power fuelling system, by consistently contributing less than 1% to the PNGS incapability, has been credited with a 6 to 20% increase in reactor capacity factor, compared to off-power fuelling schemes. (author)

  18. Online control loop tuning in Pickering Nuclear Generating Stations

    International Nuclear Information System (INIS)

    Yu, K.X.; Harrington, S.

    2008-01-01

    Most analog controllers in the Pickering B Nuclear Generating Stations adopted PID control scheme. In replacing the analog controllers with digital controllers, the PID control strategies, including the original tuning parameters were retained. The replacement strategy resulted in minimum effort on control loop tuning. In a few cases, however, it was found during commissioning that control loop tuning was required as a result of poor control loop performance, typically due to slow response and controlled process oscillation. Several factors are accounted for the necessities of control loop re-tuning. Our experience in commissioning the digital controllers showed that online control tuning posted some challenges in nuclear power plant. (author)

  19. Participation in interdisciplinary meetings on genetic diagnostics (NGS)

    NARCIS (Netherlands)

    Koole, Tom; van Burgsteden, Lotte; Harms, Paulien; van Diemen, Cleo C; van Langen, Irene M

    2017-01-01

    Diagnostics using next generation sequencing (NGS) requires high-quality interdisciplinary collaboration. In order to gain insight into this crucial collaborative process, we made video recordings of a new multidisciplinary team at work in the clinical genetics department of the University Medical

  20. Validation of an NGS mutation detection panel for melanoma.

    Science.gov (United States)

    Reiman, Anne; Kikuchi, Hugh; Scocchia, Daniela; Smith, Peter; Tsang, Yee Wah; Snead, David; Cree, Ian A

    2017-02-22

    Knowledge of the genotype of melanoma is important to guide patient management. Identification of mutations in BRAF and c-KIT lead directly to targeted treatment, but it is also helpful to know if there are driver oncogene mutations in NRAS, GNAQ or GNA11 as these patients may benefit from alternative strategies such as immunotherapy. While polymerase chain reaction (PCR) methods are often used to detect BRAF mutations, next generation sequencing (NGS) is able to determine all of the necessary information on several genes at once, with potential advantages in turnaround time. We describe here an Ampliseq hotspot panel for melanoma for use with the IonTorrent Personal Genome Machine (PGM) which covers the mutations currently of most clinical interest. We have validated this in 151 cases of skin and uveal melanoma from our files, and correlated the data with PCR based assessment of BRAF status. There was excellent agreement, with few discrepancies, though NGS does have greater coverage and picks up some mutations that would be missed by PCR. However, these are often rare and of unknown significance for treatment. PCR methods are rapid, less time-consuming and less expensive than NGS, and could be used as triage for patients requiring more extensive diagnostic workup. The NGS panel described here is suitable for clinical use with formalin-fixed paraffin-embedded (FFPE) samples.

  1. Genetic counselors’ (GC) knowledge, awareness, and understanding of clinical next-generation sequencing (NGS) genomic testing

    Science.gov (United States)

    Boland, PM; Ruth, K; Matro, JM; Rainey, KL; Fang, CY; Wong, YN; Daly, MB; Hall, MJ

    2014-01-01

    Genomic tests are increasingly complex, less expensive, and more widely available with the advent of next-generation sequencing (NGS). We assessed knowledge and perceptions among genetic counselors pertaining to NGS genomic testing via an online survey. Associations between selected characteristics and perceptions were examined. Recent education on NGS testing was common, but practical experience limited. Perceived understanding of clinical NGS was modest, specifically concerning tumor testing. Greater perceived understanding of clinical NGS testing correlated with more time spent in cancer-related counseling, exposure to NGS testing, and NGS-focused education. Substantial disagreement about the role of counseling for tumor-based testing was seen. Finally, a majority of counselors agreed with the need for more education about clinical NGS testing, supporting this approach to optimizing implementation. PMID:25523111

  2. Genetic counselors' (GC) knowledge, awareness, understanding of clinical next-generation sequencing (NGS) genomic testing.

    Science.gov (United States)

    Boland, P M; Ruth, K; Matro, J M; Rainey, K L; Fang, C Y; Wong, Y N; Daly, M B; Hall, M J

    2015-12-01

    Genomic tests are increasingly complex, less expensive, and more widely available with the advent of next-generation sequencing (NGS). We assessed knowledge and perceptions among genetic counselors pertaining to NGS genomic testing via an online survey. Associations between selected characteristics and perceptions were examined. Recent education on NGS testing was common, but practical experience limited. Perceived understanding of clinical NGS was modest, specifically concerning tumor testing. Greater perceived understanding of clinical NGS testing correlated with more time spent in cancer-related counseling, exposure to NGS testing, and NGS-focused education. Substantial disagreement about the role of counseling for tumor-based testing was seen. Finally, a majority of counselors agreed with the need for more education about clinical NGS testing, supporting this approach to optimizing implementation. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  3. A study of wet deposition of atmospheric tritium releases at the Ontario Power Generation, Pickering Nuclear Generating Station

    International Nuclear Information System (INIS)

    Crooks, G.; DeWilde, J.; Yu, L.

    2001-01-01

    The Ontario Power Generation,Pickering Nuclear Generating Station (PNGS) has been investigating deposition of atmospheric releases of tritium on their site. This study has included numerical dispersion modelling studies conducted over the past three years, as well as an ongoing field monitoring study. The following paper will present results of the field monitoring study and make comparisons to the numerical modelling. The results of this study could be of potential use to nuclear stations in quantifying tritium deposition in near field regions where building wake effects dominate pollutant dispersion

  4. Seismic response of the Pickering pressure relief duct to the 1985 Nahanni earthquake

    International Nuclear Information System (INIS)

    Ghobarah, A.

    1995-05-01

    The objective of this study is to examine the structural response of the Pickering pressure relief duct when subjected to the ground motion records of the 1985 Nahanni earthquake (December 23, 05:16 GMT, Site 1 - Iverson, N.W.T.). It also includes an estimate of the possible impact on the nuclear safety function of the duct. The structural models developed in an earlier study were used in this analysis. The response to the earthquake ground motion was determined on the basis of the estimated capacities of various components of the duct. The ability of the structure to fulfill its nuclear safety function is discussed. (author). 6 refs., 1 tab., 17 figs

  5. Reverse logistics network for municipal solid waste management: The inclusion of waste pickers as a Brazilian legal requirement.

    Science.gov (United States)

    Ferri, Giovane Lopes; Chaves, Gisele de Lorena Diniz; Ribeiro, Glaydston Mattos

    2015-06-01

    This study proposes a reverse logistics network involved in the management of municipal solid waste (MSW) to solve the challenge of economically managing these wastes considering the recent legal requirements of the Brazilian Waste Management Policy. The feasibility of the allocation of MSW material recovery facilities (MRF) as intermediate points between the generators of these wastes and the options for reuse and disposal was evaluated, as well as the participation of associations and cooperatives of waste pickers. This network was mathematically modelled and validated through a scenario analysis of the municipality of São Mateus, which makes the location model more complete and applicable in practice. The mathematical model allows the determination of the number of facilities required for the reverse logistics network, their location, capacities, and product flows between these facilities. The fixed costs of installation and operation of the proposed MRF were balanced with the reduction of transport costs, allowing the inclusion of waste pickers to the reverse logistics network. The main contribution of this study lies in the proposition of a reverse logistics network for MSW simultaneously involving legal, environmental, economic and social criteria, which is a very complex goal. This study can guide practices in other countries that have realities similar to those in Brazil of accelerated urbanisation without adequate planning for solid waste management, added to the strong presence of waste pickers that, through the characteristic of social vulnerability, must be included in the system. In addition to the theoretical contribution to the reverse logistics network problem, this study aids in decision-making for public managers who have limited technical and administrative capacities for the management of solid wastes. Copyright © 2015 Elsevier Ltd. All rights reserved.

  6. Leptospira Exposure and Waste Pickers: A Case-Control Seroprevalence Study in Durango, Mexico.

    Science.gov (United States)

    Alvarado-Esquivel, Cosme; Hernandez-Tinoco, Jesus; Sanchez-Anguiano, Luis Francisco; Ramos-Nevarez, Agar; Cerrillo-Soto, Sandra Margarita; Guido-Arreola, Carlos Alberto

    2015-08-01

    Infection with Leptospira may occur by contact with Leptospira-infected animals. Waste pickers are in contact with rodents and dogs while picking in the garbage. Whether waste pickers are at risk for Leptospira infection is largely unknown. This study was aimed to determine the association of Leptospira IgG seroprevalence with the occupation of waste picking, and to determine the epidemiological characteristics of the waste pickers with Leptospira exposure. Through a case-control study, we determined the seroprevalence of anti-Leptospira IgG antibodies in 90 waste pickers and 90 age- and gender-matched control subjects in Durango City, Mexico using an enzyme immunoassay. Data were analyzed by bivariate and multivariate analyses. The prevalence of anti-Leptospira IgG antibodies was similar in waste pickers (4/90: 4.4%) to that in control subjects (5/90: 5.6%) (P = 1.00). Bivariate analysis showed that Leptospira exposure in waste pickers was associated with increasing age (P = 0.009), no education (P = 0.008), and consumption of rat meat (P = 0.04). However, these associations were no longer found by multivariate analysis. Leptospira exposure in waste pickers was not associated with health status, duration in the activity, wearing hand gloves and facemasks, history of injuries with sharp material of the garbage, or contact with animals or soil. This is the first study about Leptospira exposure in waste pickers. Results suggest that waste pickers are not at increasing risk for Leptospira exposure in Durango City, Mexico. Further research with a larger sample size to elucidate the association of Leptospira exposure with waste picking activity is needed.

  7. Leptospira Exposure and Waste Pickers: A Case-Control Seroprevalence Study in Durango, Mexico

    Science.gov (United States)

    Alvarado-Esquivel, Cosme; Hernandez-Tinoco, Jesus; Sanchez-Anguiano, Luis Francisco; Ramos-Nevarez, Agar; Cerrillo-Soto, Sandra Margarita; Guido-Arreola, Carlos Alberto

    2015-01-01

    Background Infection with Leptospira may occur by contact with Leptospira-infected animals. Waste pickers are in contact with rodents and dogs while picking in the garbage. Whether waste pickers are at risk for Leptospira infection is largely unknown. This study was aimed to determine the association of Leptospira IgG seroprevalence with the occupation of waste picking, and to determine the epidemiological characteristics of the waste pickers with Leptospira exposure. Methods Through a case-control study, we determined the seroprevalence of anti-Leptospira IgG antibodies in 90 waste pickers and 90 age- and gender-matched control subjects in Durango City, Mexico using an enzyme immunoassay. Data were analyzed by bivariate and multivariate analyses. Results The prevalence of anti-Leptospira IgG antibodies was similar in waste pickers (4/90: 4.4%) to that in control subjects (5/90: 5.6%) (P = 1.00). Bivariate analysis showed that Leptospira exposure in waste pickers was associated with increasing age (P = 0.009), no education (P = 0.008), and consumption of rat meat (P = 0.04). However, these associations were no longer found by multivariate analysis. Leptospira exposure in waste pickers was not associated with health status, duration in the activity, wearing hand gloves and facemasks, history of injuries with sharp material of the garbage, or contact with animals or soil. Conclusions This is the first study about Leptospira exposure in waste pickers. Results suggest that waste pickers are not at increasing risk for Leptospira exposure in Durango City, Mexico. Further research with a larger sample size to elucidate the association of Leptospira exposure with waste picking activity is needed. PMID:26124911

  8. Reverse logistics network for municipal solid waste management: The inclusion of waste pickers as a Brazilian legal requirement

    Energy Technology Data Exchange (ETDEWEB)

    Ferri, Giovane Lopes, E-mail: giovane.ferri@aluno.ufes.br [Department of Engineering and Technology, Federal University of Espírito Santo – UFES, Rodovia BR 101 Norte, Km 60, Bairro Litorâneo, São Mateus, ES, 29.932-540 (Brazil); Diniz Chaves, Gisele de Lorena, E-mail: gisele.chaves@ufes.br [Department of Engineering and Technology, Federal University of Espírito Santo – UFES, Rodovia BR 101 Norte, Km 60, Bairro Litorâneo, São Mateus, ES, 29.932-540 (Brazil); Ribeiro, Glaydston Mattos, E-mail: glaydston@pet.coppe.ufrj.br [Transportation Engineering Programme, Federal University of Rio de Janeiro – UFRJ, Centro de Tecnologia, Bloco H, Sala 106, Cidade Universitária, Rio de Janeiro, 21949-900 (Brazil)

    2015-06-15

    Highlights: • We propose a reverse logistics network for MSW involving waste pickers. • A generic facility location mathematical model was validated in a Brazilian city. • The results enable to predict the capacity for screening and storage centres (SSC). • We minimise the costs for transporting MSW with screening and storage centres. • The use of SSC can be a potential source of revenue and a better use of MSW. - Abstract: This study proposes a reverse logistics network involved in the management of municipal solid waste (MSW) to solve the challenge of economically managing these wastes considering the recent legal requirements of the Brazilian Waste Management Policy. The feasibility of the allocation of MSW material recovery facilities (MRF) as intermediate points between the generators of these wastes and the options for reuse and disposal was evaluated, as well as the participation of associations and cooperatives of waste pickers. This network was mathematically modelled and validated through a scenario analysis of the municipality of São Mateus, which makes the location model more complete and applicable in practice. The mathematical model allows the determination of the number of facilities required for the reverse logistics network, their location, capacities, and product flows between these facilities. The fixed costs of installation and operation of the proposed MRF were balanced with the reduction of transport costs, allowing the inclusion of waste pickers to the reverse logistics network. The main contribution of this study lies in the proposition of a reverse logistics network for MSW simultaneously involving legal, environmental, economic and social criteria, which is a very complex goal. This study can guide practices in other countries that have realities similar to those in Brazil of accelerated urbanisation without adequate planning for solid waste management, added to the strong presence of waste pickers that, through the

  9. Reverse logistics network for municipal solid waste management: The inclusion of waste pickers as a Brazilian legal requirement

    International Nuclear Information System (INIS)

    Ferri, Giovane Lopes; Diniz Chaves, Gisele de Lorena; Ribeiro, Glaydston Mattos

    2015-01-01

    Highlights: • We propose a reverse logistics network for MSW involving waste pickers. • A generic facility location mathematical model was validated in a Brazilian city. • The results enable to predict the capacity for screening and storage centres (SSC). • We minimise the costs for transporting MSW with screening and storage centres. • The use of SSC can be a potential source of revenue and a better use of MSW. - Abstract: This study proposes a reverse logistics network involved in the management of municipal solid waste (MSW) to solve the challenge of economically managing these wastes considering the recent legal requirements of the Brazilian Waste Management Policy. The feasibility of the allocation of MSW material recovery facilities (MRF) as intermediate points between the generators of these wastes and the options for reuse and disposal was evaluated, as well as the participation of associations and cooperatives of waste pickers. This network was mathematically modelled and validated through a scenario analysis of the municipality of São Mateus, which makes the location model more complete and applicable in practice. The mathematical model allows the determination of the number of facilities required for the reverse logistics network, their location, capacities, and product flows between these facilities. The fixed costs of installation and operation of the proposed MRF were balanced with the reduction of transport costs, allowing the inclusion of waste pickers to the reverse logistics network. The main contribution of this study lies in the proposition of a reverse logistics network for MSW simultaneously involving legal, environmental, economic and social criteria, which is a very complex goal. This study can guide practices in other countries that have realities similar to those in Brazil of accelerated urbanisation without adequate planning for solid waste management, added to the strong presence of waste pickers that, through the

  10. Viscosity of the oil-in-water Pickering emulsion stabilized by surfactant-polymer and nanoparticle-surfactant-polymer system

    Science.gov (United States)

    Sharma, Tushar; Kumar, G. Suresh; Chon, Bo Hyun; Sangwai, Jitendra S.

    2014-11-01

    Information on the viscosity of Pickering emulsion is required for their successful application in upstream oil and gas industry to understand their stability at extreme environment. In this work, a novel formulation of oil-in-water (o/w) Pickering emulsion stabilized using nanoparticle-surfactant-polymer (polyacrylamide) system as formulated in our earlier work (Sharma et al., Journal of Industrial and Engineering Chemistry, 2014) is investigated for rheological stability at high pressure and high temperature (HPHT) conditions using a controlled-strain rheometer. The nanoparticle (SiO2 and clay) concentration is varied from 1.0 to 5.0 wt%. The results are compared with the rheological behavior of simple o/w emulsion stabilized by surfactant-polymer system. Both the emulsions exhibit non-Newtonian shear thinning behavior. A positive shift in this behavior is observed for surfactant-polymer stabilized emulsion at high pressure conditions. Yield stress is observed to increase with pressure for surfactant-polymer emulsion. In addition, increase in temperature has an adverse effect on the viscosity of emulsion stabilized by surfactant-polymer system. In case of nanoparticle-surfactant-polymer stabilized o/w emulsion system, the viscosity and yield stress are predominantly constant for varying pressure and temperature conditions. The viscosity data for both o/w emulsion systems are fitted by the Herschel-Bulkley model and found to be satisfactory. In general, the study indicates that the Pickering emulsion stabilized by nanoparticle-surfactant-polymer system shows improved and stable rheological properties as compared to conventional emulsion stabilized by surfactant-polymer system indicating their successful application for HPHT environment in upstream oil and gas industry.

  11. Tracking the NGS revolution: managing life science research on shared high-performance computing clusters.

    Science.gov (United States)

    Dahlö, Martin; Scofield, Douglas G; Schaal, Wesley; Spjuth, Ola

    2018-05-01

    Next-generation sequencing (NGS) has transformed the life sciences, and many research groups are newly dependent upon computer clusters to store and analyze large datasets. This creates challenges for e-infrastructures accustomed to hosting computationally mature research in other sciences. Using data gathered from our own clusters at UPPMAX computing center at Uppsala University, Sweden, where core hour usage of ∼800 NGS and ∼200 non-NGS projects is now similar, we compare and contrast the growth, administrative burden, and cluster usage of NGS projects with projects from other sciences. The number of NGS projects has grown rapidly since 2010, with growth driven by entry of new research groups. Storage used by NGS projects has grown more rapidly since 2013 and is now limited by disk capacity. NGS users submit nearly twice as many support tickets per user, and 11 more tools are installed each month for NGS projects than for non-NGS projects. We developed usage and efficiency metrics and show that computing jobs for NGS projects use more RAM than non-NGS projects, are more variable in core usage, and rarely span multiple nodes. NGS jobs use booked resources less efficiently for a variety of reasons. Active monitoring can improve this somewhat. Hosting NGS projects imposes a large administrative burden at UPPMAX due to large numbers of inexperienced users and diverse and rapidly evolving research areas. We provide a set of recommendations for e-infrastructures that host NGS research projects. We provide anonymized versions of our storage, job, and efficiency databases.

  12. Tracking the NGS revolution: managing life science research on shared high-performance computing clusters

    Science.gov (United States)

    2018-01-01

    Abstract Background Next-generation sequencing (NGS) has transformed the life sciences, and many research groups are newly dependent upon computer clusters to store and analyze large datasets. This creates challenges for e-infrastructures accustomed to hosting computationally mature research in other sciences. Using data gathered from our own clusters at UPPMAX computing center at Uppsala University, Sweden, where core hour usage of ∼800 NGS and ∼200 non-NGS projects is now similar, we compare and contrast the growth, administrative burden, and cluster usage of NGS projects with projects from other sciences. Results The number of NGS projects has grown rapidly since 2010, with growth driven by entry of new research groups. Storage used by NGS projects has grown more rapidly since 2013 and is now limited by disk capacity. NGS users submit nearly twice as many support tickets per user, and 11 more tools are installed each month for NGS projects than for non-NGS projects. We developed usage and efficiency metrics and show that computing jobs for NGS projects use more RAM than non-NGS projects, are more variable in core usage, and rarely span multiple nodes. NGS jobs use booked resources less efficiently for a variety of reasons. Active monitoring can improve this somewhat. Conclusions Hosting NGS projects imposes a large administrative burden at UPPMAX due to large numbers of inexperienced users and diverse and rapidly evolving research areas. We provide a set of recommendations for e-infrastructures that host NGS research projects. We provide anonymized versions of our storage, job, and efficiency databases. PMID:29659792

  13. NUKAB system use with the PICKER DYNA CAMERA II

    International Nuclear Information System (INIS)

    Collet, H.; Faurous, P.; Lehn, A.; Suquet, P.

    Present-day data processing units connected to scintillation gamma cameras can make use of cabled programme or recorded programme systems. The NUKAB system calls on the latter technique. The central element of the data processing unit, connected to the PICKER DYNA CAMERA II output, consists of a DIGITAL PDP 8E computer with 12-bit technological words. The use of a 12-bit technological format restricts the possibilities of digitalisation, 64x64 images representing the practical limit. However the NUKAB system appears well suited to the processing of data from gamma cameras at present in service. The addition of output terminals of the tracing panel type should widen the possibilities of the system. It seems that the 64x64 format is not a handicap in view of the resolution power of the detectors [fr

  14. Tritium in groundwater investigation at the Pickering Nuclear Generating Station

    International Nuclear Information System (INIS)

    DeWilde, J.; Yu, L.; Wootton, R.; Belanger, D.; Hansen, K.; McGurk, E.; Teare, A.

    2001-01-01

    Ontario Power Generation Inc. (OPG) investigated tritium in groundwater at the Pickering Nuclear Generating Station (PNGS). The objectives of the study were to evaluate and define the extent of radionuclides, primarily tritium, in groundwater, investigate the causes or sources of contamination, determine impacts on the natural environment, and provide recommendations to prevent future discharges. This paper provides an overview of the investigations conducted in 1999 and 2000 to identity the extent of the tritium beneath the site and the potential sources of tritium released to the groundwater. The investigation and findings are summarized with a focus on unique aspects of the investigation, on lessons learned and benefits. Some of the investigative techniques discussed include process assessments, video inspections, hydrostatic and tracer tests, Helium 3 analysis for tritium age dating, deuterium and tritium in soil analysis. The investigative techniques have widespread applications to other nuclear generating stations. (author)

  15. Colloidal formulations for probiotics delivery and Pickering systems

    DEFF Research Database (Denmark)

    Yücel Falco, Cigdem

    countries. One emerging functional food area is the efficient delivery of health-promoting probiotics. Although much progress has already been made in the development and understanding of novel microencapsulation systems, maintaining viability during gastric passage and being effective at the target site...... is still an issue for probiotics. On the other hand, one of the foremost challenges in the production of physically stable foods during the defined shelf life is the identification of new food-grade ingredients. In this context, the replacement of classical emulsifiers with solid particles is one...... of the advancing food research areas, though the number of food-grade solid particles investigated is still insufficient. Edible probiotic strains can potentially be valorised as particles similar to micron-sized fat particles in Pickering systems such as ice cream due to their low calories and their availability...

  16. Development and characterization of novel antimicrobial bilayer films based on Polylactic acid (PLA)/Pickering emulsions.

    Science.gov (United States)

    Zhu, Jun-You; Tang, Chuan-He; Yin, Shou-Wei; Yang, Xiao-Quan

    2018-02-01

    Biodegradable food packaging is sustainable and has a great application prospect. PLA is a promising alternative for petroleum-derived polymers. However, PLA packaging suffers from poor barrier properties compared with petroleum-derived ones. To address this issue, we designed bilayer films based on PLA and Pickering emulsions. The formed bilayer films were compact and uniform and double layers were combined firmly. This strategy enhanced mechanical resistance, ductility and moisture barrier of Pickering emulsion films, and concomitantly enhanced the oxygen barrier for PLA films. Thymol loadings in Pickering emulsion layer endowed them with antimicrobial and antioxidant activity. The release profile of thymol was well fitted with Fick's second law. The antimicrobial activity of the films depended on film types, and Pickering emulsion layer presented larger inhibition zone than PLA layer, hinting that the films possessed directional releasing role. This study opens a promising route to fabricate bilayer architecture creating synergism of each layer. Copyright © 2017 Elsevier Ltd. All rights reserved.

  17. Newly discovered geological features and their potential impact on Darlington and Pickering

    International Nuclear Information System (INIS)

    Wallach, J.L.

    1990-01-01

    Newly available information reveals the presence of a prominent north-northeast oriented aeromagnetic lineament and east-northeast trending, linear patterns in young sediments on the bottom of Lake Ontario. The magnetic lineament, named the Niagara-Pickering Magnetic Lineament, passes practically beneath the Pickering Nuclear Generating Station (8x1600 MW reactors), and about 30 km west of the Darlington Nuclear Generating Station (4x2800 MW reactors). Magnetic data suggest that the Niagara-Pickering Magnetic Lineament may be the signature of a fault and may connect with the Akron Magnetic Boundary in Ohio, with which several earthquakes appear to be associated. Geological data lend support to the fault hypothesis. A north-northwest trending belt of earthquake epicenters, which includes the Lockport, NY earthquake (est M=5.0) and the Attica, NY earthquake (M=5.8), lies just east of, and parallels, the entire length of Georgian Bay en route to Attica, New York. The proximity and parallelism of the Georgian Bay Linear Zone to this belt of earthquake epicenters implies that the Georgian Bay Linear Zone may be tectonically active. The Georgian Bay Linear Zone and the Niagara-Pickering Magnetic Lineament appear to intersect very near Pickering and within about 30 km from Darlington. This, combined with evidence of high horizontal stresses in the area and the implication that both lineaments may be seismically active, suggests that many of the ingredients necessary for an earthquake of at least M=5.0 to M=6.25 exist near both Darlington and Pickering. Therefore, it is necessary that the Niagara-Pickering Magnetic Lineament, the Georgian Bay Linear Zone and the other newly discovered structural features be properly evaluated in order to determine whether or not the current Design Basis Seismic Ground Motions for Darlington and Pickering are adequate

  18. Fabrication of CMC-g-PAM superporous polymer monoliths via eco-friendly Pickering-MIPEs for superior adsorption of methyl violet and methylene blue

    Science.gov (United States)

    Wang, Feng; Zhu, Yongfeng; Wang, Wenbo; Zong, Li; Lu, Taotao; Wang, Aiqin

    2017-06-01

    A series of superporous carboxymethylcellulose-graft-poly(acrylamide) (CMC-g-PAM) polymer monoliths presenting interconnected pore structure and excellent adsorption properties were prepared by one-step free-radical grafting polymerization reaction of CMC and acrylamide (AM) in the oil-in-water (O/W) Pickering-medium internal phase emulsions (Pickering-MIPEs) composed of non-toxic edible oil as a dispersion phase and natural Pal nanorods as stabilizers. The effects of Pal dosage, AM dosage, and co-surfactant Tween-20 (T-20) on the pore structures of the monoliths were studied. It was revealed that the well-defined pores were formed when the dosages of Pal and T-20 are 9-14% and 3%, respectively. The porous monolith can rapidly adsorb 1585 mg/g of methyl violet (MV) and 1625 mg/g of methylene blue (MB). After the monolith was regenerated by adsorption-desorption process for 5 times, the adsorption capacities still reached 92.1% (for MV) and 93.5% (for MB) of the initial maximum adsorption capacities. The adsorption process was fitted with Langmuir adsorption isotherm model and pseudo-second-order adsorption kinetic model very well, which indicate that mono-layer chemical adsorption mainly contribute to the high-capacity adsorption for dyes. The superporous polymer monolith prepared from eco-friendly Pickering-MIPEs shows good adsorption capacity and fast adsorption rate, which is potential adsorbent for the decontimination of dye-containing wastewater.

  19. Implementation and on-sky results of an optimal wavefront controller for the MMT NGS adaptive optics system

    Science.gov (United States)

    Powell, Keith B.; Vaitheeswaran, Vidhya

    2010-07-01

    The MMT observatory has recently implemented and tested an optimal wavefront controller for the NGS adaptive optics system. Open loop atmospheric data collected at the telescope is used as the input to a MATLAB based analytical model. The model uses nonlinear constrained minimization to determine controller gains and optimize the system performance. The real-time controller performing the adaptive optics close loop operation is implemented on a dedicated high performance PC based quad core server. The controller algorithm is written in C and uses the GNU scientific library for linear algebra. Tests at the MMT confirmed the optimal controller significantly reduced the residual RMS wavefront compared with the previous controller. Significant reductions in image FWHM and increased peak intensities were obtained in J, H and K-bands. The optimal PID controller is now operating as the baseline wavefront controller for the MMT NGS-AO system.

  20. Static yield stress of a magnetorheological fluid containing Pickering emulsion polymerized Fe2O3/polystyrene composite particles.

    Science.gov (United States)

    Seo, Youngwook P; Kwak, Soonjong; Choi, Hyoung Jin; Seo, Yongsok

    2016-02-01

    The flow behaviors of magnetorheological (MR) suspensions containing Pickering emulsion polymerized Fe2O3/polystyrene (PS) composite particles were reanalyzed using the Seo-Seo model. The experimental shear stress data obtained experimentally from the magnetorheological fluid fit well to the Seo-Seo model, indicating that this model can describe the structural reformation process of the aligned fibers at various shear rates. Unlike the dynamic yield stress obtained from the Cho-Choi-Jhon (CCJ) model, the static yield stresses obtained from the Seo-Seo model exhibit the same quadratic dependence on the magnetic field strength for both pure Fe2O3 particle suspension and Fe2O3/PS particle suspensions, which is in agreement with the predictions of the polarization model. The static yield stress plausibly explains the difference in underlying mechanism of MR fluids. Copyright © 2015 Elsevier Inc. All rights reserved.

  1. Fire fighting capability assessment program Bruce B NGS

    International Nuclear Information System (INIS)

    1995-05-01

    This is a report on the completion of work relating to the assessment of the capability of Bruce B NGS to cope with a large fire incident. This included an evaluation of an exercise scenario that would simulate a large fire incident and of their fire plans and procedures. Finally the execution of fire plans by Bruce B NGS, as demonstrated by their application of human and material resources during a simulated large fire, was observed. The fire fighting equipment and the personal protective clothing and associated equipment that was in use was all of good quality and in good condition. There had also been notable improvement in communications equipment. Similarly, the human resources that had been assigned to fire fighting and rescue crews and that were available were more than adequate. Use of a logical incident command system, and the adoption of proper policy and procedures for radio communications were equally significant improvements. Practice should correct the breakdowns that occurred in these areas during the exercise. As well, there remains a need for the development of policy on fire fighting and rescue operations with more depth and clarity. In summary, the key point to be recognized is the degree of improvement that has been realized since the previous evaluation in 1990. Clearly the Emergency Response Teams organization of Bruce B NGS is evolving into an effective fire fighting force. Providing that the deficiencies identified in this report are addressed satisfactorily, Fire Cross is confident that the organization will have the capability to provide rescue and fire fighting services that will satisfy the need. 2 figs

  2. Use of the LUS in sequence allele designations to facilitate probabilistic genotyping of NGS-based STR typing results.

    Science.gov (United States)

    Just, Rebecca S; Irwin, Jodi A

    2018-05-01

    employed. Further, these biologically based, easy-to-derive designations uphold clear relationships between parent alleles and their stutter products, enabling analysis in fully continuous probabilistic programs that model stutter while avoiding the algorithmic complexities that come with string based searches. Though using repeat unit plus LUS length as the allele designator does not capture variation that occurs outside of the core repeat regions, this straightforward approach would permit the large majority of known STR sequence variation to be used for mixture deconvolution and, in turn, result in more informative mixture statistics in the near term. Ultimately, the method could bridge the gap from current length-based probabilistic systems to facilitate broader adoption of NGS by forensic DNA testing laboratories. Copyright © 2018 The Authors. Published by Elsevier B.V. All rights reserved.

  3. Demographic inferences from large-scale NGS data

    DEFF Research Database (Denmark)

    Pedersen, Casper-Emil Tingskov

    .g. human genetics. In this thesis, the three papers presented demonstrate the advantages of NGS data in the framework of population genetics for elucidating demographic inferences, important for understanding conservation efforts, selection and mutational burdens. In the first whole-genome study...... that the demographic history of the Inuit is the most extreme in terms of population size, of any human population. We identify a slight increase in the number of deleterious alleles because of this demographic history and support our results using simulations. We use this to show that the reduction in population size...

  4. Inference with viral quasispecies diversity indices: clonal and NGS approaches.

    Science.gov (United States)

    Gregori, Josep; Salicrú, Miquel; Domingo, Esteban; Sanchez, Alex; Esteban, Juan I; Rodríguez-Frías, Francisco; Quer, Josep

    2014-04-15

    Given the inherent dynamics of a viral quasispecies, we are often interested in the comparison of diversity indices of sequential samples of a patient, or in the comparison of diversity indices of virus in groups of patients in a treated versus control design. It is then important to make sure that the diversity measures from each sample may be compared with no bias and within a consistent statistical framework. In the present report, we review some indices often used as measures for viral quasispecies complexity and provide means for statistical inference, applying procedures taken from the ecology field. In particular, we examine the Shannon entropy and the mutation frequency, and we discuss the appropriateness of different normalization methods of the Shannon entropy found in the literature. By taking amplicons ultra-deep pyrosequencing (UDPS) raw data as a surrogate of a real hepatitis C virus viral population, we study through in-silico sampling the statistical properties of these indices under two methods of viral quasispecies sampling, classical cloning followed by Sanger sequencing (CCSS) and next-generation sequencing (NGS) such as UDPS. We propose solutions specific to each of the two sampling methods-CCSS and NGS-to guarantee statistically conforming conclusions as free of bias as possible. josep.gregori@gmail.com Supplementary information: Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  5. CRISPR-DAV: CRISPR NGS data analysis and visualization pipeline.

    Science.gov (United States)

    Wang, Xuning; Tilford, Charles; Neuhaus, Isaac; Mintier, Gabe; Guo, Qi; Feder, John N; Kirov, Stefan

    2017-12-01

    The simplicity and precision of CRISPR/Cas9 system has brought in a new era of gene editing. Screening for desired clones with CRISPR-mediated genomic edits in a large number of samples is made possible by next generation sequencing (NGS) due to its multiplexing. Here we present CRISPR-DAV (CRISPR Data Analysis and Visualization) pipeline to analyze the CRISPR NGS data in a high throughput manner. In the pipeline, Burrows-Wheeler Aligner and Assembly Based ReAlignment are used for small and large indel detection, and results are presented in a comprehensive set of charts and interactive alignment view. CRISPR-DAV is available at GitHub and Docker Hub repositories: https://github.com/pinetree1/crispr-dav.git and https://hub.docker.com/r/pinetree1/crispr-dav/. xuning.wang@bms.com. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

  6. A comparison of clinical vs subclinical skin pickers in Israel.

    Science.gov (United States)

    Keuthen, Nancy J; Curley, Erin E; Tung, Esther S; Ittah, Karen; Qasem, Atheer; Murad, Sari; Odlaug, Brian L; Leibovici, Vera

    2016-05-01

    Skin-picking disorder (SPD) was recognized as its own entity for the first time in DSM-5. The existing SPD literature is limited and, to date, no study has examined the differences between clinical and sub- clinical SPD. Identifying differences between these 2 groups may improve diagnostic accuracy, treatment, and prevention efforts. Israeli adults (N = 4,325) from 2 previous studies were examined for the presence of clinical and subclinical SPD. Individuals with clinical SPD (n = 150) vs subclinical SPD (n = 219) were compared on skin-picking characteristics, psychological phenomena, and clinical correlates. There were many similarities between clinical and subclinical skin pickers. Individuals with clinical SPD, however, had more severe skin picking, greater associated functional impairment, greater perceived stress, and greater depressive and obsessive-compulsive symptoms, and were also more likely to have a first-degree relative with SPD. This study suggests that although there are some similarities between clinical and subclinical SPD, there also are distinct differences in the clinical presentation. Understanding these differences may be an important factor in treatment and prevention planning.

  7. Laboratory testing and assessment of the Pickering PRD supporting frame

    International Nuclear Information System (INIS)

    Ghobarah, A.

    1995-05-01

    The objective of this study was to design and test reinforced concrete beam-column subassemblages representing the beam, column and joint of the Centre Pier (CP) support of the Pressure Relief Duct (PRD) at the Pickering A Nuclear Generating Station. The testing program was expected to establish the failure mode of the subassemblage and to compare the performance of the existing CP with a specimen detailed in accordance with current code provisions. A one-third scale specimen of the beam-column subassemblage was designed and tested to failure when subjected to simulated seismic loads. A second specimen was constructed with shear reinforcement that was detailed according to the provisions of the CAN3-N287.3-M82 code. The second specimen was tested in the same manner as the first specimen. From the experimental data on the behaviour and mode of failure of the specimens, analytical evaluations were conducted to determine the inelastic nonlinear behaviour of the CP structural system when subjected to various levels of ground motion. (author). 11 refs., 3 tabs., 40 figs

  8. Water-in-oil Pickering emulsions stabilized by stearoylated microcrystalline cellulose.

    Science.gov (United States)

    Pang, Bo; Liu, Huan; Liu, Peiwen; Peng, Xinwen; Zhang, Kai

    2018-03-01

    Hydrophobic particles with static water contact angles larger than 90° are more like to stabilize W/O Pickering emulsions. In particular, high internal phase Pickering emulsions (HIPEs) are of great interest for diverse applications. However, W/O HIPEs have rarely been realized using sustainable biopolymers. Herein, we used stearoylated microcrystalline cellulose (SMCC) to stabilize W/O Pickering emulsions and especially, W/O HIPEs. Moreover, these W/O HIPEs can be further used as platforms for the preparation of porous materials, such as porous foams. Stearoylated microcrystalline cellulose (SMCC) was prepared by modifying MCC with stearoyl chloride under heterogeneous conditions. Using SMCC as emulsifiers, W/O medium and high internal phase Pickering emulsions (MIPEs and HIPEs) with various organic solvents as continuous phases were prepared using one-step and two-step methods, respectively. Polystyrene (PS) foams were prepared after polymerization of oil phase using HIPEs as templates and their oil/water separation capacity were studied. SMCC could efficiently stabilize W/O Pickering emulsions and HIPEs could only be prepared via the two-step method. The internal phase volume fraction of the SMCC-stabilized HIPEs reached as high as 89%. Diverse internal phase volume fractions led to distinct inner structures of foams with closed or open cells. These macroporous polystyrene (PS) foams demonstrated great potential for the effective absorption of organic solvents from underwater. Copyright © 2017 Elsevier Inc. All rights reserved.

  9. DeepPicker: A deep learning approach for fully automated particle picking in cryo-EM.

    Science.gov (United States)

    Wang, Feng; Gong, Huichao; Liu, Gaochao; Li, Meijing; Yan, Chuangye; Xia, Tian; Li, Xueming; Zeng, Jianyang

    2016-09-01

    Particle picking is a time-consuming step in single-particle analysis and often requires significant interventions from users, which has become a bottleneck for future automated electron cryo-microscopy (cryo-EM). Here we report a deep learning framework, called DeepPicker, to address this problem and fill the current gaps toward a fully automated cryo-EM pipeline. DeepPicker employs a novel cross-molecule training strategy to capture common features of particles from previously-analyzed micrographs, and thus does not require any human intervention during particle picking. Tests on the recently-published cryo-EM data of three complexes have demonstrated that our deep learning based scheme can successfully accomplish the human-level particle picking process and identify a sufficient number of particles that are comparable to those picked manually by human experts. These results indicate that DeepPicker can provide a practically useful tool to significantly reduce the time and manual effort spent in single-particle analysis and thus greatly facilitate high-resolution cryo-EM structure determination. DeepPicker is released as an open-source program, which can be downloaded from https://github.com/nejyeah/DeepPicker-python. Copyright © 2016 Elsevier Inc. All rights reserved.

  10. Estimating the possible range of recycling rates achieved by dump waste pickers: The case of Bantar Gebang in Indonesia.

    Science.gov (United States)

    Sasaki, Shunsuke; Araki, Tetsuya

    2014-06-01

    This article presents informal recycling contributions made by scavengers in the surrounding area of Bantar Gebang final disposal site for municipal solid waste generated in Jakarta. Preliminary fieldwork was conducted through daily conversations with scavengers to identify recycling actors at the site, and then quantitative field surveys were conducted twice. The first survey (n = 504 households) covered 33% of all households in the area, and the second survey (n = 69 households) was conducted to quantify transactions of recyclables among scavengers. Mathematical equations were formulated with assumptions made to estimate the possible range of recycling rates achieved by dump waste pickers. Slightly over 60% of all respondents were involved in informal recycling and over 80% of heads of households were waste pickers, normally referred to as live-in waste pickers and live-out waste pickers at the site. The largest percentage of their spouses were family workers, followed by waste pickers and housewives. Over 95% of all households of respondents had at least one waste picker or one small boss who has a coequal status of a waste picker. Average weight of recyclables collected by waste pickers at the site was estimated to be approximately 100 kg day(-1) per household on the net weight basis. The recycling rate of solid wastes collected by all scavengers at the site was estimated to be in the range of 2.8-7.5% of all solid wastes transported to the site. © The Author(s) 2014.

  11. Fragger: a protein fragment picker for structural queries [version 2; referees: 2 approved

    Directory of Open Access Journals (Sweden)

    Francois Berenger

    2018-04-01

    Full Text Available Protein modeling and design activities often require querying the Protein Data Bank (PDB with a structural fragment, possibly containing gaps. For some applications, it is preferable to work on a specific subset of the PDB or with unpublished structures. These requirements, along with specific user needs, motivated the creation of a new software to manage and query 3D protein fragments. Fragger is a protein fragment picker that allows protein fragment databases to be created and queried. All fragment lengths are supported and any set of PDB files can be used to create a database. Fragger can efficiently search a fragment database with a query fragment and a distance threshold. Matching fragments are ranked by distance to the query. The query fragment can have structural gaps and the allowed amino acid sequences matching a query can be constrained via a regular expression of one-letter amino acid codes. Fragger also incorporates a tool to compute the backbone RMSD of one versus many fragments in high throughput. Fragger should be useful for protein design, loop grafting and related structural bioinformatics tasks.

  12. Tailoring the Wettability of Colloidal Particles for Pickering Emulsions via Surface Modification and Roughness

    Directory of Open Access Journals (Sweden)

    Meina Xiao

    2018-06-01

    Full Text Available Pickering emulsions are water or oil droplets that are stabilized by colloidal particles and have been intensely studied since the late 90s. The surfactant-free nature of these emulsions has little adverse effects such as irritancy and contamination of environment and typically exhibit enhanced stability compared to surfactant-stabilized emulsions. Therefore, they offer promising applications in cosmetics, food science, controlled release, and the manufacturing of microcapsules and porous materials. The wettability of the colloidal particles is the main parameter determining the formation and stability of Pickering emulsions. Tailoring the wettability by surface chemistry or surface roughness offers considerable scope for the design of a variety of hybrid nanoparticles that may serve as novel efficient Pickering emulsion stabilizers. In this review, we will discuss the recent advances in the development of surface modification of nanoparticles.

  13. The One-Step Pickering Emulsion Polymerization Route for Synthesizing Organic-Inorganic Nanocomposite Particles

    Directory of Open Access Journals (Sweden)

    Kaushal Rege

    2010-02-01

    Full Text Available Polystyrene-silica core-shell nanocomposite particles are successfully prepared via one-step Pickering emulsion polymerization. Possible mechanisms of Pickering emulsion polymerization are addressed in the synthesis of polystyrene-silica nanocomposite particles using 2,2-azobis(2-methyl-N-(2-hydroxyethylpropionamide (VA-086 and potassium persulfate (KPS as the initiator. Motivated by potential applications of “smart” composite particles in controlled drug delivery, the one-step Pickering emulsion polymerization route is further applied to synthesize polystyrene/poly(N-isopropylacrylamide (PNIPAAm-silica core-shell nanoparticles with N-isopropylacrylamide incorporated into the core as a co-monomer. The polystyrene/PNIPAAm-silica composite nanoparticles are temperature sensitive and can be taken up by human prostate cancer (PC3-PSMA cells.

  14. Pickering interfacial catalysis for biphasic systems: from emulsion design to green reactions.

    Science.gov (United States)

    Pera-Titus, Marc; Leclercq, Loïc; Clacens, Jean-Marc; De Campo, Floryan; Nardello-Rataj, Véronique

    2015-02-09

    Pickering emulsions are surfactant-free dispersions of two immiscible fluids that are kinetically stabilized by colloidal particles. For ecological reasons, these systems have undergone a resurgence of interest to mitigate the use of synthetic surfactants and solvents. Moreover, the use of colloidal particles as stabilizers provides emulsions with original properties compared to surfactant-stabilized emulsions, microemulsions, and micellar systems. Despite these specific advantages, the application of Pickering emulsions to catalysis has been rarely explored. This Minireview describes very recent examples of hybrid and composite amphiphilic materials for the design of interfacial catalysts in Pickering emulsions with special emphasis on their assets and challenges for industrially relevant biphasic reactions in fine chemistry, biofuel upgrading, and depollution. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. Current Opportunities and Challenges of Next Generation Sequencing (NGS) of DNA; Determining Health and Diseases

    NARCIS (Netherlands)

    Robert, Vincent Albert Romain Ghislain

    2016-01-01

    Many publications have demonstrated the huge potential of NGS methods in terms of new species discovery, environment monitoring, ecological studies, etc. [24,35,92,97,103]. Undoubtedly, NGS will become one the major tools for species identification and for routine diagnostic use. While read lengths

  16. Promises and pitfalls of NGS technology in Clinic: Experience from Kolkata

    Directory of Open Access Journals (Sweden)

    Atanu Kumar Dutta

    2017-12-01

    With the help of a series of cases the utility of NGS testing and different flavors of the technology will be outlined. Specifically in the prenatal diagnostic setting dilemma related to testing and not testing will be outlined. The absence of customized CNV assays complimenting the NGS panel will be highlighted.

  17. Evolution of the Darlington NGS fuel handling computer systems

    International Nuclear Information System (INIS)

    Leung, V.; Crouse, B.

    1996-01-01

    The ability to improve the capabilities and reliability of digital control systems in nuclear power stations to meet changing plant and personnel requirements is a formidable challenge. Many of these systems have high quality assurance standards that must be met to ensure adequate nuclear safety. Also many of these systems contain obsolete hardware along with software that is not easily transported to newer technology computer equipment. Combining modern technology upgrades into a system of obsolete hardware components is not an easy task. Lastly, as users become more accustomed to using modern technology computer systems in other areas of the station (e.g. information systems), their expectations of the capabilities of the plant systems increase. This paper will present three areas of the Darlington NGS fuel handling computer system that have been or are in the process of being upgraded to current technology components within the framework of an existing fuel handling control system. (author). 3 figs

  18. Evolution of the Darlington NGS fuel handling computer systems

    Energy Technology Data Exchange (ETDEWEB)

    Leung, V; Crouse, B [Ontario Hydro, Bowmanville (Canada). Darlington Nuclear Generating Station

    1997-12-31

    The ability to improve the capabilities and reliability of digital control systems in nuclear power stations to meet changing plant and personnel requirements is a formidable challenge. Many of these systems have high quality assurance standards that must be met to ensure adequate nuclear safety. Also many of these systems contain obsolete hardware along with software that is not easily transported to newer technology computer equipment. Combining modern technology upgrades into a system of obsolete hardware components is not an easy task. Lastly, as users become more accustomed to using modern technology computer systems in other areas of the station (e.g. information systems), their expectations of the capabilities of the plant systems increase. This paper will present three areas of the Darlington NGS fuel handling computer system that have been or are in the process of being upgraded to current technology components within the framework of an existing fuel handling control system. (author). 3 figs.

  19. Multi-Unit Aspects of the Pickering Generating Station

    Energy Technology Data Exchange (ETDEWEB)

    Morison, W. G. [Atomic Energy of Canada Ltd, Sheridan Park, ON (Canada)

    1968-04-15

    The Pickering nuclear generating station is located on the north shore of Lake Ontario, about 20 miles east of the city of Toronto, Canada. The station has been planned and laid out on an eight-unit station, four units of which have now been authorized for construction. Each of these four units consists of a single heavy-water moderated and cooled CANDU-type reactor and auxiliaries coupled to a single tandem compound turbine generator with a net output of approximately 500 MW(e). The units are identical and are scheduled to come into operation at intervals of one year from 1970 to 1973. The station has been planned with central facilities for: administration maintenance laboratories, stores, change rooms, decontamination and waste management services. A common control centre, cooling water intake and discharge system, and spent fuel storage bay for four units has been arranged. A feature of the multi-unit station is a common containment system. Cost savings in building a number of identical units on the same site result from a single exclusion area, shared engineering costs, equipment purchase contracts for four identical components, and efficient use of construction plant. Operating cost savings are anticipated in the use of a common operating and maintenance staff and spare parts inventory. The plant has been arranged to minimize problems of operating, commissioning and constructing units at the same time on the same site. The layout and construction sequence have been arranged so that the first unit can be commissioned and operated with little or no interference from the construction forces working on succeeding units. During the construction phase barriers will be erected in the common control centre between operating control equipment and that being installed. Operations and construction personnel will enter the plant by separate routes and work in areas separated by physical barriers. (author)

  20. Modulation of Cyclodextrin Particle Amphiphilic Properties to Stabilize Pickering Emulsion.

    Science.gov (United States)

    Xi, Yongkang; Luo, Zhigang; Lu, Xuanxuan; Peng, Xichun

    2018-01-10

    Cyclodextrins have been proven to form complexes with linear oil molecules and stabilize emulsions. Amphiphilic properties of cyclodextrin particles were modulated through esterification reaction between β-cyclodextrin (β-CD) and octadecenyl succinic anhydride (ODSA) under alkaline conditions. ODS-β-CD particles with degree of substitution (DS) of 0.003, 0.011, and 0.019 were obtained. The introduced hydrophobic long chain that was linked within β-CD cavity led to the change of ODS-β-CD in terms of morphological structure, surface charge density, size, and contact angle, upon which the properties and stability of the emulsions stabilized by ODS-β-CD were highly dependent. The average diameter of ODS-β-CD particles ranged from 449 to 1484 nm. With the DS increased from 0.003 to 0.019, the contact angle and absolute zeta potential value of these ODS-β-CD particles improved from 25.7° to 47.3° and 48.1 to 62.8 mV, respectively. The cage structure of β-CD crystals was transformed to channel structure, then further to amorphous structure after introduction of the octadecenyl succinylation chain. ODS-β-CD particles exhibited higher emulsifying ability compared to β-CD. The resulting Pickering emulsions formed by ODS-β-CD particles were more stable during storage. This study investigates the ability of these ODS-β-CD particles to stabilize oil-in-water emulsions with respect to their amphiphilic character and structural properties.

  1. Aquivion Perfluorosulfonic Superacid as an Efficient Pickering Interfacial Catalyst for the Hydrolysis of Triglycerides.

    Science.gov (United States)

    Shi, Hui; Fan, Zhaoyu; Hong, Bing; Pera-Titus, Marc

    2017-09-11

    Rational design of the surface properties of heterogeneous catalysts can boost the interfacial activity in biphasic reactions through the generation of Pickering emulsions. This concept, termed Pickering interfacial catalysis (PIC), has shown promising credentials in acid-catalyzed transesterification, ester hydrolysis, acetalization, etherification, and alkylation reactions. PIC has now been applied to the efficient, solvent-free hydrolysis of the triglyceride glyceryl trilaurate to lauric acid, catalyzed by Aquivion perfluorosulfonic superacid at mild conditions (100 °C and ambient pressure). © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  2. Bruce used fuel dry storage project evolution from Pickering to Bruce

    International Nuclear Information System (INIS)

    Young, R.E.

    1996-01-01

    Additional fuel storage capacity is required at Bruce Nuclear Generating Station, which otherwise would soon fill up all its pool storage capacity. The recommended option was to use a dry storage container similar to that at Pickering. The changes made to the Pickering type of container included: fuel to be stored in trays; the container's capacity increased to 600 bundles; the container's lid to be changed to a metal one; the single concrete lid to be changed to a double metal lid system; the container not to be transportable; the container would be dry-loaded. 7 figs

  3. Bruce used fuel dry storage project evolution from Pickering to Bruce

    Energy Technology Data Exchange (ETDEWEB)

    Young, R E [Ontario Hydro, Tiverton, ON (Canada). Bruce Nuclear Generating Station-A

    1997-12-31

    Additional fuel storage capacity is required at Bruce Nuclear Generating Station, which otherwise would soon fill up all its pool storage capacity. The recommended option was to use a dry storage container similar to that at Pickering. The changes made to the Pickering type of container included: fuel to be stored in trays; the container`s capacity increased to 600 bundles; the container`s lid to be changed to a metal one; the single concrete lid to be changed to a double metal lid system; the container not to be transportable; the container would be dry-loaded. 7 figs.

  4. Fast admixture analysis and population tree estimation for SNP and NGS data

    DEFF Research Database (Denmark)

    Cheng, Jade Yu; Mailund, Thomas; Nielsen, Rasmus

    2017-01-01

    assumption for identifying ancestry components correctly and for inferring the correct tree. In most cases, ancestry components are inferred correctly, although sample sizes and times since admixture can influence the results. We show that the popular Gaussian approximation tends to perform poorly under......-calling associated with Next Generation Sequencing (NGS) data. We also present a new method for estimating population trees from ancestry components using a Gaussian approximation. Using coalescence simulations of diverging populations, we explore the adequacy of the STRUCTURE-style models and the Gaussian...... extreme divergence scenarios e.g. with very long branch lengths, but the topologies of the population trees are accurately inferred in all scenarios explored. The new methods are implemented together with appropriate visualization tools in the software package Ohana....

  5. Synthesis of Covalently Cross-Linked Colloidosomes from Peroxidized Pickering Emulsions

    Directory of Open Access Journals (Sweden)

    Nadiya Popadyuk

    2016-10-01

    Full Text Available A new approach to the formation of cross-linked colloidosomes was developed on the basis of Pickering emulsions that were stabilized exclusively by peroxidized colloidal particles. Free radical polymerization and a soft template technique were used to convert droplets of a Pickering emulsion into colloidosomes. The peroxidized latex particles were synthesized in the emulsion polymerization process using amphiphilic polyperoxide copolymers poly(2-tert-butylperoxy-2-methyl-5-hexen-3-ine-co-maleic acid (PM-1-MAc or poly[N-(tert-butylperoxymethylacrylamide]-co-maleic acid (PM-2-MAc, which were applied as both initiators and surfactants (inisurfs. The polymerization in the presence of the inisurfs results in latexes with a controllable amount of peroxide and carboxyl groups at the particle surface. Peroxidized polystyrene latex particles with a covalently grafted layer of inisurf PM-1-MAc or PM-2-MAc were used as Pickering stabilizers to form Pickering emulsions. A mixture of styrene and/or butyl acrylate with divinylbenzene and hexadecane was applied as a template for the synthesis of colloidosomes. Peroxidized latex particles located at the interface are involved in the radical reactions of colloidosomes formation. As a result, covalently cross-linked colloidosomes were obtained. It was demonstrated that the structure of the synthesized (using peroxidized latex particles colloidosomes depends on the amount of functional groups and pH during the synthesis. Therefore, the size and morphology of colloidosomes can be controlled by latex particle surface properties.

  6. Pickering emulsions stabilized by whey protein nanoparticles prepared by thermal cross-linking

    NARCIS (Netherlands)

    Wu, Jiande; Shi, Mengxuan; Li, Wei; Zhao, Luhai; Wang, Ze; Yan, Xinzhong; Norde, Willem; Li, Yuan

    2015-01-01

    A Pickering (o/w) emulsion was formed and stabilized by whey protein isolate nanoparticles (WPI NPs). Those WPI NPs were prepared by thermal cross-linking of denatured WPI proteins within w/o emulsion droplets at 80. °C for 15. min. During heating of w/o emulsions containing 10% (w/v) WPI

  7. Novel carboxymethyl cellulose-polyvinyl alcohol blend films stabilized by Pickering emulsion incorporation method.

    Science.gov (United States)

    Fasihi, Hadi; Fazilati, Mohammad; Hashemi, Mahdi; Noshirvani, Nooshin

    2017-07-01

    The aim of this study was to investigate the possibility of increasing the antimicrobial and antioxidant properties of biodegradable active films stabilized via Pickering emulsions. The blend films were prepared from carboxymethyl cellulose (CMC) and polyvinyl alcohol (PVA), emulsified with oleic acid (OL) and incorporated with rosemary essential oil (REO). Formation of Pickering emulsion was confirmed by scanning electron microscopy (SEM), optical microscopy, mean droplet size and emulsion stability. Morphological, optical, physical, mechanical, thermal, antifungal and antioxidant properties of the films incorporated with different concentrations of REO (0.5, 1.5 and 3%) were determined. The results showed an increase in UV absorbance and elongation at break but, a decrease in tensile strength and thermal stability of the films. Interestingly, films containing REO exhibited considerable antioxidant and antimicrobial properties. In vitro microbial tests exhibited 100% fungal inhibition against Penicillium digitatum in the films containing 3% REO. In addition, no fungal growth were observed after 60days of storage at 25°C in bread slices were stored with active films incorporated with 3% REO, could attributed to the slow and regular release of REO caused by Pickering emulsions. The results of this study suggest that Pickering emulsion is a very promising method, which significantly affects antioxidant and antimicrobial activities of the films. Copyright © 2017 Elsevier Ltd. All rights reserved.

  8. Women cotton pickers perceptions about health hazards due to pesticide use in irrigated punjab

    International Nuclear Information System (INIS)

    Abbas, M.; Mehmood, I.; Bashir, A.; Hassan, S.

    2015-01-01

    In Pakistan, cotton crop has special importance from the perspective of largest employment generation both for males and females in the production and value chains. Cotton picking is primarily a female specific activity in all cropping zones of Pakistan. Women cotton pickers mostly belong to poor rural society involved in this labour force to feed their families. Cotton pickers in Pakistan face some serious health related problems due to heavy use of pesticides on cotton crop. The present study was designed to investigate the problem faced by women cotton pickers and their role in household decision making. Overall 150 women cotton pickers were interviewed from Bahawalnagar, Sahiwal and Vehari districts of cotton-wheat zone of the Punjab. Summary statistics of women cotton pickers' showed mean average age was 33 years and had 2.4 ears of formal schooling and 10 years of cotton picking experience. The main reasons for cotton picking reported were to reduce family financial burden (30%) followed by better access to food and resource (23%) and better education of children (21%). Majority of the respondents (97.33%) reported that the mode of payments of cotton picking was in cash and the most of the respondents (83.70%) reported that they got wages in time. Only few respondents (8.70%) were aware of health hazards due to pesticides and only 10% women wear protective clothes during cotton picking. Majority of the respondents (76%) wash their clothes after cotton picking whereas almost all the respondents wash their hand after cotton picking. The women cotton pickers faced health problem, tiredness (54.5%), mental disturbance (9.90%) and fatigue (8.00%). More than 58% women reported their involvement in household decision making regarding food and groceries while 30.6% women involved in decision about education of children. It is suggested that the female cotton pickers should be educated about the importance (in terms of disease treatment and long-run health costs

  9. Fabrication of CMC-g-PAM Superporous Polymer Monoliths via Eco-Friendly Pickering-MIPEs for Superior Adsorption of Methyl Violet and Methylene Blue.

    Science.gov (United States)

    Wang, Feng; Zhu, Yongfeng; Wang, Wenbo; Zong, Li; Lu, Taotao; Wang, Aiqin

    2017-01-01

    A series of superporous carboxymethylcellulose- graft -poly(acrylamide)/palygorskite (CMC- g -PAM/Pal) polymer monoliths presenting interconnected pore structure and excellent adsorption properties were prepared by one-step free-radical grafting polymerization reaction of CMC and acrylamide (AM) in the oil-in-water (O/W) Pickering-medium internal phase emulsions (Pickering-MIPEs) composed of non-toxic edible oil as a dispersion phase and natural Pal nanorods as stabilizers. The effects of Pal dosage, AM dosage, and co-surfactant Tween-20 (T-20) on the pore structures of the monoliths were studied. It was revealed that the well-defined pores were formed when the dosages of Pal and T-20 are 9-14 and 3%, respectively. The porous monolith can rapidly adsorb 1,585 mg/g of methyl violet (MV) and 1,625 mg/g of methylene blue (MB). After the monolith was regenerated by adsorption-desorption process for five times, the adsorption capacities still reached 92.1% (for MV) and 93.5% (for MB) of the initial maximum adsorption capacities. The adsorption process was fitted with Langmuir adsorption isotherm model and pseudo-second-order adsorption kinetic model very well, which indicate that mono-layer chemical adsorption mainly contribute to the high-capacity adsorption for dyes. The superporous polymer monolith prepared from eco-friendly Pickering-MIPEs shows good adsorption capacity and fast adsorption rate, which is potential adsorbent for the decontamination of dye-containing wastewater.

  10. Fabrication of CMC-g-PAM Superporous Polymer Monoliths via Eco-Friendly Pickering-MIPEs for Superior Adsorption of Methyl Violet and Methylene Blue

    Directory of Open Access Journals (Sweden)

    Feng Wang

    2017-06-01

    Full Text Available A series of superporous carboxymethylcellulose-graft-poly(acrylamide/palygorskite (CMC-g-PAM/Pal polymer monoliths presenting interconnected pore structure and excellent adsorption properties were prepared by one-step free-radical grafting polymerization reaction of CMC and acrylamide (AM in the oil-in-water (O/W Pickering-medium internal phase emulsions (Pickering-MIPEs composed of non-toxic edible oil as a dispersion phase and natural Pal nanorods as stabilizers. The effects of Pal dosage, AM dosage, and co-surfactant Tween-20 (T-20 on the pore structures of the monoliths were studied. It was revealed that the well-defined pores were formed when the dosages of Pal and T-20 are 9–14 and 3%, respectively. The porous monolith can rapidly adsorb 1,585 mg/g of methyl violet (MV and 1,625 mg/g of methylene blue (MB. After the monolith was regenerated by adsorption-desorption process for five times, the adsorption capacities still reached 92.1% (for MV and 93.5% (for MB of the initial maximum adsorption capacities. The adsorption process was fitted with Langmuir adsorption isotherm model and pseudo-second-order adsorption kinetic model very well, which indicate that mono-layer chemical adsorption mainly contribute to the high-capacity adsorption for dyes. The superporous polymer monolith prepared from eco-friendly Pickering-MIPEs shows good adsorption capacity and fast adsorption rate, which is potential adsorbent for the decontamination of dye-containing wastewater.

  11. Preparation of Pickering emulsions through interfacial adsorption by soft cyclodextrin nanogels

    Directory of Open Access Journals (Sweden)

    Shintaro Kawano

    2015-11-01

    Full Text Available Background: Emulsions stabilized by colloidal particles are known as Pickering emulsions. To date, soft microgel particles as well as inorganic and organic particles have been utilized as Pickering emulsifiers. Although cyclodextrin (CD works as an attractive emulsion stabilizer through the formation of a CD–oil complex at the oil–water interface, a high concentration of CD is normally required. Our research focuses on an effective Pickering emulsifier based on a soft colloidal CD polymer (CD nanogel with a unique surface-active property.Results: CD nanogels were prepared by crosslinking heptakis(2,6-di-O-methyl-β-cyclodextrin with phenyl diisocyanate and subsequent immersion of the resulting polymer in water. A dynamic light scattering study shows that primary CD nanogels with 30–50 nm diameter assemble into larger CD nanogels with 120 nm diameter by an increase in the concentration of CD nanogel from 0.01 to 0.1 wt %. The CD nanogel has a surface-active property at the air–water interface, which reduces the surface tension of water. The CD nanogel works as an effective Pickering emulsion stabilizer even at a low concentration (0.1 wt %, forming stable oil-in-water emulsions through interfacial adsorption by the CD nanogels.Conclusion: Soft CD nanogel particles adsorb at the oil–water interface with an effective coverage by forming a strong interconnected network and form a stable Pickering emulsion. The adsorption property of CD nanogels on the droplet surface has great potential to become new microcapsule building blocks with porous surfaces. These microcapsules may act as stimuli-responsive nanocarriers and nanocontainers.

  12. 2015 NOAA NGS Topobathy Lidar DEM: Buzzards Bay Block3 (MA)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — These data were collected and derived by the National Oceanic Atmospheric Administration, National Geodetic Survey (NGS) Remote Sensing Division using a Riegl VQ820G...

  13. Selective separation of lambdacyhalothrin by porous/magnetic molecularly imprinted polymers prepared by Pickering emulsion polymerization.

    Science.gov (United States)

    Hang, Hui; Li, Chunxiang; Pan, Jianming; Li, Linzi; Dai, Jiangdong; Dai, Xiaohui; Yu, Ping; Feng, Yonghai

    2013-10-01

    Porous/magnetic molecularly imprinted polymers (PM-MIPs) were prepared by Pickering emulsion polymerization. The reaction was carried out in an oil/water emulsion using magnetic halloysite nanotubes as the stabilizer instead of a toxic surfactant. In the oil phase, the imprinting process was conducted by radical polymerization of functional and cross-linked monomers, and porogen chloroform generated steam under the high reaction temperature, which resulted in some pores decorated with easily accessible molecular binding sites within the as-made PM-MIPs. The characterization demonstrated that the PM-MIPs were porous and magnetic inorganic-polymer composite microparticles with magnetic sensitivity (M(s) = 0.7448 emu/g), thermal stability (below 473 K) and magnetic stability (over the pH range of 2.0-8.0). The PM-MIPs were used as a sorbent for the selective binding of lambdacyhalothrin (LC) and rapidly separated under an external magnetic field. The Freundlich isotherm model gave a good fit to the experimental data. The adsorption kinetics of the PM-MIPs was well described by pseudo-second-order kinetics, indicating that the chemical process could be the rate-limiting step in the adsorption of LC. The selective recognition experiments exhibited the outstanding selective adsorption effect of the PM-MIPs for target LC. Moreover, the PM-MIPs regeneration without significant loss in adsorption capacity was demonstrated by at least four repeated cycles. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  14. Status of NGS CORS Network and Its Contribution to the GGOS Infrastructure

    Science.gov (United States)

    Choi, K. K.; Haw, D.; Sun, L.

    2017-12-01

    Recent advancement of Satellite Geodesy techniques can now contribute to the global frame realization needed to improve worldwide accuracies. These techniques rely on coordinates computed using continuously observed GPS data and corresponding satellite orbits. The GPS-based reference system continues to depend on the physical stability of a ground-based network of points as the primary foundation for these observations. NOAA's National Geodetic Survey (NGS) has been operating Continuously Operating Reference Stations (CORS) to provide direct access to the National Spatial Reference System (NSRS). By virtue of NGS' scientific reputation and leadership in national and international geospatial issues, NGS has determined to increase its participation in the maintenance of the U.S. component of the global GPS tracking network in order to realize a long-term stable national terrestrial reference frame. NGS can do so by leveraging its national leadership role coupled with NGS' scientific expertise, in designating and upgrading a subset of the current tracking network for this purpose. This subset of stations must have the highest operational standards to serve the dual functions: being the U.S. contribution to the international frame, along with providing the link to the national datum. These stations deserve special attention to ensure that the highest possible levels of quality and stability are maintained. To meet this need, NGS is working with the international scientific groups to add and designate these reference stations based on scientific merit such as: colocation with other geodetic techniques, geographic area, and monumentation stability.

  15. A Study of Micro Finance: Special Reference to Female Waste Pickers in Pimpri Chinchwad Area in Pune

    OpenAIRE

    Hebalkar, Dr. Rashmi; Sharma, Meena Sunildutt

    2013-01-01

    Female waste pickers are the neglected section of urban women who are struggling to make ends meet, in an occupation which is hazardous for health, and are contributing to the welfare of society, without realizing it, through collecting waste and sending it forward for recycling. These women may be poorly educated but at least some of them have been unionized and their union attempts to improve their condition. Despite the existence of KKPKP union, there are female waste pickers who have not ...

  16. The interaction between popular economy, social movements and public policies: A case study of the waste pickers' movement

    OpenAIRE

    van Zeeland, Angelique J.W.M.

    2014-01-01

    This paper examines the challenges of expansion and sustainability of Social and Solidarity Economy (SSE). It focuses on the interaction between popular economy and SSE, and stresses the importance of collective action and public policies to enable the transition from the informal economy toward SSE. The main focus is on the waste pickers' movement. Experiences from Latin America, Asia and Africa show the possibilities of incorporating a significant contingent of informal waste pickers in sol...

  17. Pulse picker for synchrotron radiation driven by a surface acoustic wave.

    Science.gov (United States)

    Vadilonga, Simone; Zizak, Ivo; Roshchupkin, Dmitry; Petsiuk, Andrei; Dolbnya, Igor; Sawhney, Kawal; Erko, Alexei

    2017-05-15

    A functional test for a pulse picker for synchrotron radiation was performed at Diamond Light Source. The purpose of a pulse picker is to select which pulse from the synchrotron hybrid-mode bunch pattern reaches the experiment. In the present work, the Bragg reflection on a Si/B4C multilayer was modified using surface acoustic wave (SAW) trains. Diffraction on the SAW alters the direction of the x rays and it can be used to modulate the intensity of the x rays that reach the experimental chamber. Using electronic modulation of the SAW amplitude, it is possible to obtain different scattering conditions for different x-ray pulses. To isolate the single bunch, the state of the SAW must be changed in the short time gap between the pulses. To achieve the necessary time resolution, the measurements have been performed in conical diffraction geometry. The achieved time resolution was 120 ns.

  18. Retrofit of AECL CAN6 seals into the Pickering shutdown cooling pumps

    International Nuclear Information System (INIS)

    Rhodes, D.; Metcalfe, R.; Brown, G.

    1997-01-01

    The existing mechanical seals in the shutdown cooling (SDC) pumps at the eight-unit Pickering Nuclear Generating Station have caused as least seven forced outages in the last fifteen years. The SDC pumps were originally intended to run only during shutdowns, mostly at low pressure, except for short periods during routine testing of SDC isolation valves while the plant is operating at full pressure to verify that the emergency core injection system is available. Unfortunately, in practice, some SDC pumps must be run much more frequently than this to prevent overheating or freezing of components in the system while the plant is at power. This more severe service has decreased seal lifetime from about 8000 running hours to about 3000 running hours. Rather than tackling the difficult task of eliminating on-power running of the pumps, Pickering decided to install a more robust seal design that could withstand this. Through the process of competitive tender, AECL's CAN6 seal was chosen. This seal has a successful history in similarly demanding conditions in boiling water reactors in the USA. To supplement this and demonstrate there would be no 'surprises,' a 2000-hour test program was conducted. Testing consisted of simulating all the expected conditions, plus some special tests under abnormal conditions. This has given assurance that the seal will operate reliably in the Pickering shutdown cooling pumps. (author)

  19. Some engineering aspects of the investigation into the cracking of pressure tubes in the Pickering reactors

    International Nuclear Information System (INIS)

    Ross-Ross, P.A.; Towgood, G.R.; Hunter, T.A.

    1976-01-01

    In August 1974, Pickering Unit 3 (514 MWe) was shutdown for a period of 8 months because of cracks in 17 of the 390 pressure tubes. The cracks were a result of incorrect installation procedures during construction. Improper positioning of the rolling tool used to join the Zr-2.5 wt% Nb pressure tube to the end fitting produced very high residual tensile stresses. High stresses in combination with periods with the tubes cold caused the cracking. Crack propagation was by fracture of hydrides which are brittle when cold. Subsequent investigation confirmed that properly rolled joints are not susceptible to such cracking. The resources of Canadian industry, Ontario Hydro and Atomic Energy of Canada were coordinated to find engineering solutions to the crack program. The defective tubes were removed from reactor, thoroughly examined to identify the cause of the cracks, and thoroughly tested to prove safety. Non-destructive techniques were quickly adopted for inspection of tubes in Pickering. Tools and procedures for retubing the 17 channels were prepared and Pickering Unit 3 was returned to service at the end of March 1975. (author)

  20. Retrofit of AECL CAN6 seals into the Pickering shutdown cooling pumps

    International Nuclear Information System (INIS)

    Rhodes, D.; Metcalfe, R.; Brown, G.; Kiameh, P.; Burchett, P.

    1997-01-01

    The existing mechanical seals in the shutdown cooling (SDC) pumps at the eight-unit Pickering Nuclear Generating Station have caused at least seven forced outages in the last fifteen years. The SDC pumps were originally intended to run only during shutdowns, mostly at low pressure, except for short periods during routine testing of SDC isolation valves while the plant is operating at full pressure to verify that the emergency core injection system is available. Unfortunately, in practice, some SDC pumps must be run much more frequently than this to prevent overheating or freezing of components in the system while the plant is at power. This more severe service has decreased seal lifetime from about 8000 running hours to about 3000 running hours. Rather than tackling the difficult task of eliminating on-power running of the pumps, Pickering decided to install a more robust seal design that could withstand this. Through the process of competitive tender, AECL's CAN6 seal was chosen. This seal has a successful history in similarly demanding conditions in boiling water reactors in the USA. To supplement this and demonstrate there would be no 'surprises,' a 2000-hour test program was conducted. Testing consisted of simulating all the expected conditions, plus some special tests under abnormal conditions. This has given assurance that the seal will operate reliably in the Pickering shutdown cooling pumps. (author)

  1. QuickNGS elevates Next-Generation Sequencing data analysis to a new level of automation.

    Science.gov (United States)

    Wagle, Prerana; Nikolić, Miloš; Frommolt, Peter

    2015-07-01

    Next-Generation Sequencing (NGS) has emerged as a widely used tool in molecular biology. While time and cost for the sequencing itself are decreasing, the analysis of the massive amounts of data remains challenging. Since multiple algorithmic approaches for the basic data analysis have been developed, there is now an increasing need to efficiently use these tools to obtain results in reasonable time. We have developed QuickNGS, a new workflow system for laboratories with the need to analyze data from multiple NGS projects at a time. QuickNGS takes advantage of parallel computing resources, a comprehensive back-end database, and a careful selection of previously published algorithmic approaches to build fully automated data analysis workflows. We demonstrate the efficiency of our new software by a comprehensive analysis of 10 RNA-Seq samples which we can finish in only a few minutes of hands-on time. The approach we have taken is suitable to process even much larger numbers of samples and multiple projects at a time. Our approach considerably reduces the barriers that still limit the usability of the powerful NGS technology and finally decreases the time to be spent before proceeding to further downstream analysis and interpretation of the data.

  2. A Fast Solution to NGS Library Prep with Low Nanogram DNA Input

    Science.gov (United States)

    Liu, Pingfang; Lohman, Gregory J.S.; Cantor, Eric; Langhorst, Bradley W.; Yigit, Erbay; Apone, Lynne M.; Munafo, Daniela B.; Stewart, Fiona J.; Evans, Thomas C.; Nichols, Nicole; Dimalanta, Eileen T.; Davis, Theodore B.; Sumner, Christine

    2013-01-01

    Next Generation Sequencing (NGS) has significantly impacted human genetics, enabling a comprehensive characterization of the human genome as well as a better understanding of many genomic abnormalities. By delivering massive DNA sequences at unprecedented speed and cost, NGS promises to make personalized medicine a reality in the foreseeable future. To date, library construction with clinical samples has been a challenge, primarily due to the limited quantities of sample DNA available. Our objective here was to overcome this challenge by developing NEBNext® Ultra DNA Library Prep Kit, a fast library preparation method. Specifically, we streamlined the workflow utilizing novel NEBNext reagents and adaptors, including a new DNA polymerase that has been optimized to minimize GC bias. As a result of this work, we have developed a simple method for library construction from an amount of DNA as low as 5 ng, which can be used for both intact and fragmented DNA. Moreover, the workflow is compatible with multiple NGS platforms.

  3. Targeted NGS meets expert clinical characterization: Efficient diagnosis of spastic paraplegia type 11

    Directory of Open Access Journals (Sweden)

    Cristina Castro-Fernández

    2015-06-01

    Full Text Available Next generation sequencing (NGS is transforming the diagnostic approach for neurological disorders, since it allows simultaneous analysis of hundreds of genes, even based on just a broad, syndromic patient categorization. However, such an approach bears a high risk of incidental and uncertain genetic findings. We report a patient with spastic paraplegia whose comprehensive neurological and imaging examination raised a high clinical suspicion of SPG11. Thus, although our NGS pipeline for this group of disorders includes gene panel and exome sequencing, in this sample only the spatacsin gene region was captured and subsequently searched for mutations. Two probably pathogenic variants were quickly and clearly identified, confirming the diagnosis of SPG11. This case illustrates how combination of expert clinical characterization with highly oriented NGS protocols leads to a fast, cost-efficient diagnosis, minimizing the risk of findings with unclear significance.

  4. Tritium releases from the Pickering Nuclear Generating Station and birth defects and infant mortality in nearby communities 1971-1988

    International Nuclear Information System (INIS)

    Johnson, K.C.; Rouleau, J.

    1991-10-01

    This study was commissioned to examine whether there were elevated rates of stillbirth, birth defects, or death in the first year of life between 1971 and 1988 among offspring of residents of communities within a 25-kilometre radius of the Pickering Nuclear Generating Station. The study was also to investigate whether there were any statistical associations between the monthly airborne or waterborne tritium emissions from the Pickering Nuclear Generating Station and the rates of these reproductive outcomes. Overall analysis did not support a hypothesis of increased rates of stillbirths, neonatal mortality or infant mortality near the Pickering Nuclear Generating Station, or a hypothesis of increased birth prevalence of birth defects for 21 of 22 diagnostic categories. The prevalence of Down Syndrome was elevated in both Pickering and Ajax; however, there was no consistent pattern between tritium release levels and Down Syndrome prevalence, chance could not be ruled out for the associations between Down Syndrome and tritium releases or ground-monitored concentrations, the association was detected in an analysis where multiple testing was done which may turn up significant associations by change, and maternal residence at birth and early in pregnancy needs to be verified. The association between Down Syndrome and low-level radiation remains indeterminate when existing evidence from epidemiological studies is summed. The estimated radiation exposure from the nuclear plant for residents of Pickering and Ajax is lower by a factor of 100 than the normal natural background radiation. Further study is recommended. (21 tabs., 29 figs., 5 maps, 37 refs.)

  5. Study of the time effect on the strength of cell-cell adhesion force by a novel nano-picker

    Energy Technology Data Exchange (ETDEWEB)

    Shen, Yajing, E-mail: shen@robo.mein.naogya-u.ac.jp [Dept. of Micro-Nano Systems Engineering, Nagoya University, Nagoya 464-8603 (Japan); Nakajima, Masahiro [Center for Micro-Nano Mechatronics, Nagoya University, Nagoya 464-8603 (Japan); Kojima, Seiji; Homma, Michio [Division of Biological Science, Nagoya University, Nagoya 464-8603 (Japan); Fukuda, Toshio [Dept. of Micro-Nano Systems Engineering, Nagoya University, Nagoya 464-8603 (Japan); Center for Micro-Nano Mechatronics, Nagoya University, Nagoya 464-8603 (Japan)

    2011-06-03

    Highlights: {yields} A nano-picker is developed for single cell adhesion force measurement. {yields} The adhesion of picker-cell has no influence to the cell-cell measurement result. {yields} Cell-cell adhesion force has a rise at the first few minutes and then becomes constant. -- Abstract: Cell's adhesion is important to cell's interaction and activates. In this paper, a novel method for cell-cell adhesion force measurement was proposed by using a nano-picker. The effect of the contact time on the cell-cell adhesion force was studied. The nano-picker was fabricated from an atomic force microscopy (AFM) cantilever by nano fabrication technique. The cell-cell adhesion force was measured based on the deflection of the nano-picker beam. The result suggests that the adhesion force between cells increased with the increasing of contact time at the first few minutes. After that, the force became constant. This measurement methodology was based on the nanorobotic manipulation system inside an environmental scanning electron microscope. It can realize both the observation and manipulation of a single cell at nanoscale. The quantitative and precise cell-cell adhesion force result can be obtained by this method. It would help us to understand the single cell interaction with time and would benefit the research in medical and biological fields potentially.

  6. A Web-Hosted R Workflow to Simplify and Automate the Analysis of 16S NGS Data

    Science.gov (United States)

    Next-Generation Sequencing (NGS) produces large data sets that include tens-of-thousands of sequence reads per sample. For analysis of bacterial diversity, 16S NGS sequences are typically analyzed in a workflow that containing best-of-breed bioinformatics packages that may levera...

  7. Preparation of cellulose nanocrystals from asparagus (Asparagus officinalis L.) and their applications to palm oil/water Pickering emulsion.

    Science.gov (United States)

    Wang, Wenhang; Du, Guanhua; Li, Cong; Zhang, Hongjie; Long, Yunduo; Ni, Yonghao

    2016-10-20

    Nano cellulosic materials as promising emulsion stabilizers have attracted great interest in food industry. In this paper, five different sized cellulose nanocrystals (CNC) samples were prepared from stem of Asparagus officinalis L. using the same sulfuric acid hydrolysis conditions but different times (1.5, 2, 2.5, 3.0, and 3.5h). The sizes of these CNC ranged from 178.2 to 261.8nm, with their crystallinity of 72.4-77.2%. The CNC aqueous dispersions showed a typical shear thinning behavior. In a palm oil/water (30/70, v/v) model solution, stable Pickering emulsions were formed with the addition of CNC, and their sizes are in the range of 1-10μm based on the optical and confocal laser scanning microscopy (CLSM) observation. The CNC sample prepared at 3h hydrolysis time, showed a relative efficient emulsion capacity for palm oil droplets, among these CNCs. Other parameters including the CNC, salt, and casein concentrations on the emulsion stability were studied. Copyright © 2016 Elsevier Ltd. All rights reserved.

  8. Pickering emulsion: A novel template for microencapsulated phase change materials with polymer–silica hybrid shell

    International Nuclear Information System (INIS)

    Yin, Dezhong; Ma, Li; Liu, Jinjie; Zhang, Qiuyu

    2014-01-01

    MePCMs (microencapsulated phase change materials) with covalently bonded SiO 2 /polymer hybrid as shell were fabricated via Pickering emulsion polymerization stabilized solely by organically-modified SiO 2 particles. Morphology and core–shell structure of these microcapsules were observed by scanning electron microscopy (SEM). Thermal properties of microencapsulated 1-dodecanol were determined using DSC (differential scanning calorimetry) and TGA (thermal gravimetric analysis). The results indicate that mass ratio of St (styrene)/DVB (divinylbenzene)/dodecanol has great effect on the morphology, inner structure, microencapsulation efficiency and durability of resultant MePCMs. When ratio of St/DVB/dodecanol was 5/1/12, dodecanol content of as much as 62.8% is obtained and the utility efficiency of dodecanol reaches 94.2%. The prepared MePCMs present good durability and thermal reliability. 2.2% of core material leached away the microcapsule after suspended in water for 10 days and 5.8% of core material leached after 2000 accelerated thermal cycling. Our study demonstrated that Pickering emulsion polymerization is a simple and robust method for the preparation of MePCMs with polymer–inorganic hybrids as shell. - Highlights: • We fabricated MePCM via surfactant-free Pickering emulsion polymerization. • The shell of MePCM was composed of PS/SiO 2 organic–inorganic hybrids. • The phase change enthalpy of MePCM is 125.0 J g −1 and the utility efficiency of 1-dodecanol reached 94.2%. • Only 2.2% and 5.8% of core material lost after durability test and 2000 accelerated thermal cycling respectively

  9. KNIME4NGS: a comprehensive toolbox for next generation sequencing analysis.

    Science.gov (United States)

    Hastreiter, Maximilian; Jeske, Tim; Hoser, Jonathan; Kluge, Michael; Ahomaa, Kaarin; Friedl, Marie-Sophie; Kopetzky, Sebastian J; Quell, Jan-Dominik; Mewes, H Werner; Küffner, Robert

    2017-05-15

    Analysis of Next Generation Sequencing (NGS) data requires the processing of large datasets by chaining various tools with complex input and output formats. In order to automate data analysis, we propose to standardize NGS tasks into modular workflows. This simplifies reliable handling and processing of NGS data, and corresponding solutions become substantially more reproducible and easier to maintain. Here, we present a documented, linux-based, toolbox of 42 processing modules that are combined to construct workflows facilitating a variety of tasks such as DNAseq and RNAseq analysis. We also describe important technical extensions. The high throughput executor (HTE) helps to increase the reliability and to reduce manual interventions when processing complex datasets. We also provide a dedicated binary manager that assists users in obtaining the modules' executables and keeping them up to date. As basis for this actively developed toolbox we use the workflow management software KNIME. See http://ibisngs.github.io/knime4ngs for nodes and user manual (GPLv3 license). robert.kueffner@helmholtz-muenchen.de. Supplementary data are available at Bioinformatics online.

  10. Next Generation Sequencing Plus (NGS+) with Y-chromosomal Markers for Forensic Pedigree Searches.

    Science.gov (United States)

    Qian, Xiaoqin; Hou, Jiayi; Wang, Zheng; Ye, Yi; Lang, Min; Gao, Tianzhen; Liu, Jing; Hou, Yiping

    2017-09-12

    There is high demand for forensic pedigree searches with Y-chromosome short tandem repeat (Y-STR) profiling in large-scale crime investigations. However, when two Y-STR haplotypes have a few mismatched loci, it is difficult to determine if they are from the same male lineage because of the high mutation rate of Y-STRs. Here we design a new strategy to handle cases in which none of pedigree samples shares identical Y-STR haplotype. We combine next generation sequencing (NGS), capillary electrophoresis and pyrosequencing under the term 'NGS+' for typing Y-STRs and Y-chromosomal single nucleotide polymorphisms (Y-SNPs). The high-resolution Y-SNP haplogroup and Y-STR haplotype can be obtained with NGS+. We further developed a new data-driven decision rule, FSindex, for estimating the likelihood for each retrieved pedigree. Our approach enables positive identification of pedigree from mismatched Y-STR haplotypes. It is envisaged that NGS+ will revolutionize forensic pedigree searches, especially when the person of interest was not recorded in forensic DNA database.

  11. Pickering G.S. boiler repair: an example of planned maintenance

    International Nuclear Information System (INIS)

    Dalrymple, D.G.

    1976-04-01

    The first application of boiler repair tools and procedures is estimated to have yielded a four-fold return on the development investment. The need to develop such technology is a result of the environment in which boiler repairs must be made. As nuclear technology evolves and plants and components get bigger, equipment will increasingly have to be repaired in situ with minimum plant downtime and minimum exposure of repair personnel to radiation. This lecture traces development of the Pickering A boiler repair capability which is seen as an example of how utility and contractor should interact to anticipate and meet maintenance requirements. (author)

  12. The Vale of Pickering in the Mesolithic: uncovering the early post-glacial landscape

    Directory of Open Access Journals (Sweden)

    Tim Schadla-Hall

    2000-10-01

    Full Text Available Since 1954, when Grahame Clark published the results of his excavations at Star Carr in northeast Yorkshire, the site has been recognized as a key to understanding early Mesolithic huntergatherer settlement and subsistence in northwest Europe. In 1976, archaeological and palaeoenvironmental research in the area was resumed - since 1986 under the auspices of the Vale of Pickering Research Trust - and it is now possible to set Star Carr and nearby Mesolithic sites in the wider context of the early postglacial landscape.

  13. Next Generation Solvent (NGS): Development for Caustic-Side Solvent Extraction of Cesium

    Energy Technology Data Exchange (ETDEWEB)

    Moyer, Bruce A. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Birdwell, Jr, Joseph F. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Bonnesen, Peter V. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Bruffey, Stephanie H. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Delmau, Laetitia Helene [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Duncan, Nathan C. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Ensor, Dale [Tennessee Technological Univ., Cookeville, TN (United States); Hill, Talon G. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Lee, Denise L. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Rajbanshi, Arbin [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Roach, Benjamin D. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Szczygiel, Patricia L. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Sloop, Jr., Frederick V. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Stoner, Erica L. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Williams, Neil J. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

    2014-03-01

    This report summarizes the FY 2010 and 2011 accomplishments at Oak Ridge National Laboratory (ORNL) in developing the Next Generation Caustic-Side Solvent Extraction (NG-CSSX) process, referred to commonly as the Next Generation Solvent (NGS), under funding from the U.S. Department of Energy, Office of Environmental Management (DOE-EM), Office of Technology Innovation and Development. The primary product of this effort is a process solvent and preliminary flowsheet capable of meeting a target decontamination factor (DF) of 40,000 for worst-case Savannah River Site (SRS) waste with a concentration factor of 15 or higher in the 18-stage equipment configuration of the SRS Modular Caustic-Side Solvent Extraction Unit (MCU). In addition, the NG-CSSX process may be readily adapted for use in the SRS Salt Waste Processing Facility (SWPF) or in supplemental tank-waste treatment at Hanford upon appropriate solvent or flowsheet modifications. Efforts in FY 2010 focused on developing a solvent composition and process flowsheet for MCU implementation. In FY 2011 accomplishments at ORNL involved a wide array of chemical-development activities and testing up through single-stage hydraulic and mass-transfer tests in 5-cm centrifugal contactors. Under subcontract from ORNL, Argonne National Laboratory (ANL) designed a preliminary flowsheet using ORNL cesium distribution data, and Tennessee Technological University confirmed a chemical model for cesium distribution ratios (DCs) as a function of feed composition. Interlaboratory efforts were coordinated with complementary engineering tests carried out (and reported separately) by personnel at Savannah River National Laboratory (SRNL) and Savannah River Remediation (SRR) with helpful advice by Parsons Engineering and General Atomics on aspects of possible SWPF implementation.

  14. Review of Ontario Hydro Pickering 'A' and Bruce 'A' nuclear generating stations' accident analyses

    International Nuclear Information System (INIS)

    Serdula, K.J.

    1988-01-01

    Deterministic safety analysis for the Pickering 'A' and Bruce 'A' nuclear generating stations were reviewed. The methodology used in the evaluation and assessment was based on the concept of 'N' critical parameters defining an N-dimensional safety parameter space. The reviewed accident analyses were evaluated and assessed based on their demonstrated safety coverage for credible values and trajectories of the critical parameters within this N-dimensional safety parameter space. The reported assessment did not consider probability of occurrence of event. The reviewed analyses were extensive for potential occurrence of accidents under normal steady-state operating conditions. These analyses demonstrated an adequate assurance of safety for the analyzed conditions. However, even for these reactor conditions, items have been identified for consideration of review and/or further study, which would provide a greater assurance of safety in the event of an accident. Accident analyses based on a plant in a normal transient operating state or in an off-normal condition but within the allowable operating envelope are not as extensive. Improvements in demonstrations and/or justifications of safety upon potential occurrence of accidents would provide further assurance of adequacy of safety under these conditions. Some events under these conditions have not been analyzed because of their judged low probability; however, accident analyses in this area should be considered. Recommendations are presented relating to these items; it is also recommended that further study is needed of the Pickering 'A' special safety systems

  15. Uplifting : mobile cranes and picker trucks get higher, stronger, and safer

    Energy Technology Data Exchange (ETDEWEB)

    Budd, G.

    2008-10-15

    New crane and picker truck equipment designed for use in the oil and gas industry was discussed in this article. The longest crane in the North America is due to arrive in Calgary soon. Mobile cranes are often used for maintenance, construction, and shutdowns at natural gas plants, refineries, and oil batteries. Telescopic cranes are also used to service pump jacks and lift rolls of coiled tubing into place on drilling rigs. While cranes carry more weight, picker trucks are more mobile and flexible. Lattice boom crawler cranes were designed to pick up loads and carry them to different positions. Telescopic cranes must remain stationary, and careful planning is needed to ensure that they are used efficiently. Modern telescopic cranes have hydraulically powered booms. Advanced steel alloy technology is used to produce lightweight booms equipped with automated pin-locking mechanisms. The largest telescopic crane in North America will be used by an oil and gas operator in Alberta. The crane will have a combined boom and lattice jib height of 226 meters, and its maximum lifting capacity is 1200 tonnes. Gantry cranes are also increasingly being used by oil and gas operators due to their ability to straddle loads, thereby reducing the risk of tipping. It was concluded that gantry cranes are particularly suitable for rougher terrains. 4 figs.

  16. Heterogeneous Pd catalysts as emulsifiers in Pickering emulsions for integrated multistep synthesis in flow chemistry.

    Science.gov (United States)

    Hiebler, Katharina; Lichtenegger, Georg J; Maier, Manuel C; Park, Eun Sung; Gonzales-Groom, Renie; Binks, Bernard P; Gruber-Woelfler, Heidrun

    2018-01-01

    Within the "compartmentalised smart factory" approach of the ONE-FLOW project the implementation of different catalysts in "compartments" provided by Pickering emulsions and their application in continuous flow is targeted. We present here the development of heterogeneous Pd catalysts that are ready to be used in combination with biocatalysts for catalytic cascade synthesis of active pharmaceutical ingredients (APIs). In particular, we focus on the application of the catalytic systems for Suzuki-Miyaura cross-coupling reactions, which is the key step in the synthesis of the targeted APIs valsartan and sacubitril. An immobilised enzyme will accomplish the final product formation via hydrolysis. In order to create a large interfacial area for the catalytic reactions and to keep the reagents separated until required, the catalyst particles are used to stabilise Pickering emulsions of oil and water. A set of Ce-Sn-Pd oxides with the molecular formula Ce 0.99- x Sn x Pd 0.01 O 2-δ ( x = 0-0.99) has been prepared utilising a simple single-step solution combustion method. The high applicability of the catalysts for different functional groups and their minimal leaching behaviour is demonstrated with various Suzuki-Miyaura cross-coupling reactions in batch as well as in continuous flow employing the so-called "plug & play reactor". Finally, we demonstrate the use of these particles as the sole emulsifier of oil-water emulsions for a range of oils.

  17. Interfacial behaviour of sodium stearoyllactylate (SSL) as an oil-in-water pickering emulsion stabiliser.

    Science.gov (United States)

    Kurukji, D; Pichot, R; Spyropoulos, F; Norton, I T

    2013-11-01

    The ability of a food ingredient, sodium stearoyllactylate (SSL), to stabilise oil-in-water (O/W) emulsions against coalescence was investigated, and closely linked to its capacity to act as a Pickering stabiliser. Results showed that emulsion stability could be achieved with a relatively low SSL concentration (≥0.1 wt%), and cryogenic-scanning electron microscopy (cryo-SEM) visualisation of emulsion structure revealed the presence of colloidal SSL aggregates adsorbed at the oil-water interface. Surface properties of SSL could be modified by altering the size of these aggregates in water; a faster decrease in surface tension was observed when SSL dispersions were subjected to high pressure homogenisation (HPH). The rate of SSL adsorption at the sunflower oil-water interface also increased after HPH, and a higher interfacial tension (IFT) was observed with increasing SSL concentration. Differential scanning calorimetry (DSC) enabled a comparison of the thermal behaviour of SSL in aqueous dispersions with SSL-stabilised O/W emulsions. SSL melting enthalpy depended on emulsion interfacial area and the corresponding DSC data was used to determine the amount of SSL adsorbed at the oil-water interface. An idealised theoretical interfacial coverage calculation based on Pickering emulsion theory was in general agreement with the mass of SSL adsorbed as predicted by DSC. Copyright © 2013 The Authors. Published by Elsevier Inc. All rights reserved.

  18. Electrospun composite matrices of poly(ε-caprolactone)-montmorillonite made using tenside free Pickering emulsions

    International Nuclear Information System (INIS)

    Samanta, Archana; Takkar, Sonam; Kulshreshtha, Ritu; Nandan, Bhanu; Srivastava, Rajiv K.

    2016-01-01

    The production of composite electrospun matrices of poly(ε-caprolactone) (PCL) using an emulsifier-free emulsion, made with minimal organic solvent, as precursor is reported. Pickering emulsions of PCL were prepared using modified montmorillonite (MMT) clay as the stabilizer. Hydrophobic tallow group of the modified MMT clay resulted in analogous interaction of clay with oil and aqueous phase and its adsorption at the interface to provide stability to the resultant emulsion. Composite fibrous matrices of PCL and MMT were produced using electrospinning under controlled conditions. The fiber fineness was found to alter with PCL concentration and volume fraction of the aqueous and oil phases. A higher tensile strength and modulus was obtained with inclusion of MMT in PCL electrospun matrix in comparison to a matrix made using neat PCL. The presence of clay in the fibrous matrix did not change the cell proliferation efficiency in comparison to neat PCL matrix. Composite fibrous matrices of PCL/MMT bearing enhanced tensile properties may find applications in areas other than tissue engineering for example food packaging and filtration. - Highlights: • Tenside free, clay stabilized Pickering emulsion of PCL is made with minimal organic solvent. • Organic–inorganic composite fibrous matrices were produced via emulsion electrospinning. • Fiber fineness was efficiently controlled by variation in emulsion formulation. • Fibrous matrices of high tensile strength and modulus were obtained in comparison to neat PCL matrix. • PCL/clay matrices showed effective cell proliferation as a neat PCL matrix.

  19. Electrospun composite matrices of poly(ε-caprolactone)-montmorillonite made using tenside free Pickering emulsions

    Energy Technology Data Exchange (ETDEWEB)

    Samanta, Archana [Department of Textile Technology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016 (India); Takkar, Sonam; Kulshreshtha, Ritu [Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016 (India); Nandan, Bhanu [Department of Textile Technology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016 (India); Srivastava, Rajiv K., E-mail: rajiv@textile.iitd.ac.in [Department of Textile Technology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016 (India)

    2016-12-01

    The production of composite electrospun matrices of poly(ε-caprolactone) (PCL) using an emulsifier-free emulsion, made with minimal organic solvent, as precursor is reported. Pickering emulsions of PCL were prepared using modified montmorillonite (MMT) clay as the stabilizer. Hydrophobic tallow group of the modified MMT clay resulted in analogous interaction of clay with oil and aqueous phase and its adsorption at the interface to provide stability to the resultant emulsion. Composite fibrous matrices of PCL and MMT were produced using electrospinning under controlled conditions. The fiber fineness was found to alter with PCL concentration and volume fraction of the aqueous and oil phases. A higher tensile strength and modulus was obtained with inclusion of MMT in PCL electrospun matrix in comparison to a matrix made using neat PCL. The presence of clay in the fibrous matrix did not change the cell proliferation efficiency in comparison to neat PCL matrix. Composite fibrous matrices of PCL/MMT bearing enhanced tensile properties may find applications in areas other than tissue engineering for example food packaging and filtration. - Highlights: • Tenside free, clay stabilized Pickering emulsion of PCL is made with minimal organic solvent. • Organic–inorganic composite fibrous matrices were produced via emulsion electrospinning. • Fiber fineness was efficiently controlled by variation in emulsion formulation. • Fibrous matrices of high tensile strength and modulus were obtained in comparison to neat PCL matrix. • PCL/clay matrices showed effective cell proliferation as a neat PCL matrix.

  20. Nozzleless Fabrication of Oil-Core Biopolymeric Microcapsules by the Interfacial Gelation of Pickering Emulsion Templates.

    Science.gov (United States)

    Leong, Jun-Yee; Tey, Beng-Ti; Tan, Chin-Ping; Chan, Eng-Seng

    2015-08-05

    Ionotropic gelation has been an attractive method for the fabrication of biopolymeric oil-core microcapsules due to its safe and mild processing conditions. However, the mandatory use of a nozzle system to form the microcapsules restricts the process scalability and the production of small microcapsules (microcapsules through ionotropic gelation at the interface of an O/W Pickering emulsion. This approach involves the self-assembly of calcium carbonate (CaCO3) nanoparticles at the interface of O/W emulsion droplets followed by the addition of a polyanionic biopolymer into the aqueous phase. Subsequently, CaCO3 nanoparticles are dissolved by pH reduction, thus liberating Ca(2+) ions to cross-link the surrounding polyanionic biopolymer to form a shell that encapsulates the oil droplet. We demonstrate the versatility of this method by fabricating microcapsules from different types of polyanionic biopolymers (i.e., alginate, pectin, and gellan gum) and water-immiscible liquid cores (i.e., palm olein, cyclohexane, dichloromethane, and toluene). In addition, small microcapsules with a mean size smaller than 100 μm can be produced by selecting the appropriate conventional emulsification methods available to prepare the Pickering emulsion. The simplicity and versatility of this method allows biopolymeric microcapsules to be fabricated with ease by ionotropic gelation for numerous applications.

  1. Chemistry control at Bruce NGS 'B' from constructed to commercial operation

    International Nuclear Information System (INIS)

    Roberts, J.G.

    1987-01-01

    Pre-operational storage chemistry and flushing of the secondary side is described. The approach devised for Bruce NGS 'B' Unit 6 was unique for an Ontario Hydro Nuclear Unit. The significance of the improved Construction installation and Quality Assurance procedures, combined with those of Operations is identified. Secondary side chemistry during both commissioning and later operation is reported. It will be shown that the application of ALARA (As Low As is Reasonably Achievable) concept has resulted in tighter chemical specifications being met

  2. TUF assessment of an abnormal load rejection event at Darlington NGS

    International Nuclear Information System (INIS)

    Liauw, W.K.; Liu, W.S.

    1997-01-01

    The main purpose of reactor system code development is to support plant operation and to assist in safety analysis. To illustrate the operational support activities of the TUF code, the assessment of a simple case of abnormal load rejection event at Darlington NGS is described. The main assessment of this event examines the flow conditions at the steam generators and the possible impact on the turbine. This assessment demonstrates the TUF capability in the operational support analysis for CANDU reactors. (author)

  3. Bio-Docklets: virtualization containers for single-step execution of NGS pipelines.

    Science.gov (United States)

    Kim, Baekdoo; Ali, Thahmina; Lijeron, Carlos; Afgan, Enis; Krampis, Konstantinos

    2017-08-01

    Processing of next-generation sequencing (NGS) data requires significant technical skills, involving installation, configuration, and execution of bioinformatics data pipelines, in addition to specialized postanalysis visualization and data mining software. In order to address some of these challenges, developers have leveraged virtualization containers toward seamless deployment of preconfigured bioinformatics software and pipelines on any computational platform. We present an approach for abstracting the complex data operations of multistep, bioinformatics pipelines for NGS data analysis. As examples, we have deployed 2 pipelines for RNA sequencing and chromatin immunoprecipitation sequencing, preconfigured within Docker virtualization containers we call Bio-Docklets. Each Bio-Docklet exposes a single data input and output endpoint and from a user perspective, running the pipelines as simply as running a single bioinformatics tool. This is achieved using a "meta-script" that automatically starts the Bio-Docklets and controls the pipeline execution through the BioBlend software library and the Galaxy Application Programming Interface. The pipeline output is postprocessed by integration with the Visual Omics Explorer framework, providing interactive data visualizations that users can access through a web browser. Our goal is to enable easy access to NGS data analysis pipelines for nonbioinformatics experts on any computing environment, whether a laboratory workstation, university computer cluster, or a cloud service provider. Beyond end users, the Bio-Docklets also enables developers to programmatically deploy and run a large number of pipeline instances for concurrent analysis of multiple datasets. © The Authors 2017. Published by Oxford University Press.

  4. New Challenges in Targeting Signaling Pathways in Acute Lymphoblastic Leukemia by NGS Approaches: An Update

    Science.gov (United States)

    Hernández-Rivas, Jesús María

    2018-01-01

    The identification and study of genetic alterations involved in various signaling pathways associated with the pathogenesis of acute lymphoblastic leukemia (ALL) and the application of recent next-generation sequencing (NGS) in the identification of these lesions not only broaden our understanding of the involvement of various genetic alterations in the pathogenesis of the disease but also identify new therapeutic targets for future clinical trials. The present review describes the main deletions, amplifications, sequence mutations, epigenetic lesions, and new structural DNA rearrangements detected by NGS in B-ALL and T-ALL and their clinical importance for therapeutic procedures. We reviewed the molecular basis of pathways including transcriptional regulation, lymphoid differentiation and development, TP53 and the cell cycle, RAS signaling, JAK/STAT, NOTCH, PI3K/AKT/mTOR, Wnt/β-catenin signaling, chromatin structure modifiers, and epigenetic regulators. The implementation of NGS strategies has enabled important mutated genes in each pathway, their associations with the genetic subtypes of ALL, and their outcomes, which will be described further. We also discuss classic and new cryptic DNA rearrangements in ALL identified by mRNA-seq strategies. Novel cooperative abnormalities in ALL could be key prognostic and/or predictive biomarkers for selecting the best frontline treatment and for developing therapies after the first relapse or refractory disease. PMID:29642462

  5. NGS QC Toolkit: a toolkit for quality control of next generation sequencing data.

    Directory of Open Access Journals (Sweden)

    Ravi K Patel

    Full Text Available Next generation sequencing (NGS technologies provide a high-throughput means to generate large amount of sequence data. However, quality control (QC of sequence data generated from these technologies is extremely important for meaningful downstream analysis. Further, highly efficient and fast processing tools are required to handle the large volume of datasets. Here, we have developed an application, NGS QC Toolkit, for quality check and filtering of high-quality data. This toolkit is a standalone and open source application freely available at http://www.nipgr.res.in/ngsqctoolkit.html. All the tools in the application have been implemented in Perl programming language. The toolkit is comprised of user-friendly tools for QC of sequencing data generated using Roche 454 and Illumina platforms, and additional tools to aid QC (sequence format converter and trimming tools and analysis (statistics tools. A variety of options have been provided to facilitate the QC at user-defined parameters. The toolkit is expected to be very useful for the QC of NGS data to facilitate better downstream analysis.

  6. Design and installation of a strategically placed algae mesh barrier at OPG Pickering Nuclear Generating Station

    International Nuclear Information System (INIS)

    Marttila, D.; Patrick, P.; Gregoris, C.

    2009-01-01

    Ontario Power Generation's Pickering Nuclear has experienced a number of events in which attached algae have become entrained in the water intake costing approximately $30M over the 1995-2005 period as a result of deratings, Unit shutdowns and other operational issues. In 2005-2006 OPG and Kinectrics worked collaboratively on evaluating different potential solutions to reduce the impact of algae on the station. One of the solutions developed by Kinectrics included a strategically placed barrier net designed to regulate algae flow into the station intake. In 2006, Kinectrics designed and installed the system, the first of its kind at a Nuclear Power Plant in Canada. The system was operational by May 2007. OPG completed an effectiveness study in 2007 and concluded the barrier system had a beneficial effect on reducing algae impact on the station. (author)

  7. THE INFLUENCE OF TRUST IN THE CONSTITUTION OF A BRAZILIAN COOPERATIVE OF SELECTIVE WASTE PICKERS

    Directory of Open Access Journals (Sweden)

    Dayanne Marciane Gonçalves

    2016-03-01

    Full Text Available Since the Brazilian public policy started to encourage solidarity economy in 2003, the number of projects and enterprises in this sector has steadily increased. Embeddedness has contributed to the understanding of organizational phenomena of solidarity economy and cooperatives. The aim of this study was to understand the influence of trust, from the perspective of Mark Granovetter’s social networks, on the constitution of a cooperative of urban recyclable waste pickers in southern Brazil between 1996 until early 2012, considered the foundation period. We used the qualitative method with a historical approach to social relationships and content analysis. Possible influences of trust were analysed based on the economic, social and political history of the cooperative. Among the main results, we highlight the existence of social relations before the constitution, defined by trust due to family identity and reputation built over time.

  8. Next-generation sequencing (NGS) for assessment of microbial water quality: current progress, challenges, and future opportunities.

    Science.gov (United States)

    Tan, BoonFei; Ng, Charmaine; Nshimyimana, Jean Pierre; Loh, Lay Leng; Gin, Karina Y-H; Thompson, Janelle R

    2015-01-01

    Water quality is an emergent property of a complex system comprised of interacting microbial populations and introduced microbial and chemical contaminants. Studies leveraging next-generation sequencing (NGS) technologies are providing new insights into the ecology of microbially mediated processes that influence fresh water quality such as algal blooms, contaminant biodegradation, and pathogen dissemination. In addition, sequencing methods targeting small subunit (SSU) rRNA hypervariable regions have allowed identification of signature microbial species that serve as bioindicators for sewage contamination in these environments. Beyond amplicon sequencing, metagenomic and metatranscriptomic analyses of microbial communities in fresh water environments reveal the genetic capabilities and interplay of waterborne microorganisms, shedding light on the mechanisms for production and biodegradation of toxins and other contaminants. This review discusses the challenges and benefits of applying NGS-based methods to water quality research and assessment. We will consider the suitability and biases inherent in the application of NGS as a screening tool for assessment of biological risks and discuss the potential and limitations for direct quantitative interpretation of NGS data. Secondly, we will examine case studies from recent literature where NGS based methods have been applied to topics in water quality assessment, including development of bioindicators for sewage pollution and microbial source tracking, characterizing the distribution of toxin and antibiotic resistance genes in water samples, and investigating mechanisms of biodegradation of harmful pollutants that threaten water quality. Finally, we provide a short review of emerging NGS platforms and their potential applications to the next generation of water quality assessment tools.

  9. Large scale replacement of fuel channels in the Pickering CANDU reactor using a man-in-the-loop remote control system

    International Nuclear Information System (INIS)

    Stratton, D.

    1991-01-01

    Spar Aerospace Limited of Toronto is presently under contract to Ontario Hydro to design a Remote Manipulation and Control System (RMCS) to be used during the large scale replacement of the fuel channels in the Pickering A Nuclear Generating Station. The system is designed to support the replacement of all 390 fuel channels in each of the four reactors at the Pickering A station in a safe manner that minimizes worker radiation exposure and unit outage time

  10. High-Surface-Area, Emulsion-Templated Carbon Foams by Activation of polyHIPEs Derived from Pickering Emulsions

    Directory of Open Access Journals (Sweden)

    Robert T. Woodward

    2016-09-01

    Full Text Available Carbon foams displaying hierarchical porosity and excellent surface areas of >1400 m2/g can be produced by the activation of macroporous poly(divinylbenzene. Poly(divinylbenzene was synthesized from the polymerization of the continuous, but minority, phase of a simple high internal phase Pickering emulsion. By the addition of KOH, chemical activation of the materials is induced during carbonization, producing Pickering-emulsion-templated carbon foams, or carboHIPEs, with tailorable macropore diameters and surface areas almost triple that of those previously reported. The retention of the customizable, macroporous open-cell structure of the poly(divinylbenzene precursor and the production of a large degree of microporosity during activation leads to tailorable carboHIPEs with excellent surface areas.

  11. Hydroxyapatite-armored poly(ε-caprolactone) microspheres and hydroxyapatite microcapsules fabricated via a Pickering emulsion route.

    Science.gov (United States)

    Fujii, Syuji; Okada, Masahiro; Nishimura, Taiki; Maeda, Hayata; Sugimoto, Tatsuya; Hamasaki, Hiroyuki; Furuzono, Tsutomu; Nakamura, Yoshinobu

    2012-05-15

    Hydroxyapatite (HAp) nanoparticle-armored poly(ε-caprolactone) (PCL) microspheres were fabricated via a "Pickering-type" emulsion solvent evaporation method in the absence of any molecular surfactants. It was clarified that the interaction between carbonyl/carboxylic acid groups of PCL and the HAp nanoparticles at an oil-water interface played a crucial role in the preparation of the stable Pickering-type emulsions and the HAp nanoparticle-armored microspheres. The HAp nanoparticle-armored PCL microspheres were characterized in terms of size, size distribution, morphology, and chemical compositions using scanning electron microscopy, laser diffraction, energy dispersive X-ray microanalysis, and thermogravimetric analysis. The presence of HAp nanoparticles at the surface of the microspheres was confirmed by scanning electron microscopy and energy dispersive X-ray microanalysis. Pyrolysis of the PCL cores led to the formation of the corresponding HAp hollow microcapsules. Copyright © 2012 Elsevier Inc. All rights reserved.

  12. Application of Shuttle Remote Manipulator System technology to the replacement of fuel channels in the Pickering CANDU reactor

    International Nuclear Information System (INIS)

    Stratton, D.; Butt, C.

    1982-04-01

    Spar Aerospace Limited of Toronto was the prime contractor to the National Research Council of Canada for the design and development of the Shuttle Remote Manipulator (SRMS). Spar is presently under contract to Ontario Hydro to design and build a Remote Manipulation Control System to replace the fuel channels in the Pickering A Nuclear Generating Station. The equipment may be used to replace the fuel channels in six other early generation CANDU reactors

  13. The Effect of Storage and Routing Policies on Picker Blocking in a Real-life Narrow-aisle Warehouse

    OpenAIRE

    Van Gils, Teun; Caris, An; Ramaekers, Katrien

    2017-01-01

    Upcoming e-commerce markets force warehouses to handle a large number of orders within short time windows. Narrow-aisle order picking systems allow to store a large number of products in small areas. In manual order picking systems, narrow aisles can result in substantial waiting time compared to wide-aisle systems. The objective of this study is to analyse the joint effect of the two main operational order picking planning problems, storage location assignment and order picker routing, on or...

  14. Sample Results From The Extraction, Scrub, And Strip Test For The Blended NGS Solvent

    Energy Technology Data Exchange (ETDEWEB)

    Washington, A. L. II [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL); Peters, T. B. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL)

    2014-03-03

    This report summarizes the results of the extraction, scrub, and strip testing for the September 2013 sampling of the Next Generation Solvent (NGS) Blended solvent from the Modular Caustic Side-Solvent Extraction Unit (MCU) Solvent Hold Tank. MCU is in the process of transitioning from the BOBCalixC6 solvent to the NGS Blend solvent. As part of that transition, MCU has intentionally created a blended solvent to be processed using the Salt Batch program. This sample represents the first sample received from that blended solvent. There were two ESS tests performed where NGS blended solvent performance was assessed using either the Tank 21 material utilized in the Salt Batch 7 analyses or a simulant waste material used in the V-5/V-10 contactor testing. This report tabulates the temperature corrected cesium distribution, or DCs values, step recovery percentage, and actual temperatures recorded during the experiment. This report also identifies the sample receipt date, preparation method, and analysis performed in the accumulation of the listed values. The calculated extraction DCs values using the Tank 21H material and simulant are 59.4 and 53.8, respectively. The DCs values for two scrub and three strip processes for the Tank 21 material are 4.58, 2.91, 0.00184, 0.0252, and 0.00575, respectively. The D-values for two scrub and three strip processes for the simulant are 3.47, 2.18, 0.00468, 0.00057, and 0.00572, respectively. These values are similar to previous measurements of Salt Batch 7 feed with lab-prepared blended solvent. These numbers are considered compatible to allow simulant testing to be completed in place of actual waste due to the limited availability of feed material.

  15. Sample Results From The Extraction, Scrub, And Strip Test For The Blended NGS Solvent

    International Nuclear Information System (INIS)

    Washington, A. L. II; Peters, T. B.

    2014-01-01

    This report summarizes the results of the extraction, scrub, and strip testing for the September 2013 sampling of the Next Generation Solvent (NGS) Blended solvent from the Modular Caustic Side-Solvent Extraction Unit (MCU) Solvent Hold Tank. MCU is in the process of transitioning from the BOBCalixC6 solvent to the NGS Blend solvent. As part of that transition, MCU has intentionally created a blended solvent to be processed using the Salt Batch program. This sample represents the first sample received from that blended solvent. There were two ESS tests performed where NGS blended solvent performance was assessed using either the Tank 21 material utilized in the Salt Batch 7 analyses or a simulant waste material used in the V-5/V-10 contactor testing. This report tabulates the temperature corrected cesium distribution, or DCs values, step recovery percentage, and actual temperatures recorded during the experiment. This report also identifies the sample receipt date, preparation method, and analysis performed in the accumulation of the listed values. The calculated extraction DCs values using the Tank 21H material and simulant are 59.4 and 53.8, respectively. The DCs values for two scrub and three strip processes for the Tank 21 material are 4.58, 2.91, 0.00184, 0.0252, and 0.00575, respectively. The D-values for two scrub and three strip processes for the simulant are 3.47, 2.18, 0.00468, 0.00057, and 0.00572, respectively. These values are similar to previous measurements of Salt Batch 7 feed with lab-prepared blended solvent. These numbers are considered compatible to allow simulant testing to be completed in place of actual waste due to the limited availability of feed material

  16. Waste Picker Organizations and Their Contribution to the Circular Economy: Two Case Studies from a Global South Perspective

    Directory of Open Access Journals (Sweden)

    Jutta Gutberlet

    2017-09-01

    Full Text Available The discussion on the circular economy (CE has attracted a rising interest within global policy and business as a way of increasing the sustainability of production and consumption. Yet the literature mostly portrays a Global North perspective. There is a diverse spectrum of community-based organizations playing important roles in resource recovery and transformation, particularly, but not only, in Global South countries, providing innovative examples for grassroots involvement in waste management and in the CE. This article proposes to add a Southern lens, situated in the context of waste picker organizations, to the concept of CE. The discursive framework in this article couples ecological economy (EE with social/solidarity economy (SSE, focusing not only on environmental sustainability but also on social, economic, political and cultural dimensions involved in production, consumption and discard. We acknowledge that grassroots movements contribute to policy making and improve urban waste management systems. The paper outlines two empirical studies (Argentina, Brazil that illustrate how waste picker organizations perform selective waste collection services, engage with municipalities and industries, and practice the CE. The research reveals that social and political facets need to be added to the debate about the CE, linking environmental management and policy with community development and recognizing waste pickers as protagonists in the CE. Our findings emphasize a need for a change of persisting inequalities in public policy by recognizing the importance of popular waste management praxis and knowledge, ultimately redefining the CE.

  17. AECB staff annual assessment of the Pickering A and B Nuclear Generating Stations for the year 1994

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1995-06-01

    The Pickering Nuclear Generating Station (PNGS) is located on the north shore of Lake Ontario, about 32 km east of downtown Toronto. It consists of two stations, PNGS-A and PNGS-B. Each station contains four reactor units. PNGS-A consists of Units 1 to 4, while PNGS-B consists of Units 5 to 8. Each unit can generate about 540 megawatts of electricity. All eight units are located within a single enclosure. Ontario Hydro`s Pickering Nuclear Division has assigned one Station Director with authority over both stations, but each station has its own organization. AECB issue a separate operating licence for each station. This report presents the Atomic Energy Control Board staff assessment of the Pickering stations` safety performance in 1994 and other aspects that they consider to have significant impact on nuclear safety. AECB based their conclusions on their observations, audits, inspections and review of information that Ontario Hydro submits to them as required by the station Operating Licences. 11 tabs., 8 figs.

  18. AECB staff annual assessment of the Pickering A and B Nuclear Generating Stations for the year 1994

    International Nuclear Information System (INIS)

    1995-06-01

    The Pickering Nuclear Generating Station (PNGS) is located on the north shore of Lake Ontario, about 32 km east of downtown Toronto. It consists of two stations, PNGS-A and PNGS-B. Each station contains four reactor units. PNGS-A consists of Units 1 to 4, while PNGS-B consists of Units 5 to 8. Each unit can generate about 540 megawatts of electricity. All eight units are located within a single enclosure. Ontario Hydro's Pickering Nuclear Division has assigned one Station Director with authority over both stations, but each station has its own organization. AECB issue a separate operating licence for each station. This report presents the Atomic Energy Control Board staff assessment of the Pickering stations' safety performance in 1994 and other aspects that they consider to have significant impact on nuclear safety. AECB based their conclusions on their observations, audits, inspections and review of information that Ontario Hydro submits to them as required by the station Operating Licences. 11 tabs., 8 figs

  19. lociNGS: a lightweight alternative for assessing suitability of next-generation loci for evolutionary analysis.

    Directory of Open Access Journals (Sweden)

    Sarah M Hird

    Full Text Available Genomic enrichment methods and next-generation sequencing produce uneven coverage for the portions of the genome (the loci they target; this information is essential for ascertaining the suitability of each locus for further analysis. lociNGS is a user-friendly accessory program that takes multi-FASTA formatted loci, next-generation sequence alignments and demographic data as input and collates, displays and outputs information about the data. Summary information includes the parameters coverage per locus, coverage per individual and number of polymorphic sites, among others. The program can output the raw sequences used to call loci from next-generation sequencing data. lociNGS also reformats subsets of loci in three commonly used formats for multi-locus phylogeographic and population genetics analyses - NEXUS, IMa2 and Migrate. lociNGS is available at https://github.com/SHird/lociNGS and is dependent on installation of MongoDB (freely available at http://www.mongodb.org/downloads. lociNGS is written in Python and is supported on MacOSX and Unix; it is distributed under a GNU General Public License.

  20. Analysis and Visualization of ChIP-Seq and RNA-Seq Sequence Alignments Using ngs.plot.

    Science.gov (United States)

    Loh, Yong-Hwee Eddie; Shen, Li

    2016-01-01

    The continual maturation and increasing applications of next-generation sequencing technology in scientific research have yielded ever-increasing amounts of data that need to be effectively and efficiently analyzed and innovatively mined for new biological insights. We have developed ngs.plot-a quick and easy-to-use bioinformatics tool that performs visualizations of the spatial relationships between sequencing alignment enrichment and specific genomic features or regions. More importantly, ngs.plot is customizable beyond the use of standard genomic feature databases to allow the analysis and visualization of user-specified regions of interest generated by the user's own hypotheses. In this protocol, we demonstrate and explain the use of ngs.plot using command line executions, as well as a web-based workflow on the Galaxy framework. We replicate the underlying commands used in the analysis of a true biological dataset that we had reported and published earlier and demonstrate how ngs.plot can easily generate publication-ready figures. With ngs.plot, users would be able to efficiently and innovatively mine their own datasets without having to be involved in the technical aspects of sequence coverage calculations and genomic databases.

  1. Integrated systems for NGS data management and analysis: open issues and available solutions

    Directory of Open Access Journals (Sweden)

    Valerio eBianchi

    2016-05-01

    Full Text Available Next-generation sequencing (NGS technologies have deeply changed our understanding of cellular processes by delivering an astonishing amount of data at affordable prices; nowadays, many biology laboratories have already accumulated a large number of sequenced samples. However, managing and analyzing these data poses new challenges, which may easily be underestimated by research groups devoid of IT and quantitative skills. In this perspective, we identify five issues that should be carefully addressed by research groups approaching NGS technologies. In particular, the five key issues to be considered concern: 1 adopting a laboratory management system (LIMS and safeguard the resulting raw data structure in downstream analyses; 2 monitoring the flow of the data and standardizing input and output directories and file names, even when multiple analysis protocols are used on the same data; 3 ensuring complete traceability of the analysis performed; 4 enabling non-experienced users to run analyses through a graphical user interface (GUI acting as a front-end for the pipelines; 5 relying on standard metadata to annotate the datasets, and when possible using controlled vocabularies, ideally derived from biomedical ontologies. Finally, we discuss the currently available tools in the light of these issues, and we introduce HTS-flow, a new workflow management system (WMS conceived to address the concerns we raised. HTS-flow is able to retrieve information from a LIMS database, manages data analyses through a simple GUI, outputs data in standard locations and allows the complete traceability of datasets, accompanying metadata and analysis scripts.

  2. NGS testing for cardiomyopathy: Utility of adding RASopathy-associated genes.

    Science.gov (United States)

    Ceyhan-Birsoy, Ozge; Miatkowski, Maya M; Hynes, Elizabeth; Funke, Birgit H; Mason-Suares, Heather

    2018-04-25

    RASopathies include a group of syndromes caused by pathogenic germline variants in RAS-MAPK pathway genes and typically present with facial dysmorphology, cardiovascular disease, and musculoskeletal anomalies. Recently, variants in RASopathy-associated genes have been reported in individuals with apparently nonsyndromic cardiomyopathy, suggesting that subtle features may be overlooked. To determine the utility and burden of adding RASopathy-associated genes to cardiomyopathy panels, we tested 11 RASopathy-associated genes by next-generation sequencing (NGS), including NGS-based copy number variant assessment, in 1,111 individuals referred for genetic testing for hypertrophic cardiomyopathy (HCM) or dilated cardiomyopathy (DCM). Disease-causing variants were identified in 0.6% (four of 692) of individuals with HCM, including three missense variants in the PTPN11, SOS1, and BRAF genes. Overall, 36 variants of uncertain significance (VUSs) were identified, averaging ∼3VUSs/100 cases. This study demonstrates that adding a subset of the RASopathy-associated genes to cardiomyopathy panels will increase clinical diagnoses without significantly increasing the number of VUSs/case. © 2018 Wiley Periodicals, Inc.

  3. Non-Aqueous Titration Method for Determining Suppressor Concentration in the MCU Next Generation Solvent (NGS)

    Energy Technology Data Exchange (ETDEWEB)

    Taylor-Pashow, Kathryn M. L. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL); Jones, Daniel H. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL)

    2017-10-23

    A non-aqueous titration method has been used for quantifying the suppressor concentration in the MCU solvent hold tank (SHT) monthly samples since the Next Generation Solvent (NGS) was implemented in 2013. The titration method measures the concentration of the NGS suppressor (TiDG) as well as the residual tri-n-octylamine (TOA) that is a carryover from the previous solvent. As the TOA concentration has decreased over time, it has become difficult to resolve the TiDG equivalence point as the TOA equivalence point has moved closer. In recent samples, the TiDG equivalence point could not be resolved, and therefore, the TiDG concentration was determined by subtracting the TOA concentration as measured by semi-volatile organic analysis (SVOA) from the total base concentration as measured by titration. In order to improve the titration method so that the TiDG concentration can be measured directly, without the need for the SVOA data, a new method has been developed that involves spiking of the sample with additional TOA to further separate the two equivalence points in the titration. This method has been demonstrated on four recent SHT samples and comparison to results obtained using the SVOA TOA subtraction method shows good agreement. Therefore, it is recommended that the titration procedure be revised to include the TOA spike addition, and this to become the primary method for quantifying the TiDG.

  4. Non-Aqueous Titration Method for Determining Suppressor Concentration in the MCU Next Generation Solvent (NGS)

    International Nuclear Information System (INIS)

    Taylor-Pashow, Kathryn M. L.; Jones, Daniel H.

    2017-01-01

    A non-aqueous titration method has been used for quantifying the suppressor concentration in the MCU solvent hold tank (SHT) monthly samples since the Next Generation Solvent (NGS) was implemented in 2013. The titration method measures the concentration of the NGS suppressor (TiDG) as well as the residual tri-n-octylamine (TOA) that is a carryover from the previous solvent. As the TOA concentration has decreased over time, it has become difficult to resolve the TiDG equivalence point as the TOA equivalence point has moved closer. In recent samples, the TiDG equivalence point could not be resolved, and therefore, the TiDG concentration was determined by subtracting the TOA concentration as measured by semi-volatile organic analysis (SVOA) from the total base concentration as measured by titration. In order to improve the titration method so that the TiDG concentration can be measured directly, without the need for the SVOA data, a new method has been developed that involves spiking of the sample with additional TOA to further separate the two equivalence points in the titration. This method has been demonstrated on four recent SHT samples and comparison to results obtained using the SVOA TOA subtraction method shows good agreement. Therefore, it is recommended that the titration procedure be revised to include the TOA spike addition, and this to become the primary method for quantifying the TiDG.

  5. AECB staff review of Bruce NGS 'A' operation for the year 1989

    International Nuclear Information System (INIS)

    1990-06-01

    The operation of the Bruce Nuclear Generating Station 'B' is monitored and licensing requirements are enforced by the Atomic Energy Control Board (AECB). This report records the conclusions of the AECB staff assessment of Bruce NGS 'A' during 1989 and the early part of 1990. Overall operation of the station met acceptable safety standards. Despite numerous problems and technical difficulties encountered, station management and supervisory personnel acted with due caution and made decisions in the interests of safety. There was evidence of improvement in a number of key areas, supported by pertinent indicators in the objective measures table. The extensive inspection and maintenance programs carried out during the year revealed the extent of component deterioration due to aging to be larger than expected. Hydrogen embrittlement of pressure tubes, erosion/corrosion of steam and feed water valves, heat exchanger tubes and piping, fouling of boilers and heat exchangers, and environmental damage of electrical equipment are examples. Continued aging of plant equipment and its potential for reducing the margins for safe operation must be taken into account by Ontario Hydro in establishing priorities and target dates for completion of actions to resolve identified problems at Bruce NGS 'A'. (2 tabs.)

  6. panelcn.MOPS: Copy-number detection in targeted NGS panel data for clinical diagnostics.

    Science.gov (United States)

    Povysil, Gundula; Tzika, Antigoni; Vogt, Julia; Haunschmid, Verena; Messiaen, Ludwine; Zschocke, Johannes; Klambauer, Günter; Hochreiter, Sepp; Wimmer, Katharina

    2017-07-01

    Targeted next-generation-sequencing (NGS) panels have largely replaced Sanger sequencing in clinical diagnostics. They allow for the detection of copy-number variations (CNVs) in addition to single-nucleotide variants and small insertions/deletions. However, existing computational CNV detection methods have shortcomings regarding accuracy, quality control (QC), incidental findings, and user-friendliness. We developed panelcn.MOPS, a novel pipeline for detecting CNVs in targeted NGS panel data. Using data from 180 samples, we compared panelcn.MOPS with five state-of-the-art methods. With panelcn.MOPS leading the field, most methods achieved comparably high accuracy. panelcn.MOPS reliably detected CNVs ranging in size from part of a region of interest (ROI), to whole genes, which may comprise all ROIs investigated in a given sample. The latter is enabled by analyzing reads from all ROIs of the panel, but presenting results exclusively for user-selected genes, thus avoiding incidental findings. Additionally, panelcn.MOPS offers QC criteria not only for samples, but also for individual ROIs within a sample, which increases the confidence in called CNVs. panelcn.MOPS is freely available both as R package and standalone software with graphical user interface that is easy to use for clinical geneticists without any programming experience. panelcn.MOPS combines high sensitivity and specificity with user-friendliness rendering it highly suitable for routine clinical diagnostics. © 2017 The Authors. Human Mutation published by Wiley Periodicals, Inc.

  7. A case study for cloud based high throughput analysis of NGS data using the globus genomics system

    Directory of Open Access Journals (Sweden)

    Krithika Bhuvaneshwar

    2015-01-01

    Full Text Available Next generation sequencing (NGS technologies produce massive amounts of data requiring a powerful computational infrastructure, high quality bioinformatics software, and skilled personnel to operate the tools. We present a case study of a practical solution to this data management and analysis challenge that simplifies terabyte scale data handling and provides advanced tools for NGS data analysis. These capabilities are implemented using the “Globus Genomics” system, which is an enhanced Galaxy workflow system made available as a service that offers users the capability to process and transfer data easily, reliably and quickly to address end-to-endNGS analysis requirements. The Globus Genomics system is built on Amazon's cloud computing infrastructure. The system takes advantage of elastic scaling of compute resources to run multiple workflows in parallel and it also helps meet the scale-out analysis needs of modern translational genomics research.

  8. Quinoa starch granules as stabilizing particles for production of Pickering emulsions.

    Science.gov (United States)

    Rayner, Marilyn; Sjöö, Malin; Timgren, Anna; Dejmek, Petr

    2012-01-01

    Intact starch granules isolated from quinoa (Chenopodium quinoa Willd.) were used to stabilize emulsion drops in so-called Pickering emulsions. Miglyol 812 was used as dispersed phase and a phosphate buffer (pH7) with different salt (NaCl) concentrations was used as the continuous phase. The starch granules were hydrophobically modified to different degrees by octenyl succinic anhydride (OSA) or by dry heat treatment at 120 degrees C in order to study the effect on the resulting emulsion drop size. The degree of OSA-modification had a low to moderate impact on drop size. The highest level of modification (4.66%) showed the largest mean drop size, and lowest amount of free starch, which could be an effect of a higher degree of aggregation of the starch granules and, thereby, also the emulsion drops stabilized by them. The heat treated starch granules had a poor stabilizing ability and only the starch heated for the longest time (150 min at 120 degrees C) had a better emulsifying capacity than the un-modified native starch granules. The effect of salt concentration was rather limited. However, an increased concentration of salt slightly increased the mean drop size and the elastic modulus.

  9. Evaluation of severe accident risk in the Pickering a risk assessment

    International Nuclear Information System (INIS)

    Dinnie, K.S.; Raina, V.M.

    1997-01-01

    The nature of the design of commercial power plants is such that significant impacts on public health can only occur if a number of barriers fail. Rigorous design and licensing requirements ensure that the more likely accidents do not fail all these barriers and their contribution to risk is likely to be small. The task of estimating accident risk must, therefore, focus more towards those less likely but potentially more serious combinations of failures that are characterized by the following: a) a large release of fission products into the containment atmosphere, b) a breach in the containment envelope, and c) the existence of a driving force to expel the containment atmosphere to the outside environment. The likelihood of such conditions existing simultaneously during the course of an accident is expected to be small, such that experience and data regarding the behaviour of plant systems under such conditions is sparse or non-existent. The challenge of Probabilistic Safety Assessments (PSAs) is to examine the potential for severe accidents using approaches that are sufficiently detailed and realistic to provide valid information regarding plant risk and susceptibilities, while simple enough to keep the analysis manageable. This paper outlines the key features of the Pickering A Risk Assessment (PARA) (1) and the manner in which it addresses these issues, and provides some insights into the results and conclusions drawn from the study. (author)

  10. Electrospun composite matrices of poly(ε-caprolactone)-montmorillonite made using tenside free Pickering emulsions.

    Science.gov (United States)

    Samanta, Archana; Takkar, Sonam; Kulshreshtha, Ritu; Nandan, Bhanu; Srivastava, Rajiv K

    2016-12-01

    The production of composite electrospun matrices of poly(ε-caprolactone) (PCL) using an emulsifier-free emulsion, made with minimal organic solvent, as precursor is reported. Pickering emulsions of PCL were prepared using modified montmorillonite (MMT) clay as the stabilizer. Hydrophobic tallow group of the modified MMT clay resulted in analogous interaction of clay with oil and aqueous phase and its adsorption at the interface to provide stability to the resultant emulsion. Composite fibrous matrices of PCL and MMT were produced using electrospinning under controlled conditions. The fiber fineness was found to alter with PCL concentration and volume fraction of the aqueous and oil phases. A higher tensile strength and modulus was obtained with inclusion of MMT in PCL electrospun matrix in comparison to a matrix made using neat PCL. The presence of clay in the fibrous matrix did not change the cell proliferation efficiency in comparison to neat PCL matrix. Composite fibrous matrices of PCL/MMT bearing enhanced tensile properties may find applications in areas other than tissue engineering for example food packaging and filtration. Copyright © 2016 Elsevier B.V. All rights reserved.

  11. Production of Concentrated Pickering Emulsions with Narrow Size Distributions Using Stirred Cell Membrane Emulsification.

    Science.gov (United States)

    Manga, Mohamed S; York, David W

    2017-09-12

    Stirred cell membrane emulsification (SCME) has been employed to prepare concentrated Pickering oil in water emulsions solely stabilized by fumed silica nanoparticles. The optimal conditions under which highly stable and low-polydispersity concentrated emulsions using the SCME approach are highlighted. Optimization of the oil flux rates and the paddle stirrer speeds are critical to achieving control over the droplet size and size distribution. Investigating the influence of oil volume fraction highlights the criticality of the initial particle loading in the continuous phase on the final droplet size and polydispersity. At a particle loading of 4 wt %, both the droplet size and polydispersity increase with increasing of the oil volume fraction above 50%. As more interfacial area is produced, the number of particles available in the continuous phase diminishes, and coincidently a reduction in the kinetics of particle adsorption to the interface resulting in larger polydisperse droplets occurs. Increasing the particle loading to 10 wt % leads to significant improvements in both size and polydispersity with oil volume fractions as high as 70% produced with coefficient of variation values as low as ∼30% compared to ∼75% using conventional homogenization techniques.

  12. Intestinal parasitism among waste pickers in Mato Grosso do Sul, Midwest Brazil

    Directory of Open Access Journals (Sweden)

    Minoru German Higa Júnior

    2017-12-01

    Full Text Available ABSTRACT The purpose of this study was to estimate the prevalence of intestinal parasites in both cooperative-affiliated and independent waste pickers operating at the municipal sanitary landfill in Campo Grande, Mato Grosso do Sul, Brazil, and associate these findings with hemoglobin, eosinophils, vitamin A and C levels and interleukin 5 and 10 (IL-5 and IL-10 production. Biological samples were collected, in addition to clinical, epidemiological, and sociodemographic data. Stool analyzes were based on sedimentation by centrifugation and on spontaneous sedimentation. High-performance liquid chromatography was used to determine vitamin A and C levels. ELISA was employed to quantify interleukins. Intestinal parasites were found in 29 of the 66 subjects assessed (43.9%. Endolimax nana (22.7%, Entamoeba coli (21.1%, Giardia lamblia (6.1%, Entamoeba histolytica/E. dispar (4.5%, and Ascaris lumbricoides (4.5% were the most prevalent species. Pathogenic parasites were detected in 11 individuals (16.7%. Hypovitaminoses A and C were detected in 19.6% (13/66 and 98.4% (65/66 of subjects, respectively. IL-5 and IL-10 production was observed in 21 (31.8% and 32 (48.4% subjects, respectively. Infection with pathogenic intestinal parasites was not a cause of vitamin A and C deficiency or IL-5 and IL-10 production among these workers.

  13. Next-generation sequencing (NGS for assessment of microbial water quality: current progress, challenges, and future opportunities

    Directory of Open Access Journals (Sweden)

    BoonFei eTan

    2015-09-01

    Full Text Available Water quality is an emergent property of a complex system comprised of interacting microbial populations and introduced microbial and chemical contaminants. Studies leveraging next-generation sequencing (NGS technologies are providing new insights into the ecology of microbially mediated processes that influence fresh water quality such as algal blooms, contaminant biodegradation, and pathogen dissemination. In addition, sequencing methods targeting small subunit (SSU rRNA hypervariable regions have allowed identification of signature microbial species that serve as bioindicators for sewage contamination in these environments. Beyond amplicon sequencing, metagenomic and metatranscriptomic analyses of microbial communities in fresh water environments reveal the genetic capabilities and interplay of waterborne microorganisms, shedding light on the mechanisms for production and biodegradation of toxins and other contaminants. This review discusses the challenges and benefits of applying NGS-based methods to water quality research and assessment. We will consider the suitability and biases inherent in the application of NGS as a screening tool for assessment of biological risks and discuss the potential and limitations for direct quantitative interpretation of NGS data. Secondly, we will examine case studies from recent literature where NGS based methods have been applied to topics in water quality assessment, including development of bioindicators for sewage pollution and microbial source tracking, characterizing the distribution of toxin and antibiotic resistance genes in water samples, and investigating mechanisms of biodegradation of harmful pollutants that threaten water quality. Finally, we provide a short review of emerging NGS platforms and their potential applications to the next generation of water quality assessment tools.

  14. Evaluation of a pilot fish handling system at Bruce NGS 'A'

    International Nuclear Information System (INIS)

    Griffiths, J.S.

    1985-10-01

    A pilot fish recovery system using a Hidrostal fish pump was tested in the Bruce NGS 'A' forebay during June, 1984. Despite low forebay fish concentrations, the system was capable of capturing 97,000 alewife/day (3900 kg) if operated continuously. Post-pumping survival averaged 97%. It is estimated that a single pump could handle alewife runs in the 40,000 to 70,000 kg range, but multiple pumps or a single larger pump would be required to assure station protection from the largest runs (>100,000 kg). Results indicate that tank/trailer return of pumped fish is feasible, but other alternatives for returning fish to Lake Huron are also being considered

  15. AECB staff review of Bruce NGS 'B' operation for the year 1989

    International Nuclear Information System (INIS)

    1990-06-01

    The operation of the Bruce Nuclear Generating Station 'B' is monitored and licensing requirements are enforced by the Atomic Energy Control Board (AECB), which observes operation of the reactors, conducts audits, witnesses important activities, reviews station documentation and reports, and issue approvals, where appropriate, in accordance with licence conditions. This report records the conclusions of the AECB staff assessment of Bruce NGS 'B' during 1989. In general, the station operated within acceptable safety standards. Quality improvement initiatives started in 1989 should lead to improved station maintenance and operation in coming years. Ontario Hydro still needs to improve the administration of operating memos, deficiency reports and call-ups. Station management must ensure that shift supervisors and reactor first operators operate the station in a conservative manner at all times and put safety interests first when responding to a unit upset. (2 tabs.)

  16. AECB staff annual report of Bruce NGS 'B' for the year 1988

    International Nuclear Information System (INIS)

    1989-05-01

    The operation of the Bruce 'B' Nuclear Generating Station is monitored and licensing requirements are enforced by the Atomic Energy Control Board (AECB) Bruce project staff, with appropriate support from other AECB personnel. The staff observes operation of the reactors, conducts audits, witnesses important activities, reviews station documentation and reports, and issues approvals where appropriate in accordance with license conditions. As required by a condition of its Operating Licence, Ontario Hydro each year submits Technical Reports which summarize various aspects of the operation of Bruce NGS 'B' during the year. When these reports have been reviewed by AECB staff, a formal Annual Review Meeting is held with the station management to discuss safety-related aspects of the station operation, and to inform Ontario Hydro of AECB staff conclusions with respect to the performance of Ontario Hydro in operating the station during the year

  17. Update of the Picker C9 irradiator control system of the gamma II room of the secondary laboratory of dosimetric calibration

    International Nuclear Information System (INIS)

    Simon S, L. E.

    2016-01-01

    The Picker C9 irradiator is responsible for the calibration of different radiological equipment and the control system that maintains it in operation is designed in the graphical programming software LabVIEW (Laboratory Virtual Instrumentation Engineering Workbench), being its major advantages: the different types of communication, easy interconnection with other software and the recognition of different hardware devices, among others. Operation of the irradiator control system is performed with the NI-Usb-6008 (DAQ) data acquisition module of the National Instruments Company. The purpose of this work is to update the routines that make the Picker C9 control system of the gamma II room of the secondary laboratory of dosimetric calibration, using the graphic programming software LabVIEW, as well as to configure the new acquisition hardware of data that is implemented to control the Picker C9 irradiator system and ensure its operation. (Author)

  18. Effects of Occupational Exposure on the Health of Rag Pickers Due to Fungal Contamination at Waste Dumping Sites in Gwalipor (India

    Directory of Open Access Journals (Sweden)

    Harandra K. Sharma

    2017-02-01

    Full Text Available We investigated fungal contamination near different waste dumping sites and assessed the health risk factors of rag pickers associated with collection of waste in Gwalior during the year 2014-15. Petri plates were exposed at waste dumping sites and were transferred to the laboratory, analysis and identification was mainly carried out by culturing the fungal colonies by following standard procedures. A pretested questionnaire was used to evaluate the health problems among the rag pickers. Results indicated that all the dumping sites are contaminated with different types of fungal pathogens like Alternaria alternate, Aspergillus flavus, A. fumigates, A. niger, Cladosporium, Fusarium, Mucor, Penicillium and Rhizopus. Our study reported higher incidence of musculoskeletal and respiratory diseases among rag pickers. There is also strong need for carrying out similar assessment studies for other cities too. This will entail generation of more precise site specific information regarding fungal species and associated health risk factor.

  19. Effects of Occupational Exposure on the Health of Rag Pickers Due to Fungal Contamination at Waste Dumping Sites in Gwalior (India

    Directory of Open Access Journals (Sweden)

    Harandra K. Sharma

    2017-02-01

    Full Text Available We investigated fungal contamination near different waste dumping sites and assessed the health risk factors of rag pickers associated with collection of waste in Gwalior during the year 2014-15. Petri plates were exposed at waste dumping sites and were transferred to the laboratory, analysis and identification was mainly carried out by culturing the fungal colonies by following standard procedures. A pretested questionnaire was used to evaluate the health problems among the rag pickers. Results indicated that all the dumping sites are contaminated with different types of fungal pathogens like Alternaria alternate, Aspergillus flavus, A. fumigates, A. niger, Cladosporium, Fusarium, Mucor, Penicillium and Rhizopus. Our study reported higher incidence of musculoskeletal and respiratory diseases among rag pickers. There is also strong need for carrying out similar assessment studies for other cities too. This will entail generation of more precise site specific information regarding fungal species and associated health risk factor.

  20. What Is the Best NGS Enrichment Method for the Molecular Diagnosis of Monogenic Diabetes and Obesity?

    Directory of Open Access Journals (Sweden)

    Julien Philippe

    Full Text Available Molecular diagnosis of monogenic diabetes and obesity is of paramount importance for both the patient and society, as it can result in personalized medicine associated with a better life and it eventually saves health care spending. Genetic clinical laboratories are currently switching from Sanger sequencing to next-generation sequencing (NGS approaches but choosing the optimal protocols is not easy. Here, we compared the sequencing coverage of 43 genes involved in monogenic forms of diabetes and obesity, and variant detection rates, resulting from four enrichment methods based on the sonication of DNA (Agilent SureSelect, RainDance technologies, or using enzymes for DNA fragmentation (Illumina Nextera, Agilent HaloPlex. We analyzed coding exons and untranslated regions of the 43 genes involved in monogenic diabetes and obesity. We found that none of the methods achieves yet full sequencing of the gene targets. Nonetheless, the RainDance, SureSelect and HaloPlex enrichment methods led to the best sequencing coverage of the targets; while the Nextera method resulted in the poorest sequencing coverage. Although the sequencing coverage was high, we unexpectedly found that the HaloPlex method missed 20% of variants detected by the three other methods and Nextera missed 10%. The question of which NGS technique for genetic diagnosis yields the highest diagnosis rate is frequently discussed in the literature and the response is still unclear. Here, we showed that the RainDance enrichment method as well as SureSelect, which are both based on the sonication of DNA, resulted in a good sequencing quality and variant detection, while the use of enzymes to fragment DNA (HaloPlex or Nextera might not be the best strategy to get an accurate sequencing.

  1. AECB staff annual report of Bruce B NGS for the year 1991

    International Nuclear Information System (INIS)

    1992-11-01

    In this account of Bruce NGS B station operation during the year 1991 AECB staff have pointed out non-compliances with the operating licence, which have been few in number and minor in degree of seriousness. There were no exposures of workers to radiation in excess of regulatory limits, but there were contraventions of the ALARA principle. Releases of radioactive material to the environment have been well below the target levels. The performance of the four special safety systems has been good, except for the containment system. A review of the significant event reports and the causes of the events has revealed a lack of a system by which operations and maintenance work could be verified to have been carried out as intended. In operations and maintenance the backlog of work to be done to regularize temporary changes to equipment (removal of jumpers), to carry out preventive maintenance (call-ups), and to make repairs (deficiency reports) has increased from that of the previous year. On the other hand, the station has reduced the number of temporary operating instructions (operating memos) to half of what it was last year. The fretting of steam generator tubes reported last year has not become worse. Nevertheless, inspections continue and modifications to the tube supports are underway. Overall plant chemistry has been acceptable. An Ontario Hydro assessment of the station found the station management's expectations for maintaining the margin of safety in the plant had not been properly communicated to all levels of station staff. The station is now attempting to correct this. Infractions of work protection procedures, which were the subject of many significant events, have led to changes in the procedures and resulted in a major training effort. AECB staff believe that Ontario Hydro has continued to operate Bruce NGS B in a safe manner, but have pointed out areas where improvement is required. (Author)

  2. DEVELOPMENT OF ANALYTICAL METHODS FOR DETERMINING SUPPRESSOR CONCENTRATION IN THE MCU NEXT GENERATION SOLVENT (NGS)

    Energy Technology Data Exchange (ETDEWEB)

    Taylor-Pashow, K.; Fondeur, F.; White, T.; Diprete, D.; Milliken, C.

    2013-07-31

    Savannah River National Laboratory (SRNL) was tasked with identifying and developing at least one, but preferably two methods for quantifying the suppressor in the Next Generation Solvent (NGS) system. The suppressor is a guanidine derivative, N,N',N"-tris(3,7-dimethyloctyl)guanidine (TiDG). A list of 10 possible methods was generated, and screening experiments were performed for 8 of the 10 methods. After completion of the screening experiments, the non-aqueous acid-base titration was determined to be the most promising, and was selected for further development as the primary method. {sup 1}H NMR also showed promising results from the screening experiments, and this method was selected for further development as the secondary method. Other methods, including {sup 36}Cl radiocounting and ion chromatography, also showed promise; however, due to the similarity to the primary method (titration) and the inability to differentiate between TiDG and TOA (tri-n-ocytlamine) in the blended solvent, {sup 1}H NMR was selected over these methods. Analysis of radioactive samples obtained from real waste ESS (extraction, scrub, strip) testing using the titration method showed good results. Based on these results, the titration method was selected as the method of choice for TiDG measurement. {sup 1}H NMR has been selected as the secondary (back-up) method, and additional work is planned to further develop this method and to verify the method using radioactive samples. Procedures for analyzing radioactive samples of both pure NGS and blended solvent were developed and issued for the both methods.

  3. FASTQSim: platform-independent data characterization and in silico read generation for NGS datasets.

    Science.gov (United States)

    Shcherbina, Anna

    2014-08-15

    High-throughput next generation sequencing technologies have enabled rapid characterization of clinical and environmental samples. Consequently, the largest bottleneck to actionable data has become sample processing and bioinformatics analysis, creating a need for accurate and rapid algorithms to process genetic data. Perfectly characterized in silico datasets are a useful tool for evaluating the performance of such algorithms. Background contaminating organisms are observed in sequenced mixtures of organisms. In silico samples provide exact truth. To create the best value for evaluating algorithms, in silico data should mimic actual sequencer data as closely as possible. FASTQSim is a tool that provides the dual functionality of NGS dataset characterization and metagenomic data generation. FASTQSim is sequencing platform-independent, and computes distributions of read length, quality scores, indel rates, single point mutation rates, indel size, and similar statistics for any sequencing platform. To create training or testing datasets, FASTQSim has the ability to convert target sequences into in silico reads with specific error profiles obtained in the characterization step. FASTQSim enables users to assess the quality of NGS datasets. The tool provides information about read length, read quality, repetitive and non-repetitive indel profiles, and single base pair substitutions. FASTQSim allows the user to simulate individual read datasets that can be used as standardized test scenarios for planning sequencing projects or for benchmarking metagenomic software. In this regard, in silico datasets generated with the FASTQsim tool hold several advantages over natural datasets: they are sequencing platform independent, extremely well characterized, and less expensive to generate. Such datasets are valuable in a number of applications, including the training of assemblers for multiple platforms, benchmarking bioinformatics algorithm performance, and creating challenge

  4. RAP: RNA-Seq Analysis Pipeline, a new cloud-based NGS web application.

    Science.gov (United States)

    D'Antonio, Mattia; D'Onorio De Meo, Paolo; Pallocca, Matteo; Picardi, Ernesto; D'Erchia, Anna Maria; Calogero, Raffaele A; Castrignanò, Tiziana; Pesole, Graziano

    2015-01-01

    The study of RNA has been dramatically improved by the introduction of Next Generation Sequencing platforms allowing massive and cheap sequencing of selected RNA fractions, also providing information on strand orientation (RNA-Seq). The complexity of transcriptomes and of their regulative pathways make RNA-Seq one of most complex field of NGS applications, addressing several aspects of the expression process (e.g. identification and quantification of expressed genes and transcripts, alternative splicing and polyadenylation, fusion genes and trans-splicing, post-transcriptional events, etc.). In order to provide researchers with an effective and friendly resource for analyzing RNA-Seq data, we present here RAP (RNA-Seq Analysis Pipeline), a cloud computing web application implementing a complete but modular analysis workflow. This pipeline integrates both state-of-the-art bioinformatics tools for RNA-Seq analysis and in-house developed scripts to offer to the user a comprehensive strategy for data analysis. RAP is able to perform quality checks (adopting FastQC and NGS QC Toolkit), identify and quantify expressed genes and transcripts (with Tophat, Cufflinks and HTSeq), detect alternative splicing events (using SpliceTrap) and chimeric transcripts (with ChimeraScan). This pipeline is also able to identify splicing junctions and constitutive or alternative polyadenylation sites (implementing custom analysis modules) and call for statistically significant differences in genes and transcripts expression, splicing pattern and polyadenylation site usage (using Cuffdiff2 and DESeq). Through a user friendly web interface, the RAP workflow can be suitably customized by the user and it is automatically executed on our cloud computing environment. This strategy allows to access to bioinformatics tools and computational resources without specific bioinformatics and IT skills. RAP provides a set of tabular and graphical results that can be helpful to browse, filter and export

  5. ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases.

    Science.gov (United States)

    Shen, Li; Shao, Ningyi; Liu, Xiaochuan; Nestler, Eric

    2014-04-15

    Understanding the relationship between the millions of functional DNA elements and their protein regulators, and how they work in conjunction to manifest diverse phenotypes, is key to advancing our understanding of the mammalian genome. Next-generation sequencing technology is now used widely to probe these protein-DNA interactions and to profile gene expression at a genome-wide scale. As the cost of DNA sequencing continues to fall, the interpretation of the ever increasing amount of data generated represents a considerable challenge. We have developed ngs.plot - a standalone program to visualize enrichment patterns of DNA-interacting proteins at functionally important regions based on next-generation sequencing data. We demonstrate that ngs.plot is not only efficient but also scalable. We use a few examples to demonstrate that ngs.plot is easy to use and yet very powerful to generate figures that are publication ready. We conclude that ngs.plot is a useful tool to help fill the gap between massive datasets and genomic information in this era of big sequencing data.

  6. ngs (notochord granular surface) gene encodes a novel type of intermediate filament family protein essential for notochord maintenance in zebrafish.

    Science.gov (United States)

    Tong, Xiangjun; Xia, Zhidan; Zu, Yao; Telfer, Helena; Hu, Jing; Yu, Jingyi; Liu, Huan; Zhang, Quan; Sodmergen; Lin, Shuo; Zhang, Bo

    2013-01-25

    The notochord is an important organ involved in embryonic patterning and locomotion. In zebrafish, the mature notochord consists of a single stack of fully differentiated, large vacuolated cells called chordocytes, surrounded by a single layer of less differentiated notochordal epithelial cells called chordoblasts. Through genetic analysis of zebrafish lines carrying pseudo-typed retroviral insertions, a mutant exhibiting a defective notochord with a granular appearance was isolated, and the corresponding gene was identified as ngs (notochord granular surface), which was specifically expressed in the notochord. In the mutants, the notochord started to degenerate from 32 hours post-fertilization, and the chordocytes were then gradually replaced by smaller cells derived from chordoblasts. The granular notochord phenotype was alleviated by anesthetizing the mutant embryos with tricaine to prevent muscle contraction and locomotion. Phylogenetic analysis showed that ngs encodes a new type of intermediate filament (IF) family protein, which we named chordostatin based on its function. Under the transmission electron microcopy, bundles of 10-nm-thick IF-like filaments were enriched in the chordocytes of wild-type zebrafish embryos, whereas the chordocytes in ngs mutants lacked IF-like structures. Furthermore, chordostatin-enhanced GFP (EGFP) fusion protein assembled into a filamentous network specifically in chordocytes. Taken together, our work demonstrates that ngs encodes a novel type of IF protein and functions to maintain notochord integrity for larval development and locomotion. Our work sheds light on the mechanisms of notochord structural maintenance, as well as the evolution and biological function of IF family proteins.

  7. MutAid: Sanger and NGS Based Integrated Pipeline for Mutation Identification, Validation and Annotation in Human Molecular Genetics.

    Directory of Open Access Journals (Sweden)

    Ram Vinay Pandey

    Full Text Available Traditional Sanger sequencing as well as Next-Generation Sequencing have been used for the identification of disease causing mutations in human molecular research. The majority of currently available tools are developed for research and explorative purposes and often do not provide a complete, efficient, one-stop solution. As the focus of currently developed tools is mainly on NGS data analysis, no integrative solution for the analysis of Sanger data is provided and consequently a one-stop solution to analyze reads from both sequencing platforms is not available. We have therefore developed a new pipeline called MutAid to analyze and interpret raw sequencing data produced by Sanger or several NGS sequencing platforms. It performs format conversion, base calling, quality trimming, filtering, read mapping, variant calling, variant annotation and analysis of Sanger and NGS data under a single platform. It is capable of analyzing reads from multiple patients in a single run to create a list of potential disease causing base substitutions as well as insertions and deletions. MutAid has been developed for expert and non-expert users and supports four sequencing platforms including Sanger, Illumina, 454 and Ion Torrent. Furthermore, for NGS data analysis, five read mappers including BWA, TMAP, Bowtie, Bowtie2 and GSNAP and four variant callers including GATK-HaplotypeCaller, SAMTOOLS, Freebayes and VarScan2 pipelines are supported. MutAid is freely available at https://sourceforge.net/projects/mutaid.

  8. MutAid: Sanger and NGS Based Integrated Pipeline for Mutation Identification, Validation and Annotation in Human Molecular Genetics.

    Science.gov (United States)

    Pandey, Ram Vinay; Pabinger, Stephan; Kriegner, Albert; Weinhäusel, Andreas

    2016-01-01

    Traditional Sanger sequencing as well as Next-Generation Sequencing have been used for the identification of disease causing mutations in human molecular research. The majority of currently available tools are developed for research and explorative purposes and often do not provide a complete, efficient, one-stop solution. As the focus of currently developed tools is mainly on NGS data analysis, no integrative solution for the analysis of Sanger data is provided and consequently a one-stop solution to analyze reads from both sequencing platforms is not available. We have therefore developed a new pipeline called MutAid to analyze and interpret raw sequencing data produced by Sanger or several NGS sequencing platforms. It performs format conversion, base calling, quality trimming, filtering, read mapping, variant calling, variant annotation and analysis of Sanger and NGS data under a single platform. It is capable of analyzing reads from multiple patients in a single run to create a list of potential disease causing base substitutions as well as insertions and deletions. MutAid has been developed for expert and non-expert users and supports four sequencing platforms including Sanger, Illumina, 454 and Ion Torrent. Furthermore, for NGS data analysis, five read mappers including BWA, TMAP, Bowtie, Bowtie2 and GSNAP and four variant callers including GATK-HaplotypeCaller, SAMTOOLS, Freebayes and VarScan2 pipelines are supported. MutAid is freely available at https://sourceforge.net/projects/mutaid.

  9. AECB staff annual assessment of the Pickering A and B Nuclear Generating Stations for the year 1995

    International Nuclear Information System (INIS)

    1996-06-01

    This report is the Atomic Energy Control Board (AECB) staff assessment of safety at the Pickering Nuclear Generating Station (PNGS-A and PNGS-B) for 1995. Our on-site Project Officers and Ottawa-based specialists monitored the stations throughout the year. In 1995, compliance with the Transportation Packaging of Radioactive Materials Regulations and the Cost Recovery Fees Regulations was satisfactory. The performance of the special safety systems was good. Releases of radioactive materials from the station were low and well below the legal limits for public safety. 10 tabs., 7 figs

  10. Interpretation of 131I hippuran renocystogram using vascular invasion segment systemic flow, and DYNA CAMERA II Picker

    International Nuclear Information System (INIS)

    Morcellet, J.L.; Baret, A.

    A quantitative approximation of flows of fluids from each kidney (renal clearances urinary flows), of the hippuran mean stay time into each kidney was proposed. These times are decomposed into cortical transit mean time and into pyelocavities mean stay time. The use of a dual isotope scintillation Dyna Camera II Picker changes the collecting of the data and permits the simultaneous measurement of cardiac output which is required for their treatment. This treatment is carried out by the mean of a videotape recorder which authorizes delayed time work and by the mean of a hundred channels computer, which displays numerical data and their integration [fr

  11. BioVLAB-MMIA-NGS: microRNA-mRNA integrated analysis using high-throughput sequencing data.

    Science.gov (United States)

    Chae, Heejoon; Rhee, Sungmin; Nephew, Kenneth P; Kim, Sun

    2015-01-15

    It is now well established that microRNAs (miRNAs) play a critical role in regulating gene expression in a sequence-specific manner, and genome-wide efforts are underway to predict known and novel miRNA targets. However, the integrated miRNA-mRNA analysis remains a major computational challenge, requiring powerful informatics systems and bioinformatics expertise. The objective of this study was to modify our widely recognized Web server for the integrated mRNA-miRNA analysis (MMIA) and its subsequent deployment on the Amazon cloud (BioVLAB-MMIA) to be compatible with high-throughput platforms, including next-generation sequencing (NGS) data (e.g. RNA-seq). We developed a new version called the BioVLAB-MMIA-NGS, deployed on both Amazon cloud and on a high-performance publicly available server called MAHA. By using NGS data and integrating various bioinformatics tools and databases, BioVLAB-MMIA-NGS offers several advantages. First, sequencing data is more accurate than array-based methods for determining miRNA expression levels. Second, potential novel miRNAs can be detected by using various computational methods for characterizing miRNAs. Third, because miRNA-mediated gene regulation is due to hybridization of an miRNA to its target mRNA, sequencing data can be used to identify many-to-many relationship between miRNAs and target genes with high accuracy. http://epigenomics.snu.ac.kr/biovlab_mmia_ngs/. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  12. Pickering emulsion stabilized by cashew gum- poly-l-lactide copolymer nanoparticles: Synthesis, characterization and amphotericin B encapsulation.

    Science.gov (United States)

    Richter, A R; Feitosa, J P A; Paula, H C B; Goycoolea, F M; de Paula, R C M

    2018-04-01

    In this work, we provide proof-of-concept of formation, physical characteristics and potential use as a drug delivery formulation of Pickering emulsions (PE) obtained by a novel method that combines nanoprecipitation with subsequent spontaneous emulsification process. To this end, pre-formed ultra-small (d.∼10 nm) nanoprecipitated nanoparticles of hydrophobic derivatives of cashew tree gum grafted with polylactide (CGPLAP), were conceived to stabilize Pickering emulsions obtained by spontaneous emulsification. These were also loaded with Amphotericin B (AmB), a drug of low oral bioavailability used in the therapy of neglected diseases such as leishmaniasis. The graft reaction was performed in two CG/PLA molar ratio conditions (1:1 and 1:10). Emulsions were prepared by adding the organic phase (Miglyol 812 ® ) in the aqueous phase (nanoprecipitated CGPLAP), resulting the immediate emulsion formation. The isolation by centrifugation does not destabilize or separate the nanoparticles from oil droplets of the PE emulsion. Emulsions with CGPLAP 1:1 presented unimodal distributions at different CGPLA concentration, lower values in size and PDI and the best stability over time. The AmB was incorporated in the emulsions with a process efficiency of 21-47%, as determined by UV-vis. AmB in CGPLAP emulsions is in less aggregated state than observed in commercial AmB formulation. Copyright © 2018 Elsevier B.V. All rights reserved.

  13. Ring thermal shield piping modification at Pickering Nuclear Generating Station 'A' Unit 1

    International Nuclear Information System (INIS)

    Brown, R.; Cobanoglu, M.M.

    1995-01-01

    Each of the four Pickering Nuclear Generating Station A (PNGSA) CANDU units was constructed with its reactor and dump tank surrounded by a concrete Calandria Vault (CV). The Ring Thermal Shield (RTS) system at PNGSA units is a water cooled structure with internal cooling channels with the purpose of attenuating excessive heat flux from the calandria shell to the end shield rings and adjoining concrete (Figure 1). In newer CANDU units the reactor calandria vessel is surrounded by a large water filled shield tank which eliminates the requirement for the RTS system. The RTS structures are situated in the space between the calandria and the vault walls. Each RTS is assembled from eight flat sided carbon steel segments, tilted towards the calandria and supported from the end shield rings. Cooling water to the RTS is supplied by carbon steel cooling pipes with a portion of the pipe run embedded in the vault walls. Flow through each RTS is divided into two independent circuits, having an inlet and an outlet cooling line. There are four locations of RTS inlet and outlet cooling lines. The inlet lines are located at the bottom and the outlet lines at the top of the RTS. The 'L' shaped section of RTS inlet and outlet cooling lines, from the RTS waterbox to the start of embedded portion at the concrete wall, had become defective due to corrosion induced by excessive Moisture levels in the calandria vaults. An on-line leak sealing capability was developed and placed in service in all four PNGSA units. However, a leak found during the 1994 Unit 1 outage was too large,to seal with the current capability, forcing Ontario Hydro (OH) to develop a method to replace the corroded pipes. The repair project was subject to some lofty performance targets. All tools had to be able to withstand dose rates of up to 3000 Rem/hour. These tools, along with procedures and personnel had to successfully repair the RTS system within 6 months otherwise a costly outage extension would result. This

  14. Exploring the role of picker personality in predicting picking performance with pick by voice, pick to light and RF-terminal picking

    NARCIS (Netherlands)

    de Vries, J.; de Koster, R.; Stam, D.

    2016-01-01

    Order pickers and individual differences between them could have a substantial impact on picking performance, but are largely ignored in studies on order picking. This paper explores the role of individual differences in picking performance with various picking tools (pick by voice, RF-terminal

  15. Waste picker livelihoods and inclusive neoliberal municipal solid waste management policies: The case of the La Chureca garbage dump site in Managua, Nicaragua.

    Science.gov (United States)

    Hartmann, Chris

    2018-01-01

    The modernization (i.e. mechanization, formalization, and capital intensification) and enclosure of municipal solid waste management (MSWM) systems threaten waste picker livelihoods. From 2009 to 2013, a major development project, embodying traditional neoliberal policies with inclusive social policies, transformed the Managua, Nicaragua, municipal solid waste site from an open-air dump where as many as 2,000 informal waste pickers toiled to a sanitary landfill. To investigate waste pickers' social and economic condition, including labor characteristics, household income, and poverty incidence, after the project's completion, 146 semi-structured survey questionnaires were administered to four communities adjacent to the landfill and 45 semi-structured interviews were completed with key stakeholders. Findings indicate that hundreds of waste pickers were displaced by the project, employment benefits from the project were unevenly distributed by neighborhood, and informal waste picking endures due to persistent impoverishment, thereby contributing to continued social and economic marginalization and environmental degradation. The findings highlight the limitations of inclusive neoliberal development efforts to transform MSWM in a low-income country. Copyright © 2017 Elsevier Ltd. All rights reserved.

  16. Preparation of stable Pickering emulsions with short, medium and long chain fats and starch nanocrystals and their in vitro digestion properties

    Science.gov (United States)

    Pickering emulsions are receiving more attention as delivery systems in food and pharmaceuticals because they can be formulated with nontoxic food ingredients to form stable emulsions. In this study, 40-100 nm starch nanocrystals (SNCs) prepared from acid hydrolysis of waxy maize starches were used ...

  17. NGS Analysis of Human Embryo Culture Media Reveals miRNAs of Extra Embryonic Origin.

    Science.gov (United States)

    Sánchez-Ribas, Immaculada; Diaz-Gimeno, Patricia; Quiñonero, Alicia; Ojeda, María; Larreategui, Zaloa; Ballesteros, Agustín; Domínguez, Francisco

    2018-01-01

    Our objective in this work was to isolate, identify, and compare micro-RNAs (miRNAs) found in spent culture media of euploid and aneuploid in vitro fertilization (IVF) embryos. Seventy-two embryos from 62 patients were collected, and their spent media were retained. A total of 108 spent conditioned media samples were analyzed (n = 36 day 3 euploid embryos, n = 36 day 3 aneuploid embryos, and n = 36 matched control media). Fifty hed-control media embryos were analyzed using next-generation sequencing (NGS) technology. We detected 53 known human miRNAs present in the spent conditioned media of euploid and aneuploid IVF embryos. miR-181b-5p and miR-191-5p were found the most represented. We validated our results by quantitative polymerase chain reaction (qPCR), but no significant results were obtained between the groups. In conclusion, we obtained the list of miRNAs present in the spent conditioned media from euploid and aneuploid IVF embryos, but our data suggest that these miRNAs could have a nonembryonic origin.

  18. NGS combined with phylogenetic analysis to detect HIV-1 dual infection in Romanian people who inject drugs.

    Science.gov (United States)

    Popescu, Bogdan; Banica, Leontina; Nicolae, Ionelia; Radu, Eugen; Niculescu, Iulia; Abagiu, Adrian; Otelea, Dan; Paraschiv, Simona

    2018-04-04

    Dual HIV infections are possible and likely in people who inject drugs (PWID). Thirty-eight newly diagnosed patients, 19 PWID and 19 heterosexually HIV infected were analysed. V2-V3 loop of HIV-1 env gene was sequenced on the NGS platform 454 GSJunior (Roche). HIV-1 dual/multiple infections were identified in five PWID. For three of these patients, the reconstructed variants belonged to pure F1 subtype and CRF14_BG strains according to phylogenetic analysis. New recombinant forms between these parental strains were identified in two PWID samples. NGS data can provide, with the help of phylogenetic analysis, important insights about the intra-host sub-population structure. Copyright © 2018. Published by Elsevier Masson SAS.

  19. Update of the Picker C9 irradiator control system of the gamma II room of the secondary laboratory of dosimetric calibration; Actualizacion del sistema de control del irradiador Picker C9 de la sala gamma II del laboratorio secundario de calibracion dosimetrica

    Energy Technology Data Exchange (ETDEWEB)

    Simon S, L. E.

    2016-07-01

    The Picker C9 irradiator is responsible for the calibration of different radiological equipment and the control system that maintains it in operation is designed in the graphical programming software LabVIEW (Laboratory Virtual Instrumentation Engineering Workbench), being its major advantages: the different types of communication, easy interconnection with other software and the recognition of different hardware devices, among others. Operation of the irradiator control system is performed with the NI-Usb-6008 (DAQ) data acquisition module of the National Instruments Company. The purpose of this work is to update the routines that make the Picker C9 control system of the gamma II room of the secondary laboratory of dosimetric calibration, using the graphic programming software LabVIEW, as well as to configure the new acquisition hardware of data that is implemented to control the Picker C9 irradiator system and ensure its operation. (Author)

  20. Next-generation sequencing (NGS) for assessment of microbial water quality: current progress, challenges, and future opportunities

    OpenAIRE

    BoonFei eTan; Charmaine Marie Ng; Jean Pierre Nshimyimana; Jean Pierre Nshimyimana; Lay-Leng eLoh; Lay-Leng eLoh; Karina Yew-Hoong Gin; Janelle Renee Thompson; Janelle Renee Thompson

    2015-01-01

    Water quality is an emergent property of a complex system comprised of interacting microbial populations and introduced microbial and chemical contaminants. Studies leveraging next-generation sequencing (NGS) technologies are providing new insights into the ecology of microbially mediated processes that influence fresh water quality such as algal blooms, contaminant biodegradation, and pathogen dissemination. In addition, sequencing methods targeting small subunit (SSU) rRNA hypervariable reg...

  1. ngs (Notochord Granular Surface) Gene Encodes a Novel Type of Intermediate Filament Family Protein Essential for Notochord Maintenance in Zebrafish*

    Science.gov (United States)

    Tong, Xiangjun; Xia, Zhidan; Zu, Yao; Telfer, Helena; Hu, Jing; Yu, Jingyi; Liu, Huan; Zhang, Quan; Sodmergen; Lin, Shuo; Zhang, Bo

    2013-01-01

    The notochord is an important organ involved in embryonic patterning and locomotion. In zebrafish, the mature notochord consists of a single stack of fully differentiated, large vacuolated cells called chordocytes, surrounded by a single layer of less differentiated notochordal epithelial cells called chordoblasts. Through genetic analysis of zebrafish lines carrying pseudo-typed retroviral insertions, a mutant exhibiting a defective notochord with a granular appearance was isolated, and the corresponding gene was identified as ngs (notochord granular surface), which was specifically expressed in the notochord. In the mutants, the notochord started to degenerate from 32 hours post-fertilization, and the chordocytes were then gradually replaced by smaller cells derived from chordoblasts. The granular notochord phenotype was alleviated by anesthetizing the mutant embryos with tricaine to prevent muscle contraction and locomotion. Phylogenetic analysis showed that ngs encodes a new type of intermediate filament (IF) family protein, which we named chordostatin based on its function. Under the transmission electron microcopy, bundles of 10-nm-thick IF-like filaments were enriched in the chordocytes of wild-type zebrafish embryos, whereas the chordocytes in ngs mutants lacked IF-like structures. Furthermore, chordostatin-enhanced GFP (EGFP) fusion protein assembled into a filamentous network specifically in chordocytes. Taken together, our work demonstrates that ngs encodes a novel type of IF protein and functions to maintain notochord integrity for larval development and locomotion. Our work sheds light on the mechanisms of notochord structural maintenance, as well as the evolution and biological function of IF family proteins. PMID:23132861

  2. Biodiversity Monitoring Using NGS Approaches on Unusual Substrates (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)

    Energy Technology Data Exchange (ETDEWEB)

    Gilbert, Tom

    2013-03-01

    Tom Gilbert of the Natural History Museum of Denmark on "Biodiversity monitoring using NGS approaches on unusual substrates" at the 8th Annual Genomics of Energy & Environment Meeting in Walnut Creek, Calif.

  3. Effective Analysis of NGS Metagenomic Data with Ultra-Fast Clustering Algorithms (MICW - Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    Energy Technology Data Exchange (ETDEWEB)

    Li, Weizhong

    2011-10-12

    San Diego Supercomputer Center's Weizhong Li on "Effective Analysis of NGS Metagenomic Data with Ultra-fast Clustering Algorithms" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

  4. Radiological pathways analysis for spent solvents from the boiler chemical cleaning at the Pickering Nuclear Site

    International Nuclear Information System (INIS)

    Garisto, N.C.; Eslami, Z.; Hodgins, S.; Beaman, T.; Von Svoboda, S.; Marczak, J.

    2006-01-01

    Spent solvents are generated as a result of Boiler Chemical Cleanings (BCC) at CANDU reactor sites. These solutions contain small amount of radioactivity from a number of different sources including: Cut tubes - short sections of boiler tubes are infrequently removed from the boilers for a detailed characterization. These tubes are typically only plugged at the tubesheet allowing the primary side deposits to be exposed to BCC solvents. Tube leaks - primary to secondary side leaks also occur infrequently as a result of tube degradation. Radioactivity from the leaking fluid can consequently be deposited in the sludge on the secondary side of the tubes. Diffusion of tritium - during normal operation of the reactor units, tritium slowly diffuses from the heavy water in the primary heat-transfer system to the light-water coolant on the secondary side. Some of this tritium is retained in the secondary side deposits. The Pickering Nuclear Generating Station (PNGS) would like the flexibility to have several options for handling the spent solvent waste and associated rinse water from BCC. To this end, a radiological pathways analysis was undertaken to determine dose consequences associated with each option. Sample results from this study are included in this paper. The pathways analysis is used in this study to calculate dose to hypothetical receptors including individuals such as truck drivers, incinerator workers, residue (ash) handlers, residents who live near the landfill, inadvertent intruders into the landfill after closure and residents who live near the outfall. This dose is compared to a de minimis dose. A de minimis dose or dose rate represents a level of risk, which is generally accepted as being of no significance. Shipments of spent solvents and rinse water with corresponding doses below de minimis can be sent to conventional (i.e., non-radioactive) landfills for incineration and disposal as the radioactive dose associated with them is much less than natural

  5. Automated phase picker and source location algorithm for local distances using a single three component seismic station

    International Nuclear Information System (INIS)

    Saari, J.

    1989-12-01

    The paper describes procedures for automatic location of local events by using single-site, three-component (3c) seismogram records. Epicentral distance is determined from the time difference between P- and S-onsets. For onset time estimates a special phase picker algorithm is introduced. Onset detection is accomplished by comparing short-term average with long-term average after multiplication of north, east and vertical components of recording. For epicentral distances up to 100 km, errors seldom exceed 5 km. The slowness vector, essentially the azimuth, is estimated independently by using the Christoffersson et al. (1988) 'polarization' technique, although a priori knowledge of the P-onset time gives the best results. Differences between 'true' and observed azimuths are generally less than 12 deg C. Practical examples are given by demonstrating the viability of the procedures for automated 3c seismogram analysis. The results obtained compare favourably with those achieved by a miniarray of three stations. (orig.)

  6. Facile Route to Transparent, Strong, and Thermally Stable Nanocellulose/Polymer Nanocomposites from an Aqueous Pickering Emulsion.

    Science.gov (United States)

    Fujisawa, Shuji; Togawa, Eiji; Kuroda, Katsushi

    2017-01-09

    Cellulose nanofibril (CNF) is a promising nanofiller for polymer nanocomposite materials, and a critical challenge in designing these materials is organization of the nanostructure using a facile process. Here, we report a facile aqueous preparation process for nanostructured polystyrene (PS)/CNF composites via the formation of a CNF-stabilized Pickering emulsion. PS nanoparticles, with a narrow size distribution, were synthesized by free radical polymerization in water using CNF as a stabilizer. The nanoparticles were easily collected by filtration, and the resulting material had a composite structure of PS nanoparticles embedded in a CNF framework. The PS/CNF nanocomposite showed high optical transparency, strength, and thermal dimensional stability. Thus, this technique provides a simple and environmentally friendly method for the preparation of novel CNF/polymer nanocomposite materials.

  7. Investigations of titamium and zirconium hydrides to determine suitability of recoverable tritium immobilization for the Pickering tritium removal system

    International Nuclear Information System (INIS)

    Noga, J.O.

    1981-11-01

    A tritium removal system will be constructed at Pickering Nuclear Generating station to reduce the adverse effects of this radioactive hydrogen isotope. This report summarizes various properties of titanium and zirconium sponge hydrides which have been selected as suitable candidates for tritium product immobilization. Equilibrium pressure-composition-temperature data indicates that both materials behave suitably to provide a safe, solid form of tritium storage. Titanium tritide is recommended as the best choice due to higher dissociation pressures which can be achieved at equivalent temperatures when compared to zirconium tritide. Higher dissociation pressures would result in faster and more efficient recovery of tritium gas from the immobilized state. It is evident from the stability of these compounds that their utilization as tritides will greatly enhance the integrity of tritium storage

  8. A random forest classifier for detecting rare variants in NGS data from viral populations

    Directory of Open Access Journals (Sweden)

    Raunaq Malhotra

    Full Text Available We propose a random forest classifier for detecting rare variants from sequencing errors in Next Generation Sequencing (NGS data from viral populations. The method utilizes counts of varying length of k-mers from the reads of a viral population to train a Random forest classifier, called MultiRes, that classifies k-mers as erroneous or rare variants. Our algorithm is rooted in concepts from signal processing and uses a frame-based representation of k-mers. Frames are sets of non-orthogonal basis functions that were traditionally used in signal processing for noise removal. We define discrete spatial signals for genomes and sequenced reads, and show that k-mers of a given size constitute a frame.We evaluate MultiRes on simulated and real viral population datasets, which consist of many low frequency variants, and compare it to the error detection methods used in correction tools known in the literature. MultiRes has 4 to 500 times less false positives k-mer predictions compared to other methods, essential for accurate estimation of viral population diversity and their de-novo assembly. It has high recall of the true k-mers, comparable to other error correction methods. MultiRes also has greater than 95% recall for detecting single nucleotide polymorphisms (SNPs and fewer false positive SNPs, while detecting higher number of rare variants compared to other variant calling methods for viral populations. The software is available freely from the GitHub link https://github.com/raunaq-m/MultiRes. Keywords: Sequencing error detection, Reference free methods, Next-generation sequencing, Viral populations, Multi-resolution frames, Random forest classifier

  9. Vipie: web pipeline for parallel characterization of viral populations from multiple NGS samples.

    Science.gov (United States)

    Lin, Jake; Kramna, Lenka; Autio, Reija; Hyöty, Heikki; Nykter, Matti; Cinek, Ondrej

    2017-05-15

    Next generation sequencing (NGS) technology allows laboratories to investigate virome composition in clinical and environmental samples in a culture-independent way. There is a need for bioinformatic tools capable of parallel processing of virome sequencing data by exactly identical methods: this is especially important in studies of multifactorial diseases, or in parallel comparison of laboratory protocols. We have developed a web-based application allowing direct upload of sequences from multiple virome samples using custom parameters. The samples are then processed in parallel using an identical protocol, and can be easily reanalyzed. The pipeline performs de-novo assembly, taxonomic classification of viruses as well as sample analyses based on user-defined grouping categories. Tables of virus abundance are produced from cross-validation by remapping the sequencing reads to a union of all observed reference viruses. In addition, read sets and reports are created after processing unmapped reads against known human and bacterial ribosome references. Secured interactive results are dynamically plotted with population and diversity charts, clustered heatmaps and a sortable and searchable abundance table. The Vipie web application is a unique tool for multi-sample metagenomic analysis of viral data, producing searchable hits tables, interactive population maps, alpha diversity measures and clustered heatmaps that are grouped in applicable custom sample categories. Known references such as human genome and bacterial ribosomal genes are optionally removed from unmapped ('dark matter') reads. Secured results are accessible and shareable on modern browsers. Vipie is a freely available web-based tool whose code is open source.

  10. Networks of recyclable material waste-picker's cooperatives: an alternative for the solid waste management in the city of Rio de Janeiro.

    Science.gov (United States)

    Tirado-Soto, Magda Martina; Zamberlan, Fabio Luiz

    2013-04-01

    The objective of this study is to discuss the role of networks formed of waste-picker cooperatives in ameliorating problems of final disposal of solid waste in the city of Rio de Janeiro, since the city's main landfill will soon have to close because of exhausted capacity. However, it is estimated that in the city of Rio de Janeiro there are around five thousand waste-pickers working in poor conditions, with lack of physical infrastructure and training, but contributing significantly by diverting solid waste from landfills. According to the Sustainable Development Indicators (IBGE, 2010a,b) in Brazil, recycling rates hover between 45% and 55%. In the municipality of Rio de Janeiro, only 1% of the waste produced is collected selectively by the government (COMLURB, 2010), demonstrating that recycling is mainly performed by waste-pickers. Furthermore, since the recycling market is an oligopsony that requires economies of scale to negotiate directly with industries, the idea of working in networks of cooperatives meets the demands for joint marketing of recyclable materials. Thus, this work presents a method for creating and structuring a network of recycling cooperatives, with prior training for working in networks, so that the expected synergies and joint efforts can lead to concrete results. We intend to demonstrate that it is first essential to strengthen the waste-pickers' cooperatives in terms of infrastructure, governance and training so that solid waste management can be environmentally, socially and economically sustainable in the city of Rio de Janeiro. Copyright © 2012 Elsevier Ltd. All rights reserved.

  11. An Infrared Census of DUST in Nearby Galaxies with Spitzer (DUSTiNGS). IV. Discovery of High-redshift AGB Analogs

    Science.gov (United States)

    Boyer, M. L.; McQuinn, K. B. W.; Groenewegen, M. A. T.; Zijlstra, A. A.; Whitelock, P. A.; van Loon, J. Th.; Sonneborn, G.; Sloan, G. C.; Skillman, E. D.; Meixner, M.; McDonald, I.; Jones, O. C.; Javadi, A.; Gehrz, R. D.; Britavskiy, N.; Bonanos, A. Z.

    2017-12-01

    The survey for DUST in Nearby Galaxies with Spitzer (DUSTiNGS) identified several candidate Asymptotic Giant Branch (AGB) stars in nearby dwarf galaxies and showed that dust can form even in very metal-poor systems ({\\boldsymbol{Z}}∼ 0.008 {Z}ȯ ). Here, we present a follow-up survey with WFC3/IR on the Hubble Space Telescope (HST), using filters that are capable of distinguishing carbon-rich (C-type) stars from oxygen-rich (M-type) stars: F127M, F139M, and F153M. We include six star-forming DUSTiNGS galaxies (NGC 147, IC 10, Pegasus dIrr, Sextans B, Sextans A, and Sag DIG), all more metal-poor than the Magellanic Clouds and spanning 1 dex in metallicity. We double the number of dusty AGB stars known in these galaxies and find that most are carbon rich. We also find 26 dusty M-type stars, mostly in IC 10. Given the large dust excess and tight spatial distribution of these M-type stars, they are most likely on the upper end of the AGB mass range (stars undergoing Hot Bottom Burning). Theoretical models do not predict significant dust production in metal-poor M-type stars, but we see evidence for dust excess around M-type stars even in the most metal-poor galaxies in our sample (12+{log}({{O}}/{{H}})=7.26{--}7.50). The low metallicities and inferred high stellar masses (up to ∼10 {M}ȯ ) suggest that AGB stars can produce dust very early in the evolution of galaxies (∼30 Myr after they form), and may contribute significantly to the dust reservoirs seen in high-redshift galaxies. Based on observations made with the NASA/ESA Hubble Space Telescope at the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS 5-26555. These observations are associated with program GO-14073.

  12. Hungarian Marfan family with large FBN1 deletion calls attention to copy number variation detection in the current NGS era

    Science.gov (United States)

    Ágg, Bence; Meienberg, Janine; Kopps, Anna M.; Fattorini, Nathalie; Stengl, Roland; Daradics, Noémi; Pólos, Miklós; Bors, András; Radovits, Tamás; Merkely, Béla; De Backer, Julie; Szabolcs, Zoltán; Mátyás, Gábor

    2018-01-01

    Copy number variations (CNVs) comprise about 10% of reported disease-causing mutations in Mendelian disorders. Nevertheless, pathogenic CNVs may have been under-detected due to the lack or insufficient use of appropriate detection methods. In this report, on the example of the diagnostic odyssey of a patient with Marfan syndrome (MFS) harboring a hitherto unreported 32-kb FBN1 deletion, we highlight the need for and the feasibility of testing for CNVs (>1 kb) in Mendelian disorders in the current next-generation sequencing (NGS) era. PMID:29850152

  13. Histidine-functionalized carbon-based dot-Zinc(II) nanoparticles as a novel stabilizer for Pickering emulsion synthesis of polystyrene microspheres.

    Science.gov (United States)

    Ruiyi, Li; Zaijun, Li; Junkang, Liu

    2017-05-01

    Carbon-based dots (CDs) are nanoparticles with size-dependent optical and electronic properties that have been widely applied in energy-efficient displays and lighting, photovoltaic devices and biological markers. However, conventional CDs are difficult to be used as ideal stabilizer for Pickering emulsion due to its irrational amphiphilic structure. The study designed and synthesized a new histidine-functionalized carbon dot-Zinc(II) nanoparticles, which is termed as His-CD-Zn. The His-CD was made via one-step hydrothermal treatment of histidine and maleic acid. The His-CD reacted with Zn 2+ to form His-CD-Zn. The as-prepared His-CD-Zn was used as a solid particle surfactant for stabilizing styrene-in-water emulsion. The Pickering emulsion exhibits high stability and sensitive pH-switching behaviour. The introduction of S 2 O 8 2- triggers the emulsion polymerization of styrene. The resulted polystyrene microsphere was well coated with His-CDs on the surface. It was successfully used as an ideal adsorbent for removal of heavy metallic ions from water with high adsorption capacity. The study also provides a prominent approach for fabrication of amphiphilic carbon-based nanoparticles for stabilizing Pickering emulsion. Copyright © 2017 Elsevier Inc. All rights reserved.

  14. Introduction of the Python script STRinNGS for analysis of STR regions in FASTQ or BAM files and expansion of the Danish STR sequence database to 11 STRs

    DEFF Research Database (Denmark)

    Friis, Susanne L; Buchard, Anders; Rockenbauer, Eszter

    2016-01-01

    This work introduces the in-house developed Python application STRinNGS for analysis of STR sequence elements in BAM or FASTQ files. STRinNGS identifies sequence reads with STR loci by their flanking sequences, it analyses the STR sequence and the flanking regions, and generates a report with the......This work introduces the in-house developed Python application STRinNGS for analysis of STR sequence elements in BAM or FASTQ files. STRinNGS identifies sequence reads with STR loci by their flanking sequences, it analyses the STR sequence and the flanking regions, and generates a report...

  15. ALF: a strategy for identification of unauthorized GMOs in complex mixtures by a GW-NGS method and dedicated bioinformatics analysis.

    Science.gov (United States)

    Košir, Alexandra Bogožalec; Arulandhu, Alfred J; Voorhuijzen, Marleen M; Xiao, Hongmei; Hagelaar, Rico; Staats, Martijn; Costessi, Adalberto; Žel, Jana; Kok, Esther J; Dijk, Jeroen P van

    2017-10-26

    The majority of feed products in industrialised countries contains materials derived from genetically modified organisms (GMOs). In parallel, the number of reports of unauthorised GMOs (UGMOs) is gradually increasing. There is a lack of specific detection methods for UGMOs, due to the absence of detailed sequence information and reference materials. In this research, an adapted genome walking approach was developed, called ALF: Amplification of Linearly-enriched Fragments. Coupling of ALF to NGS aims for simultaneous detection and identification of all GMOs, including UGMOs, in one sample, in a single analysis. The ALF approach was assessed on a mixture made of DNA extracts from four reference materials, in an uneven distribution, mimicking a real life situation. The complete insert and genomic flanking regions were known for three of the included GMO events, while for MON15985 only partial sequence information was available. Combined with a known organisation of elements, this GMO served as a model for a UGMO. We successfully identified sequences matching with this organisation of elements serving as proof of principle for ALF as new UGMO detection strategy. Additionally, this study provides a first outline of an automated, web-based analysis pipeline for identification of UGMOs containing known GM elements.

  16. Using GC-FID to Quantify the Removal of 4-sec-Butylphenol from NGS Solvent by NaOH

    Energy Technology Data Exchange (ETDEWEB)

    Sloop, Jr., Frederick V. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Moyer, Bruce A. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

    2014-12-01

    A caustic wash of the solvent used in the Next-Generation Caustic-Side Solvent Extraction (NG-CSSX) process was found to remove the modifier breakdown product 4-sec-butylphenol (SBP) with varying efficiency depending on the aqueous NaOH concentration. Recent efforts at ORNL have aimed at characterizing the flowsheet chemistry and reducing the technical uncertainties of the NG-CSSX process. One technical uncertainty has been the efficacy of caustic washing of the solvent for the removal of lipophilic anions, in particular, the efficient removal of SBP, an important degradation product of the solvent modifier, Cs-7SB. In order to make this determination, it was necessary to develop a sensitive and reliable analytical technique for the detection and quantitation of SBP. This report recounts the development of a GC-FID-based (Gas Chromatography Flame Ionization Detection) technique for analyzing SBP and the utilization of the technique to subsequently confirm the ability of the caustic wash to efficiently remove SBP from the Next Generation Solvent (NGS) used in NG-CSSX. In particular, the developed technique was used to monitor the amount of SBP removed from a simple solvent and the full NGS by contact with sodium hydroxide wash solutions over a range of concentrations. The results show that caustic washing removes SBP with effectively the same efficiency as it did in the original Caustic-Side Solvent Extraction (CSSX) process.

  17. Bruce NGS a loss of flow analysis for effectiveness of level 2 defence-in-depth provisions

    International Nuclear Information System (INIS)

    Won, W.; Jiang, Y.; Kwee, M.; Xue, J.

    2014-01-01

    The concept of defence-in-depth is applied to CANDU (CANada Deuterium Uranium) reactor designs and operations to provide series of levels of defence to prevent accidents progressing and to provide protection for reactor and public safety. The level 2 defence-in-depth provisions are designed to detect and intercept deviation from normal operation in order to prevent anticipated operating occurrences (AOOs) from escalating to accident conditions, and to return the plant to a state of normal operations, according to the Canada Nuclear Safety Commission (CNSC) regulatory document RD-337. Historically, safety analysis has focused on the effectiveness of level 3 defence-in-depth provisions in accident conditions, and the effectiveness of level 2 defence-in-depth has not been assessed. In this study, the effectiveness of Level 2 defence-in-depth is assessed for loss of flow (LOF) events for Bruce Nuclear Generating Station (NGS) A reactors. The level 2 defence-in-depth in Bruce NGS A design is identified to be the stepback function of reactor regulating system (RRS). The behavior of RRS stepback following the initiation of loss of flow event is simulated using RFSP/TUF/RRS - em coupled code. The behavior of full system and single channel is simulated and assessed against the acceptance criteria - fitness for service of systems, structures and components (SSCs). (author)

  18. Bruce NGS a loss of flow analysis for effectiveness of level 2 defence-in-depth provisions

    Energy Technology Data Exchange (ETDEWEB)

    Won, W. [AMEC NSS, Toronto, ON (Canada); Jiang, Y.; Kwee, M.; Xue, J. [Bruce Power, Toronto, ON (Canada)

    2014-07-01

    The concept of defence-in-depth is applied to CANDU (CANada Deuterium Uranium) reactor designs and operations to provide series of levels of defence to prevent accidents progressing and to provide protection for reactor and public safety. The level 2 defence-in-depth provisions are designed to detect and intercept deviation from normal operation in order to prevent anticipated operating occurrences (AOOs) from escalating to accident conditions, and to return the plant to a state of normal operations, according to the Canada Nuclear Safety Commission (CNSC) regulatory document RD-337. Historically, safety analysis has focused on the effectiveness of level 3 defence-in-depth provisions in accident conditions, and the effectiveness of level 2 defence-in-depth has not been assessed. In this study, the effectiveness of Level 2 defence-in-depth is assessed for loss of flow (LOF) events for Bruce Nuclear Generating Station (NGS) A reactors. The level 2 defence-in-depth in Bruce NGS A design is identified to be the stepback function of reactor regulating system (RRS). The behavior of RRS stepback following the initiation of loss of flow event is simulated using RFSP/TUF/RRS{sub -}em coupled code. The behavior of full system and single channel is simulated and assessed against the acceptance criteria - fitness for service of systems, structures and components (SSCs). (author)

  19. Anemia em catadores de material reciclável que utilizam carrinho de propulsão humana no município de Santos Anemia in recyclable waste pickers using human driven pushcarts in the city of Santos, southeastern Brazil

    Directory of Open Access Journals (Sweden)

    Mauro Abrahão Rozman

    2010-06-01

    evaluation and venous blood was drawn for complete blood count and serological testing for HIV, HCV, HBV, and syphilis. Statistical analysis included univariate and multivariate (logistic regression analyses testing for the association between anemia and risk factors. RESULTS: The prevalence of anemia was 38.3%. Variables independently associated with anemia in the multivariate model were: gender (OR 2.8; 95% CI: 1.25-6.5, HIV infection (OR 6.45; 95% CI: 2.11-21.06, BMI (χ2 for trend, p < 0.01, length of time working as a picker (χ2 for trend, p < 0.01, and consumption of milk (χ2 for trend, p < 0.01 and animal protein (OR 0.30; 95% CI: 0.13-0.68. CONCLUSIONS: The prevalence of anemia among recyclable waste pickers is high even after the compulsory addition of iron to wheat and corn flours. Waste pickers have not benefited from the actions for workers' health protection established by law. Health actions targeting this occupational category should be implemented to ensure their access to health services.

  20. Os catadores de lixo e o processo de emancipação social Waste material pickers and emancipation process

    Directory of Open Access Journals (Sweden)

    Marta Pimenta Velloso

    2005-12-01

    Full Text Available O artigo tece comentários sobre o processo de organização de duas associações de catadores de materiais recicláveis. Traz à tona a problemática da exclusão, enfatizando a necessidade de inserção dos segmentos sociais marginalizados. Focaliza, como caminho de inserção, a recriação de espaços com ambiente apropriado ao desenvolvimento da criatividade e, conseqüentemente, ao processo de emancipação social. Apresenta o Pequeno Grupo como solo provisório para existência humana, onde o poder decisório se manifesta a partir da interação dinâmica entre o singular e o coletivo.The article describes the organizing process of two associations of waste and recyclings material pickers. The question of social exclusion emerges emphasizing therefore the urgent socially comeback of left out segments of people. It shows that the way to resocializing is the creation of environmentally approprieted spaces to develop creativity leading thus to self emancipation. The small group is seen as a transitory ground of human life, where the power to decide comes out as an interplay of individuals and collectives bodies.

  1. Preparation of Lignin/Sodium Dodecyl Sulfate Composite Nanoparticles and Their Application in Pickering Emulsion Template-Based Microencapsulation.

    Science.gov (United States)

    Pang, Yuxia; Wang, Shengwen; Qiu, Xueqing; Luo, Yanling; Lou, Hongming; Huang, Jinhao

    2017-12-20

    Lignin is a vastly underutilized biomass resource. The preparation of water-dispersed lignin nanoparticles is an effective way to realize the high-value utilization of lignin. However, the currently reported preparation methods of lignin nanoparticles still have some drawbacks, such as the requirement for toxic organic solvent or chemical modification, complicated operation process, and poor dispersibility. Here, lignin/sodium dodecyl sulfate (SDS) composite nanoparticles (LSNPs) with outstanding water dispersibility and a size range of 70-200 nm were facilely prepared via acidifying the mixed basic solution of alkaline lignin and SDS. No harsh chemical was needed. The formation mechanism was systematically studied. Results indicated that the LSNPs were obtained by acid precipitation of the mixed micelles formed by the self-assembly of lignin and SDS. In addition, on the basis of the LSNP-stabilized Pickering emulsions, lignin/polyurea composite microcapsules combining the excellent chemical stability of a synthetic polyurea shell with the fantastic antiphotolysis and antioxidant properties of lignin were successfully prepared.

  2. Joint Effects of Granule Size and Degree of Substitution on Octenylsuccinated Sweet Potato Starch Granules As Pickering Emulsion Stabilizers.

    Science.gov (United States)

    Li, Jinfeng; Ye, Fayin; Lei, Lin; Zhou, Yun; Zhao, Guohua

    2018-05-02

    The granules of sweet potato starch were size fractionated into three portions with significantly different median diameters ( D 50 ) of 6.67 (small-sized), 11.54 (medium-sized), and 16.96 μm (large-sized), respectively. Each portion was hydrophobized at the mass-based degrees of substitution (DS m ) of approximately 0.0095 (low), 0.0160 (medium), and 0.0230 (high). The Pickering emulsion-stabilizing capacities of modified granules were tested, and the resultant emulsions were characterized. The joint effects of granule size and DS m on emulsifying capacity (EC) were investigated by response surface methodology. For small-, medium-, and large-sized fractions, their highest emulsifying capacities are comparable but, respectively, encountered at high (0.0225), medium (0.0158), and low (0.0095) DS m levels. The emulsion droplet size increased with granule size, and the number of freely scattered granules in emulsions decreased with DS m . In addition, the term of surface density of the octenyl succinic group (SD -OSG ) was first proposed for modified starch granules, and it was proved better than DS m in interpreting the emulsifying capacities of starch granules with varying sizes. The present results implied that, as the particulate stabilizers, the optimal DS m of modified starch granules is size specific.

  3. Combining Pickering Emulsion Polymerization with Molecular Imprinting to Prepare Polymer Microspheres for Selective Solid-Phase Extraction of Malachite Green

    Directory of Open Access Journals (Sweden)

    Weixin Liang

    2017-08-01

    Full Text Available Malachite green (MG is currently posing a carcinogenic threat to the safety of human lives; therefore, it is highly desirable to develop an effective method for fast trace detection of MG. Herein, for the first time, this paper presents a systematic study on polymer microspheres, being prepared by combined Pickering emulsion polymerization and molecular imprinting, to detect and purify MG. The microspheres, molecularly imprinted with MG, show enhanced adsorption selectivity to MG, despite a somewhat lowered adsorption capacity, as compared to the counterpart without molecular imprinting. Structural features and adsorption performance of these microspheres are elucidated by different characterizations and kinetic and thermodynamic analyses. The surface of the molecularly imprinted polymer microspheres (M-PMs exhibits regular pores of uniform pore size distribution, endowing M-PMs with impressive adsorption selectivity to MG. In contrast, the microspheres without molecular imprinting show a larger average particle diameter and an uneven porous surface (with roughness and a large pore size, causing a lower adsorption selectivity to MG despite a higher adsorption capacity. Various adsorption conditions are investigated, such as pH and initial concentration of the solution with MG, for optimizing the adsorption performance of M-PMs in selectively tackling MG. The adsorption kinetics and thermodynamics are deeply discussed and analyzed, so as to provide a full picture of the adsorption behaviors of the polymer microspheres with and without the molecular imprinting. Significantly, M-PMs show promising solid-phase extraction column applications for recovering MG in a continuous extraction manner.

  4. Self-Assembled Colloidal Particle Clusters from In Situ Pickering-Like Emulsion Polymerization via Single Electron Transfer Mechanism.

    Science.gov (United States)

    Yuan, Jinfeng; Zhao, Weiting; Pan, Mingwang; Zhu, Lei

    2016-08-01

    A simple route is reported to synthesize colloidal particle clusters (CPCs) from self-assembly of in situ poly(vinylidene fluoride)/poly(styrene-co-tert-butyl acrylate) [PVDF/P(St-co-tBA)] Janus particles through one-pot seeded emulsion single electron transfer radical polymerization. In the in situ Pickering-like emulsion polymerization, the tBA/St/PVDF feed ratio and polymerization temperature are important for the formation of well-defined CPCs. When the tBA/St/PVDF feed ratio is 0.75 g/2.5 g/0.5 g and the reaction temperature is 35 °C, relatively uniform raspberry-like CPCs are obtained. The hydrophobicity of the P(St-co-tBA) domains and the affinity of PVDF to the aqueous environment are considered to be the driving force for the self-assembly of the in situ formed PVDF/P(St-co-tBA) Janus particles. The resultant raspberry-like CPCs with PVDF particles protruding outward may be promising for superhydrophobic smart coatings. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  5. Production of starch nanoparticles by dissolution and non-solvent precipitation for use in food-grade Pickering emulsions.

    Science.gov (United States)

    Saari, Hisfazilah; Fuentes, Catalina; Sjöö, Malin; Rayner, Marilyn; Wahlgren, Marie

    2017-02-10

    The aim of this study was to investigate non-solvent precipitation of starch to produce nanoparticles that could be used in Pickering emulsions. The material used was waxy maize, modified with octenyl succinic anhydride. Different methods of non-solvent precipitation were investigated, and a method based on direct mixing of an 8% starch solution and ethanol (ratio 1:1) was found to produce the smallest particles. The particle size was measured using AFM and AF4, and was found to be in the range 100-200nm. However, both larger particles and aggregates of nanoparticles were observed. The emulsion produced using the precipitated starch particles had a droplet size that between 0.5 and 45μm, compared to emulsions produced from waxy maize granules, in which had a size of 10-100μm. The drop in size contributed to increased stability against creaming. The amount of starch used for emulsion stabilization could also be substantially reduced. Copyright © 2016 The Author(s). Published by Elsevier Ltd.. All rights reserved.

  6. AECB staff annual assessment of the Pickering A and B Nuclear Generating Stations for the year 1996

    International Nuclear Information System (INIS)

    1997-06-01

    The Atomic Energy Control Board is the independent federal agency that controls all nuclear activities in Canada. A major use of nuclear energy in Canada is electricity production. The AECB assesses every station's performance against legal requirements, including the conditions in the operating licence. Each station is inspected and all aspects of the station's operation and management is reviewed. This report is the AECB staff assessment of reactor safety at the Pickering A and B Generating Stations for 1996. PNGS-A and PNGS-B operated safely during 1996. Although the risk to the workers and the public is low, major safety related changes are necessary at the stations and the sustainability of those changes needs to be demonstrated. Improvement is needed by Ontario Hydro in meeting the time limits for reporting reportable events. Ontario Hydro's follow up to events and causal factor analyses continue to need improvements. Improvements are needed to operational safety and reactor maintenance at both A and B. There are signs of improvement through Ontario Hydro's plan for recovery, and in station management changes. There also appears to be commitment to safety expressed at the highest level of the utility

  7. Load modeling for sharp V-cutter cutting litchi ( Litchi chinensis Sonn ...

    African Journals Online (AJOL)

    harvesting. Cutting load is a key parameter for 'hand-held auto-picker' operation. However, there is still no suitable model for cutting load setting. Hence, a model describing the relationship among cutting load, blade angle and friction coefficient was developed for cutting operation by sharp V-cutters. The model was based ...

  8. ChimericSeq: An open-source, user-friendly interface for analyzing NGS data to identify and characterize viral-host chimeric sequences

    Science.gov (United States)

    Shieh, Fwu-Shan; Jongeneel, Patrick; Steffen, Jamin D.; Lin, Selena; Jain, Surbhi; Song, Wei

    2017-01-01

    Identification of viral integration sites has been important in understanding the pathogenesis and progression of diseases associated with particular viral infections. The advent of next-generation sequencing (NGS) has enabled researchers to understand the impact that viral integration has on the host, such as tumorigenesis. Current computational methods to analyze NGS data of virus-host junction sites have been limited in terms of their accessibility to a broad user base. In this study, we developed a software application (named ChimericSeq), that is the first program of its kind to offer a graphical user interface, compatibility with both Windows and Mac operating systems, and optimized for effectively identifying and annotating virus-host chimeric reads within NGS data. In addition, ChimericSeq’s pipeline implements custom filtering to remove artifacts and detect reads with quantitative analytical reporting to provide functional significance to discovered integration sites. The improved accessibility of ChimericSeq through a GUI interface in both Windows and Mac has potential to expand NGS analytical support to a broader spectrum of the scientific community. PMID:28829778

  9. ChimericSeq: An open-source, user-friendly interface for analyzing NGS data to identify and characterize viral-host chimeric sequences.

    Directory of Open Access Journals (Sweden)

    Fwu-Shan Shieh

    Full Text Available Identification of viral integration sites has been important in understanding the pathogenesis and progression of diseases associated with particular viral infections. The advent of next-generation sequencing (NGS has enabled researchers to understand the impact that viral integration has on the host, such as tumorigenesis. Current computational methods to analyze NGS data of virus-host junction sites have been limited in terms of their accessibility to a broad user base. In this study, we developed a software application (named ChimericSeq, that is the first program of its kind to offer a graphical user interface, compatibility with both Windows and Mac operating systems, and optimized for effectively identifying and annotating virus-host chimeric reads within NGS data. In addition, ChimericSeq's pipeline implements custom filtering to remove artifacts and detect reads with quantitative analytical reporting to provide functional significance to discovered integration sites. The improved accessibility of ChimericSeq through a GUI interface in both Windows and Mac has potential to expand NGS analytical support to a broader spectrum of the scientific community.

  10. Eddy current magnetic bias x-probe qualification and inspection of steam generator Monel 400 tubing in Pickering Nuclear Generating Station

    International Nuclear Information System (INIS)

    Lepine, B.A.; Van Langen, J.; Obrutsky, L.

    2006-01-01

    This paper presents an overview of the x-probe MB 350 eddy current inspection array probe, for detection of open OD axial crack-like flaws in Monel 400 tubes at Pickering Nuclear Generating Station. This report contains a selection of inspection results from the field inspections performed with this probe during the 2003 and 2004 period at Pickering Nuclear Generating Station A and B. During the 2003 in-service eddy current inspection results of Pickering Nuclear Generating Station A (PNGS-A) Unit 2, a 13 mm (0.5 inch) long axial indication was detected by the CTR1 bobbin and CTR2-C4 array probes in Tube R25-C52 of Steam Generator (SG) 11 in the hot leg sludge pile region. An experimental magnetic bias X-probe, specially designed by Zetec for inspection of Monel 400 tubing, was deployed and the indication was characterized as a potential out diameter (OD) axially oriented crack. Post-inspection tube pulling and destructive examination confirmed the presence of an Environmentally Assisted Crack (EAC), approximately 80% deep and 13mm long. Due to the significance of this discovery, Ontario Power Generation (OPG) requested AECL to initiate a program for qualification of the X-probe MB 350 for the detection of OD axial cracks in medium to high magnetic permeability μ r Monel 400 PNGS-A and B steam generator tubing at different locations. The X-probe MB 350 subsequently has been deployed as a primary inspection probe for crack detection for PNGS steam generators. (author)

  11. Evaluation of NGS and RT-PCR Methods for ALK Rearrangement in European NSCLC Patients: Results from the European Thoracic Oncology Platform Lungscape Project.

    Science.gov (United States)

    Letovanec, Igor; Finn, Stephen; Zygoura, Panagiota; Smyth, Paul; Soltermann, Alex; Bubendorf, Lukas; Speel, Ernst-Jan; Marchetti, Antonio; Nonaka, Daisuke; Monkhorst, Kim; Hager, Henrik; Martorell, Miguel; Sejda, Aleksandra; Cheney, Richard; Hernandez-Losa, Javier; Verbeken, Eric; Weder, Walter; Savic, Spasenija; Di Lorito, Alessia; Navarro, Atilio; Felip, Enriqueta; Warth, Arne; Baas, Paul; Meldgaard, Peter; Blackhall, Fiona; Dingemans, Anne-Marie; Dienemann, Hendrik; Dziadziuszko, Rafal; Vansteenkiste, Johan; O'Brien, Cathal; Geiger, Thomas; Sherlock, Jon; Schageman, Jeoffrey; Dafni, Urania; Kammler, Roswitha; Kerr, Keith; Thunnissen, Erik; Stahel, Rolf; Peters, Solange

    2018-03-01

    The reported prevalence of ALK receptor tyrosine kinase gene (ALK) rearrangement in NSCLC ranges from 2% to 7%. The primary standard diagnostic method is fluorescence in situ hybridization (FISH). Recently, immunohistochemistry (IHC) has also proved to be a reproducible and sensitive technique. Reverse-transcriptase polymerase chain reaction (RT-PCR) has also been advocated, and most recently, the advent of targeted next-generation sequencing (NGS) for ALK and other fusions has become possible. This study compares anaplastic lymphoma kinase (ALK) evaluation with all four techniques in resected NSCLC from the large European Thoracic Oncology Platform Lungscape cohort. A total of 96 cases from the European Thoracic Oncology Platform Lungscape iBiobank, with any ALK immunoreactivity were examined by FISH, central RT-PCR, and NGS. An H-score higher than 120 defines IHC positivity. RNA was extracted from the same formalin-fixed, paraffin-embedded tissues. For RT-PCR, primers covered the most frequent ALK translocations. For NGS, the Oncomine Solid Tumour Fusion Transcript Kit (Thermo Fisher Scientific, Waltham, MA) was used. The concordance was assessed using the Cohen κ coefficient (two-sided α ≤ 5%). NGS provided results for 77 of the 95 cases tested (81.1%), whereas RT-PCR provided results for 77 of 96 (80.2%). Concordance occurred in 55 cases of the 60 cases tested with all four methods (43 ALK negative and 12 ALK positive). Using ALK copositivity for IHC and FISH as the criterion standard, we derived a sensitivity for RT-PCR/NGS of 70.0%/85.0%, with a specificity of 87.1%/79.0%. When either RT-PCR or NGS was combined with IHC, the sensitivity remained the same, whereas the specificity increased to 88.7% and 83.9% respectively. NGS evaluation with the Oncomine Solid Tumour Fusion transcript kit and RT-PCR proved to have high sensitivity and specificity, advocating their use in routine practice. For maximal sensitivity and specificity, ALK status should be

  12. A framework for organizing cancer-related variations from existing databases, publications and NGS data using a High-performance Integrated Virtual Environment (HIVE).

    Science.gov (United States)

    Wu, Tsung-Jung; Shamsaddini, Amirhossein; Pan, Yang; Smith, Krista; Crichton, Daniel J; Simonyan, Vahan; Mazumder, Raja

    2014-01-01

    Years of sequence feature curation by UniProtKB/Swiss-Prot, PIR-PSD, NCBI-CDD, RefSeq and other database biocurators has led to a rich repository of information on functional sites of genes and proteins. This information along with variation-related annotation can be used to scan human short sequence reads from next-generation sequencing (NGS) pipelines for presence of non-synonymous single-nucleotide variations (nsSNVs) that affect functional sites. This and similar workflows are becoming more important because thousands of NGS data sets are being made available through projects such as The Cancer Genome Atlas (TCGA), and researchers want to evaluate their biomarkers in genomic data. BioMuta, an integrated sequence feature database, provides a framework for automated and manual curation and integration of cancer-related sequence features so that they can be used in NGS analysis pipelines. Sequence feature information in BioMuta is collected from the Catalogue of Somatic Mutations in Cancer (COSMIC), ClinVar, UniProtKB and through biocuration of information available from publications. Additionally, nsSNVs identified through automated analysis of NGS data from TCGA are also included in the database. Because of the petabytes of data and information present in NGS primary repositories, a platform HIVE (High-performance Integrated Virtual Environment) for storing, analyzing, computing and curating NGS data and associated metadata has been developed. Using HIVE, 31 979 nsSNVs were identified in TCGA-derived NGS data from breast cancer patients. All variations identified through this process are stored in a Curated Short Read archive, and the nsSNVs from the tumor samples are included in BioMuta. Currently, BioMuta has 26 cancer types with 13 896 small-scale and 308 986 large-scale study-derived variations. Integration of variation data allows identifications of novel or common nsSNVs that can be prioritized in validation studies. Database URL: BioMuta: http

  13. Effects of variable-row-spacing harvesting picker platform scraping plates on cotton fiber quality and quantity

    Directory of Open Access Journals (Sweden)

    Cíntia Michele de Campos Baraviera

    2017-06-01

    Full Text Available There have been increasing demands for high-quality cotton fibers that meet the textile industry quality standards. Concurrently, there have been efforts to reduce contaminants during harvesting to reduce harvesting costs. The goal of this research was to evaluate the efficiency of the picker platform with Variable-Row-Spacing (VRS for harvesting cotton in narrow rows, over two harvest seasons in two regions within the state of Mato Grosso, Brazil. In this study, how the presence vs. absence of scraping plates and variations in travel speed was related to quantifiable levels of impurities the harvested fibers was examined. The research was divided into three experiments (Exp. I, II, and III, using cotton varieties FM 975 WS, IMA 5672 B2 RF, and IMA 5675 B2 RF, with row spacing of 0.45 m. The experimental design was randomized blocks, in a 2 ? 3 factorial design, using the presence/absence of the plate and three speeds (0.61, 1.0, and 1.42 m·s-¹, with seven repetitions, totaling 42 experimental plots. The plot size was 108 m² (3.6 ? 30 m. The data were analyzed using the F test in ANOVA and the post-hoc Tukey test (p < 0.05. The results showed that scraping plates increased the number of stems and cones, and reduced the harvest efficiency of cotton planted in narrow rows in the region of Sorriso-MT during the 2013/2014 harvest. For the 2014/2015 harvest, the highest speed and the presence of the scraping plates increased the number of cones in the cotton samples. In the experiment conducted in Serra da Petrovina, the removal of the scraping plates decreased the amount of cones in the harvested cotton.

  14. Glacial Lake Pickering: stratigraphy and chronology of a proglacial lake dammed by the North Sea Lobe of the British-Irish Ice Sheet

    OpenAIRE

    Evans, David J.A.; Bateman, Mark D.; Roberts, David H.; Medialdea, Alicia; Hayes, Laura; Duller, Geoff A.T.; Fabel, Derek; Clark, Chris D.

    2016-01-01

    We report the first chronology, using four new optically stimulated luminescence dates, on the sedimentary record of Glacial Lake Pickering, dammed by the North Sea Lobe of the British–Irish Ice Sheet during the Dimlington Stadial (24–11 ka cal BP). Dates range from 17.6 ± 1.0 to 15.8 ± 0.9 ka for the sedimentation of the Sherburn Sands at East Heslerton, which were formed by multiple coalescing alluvial fans prograding into the falling water levels of the lake and fed by progressively larger...

  15. Interconnectivity of macroporous molecularly imprinted polymers fabricated by hydroxyapatite-stabilized Pickering high internal phase emulsions-hydrogels for the selective recognition of protein.

    Science.gov (United States)

    Sun, Yanhua; Li, Yuqing; Xu, Jiangfeng; Huang, Ling; Qiu, Tianyun; Zhong, Shian

    2017-07-01

    Hydroxyapatite hybridized molecularly imprinted polydopamine polymers with selective recognition of bovine hemoglobin (BHb) were successfully prepared via Pickering oil-in-water high internal phase emulsions-hydrogels and molecularly imprinting technique. The emulsions were stabilized by hydroxyapatite of which the wettability was modified by 3-methacryloxypropyltrimethoxysilane. The materials were characterized by SEM, IR and TGA. The results showed that the BHb imprinted polymers based on Pickering hydrogels (Hydro-MIPs) possess macropores ranging from 20μm to 50μm, and their large numbers of amino groups and hydroxyl groups result in a favorable adsorption capacity for BHb. The maximum adsorption capacity of Hydro-MIPs for BHb was 438mg/g, 3.27 times more than that of the non-imprinted polymers (Hydro-NIPs). The results indicated that Hydro-MIPs possessing well-defined hierarchical porous structures exhibited outstanding recognition behavior towards the target protein molecules. This work provided a promising alternative method for the fabrication of polymer materials with tunable and interconnected pores structures for the separation and purification of protein in vitro. Copyright © 2017. Published by Elsevier B.V.

  16. Robust species taxonomy assignment algorithm for 16S rRNA NGS reads: application to oral carcinoma samples

    Directory of Open Access Journals (Sweden)

    Nezar Noor Al-Hebshi

    2015-09-01

    Full Text Available Background: Usefulness of next-generation sequencing (NGS in assessing bacteria associated with oral squamous cell carcinoma (OSCC has been undermined by inability to classify reads to the species level. Objective: The purpose of this study was to develop a robust algorithm for species-level classification of NGS reads from oral samples and to pilot test it for profiling bacteria within OSCC tissues. Methods: Bacterial 16S V1-V3 libraries were prepared from three OSCC DNA samples and sequenced using 454's FLX chemistry. High-quality, well-aligned, and non-chimeric reads ≥350 bp were classified using a novel, multi-stage algorithm that involves matching reads to reference sequences in revised versions of the Human Oral Microbiome Database (HOMD, HOMD extended (HOMDEXT, and Greengene Gold (GGG at alignment coverage and percentage identity ≥98%, followed by assignment to species level based on top hit reference sequences. Priority was given to hits in HOMD, then HOMDEXT and finally GGG. Unmatched reads were subject to operational taxonomic unit analysis. Results: Nearly, 92.8% of the reads were matched to updated-HOMD 13.2, 1.83% to trusted-HOMDEXT, and 1.36% to modified-GGG. Of all matched reads, 99.6% were classified to species level. A total of 228 species-level taxa were identified, representing 11 phyla; the most abundant were Proteobacteria, Bacteroidetes, Firmicutes, Fusobacteria, and Actinobacteria. Thirty-five species-level taxa were detected in all samples. On average, Prevotella oris, Neisseria flava, Neisseria flavescens/subflava, Fusobacterium nucleatum ss polymorphum, Aggregatibacter segnis, Streptococcus mitis, and Fusobacterium periodontium were the most abundant. Bacteroides fragilis, a species rarely isolated from the oral cavity, was detected in two samples. Conclusion: This multi-stage algorithm maximizes the fraction of reads classified to the species level while ensuring reliable classification by giving priority to the

  17. Preparation and documentation of a CATHENA input file for Darlington NGS

    International Nuclear Information System (INIS)

    1989-03-01

    A CATHENA input model has been developed and documented for the heat transport system of the Darlington Nuclear Generating Station. CATHENA, an advanced two-fluid thermalhydraulic computer code, has been designed for analysis of postulated loss-of-coolant accidents (LOCA) and upset conditions in the CANDU system. This report describes the Darlington input model (or idealization), and gives representative results for a simulation of a small break at an inlet header

  18. The dew point response of the annulus gas system of Bruce NGS A

    International Nuclear Information System (INIS)

    Kenchington, J.; Ellis, P.J.; Meranda, D.

    1983-01-01

    The dew point response of the Annulus Gas System in Bruce A, Units 1 and 2 has been modelled in order to alert the operator of the presence of heavy water and to estimate the leak rate into the annulus. The computer model can be easily adapted to determine the Annulus Gas System dew point response in any station. It models the complex arrangement of the system and the transportation of moisture through the annuli by a combination of plug flow and mixing of CO 2 and D 2 O vapor. It predicts the response of the dew point monitor for a range of specified leak rates and positions of a leaking channel in a string of channels. This model has been used to calculate the variation of dew point and rate of change of dew point with respect to time (t). It shows that there is a maximum in the rate of dew point change (dT/dt) with respect to the corresponding dew point (T). This maximum is unique for a given leak rate and channel position. It is independent of the starting time for the leak. The computer programme has been verified by an analytical solution for the model

  19. The ICR96 exon CNV validation series: a resource for orthogonal assessment of exon CNV calling in NGS data [version 1; referees: 2 approved

    Directory of Open Access Journals (Sweden)

    Shazia Mahamdallie

    2017-05-01

    Full Text Available Detection of deletions and duplications of whole exons (exon CNVs is a key requirement of genetic testing. Accurate detection of this variant type has proved very challenging in targeted next-generation sequencing (NGS data, particularly if only a single exon is involved. Many different NGS exon CNV calling methods have been developed over the last five years. Such methods are usually evaluated using simulated and/or in-house data due to a lack of publicly-available datasets with orthogonally generated results. This hinders tool comparisons, transparency and reproducibility. To provide a community resource for assessment of exon CNV calling methods in targeted NGS data, we here present the ICR96 exon CNV validation series. The dataset includes high-quality sequencing data from a targeted NGS assay (the TruSight Cancer Panel together with Multiplex Ligation-dependent Probe Amplification (MLPA results for 96 independent samples. 66 samples contain at least one validated exon CNV and 30 samples have validated negative results for exon CNVs in 26 genes. The dataset includes 46 exon CNVs in BRCA1, BRCA2, TP53, MLH1, MSH2, MSH6, PMS2, EPCAM or PTEN, giving excellent representation of the cancer predisposition genes most frequently tested in clinical practice. Moreover, the validated exon CNVs include 25 single exon CNVs, the most difficult type of exon CNV to detect. The FASTQ files for the ICR96 exon CNV validation series can be accessed through the European-Genome phenome Archive (EGA under the accession number EGAS00001002428.

  20. Automatic picker of P & S first arrivals and robust event locator

    Science.gov (United States)

    Pinsky, V.; Polozov, A.; Hofstetter, A.

    2003-12-01

    We report on further development of automatic all distances location procedure designed for a regional network. The procedure generalizes the previous "loca l" (R ratio of two STAs, calculated in two consecutive and equal time windows (instead of previously used Akike Information Criterion). "Teleseismic " location is split in two stages: preliminary and final one. The preliminary part estimates azimuth and apparent velocity by fitting a plane wave to the P automatic pickings. The apparent velocity criterion is used to decide about strategy of the following computations: teleseismic or regional. The preliminary estimates of azimuth and apparent velocity provide starting value for the final teleseismic and regional location. Apparent velocity is used to get first a pproximation distance to the source on the basis of the P, Pn, Pg travel-timetables. The distance estimate together with the preliminary azimuth estimate provides first approximations of the source latitude and longitude via sine and cosine theorems formulated for the spherical triangle. Final location is based on robust grid-search optimization procedure, weighting the number of pickings that simultaneously fit the model travel times. The grid covers initial location and becomes finer while approaching true hypocenter. The target function is a sum of the bell-shaped characteristic functions, used to emphasize true pickings and eliminate outliers. The final solution is a grid point that provides maximum to the target function. The procedure was applied to a list of ML > 4 earthquakes recorded by the Israel Seismic Network (ISN) in the 1999-2002 time period. Most of them are badly constrained relative the network. However, the results of location with average normalized error relative bulletin solutions e=dr/R of 5% were obtained, in each of the distance ranges. The first version of the procedure was incorporated in the national Early Warning System in 2001. Recently, we started to send automatic Early

  1. Preference of multi-walled carbon nanotube (MWCNT) to single-walled carbon nanotube (SWCNT) and activated carbon for preparing silica nanohybrid pickering emulsion for chemical enhanced oil recovery (C-EOR)

    Energy Technology Data Exchange (ETDEWEB)

    AfzaliTabar, M. [Department of Chemistry, Islamic Azad University Branch of Tehran North, Tehran (Iran, Islamic Republic of); Alaei, M., E-mail: alaiem@ripi.ir [Nanotechnology Research Center, Research Institute of Petroleum Industry (RIPI), Tehran (Iran, Islamic Republic of); Ranjineh Khojasteh, R.; Motiee, F. [Department of Chemistry, Islamic Azad University Branch of Tehran North, Tehran (Iran, Islamic Republic of); Rashidi, A.M. [Nanotechnology Research Center, Research Institute of Petroleum Industry (RIPI), Tehran (Iran, Islamic Republic of)

    2017-01-15

    The aim of this research was to determine the best nano hybrid that can be used as a Pickering emulsion Chemical Enhanced Oil Recovery (C-EOR). Therefore, we have prepared different carbon structures nano hybrids with SiO{sub 2} nano particles with different weight percent using sol-gel method. The as-prepared nano materials were characterized with X-Ray Diffraction (XRD), Field Emission Scanning Electron Microscopy (FE-SEM) and Thermal Gravimetric Analysis (TGA). Pickering emulsions of these nanohybrids were prepared at pH=7 in ambient temperature and with distilled water. Stability of the mentioned Pickering emulsions was controlled for one month. Emulsion phase morphology was investigated using optical microscopic imaging. Evaluation results demonstrated that the best sample is the 70% MWCNT/SiO{sub 2} nanohybrid. Stability of the selected nanohybrid (70% MWCNT/SiO{sub 2} nanohybrid) was investigated by alteration of salinity, pH and temperature. Results showed that the mentioned Pickering emulsion has very good stability at 0.1%, 1% salinity, moderate and high temperature (25 °C and 90 °C) and neutral and alkaline pH (7, 10) that is suitable for the oil reservoirs conditions. The effect of the related nano fluid on the wettability of carbonate rock was investigated by measuring the contact angle and interfacial tension. Results show that the nanofluid could significantly change the wettability of the carbonate rock from oil wet to water wet and can decrease the interfacial tension. Therefore, the 70% MWCNT/SiO{sub 2} nanohybrid Pickering emulsion can be used for Chemical Enhanced Oil Recovery (C-EOR).

  2. Preference of multi-walled carbon nanotube (MWCNT) to single-walled carbon nanotube (SWCNT) and activated carbon for preparing silica nanohybrid pickering emulsion for chemical enhanced oil recovery (C-EOR)

    International Nuclear Information System (INIS)

    AfzaliTabar, M.; Alaei, M.; Ranjineh Khojasteh, R.; Motiee, F.; Rashidi, A.M.

    2017-01-01

    The aim of this research was to determine the best nano hybrid that can be used as a Pickering emulsion Chemical Enhanced Oil Recovery (C-EOR). Therefore, we have prepared different carbon structures nano hybrids with SiO 2 nano particles with different weight percent using sol-gel method. The as-prepared nano materials were characterized with X-Ray Diffraction (XRD), Field Emission Scanning Electron Microscopy (FE-SEM) and Thermal Gravimetric Analysis (TGA). Pickering emulsions of these nanohybrids were prepared at pH=7 in ambient temperature and with distilled water. Stability of the mentioned Pickering emulsions was controlled for one month. Emulsion phase morphology was investigated using optical microscopic imaging. Evaluation results demonstrated that the best sample is the 70% MWCNT/SiO 2 nanohybrid. Stability of the selected nanohybrid (70% MWCNT/SiO 2 nanohybrid) was investigated by alteration of salinity, pH and temperature. Results showed that the mentioned Pickering emulsion has very good stability at 0.1%, 1% salinity, moderate and high temperature (25 °C and 90 °C) and neutral and alkaline pH (7, 10) that is suitable for the oil reservoirs conditions. The effect of the related nano fluid on the wettability of carbonate rock was investigated by measuring the contact angle and interfacial tension. Results show that the nanofluid could significantly change the wettability of the carbonate rock from oil wet to water wet and can decrease the interfacial tension. Therefore, the 70% MWCNT/SiO 2 nanohybrid Pickering emulsion can be used for Chemical Enhanced Oil Recovery (C-EOR).

  3. Phytotoxicology section investigation in the vicinity of the Bruce Nuclear Power Development, the Pickering Nuclear Generating Station and the Darlington Nuclear Generating Station, in October, 1989

    International Nuclear Information System (INIS)

    1991-02-01

    The Phytotoxicology Section, Air Resources Branch is a participant in the Pickering and Bruce Nuclear Contingency Plans. The Phytotoxicology Emergency Response Team is responsible for collecting vegetation samples in the event of a nuclear emergency at any of the nuclear generating stations in the province. As part of its responsibility the Phytotoxicology Section collects samples around the nuclear generating stations for comparison purposes in the event of an emergency. Because of the limited frequency of sampling, the data from the surveys are not intended to be used as part of a regulatory monitoring program. These data represent an effort by the MOE to begin to establish a data base of tritium concentrations in vegetation. The Phytotoxicology Section has carried out seven surveys in the vicinity of Ontario Hydro nuclear generating stations since 1981. Surveys were conducted for tritium in snow in the vicinity of Bruce Nuclear Power Development (BNPD), February, 1981; tritium in cell-free water of white ash in the vicinity of BNPD, September, 1981; tritium in snow in the vicinity of BNPD, March, 1982; tritium in tree sap in the vicinity of BNPD, April, 1982; tritium in tree sap in the vicinity of BNPD, April, 1984, tritium in the cell-free water of white ash in the vicinity of BNPD, September, 1985; and, tritium in cell-free water of grass in the vicinity of Pickering Nuclear Generation Station (PNGS), October 1986. In all cases a pattern of decreasing tritium levels with increasing distance from the stations was observed. In October, 1989, assessment surveys were conducted around Bruce Nuclear Power Development, the Pickering Nuclear Generating Station and the new Darlington Nuclear Generating Station (DNGS). The purpose of these surveys was to provide baseline data for tritium in cell-free water of grass at all three locations at the same time of year. As none of the reactor units at DNGS had been brought on line at the time of the survey, this data was to be

  4. Evolution in the Amphi-Atlantic tropical genus Guibourtia (Fabaceae, Detarioideae), combining NGS phylogeny and morphology.

    Science.gov (United States)

    Tosso, Félicien; Hardy, Olivier J; Doucet, Jean-Louis; Daïnou, Kasso; Kaymak, Esra; Migliore, Jérémy

    2018-03-01

    Tropical rain forests support a remarkable diversity of tree species, questioning how and when this diversity arose. The genus Guibourtia (Fabaceae, Detarioideae), characterized by two South American and 13 African tree species growing in various tropical biomes, is an interesting model to address the role of biogeographic processes and adaptation to contrasted environments on species diversification. Combining whole plastid genome sequencing and morphological characters analysis, we studied the timing of speciation and diversification processes in Guibourtia through molecular dating and ancestral habitats reconstruction. All species except G. demeusei and G. copallifera appear monophyletic. Dispersal from Africa to America across the Atlantic Ocean is the most plausible hypothesis to explain the occurrence of Neotropical Guibourtia species, which diverged ca. 11.8 Ma from their closest African relatives. The diversification of the three main clades of African Guibourtia is concomitant to Miocene global climate changes, highlighting pre-Quaternary speciation events. These clades differ by their reproductive characters, which validates the three subgenera previously described: Pseudocopaiva, Guibourtia and Gorskia. Within most monophyletic species, plastid lineages start diverging from each other during the Pliocene or early Pleistocene, suggesting that these species already arose during this period. The multiple transitions between rain forests and dry forests/savannahs inferred here through the plastid phylogeny in each Guibourtia subgenus address thus new questions about the role of phylogenetic relationships in shaping ecological niche and morphological similarity among taxa. Copyright © 2017 Elsevier Inc. All rights reserved.

  5. Molecularly imprinted polymer microspheres prepared by Pickering emulsion polymerization for selective solid-phase extraction of eight bisphenols from human urine samples

    International Nuclear Information System (INIS)

    Yang, Jiajia; Li, Yun; Wang, Jincheng; Sun, Xiaoli; Cao, Rong; Sun, Hao; Huang, Chaonan; Chen, Jiping

    2015-01-01

    Highlights: • BPA imprinted polymer microspheres were prepared by Pickering emulsion polymerization. • Regular spherical shape and narrow diameter distribution. • Good specific adsorption capacity for BPA. • Good class-selectivity and clean-up efficiency for bisphenols in human urine under SPE mode. • Good recoveries and sensitivity for bisphenols using the MIPMS-SPE coupled with HPLC-DAD method. - Abstract: The bisphenol A (BPA) imprinted polymer microspheres were prepared by simple Pickering emulsion polymerization. Compared to traditional bulk polymerization, both high yields of polymer and good control of particle sizes were achieved. The characterization results of scanning electron microscopy and nitrogen adsorption–desorption measurements showed that the obtained molecularly imprinted polymer microsphere (MIPMS) particles possessed regular spherical shape, narrow diameter distribution (30–60 μm), a specific surface area (S BET ) of 281.26 m 2 g −1 and a total pore volume (V t ) of 0.459 cm 3 g −1 . Good specific adsorption capacity for BPA was obtained in the sorption experiment and good class selectivity for BPA and its seven structural analogs (bisphenol F, bisphenol B, bisphenol E, bisphenol AF, bisphenol S, bisphenol AP and bisphenol Z) was demonstrated by the chromatographic evaluation experiment. The MIPMS as solid-phase extraction (SPE) packing material was then evaluated for extraction and clean-up of these bisphenols (BPs) from human urine samples. An accurate and sensitive analytical method based on the MIPMS-SPE coupled with HPLC-DAD has been successfully established for simultaneous determination of eight BPs from human urine samples with detection limits of 1.2–2.2 ng mL −1 . The recoveries of BPs for urine samples at two spiking levels (100 and 500 ng mL −1 for each BP) were in the range of 81.3–106.7% with RSD values below 8.3%

  6. Fabrication and evaluation of chitosan/NaYF4:Yb3+/Tm3+ upconversion nanoparticles composite beads based on the gelling of Pickering emulsion droplets

    International Nuclear Information System (INIS)

    Yan, Huiqiong; Chen, Xiuqiong; Shi, Jia; Shi, Zaifeng; Sun, Wei; Lin, Qiang; Wang, Xianghui; Dai, Zihao

    2017-01-01

    The rare earth ion doped upconversion nanoparticles (UCNPs) synthesized by hydrophobic organic ligands possess poor solubility and low fluorescence quantum yield in aqueous media. To conquer this issue, NaYF 4 :Yb 3+ /Tm 3+ UCNPs, synthesized by a hydrothermal method, were coated with F127 and then assembled with chitosan to fabricate the chitosan/NaYF 4 :Yb 3+ /Tm 3+ composite beads (CS/NaYF 4 :Yb 3+ /Tm 3+ CBs) by Pickering emulsion system. The characterization results revealed that the as-synthesized NaYF 4 :Yb 3+ /Tm 3+ UCNPs with an average size of 20 nm exhibited spherical morphology, high crystallinity and characteristic emission upconversion fluorescence with an overall blue color output. The NaYF 4 :Yb 3+ /Tm 3+ UCNPs were successfully conjugated on the surface of chitosan beads by the gelling of emulsion droplets. The resultant CS/NaYF 4 :Yb 3+ /Tm 3+ CBs showed good upconversion luminescent property, drug-loading capacity, release performance and excellent biocompatibility, exhibiting great potentials in targeted drug delivery and tissue engineering with potential tracking capability and lasting release performance. - Highlights: • NaYF 4 :Yb 3+ /Tm 3+ UCNPs were coated by F127 to improve aqueous dispersibility. • NaYF 4 :Yb 3+ /Tm 3+ UCNPs were assembled with chitosan to fabricate the composite beads (CMs). • Pickering emulsions stabilized by UCNPs exhibited uniform and satisfactory emulsion droplets. • The CMs prepared by the gelling of emulsion droplet preserved upconversion luminescent property. • The resultant CMs showed good drug-loading capacity, release performance and biocompatibility.

  7. No more non-model species: the promise of next generation sequencing for comparative immunology.

    Science.gov (United States)

    Dheilly, Nolwenn M; Adema, Coen; Raftos, David A; Gourbal, Benjamin; Grunau, Christoph; Du Pasquier, Louis

    2014-07-01

    Next generation sequencing (NGS) allows for the rapid, comprehensive and cost effective analysis of entire genomes and transcriptomes. NGS provides approaches for immune response gene discovery, profiling gene expression over the course of parasitosis, studying mechanisms of diversification of immune receptors and investigating the role of epigenetic mechanisms in regulating immune gene expression and/or diversification. NGS will allow meaningful comparisons to be made between organisms from different taxa in an effort to understand the selection of diverse strategies for host defence under different environmental pathogen pressures. At the same time, it will reveal the shared and unique components of the immunological toolkit and basic functional aspects that are essential for immune defence throughout the living world. In this review, we argue that NGS will revolutionize our understanding of immune responses throughout the animal kingdom because the depth of information it provides will circumvent the need to concentrate on a few "model" species. Copyright © 2014 Elsevier Ltd. All rights reserved.

  8. Exploring the genes of yerba mate (Ilex paraguariensis A. St.-Hil. by NGS and de novo transcriptome assembly.

    Directory of Open Access Journals (Sweden)

    Humberto J Debat

    Full Text Available Yerba mate (Ilex paraguariensis A. St.-Hil. is an important subtropical tree crop cultivated on 326,000 ha in Argentina, Brazil and Paraguay, with a total yield production of more than 1,000,000 t. Yerba mate presents a strong limitation regarding sequence information. The NCBI GenBank lacks an EST database of yerba mate and depicts only 80 DNA sequences, mostly uncharacterized. In this scenario, in order to elucidate the yerba mate gene landscape by means of NGS, we explored and discovered a vast collection of I. paraguariensis transcripts. Total RNA from I. paraguariensis was sequenced by Illumina HiSeq-2000 obtaining 72,031,388 pair-end 100 bp sequences. High quality reads were de novo assembled into 44,907 transcripts encompassing 40 million bases with an estimated coverage of 180X. Multiple sequence analysis allowed us to predict that yerba mate contains ∼ 32,355 genes and 12,551 gene variants or isoforms. We identified and categorized members of more than 100 metabolic pathways. Overall, we have identified ∼ 1,000 putative transcription factors, genes involved in heat and oxidative stress, pathogen response, as well as disease resistance and hormone response. We have also identified, based in sequence homology searches, novel transcripts related to osmotic, drought, salinity and cold stress, senescence and early flowering. We have also pinpointed several members of the gene silencing pathway, and characterized the silencing effector Argonaute1. We predicted a diverse supply of putative microRNA precursors involved in developmental processes. We present here the first draft of the transcribed genomes of the yerba mate chloroplast and mitochondrion. The putative sequence and predicted structure of the caffeine synthase of yerba mate is presented. Moreover, we provide a collection of over 10,800 SSR accessible to the scientific community interested in yerba mate genetic improvement. This contribution broadly expands the limited knowledge

  9. Exploring the Genes of Yerba Mate (Ilex paraguariensis A. St.-Hil.) by NGS and De Novo Transcriptome Assembly

    Science.gov (United States)

    Aguilera, Patricia M.; Bubillo, Rosana E.; Otegui, Mónica B.; Ducasse, Daniel A.; Zapata, Pedro D.; Marti, Dardo A.

    2014-01-01

    Yerba mate (Ilex paraguariensis A. St.-Hil.) is an important subtropical tree crop cultivated on 326,000 ha in Argentina, Brazil and Paraguay, with a total yield production of more than 1,000,000 t. Yerba mate presents a strong limitation regarding sequence information. The NCBI GenBank lacks an EST database of yerba mate and depicts only 80 DNA sequences, mostly uncharacterized. In this scenario, in order to elucidate the yerba mate gene landscape by means of NGS, we explored and discovered a vast collection of I. paraguariensis transcripts. Total RNA from I. paraguariensis was sequenced by Illumina HiSeq-2000 obtaining 72,031,388 pair-end 100 bp sequences. High quality reads were de novo assembled into 44,907 transcripts encompassing 40 million bases with an estimated coverage of 180X. Multiple sequence analysis allowed us to predict that yerba mate contains ∼32,355 genes and 12,551 gene variants or isoforms. We identified and categorized members of more than 100 metabolic pathways. Overall, we have identified ∼1,000 putative transcription factors, genes involved in heat and oxidative stress, pathogen response, as well as disease resistance and hormone response. We have also identified, based in sequence homology searches, novel transcripts related to osmotic, drought, salinity and cold stress, senescence and early flowering. We have also pinpointed several members of the gene silencing pathway, and characterized the silencing effector Argonaute1. We predicted a diverse supply of putative microRNA precursors involved in developmental processes. We present here the first draft of the transcribed genomes of the yerba mate chloroplast and mitochondrion. The putative sequence and predicted structure of the caffeine synthase of yerba mate is presented. Moreover, we provide a collection of over 10,800 SSR accessible to the scientific community interested in yerba mate genetic improvement. This contribution broadly expands the limited knowledge of yerba mate genes

  10. NGS Reveals Molecular Pathways Affected by Obesity and Weight Loss-Related Changes in miRNA Levels in Adipose Tissue

    Directory of Open Access Journals (Sweden)

    Alina Kuryłowicz

    2017-12-01

    Full Text Available Both obesity and weight loss may cause molecular changes in adipose tissue. This study aimed to characterize changes in adipose tissue miRNome in order to identify molecular pathways affected by obesity and weight changes. Next generation sequencing (NGS was applied to identify microRNAs (miRNAs differentially expressed in 47 samples of visceral (VAT and subcutaneous (SAT adipose tissues from normal-weight (N, obese (O and obese after surgery-induced weight loss (PO individuals. Subsequently miRNA expression was validated by real-time PCR in 197 adipose tissues and bioinformatics analysis performed to identify molecular pathways affected by obesity-related changes in miRNA expression. NGS identified 344 miRNAs expressed in adipose tissues with ≥5 reads per million. Using >2 and <−2 fold change as cut-offs we showed that the expression of 54 miRNAs differed significantly between VAT-O and SAT-O. Equally, between SAT-O and SAT-N, the expression of 20 miRNAs differed significantly, between SAT-PO and SAT-N the expression of 79 miRNAs differed significantly, and between SAT-PO and SAT-O, the expression of 61 miRNAs differed significantly. Ontological analyses disclosed several molecular pathways regulated by these miRNAs in adipose tissue. NGS-based miRNome analysis characterized changes of the miRNA profile of adipose tissue, which are associated with changes of weight possibly responsible for a differential regulation of molecular pathways in adipose tissue when the individual is obese and after the individual has lost weight.

  11. Validation and comparison of two NGS assays for the detection of EGFR T790M resistance mutation in liquid biopsies of NSCLC patients.

    Science.gov (United States)

    Vollbrecht, Claudia; Lehmann, Annika; Lenze, Dido; Hummel, Michael

    2018-04-06

    Analysis of circulating cell-free DNA (cfDNA) derived from peripheral blood ("liquid biopsy") is an attractive alternative to identify non-small cell lung cancer (NSCLC) patients with the EGFR T790M mutation eligible for 3rd generation tyrosine kinase inhibitor therapy. We evaluated two PCR-based next generation sequencing (NGS) approaches, one including unique molecular identifiers (UMI), with focus on highly sensitive EGFR T790M mutation detection. Therefore, we extracted and sequenced cfDNA from synthetic plasma samples spiked with mutated DNA at decreasing allele frequencies and from 21 diagnostic NSCLC patients. Data evaluation was performed to determine the limit of detection (LoD), accuracy, specificity and sensitivity of both assays. Considering all tested reference dilutions and mutations the UMI assay performed best in terms of LoD (1% vs. 5%), sensitivity (95.8% vs. 81.3%), specificity (100% vs. 93.8%) and accuracy (96.9% vs. 84.4%). Comparing mutation status of diagnostic samples with both assays showed 81.3% concordance with primary mutation verifiable in 52% of cases. EGFR T790M was detected concordantly in 6/7 patients with allele frequencies from 0.1% to 27%. In one patient, the T790M mutation was exclusively detectable with the UMI assay. Our data demonstrate that both assays are applicable as multi-biomarker NGS tools enabling the simultaneous detection of primary EGFR driver and resistance mutations. However, for mutations with low allelic frequencies the use of NGS panels with UMI facilitates a more sensitive and reliable detection.

  12. Use of the Ion PGM and the GeneReader NGS Systems in Daily Routine Practice for Advanced Lung Adenocarcinoma Patients: A Practical Point of View Reporting a Comparative Study and Assessment of 90 Patients

    Directory of Open Access Journals (Sweden)

    Simon Heeke

    2018-03-01

    Full Text Available Background: With the integration of various targeted therapies into the clinical management of patients with advanced lung adenocarcinoma, next-generation sequencing (NGS has become the technology of choice and has led to an increase in simultaneously interrogated genes. However, the broader adoption of NGS for routine clinical practice is still hampered by sophisticated workflows, complex bioinformatics analysis and medical interpretation. Therefore, the performance of the novel QIAGEN GeneReader NGS system was compared to an in-house ISO-15189 certified Ion PGM NGS platform. Methods: Clinical samples from 90 patients (60 Retrospectively and 30 Prospectively with lung adenocarcinoma were sequenced with both systems. Mutations were analyzed and EGFR, KRAS, BRAF, NRAS, ALK, PIK3CA and ERBB2 genes were compared and sampling time and suitability for clinical testing were assessed. Results: Both sequencing systems showed perfect concordance for the overlapping genes. Correlation of allele frequency was r2 = 0.93 for the retrospective patients and r2 = 0.81 for the prospective patients. Hands-on time and total run time were shorter using the PGM system, while the GeneReader platform provided good traceability and up-to-date interpretation of the results. Conclusion: We demonstrated the suitability of the GeneReader NGS system in routine practice in a clinical pathology laboratory setting.

  13. Molecularly imprinted polymer microspheres prepared by Pickering emulsion polymerization for selective solid-phase extraction of eight bisphenols from human urine samples

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Jiajia [Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023 (China); University of Chinese Academy of Sciences, Beijing 100049 (China); Li, Yun; Wang, Jincheng [Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023 (China); Sun, Xiaoli; Cao, Rong [Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023 (China); University of Chinese Academy of Sciences, Beijing 100049 (China); Sun, Hao [Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023 (China); Department of Chemistry, Liaoning University, Shenyang 110000 (China); Huang, Chaonan [Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023 (China); University of Chinese Academy of Sciences, Beijing 100049 (China); Chen, Jiping, E-mail: chenjp@dicp.ac.cn [Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023 (China)

    2015-05-04

    Highlights: • BPA imprinted polymer microspheres were prepared by Pickering emulsion polymerization. • Regular spherical shape and narrow diameter distribution. • Good specific adsorption capacity for BPA. • Good class-selectivity and clean-up efficiency for bisphenols in human urine under SPE mode. • Good recoveries and sensitivity for bisphenols using the MIPMS-SPE coupled with HPLC-DAD method. - Abstract: The bisphenol A (BPA) imprinted polymer microspheres were prepared by simple Pickering emulsion polymerization. Compared to traditional bulk polymerization, both high yields of polymer and good control of particle sizes were achieved. The characterization results of scanning electron microscopy and nitrogen adsorption–desorption measurements showed that the obtained molecularly imprinted polymer microsphere (MIPMS) particles possessed regular spherical shape, narrow diameter distribution (30–60 μm), a specific surface area (S{sub BET}) of 281.26 m{sup 2} g{sup −1} and a total pore volume (V{sub t}) of 0.459 cm{sup 3} g{sup −1}. Good specific adsorption capacity for BPA was obtained in the sorption experiment and good class selectivity for BPA and its seven structural analogs (bisphenol F, bisphenol B, bisphenol E, bisphenol AF, bisphenol S, bisphenol AP and bisphenol Z) was demonstrated by the chromatographic evaluation experiment. The MIPMS as solid-phase extraction (SPE) packing material was then evaluated for extraction and clean-up of these bisphenols (BPs) from human urine samples. An accurate and sensitive analytical method based on the MIPMS-SPE coupled with HPLC-DAD has been successfully established for simultaneous determination of eight BPs from human urine samples with detection limits of 1.2–2.2 ng mL{sup −1}. The recoveries of BPs for urine samples at two spiking levels (100 and 500 ng mL{sup −1} for each BP) were in the range of 81.3–106.7% with RSD values below 8.3%.

  14. Trends in IT Innovation to Build a Next Generation Bioinformatics Solution to Manage and Analyse Biological Big Data Produced by NGS Technologies

    Directory of Open Access Journals (Sweden)

    Alexandre G. de Brevern

    2015-01-01

    Full Text Available Sequencing the human genome began in 1994, and 10 years of work were necessary in order to provide a nearly complete sequence. Nowadays, NGS technologies allow sequencing of a whole human genome in a few days. This deluge of data challenges scientists in many ways, as they are faced with data management issues and analysis and visualization drawbacks due to the limitations of current bioinformatics tools. In this paper, we describe how the NGS Big Data revolution changes the way of managing and analysing data. We present how biologists are confronted with abundance of methods, tools, and data formats. To overcome these problems, focus on Big Data Information Technology innovations from web and business intelligence. We underline the interest of NoSQL databases, which are much more efficient than relational databases. Since Big Data leads to the loss of interactivity with data during analysis due to high processing time, we describe solutions from the Business Intelligence that allow one to regain interactivity whatever the volume of data is. We illustrate this point with a focus on the Amadea platform. Finally, we discuss visualization challenges posed by Big Data and present the latest innovations with JavaScript graphic libraries.

  15. Trends in IT Innovation to Build a Next Generation Bioinformatics Solution to Manage and Analyse Biological Big Data Produced by NGS Technologies

    Science.gov (United States)

    de Brevern, Alexandre G.; Meyniel, Jean-Philippe; Fairhead, Cécile; Neuvéglise, Cécile; Malpertuy, Alain

    2015-01-01

    Sequencing the human genome began in 1994, and 10 years of work were necessary in order to provide a nearly complete sequence. Nowadays, NGS technologies allow sequencing of a whole human genome in a few days. This deluge of data challenges scientists in many ways, as they are faced with data management issues and analysis and visualization drawbacks due to the limitations of current bioinformatics tools. In this paper, we describe how the NGS Big Data revolution changes the way of managing and analysing data. We present how biologists are confronted with abundance of methods, tools, and data formats. To overcome these problems, focus on Big Data Information Technology innovations from web and business intelligence. We underline the interest of NoSQL databases, which are much more efficient than relational databases. Since Big Data leads to the loss of interactivity with data during analysis due to high processing time, we describe solutions from the Business Intelligence that allow one to regain interactivity whatever the volume of data is. We illustrate this point with a focus on the Amadea platform. Finally, we discuss visualization challenges posed by Big Data and present the latest innovations with JavaScript graphic libraries. PMID:26125026

  16. Impact of NGS in the medical sciences: Genetic syndromes with an increased risk of developing cancer as an example of the use of new technologies

    Science.gov (United States)

    Lapunzina, Pablo; López, Rocío Ortiz; Rodríguez-Laguna, Lara; García-Miguel, Purificación; Martínez, Augusto Rojas; Martínez-Glez, Víctor

    2014-01-01

    The increased speed and decreasing cost of sequencing, along with an understanding of the clinical relevance of emerging information for patient management, has led to an explosion of potential applications in healthcare. Currently, SNP arrays and Next-Generation Sequencing (NGS) technologies are relatively new techniques used to scan genomes for gains and losses, losses of heterozygosity (LOH), SNPs, and indel variants as well as to perform complete sequencing of a panel of candidate genes, the entire exome (whole exome sequencing) or even the whole genome. As a result, these new high-throughput technologies have facilitated progress in the understanding and diagnosis of genetic syndromes and cancers, two disorders traditionally considered to be separate diseases but that can share causal genetic alterations in a group of developmental disorders associated with congenital malformations and cancer risk. The purpose of this work is to review these syndromes as an example of a group of disorders that has been included in a panel of genes for NGS analysis. We also highlight the relationship between development and cancer and underline the connections between these syndromes. PMID:24764758

  17. Trends in IT Innovation to Build a Next Generation Bioinformatics Solution to Manage and Analyse Biological Big Data Produced by NGS Technologies.

    Science.gov (United States)

    de Brevern, Alexandre G; Meyniel, Jean-Philippe; Fairhead, Cécile; Neuvéglise, Cécile; Malpertuy, Alain

    2015-01-01

    Sequencing the human genome began in 1994, and 10 years of work were necessary in order to provide a nearly complete sequence. Nowadays, NGS technologies allow sequencing of a whole human genome in a few days. This deluge of data challenges scientists in many ways, as they are faced with data management issues and analysis and visualization drawbacks due to the limitations of current bioinformatics tools. In this paper, we describe how the NGS Big Data revolution changes the way of managing and analysing data. We present how biologists are confronted with abundance of methods, tools, and data formats. To overcome these problems, focus on Big Data Information Technology innovations from web and business intelligence. We underline the interest of NoSQL databases, which are much more efficient than relational databases. Since Big Data leads to the loss of interactivity with data during analysis due to high processing time, we describe solutions from the Business Intelligence that allow one to regain interactivity whatever the volume of data is. We illustrate this point with a focus on the Amadea platform. Finally, we discuss visualization challenges posed by Big Data and present the latest innovations with JavaScript graphic libraries.

  18. Hétérogenéité quantitative et qualitative de la matière organique dans les argiles du Kimmeridgien du val de Pickering (Yorkshire, UK). Cadre sédimentologique et stratigraphique Quantitative and Qualitative Heterogeneity of the Organic Matter Within the Kimmeridge Clay of the Vale of Pickering (Yorkshire, Uk). Sedimentological and Stratigraphical Framework

    OpenAIRE

    Penn I. E.; Herbin J. P.; Muller C.; Geyssant J. R.; Melieres F.

    2006-01-01

    Les argiles du Kimméridgien contribuent à l'alimentation de nombreux gisements en mer du Nord. L'étude de quatre puits localisés sur une coupe Est-Ouest dans le Val de Pickering (Bassin de Cleveland) permet d'illustrer dans cette formation l'hétérogénéité de distribution verticale et latérale de la matière organique en terme de quantité et de qualité. La coupe étudiée (35 km de long, 200 m de haut) représente environ 6,5 millions d'années d'histoire géologique. Les analyses minéralogiques mon...

  19. Upper limit to the deuterium abundance and a measurement of the pickering-β line in the low excitation planetary IC 418

    International Nuclear Information System (INIS)

    Le Vaux, H.A.

    1977-01-01

    The problem of detecting a weak spectrum line, deuterium alpha, very near in wavelength to H/sub alpha/, assumed to be thousands of times as strong, is discussed from the point of view of optimizing the signal-to-noise ratio. A spectrometer consisting of three pressure scanning Fabry-Perot etalons with low reflectivity coatings was found to be the best instrument for this experiment. While no feature attributable to deuterium was detected in the planetary nebula IC 418, an upper limit relative to hydrogen of 3.4 x 10 -5 was established at the 95% confidence level. The significance of this result is discussed in light of the role played by deuterium in cosmology. The intensity ratio of the Pickering beta line (n'' = 6, n' = 4 transition of ionized helium) relative to H/sub alpha/ was measured to be 6.5 x 10 -5 . Observations of the nebular continuum made at five wavelengths in the red and near infrared are summarized and compared with predicted intensities

  20. Fabrication of magnetic hydroxypropyl cellulose-g-poly(acrylic acid) porous spheres via Pickering high internal phase emulsion for removal of Cu(2+) and Cd(2.).

    Science.gov (United States)

    Zhu, Yongfeng; Zheng, Yian; Zong, Li; Wang, Feng; Wang, Aiqin

    2016-09-20

    A series of magnetic hydroxypropyl cellulose-g-poly(acrylic acid) porous spheres were prepared via O/W Pickering high internal phase emulsions (HIPEs) integrated precipitation polymerization. The structure and composition of modified Fe3O4 and porous structures were characterized by TEM, XRD, TGA and SEM. The results indicated that the silanized Fe3O4 can influence greatly the pore structure of magnetic porous sphere in addition to non-negligible impacts of the proportion of mixed solvent and co-surfactant. The adsorption experiment demonstrated that the adsorption equilibrium can be reached within 40min and the maximal adsorption capacity was 300.00mg/g for Cd(2+) and 242.72mg/g for Cu(2+), suggesting its fast adsorption kinetics and high adsorption capacity. After five adsorption-desorption cycles, no significant changes in the adsorption capacity were observed, suggesting its excellent reusability. The magnetic porous sphere can be easily separated from the solution and then find its potential as a recyclable material for highly efficient removal of heavy metals. Copyright © 2016 Elsevier Ltd. All rights reserved.

  1. Fabrication and evaluation of chitosan/NaYF4:Yb3+/Tm3+ upconversion nanoparticles composite beads based on the gelling of Pickering emulsion droplets.

    Science.gov (United States)

    Yan, Huiqiong; Chen, Xiuqiong; Shi, Jia; Shi, Zaifeng; Sun, Wei; Lin, Qiang; Wang, Xianghui; Dai, Zihao

    2017-02-01

    The rare earth ion doped upconversion nanoparticles (UCNPs) synthesized by hydrophobic organic ligands possess poor solubility and low fluorescence quantum yield in aqueous media. To conquer this issue, NaYF 4 :Yb 3+ /Tm 3+ UCNPs, synthesized by a hydrothermal method, were coated with F127 and then assembled with chitosan to fabricate the chitosan/NaYF 4 :Yb 3+ /Tm 3+ composite beads (CS/NaYF 4 :Yb 3+ /Tm 3+ CBs) by Pickering emulsion system. The characterization results revealed that the as-synthesized NaYF 4 :Yb 3+ /Tm 3+ UCNPs with an average size of 20nm exhibited spherical morphology, high crystallinity and characteristic emission upconversion fluorescence with an overall blue color output. The NaYF 4 :Yb 3+ /Tm 3+ UCNPs were successfully conjugated on the surface of chitosan beads by the gelling of emulsion droplets. The resultant CS/NaYF 4 :Yb 3+ /Tm 3+ CBs showed good upconversion luminescent property, drug-loading capacity, release performance and excellent biocompatibility, exhibiting great potentials in targeted drug delivery and tissue engineering with potential tracking capability and lasting release performance. Copyright © 2016 Elsevier B.V. All rights reserved.

  2. A machine learning model to determine the accuracy of variant calls in capture-based next generation sequencing.

    Science.gov (United States)

    van den Akker, Jeroen; Mishne, Gilad; Zimmer, Anjali D; Zhou, Alicia Y

    2018-04-17

    Next generation sequencing (NGS) has become a common technology for clinical genetic tests. The quality of NGS calls varies widely and is influenced by features like reference sequence characteristics, read depth, and mapping accuracy. With recent advances in NGS technology and software tools, the majority of variants called using NGS alone are in fact accurate and reliable. However, a small subset of difficult-to-call variants that still do require orthogonal confirmation exist. For this reason, many clinical laboratories confirm NGS results using orthogonal technologies such as Sanger sequencing. Here, we report the development of a deterministic machine-learning-based model to differentiate between these two types of variant calls: those that do not require confirmation using an orthogonal technology (high confidence), and those that require additional quality testing (low confidence). This approach allows reliable NGS-based calling in a clinical setting by identifying the few important variant calls that require orthogonal confirmation. We developed and tested the model using a set of 7179 variants identified by a targeted NGS panel and re-tested by Sanger sequencing. The model incorporated several signals of sequence characteristics and call quality to determine if a variant was identified at high or low confidence. The model was tuned to eliminate false positives, defined as variants that were called by NGS but not confirmed by Sanger sequencing. The model achieved very high accuracy: 99.4% (95% confidence interval: +/- 0.03%). It categorized 92.2% (6622/7179) of the variants as high confidence, and 100% of these were confirmed to be present by Sanger sequencing. Among the variants that were categorized as low confidence, defined as NGS calls of low quality that are likely to be artifacts, 92.1% (513/557) were found to be not present by Sanger sequencing. This work shows that NGS data contains sufficient characteristics for a machine-learning-based model to

  3. Increased genetic diversity and prevalence of co-infection with Trypanosoma spp. in koalas (Phascolarctos cinereus and their ticks identified using next-generation sequencing (NGS.

    Directory of Open Access Journals (Sweden)

    Amanda D Barbosa

    Full Text Available Infections with Trypanosoma spp. have been associated with poor health and decreased survival of koalas (Phascolarctos cinereus, particularly in the presence of concurrent pathogens such as Chlamydia and koala retrovirus. The present study describes the application of a next-generation sequencing (NGS-based assay to characterise the prevalence and genetic diversity of trypanosome communities in koalas and two native species of ticks (Ixodes holocyclus and I. tasmani removed from koala hosts. Among 168 koalas tested, 32.2% (95% CI: 25.2-39.8% were positive for at least one Trypanosoma sp. Previously described Trypanosoma spp. from koalas were identified, including T. irwini (32.1%, 95% CI: 25.2-39.8%, T. gilletti (25%, 95% CI: 18.7-32.3%, T. copemani (27.4%, 95% CI: 20.8-34.8% and T. vegrandis (10.1%, 95% CI: 6.0-15.7%. Trypanosoma noyesi was detected for the first time in koalas, although at a low prevalence (0.6% 95% CI: 0-3.3%, and a novel species (Trypanosoma sp. AB-2017 was identified at a prevalence of 4.8% (95% CI: 2.1-9.2%. Mixed infections with up to five species were present in 27.4% (95% CI: 21-35% of the koalas, which was significantly higher than the prevalence of single infections 4.8% (95% CI: 2-9%. Overall, a considerably higher proportion (79.7% of the Trypanosoma sequences isolated from koala blood samples were identified as T. irwini, suggesting this is the dominant species. Co-infections involving T. gilletti, T. irwini, T. copemani, T. vegrandis and Trypanosoma sp. AB-2017 were also detected in ticks, with T. gilletti and T. copemani being the dominant species within the invertebrate hosts. Direct Sanger sequencing of Trypanosoma 18S rRNA gene amplicons was also performed and results revealed that this method was only able to identify the genotypes with greater amount of reads (according to NGS within koala samples, which highlights the advantages of NGS in detecting mixed infections. The present study provides new insights

  4. Increased genetic diversity and prevalence of co-infection with Trypanosoma spp. in koalas (Phascolarctos cinereus) and their ticks identified using next-generation sequencing (NGS).

    Science.gov (United States)

    Barbosa, Amanda D; Gofton, Alexander W; Paparini, Andrea; Codello, Annachiara; Greay, Telleasha; Gillett, Amber; Warren, Kristin; Irwin, Peter; Ryan, Una

    2017-01-01

    Infections with Trypanosoma spp. have been associated with poor health and decreased survival of koalas (Phascolarctos cinereus), particularly in the presence of concurrent pathogens such as Chlamydia and koala retrovirus. The present study describes the application of a next-generation sequencing (NGS)-based assay to characterise the prevalence and genetic diversity of trypanosome communities in koalas and two native species of ticks (Ixodes holocyclus and I. tasmani) removed from koala hosts. Among 168 koalas tested, 32.2% (95% CI: 25.2-39.8%) were positive for at least one Trypanosoma sp. Previously described Trypanosoma spp. from koalas were identified, including T. irwini (32.1%, 95% CI: 25.2-39.8%), T. gilletti (25%, 95% CI: 18.7-32.3%), T. copemani (27.4%, 95% CI: 20.8-34.8%) and T. vegrandis (10.1%, 95% CI: 6.0-15.7%). Trypanosoma noyesi was detected for the first time in koalas, although at a low prevalence (0.6% 95% CI: 0-3.3%), and a novel species (Trypanosoma sp. AB-2017) was identified at a prevalence of 4.8% (95% CI: 2.1-9.2%). Mixed infections with up to five species were present in 27.4% (95% CI: 21-35%) of the koalas, which was significantly higher than the prevalence of single infections 4.8% (95% CI: 2-9%). Overall, a considerably higher proportion (79.7%) of the Trypanosoma sequences isolated from koala blood samples were identified as T. irwini, suggesting this is the dominant species. Co-infections involving T. gilletti, T. irwini, T. copemani, T. vegrandis and Trypanosoma sp. AB-2017 were also detected in ticks, with T. gilletti and T. copemani being the dominant species within the invertebrate hosts. Direct Sanger sequencing of Trypanosoma 18S rRNA gene amplicons was also performed and results revealed that this method was only able to identify the genotypes with greater amount of reads (according to NGS) within koala samples, which highlights the advantages of NGS in detecting mixed infections. The present study provides new insights on the

  5. Web-based NGS data analysis using miRMaster: a large-scale meta-analysis of human miRNAs.

    Science.gov (United States)

    Fehlmann, Tobias; Backes, Christina; Kahraman, Mustafa; Haas, Jan; Ludwig, Nicole; Posch, Andreas E; Würstle, Maximilian L; Hübenthal, Matthias; Franke, Andre; Meder, Benjamin; Meese, Eckart; Keller, Andreas

    2017-09-06

    The analysis of small RNA NGS data together with the discovery of new small RNAs is among the foremost challenges in life science. For the analysis of raw high-throughput sequencing data we implemented the fast, accurate and comprehensive web-based tool miRMaster. Our toolbox provides a wide range of modules for quantification of miRNAs and other non-coding RNAs, discovering new miRNAs, isomiRs, mutations, exogenous RNAs and motifs. Use-cases comprising hundreds of samples are processed in less than 5 h with an accuracy of 99.4%. An integrative analysis of small RNAs from 1836 data sets (20 billion reads) indicated that context-specific miRNAs (e.g. miRNAs present only in one or few different tissues / cell types) still remain to be discovered while broadly expressed miRNAs appear to be largely known. In total, our analysis of known and novel miRNAs indicated nearly 22 000 candidates of precursors with one or two mature forms. Based on these, we designed a custom microarray comprising 11 872 potential mature miRNAs to assess the quality of our prediction. MiRMaster is a convenient-to-use tool for the comprehensive and fast analysis of miRNA NGS data. In addition, our predicted miRNA candidates provided as custom array will allow researchers to perform in depth validation of candidates interesting to them. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  6. Applicability and Efficiency of NGS in Routine Diagnosis: In-Depth Performance Analysis of a Complete Workflow for CFTR Mutation Analysis.

    Directory of Open Access Journals (Sweden)

    Adrien Pagin

    Full Text Available Actually, about 2000 sequence variations have been documented in the CFTR gene requiring extensive and multi-step genetic testing in the diagnosis of cystic fibrosis and CFTR-related disorders. We present a two phases study, with validation and performance monitoring, of a single experiment methodology based on multiplex PCR and high throughput sequencing that allows detection of all variants, including large rearrangements, affecting the coding regions plus three deep intronic loci.A total of 340 samples, including 257 patients and 83 previously characterized control samples, were sequenced in 17 MiSeq runs and analyzed with two bioinformatic pipelines in routine diagnostic conditions. We obtained 100% coverage for all the target regions in every tested sample.We correctly identified all the 87 known variants in the control samples and successfully confirmed the 62 variants identified among the patients without observing false positive results. Large rearrangements were identified in 18/18 control samples. Only 17 patient samples showed false positive signals (6.6%, 12 of which showed a borderline result for a single amplicon. We also demonstrated the ability of the assay to detect allele specific dropout of amplicons when a sequence variation occurs at a primer binding site thus limiting the risk for false negative results.We described here the first NGS workflow for CFTR routine analysis that demonstrated equivalent diagnostic performances compared to Sanger sequencing and multiplex ligation-dependent probe amplification. This study illustrates the advantages of NGS in term of scalability, workload reduction and cost-effectiveness in combination with an improvement of the overall data quality due to the simultaneous detection of SNVs and large rearrangements.

  7. A rapid NGS strategy for comprehensive molecular diagnosis of Birt-Hogg-Dubé syndrome in patients with primary spontaneous pneumothorax.

    Science.gov (United States)

    Zhang, Xinxin; Ma, Dehua; Zou, Wei; Ding, Yibing; Zhu, Chengchu; Min, Haiyan; Zhang, Bin; Wang, Wei; Chen, Baofu; Ye, Minhua; Cai, Minghui; Pan, Yanqing; Cao, Lei; Wan, Yueming; Jin, Yu; Gao, Qian; Yi, Long

    2016-05-27

    Primary spontaneous pneumothorax (PSP) or pulmonary cysts is one of the manifestations of Birt-Hogg-Dube syndrome (BHDS) that is caused by heterozygous mutations in FLCN gene. Most of the mutations are SNVs and small indels, and there are also approximately 10 % large intragenic deletions and duplications of the mutations. These molecular findings are generally obtained by disparate methods including Sanger sequencing and Multiple Ligation-dependent Probe Amplification in the clinical laboratory. In addition, as a genetically heterogeneous disorder, PSP may be caused by mutations in multiple genes include FBN1, COL3A1, CBS, SERPINA1 and TSC1/TSC2 genes. For differential diagnosis, these genes should also be screened which makes the diagnostic procedure more time-consuming and labor-intensive. Forty PSP patients were divided into 2 groups. Nineteen patients with different pathogenic mutations of FLCN previously identified by conventional Sanger sequencing and MLPA were included in test group, 21 random PSP patients without any genetic screening were included in blinded sample group. 7 PSP genes including FLCN, FBN1, COL3A1, CBS, SERPINA1 and TSC1/TSC2 were designed and enriched by Haloplex system, sequenced on a Miseq platform and analyzed in the 40 patients to evaluate the performance of the targeted-NGS method. We demonstrated that the full spectrum of genes associated with pneumothorax including FLCN gene mutations can be identified simultaneously in multiplexed sequence data. Noteworthy, by our in-house copy number analysis of the sequence data, we could not only detect intragenic deletions, but also determine approximate deletion junctions simultaneously. NGS based Haloplex target enrichment technology is proved to be a rapid and cost-effective screening strategy for the comprehensive molecular diagnosis of BHDS in PSP patients, as it can replace Sanger sequencing and MLPA by simultaneously detecting exonic and intronic SNVs, small indels, large intragenic

  8. Molecularly imprinted polymer microspheres prepared by Pickering emulsion polymerization for selective solid-phase extraction of eight bisphenols from human urine samples.

    Science.gov (United States)

    Yang, Jiajia; Li, Yun; Wang, Jincheng; Sun, Xiaoli; Cao, Rong; Sun, Hao; Huang, Chaonan; Chen, Jiping

    2015-05-04

    The bisphenol A (BPA) imprinted polymer microspheres were prepared by simple Pickering emulsion polymerization. Compared to traditional bulk polymerization, both high yields of polymer and good control of particle sizes were achieved. The characterization results of scanning electron microscopy and nitrogen adsorption-desorption measurements showed that the obtained molecularly imprinted polymer microsphere (MIPMS) particles possessed regular spherical shape, narrow diameter distribution (30-60 μm), a specific surface area (S(BET)) of 281.26 m(2) g(-1) and a total pore volume (V(t)) of 0.459 cm(3) g(-1). Good specific adsorption capacity for BPA was obtained in the sorption experiment and good class selectivity for BPA and its seven structural analogs (bisphenol F, bisphenol B, bisphenol E, bisphenol AF, bisphenol S, bisphenol AP and bisphenol Z) was demonstrated by the chromatographic evaluation experiment. The MIPMS as solid-phase extraction (SPE) packing material was then evaluated for extraction and clean-up of these bisphenols (BPs) from human urine samples. An accurate and sensitive analytical method based on the MIPMS-SPE coupled with HPLC-DAD has been successfully established for simultaneous determination of eight BPs from human urine samples with detection limits of 1.2-2.2 ng mL(-1). The recoveries of BPs for urine samples at two spiking levels (100 and 500 ng mL(-1) for each BP) were in the range of 81.3-106.7% with RSD values below 8.3%. Copyright © 2015 Elsevier B.V. All rights reserved.

  9. Facile fabrication of poly(L-lactic acid) microsphere-incorporated calcium alginate/hydroxyapatite porous scaffolds based on Pickering emulsion templates.

    Science.gov (United States)

    Hu, Yang; Ma, Shanshan; Yang, Zhuohong; Zhou, Wuyi; Du, Zhengshan; Huang, Jian; Yi, Huan; Wang, Chaoyang

    2016-04-01

    In this study, we develop a facile one-pot approach to the fabrication of poly(L-lactic acid) (PLLA) microsphere-incorporated calcium alginate (ALG-Ca)/hydroxyapatite (HAp) porous scaffolds based on HAp nanoparticle-stabilized oil-in-water Pickering emulsion templates, which contain alginate in the aqueous phase and PLLA in the oil phase. The emulsion aqueous phase is solidified by in situ gelation of alginate with Ca(2+) released from HAp by decreasing pH with slow hydrolysis of D-gluconic acid δ-lactone (GDL) to produce emulsion droplet-incorporated gels, followed by freeze-drying to form porous scaffolds containing microspheres. The pore structure of porous scaffolds can be adjusted by varying the HAp or GDL concentration. The compressive tests show that the increase of HAp or GDL concentration is beneficial to improve the compressive property of porous scaffolds, while the excessive HAp can lead to the decrease in compressive property. Moreover, the swelling behavior studies display that the swelling ratios of porous scaffolds reduce with increasing HAp or GDL concentration. Furthermore, hydrophobic drug ibuprofen (IBU) and hydrophilic drug bovine serum albumin (BSA) are loaded into the microspheres and scaffold matrix, respectively. In vitro drug release results indicate that BSA has a rapid release while IBU has a sustained release in the dual drug-loaded scaffolds. In vitro cell culture experiments verify that mouse bone mesenchymal stem cells can proliferate on the porous scaffolds well, indicating the good biocompatibility of porous scaffolds. All these results demonstrate that the PLLA microsphere-incorporated ALG-Ca/HAp porous scaffolds have a promising potential for tissue engineering and drug delivery applications. Copyright © 2016 Elsevier B.V. All rights reserved.

  10. Non-synonymous variations in cancer and their effects on the human proteome: workflow for NGS data biocuration and proteome-wide analysis of TCGA data.

    Science.gov (United States)

    Cole, Charles; Krampis, Konstantinos; Karagiannis, Konstantinos; Almeida, Jonas S; Faison, William J; Motwani, Mona; Wan, Quan; Golikov, Anton; Pan, Yang; Simonyan, Vahan; Mazumder, Raja

    2014-01-27

    Next-generation sequencing (NGS) technologies have resulted in petabytes of scattered data, decentralized in archives, databases and sometimes in isolated hard-disks which are inaccessible for browsing and analysis. It is expected that curated secondary databases will help organize some of this Big Data thereby allowing users better navigate, search and compute on it. To address the above challenge, we have implemented a NGS biocuration workflow and are analyzing short read sequences and associated metadata from cancer patients to better understand the human variome. Curation of variation and other related information from control (normal tissue) and case (tumor) samples will provide comprehensive background information that can be used in genomic medicine research and application studies. Our approach includes a CloudBioLinux Virtual Machine which is used upstream of an integrated High-performance Integrated Virtual Environment (HIVE) that encapsulates Curated Short Read archive (CSR) and a proteome-wide variation effect analysis tool (SNVDis). As a proof-of-concept, we have curated and analyzed control and case breast cancer datasets from the NCI cancer genomics program - The Cancer Genome Atlas (TCGA). Our efforts include reviewing and recording in CSR available clinical information on patients, mapping of the reads to the reference followed by identification of non-synonymous Single Nucleotide Variations (nsSNVs) and integrating the data with tools that allow analysis of effect nsSNVs on the human proteome. Furthermore, we have also developed a novel phylogenetic analysis algorithm that uses SNV positions and can be used to classify the patient population. The workflow described here lays the foundation for analysis of short read sequence data to identify rare and novel SNVs that are not present in dbSNP and therefore provides a more comprehensive understanding of the human variome. Variation results for single genes as well as the entire study are available

  11. Pre-Analytical Considerations for Successful Next-Generation Sequencing (NGS: Challenges and Opportunities for Formalin-Fixed and Paraffin-Embedded Tumor Tissue (FFPE Samples

    Directory of Open Access Journals (Sweden)

    Gladys Arreaza

    2016-09-01

    Full Text Available In cancer drug discovery, it is important to investigate the genetic determinants of response or resistance to cancer therapy as well as factors that contribute to adverse events in the course of clinical trials. Despite the emergence of new technologies and the ability to measure more diverse analytes (e.g., circulating tumor cell (CTC, circulating tumor DNA (ctDNA, etc., tumor tissue is still the most common and reliable source for biomarker investigation. Because of its worldwide use and ability to preserve samples for many decades at ambient temperature, formalin-fixed, paraffin-embedded tumor tissue (FFPE is likely to be the preferred choice for tissue preservation in clinical practice for the foreseeable future. Multiple analyses are routinely performed on the same FFPE samples (such as Immunohistochemistry (IHC, in situ hybridization, RNAseq, DNAseq, TILseq, Methyl-Seq, etc.. Thus, specimen prioritization and optimization of the isolation of analytes is critical to ensure successful completion of each assay. FFPE is notorious for producing suboptimal DNA quality and low DNA yield. However, commercial vendors tend to request higher DNA sample mass than what is actually required for downstream assays, which restricts the breadth of biomarker work that can be performed. We evaluated multiple genomics service laboratories to assess the current state of NGS pre-analytical processing of FFPE. Significant differences in pre-analytical capabilities were observed. Key aspects are highlighted and recommendations are made to improve the current practice in translational research.

  12. NGS tools for traceability in candies as high processed food products: Ion Torrent PGM versus conventional PCR-cloning.

    Science.gov (United States)

    Muñoz-Colmenero, Marta; Martínez, Jose Luis; Roca, Agustín; Garcia-Vazquez, Eva

    2017-01-01

    The Next Generation Sequencing methodologies are considered the next step within DNA-based methods and their applicability in different fields is being evaluated. Here, we tested the usefulness of the Ion Torrent Personal Genome Machine (PGM) in food traceability analyzing candies as a model of high processed foods, and compared the results with those obtained by PCR-cloning-sequencing (PCR-CS). The majority of samples exhibited consistency between methodologies, yielding more information and species per product from the PGM platform than PCR-CS. Significantly higher AT-content in sequences of the same species was also obtained from PGM. This together with some taxonomical discrepancies between methodologies suggest that the PGM platform is still pre-mature for its use in food traceability of complex highly processed products. It could be a good option for analysis of less complex food, saving time and cost per sample. Copyright © 2016 Elsevier Ltd. All rights reserved.

  13. The distribution and abundance of gamma emitting radionuclides in Lake Ontario sediments

    International Nuclear Information System (INIS)

    McKinley, R.S.

    1985-03-01

    The distribution of gamma emitting radionuclides in Lake Ontario sediments was investigated. Samples were collected using a systematic design in the vicinity of Pickering and Darlington, and supplemented by lakewide offshore samples. Naturally occurring 40 K was the predominant source of gamma activity. 60 Co was the only potentially CANDU released radionuclide which showed a distributional association with the Pickering 'A' NGS discharge

  14. A NGS approach to the encrusting Mediterranean sponge Crella elegans (Porifera, Demospongiae, Poecilosclerida): transcriptome sequencing, characterization and overview of the gene expression along three life cycle stages.

    Science.gov (United States)

    Pérez-Porro, A R; Navarro-Gómez, D; Uriz, M J; Giribet, G

    2013-05-01

    Sponges can be dominant organisms in many marine and freshwater habitats where they play essential ecological roles. They also represent a key group to address important questions in early metazoan evolution. Recent approaches for improving knowledge on sponge biological and ecological functions as well as on animal evolution have focused on the genetic toolkits involved in ecological responses to environmental changes (biotic and abiotic), development and reproduction. These approaches are possible thanks to newly available, massive sequencing technologies-such as the Illumina platform, which facilitate genome and transcriptome sequencing in a cost-effective manner. Here we present the first NGS (next-generation sequencing) approach to understanding the life cycle of an encrusting marine sponge. For this we sequenced libraries of three different life cycle stages of the Mediterranean sponge Crella elegans and generated de novo transcriptome assemblies. Three assemblies were based on sponge tissue of a particular life cycle stage, including non-reproductive tissue, tissue with sperm cysts and tissue with larvae. The fourth assembly pooled the data from all three stages. By aggregating data from all the different life cycle stages we obtained a higher total number of contigs, contigs with blast hit and annotated contigs than from one stage-based assemblies. In that multi-stage assembly we obtained a larger number of the developmental regulatory genes known for metazoans than in any other assembly. We also advance the differential expression of selected genes in the three life cycle stages to explore the potential of RNA-seq for improving knowledge on functional processes along the sponge life cycle. © 2013 Blackwell Publishing Ltd.

  15. Next-generation sequence analysis of cancer xenograft models.

    Directory of Open Access Journals (Sweden)

    Fernando J Rossello

    Full Text Available Next-generation sequencing (NGS studies in cancer are limited by the amount, quality and purity of tissue samples. In this situation, primary xenografts have proven useful preclinical models. However, the presence of mouse-derived stromal cells represents a technical challenge to their use in NGS studies. We examined this problem in an established primary xenograft model of small cell lung cancer (SCLC, a malignancy often diagnosed from small biopsy or needle aspirate samples. Using an in silico strategy that assign reads according to species-of-origin, we prospectively compared NGS data from primary xenograft models with matched cell lines and with published datasets. We show here that low-coverage whole-genome analysis demonstrated remarkable concordance between published genome data and internal controls, despite the presence of mouse genomic DNA. Exome capture sequencing revealed that this enrichment procedure was highly species-specific, with less than 4% of reads aligning to the mouse genome. Human-specific expression profiling with RNA-Seq replicated array-based gene expression experiments, whereas mouse-specific transcript profiles correlated with published datasets from human cancer stroma. We conclude that primary xenografts represent a useful platform for complex NGS analysis in cancer research for tumours with limited sample resources, or those with prominent stromal cell populations.

  16. Suppression substractive hybridisation and NGS reveal differential transcriptome expression profiles in Wayfaring Tree (Viburnum lantana L. treated with ozone

    Directory of Open Access Journals (Sweden)

    Elena eGottardini

    2016-06-01

    specific transcription factors (MYB and WRKY. This study demonstrates that a complex sequence of events takes place in the cells at intracellular and membrane level following O3 exposure and elucidates the effects of this oxidative stress on the transcriptional machinery of the non-model plant species V. lantana, with the final aim to provide the molecular supportive knowledge for the use of this plant as O3-bioindicator.

  17. Fabrication and evaluation of chitosan/NaYF{sub 4}:Yb{sup 3+}/Tm{sup 3+} upconversion nanoparticles composite beads based on the gelling of Pickering emulsion droplets

    Energy Technology Data Exchange (ETDEWEB)

    Yan, Huiqiong; Chen, Xiuqiong; Shi, Jia; Shi, Zaifeng; Sun, Wei; Lin, Qiang, E-mail: linqianggroup@163.com; Wang, Xianghui; Dai, Zihao

    2017-02-01

    The rare earth ion doped upconversion nanoparticles (UCNPs) synthesized by hydrophobic organic ligands possess poor solubility and low fluorescence quantum yield in aqueous media. To conquer this issue, NaYF{sub 4}:Yb{sup 3+}/Tm{sup 3+} UCNPs, synthesized by a hydrothermal method, were coated with F127 and then assembled with chitosan to fabricate the chitosan/NaYF{sub 4}:Yb{sup 3+}/Tm{sup 3+} composite beads (CS/NaYF{sub 4}:Yb{sup 3+}/Tm{sup 3+} CBs) by Pickering emulsion system. The characterization results revealed that the as-synthesized NaYF{sub 4}:Yb{sup 3+}/Tm{sup 3+} UCNPs with an average size of 20 nm exhibited spherical morphology, high crystallinity and characteristic emission upconversion fluorescence with an overall blue color output. The NaYF{sub 4}:Yb{sup 3+}/Tm{sup 3+} UCNPs were successfully conjugated on the surface of chitosan beads by the gelling of emulsion droplets. The resultant CS/NaYF{sub 4}:Yb{sup 3+}/Tm{sup 3+} CBs showed good upconversion luminescent property, drug-loading capacity, release performance and excellent biocompatibility, exhibiting great potentials in targeted drug delivery and tissue engineering with potential tracking capability and lasting release performance. - Highlights: • NaYF{sub 4}:Yb{sup 3+}/Tm{sup 3+} UCNPs were coated by F127 to improve aqueous dispersibility. • NaYF{sub 4}:Yb{sup 3+}/Tm{sup 3+} UCNPs were assembled with chitosan to fabricate the composite beads (CMs). • Pickering emulsions stabilized by UCNPs exhibited uniform and satisfactory emulsion droplets. • The CMs prepared by the gelling of emulsion droplet preserved upconversion luminescent property. • The resultant CMs showed good drug-loading capacity, release performance and biocompatibility.

  18. Gentilly - 2 NGS ALARA program

    International Nuclear Information System (INIS)

    Rheaume, Michel R.

    1998-01-01

    This is a slide-based oral presentation given to the COG/IAEA: Fifth technical committee meeting on 'Exchange of operating experience of pressurized heavy water reactors' held in Mangalia, Romania on 7-10 September 1998. The operation experience of Gentilly -1 and Gentilly - 2 nuclear power stations is summarized. The radiation protection philosophy is addressed, the orange/yellow/green RP qualifications are explained and the ALARA Program objectives are described. The criteria used to develop the Gentilly - 2 station ALARA Program are presented. The program is based on: strong Hydro Quebec commitments, organization (responsibilities well defined); ALARA Committee; tools; procedures; good documentation. Description of the program is given then in details. Measures for dose and radioactive sources reduction are presented. Collective doses recorded at Gentilly - 2 between 1984 and 1997 are plotted and figures are given in a table

  19. Evaluation of the zebrafish embryo as an alternative model for hepatotoxicity testing

    NARCIS (Netherlands)

    Driessen, Marja

    2014-01-01

    In this thesis we showed the applicability of the zebrafish embryo as an alternative model for hepatotoxicity testing using analysis of mechanisms through toxicogenomics. By applying a variety of toxicogenomics techniques, we were able to characterize specific responses. NGS revealed that

  20. Mixture model with multiple allocations for clustering spatially correlated observations in the analysis of ChIP-Seq data

    NARCIS (Netherlands)

    Ranciati, Saverio; Viroli, Cinzia; Wit, Ernst C.

    2017-01-01

    Model-based clustering is a technique widely used to group a collection of units into mutually exclusive groups. There are, however, situations in which an observation could in principle belong to more than one cluster. In the context of next-generation sequencing (NGS) experiments, for example, the

  1. Hétérogenéité quantitative et qualitative de la matière organique dans les argiles du Kimmeridgien du val de Pickering (Yorkshire, UK. Cadre sédimentologique et stratigraphique Quantitative and Qualitative Heterogeneity of the Organic Matter Within the Kimmeridge Clay of the Vale of Pickering (Yorkshire, Uk. Sedimentological and Stratigraphical Framework

    Directory of Open Access Journals (Sweden)

    Penn I. E.

    2006-11-01

    Full Text Available Les argiles du Kimméridgien contribuent à l'alimentation de nombreux gisements en mer du Nord. L'étude de quatre puits localisés sur une coupe Est-Ouest dans le Val de Pickering (Bassin de Cleveland permet d'illustrer dans cette formation l'hétérogénéité de distribution verticale et latérale de la matière organique en terme de quantité et de qualité. La coupe étudiée (35 km de long, 200 m de haut représente environ 6,5 millions d'années d'histoire géologique. Les analyses minéralogiques montrent que la formation est caractérisée par une grande homogénéité des apports sédimentaires, ce qui suppose des conditions de sédimentation stables dans le temps et dans l'espace. Le matériel sédimentaire, déposé dans un environnement calme, est composé de minéraux argileux (kaolinite, illite, et interstratifiés irréguliers illite/smectite avec des niveaux carbonatés résultant d'une production biogénique. Ces niveaux carbonatés intercalés au sein des argiles peuvent être corrélés entre les puits. Pour la plupart dolomitisés, ils résultent d'une transformation plus importante àl'ouest (Marton qu'à l'est (Reighton de couches presque exclusivement formées de coccolithes. L'extension horizontale de ces niveaux indique qu'ils correspondent à des événements géodynamiques régionaux. L'étude des ammonites permet de reconnaitre, dans le Yorkshire, la succession de 10 zones du Kimméridgien (sensu anglico et d'identifier 8 sous-zones depuis la zone à Cymodoce (- 144 m. a. jusqu'à celle à Pectinatus (- 137,5 m. a. . Les zonations reconnues permettent de corréler ces quatre puits avec les autres régions d'Angleterre. L'existence de repères stratigraphiques et de repères diagraphiques caractéristiques au sein des zones d'ammonites permet d'établir des zones de corrélation entre une partie bassin (puits de Marton 87, Ebberston 87, Flixton 87 et une zone haute appartenant à la plate-forme Est de l

  2. Harnessing NGS and Big Data Optimally: Comparison of miRNA Prediction from Assembled versus Non-assembled Sequencing Data--The Case of the Grass Aegilops tauschii Complex Genome.

    Science.gov (United States)

    Budak, Hikmet; Kantar, Melda

    2015-07-01

    MicroRNAs (miRNAs) are small, endogenous, non-coding RNA molecules that regulate gene expression at the post-transcriptional level. As high-throughput next generation sequencing (NGS) and Big Data rapidly accumulate for various species, efforts for in silico identification of miRNAs intensify. Surprisingly, the effect of the input genomics sequence on the robustness of miRNA prediction was not evaluated in detail to date. In the present study, we performed a homology-based miRNA and isomiRNA prediction of the 5D chromosome of bread wheat progenitor, Aegilops tauschii, using two distinct sequence data sets as input: (1) raw sequence reads obtained from 454-GS FLX Titanium sequencing platform and (2) an assembly constructed from these reads. We also compared this method with a number of available plant sequence datasets. We report here the identification of 62 and 22 miRNAs from raw reads and the assembly, respectively, of which 16 were predicted with high confidence from both datasets. While raw reads promoted sensitivity with the high number of miRNAs predicted, 55% (12 out of 22) of the assembly-based predictions were supported by previous observations, bringing specificity forward compared to the read-based predictions, of which only 37% were supported. Importantly, raw reads could identify several repeat-related miRNAs that could not be detected with the assembly. However, raw reads could not capture 6 miRNAs, for which the stem-loops could only be covered by the relatively longer sequences from the assembly. In summary, the comparison of miRNA datasets obtained by these two strategies revealed that utilization of raw reads, as well as assemblies for in silico prediction, have distinct advantages and disadvantages. Consideration of these important nuances can benefit future miRNA identification efforts in the current age of NGS and Big Data driven life sciences innovation.

  3. Catadoras de caranguejo e saberes tradicionais na conservação de manguezais da Amazônia brasileira Crab pickers and traditional knowledge in the conservation of brazilian Amazonian mangroves

    Directory of Open Access Journals (Sweden)

    Denise Machado

    2007-08-01

    Full Text Available A catação de caranguejo (Ucides cordatus desenvolvida por mulheres caboclas em áreas do litoral norte da região amazônica, precisamente no nordeste paraense, possibilita a análise da problemática ambiental e relações de gênero a partir de uma abordagem antropológica sobre uma parcela da população tradicional amazônica. Quanto à questão ambiental, é tratada em termos de conservação, manejo e conhecimento de recursos ambientais. Evidenciou-se que a pesca desenvolvida nas áreas de manguezais na vila de Guarajubal é feita artesanalmente e direcionada à captura e beneficiamento do caranguejo, com o trabalho decisivo das mulheres a partir da maior demanda nos centros urbanos próximos. O trabalho das catadoras lhes possibilita manifestarem-se em relação aos problemas ambientais, ainda que no contexto local.The crab (Ucides cordatus picking, done by cabocla women in Northeast Pará of the North Coastal Amazon Region, permits the analysis of the environmental question and of gender relations from an anthropological approach on a specific Amazonian traditional population. The environmental question is dealt with in terms of conservation, handling and knowledge about environmental resources. Evidence shows that crab picking is an artisan activity developed in mangrove swamp areas near the town of Guarajubal in which catching and doing product betterment of the crab are women's work, stimulated by the growing demand from nearby urban centers. The work of the catadoras (pickers allows them to manifest their opinions in relation to the environmental problems, albeit in the local context.

  4. A computer model for hydride blister growth in zirconium alloys

    International Nuclear Information System (INIS)

    White, A.J.; Sawatzky, A.; Woo, C.H.

    1985-06-01

    The failure of a Zircaloy-2 pressure tube in the Pickering unit 2 reactor started at a series of zirconium hydride blisters on the outside of the pressure tube. These blisters resulted from the thermal diffusion of hydrogen to the cooler regions of the pressure tube. In this report the physics of thermal diffusion of hydrogen in zirconium is reviewed and a computer model for blister growth in two-dimensional Cartesian geometry is described. The model is used to show that the blister-growth rate in a two-phase zirconium/zirconium-hydride region does not depend on the initial hydrogen concentration nor on the hydrogen pick-up rate, and that for a fixed far-field temperature there is an optimum pressure-type/calandria-tube contact temperature for growing blisters. The model described here can also be used to study large-scale effects, such as hydrogen-depletion zones around hydride blisters

  5. Monte Carlo modeling of the Fastscan whole body counter response

    International Nuclear Information System (INIS)

    Graham, H.R.; Waller, E.J.

    2015-01-01

    Monte Carlo N-Particle (MCNP) was used to make a model of the Fastscan for the purpose of calibration. Two models were made one for the Pickering Nuclear Site, and one for the Darlington Nuclear Site. Once these models were benchmarked and found to be in good agreement, simulations were run to study the effect different sized phantoms had on the detected response, and the shielding effect of torso fat was not negligible. Simulations into the nature of a source being positioned externally on the anterior or posterior of a person were also conducted to determine a ratio that could be used to determine if a source is externally or internally placed. (author)

  6. Pickering dry storage - commissioning and initial operation

    International Nuclear Information System (INIS)

    Jonjev, S.

    1996-01-01

    Having commissioned all individual conventional and nuclear systems, the first Dry Storage Container (DSC) was loaded with four modules of 17 year cooled irradiated fuel (366 bundles) in the Auxiliary Irradiated Fuel Bay (AIFB) on November 29, 1995. After decontamination of the outer surface, and draining of water, the DSC was transported to the Used Fuel Dry Storage Facility (UFDSF) workshop, where it was vacuum dried, and then the lid was welded on. Following successful radiography test of the lid weld, the DSC was vacuum dried again and backfilled with Helium to a pressure of 930 mbar(a). The Helium leak test showed zero leakage (allowable leak rate is 1x10 -5 cc/sec). Finally, after loose contamination checks were performed and permanent safeguards seals were applied, the DSC was placed in the UFDSF storage area on January 23, 1996. Radiation fields at contact with the DSC surface were < 0.6 mrem/hr, and at the exterior surface of the storage building wall only 33 micro-rem/hr (far below the target of 250 micro-rem/hr). Therefore, the actual dose rates to general public (at the exclusion zone boundary) will be well below the design target of 1 % of the regulatory limit. (author). 3 refs., 2 tabs., 5 figs

  7. Pickering dry storage - commissioning and initial operation

    Energy Technology Data Exchange (ETDEWEB)

    Jonjev, S [Ontario Hydro, Pickering, ON (Canada). Pickering Generating Station

    1997-12-31

    Having commissioned all individual conventional and nuclear systems, the first Dry Storage Container (DSC) was loaded with four modules of 17 year cooled irradiated fuel (366 bundles) in the Auxiliary Irradiated Fuel Bay (AIFB) on November 29, 1995. After decontamination of the outer surface, and draining of water, the DSC was transported to the Used Fuel Dry Storage Facility (UFDSF) workshop, where it was vacuum dried, and then the lid was welded on. Following successful radiography test of the lid weld, the DSC was vacuum dried again and backfilled with Helium to a pressure of 930 mbar(a). The Helium leak test showed zero leakage (allowable leak rate is 1x10{sup -5} cc/sec). Finally, after loose contamination checks were performed and permanent safeguards seals were applied, the DSC was placed in the UFDSF storage area on January 23, 1996. Radiation fields at contact with the DSC surface were < 0.6 mrem/hr, and at the exterior surface of the storage building wall only 33 micro-rem/hr (far below the target of 250 micro-rem/hr). Therefore, the actual dose rates to general public (at the exclusion zone boundary) will be well below the design target of 1 % of the regulatory limit. (author). 3 refs., 2 tabs., 5 figs.

  8. 2015 NOAA NGS Topobathy Lidar: Puerto Rico

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — These data were collected by the National Oceanic Atmospheric Administration National Geodetic Survey Remote Sensing Division using a Riegl VQ-820G system. The data...

  9. Nuclear safety management at the Wolsong NGS

    Energy Technology Data Exchange (ETDEWEB)

    Bong-Seob, Han [Korea Electric Power Corp., Wolson NPP no. 1 and 2 (Korea, Republic of)

    1997-12-01

    Nuclear safety management at the Wolsong nuclear power plant is described, including the following issues: site selection; plant history; operational goals; operational guidelines; reactor safety; safety training; plant maintenance; management of plant equipment lifetime; future tasks.

  10. Nuclear safety management at the Wolsong NGS

    International Nuclear Information System (INIS)

    Han Bong-Seob

    1997-01-01

    Nuclear safety management at the Wolsong nuclear power plant is described, including the following issues: site selection; plant history; operational goals; operational guidelines; reactor safety; safety training; plant maintenance; management of plant equipment lifetime; future tasks

  11. 2014 NOAA NGS Topobathy Lidar: Connecticut

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — These data were collected by the National Oceanic Atmospheric Administration National Geodetic Survey Remote Sensing Division using a Riegl VQ820G system. The data...

  12. MOV predictive maintenance program at Darlington NGS

    International Nuclear Information System (INIS)

    Morrison, J.F.

    1992-01-01

    This paper details the Motor Operated Valve (MOV) Predictive Maintenance program at Darlington Nuclear Generating Station. The program encompasses the use of diagnostics tooling in conjunction with more standard maintenance techniques, with the goal of improving performance of MOV's. Problems encountered and solutions developed during the first two phases of this program are presented, along with proposed actions for the final trending phase of the program. This paper also touches on the preventive and corrective maintenance aspects of an overall MOV maintenance program. 6 refs., 6 tabs., 6 figs

  13. Planning the location of facilities to implement a reverse logistic system of post-consumer packaging using a location mathematical model.

    Science.gov (United States)

    Couto, Maria Claudia Lima; Lange, Liséte Celina; Rosa, Rodrigo de Alvarenga; Couto, Paula Rogeria Lima

    2017-12-01

    The implementation of reverse logistics systems (RLS) for post-consumer products provides environmental and economic benefits, since it increases recycling potential. However, RLS implantation and consolidation still face problems. The main shortcomings are the high costs and the low expectation of broad implementation worldwide. This paper presents two mathematical models to decide the number and the location of screening centers (SCs) and valorization centers (VCs) to implement reverse logistics of post-consumer packages, defining the optimum territorial arrangements (OTAs), allowing the inclusion of small and medium size municipalities. The paper aims to fill a gap in the literature on RLS location facilities that not only aim at revenue optimization, but also the participation of the population, the involvement of pickers and the service universalization. The results showed that implementation of VCs can lead to revenue/cost ratio higher than 100%. The results of this study can supply companies and government agencies with a global view on the parameters that influence RLS sustainability and help them make decisions about the location of these facilities and the best reverse flows with the social inclusion of pickers and serving the population of small and medium-sized municipalities.

  14. Aquatic dispersion modelling of a tritium plume in Lake Ontario

    International Nuclear Information System (INIS)

    Klukas, M.H.; Moltyaner, G.L.

    1996-05-01

    Approximately 2900 kg of tritiated water, containing 2.3E+15 Bq of tritium, were released to Lake Ontario via the cooling water discharge when a leak developed in a moderator heat exchanger in Unit 1 at the Pickering Nuclear Generating Station (PNGS) on 1992 August 2. The release provided the opportunity to study the dispersion of a tritium plume in the coastal zone of Lake Ontario. Current direction over the two-week period following the release was predominantly parallel to the shore, and elevated tritium concentrations were observed up to 20 km east and 85 km west of the PNGS. Predictions of the tritium plume movement were made using current velocity measurements taken at 8-m depth, 2.5 km offshore from Darlington and using a empirical relationship where alongshore current speed is assumed to be proportional to the alongshore component of the wind speed. The tritium migration was best described using current velocity measurements. The tritium plume dispersion is modelled using the one-dimensional advection-dispersion equation. Transport parameters are the alongshore current speed and longitudinal dispersion coefficient. Longitudinal dispersion coefficients, estimated by fitting the solution of the advection-dispersion equation to measured concentration distance profiles ranged from 3.75 to 10.57 m 2 s -1 . Simulations using the fitted values of the dispersion coefficient were able to describe maximum tritium concentrations measured at water supply plants located within 25 km of Pickering to within a factor of 3. The dispersion coefficient is a function of spatial and temporal variability in current velocity and the fitted dispersion coefficients estimated here may not be suitable for predicting tritium plume dispersion under different current conditions. The sensitivity of the dispersion coefficient to variability in current conditions should be evaluated in further field experiments. (author). 13 refs., 7 tabs., 12 figs

  15. National Geodetic Control Stations, Geographic NAD83, NGS (2004) [geodetic_ctrl_point_la_NGS_2004

    Data.gov (United States)

    Louisiana Geographic Information Center — This data contains a set of geodetic control stations maintained by the National Geodetic Survey. Each geodetic control station in this dataset has either a precise...

  16. HTO transfer from contaminated surfaces to the atmosphere: a database for model validation

    International Nuclear Information System (INIS)

    Davis, P.A.; Amiro, B.D.; Workman, W.J.G.; Corbett, B.J.

    1996-12-01

    This report comprises a detailed database that can be used to validate models of the emission of tritiated water vapour (HTO) from natural contaminated surfaces to the atmosphere. The data were collected in 1992 July during an intensive field study based on the flux-gradient method of micrometeorology. The measurements were made over a wetland area at the Chalk River Laboratories, and over a grassed field near the Pickering Nuclear Generating Station. The study sites, the sampling protocols and the analytical techniques are described in detail, and the measured fluxes are presented. The report also contains a detailed listing of HTO concentrations in air at two heights, HTO concentrations in the source compartments (soil, surface water and vegetation), supporting meteorological data, and various vegetation and soil properties. The uncertainties in all of the measured data are estimated. (author). 15 refs., 23 tabs., 9 figs

  17. biomvRhsmm: Genomic Segmentation with Hidden Semi-Markov Model

    Directory of Open Access Journals (Sweden)

    Yang Du

    2014-01-01

    Full Text Available High-throughput technologies like tiling array and next-generation sequencing (NGS generate continuous homogeneous segments or signal peaks in the genome that represent transcripts and transcript variants (transcript mapping and quantification, regions of deletion and amplification (copy number variation, or regions characterized by particular common features like chromatin state or DNA methylation ratio (epigenetic modifications. However, the volume and output of data produced by these technologies present challenges in analysis. Here, a hidden semi-Markov model (HSMM is implemented and tailored to handle multiple genomic profile, to better facilitate genome annotation by assisting in the detection of transcripts, regulatory regions, and copy number variation by holistic microarray or NGS. With support for various data distributions, instead of limiting itself to one specific application, the proposed hidden semi-Markov model is designed to allow modeling options to accommodate different types of genomic data and to serve as a general segmentation engine. By incorporating genomic positions into the sojourn distribution of HSMM, with optional prior learning using annotation or previous studies, the modeling output is more biologically sensible. The proposed model has been compared with several other state-of-the-art segmentation models through simulation benchmarking, which shows that our efficient implementation achieves comparable or better sensitivity and specificity in genomic segmentation.

  18. Self-, other-, and joint monitoring using forward models

    Directory of Open Access Journals (Sweden)

    Martin John Pickering

    2014-03-01

    Full Text Available In the psychology of language, most accounts of self-monitoring assume that it is based on comprehension. Here we outline and develop the alternative account proposed by Pickering and Garrod (2013, in which speakers construct forward models of their upcoming utterances and compare them with the utterance as they produce them. We propose that speakers compute inverse models derived from the discrepancy (error between the utterance and the predicted utterance and use that to modify their production command or (occasionally begin anew. We then propose that comprehenders monitor other people’s speech by simulating their utterances using covert imitation and forward models, and then comparing those forward models with what they hear. They use the discrepancy to compute inverse models and modify their representation of the speaker’s production command, or realize that their representation is incorrect and may develop a new production command. We then discuss monitoring in dialogue, paying attention to sequential contributions, concurrent feedback, and the relationship between monitoring and alignment.

  19. Beta-Binomial Model for the Detection of Rare Mutations in Pooled Next-Generation Sequencing Experiments.

    Science.gov (United States)

    Jakaitiene, Audrone; Avino, Mariano; Guarracino, Mario Rosario

    2017-04-01

    Against diminishing costs, next-generation sequencing (NGS) still remains expensive for studies with a large number of individuals. As cost saving, sequencing genome of pools containing multiple samples might be used. Currently, there are many software available for the detection of single-nucleotide polymorphisms (SNPs). Sensitivity and specificity depend on the model used and data analyzed, indicating that all software have space for improvement. We use beta-binomial model to detect rare mutations in untagged pooled NGS experiments. We propose a multireference framework for pooled data with ability being specific up to two patients affected by neuromuscular disorders (NMD). We assessed the results comparing with The Genome Analysis Toolkit (GATK), CRISP, SNVer, and FreeBayes. Our results show that the multireference approach applying beta-binomial model is accurate in predicting rare mutations at 0.01 fraction. Finally, we explored the concordance of mutations between the model and software, checking their involvement in any NMD-related gene. We detected seven novel SNPs, for which the functional analysis produced enriched terms related to locomotion and musculature.

  20. The Effect of Improved Sub-Daily Earth Rotation Models on Global GPS Data Processing

    Science.gov (United States)

    Yoon, S.; Choi, K. K.

    2017-12-01

    Throughout the various International GNSS Service (IGS) products, strong periodic signals have been observed around the 14 day period. This signal is clearly visible in all IGS time-series such as those related to orbit ephemerides, Earth rotation parameters (ERP) and ground station coordinates. Recent studies show that errors in the sub-daily Earth rotation models are the main factors that induce such noise. Current IGS orbit processing standards adopted the IERS 2010 convention and its sub-daily Earth rotation model. Since the IERS convention had published, recent advances in the VLBI analysis have made contributions to update the sub-daily Earth rotation models. We have compared several proposed sub-daily Earth rotation models and show the effect of using those models on orbit ephemeris, Earth rotation parameters and ground station coordinates generated by the NGS global GPS data processing strategy.

  1. Radioactive release data from Canadian nuclear generating stations 1872-1987

    International Nuclear Information System (INIS)

    1989-03-01

    All nuclear generating stations emit small quantities of radioactive effluent both into the atmosphere and in the form of liquid effluent, into the adjoining water body, be it river, lake or sea. The purpose of this document is to report on the magnitude of these emissions for each nuclear generating station in Canada and to indicate how these emissions compare with the relevant limitations imposed by the Atomic Energy Control Board as part of its regulatory and licensing program. This report incorporates histograms indicating the annual releases of tritium in air, noble gases, iodine-131, airborne particulates, tritium in water and waterborne gross beta activity for each nuclear generating station. In addition, for Pickering NGS 'A', annual released of carbon-14 are depicted for the years 1986 and 1987. In each case the emission data are compared to the Derived Emission Limit (DEL) in order that the data may be placed in perspective. At present, only Pickering NGS 'A' is required to monitor and report carbon-14 emissions. Environmental monitoring for C-14 is conducted around the Bruce site to determine the environmental impact of its emission and whether effluent monitoring will be necessary in future years. Three nuclear generating stations have been permanently taken out of service during the last few years (Gentilly NGS-1, Douglas Point NGS and NPD NGS). Some small emissions from these sites do still occur, however, due to decontamination and decommissioning operations. (11 tabs., 26 figs.)

  2. Modelling

    CERN Document Server

    Spädtke, P

    2013-01-01

    Modeling of technical machines became a standard technique since computer became powerful enough to handle the amount of data relevant to the specific system. Simulation of an existing physical device requires the knowledge of all relevant quantities. Electric fields given by the surrounding boundary as well as magnetic fields caused by coils or permanent magnets have to be known. Internal sources for both fields are sometimes taken into account, such as space charge forces or the internal magnetic field of a moving bunch of charged particles. Used solver routines are briefly described and some bench-marking is shown to estimate necessary computing times for different problems. Different types of charged particle sources will be shown together with a suitable model to describe the physical model. Electron guns are covered as well as different ion sources (volume ion sources, laser ion sources, Penning ion sources, electron resonance ion sources, and H$^-$-sources) together with some remarks on beam transport.

  3. Near-surface traveltime tomographic inversion using multiple first break picks

    KAUST Repository

    Saragiotis, Christos; Choi, Yun Seok; Keho, T.; Alkhalifah, Tariq Ali

    2013-01-01

    The input data for refraction traveltime tomography are the traveltimes of the first breaks, which are picked using automatic pickers. Although automatic pickers perform satisfactorily overall, no one automatic picker can be characterized as the best one; one picker might fail for traces for which other pickers are accurate and vice versa for other traces. We introduce an iterative method for traveltime tomography, which takes as input traveltimes from a number of pickers. During the inversion scheme inconsistent traveltimes are replaced with more meaningful ones to obtain a smooth near-surface velocity model. The scheme is easily parallelizable and a byproduct of the inversion scheme is a set of consistent traveltimes which is close to the actual traveltimes of the first breaks.

  4. Order picker routing with product returns and interaction delays

    NARCIS (Netherlands)

    Schrotenboer, Albert H.; Wruck, Susanne; Roodbergen, Kees Jan; Veenstra, Marjolein; Dijkstra, Arjan

    2017-01-01

    E-commerce companies often use manual order-picking systems in their warehouses since these systems can provide the required flexibility and scalability. Manual systems have been widely studied, but the operating policies may require significant changes for e-commerce settings. First, to maintain

  5. A comparison of clinical vs subclinical skin pickers in Israel

    DEFF Research Database (Denmark)

    Keuthen, Nancy J.; Curley, Erin E.; Tung, Esther S.

    2016-01-01

    BACKGROUND: Skin-picking disorder (SPD) was recognized as its own entity for the first time in DSM-5. The existing SPD literature is limited and, to date, no study has examined the differences between clinical and sub- clinical SPD. Identifying differences between these 2 groups may improve diagn...

  6. A low-cost real color picker based on Arduino.

    Science.gov (United States)

    Agudo, Juan Enrique; Pardo, Pedro J; Sánchez, Héctor; Pérez, Ángel Luis; Suero, María Isabel

    2014-07-07

    Color measurements have traditionally been linked to expensive and difficult to handle equipment. The set of mathematical transformations that are needed to transfer a color that we observe in any object that doesn't emit its own light (which is usually called a color-object) so that it can be displayed on a computer screen or printed on paper is not at all trivial. This usually requires a thorough knowledge of color spaces, colorimetric transformations and color management systems. The TCS3414CS color sensor (I2C Sensor Color Grove), a system for capturing, processing and color management that allows the colors of any non-self-luminous object using a low-cost hardware based on Arduino, is presented in this paper. Specific software has been developed in Matlab and a study of the linearity of chromatic channels and accuracy of color measurements for this device has been undertaken. All used scripts (Arduino and Matlab) are attached as supplementary material. The results show acceptable accuracy values that, although obviously do not reach the levels obtained with the other scientific instruments, for the price difference they present a good low cost option.

  7. From bijels to Pickering emulsions: A lattice Boltzmann study

    NARCIS (Netherlands)

    Jansen, F.; Harting, J.

    2011-01-01

    Particle stabilized emulsions are ubiquitous in the food and cosmetics industry, but our understanding of the influence of microscopic fluid-particle and particle-particle interactions on the macroscopic rheology is still limited. In this paper we present a simulation algorithm based on a

  8. The attached algal community near Pickering GS: (II)

    International Nuclear Information System (INIS)

    McKinley, S.R.

    1982-01-01

    Environmental parameters correlated with attached algal standing crop are investigated in this report. Three groups were recognized on the basis of standing crop levels and seasonal standing crop patterns. Factors which appeared to influence the separation among the three groups were substrate size and water temperature. Standing crop levels among the discharge transects, intake and areas outside the station were found to be correlated with a combination of parameters. Standing crop levels outside the station were inversely correlated with wind speed but positively correlated with substrate particle size and depth. Algal standing crop at the intake also was inversely correlated with wind speed. Differences in standing crop levels between the intake and areas outside the station may have been attributed to substrate particle size. Low standing crop level among the discharge transects may have been attributed to higher current velocities and periodically to high water temperature

  9. What Works: Real Research or a Cherry Picker's Paradise?

    Science.gov (United States)

    Dainton, Sheila

    2006-01-01

    The purpose of this article is to consider the evidence base for some of the proposals in the Education White Paper, Higher Standards: better schools for all. In particular, the article challenges the assertion by the Secretary of State for Education and Skills that the White Paper is based on knowledge of "what works." Using the issue…

  10. Women waste pickers: living conditions, work, and health.

    Science.gov (United States)

    Coelho, Alexa Pupiara Flores; Beck, Carmem Lúcia Colomé; Fernandes, Marcelo Nunes da Silva; Freitas, Natiellen Quatrin; Prestes, Francine Cassol; Tonel, Juliana Zancan

    2016-09-29

    To know the elements of work, health, and living conditions of women who pick recyclable waste and are members of a waste cooperative in a town of the state of Rio Grande do Sul, Brazil. This is a qualitative, exploratory and descriptive study with seven subjects. Data were collected through participative observation, semi structured interview, and a focus group from July to August of 2013. The data were subjected to content analysis. The following thematic categories emerged: Women's work, informality and precariousness; Experiences of job satisfaction; and Working conditions and health: experiences with accidents, illness and health services. It was concluded that the women who collect recyclable material are exposed to precarious work conditions and potential health risks, such as work overload, accidents, illness, and social insecurity, and that nurses are responsible for promoting actions that ensure the health and inclusion of these workers.

  11. Pickering emulsions stabilized by paraffin wax and Laponite clay particles.

    Science.gov (United States)

    Li, Caifu; Liu, Qian; Mei, Zhen; Wang, Jun; Xu, Jian; Sun, Dejun

    2009-08-01

    Emulsions containing wax in dispersed droplets stabilized by disc-like Laponite clay particles are prepared. Properties of the emulsions prepared at different temperatures are examined using stability, microscopy and droplet-size analysis. At low temperature, the wax crystals in the oil droplets can protrude through the interface, leading to droplet coalescence. But at higher temperatures, the droplet size decreases with wax concentration. Considering the viscosity of the oil phase and the interfacial tension, we conclude that the wax is liquid-like during the high temperature emulsification process, but during cooling wax crystals appear around the oil/water interface and stabilize the droplets. The oil/water ratio has minimal effect on the emulsions between ratios of 3:7 and 7:3. The Laponite is believed to stabilize the emulsions by increasing the viscosity of the continuous phase and also by adsorbing at the oil/water interface, thus providing a physical barrier to coalescence.

  12. Operator training and the training simulator experience

    International Nuclear Information System (INIS)

    Mills, D.

    The author outlines the approach used by Ontario Hydro to train operators from the day they are hired as Operators-in-Training until they are Authorized Unit First Operators. He describes in detail the use of the simulator in the final year of the authorization program, drawing on experience with the Pickering NGS A simulator. Simulators, he concludes, are important aids to training but by no means all that is required to guarantee capable First Operators

  13. DOMINO: development of informative molecular markers for phylogenetic and genome-wide population genetic studies in non-model organisms.

    Science.gov (United States)

    Frías-López, Cristina; Sánchez-Herrero, José F; Guirao-Rico, Sara; Mora, Elisa; Arnedo, Miquel A; Sánchez-Gracia, Alejandro; Rozas, Julio

    2016-12-15

    The development of molecular markers is one of the most important challenges in phylogenetic and genome wide population genetics studies, especially in studies with non-model organisms. A highly promising approach for obtaining suitable markers is the utilization of genomic partitioning strategies for the simultaneous discovery and genotyping of a large number of markers. Unfortunately, not all markers obtained from these strategies provide enough information for solving multiple evolutionary questions at a reasonable taxonomic resolution. We have developed Development Of Molecular markers In Non-model Organisms (DOMINO), a bioinformatics tool for informative marker development from both next generation sequencing (NGS) data and pre-computed sequence alignments. The application implements popular NGS tools with new utilities in a highly versatile pipeline specifically designed to discover or select personalized markers at different levels of taxonomic resolution. These markers can be directly used to study the taxa surveyed for their design, utilized for further downstream PCR amplification in a broader set taxonomic scope, or exploited as suitable templates to bait design for target DNA enrichment techniques. We conducted an exhaustive evaluation of the performance of DOMINO via computer simulations and illustrate its utility to find informative markers in an empirical dataset. DOMINO is freely available from www.ub.edu/softevol/domino CONTACT: elsanchez@ub.edu or jrozas@ub.eduSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  14. Modeling Cancer Metastasis using Global, Quantitative and Integrative Network Biology

    DEFF Research Database (Denmark)

    Schoof, Erwin; Erler, Janine

    understanding of molecular processes which are fundamental to tumorigenesis. In Article 1, we propose a novel framework for how cancer mutations can be studied by taking into account their effect at the protein network level. In Article 2, we demonstrate how global, quantitative data on phosphorylation dynamics...... can be generated using MS, and how this can be modeled using a computational framework for deciphering kinase-substrate dynamics. This framework is described in depth in Article 3, and covers the design of KinomeXplorer, which allows the prediction of kinases responsible for modulating observed...... phosphorylation dynamics in a given biological sample. In Chapter III, we move into Integrative Network Biology, where, by combining two fundamental technologies (MS & NGS), we can obtain more in-depth insights into the links between cellular phenotype and genotype. Article 4 describes the proof...

  15. Resource Reviews Bronmater i a a I bespreki ngs

    African Journals Online (AJOL)

    Campbell has employed poetic licence to allow his. Noah to beach the ark in the midst of the African continent ... 11 The ant has made himself illustrious. Through constant industry industrious. So what? Would you ... of worksheets with cartoon ants for 15 year old pupils. The environmentally aware teacher, youth leader and.

  16. Airborne Gravity: NGS' Gravity Data for EN08 (2013)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Airborne gravity data for New York, Vermont, New Hampshire, Massachusettes, Maine, and Canada collected in 2013 over 1 survey. This data set is part of the Gravity...

  17. Capistrano unified school district works with San Onofre NGS

    International Nuclear Information System (INIS)

    Osterfield, M.A.; Cramer, E.N.

    1992-01-01

    A unique arrangement has the science coordinator for Capistrano Unified School District's (CUSD) grades kindergarten through eight (K-8) as a part-time contract employee at San Onofre Nuclear Generating Station (SONGS). The purpose is to assess the science capabilities at SONGS useful to CUSD teachers and to assist in making them available. This is different from the usual single-teacher renewal program or from part-time employment. This creates several unique situations for SONGS and the 23 K-8 schools in CUSD, supplementing the existing program of optional science field trips to SONGS. This approach also interests the developing mind in science before being turned off by uninteresting, user-unfriendly, bookish approaches

  18. Bruce NGS B risk assessment (BBRA) peer review process

    International Nuclear Information System (INIS)

    Kaasalainen, S.; Crocker, W.P.; Webb, W.A.

    2001-01-01

    Risk-informed decision making is considered an effective approach to managing the risk of nuclear power plant operation in a competitive market. Hence, increased reliance on the station probabilistic risk assessments (PRAs) to provide risk perspective inputs is inevitable. With increased reliance on the PRAs it is imperative that PRAs have the characteristics necessary to provide the required information. Recognizing the increased requirements on nuclear power plant PRAs the nuclear industry in the United States has expended significant effort over the past few years defining the required characteristics of a PRA for various applications. More recently several owners groups have drafted guidelines for PRA certification and several U.S. utilities have had their PRAs certified. During the year 2000 Ontario Power Generation, Nuclear (OPG,N) subjected the PRA of one of its stations to the U.S. style certification process. The PRA selected for this process was the Bruce B Risk Assessment (BBRA). BBRA was chosen for this process since it is the first OPG, N PRA to be used for risk-informed applications. However, the strengths of the BBRA identified from the certification process and the lessons learned are also largely applicable to the other OPG, N plant PRAs due to the use of similar methods and tools

  19. 2016 NOAA NGS Topobathy Lidar DEM: Key West (FL)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — These data were collected by the National Oceanic Atmospheric Administration National Geodetic Survey Remote Sensing Division using a Riegl VQ820G system. The data...

  20. 2015 NOAA NGS Topobathy Lidar DEM: Puerto Rico

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — These data were collected by the National Oceanic Atmospheric Administration National Geodetic Survey Remote Sensing Division using a Riegl VQ-820G system. The data...

  1. Resource Reviews Bronmater i a a I bespreki ngs

    African Journals Online (AJOL)

    organisations, businesses, institutes, and ... The reoort focuses on 'environment development' issues, using the two .... William Plomer and Thomas Pringle and poems from West. African .... moral values that could seriously affect the very.

  2. NGS Gravity Station Data for the U.S.

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The gravity station data (1,633,499 records) were gathered by various governmental organizations (and academia) using a variety of methods. This data base was...

  3. Fuel handling solutions to power pulse at Bruce NGS A

    International Nuclear Information System (INIS)

    Day, R.C.

    1996-01-01

    In response to the discovery of the power pulse problem in March of 1993, Bruce A has installed flow straightening shield plugs in the inner zone channels of all units to partially reduce the gap and gain an increase in reactor power to 75%. After review and evaluation of solutions to manage the gap, including creep compensators and long fuel bundles, efforts have focused on a different solution involving reordering the fuel bundles to reverse the burnup profile. This configuration is maintained by fuelling with the flow and providing better support to the highly irradiated downstream fuel bundles by changing the design of the outlet shield plug. Engineering changes to the fuel handling control system and outlet shield plug are planned to be implemented starting in June 1996, thereby eliminating the power pulse problem and restrictions on reactor operating power. (author). 2 refs., 1 tab., 2 figs

  4. Airborne Gravity: NGS' Gravity Data for AN05 (2011)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Airborne gravity data for Alaska collected in 2011 over 1 survey. This data set is part of the Gravity for the Re-definition of the American Vertical Datum (GRAV-D)...

  5. Airborne Gravity: NGS' Gravity Data for ES03 (2013)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Airborne gravity data for Maryland, Pennsylvania, New Jersey, West Virginia, Virginia, Delaware, and the Atlantic Ocean collected in 2013 over 1 survey. This data...

  6. Airborne Gravity: NGS' Gravity Data for TS01 (2014)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Airborne gravity data for Puerto Rico and the Virgin Islands collected in 2009 over 1 survey. This data set is part of the Gravity for the Re-definition of the...

  7. Airborne Gravity: NGS' Gravity Data for EN10 (2013)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Airborne gravity data for New York, Pennsylvania, New Jersey, Connecticut and the Atlantic Ocean collected in 2013 over 1 survey. This data set is part of the...

  8. Airborne Gravity: NGS' Gravity Data for AN06 (2011)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Airborne gravity data for Alaska collected in 2011 over 1 survey. This data set is part of the Gravity for the Re-definition of the American Vertical Datum (GRAV-D)...

  9. Airborne Gravity: NGS' Gravity Data for AN08 (2016)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Airborne gravity data for Alaska collected in 2016 over one survey. This data set is part of the Gravity for the Re-definition of the American Vertical Datum...

  10. Airborne Gravity: NGS' Gravity Data for EN09 (2016)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Airborne gravity data for Massachusetts, Connecticut, Rhode Island, New Hampshire, New York, and the Atlantic Ocean collected in 2012 over 1 survey. This data set is...

  11. Airborne Gravity: NGS' Gravity Data for CN02 (2013 & 2014)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Airborne gravity data for Nebraska collected in 2013 & 2014 over 3 surveys. This data set is part of the Gravity for the Re-definition of the American Vertical...

  12. Airborne Gravity: NGS' Gravity Data for CS08 (2015)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Airborne gravity data for CS08 collected in 2006 over 1 survey. This data set is part of the Gravity for the Re-definition of the American Vertical Datum (GRAV-D)...

  13. Airborne Gravity: NGS' Gravity Data for AS02 (2010)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Airborne gravity data for Alaska collected in 2010 over 2 surveys. This data set is part of the Gravity for the Re-definition of the American Vertical Datum (GRAV-D)...

  14. Airborne Gravity: NGS' Gravity Data for EN01 (2011)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Airborne gravity data for New York, Canada, and Lake Ontario collected in 2011 over 1 survey. This data set is part of the Gravity for the Re-definition of the...

  15. Airborne Gravity: NGS' Gravity Data for AN03 (2010)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Airborne gravity data for Alaska collected in 2010 and 2012 over 2 surveys. This data set is part of the Gravity for the Re-definition of the American Vertical Datum...

  16. Airborne Gravity: NGS' Gravity Data for MS02 (2016)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Airborne gravity data over southern Arizona and New Mexico overlapping into Mexico collected in 2016 over 2 surveys, AZ16-1 and AZ16-2. This data set is part of the...

  17. Airborne Gravity: NGS' Gravity Data for ES02 (2013)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Airborne gravity data for Florida and the Gulf of Mexico collected in 2013 over 1 survey. This data set is part of the Gravity for the Re-definition of the American...

  18. Airborne Gravity: NGS' Gravity Data for AN04 (2010)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Airborne gravity data for Alaska collected in 2010 over 1 survey. This data set is part of the Gravity for the Re-definition of the American Vertical Datum (GRAV-D)...

  19. Airborne Gravity: NGS' Gravity Data for CS05 (2014)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Airborne gravity data for Texas collected in 2014 over 2 surveys. This data set is part of the Gravity for the Re-definition of the American Vertical Datum (GRAV-D)...

  20. Airborne Gravity: NGS' Gravity Data for CS07 (2014 & 2016)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Airborne gravity data for Texas collected in 2014 & 2016 over 3 surveys,TX14-2, TX16-1 and TX16-2. This data set is part of the Gravity for the Re-definition of...

  1. Response to IPE and IPEEE results at Palo Verde NGS

    International Nuclear Information System (INIS)

    Lindquist, R.C.

    1992-01-01

    Insights gained from the internal events probabilistic risk assessment (PRA) and from the pilot plant demonstration of the fire-induced vulnerability evaluation (FIVE) have been used to initiate corrective actions in the form of administrative controls, compensatory measures, and plant modifications to reduce the risks associated with significant core-damage sequences. Palo Verde was a pilot demonstration plant for the FIVE methodology developed by the Electrical Power Research Institute and sponsored by the Nuclear Utility Management and Resources Council. Several findings emerged from the application of FIVE and have been acted upon to reduce the impact of fire in several compartments of the plant

  2. Airborne Gravity: NGS' Gravity Data for AS01 (2008)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Airborne gravity data for Alaska collected in 2008 over 1 survey. This data set is part of the Gravity for the Re-definition of the American Vertical Datum (GRAV-D)...

  3. Airborne Gravity: NGS' Gravity Data for CS04 (2009)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Airborne gravity data for Texas collected in 2009 over 1 survey. This data set is part of the Gravity for the Re-definition of the American Vertical Datum (GRAV-D)...

  4. 2016 NOAA NGS Topobathy Lidar: Key West (FL)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — These data were collected by the National Oceanic Atmospheric Administration National Geodetic Survey Remote Sensing Division using a Riegl VQ820G system. The data...

  5. Bruce NGS A Unit 4 preheater divider plate failure

    International Nuclear Information System (INIS)

    Landridge, M.; McInnes, D.

    1995-01-01

    On May 19, 1995, without any prior operational indications, Bruce A discovered preheater divider plate damage in Unit 4 that had the potential to have a major impact on the continued safe operation of the station. Further investigations indicated that Unit 4 may have been operating with this damage for as long as ten years. In the two months following the discovery, Bruce A has procured and replaced the 4 divider plates, located most of the missing pieces, retrieved pieces from the PHT system, investigated historical operational information, performed detailed analytical investigations, investigated root cause, performed in-situ and mock-up testing, updated operational procedures and installed DP monitoring equipment

  6. Assessment of causes for degrading fuel performance at Darlington NGS

    International Nuclear Information System (INIS)

    Judah, J.; Goodchild, S.

    2013-01-01

    Fuel performance at the Darlington nuclear generating station has historically been excellent. Until recently, the majority of these few fuel defects have been attributed to fretting by heat transport system debris. The minority have been linked to manufacturing issues. Recently, Darlington has experienced an increase in the number of fuel defects. Although the defect rate remains low with respect to industry standards, this defect experience is considered to be unacceptable given current industry expectations and the OPG zero defect policy. Nine fuel defects have been discharged since 2007 from the four Darlington reactors. This represents a fuel defect rate of just 0.35 defects per year per reactor. At the time of this writing three additional defects are suspected to be in core. Although a definitive defect cause has yet to be identified, these fuel performance issues appear to be due to the coincidental degradation of manufacturing and operational factors, thereby decreasing the margins to fuel failure due to fuelling power ramps. All of the confirmed defected bundles have been long bundles and all experienced a relatively high power ramp when shifted from Position 2 to Position 6. High bundle uranium masses and low internal clearances are thought to be significant contributing factors. Bundle burnups at the time of the power ramps were low and these bundles were not identified by existing power ramp defect predictive tools. Our assessment has resulted in a number of recommendations which are designed to mitigate these adverse conditions by restoring the margins to power ramp failures. These recommendations impact broadly across a number of organizations including reactor physics, fuel design, fuel manufacturing, reactor design, inspections and PIE. (author)

  7. NGS Gravity Network Data for the U.S.

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The gravity network data (7,298 records) were gathered by various governmental organizations (and academia) using a variety of methods.

  8. Airborne Gravity: NGS' Gravity Data for EN06 (2016)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Airborne gravity data for Maine, Canada, and the Atlantic Ocean collected in 2012 over 2 surveys. This data set is part of the Gravity for the Re-definition of the...

  9. Spent fuel bundle counter sequence error manual - BRUCE NGS

    International Nuclear Information System (INIS)

    Nicholson, L.E.

    1992-01-01

    The Spent Fuel Bundle Counter (SFBC) is used to count the number and type of spent fuel transfers that occur into or out of controlled areas at CANDU reactor sites. However if the transfers are executed in a non-standard manner or the SFBC is malfunctioning, the transfers are recorded as sequence errors. Each sequence error message typically contains adequate information to determine the cause of the message. This manual provides a guide to interpret the various sequence error messages that can occur and suggests probable cause or causes of the sequence errors. Each likely sequence error is presented on a 'card' in Appendix A. Note that it would be impractical to generate a sequence error card file with entries for all possible combinations of faults. Therefore the card file contains sequences with only one fault at a time. Some exceptions have been included however where experience has indicated that several faults can occur simultaneously

  10. Spent fuel bundle counter sequence error manual - DARLINGTON NGS

    International Nuclear Information System (INIS)

    Nicholson, L.E.

    1992-01-01

    The Spent Fuel Bundle Counter (SFBC) is used to count the number and type of spent fuel transfers that occur into or out of controlled areas at CANDU reactor sites. However if the transfers are executed in a non-standard manner or the SFBC is malfunctioning, the transfers are recorded as sequence errors. Each sequence error message typically contains adequate information to determine the cause of the message. This manual provides a guide to interpret the various sequence error messages that can occur and suggests probable cause or causes of the sequence errors. Each likely sequence error is presented on a 'card' in Appendix A. Note that it would be impractical to generate a sequence error card file with entries for all possible combinations of faults. Therefore the card file contains sequences with only one fault at a time. Some exceptions have been included however where experience has indicated that several faults can occur simultaneously

  11. 2014 NOAA NGS Lidar: Intracoastal Waterway, Florida Keys (FL)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — These data were collected by the National Oceanic Atmospheric Administration National Geodetic Survey Remote Sensing Division using a Riegl VQ820G system. The data...

  12. Spent fuel dry storage experience at Gentilly 2 NGS

    International Nuclear Information System (INIS)

    Macici, N.

    1997-01-01

    In order to provide the needed interim storage facility for the spent fuel, Hydro-Quebec chose the dry storage CANSTOR module developed by the Atomic Energy of Canada Ltd (AECL). The decision was made based upon the technical feasibility, public and environmental protection criteria, operational flexibility, economic and space saving advantages. Before the commissioning of the spent fuel dry storage facility, the project received all the required approvals. A joint provincial - federal public hearings was held in summer of 1994 in order to assess the project in term of its impact on the environment. In September 1995 took place the first transfer of spent fuel from the station bay to the dry storage facility and since then 21000 bundles of spent fuel were transferred in the two CANSTOR modules built on the station site located within the protected area of the Gentilly-2 station. To date, the expected performance of the dry storage units and equipment have been met. A third CANSTOR module is to be built in summer of 1997 on the station site. (author)

  13. Airborne Gravity: NGS' Gravity Data for AN02 (2010)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Airborne gravity data for Alaska collected in 2010 over 1 survey. This data set is part of the Gravity for the Re-definition of the American Vertical Datum (GRAV-D)...

  14. Fuel handling solutions to power pulse at Bruce NGS A

    Energy Technology Data Exchange (ETDEWEB)

    Day, R C [Ontario Hydro, Tiverton, ON (Canada). Bruce Nuclear Generating Station-A

    1997-12-31

    In response to the discovery of the power pulse problem in March of 1993, Bruce A has installed flow straightening shield plugs in the inner zone channels of all units to partially reduce the gap and gain an increase in reactor power to 75%. After review and evaluation of solutions to manage the gap, including creep compensators and long fuel bundles, efforts have focused on a different solution involving reordering the fuel bundles to reverse the burnup profile. This configuration is maintained by fuelling with the flow and providing better support to the highly irradiated downstream fuel bundles by changing the design of the outlet shield plug. Engineering changes to the fuel handling control system and outlet shield plug are planned to be implemented starting in June 1996, thereby eliminating the power pulse problem and restrictions on reactor operating power. (author). 2 refs., 1 tab., 2 figs.

  15. RESEARCH NOTE Clinical Utility of a 377 gene custom NGS ...

    Indian Academy of Sciences (India)

    2016-11-11

    Nov 11, 2016 ... panel, pre and post bioinformatic analysis protocols, as well as reporting criteria, ... panel/) resulted in a 47.8% decline inpositive reporting (Figure 1c)with a final yieldof 7.9% (24 .... as well as the analytical sensitivity and accuracy of reportable variants are what aid the ... Maple syrup urine disease, type Ia.

  16. Airborne Gravity: NGS' Gravity Data for ES01 (2013)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Airborne gravity data for Florida, the Bahamas, and the Atlantic Ocean collected in 2013 over 1 survey. This data set is part of the Gravity for the Re-definition of...

  17. Stress corrosion cracking experience in steam generators at Bruce NGS

    International Nuclear Information System (INIS)

    King, P.J.; Gonzalez, F.; Brown, J.

    1993-01-01

    In late 1990 and through 1991, units 1 and 2 at the Bruce A Nuclear Generating Station (BNGS-A) experienced a number of steam generator tube leaks. Tube failures were identified by eddy current to be circumferential cracks at U-bend supports on the hot-leg side of the boilers. In late 1991, tubes were removed from these units for failure characterization. Two active failure modes were found: corrosion fatigue in both units 1 and 2 and stress corrosion cracking (SCC) in unit 2. In unit 2, lead was found in deposits, on tubes, and in cracks, and the cracking was mixed-mode: transgranular and intergranular. This convincingly indicated the involvement of lead in the stress corrosion cracking failures. A program of inspection and tube removals was carried out to investigate more fully the extent of the problem. This program found significant cracking only in lead-affected boilers in unit 2, and also revealed a limited extent of non-lead-related intergranular stress corrosion cracking in other boilers and units. Various aspects of the failures and tube examinations are presented in this paper. Included is discussion of the cracking morphology, measured crack size distributions, and chemical analysis of tube surfaces, crack faces, and deposits -- with particular emphasis on lead

  18. LinkImputeR: user-guided genotype calling and imputation for non-model organisms.

    Science.gov (United States)

    Money, Daniel; Migicovsky, Zoë; Gardner, Kyle; Myles, Sean

    2017-07-10

    Genomic studies such as genome-wide association and genomic selection require genome-wide genotype data. All existing technologies used to create these data result in missing genotypes, which are often then inferred using genotype imputation software. However, existing imputation methods most often make use only of genotypes that are successfully inferred after having passed a certain read depth threshold. Because of this, any read information for genotypes that did not pass the threshold, and were thus set to missing, is ignored. Most genomic studies also choose read depth thresholds and quality filters without investigating their effects on the size and quality of the resulting genotype data. Moreover, almost all genotype imputation methods require ordered markers and are therefore of limited utility in non-model organisms. Here we introduce LinkImputeR, a software program that exploits the read count information that is normally ignored, and makes use of all available DNA sequence information for the purposes of genotype calling and imputation. It is specifically designed for non-model organisms since it requires neither ordered markers nor a reference panel of genotypes. Using next-generation DNA sequence (NGS) data from apple, cannabis and grape, we quantify the effect of varying read count and missingness thresholds on the quantity and quality of genotypes generated from LinkImputeR. We demonstrate that LinkImputeR can increase the number of genotype calls by more than an order of magnitude, can improve genotyping accuracy by several percent and can thus improve the power of downstream analyses. Moreover, we show that the effects of quality and read depth filters can differ substantially between data sets and should therefore be investigated on a per-study basis. By exploiting DNA sequence data that is normally ignored during genotype calling and imputation, LinkImputeR can significantly improve both the quantity and quality of genotype data generated from

  19. Peer evaluation and some valuable lessons

    Energy Technology Data Exchange (ETDEWEB)

    Holt, A G [Ontario Hydro, Toronto, ON (Canada)

    1991-04-01

    In the mid 1980s there were some signs that Ontario Hydro's nuclear program performance was deteriorating. Such signs included increased maintenance backlog, increased number of jumpers, decreased capacity factors and increasing regulatory concerns. Factors influencing this deterioration were: (a) Pressure tube creep and hydriding rates were excessive leading to increased reactor maintenance and early pressure tube replacement in Pickering NGS-A and Bruce NGS-A. (b) Preventive maintenance was reduced to a minimum owing to manpower and budget restraints. This led to more forced outages, deratings and breakdown maintenance as the urgent was dealt with rather than the important. (c) New systems were installed in the older units, Pickering NGS-A and Bruce NGS-A, in order to backfit safety related system improvements principally to meet increased regulatory requirements. This put additional strain on tight resources to assist with the installation, commissioning, testing and maintenance of these systems that generally increased the complexity of units. Again this led to a reduction of preventive maintenance.

  20. Peer evaluation and some valuable lessons

    International Nuclear Information System (INIS)

    Holt, A.G.

    1991-01-01

    In the mid 1980s there were some signs that Ontario Hydro's nuclear program performance was deteriorating. Such signs included increased maintenance backlog, increased number of jumpers, decreased capacity factors and increasing regulatory concerns. Factors influencing this deterioration were: (a) Pressure tube creep and hydriding rates were excessive leading to increased reactor maintenance and early pressure tube replacement in Pickering NGS-A and Bruce NGS-A. (b) Preventive maintenance was reduced to a minimum owing to manpower and budget restraints. This led to more forced outages, deratings and breakdown maintenance as the urgent was dealt with rather than the important. (c) New systems were installed in the older units, Pickering NGS-A and Bruce NGS-A, in order to backfit safety related system improvements principally to meet increased regulatory requirements. This put additional strain on tight resources to assist with the installation, commissioning, testing and maintenance of these systems that generally increased the complexity of units. Again this led to a reduction of preventive maintenance

  1. Observed and Modeled Tritium Concentrations in the Terrestrial Food Chain near a Continuous Atmospheric Source

    International Nuclear Information System (INIS)

    Davis, P.A.; Kim, S.B.; Chouhan, S.L.; Workman, W.J.G.

    2005-01-01

    Tritium concentrations were measured in a large number of environmental and biological samples collected during 2002 at two dairy farms and a hobby farm near Pickering Nuclear Generating Station in Ontario, Canada. The data cover most compartments of the terrestrial food chain in an agricultural setting and include detailed information on the diets of the local farm animals. Ratios of plant OBT concentration to air moisture HTO varied between 0.12 and 0.56, and were generally higher for the forage crops collected at the dairy farms than for the garden vegetables sampled at the hobby farm. Animal OBT to air HTO ratios were more uniform, ranging from 0.18 to 0.45, and were generally higher for the milk and beef samples from the dairy farms than for the chicken products from the hobby farm. The observed OBT concentrations in plants and animals were compared with predictions of IMPACT, the model used by the Canadian nuclear industry to calculate annual average doses due to routine releases. The model performed well on average for the animal endpoints but overestimated concentrations in plants by a factor of 2

  2. Modeling and interoperability of heterogeneous genomic big data for integrative processing and querying.

    Science.gov (United States)

    Masseroli, Marco; Kaitoua, Abdulrahman; Pinoli, Pietro; Ceri, Stefano

    2016-12-01

    While a huge amount of (epi)genomic data of multiple types is becoming available by using Next Generation Sequencing (NGS) technologies, the most important emerging problem is the so-called tertiary analysis, concerned with sense making, e.g., discovering how different (epi)genomic regions and their products interact and cooperate with each other. We propose a paradigm shift in tertiary analysis, based on the use of the Genomic Data Model (GDM), a simple data model which links genomic feature data to their associated experimental, biological and clinical metadata. GDM encompasses all the data formats which have been produced for feature extraction from (epi)genomic datasets. We specifically describe the mapping to GDM of SAM (Sequence Alignment/Map), VCF (Variant Call Format), NARROWPEAK (for called peaks produced by NGS ChIP-seq or DNase-seq methods), and BED (Browser Extensible Data) formats, but GDM supports as well all the formats describing experimental datasets (e.g., including copy number variations, DNA somatic mutations, or gene expressions) and annotations (e.g., regarding transcription start sites, genes, enhancers or CpG islands). We downloaded and integrated samples of all the above-mentioned data types and formats from multiple sources. The GDM is able to homogeneously describe semantically heterogeneous data and makes the ground for providing data interoperability, e.g., achieved through the GenoMetric Query Language (GMQL), a high-level, declarative query language for genomic big data. The combined use of the data model and the query language allows comprehensive processing of multiple heterogeneous data, and supports the development of domain-specific data-driven computations and bio-molecular knowledge discovery. Copyright © 2016 Elsevier Inc. All rights reserved.

  3. Combining next-generation sequencing and online databases for microsatellite development in non-model organisms.

    Science.gov (United States)

    Rico, Ciro; Normandeau, Eric; Dion-Côté, Anne-Marie; Rico, María Inés; Côté, Guillaume; Bernatchez, Louis

    2013-12-03

    Next-generation sequencing (NGS) is revolutionising marker development and the rapidly increasing amount of transcriptomes published across a wide variety of taxa is providing valuable sequence databases for the identification of genetic markers without the need to generate new sequences. Microsatellites are still the most important source of polymorphic markers in ecology and evolution. Motivated by our long-term interest in the adaptive radiation of a non-model species complex of whitefishes (Coregonus spp.), in this study, we focus on microsatellite characterisation and multiplex optimisation using transcriptome sequences generated by Illumina® and Roche-454, as well as online databases of Expressed Sequence Tags (EST) for the study of whitefish evolution and demographic history. We identified and optimised 40 polymorphic loci in multiplex PCR reactions and validated the robustness of our analyses by testing several population genetics and phylogeographic predictions using 494 fish from five lakes and 2 distinct ecotypes.

  4. Combining independent de novo assemblies optimizes the coding transcriptome for nonconventional model eukaryotic organisms.

    Science.gov (United States)

    Cerveau, Nicolas; Jackson, Daniel J

    2016-12-09

    Next-generation sequencing (NGS) technologies are arguably the most revolutionary technical development to join the list of tools available to molecular biologists since PCR. For researchers working with nonconventional model organisms one major problem with the currently dominant NGS platform (Illumina) stems from the obligatory fragmentation of nucleic acid material that occurs prior to sequencing during library preparation. This step creates a significant bioinformatic challenge for accurate de novo assembly of novel transcriptome data. This challenge becomes apparent when a variety of modern assembly tools (of which there is no shortage) are applied to the same raw NGS dataset. With the same assembly parameters these tools can generate markedly different assembly outputs. In this study we present an approach that generates an optimized consensus de novo assembly of eukaryotic coding transcriptomes. This approach does not represent a new assembler, rather it combines the outputs of a variety of established assembly packages, and removes redundancy via a series of clustering steps. We test and validate our approach using Illumina datasets from six phylogenetically diverse eukaryotes (three metazoans, two plants and a yeast) and two simulated datasets derived from metazoan reference genome annotations. All of these datasets were assembled using three currently popular assembly packages (CLC, Trinity and IDBA-tran). In addition, we experimentally demonstrate that transcripts unique to one particular assembly package are likely to be bioinformatic artefacts. For all eight datasets our pipeline generates more concise transcriptomes that in fact possess more unique annotatable protein domains than any of the three individual assemblers we employed. Another measure of assembly completeness (using the purpose built BUSCO databases) also confirmed that our approach yields more information. Our approach yields coding transcriptome assemblies that are more likely to be

  5. Next-generation sequencing analysis of gene regulation in the rat model of retinopathy of prematurity.

    Science.gov (United States)

    Griffith, Rachel M; Li, Hu; Zhang, Nan; Favazza, Tara L; Fulton, Anne B; Hansen, Ronald M; Akula, James D

    2013-08-01

    The purpose of this study was to identify the genes, biochemical signaling pathways, and biological themes involved in the pathogenesis of retinopathy of prematurity (ROP). Next-generation sequencing (NGS) was performed on the RNA transcriptome of rats with the Penn et al. (Pediatr Res 36:724-731, 1994) oxygen-induced retinopathy model of ROP at the height of vascular abnormality, postnatal day (P) 19, and normalized to age-matched, room-air-reared littermate controls. Eight custom-developed pathways with potential relevance to known ROP sequelae were evaluated for significant regulation in ROP: The three major Wnt signaling pathways, canonical, planar cell polarity (PCP), and Wnt/Ca(2+); two signaling pathways mediated by the Rho GTPases RhoA and Cdc42, which are, respectively, thought to intersect with canonical and non-canonical Wnt signaling; nitric oxide signaling pathways mediated by two nitric oxide synthase (NOS) enzymes, neuronal (nNOS) and endothelial (eNOS); and the retinoic acid (RA) signaling pathway. Regulation of other biological pathways and themes was detected by gene ontology using the Kyoto Encyclopedia of Genes and Genomes and the NIH's Database for Annotation, Visualization, and Integrated Discovery's GO terms databases. Canonical Wnt signaling was found to be regulated, but the non-canonical PCP and Wnt/Ca(2+) pathways were not. Nitric oxide signaling, as measured by the activation of nNOS and eNOS, was also regulated, as was RA signaling. Biological themes related to protein translation (ribosomes), neural signaling, inflammation and immunity, cell cycle, and cell death were (among others) highly regulated in ROP rats. These several genes and pathways identified by NGS might provide novel targets for intervention in ROP.

  6. Next Generation Sequencing Analysis of Gene Regulation in the Rat Model of Retinopathy of Prematurity

    Science.gov (United States)

    Griffith, Rachel M.; Li, Hu; Zhang, Nan; Favazza, Tara L.; Fulton, Anne B.; Hansen, Ronald M.; Akula, James D.

    2013-01-01

    Purpose To identify the genes, biochemical signaling pathways and biological themes involved in the pathogenesis of retinopathy of prematurity (ROP). Methods Next-generation sequencing (NGS) was performed on the RNA transcriptome of rats with the Penn et al. (1994) oxygen-induced retinopathy (OIR) model of ROP at the height of vascular abnormality, postnatal day (P) 19, and normalized to age-matched, room-air-reared littermate controls. Eight custom developed pathways with potential relevance to known ROP sequelae were evaluated for significant regulation in ROP: The three major Wnt signaling pathways, canonical, planar cell polarity (PCP), and Wnt/Ca2+, two signaling pathways mediated by the Rho GTPases RhoA and Cdc42, which are respectively thought to intersect with canonical and noncanonical Wnt signaling, nitric oxide signaling pathways mediated by two nitrox oxide synthase (NOS) enzymes, neuronal (nNOS) and endothelial (eNOS), and the retinoic acid (RA) signaling pathway. Regulation of other biological pathways and themes were detected by gene ontology using the Kyoto Encyclopedia of Genes and Genomes (KEGG) and the NIH's Database for Annotation, Visualization and Integrated Discovery (DAVID)'s GO terms databases. Results Canonical Wnt signaling was found to be regulated, but the non-canonical PCP and Wnt/Ca2+ pathways were not. Nitric oxide (NO) signaling, as measured by the activation of nNOS eNOS, was also regulated, as was RA signaling. Biological themes related to protein translation (ribosomes), neural signaling, inflammation and immunity, cell cycle and cell death, were (among others) highly regulated in ROP rats. Conclusions These several genes and pathways identified by NGS might provide novel targets for intervention in ROP. PMID:23775346

  7. Forest food chain and dose model (FDMF) for RODOS. Model description

    International Nuclear Information System (INIS)

    Rantavaara, A.; Vetikko, V.; Calmon, P.; Wendt, J.

    2001-12-01

    In the early phase of a large-scale fallout situation, both access to forests and the use of wild foods may need temporal restrictions. In a later phase wild foods and internal doses received through them may still need surveillance of radioactivity. After accidental fallout a major source of external radiation are the ground deposits, and in forests contaminated overstorey can also be a considerable source. For consideration of dose pathways related to forests during a nuclear emergency the Forest Food Chain and Dose Model (FDMF) was developed. It is an integral part of RODOS, a real-time, on-line decision support system for off-site emergency management in Europe. The forest module FDMF receives radionuclide concentrations in air as input from the air dispersion model of RODOS, and calculates activities deposited on various parts of the forest. The model simulates the transfer of radionuclides in the forest ecosystem. It quantifies the dynamic changes for three types of forests, typical of a region. The model gives the contamination of forest products and dose rate for external radiation as a function of time. External and internal radiation doses for various population groups according to their stay in forests and their use of forest products can be assessed since the first year until the 50 th year after the fallout event. Doses are calculated for children and adults representing the public, and ingestion doses also for pickers of berries and mushrooms, and hunters. Forest workers are a special group due to their potentially enhanced external dose from outdoor working. The model results can be shown as spatial distributions on top of geographical maps. Many parameters in the FDMF database are regional and have to be adjusted when the model is adapted for local conditions or new radioecological regions. Long-term predictions will be considerably improved when site-specific parameters are used. STUK developed the forest module together with IPSN (Institut de

  8. Assessment of field training for nuclear operations personnel

    International Nuclear Information System (INIS)

    White, M.

    1995-08-01

    Training of station personnel is an important component of the safe operation of the nuclear generating station. On-the-job training (OJT) is an important component of training. The AECB initiated this project to develop a process to assess the effectiveness of OJT for field operators, and perform an initial trial of the developed process. This report describes the recommended process to assess the effectiveness of OJT for field operators, as well as the results of the initial assessment at Pickering Nuclear Generating Station. The assessment's conclusions included: (1) Ontario Hydro policies and procedures are generally consistent with industry guidelines requiring a systematic approach to training; (2) Pickering NGS field operator performance is not always consistent with documented station requirements and standards, nor industry guidelines and practices; and (3) The Pickering NGS field operator on-the-job training is not consistent with a systematic approach to training, a requirement recognized in Ontario Hydro's Policy NGD 113, and does not contribute to a high level of performance in field operator tasks. Recommendations are made regarding the use of the developed process for future assessments of on-the-job training at nuclear power plants. (author). 36 refs., 4 tabs., 3 figs

  9. Assessment of field training for nuclear operations personnel

    Energy Technology Data Exchange (ETDEWEB)

    White, M [Safety Management Services, Inc. (Canada)

    1995-08-01

    Training of station personnel is an important component of the safe operation of the nuclear generating station. On-the-job training (OJT) is an important component of training. The AECB initiated this project to develop a process to assess the effectiveness of OJT for field operators, and perform an initial trial of the developed process. This report describes the recommended process to assess the effectiveness of OJT for field operators, as well as the results of the initial assessment at Pickering Nuclear Generating Station. The assessment`s conclusions included: (1) Ontario Hydro policies and procedures are generally consistent with industry guidelines requiring a systematic approach to training; (2) Pickering NGS field operator performance is not always consistent with documented station requirements and standards, nor industry guidelines and practices; and (3) The Pickering NGS field operator on-the-job training is not consistent with a systematic approach to training, a requirement recognized in Ontario Hydro`s Policy NGD 113, and does not contribute to a high level of performance in field operator tasks. Recommendations are made regarding the use of the developed process for future assessments of on-the-job training at nuclear power plants. (author). 36 refs., 4 tabs., 3 figs.

  10. Ontario hydro development program for steam generator waterlancing applications

    International Nuclear Information System (INIS)

    Malaugh, J.

    1992-01-01

    In the early 1980s, Ontario Hydro's main focus on waterlancing applications was in the development of technology for cleaning tubesheet sludge piles. In 1988, when Unit 2 at the Bruce Nuclear Generating Station (BNGS) was derated to 70% of full power due to severely blocked broach plates, high pressure waterlancing was proposed as a short-term solution. Due to the tight geometry that exist in the BNGS SGs (Steam Generator), an innovative approach was needed to deliver high pressure water to the broach hole locations. The initial lances and guides were modelled after a fiber-optic inspection system used for visual measurements of the broach openings. The waterlancing technology that was first developed for cleaning BNGS Unit 2 has evolved considerably since 1988. Both Units 1 and 2 upper broach plates have been successfully cleaned by waterlancing. At Pickering NGS, this technology is being further developed for use in cleaning broach plates and for tubesheet sludge lancing. This paper describes the development of the waterlance from the initial low pressure stainless steel lances to the current high pressure 'kevlar' lances. The major advances in this technology were borne out of a need to overcome the challenges presented by the SG geometry restrictions and the tenacity of the deposits that were encountered

  11. Distribution of the active liquid waste discharge concentration

    International Nuclear Information System (INIS)

    Chan, A.H.C.

    1985-03-01

    In assessing the proposal for removing the on-line liquid effluent monitor (LEM) from the Darlington NGS-A design, it was required to estimate the probability that the concentration of β-y emitters in the active liquid waste (ALW) tank discharges exceeds a specified level. To achieve this, it was necessary to know the underlying distribution of the ALW discharge concentration. Since the distribution could only be estimated from the historical data, it was also important to provide the confidence interval for the estimated probability. Using the ALW discharge records of Pickering and Bruce NGS-A, it was found that the log-normal distribution provided the best fit for the data. The frequency of the tank concentration exceeding the specified level of 24000μCi/m 3 was estimated to be 1 in 200,000 years at Bruce NGS-A and 1 in 100,000 years at Pickering. The 99% upper confidence limits are 1 in 2777 years and 1 in 77 years, respectively

  12. Estimating Gravity Biases with Wavelets in Support of a 1-cm Accurate Geoid Model

    Science.gov (United States)

    Ahlgren, K.; Li, X.

    2017-12-01

    Systematic errors that reside in surface gravity datasets are one of the major hurdles in constructing a high-accuracy geoid model at high resolutions. The National Oceanic and Atmospheric Administration's (NOAA) National Geodetic Survey (NGS) has an extensive historical surface gravity dataset consisting of approximately 10 million gravity points that are known to have systematic biases at the mGal level (Saleh et al. 2013). As most relevant metadata is absent, estimating and removing these errors to be consistent with a global geopotential model and airborne data in the corresponding wavelength is quite a difficult endeavor. However, this is crucial to support a 1-cm accurate geoid model for the United States. With recently available independent gravity information from GRACE/GOCE and airborne gravity from the NGS Gravity for the Redefinition of the American Vertical Datum (GRAV-D) project, several different methods of bias estimation are investigated which utilize radial basis functions and wavelet decomposition. We estimate a surface gravity value by incorporating a satellite gravity model, airborne gravity data, and forward-modeled topography at wavelet levels according to each dataset's spatial wavelength. Considering the estimated gravity values over an entire gravity survey, an estimate of the bias and/or correction for the entire survey can be found and applied. In order to assess the accuracy of each bias estimation method, two techniques are used. First, each bias estimation method is used to predict the bias for two high-quality (unbiased and high accuracy) geoid slope validation surveys (GSVS) (Smith et al. 2013 & Wang et al. 2017). Since these surveys are unbiased, the various bias estimation methods should reflect that and provide an absolute accuracy metric for each of the bias estimation methods. Secondly, the corrected gravity datasets from each of the bias estimation methods are used to build a geoid model. The accuracy of each geoid model

  13. The Transcriptome Analysis and Comparison Explorer--T-ACE: a platform-independent, graphical tool to process large RNAseq datasets of non-model organisms.

    Science.gov (United States)

    Philipp, E E R; Kraemer, L; Mountfort, D; Schilhabel, M; Schreiber, S; Rosenstiel, P

    2012-03-15

    Next generation sequencing (NGS) technologies allow a rapid and cost-effective compilation of large RNA sequence datasets in model and non-model organisms. However, the storage and analysis of transcriptome information from different NGS platforms is still a significant bottleneck, leading to a delay in data dissemination and subsequent biological understanding. Especially database interfaces with transcriptome analysis modules going beyond mere read counts are missing. Here, we present the Transcriptome Analysis and Comparison Explorer (T-ACE), a tool designed for the organization and analysis of large sequence datasets, and especially suited for transcriptome projects of non-model organisms with little or no a priori sequence information. T-ACE offers a TCL-based interface, which accesses a PostgreSQL database via a php-script. Within T-ACE, information belonging to single sequences or contigs, such as annotation or read coverage, is linked to the respective sequence and immediately accessible. Sequences and assigned information can be searched via keyword- or BLAST-search. Additionally, T-ACE provides within and between transcriptome analysis modules on the level of expression, GO terms, KEGG pathways and protein domains. Results are visualized and can be easily exported for external analysis. We developed T-ACE for laboratory environments, which have only a limited amount of bioinformatics support, and for collaborative projects in which different partners work on the same dataset from different locations or platforms (Windows/Linux/MacOS). For laboratories with some experience in bioinformatics and programming, the low complexity of the database structure and open-source code provides a framework that can be customized according to the different needs of the user and transcriptome project.

  14. Topogrid Derived 10 Meter Resolution Digital Elevation Model of the Shenandoah National Park and Surrounding Region, Virginia

    Science.gov (United States)

    Chirico, Peter G.; Tanner, Seth D.

    2004-01-01

    Explanation The purpose of developing a new 10m resolution DEM of the Shenandoah National Park Region was to more accurately depict geologic structure, surfical geology, and landforms of the Shenandoah National Park Region in preparation for automated landform classification. Previously, only a 30m resolution DEM was available through the National Elevation Dataset (NED). During production of the Shenandoah10m DEM of the Park the Geography Discipline of the USGS completed a revised 10m DEM to be included into the NED. However, different methodologies were used to produce the two similar DEMs. The ANUDEM algorithm was used to develop the Shenadoah DEM data. This algorithm allows for the inclusion of contours, streams, rivers, lake and water body polygons as well as spot height data to control the elevation model. A statistical analysis using over 800 National Geodetic Survey (NGS) first and second order vertical control points reveals that the Shenandoah10m DEM, produced as a part of the Appalachian Blue Ridge Landscape project, has a vertical accuracy of ?4.87 meters. The metadata for the 10m NED data reports a vertical accuracy of ?7m. A table listing the NGS control points, the elevation comparison, and the RMSE for the Shenandoah10m DEM is provided. The process of automated terrain classification involves developing statistical signatures from the DEM for each type of surficial deposit and landform type. The signature will be a measure of several characteristics derived from the elevation data including slope, aspect, planform curvature, and profile curvature. The quality of the DEM is of critical importance when extracting terrain signatures. The highest possible horizontal and vertical accuracy is required. The more accurate Shenandoah 10m DEM can now be analyzed and integrated with the geologic observations to yield statistical correlations between the two in the development of landform and surface geology mapping projects.

  15. Recent experience related to neutronic transients in Ontario Hydro CANDU nuclear generating stations

    International Nuclear Information System (INIS)

    Frescura, G.M.; Smith, A.J.; Lau, J.H.

    1991-01-01

    Ontario Hydro presently operates 18 CANDU reactors in the province of Ontario, Canada. All of these reactors are of the CANDU Pressurized Heavy Water design, although their design features differ somewhat reflecting the evolution that has taken place from 1971 when the first Pickering unit started operation to the present as the Darlington units are being placed in service. Over the last three years, two significant neutronic transients took place at the Pickering Nuclear Generating Station 'A' (NGS A) one of which resulted in a number of fuel failures. Both events provided valuable lessons in the areas of operational safety, fuel performance And accident analysis. The events and the lessons learned are discussed in this paper

  16. Microbial speciation and biofouling potential of cooling water used by Ontario Hydro

    International Nuclear Information System (INIS)

    Sharpe, V.J.

    1985-02-01

    The cooling water composition and microbial components of biofilms attached to stainless steel wafers submerged in three lake water types were evaluated to determine whether their biofouling potential differed in a predictable manner. The composition of the lake waters was different which affected biofilm composition, where the predominance of specific microbial groups varied between test systems and with time. Some prediction of biofouling potential was possible, and it was concluded that the cooling water in the vicinity of Bruce NGS had the lowest biofouling potential whereas greater biofouling could be expected in the Pickering and Nanticoke stations

  17. Operational readiness of filtered air discharge monitoring systems

    International Nuclear Information System (INIS)

    Lafortune, J.F.; Jamieson, T.J.

    1993-08-01

    An assessment of the operational readiness of the Filtered Air Discharge (FAD) Stack Monitoring systems, installed in Canadian CANDU nuclear power plants, was performed in this project. Relevant Canadian and foreign standards and regulatory requirements have been reviewed and documentation on FAD stack monitoring system design, operation, testing and maintenance have been assessed to identify likely causes and potential failures of FAD stack monitoring systems and their components under both standby and accident conditions. Recommendations have also been provided in this report for design and performance review guidelines for CANDU stations. A case study of the FAD stack monitoring system at Pickering NGS is also documented in this report

  18. Methods for MHC genotyping in non-model vertebrates.

    Science.gov (United States)

    Babik, W

    2010-03-01

    Genes of the major histocompatibility complex (MHC) are considered a paradigm of adaptive evolution at the molecular level and as such are frequently investigated by evolutionary biologists and ecologists. Accurate genotyping is essential for understanding of the role that MHC variation plays in natural populations, but may be extremely challenging. Here, I discuss the DNA-based methods currently used for genotyping MHC in non-model vertebrates, as well as techniques likely to find widespread use in the future. I also highlight the aspects of MHC structure that are relevant for genotyping, and detail the challenges posed by the complex genomic organization and high sequence variation of MHC loci. Special emphasis is placed on designing appropriate PCR primers, accounting for artefacts and the problem of genotyping alleles from multiple, co-amplifying loci, a strategy which is frequently necessary due to the structure of the MHC. The suitability of typing techniques is compared in various research situations, strategies for efficient genotyping are discussed and areas of likely progress in future are identified. This review addresses the well established typing methods such as the Single Strand Conformation Polymorphism (SSCP), Denaturing Gradient Gel Electrophoresis (DGGE), Reference Strand Conformational Analysis (RSCA) and cloning of PCR products. In addition, it includes the intriguing possibility of direct amplicon sequencing followed by the computational inference of alleles and also next generation sequencing (NGS) technologies; the latter technique may, in the future, find widespread use in typing complex multilocus MHC systems. © 2009 Blackwell Publishing Ltd.

  19. [Employee satisfaction in hospitals - validation of the Picker employee questionnaire: the German version of the "survey of employee perceptions of health care delivery" (Picker Institute Boston)].

    Science.gov (United States)

    Riechmann, M; Stahl, K

    2013-05-01

    The aim of this study was the validation of a questionnaire specially developed for the German health-care market to measure workplace-related satisfaction of all employees in direct or indirect contact to patients. Beside this, its suitability for use in human resource and quality management was tested. Based on data from a postal survey of 38 054 employees from 37 hospitals a psychometric evaluation was done via exploratory factor analysis and reliability as well as regression analysis. For testing the capability to differentiate, subgroup analyses were conducted. 14 factors (Cronbach's alpha between 0.6 and 0.9) were extracted, explaining 44% of the variance. The factors leadership and organisational culture, conditions of employment, work load and relationship to direct line manager had the strongest influence on overall employee satisfaction. Age, gender, employment status, and senior position influence job satisfaction or relevant satisfaction-related factors. Psychometric properties, the ability to differentiate between employee groups and practicability render the questionnaire well suited for use in human resource and quality management of hospitals. © Georg Thieme Verlag KG Stuttgart · New York.

  20. Novel approaches to develop community-built biological network models for potential drug discovery.

    Science.gov (United States)

    Talikka, Marja; Bukharov, Natalia; Hayes, William S; Hofmann-Apitius, Martin; Alexopoulos, Leonidas; Peitsch, Manuel C; Hoeng, Julia

    2017-08-01

    Hundreds of thousands of data points are now routinely generated in clinical trials by molecular profiling and NGS technologies. A true translation of this data into knowledge is not possible without analysis and interpretation in a well-defined biology context. Currently, there are many public and commercial pathway tools and network models that can facilitate such analysis. At the same time, insights and knowledge that can be gained is highly dependent on the underlying biological content of these resources. Crowdsourcing can be employed to guarantee the accuracy and transparency of the biological content underlining the tools used to interpret rich molecular data. Areas covered: In this review, the authors describe crowdsourcing in drug discovery. The focal point is the efforts that have successfully used the crowdsourcing approach to verify and augment pathway tools and biological network models. Technologies that enable the building of biological networks with the community are also described. Expert opinion: A crowd of experts can be leveraged for the entire development process of biological network models, from ontologies to the evaluation of their mechanistic completeness. The ultimate goal is to facilitate biomarker discovery and personalized medicine by mechanistically explaining patients' differences with respect to disease prevention, diagnosis, and therapy outcome.

  1. Negative binomial mixed models for analyzing microbiome count data.

    Science.gov (United States)

    Zhang, Xinyan; Mallick, Himel; Tang, Zaixiang; Zhang, Lei; Cui, Xiangqin; Benson, Andrew K; Yi, Nengjun

    2017-01-03

    Recent advances in next-generation sequencing (NGS) technology enable researchers to collect a large volume of metagenomic sequencing data. These data provide valuable resources for investigating interactions between the microbiome and host environmental/clinical factors. In addition to the well-known properties of microbiome count measurements, for example, varied total sequence reads across samples, over-dispersion and zero-inflation, microbiome studies usually collect samples with hierarchical structures, which introduce correlation among the samples and thus further complicate the analysis and interpretation of microbiome count data. In this article, we propose negative binomial mixed models (NBMMs) for detecting the association between the microbiome and host environmental/clinical factors for correlated microbiome count data. Although having not dealt with zero-inflation, the proposed mixed-effects models account for correlation among the samples by incorporating random effects into the commonly used fixed-effects negative binomial model, and can efficiently handle over-dispersion and varying total reads. We have developed a flexible and efficient IWLS (Iterative Weighted Least Squares) algorithm to fit the proposed NBMMs by taking advantage of the standard procedure for fitting the linear mixed models. We evaluate and demonstrate the proposed method via extensive simulation studies and the application to mouse gut microbiome data. The results show that the proposed method has desirable properties and outperform the previously used methods in terms of both empirical power and Type I error. The method has been incorporated into the freely available R package BhGLM ( http://www.ssg.uab.edu/bhglm/ and http://github.com/abbyyan3/BhGLM ), providing a useful tool for analyzing microbiome data.

  2. Bayesian state space models for dynamic genetic network construction across multiple tissues.

    Science.gov (United States)

    Liang, Yulan; Kelemen, Arpad

    2016-08-01

    Construction of gene-gene interaction networks and potential pathways is a challenging and important problem in genomic research for complex diseases while estimating the dynamic changes of the temporal correlations and non-stationarity are the keys in this process. In this paper, we develop dynamic state space models with hierarchical Bayesian settings to tackle this challenge for inferring the dynamic profiles and genetic networks associated with disease treatments. We treat both the stochastic transition matrix and the observation matrix time-variant and include temporal correlation structures in the covariance matrix estimations in the multivariate Bayesian state space models. The unevenly spaced short time courses with unseen time points are treated as hidden state variables. Hierarchical Bayesian approaches with various prior and hyper-prior models with Monte Carlo Markov Chain and Gibbs sampling algorithms are used to estimate the model parameters and the hidden state variables. We apply the proposed Hierarchical Bayesian state space models to multiple tissues (liver, skeletal muscle, and kidney) Affymetrix time course data sets following corticosteroid (CS) drug administration. Both simulation and real data analysis results show that the genomic changes over time and gene-gene interaction in response to CS treatment can be well captured by the proposed models. The proposed dynamic Hierarchical Bayesian state space modeling approaches could be expanded and applied to other large scale genomic data, such as next generation sequence (NGS) combined with real time and time varying electronic health record (EHR) for more comprehensive and robust systematic and network based analysis in order to transform big biomedical data into predictions and diagnostics for precision medicine and personalized healthcare with better decision making and patient outcomes.

  3. Safety assessment of starch-based personal care products: Nanocapsules and pickering emulsions.

    Science.gov (United States)

    Marto, J; Pinto, P; Fitas, M; Gonçalves, L M; Almeida, A J; Ribeiro, H M

    2018-03-01

    The safety profile of the ingredients used in topical dosage forms and its evaluation is an issue of utmost importance. A suitable equilibrium between safety and efficacy is crucial before promoting a dermatological product. The aim of this work was to assess the safety and biological effects of starch-based vehicles (St-BV) used in such products. The hazard, exposure and dose-response assessment were used to characterize the risk of each ingredient. The EpiSkin™ assay and human repeat insult patch tests were performed to compare the theoretical safety assessment to in vitro and in vivo data. The efficacy of the St-BV was studied using biophysical measurements in human volunteers during 28 days, showing that all ingredients and their combinations were safe for the consumer. Tissue viability determined using the EpiSkin™ testing reached values between 84.0 ± 5.0% and 98.0 ± 8.6% after application of St-BV, which were considered as non-irritant to the skin. These observations were confirmed by the in vivo studies where the St-BV did not induce any sensitization on the volunteers, being safe for human use. Moreover, St-BV increased skin hydration and microcirculation, emerging as an attractive alternative to chemical raw materials. Copyright © 2018 Elsevier Inc. All rights reserved.

  4. Extending Pickering Fuel Channel Life to 247,000 EFPH (2020)

    International Nuclear Information System (INIS)

    Malek, I.

    2013-01-01

    This presentation is about extending the life of PNGS Pressure tubes from 210,000 EFPH (Effective Full Power Hours) to 247,000 EFPH. The l license renewal is in 2013 (R & D defined in 2009). The unknowns are the extent of degradation in some key areas. There are regulatory requirements for fuel channel extended life. It is necessary to integrate inspection capability and do-ability in outages. This would result in safe operation and demonstrated margin to extend life with operation to 2020.

  5. Preparation of novel film-forming armoured latexes using silica nanoparticles as a pickering emulsion stabiliser.

    Science.gov (United States)

    Shiraz, Hana; Peake, Simon J; Davey, Tim; Cameron, Neil R; Tabor, Rico F

    2018-05-15

    Film-forming polymer latex particles of diameter acrylate (BA) as co-monomers, potassium persulphate (KPS) as an initiator and a commercially available colloidal nano-silica (Ludox®-TM40). It was found that pH control before polymerisation using methacrylic acid (MAA) facilitated the formation of armoured latexes, and mechanistic features of this process are discussed. An alternative, more robust protocol was developed whereby addition of vinyltriethoxysilane (VTES) to control wettability resulted in latexes completely armoured in colloidal nano-silica. The latexes were characterised using SEM, cryo-TEM and AFM imaging techniques. The mechanism behind the adsorption was investigated through surface pressure and contact angle measurements to understand the factors that influence this irreversible adsorption. Results indicate that nanoparticle attachment (but intriguingly not latex size) is dependent on particle wettability, providing new insight into the formation of nanoparticle-armoured latexes, along with opportunities for further development of diversely functionalized inorganic/organic polymer composite particles. Copyright © 2018 Elsevier Inc. All rights reserved.

  6. Tuning hydrophobicity of zein nanoparticles to control rheological behavior of Pickering emulsions

    NARCIS (Netherlands)

    Zou, Yuan; Baalen, van Carlijn; Yang, Xiaoquan; Scholten, E.

    2018-01-01

    In the present work, the influence of hydrophobicity of zein/tannic acid complex particles (ZTPs) on the rheological behavior of ZTP-stabilized emulsion gels is described. The hydrophobicity of the particles was controlled by the incorporation of different amounts of hydrophilic tannic acid, while

  7. A User’s Manual for Fiber Diffraction: The Automated Picker and Huber Diffractometers

    Science.gov (United States)

    1990-07-01

    17 3. Layer line scan of degummed silk ( Bombyx mori ) ................................. 18...index (arbitrary units) Figure 3. Layer line scan of degummed silk ( Bombyx mori ) showing layers 0 through 6. If the fit is rejected, new values for... originally made at intervals larger than 0.010. The smoothing and interpolation is done by a least-squares polynomial fit to segments of the data. The number

  8. Oxygen octahedra picker: A software tool to extract quantitative information from STEM images

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Yi, E-mail: y.wang@fkf.mpg.de; Salzberger, Ute; Sigle, Wilfried; Eren Suyolcu, Y.; Aken, Peter A. van

    2016-09-15

    In perovskite oxide based materials and hetero-structures there are often strong correlations between oxygen octahedral distortions and functionality. Thus, atomistic understanding of the octahedral distortion, which requires accurate measurements of atomic column positions, will greatly help to engineer their properties. Here, we report the development of a software tool to extract quantitative information of the lattice and of BO{sub 6} octahedral distortions from STEM images. Center-of-mass and 2D Gaussian fitting methods are implemented to locate positions of individual atom columns. The precision of atomic column distance measurements is evaluated on both simulated and experimental images. The application of the software tool is demonstrated using practical examples. - Highlights: • We report a software tool for mapping atomic positions from HAADF and ABF images. • It enables quantification of both crystal lattice and oxygen octahedral distortions. • We test the measurement accuracy and precision on simulated and experimental images. • It works well for different orientations of perovskite structures and interfaces.

  9. Size-dependent properties of silica nanoparticles for Pickering stabilization of emulsions and foams

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Ijung, E-mail: ijungkim@utexas.edu [The University of Texas at Austin, Department of Petroleum and Geosystems Engineering (United States); Worthen, Andrew J.; Johnston, Keith P. [The University of Texas at Austin, McKetta Department of Chemical Engineering (United States); DiCarlo, David A.; Huh, Chun [The University of Texas at Austin, Department of Petroleum and Geosystems Engineering (United States)

    2016-04-15

    Nanoparticles are a promising alternative to surfactants to stabilize emulsions or foams in enhanced oil recovery (EOR) processes due to their effectiveness in very harsh environments found in many of the oilfields around the world. While the size-dependent properties of nanoparticles have been extensively studied in the area of optics or cellular uptake, little is known on the effects of nanoparticle size on emulsion/foam generation, especially for EOR applications. In this study, silica nanoparticles with four different sizes (5, 12, 25, and 80 nm nominal diameter) but with the same surface treatment were employed to test their emulsion or foam generation behavior in high-salinity conditions. The decane-in-brine emulsion generated by sonication or flowing through sandpack showed smaller droplet size and higher apparent viscosity as the nanoparticle size decreased. Similarly, the CO{sub 2}-in-brine foam generation in sandstone or sandpacks was also significantly affected by the nanoparticle size, exhibiting higher apparent foam viscosity as the nanoparticle size decreased. In case of foam generation in sandstone cores with 5 nm nanoparticles, a noticeable hysteresis occurred when the flow velocity was initially increased and then decreased, implying a strong foam generation initially; and then the trapping of the generated foam in the rock pores, as the flow velocity decreased. On the other hand, weak foams stabilized with larger nanoparticles indicated a rapid coalescence of bubbles which prevented foam generation. Overall, stable emulsions/foams were achievable by the smaller particles as a result of greater diffusivity and/or higher number concentration, thus allowing more nanoparticles with higher surface area to volume ratio to be adsorbed at the fluid/fluid interfaces of the emulsion/foam dispersion.Graphical abstract.

  10. Mixing Time, Inversion and Multiple Emulsion Formation in a Limonene and Water Pickering Emulsion

    Directory of Open Access Journals (Sweden)

    Laura Sawiak

    2018-05-01

    Full Text Available It has previously been demonstrated that particle-stabilized emulsions comprised of limonene, water and fumed silica particles exhibit complex emulsification behavior as a function of composition and the duration of the emulsification step. Most notably the system can invert from being oil-continuous to being water-continuous under prolonged mixing. Here we investigate this phenomenon experimentally for the regime where water is the majority liquid. We prepare samples using a range of different emulsification times and we examine the final properties in bulk and via confocal microscopy. We use the images to quantitatively track the sizes of droplets and clusters of particles. We find that a dense emulsion of water droplets forms initially which is transformed, in time, into a water-in-oil-in-water multiple emulsion with concomitant changes in droplet and cluster sizes. In parallel we carry out rheological studies of water-in-limonene emulsions using different concentrations of fumed silica particles. We unite our observations to propose a mechanism for inversion based on the changes in flow properties and the availability of particles during emulsification.

  11. Food-grade Pickering stabilisation of foams by in situ hydrophobisation of calcium carbonate particles

    NARCIS (Netherlands)

    Binks, Bernard P.; Muijlwijk, K.; Koman, Henriëtte; Poortinga, A.T.

    2017-01-01

    The aim of this study was to investigate the possibility of stabilising foam bubbles in water by adsorption of calcium carbonate (CaCO3) particles. Because CaCO3 is hydrophilic and not surface-active, particles were hydrophobised in situ with several emulsifiers. The used emulsifiers were food-grade

  12. Food-grade pickering stabilisation of foams by in situ hydrophobisation of calcium carbonate particles

    NARCIS (Netherlands)

    Binks, B.P.; Muijlwijk, K.; Koman, H.; Poortinga, A.T.

    2017-01-01

    The aim of this study was to investigate the possibility of stabilising foam bubbles in water by adsorption of calcium carbonate (CaCO3) particles. Because CaCO3 is hydrophilic and not surface-active, particles were hydrophobised in situ with several emulsifiers. The used emulsifiers were food-grade

  13. Flash pulmonary edema in patients with renal artery stenosis--the Pickering Syndrome

    DEFF Research Database (Denmark)

    Pelta, Anna; Andersen, Ulrik B; Just, Sven

    2010-01-01

    We report the prevalence of flash pulmonary edema in patients consecutively referred for balloon angioplasty of uni- or bilateral renal artery stenosis (PTRA), and describe the characteristics of this special fraction of the patients. We further report two unusual cases.......We report the prevalence of flash pulmonary edema in patients consecutively referred for balloon angioplasty of uni- or bilateral renal artery stenosis (PTRA), and describe the characteristics of this special fraction of the patients. We further report two unusual cases....

  14. Genetics of Adiposity in Large Animal Models for Human Obesity-Studies on Pigs and Dogs.

    Science.gov (United States)

    Stachowiak, M; Szczerbal, I; Switonski, M

    2016-01-01

    The role of domestic mammals in the development of human biomedical sciences has been widely documented. Among these model species the pig and dog are of special importance. Both are useful for studies on the etiology of human obesity. Genome sequences of both species are known and advanced genetic tools [eg, microarray SNP for genome wide association studies (GWAS), next generation sequencing (NGS), etc.] are commonly used in such studies. In the domestic pig the accumulation of adipose tissue is an important trait, which influences meat quality and fattening efficiency. Numerous quantitative trait loci (QTLs) for pig fatness traits were identified, while gene polymorphisms associated with these traits were also described. The situation is different in dog population. Generally, excessive accumulation of adipose tissue is considered, similar to humans, as a complex disease. However, research on the genetic background of canine obesity is still in its infancy. Between-breed differences in terms of adipose tissue accumulation are well known in both animal species. In this review we show recent advances of studies on adipose tissue accumulation in pigs and dogs, and their potential importance for studies on human obesity. Copyright © 2016 Elsevier Inc. All rights reserved.

  15. SNP markers retrieval for a non-model species: a practical approach

    Directory of Open Access Journals (Sweden)

    Shahin Arwa

    2012-01-01

    Full Text Available Abstract Background SNP (Single Nucleotide Polymorphism markers are rapidly becoming the markers of choice for applications in breeding because of next generation sequencing technology developments. For SNP development by NGS technologies, correct assembly of the huge amounts of sequence data generated is essential. Little is known about assembler's performance, especially when dealing with highly heterogeneous species that show a high genome complexity and what the possible consequences are of differences in assemblies on SNP retrieval. This study tested two assemblers (CAP3 and CLC on 454 data from four lily genotypes and compared results with respect to SNP retrieval. Results CAP3 assembly resulted in higher numbers of contigs, lower numbers of reads per contig, and shorter average read lengths compared to CLC. Blast comparisons showed that CAP3 contigs were highly redundant. Contrastingly, CLC in rare cases combined paralogs in one contig. Redundant and chimeric contigs may lead to erroneous SNPs. Filtering for redundancy can be done by blasting selected SNP markers to the contigs and discarding all the SNP markers that show more than one blast hit. Results on chimeric contigs showed that only four out of 2,421 SNP markers were selected from chimeric contigs. Conclusion In practice, CLC performs better in assembling highly heterogeneous genome sequences compared to CAP3, and consequently SNP retrieval is more efficient. Additionally a simple flow scheme is suggested for SNP marker retrieval that can be valid for all non-model species.

  16. Modeling of Habitat and Foraging Behavior of Beaked Whales in the Southern California Bight

    Science.gov (United States)

    2015-09-30

    a species label. Data from acoustic line-transect surveys (2008-2011) carried out by NOAA Southwest Fisheries Science Center (Jay Barlow ) in...published, refereed] Baumann-Pickering S, Yack TM, Barlow J, Wiggins SM, Hildebrand JA (2013) Baird’s beaked whale echolocation signals. J Acoust Soc Am 133...4321-4331 [published, refereed] Yack TM, Barlow J, Calambokidis J, Southall B, and Coates S (2013) Identification of previously unknown beaked

  17. Oocyte mitochondrial deletions and heteroplasmy in a bovine model of ageing and ovarian stimulation.

    Science.gov (United States)

    Hammond, Elizabeth R; Green, Mark P; Shelling, Andrew N; Berg, Martin C; Peek, John C; Cree, Lynsey M

    2016-04-01

    Maternal ageing and ovarian stimulation result in the accumulation of mitochondrial DNA (mtDNA) deletions and heteroplasmy in individual oocytes from a novel bovine model for human assisted reproductive technology (ART). The levels of mtDNA deletions detected in oocytes increased with ovarian ageing. Low levels of mtDNA heteroplasmy were apparent across oocytes and no relationship was identified with respect to ovarian ageing or ovarian stimulation. Oocyte quality decreases with ovarian ageing and it is postulated that the mtDNA may have a role in this decline. The impact of ovarian stimulation on oocyte quality is poorly understood. Human studies investigating these effects are often limited by the use of low quality oocytes and embryos, variation in age and ovarian stimulation regimens within the patients studied, as well as genetic and environmental variability. Further, no study has investigated mtDNA heteroplasmy in individual oocytes using next-generation sequencing (NGS), and little is known about whether the oocyte accumulates heteroplasmic mtDNA mutations following ageing or ovarian stimulation. A novel bovine model for the effect of stimulation and age in human ART was undertaken using cows generated by somatic cell nuclear transfer (SCNT) from one founder, to produce a homogeneous population with reduced genetic and environmental variability. Oocytes and somatic tissues were collected from young (3 years of age; n = 4 females) and old (10 years of age; n = 5 females) cow clones following multiple natural ovarian cycles, as well as oocytes following multiple mild (FSH only) and standard (based on human a long GnRH agonist protocol) ovarian stimulation cycles. In addition, oocytes were recovered in a natural cycle from naturally conceived cows aged 4-13.5 years (n = 10) to provide a heterogeneous cohort for mtDNA deletion studies. The presence or absence of mtDNA deletions were investigated using long-range PCR in individual oocytes (n = 62). To determine

  18. A general model for likelihood computations of genetic marker data accounting for linkage, linkage disequilibrium, and mutations.

    Science.gov (United States)

    Kling, Daniel; Tillmar, Andreas; Egeland, Thore; Mostad, Petter

    2015-09-01

    Several applications necessitate an unbiased determination of relatedness, be it in linkage or association studies or in a forensic setting. An appropriate model to compute the joint probability of some genetic data for a set of persons given some hypothesis about the pedigree structure is then required. The increasing number of markers available through high-density SNP microarray typing and NGS technologies intensifies the demand, where using a large number of markers may lead to biased results due to strong dependencies between closely located loci, both within pedigrees (linkage) and in the population (allelic association or linkage disequilibrium (LD)). We present a new general model, based on a Markov chain for inheritance patterns and another Markov chain for founder allele patterns, the latter allowing us to account for LD. We also demonstrate a specific implementation for X chromosomal markers that allows for computation of likelihoods based on hypotheses of alleged relationships and genetic marker data. The algorithm can simultaneously account for linkage, LD, and mutations. We demonstrate its feasibility using simulated examples. The algorithm is implemented in the software FamLinkX, providing a user-friendly GUI for Windows systems (FamLinkX, as well as further usage instructions, is freely available at www.famlink.se ). Our software provides the necessary means to solve cases where no previous implementation exists. In addition, the software has the possibility to perform simulations in order to further study the impact of linkage and LD on computed likelihoods for an arbitrary set of markers.

  19. Development of chromosome-arm-specific microsatellite markers in Triticum aestivum (Poaceae) using NGS technology

    Czech Academy of Sciences Publication Activity Database

    Nie, X.; Li, B.; Wang, L.; Liu, P.; Biradar, S. S.; Li, T.; Doležel, Jaroslav; Edwards, D.; Luo, M.; Weining, S.

    2012-01-01

    Roč. 99, č. 9 (2012), e369-e371 ISSN 0002-9122 Institutional research plan: CEZ:AV0Z50380511 Keywords : chromosome-arm-specific DNA * flow-sorted chromosomes * next-generation sequencing Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 2.586, year: 2012

  20. 2016 NOAA NGS Ortho-rectified Color Mosaic of Anchorage, Alaska

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This data set contains ortho-rectified mosaic tiles, created as a product from the NOAA Integrated Ocean and Coastal Mapping (IOCM) initiative. The source imagery...

  1. 2016 NOAA NGS Ortho-rectified Near-Infrared Mosaic of Cleveland, Ohio

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This data set contains ortho-rectified mosaic tiles, created as a product from the NOAA Integrated Ocean and Coastal Mapping (IOCM) initiative. The source imagery...

  2. Improvements to the annunciation and display systems at Gentilly 2 NGS - An integrated approach

    Energy Technology Data Exchange (ETDEWEB)

    Dufresne, R; Desaulniers, M [Central Nucleaire Gentilly, PQ (Canada)

    1997-09-01

    Since 1990, Gentilly 2 Nuclear Generating Station has revised its overall strategy during upsets and abnormal events and has also completely revised its Emergency Operating Procedures (EOP), its abnormal General Operating Procedures (GOP) and is near completing the revision of its Operating Manuals (OM). This strategy, these new EOPs, abnormal GOPs and the abnormal OMs were validated on our full scale simulator when applicable by a multidisciplinary team composed of authorized staff, technical and safety specialists and also candidates in training for authorization. We have identified significant weakness in the annunciation and display systems impairing the management of these events. To benefit from CANDU Owner`s Group (COG) expertise, we met in some occasions the CRNL`s research team on CAMLS project (CANDU Annunciation Message List System). In order to have more immediate benefits, we chose to improve the actual annunciation and display systems using, in some cases, ideas and/or principles used in the prototype CAMLS. After a brief history, we will present the global approach used at Gentilly 2 for upset and event management and, we will therefore describe in more detail each of the improvements on annunciation and display systems which contributed to reinforce this global approach. Hereafter are some of these improvements: prioritization via color coding of window alarms, re-prioritization (major/minor) of all CRT alarms, coalescence of multi-channel analog and contact CRT alarms, increase in the amount of trends and bar charts for upset management, special alarm summary functions (contextual) for startup after a trip. We did also identify certain needs which are not yet fulfilled with the actual improved system. Finally we will describe some other proposed improvements to the annunciation and display systems that we foresee in the near future. (author). 3 refs, figs.

  3. AECB staff review of Bruce NGS 'A' operation for the year 1988

    International Nuclear Information System (INIS)

    1989-05-01

    AECB project staff believes that overall performance of the station in 1988 was generally satisfactory and better than in 1987. However, this assessment is not supported by some of the key performance indicators, although the indicators in areas where AECB staff had specific concerns do support it. For example, the percentage of reported significant events attributable to human error, the number of operating memos beyond the review date, scheduled emergency drills completed, the number of completed reactor trips all show a significant improvement over the 1987 value. In addition, AECB staff has been encouraged by the licensee's implementation of effective review processes for operator and maintenance call-ups, routines and deficiencies, and the establishment of supervisor inspection tours and operator rounds programs. Nevertheless, it is the opinion of AECB staff that to achieve standards of operation which would be considered fully satisfactory, the backlog of maintenance work must be reduced, the quality of work performed in the plant improved, and assurance provided that the required quality standards are being consistently achieved and maintained

  4. Mapsembler, targeted and micro assembly of large NGS datasets on a desktop computer

    Directory of Open Access Journals (Sweden)

    Peterlongo Pierre

    2012-03-01

    Full Text Available Abstract Background The analysis of next-generation sequencing data from large genomes is a timely research topic. Sequencers are producing billions of short sequence fragments from newly sequenced organisms. Computational methods for reconstructing whole genomes/transcriptomes (de novo assemblers are typically employed to process such data. However, these methods require large memory resources and computation time. Many basic biological questions could be answered targeting specific information in the reads, thus avoiding complete assembly. Results We present Mapsembler, an iterative micro and targeted assembler which processes large datasets of reads on commodity hardware. Mapsembler checks for the presence of given regions of interest that can be constructed from reads and builds a short assembly around it, either as a plain sequence or as a graph, showing contextual structure. We introduce new algorithms to retrieve approximate occurrences of a sequence from reads and construct an extension graph. Among other results presented in this paper, Mapsembler enabled to retrieve previously described human breast cancer candidate fusion genes, and to detect new ones not previously known. Conclusions Mapsembler is the first software that enables de novo discovery around a region of interest of repeats, SNPs, exon skipping, gene fusion, as well as other structural events, directly from raw sequencing reads. As indexing is localized, the memory footprint of Mapsembler is negligible. Mapsembler is released under the CeCILL license and can be freely downloaded from http://alcovna.genouest.org/mapsembler/.

  5. Evaluation of NGS and RT-PCR methods for ALK rearrangement in European NSCLC patients

    DEFF Research Database (Denmark)

    Letovanec, Igor; Finn, Stephen; Zygoura, Panagiota

    2018-01-01

    INTRODUCTION: The reported prevalence of ALK rearrangement in NSCLC ranges from 2%-7%. The primary standard diagnostic method is fluorescence in situ hybridization (FISH). Recently, immunohistochemistry (IHC) has also proven to be a reproducible and sensitive technique. Reverse transcriptase...

  6. Detection of a novel DSPP mutation by NGS in a population isolate in Madagascar

    Directory of Open Access Journals (Sweden)

    Agnes eBloch-Zupan

    2016-03-01

    Full Text Available A large family from a small village in Madagascar, Antanetilava, is known to present with coloured teeth. Through previous collaboration and 4 successive visits in 1994, 2004, 2005 and 2012, we provided dental care to the inhabitants and diagnosed dentinogenesis imperfecta. Recently, using whole exome sequencing we confirmed the clinical diagnosis by identifying a novel single nucleotide deletion in exon 5 of DSPP. This paper underlines the necessity of long run research, the importance of international and interpersonal collaborations as well as the major contribution of next generation sequencing tools in the genetic diagnosis of rare oro-dental anomalies. This study is registered in ClinicalTrials (https://clinicaltrials.gov under the number NCT02397824.

  7. Top of tubesheet cracking in Bruce A NGS steam generator tubing - recent experience

    International Nuclear Information System (INIS)

    Clark, M.A.; Lepik, O.; Mirzai, M.; Thompson, I.

    1998-01-01

    During the Bruce A Nuclear Generating Station (BNGS-A) Unit 1 1997 planned outage, a dew point search method identified a leak in one steam generator(SG) tube. Subsequently, the tube was inspected with all available eddy current probes and removed for examination. The initial inspection results and metallurgical examination of the removed tube confirmed that the leak was due to intergranular attack/stress corrosion cracking (IGA/SCC) emanating from the secondary side of the tube at the top of the tubesheet location. Subsequently, eddy current and ultrasonic indications were found at the top of the tubesheet of other Alloy 600 SG tubes. To investigate the source of the indications and to validate the inspection probes, sections of 40 tubes with various levels of damage were removed. The metallurgical examination of the removed sections showed that both secondary side and primary side initiated, circumferential, stress corrosion cracking and intergranular attack occurred in the BNGS-A SG tubing. Significant degradation from both mechanisms was found, invariably located in the roll transition region of the top expansion joint between the tube and the tubesheet on the hot leg (304 degrees C) side of the tube. Various aspects of the failures and tube examinations are presented in this paper, including presentation of the cracking morphology, measured crack size distributions, and discussion of some factors possibly affecting the cracking. (author)

  8. Building A NGS Genomic Resource: Towards Molecular Breeding In L. Perenne

    DEFF Research Database (Denmark)

    Ruttink, Tom; Roldán-Ruiz, Isabel; Asp, Torben

    To advance the application of molecular breeding in Lolium perenne, we have generated a sequence resource to facilitate gene discovery and SNP marker development. Illumina GAII transcriptome sequencing was performed on meristem-enriched samples of 14 Lolium genotypes. De novo assemblies for indiv......To advance the application of molecular breeding in Lolium perenne, we have generated a sequence resource to facilitate gene discovery and SNP marker development. Illumina GAII transcriptome sequencing was performed on meristem-enriched samples of 14 Lolium genotypes. De novo assemblies...... of SNP markers in selected candidate genes. In parallel, a germplasm collection of 602 Lolium genotypes was established and is being phenotyped for plant architecture, reproductive characteristics, flowering time, and forage quality traits. We will test through association genetics whether phenotypic...

  9. Airborne Gravity: NGS' Airborne Gravity Data for AN01 (2009-2010)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Airborne gravity data for Alaska collected in 2009-2010 over 2 surveys. This data set is part of the Gravity for the Re-definition of the American Vertical Datum...

  10. Airborne Gravity: NGS' Gravity Data for ES04 (2013-2014)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Airborne gravity data for North Carolina, South Carolina, Virginia, and the Atlantic Ocean collected in 2013 and 2014 over two surveys. This data set is part of the...

  11. Airborne Gravity: NGS' Gravity Data for EN07 (2012-2013)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Airborne gravity data for Maine and Canada collected in 2012 and 2013 over 2 surveys. This data set is part of the Gravity for the Re-definition of the American...

  12. Airborne Gravity: NGS' Gravity Data for ES05 (2015-2016)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Airborne gravity data for Florida and the Atlantic Ocean collected in two surveys, FL15-1 and FL15-2. This data set is part of the Gravity for the Re-definition of...

  13. Airborne Gravity: NGS' Gravity Data for AS03 (2010-2012)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Airborne gravity data for Alaska collected in 2010 and 2012 over 2 surveys. This data set is part of the Gravity for the Re-definition of the American Vertical Datum...

  14. Airborne Gravity: NGS' Gravity Data for CS02 (2008-2009)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Airborne gravity data for Louisana and Mississippi collected in 2008-2009 over 2 surveys. This data set is part of the Gravity for the Re-definition of the American...

  15. NUWE ONTWlKKELlNGS BINNE CHOMSKY SE TEORlE VAN ...

    African Journals Online (AJOL)

    Sinclair (1978) se oorsigtelike weergawe van .die inhoud van die reels wat binne die OB-raamwerk representasies in LF aflei, hier aan te vul met betre~ing tot. (i) aspekte van die ... van die GB-teorie. In. §3 word ingegaan op hoe die OB-teorie gemodifiseer is tot die GB-teorie ...... linguistic phenomena. That is something ...

  16. AECB staff annual report of Darlington NGS 'A' for the year 1990

    International Nuclear Information System (INIS)

    1991-06-01

    This report presents the AECB staff review of major licensing issues and of the operational performance of the station during 1990. In addition to the reports mentioned above, other Ontario Hydro reports, official correspondence, and observations of AECB site staff have been taken into consideration. The report is limited to those aspects of station performance that AECB staff consider to have some safety significance. Developments of significance associated with issues addressed in the report that occurred in the early part of 1991 are also mentioned

  17. From NGS assembly challenges to instability of fungal mitochondrial genomes: A case study in genome complexity.

    Science.gov (United States)

    Misas, Elizabeth; Muñoz, José Fernando; Gallo, Juan Esteban; McEwen, Juan Guillermo; Clay, Oliver Keatinge

    2016-04-01

    The presence of repetitive or non-unique DNA persisting over sizable regions of a eukaryotic genome can hinder the genome's successful de novo assembly from short reads: ambiguities in assigning genome locations to the non-unique subsequences can result in premature termination of contigs and thus overfragmented assemblies. Fungal mitochondrial (mtDNA) genomes are compact (typically less than 100 kb), yet often contain short non-unique sequences that can be shown to impede their successful de novo assembly in silico. Such repeats can also confuse processes in the cell in vivo. A well-studied example is ectopic (out-of-register, illegitimate) recombination associated with repeat pairs, which can lead to deletion of functionally important genes that are located between the repeats. Repeats that remain conserved over micro- or macroevolutionary timescales despite such risks may indicate functionally or structurally (e.g., for replication) important regions. This principle could form the basis of a mining strategy for accelerating discovery of function in genome sequences. We present here our screening of a sample of 11 fully sequenced fungal mitochondrial genomes by observing where exact k-mer repeats occurred several times; initial analyses motivated us to focus on 17-mers occurring more than three times. Based on the diverse repeats we observe, we propose that such screening may serve as an efficient expedient for gaining a rapid but representative first insight into the repeat landscapes of sparsely characterized mitochondrial chromosomes. Our matching of the flagged repeats to previously reported regions of interest supports the idea that systems of persisting, non-trivial repeats in genomes can often highlight features meriting further attention. Copyright © 2016 Elsevier Ltd. All rights reserved.

  18. BAL31-NGS approach for identification of telomeres de novo in large genomes

    Czech Academy of Sciences Publication Activity Database

    Peška, Vratislav; Sitová, Z.; Fajkus, Petr; Fajkus, Jiří

    2017-01-01

    Roč. 114, FEB2017 (2017), s. 16-27 ISSN 1046-2023 Institutional support: RVO:68081707 Keywords : alga cyanidioschyzon-merolae * macronuclear dna * (tttaggg)(n) telomeres Subject RIV: CE - Biochemistry OBOR OECD: Biochemistry and molecular biology Impact factor: 3.802, year: 2016

  19. AECB staff annual report of Darlington NGS for the year 1991

    International Nuclear Information System (INIS)

    1992-11-01

    Ontario Hydro operated Darlington in a safe manner in 1991. Ontario Hydro violated the Atomic Energy Control Regulations once and the physical security regulations three times in 1991. They failed to observe the Operating Licence conditions on ten occasions. The AECB did not find that the individual events had a significant impact on safety. There were no violations of the construction licence. None of the station staff received a radiation dose in excess of the regulatory limit. Radioactive emissions from the station were far below the regulatory limit. Special safety system performance was not fully satisfactory. Ontario Hydro failed to meet the unavailability targets for shutdown system one and the negative pressure containment system. Ontario Hydro reported seventeen incidents under conditions of the Operating and Construction licences. Units 1 and 2 remained shut down for most of 1991 because of unexplained fuel bundle damage in the reactor core. Ontario Hydro has decided to replace the main generator rotors because of cracks discovered on the rotor shaft. A fully modified rotor was installed on Unit 1. Ontario Hydro staff have a significant backlog of maintenance work. The Quality Improvement Program seemed to work well, resulting in some noticeable improvements. Three Shift Supervisors and four Control Operators were licensed this year. All planned emergency exercises and drills took place as scheduled. Ontario Hydro identified and are addressing several areas for improvement during the drills. Except for a power supply interruption to some IAEA equipment, Ontario Hydro achieved all its safeguards goals at Darlington in 1991. The Tritium Removal Facility (TRF) operated intermittently during 1991. Ontario Hydro is proceeding with the design and planning of an annex to the TRF to replace the present temporary facilities. (Author)

  20. 30~kb~sp•.k.ngs' 300k R~~.~ws

    African Journals Online (AJOL)

    AND THE AUSTRALIAN. GOVERNMENT. PUBLISHING SERVICE. In all facets of life there are professional men who follow a career according to well-established prin- ciples, and others who attempt things for which they are not equipped. History writing is not short of amateur practitioners; perhaps this is because it.

  1. National Geodetic Survey (NGS) Geodetic Control Stations, (Horizontal and/or Vertical Control), March 2009

    Data.gov (United States)

    Earth Data Analysis Center, University of New Mexico — This data contains a set of geodetic control stations maintained by the National Geodetic Survey. Each geodetic control station in this dataset has either a precise...

  2. AECB staff review of Bruce NGS'A' operation for the year 1987

    International Nuclear Information System (INIS)

    1988-06-01

    This report presents AECB project staff's review of major licensing issues and of the operational performance of the station during 1987. Ontario Hydro reports and official correspondence and observations on AECB staff at site have been taken into consideration. The report is limited to aspects of the station performance that AECB staff considers to have a safety significance. Where significant developments associated with issues addressed in the report occurred in the early part of 1988 (up to the time of writing), these are mentioned where appropriate. Ontario Hydro's Quarterly Reports for 1987 contain detailed technical information on the performance of the station, individual units and unit systems. It is the opinion of AECB project staff that despite a number of commendable actions and achievements which are identified in this report, the performance of the station in 1987 was only marginally satisfactory and less satisfactory than in 1986. This assessment is supported by key performance indicators such as the number of reportable significant events, the number of events caused by or influenced by human error and the reactor trip frequency, all of which exceeded 1986 levels, and also by the lack of satisfactory progress made during the year on actions to address the findings of the Fall '86 AECB Assessment of Operating Practices. AECB staff considers that the outstanding operations and maintenance problems that were identified in the 1986 Assessment are due, in part, to an ineffective quality assurance program, and in part to a shortage of resources

  3. AECB staff annual report of BRUCE NGS 'B' for the year 1990

    International Nuclear Information System (INIS)

    1991-06-01

    This report presents the AECB staff review of major licensing issues and of the operational performance of the station during 1990. The report is limited to those aspects of station performance that AECB staff considers to have safety significance. Where developments of significance, associated with issues addressed in the report, occurred in the early part of 1991, these are also mentioned

  4. Airborne Gravity: NGS' Gravity Data for AS04 (2015-2016)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Airborne gravity data for Alaska collected in 2015 and 2016 over 2 surveys, AK15 and AK16. This data set is part of the Gravity for the Re-definition of the American...

  5. Je, a versatile suite to handle multiplexed NGS libraries with unique molecular identifiers.

    Science.gov (United States)

    Girardot, Charles; Scholtalbers, Jelle; Sauer, Sajoscha; Su, Shu-Yi; Furlong, Eileen E M

    2016-10-08

    The yield obtained from next generation sequencers has increased almost exponentially in recent years, making sample multiplexing common practice. While barcodes (known sequences of fixed length) primarily encode the sample identity of sequenced DNA fragments, barcodes made of random sequences (Unique Molecular Identifier or UMIs) are often used to distinguish between PCR duplicates and transcript abundance in, for example, single-cell RNA sequencing (scRNA-seq). In paired-end sequencing, different barcodes can be inserted at each fragment end to either increase the number of multiplexed samples in the library or to use one of the barcodes as UMI. Alternatively, UMIs can be combined with the sample barcodes into composite barcodes, or with standard Illumina® indexing. Subsequent analysis must take read duplicates and sample identity into account, by identifying UMIs. Existing tools do not support these complex barcoding configurations and custom code development is frequently required. Here, we present Je, a suite of tools that accommodates complex barcoding strategies, extracts UMIs and filters read duplicates taking UMIs into account. Using Je on publicly available scRNA-seq and iCLIP data containing UMIs, the number of unique reads increased by up to 36 %, compared to when UMIs are ignored. Je is implemented in JAVA and uses the Picard API. Code, executables and documentation are freely available at http://gbcs.embl.de/Je . Je can also be easily installed in Galaxy through the Galaxy toolshed.

  6. Je, a versatile suite to handle multiplexed NGS libraries with unique molecular identifiers

    OpenAIRE

    Girardot, Charles; Scholtalbers, Jelle; Sauer, Sajoscha; Su, Shu-Yi; Furlong, Eileen E.M.

    2016-01-01

    Background The yield obtained from next generation sequencers has increased almost exponentially in recent years, making sample multiplexing common practice. While barcodes (known sequences of fixed length) primarily encode the sample identity of sequenced DNA fragments, barcodes made of random sequences (Unique Molecular Identifier or UMIs) are often used to distinguish between PCR duplicates and transcript abundance in, for example, single-cell RNA sequencing (scRNA-seq). In paired-end sequ...

  7. UrQt: an efficient software for the Unsupervised Quality trimming of NGS data.

    Science.gov (United States)

    Modolo, Laurent; Lerat, Emmanuelle

    2015-04-29

    Quality control is a necessary step of any Next Generation Sequencing analysis. Although customary, this step still requires manual interventions to empirically choose tuning parameters according to various quality statistics. Moreover, current quality control procedures that provide a "good quality" data set, are not optimal and discard many informative nucleotides. To address these drawbacks, we present a new quality control method, implemented in UrQt software, for Unsupervised Quality trimming of Next Generation Sequencing reads. Our trimming procedure relies on a well-defined probabilistic framework to detect the best segmentation between two segments of unreliable nucleotides, framing a segment of informative nucleotides. Our software only requires one user-friendly parameter to define the minimal quality threshold (phred score) to consider a nucleotide to be informative, which is independent of both the experiment and the quality of the data. This procedure is implemented in C++ in an efficient and parallelized software with a low memory footprint. We tested the performances of UrQt compared to the best-known trimming programs, on seven RNA and DNA sequencing experiments and demonstrated its optimality in the resulting tradeoff between the number of trimmed nucleotides and the quality objective. By finding the best segmentation to delimit a segment of good quality nucleotides, UrQt greatly increases the number of reads and of nucleotides that can be retained for a given quality objective. UrQt source files, binary executables for different operating systems and documentation are freely available (under the GPLv3) at the following address: https://lbbe.univ-lyon1.fr/-UrQt-.html .

  8. Report on the NGS3 Working Group on Safeguards by Design For Aqueous Reprocessing Plants

    Energy Technology Data Exchange (ETDEWEB)

    Johnson, Shirley J.; Ehinger, Michael; Schanfein, Mark

    2011-02-01

    The objective of the Working Group on SBD for Aqueous Reprocessing Facilities was to provide recommendations, for facility operators and designers, which would aid in the coordination and integration of nuclear material accountancy and the safeguards requirements of all concerned parties - operators, state/regional authorities, and the IAEA. The recommendations, which are to be provided to the IAEA, are intended to assist in optimizing facility design and operating parameters to ensure the safeguardability of the facility while minimizing impact on the operations. The one day Working Group session addressed a wide range of design and operating topics.

  9. 2016 NOAA NGS Ortho-rectified Color Mosaic of Whittier, Alaska

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This data set contains ortho-rectified mosaic tiles, created as a product from the NOAA Integrated Ocean and Coastal Mapping (IOCM) initiative. The source imagery...

  10. 2017 NOAA NGS Ortho-rectified Color Mosaic of Houston Ship Channel, Texas

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This data set contains ortho-rectified mosaic tiles, created as a product from the NOAA Integrated Ocean and Coastal Mapping (IOCM) initiative. The source imagery...

  11. The CERN neutrino beam to Gran Sasso (NGS). Conceptual technical design

    Energy Technology Data Exchange (ETDEWEB)

    Elsener, K [ed.; Acquistapace, G; Baldy, J L; Ball, A E; Bonnal, P; Buhler-Broglin, M; Carminati, F; Cennini, E; Ereditato, A; Falaleev, V; Faugeras, P; Ferrari, A; Foa, L; Fortuna, G; Genand, R; Grant, A L; Henny, L; Hilaire, A; Huebner, K; Inigo-Golfin, J; Kissler, K H; Lopez-Hernandez, L A; Maugain, J M; Mayoud, M; Migliozzi, P; Missiaen, D; Palladino, V; Papadopoulos, I M; Peraire, S; Pietropaolo, F; Rangod, S; Revol, J P; Roche, J; Sala, P; Sanelli, C; Stevenson, G R; Tomat, B; Tsesmelis, E; Valbuena, R; Vincke, H; Weisse, E; Wilhelmsson, M

    1998-05-19

    The conceptual design of a new neutrino facility at CERN is presented. Starting with 400 GeV/c protons from the Super Proton Synchrotron (SPS), a neutrino beam is produced which is directed towards the underground Gran Sasso Laboratory in Italy, 732 km away from CERN, where large, complex detectors will allow long-baseline experiments searching for neutrino oscillation phenomena to be performed. (orig.)

  12. 2016 NOAA NGS Ortho-rectified Mean High Water Color Mosaic of Venice Inlet ICW, Florida

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This data set contains ortho-rectified mosaic tiles, created as a product from the NOAA Integrated Ocean and Coastal Mapping (IOCM) initiative. The source imagery...

  13. 2016 NOAA NGS Topobathy Lidar DEM: Florida Keys Outer Reef Block 03

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — These data were collected by the National Oceanic Atmospheric Administration National Geodetic Survey Remote Sensing Division using a Riegl VQ820G system. The data...

  14. Improvements to the annunciation and display systems at Gentilly 2 NGS - An integrated approach

    International Nuclear Information System (INIS)

    Dufresne, R.; Desaulniers, M.

    1997-01-01

    Since 1990, Gentilly 2 Nuclear Generating Station has revised its overall strategy during upsets and abnormal events and has also completely revised its Emergency Operating Procedures (EOP), its abnormal General Operating Procedures (GOP) and is near completing the revision of its Operating Manuals (OM). This strategy, these new EOPs, abnormal GOPs and the abnormal OMs were validated on our full scale simulator when applicable by a multidisciplinary team composed of authorized staff, technical and safety specialists and also candidates in training for authorization. We have identified significant weakness in the annunciation and display systems impairing the management of these events. To benefit from CANDU Owner's Group (COG) expertise, we met in some occasions the CRNL's research team on CAMLS project (CANDU Annunciation Message List System). In order to have more immediate benefits, we chose to improve the actual annunciation and display systems using, in some cases, ideas and/or principles used in the prototype CAMLS. After a brief history, we will present the global approach used at Gentilly 2 for upset and event management and, we will therefore describe in more detail each of the improvements on annunciation and display systems which contributed to reinforce this global approach. Hereafter are some of these improvements: prioritization via color coding of window alarms, re-prioritization (major/minor) of all CRT alarms, coalescence of multi-channel analog and contact CRT alarms, increase in the amount of trends and bar charts for upset management, special alarm summary functions (contextual) for startup after a trip. We did also identify certain needs which are not yet fulfilled with the actual improved system. Finally we will describe some other proposed improvements to the annunciation and display systems that we foresee in the near future. (author). 3 refs, figs

  15. Steam generator waterlancing at Darlington NGS (system development and field application)

    International Nuclear Information System (INIS)

    Seppala, D.; Malaugh, J.; Kiisel, E.; Kamler, F.

    1996-01-01

    From the initial steam generator (SG) inspections at Darlington Nuclear Generating Station (DNGS), the authors know that the sludge accumulations on the secondary side tubesheets have been minimal. DNGS is a fairly new station but the experience at the older Ontario Hydro plants have shown that significant accumulations will happen. A pro-active strategy has been adopted for maintaining SGs that will minimize corrosion product accumulation and the potential for component degradation. During the four year planned Unit maintenance outages, SGs will be inspected and waterlanced using a waterlance system designed and built by Babcock and Wilcox International. This automated state-of-the-art system also allows fully recorded inspections of the tubesheet/first half-lattice supports. Some of the key elements covered include results of the initial field application (May, 1995), system development and design, system qualification, cleaning performance, and lessons learned for future outages

  16. An integrated strategy combining DNA walking and NGS to detect GMOs.

    Science.gov (United States)

    Fraiture, Marie-Alice; Herman, Philippe; Papazova, Nina; De Loose, Marc; Deforce, Dieter; Ruttink, Tom; Roosens, Nancy H

    2017-10-01

    Recently, we developed a DNA walking system for the detection and characterization of a broad spectrum of GMOs in routine analysis of food/feed matrices. Here, we present a new version with improved throughput and sensitivity by coupling the DNA walking system to Pacific Bioscience® Next-generation sequencing technology. The performance of the new strategy was thoroughly assessed through several assays. First, we tested its detection and identification capability on grains with high or low GMO content. Second, the potential impacts of food processing were investigated using rice noodle samples. Finally, GMO mixtures and a real-life sample were analyzed to illustrate the applicability of the proposed strategy in routine GMO analysis. In all tested samples, the presence of multiple GMOs was unambiguously proven by the characterization of transgene flanking regions and the combinations of elements that are typical for transgene constructs. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

  17. 2016 NOAA NGS Ortho-rectified Color Mosaic of Baton Rouge, Louisiana

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This data set contains ortho-rectified mosaic tiles, created as a product from the NOAA Integrated Ocean and Coastal Mapping (IOCM) initiative. The source imagery...

  18. Feasibility of a tracer gas technique for containment leakage characterization at Bruce NGS

    International Nuclear Information System (INIS)

    Singh, V.P.

    1985-11-01

    Methods for tracer gas test have been conceived and are proposed for use in conjunction with other techniques used during off-power pressurization tests. During pressurization tests is appears possible to quantify leaks through containment boundaries which make up one of the walls in adjacent rooms but quantification of leaks to open areas will require further development. Several gases may be used as tracers during pressurization tests but the preferred tracer gas is sulphur hexafluoride (SF 6 ) at an in-vault concentration of 100 μL/L if open area sampling is to be carried out of 10 μL/L if only closed room sampling is to be performed. Large values of the ratio (tracer gas concentration in containment/lower detection limit) are necessary for identification of leak sites in open areas having significant ventilation flow. It is recommended that in-station trials be carried out to test the validity of this technique. In addition, a tracer gas technique for use during on-power operation is also proposed but leak site identification and quantification during on-power tests is only possible for containment boundaries which make up the wall(s) of adjacent rooms. The use of SF 6 is required for tests conducted during on-power operation. The recommended in-vault concentration is 10 μL/L. Recommendations are made for future work, including leak tests during on-power operation

  19. Experience gained in the production of licensable safety-critical software for Darlington NGS

    International Nuclear Information System (INIS)

    Crane, R.H.

    1992-01-01

    The Darlington Nuclear Generating Station is a new station, consisting of four 935 Mw units, built by Ontario Hydro, on the north shore of Lake Ontario, approximately 50 miles east of Toronto. In May, 1987, the first of the four units of this station was approaching the point where Ontario Hydro would be requesting a license to load fuel, and then proceed to first criticality. At this point, however, the regulatory authority, the Atomic Energy Control Board (AECB) started to show increasing concerns related to the Trip Computer Software associated with Darlington's newly-designed computerized shutdown systems. The concerns centered around whether or not the safety reliability, reviewability, and maintainability of this software could be demonstrated by Ontario Hydro or the system designer, Atomic Energy of Canada Limited (AECL). In order to back up the validity of their concerns, they hired a well-known consultant, who reviewed the code, and made recommendations concerning its design, implementation, and documentation. Considerable effort was required by Ontario Hydro and AECL in order to comply with those recommendations. This paper describes those efforts, outlines the difficulties encountered, and assesses the lessons learned from them

  20. Airborne Gravity: NGS' Gravity Data for EN02 (2011-2012)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Airborne gravity data for New York, Pennsylvania, Ohio, Michigan, Canada and Lake Erie collected in 2011 and 2012 over 3 surveys. This data set is part of the...

  1. 2008 NOAA/NGS Integrated Ocean and Coastal Mapping (IOCM) LIDAR: Kenai Peninsula Alaska

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — These data were collected by the National Oceanic Atmospheric Administration National Geodetic Survey Remote Sensing Division using an OPTECH ALTM system. The data...

  2. AECB staff annual report of Bruce A NGS for the year 1991

    International Nuclear Information System (INIS)

    1992-11-01

    In this report on Bruce A operations during 1991, AECB staff itemizes non-compliances with the operating licence. Non of the violations that occurred at Bruce A resulted in any significant threat to public safety or well-being. There were no exposures of workers to radiation in excess of the regulatory requirements; however, there have been instances of uncontrolled contaminated areas and spread of contamination in the station. Releases of radioactive material to the environment were much below target. The performance of the four special safety systems has been good, with the exception of shutdown system number two on Unit 3. A review of significant event reports and their causes has revealed an apparent lack of a system by which operations and maintenance work is verified as having been carried out correctly. There is a large backlog of maintenance work. Initiatives have been taken to correct this problem. Two important safety issues are discussed in detail. These are the chronic problem of leaking boiler tubes, and the potentially serious problem of fret marks on pressure tubes caused by abnormal fuel support. (Author)

  3. 2016 NOAA NGS Ortho-rectified Color Mosaic of Kenai and Nikiski, Alaska

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This data set contains ortho-rectified mosaic tiles, created as a product from the NOAA Integrated Ocean and Coastal Mapping (IOCM) initiative. The source imagery...

  4. 2016 NOAA NGS Ortho-rectified Color Mosaic of Cleveland, Ohio

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This data set contains ortho-rectified mosaic tiles, created as a product from the NOAA Integrated Ocean and Coastal Mapping (IOCM) initiative. The source imagery...

  5. 2015 NOAA NGS Ortho-rectified Near-Infrared Mosaic of Port Canaveral, Florida

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This data set contains ortho-rectified mosaic tiles, created as a product from the NOAA Integrated Ocean and Coastal Mapping (IOCM) initiative. The source imagery...

  6. AECB staff annual report of Point Lepreau NGS for the year 1991

    International Nuclear Information System (INIS)

    1992-11-01

    This report is the Atomic Energy Control Board (AECB) assessment of the operation of Point Lepreau nuclear generating station during 1991. On-site project officers and Ottawa-based specialists monitored the plant throughout the year. The AECB believes that New Brunswick Power is operating the reactor safely and in accordance with its operating licence. New Brunswick Power have made good progress with changes to make sure the special safety systems are operated to the highest possible standards. NB Power's financial restraints have not affected safe operation of the reactor; however, limited resources and an ambitious program of support for the first Romanian reactor could affect future operation

  7. The CERN neutrino beam to Gran Sasso (NGS). Conceptual technical design

    International Nuclear Information System (INIS)

    Elsener, K.; Acquistapace, G.; Baldy, J.L.; Ball, A.E.; Bonnal, P.; Buhler-Broglin, M.; Carminati, F.; Cennini, E.; Ereditato, A.; Falaleev, V.; Faugeras, P.; Ferrari, A.; Foa, L.; Fortuna, G.; Genand, R.; Grant, A.L.; Henny, L.; Hilaire, A.; Huebner, K.; Inigo-Golfin, J.; Kissler, K.H.; Lopez-Hernandez, L.A.; Maugain, J.M.; Mayoud, M.; Migliozzi, P.; Missiaen, D.; Palladino, V.; Papadopoulos, I.M.; Peraire, S.; Pietropaolo, F.; Rangod, S.; Revol, J.P.; Roche, J.; Sala, P.; Sanelli, C.; Stevenson, G.R.; Tomat, B.; Tsesmelis, E.; Valbuena, R.; Vincke, H.; Weisse, E.; Wilhelmsson, M.

    1998-01-01

    The conceptual design of a new neutrino facility at CERN is presented. Starting with 400 GeV/c protons from the Super Proton Synchrotron (SPS), a neutrino beam is produced which is directed towards the underground Gran Sasso Laboratory in Italy, 732 km away from CERN, where large, complex detectors will allow long-baseline experiments searching for neutrino oscillation phenomena to be performed. (orig.)

  8. KinLinks: Software Toolkit for Kinship Analysis and Pedigree Generation from NGS Datasets

    Science.gov (United States)

    2015-04-21

    combined into multi-generation 2 pedigrees via a set of heuristics to resolve relationship type (half siblings vs avuncular vs grandparent...this metric is able to differentiate parent- child relationships from siblings . • Kinship Coefficient as calculated by the KING algorithm [22]. The...second classifier predicts the exact relationship among a pair of samples (i.e. parent/ child , sibling , grandparent, avuncular, cousin, unrelated). Both

  9. Mining and Development of Novel SSR Markers Using Next Generation Sequencing (NGS Data in Plants

    Directory of Open Access Journals (Sweden)

    Sima Taheri

    2018-02-01

    Full Text Available Microsatellites, or simple sequence repeats (SSRs, are one of the most informative and multi-purpose genetic markers exploited in plant functional genomics. However, the discovery of SSRs and development using traditional methods are laborious, time-consuming, and costly. Recently, the availability of high-throughput sequencing technologies has enabled researchers to identify a substantial number of microsatellites at less cost and effort than traditional approaches. Illumina is a noteworthy transcriptome sequencing technology that is currently used in SSR marker development. Although 454 pyrosequencing datasets can be used for SSR development, this type of sequencing is no longer supported. This review aims to present an overview of the next generation sequencing, with a focus on the efficient use of de novo transcriptome sequencing (RNA-Seq and related tools for mining and development of microsatellites in plants.

  10. Spent fuel bundle counter sequence error manual - RAPPS (200 MW) NGS

    International Nuclear Information System (INIS)

    Nicholson, L.E.

    1992-01-01

    The Spent Fuel Bundle Counter (SFBC) is used to count the number and type of spent fuel transfers that occur into or out of controlled areas at CANDU reactor sites. However if the transfers are executed in a non-standard manner or the SFBC is malfunctioning, the transfers are recorded as sequence errors. Each sequence error message typically contains adequate information to determine the cause of the message. This manual provides a guide to interpret the various sequence error messages that can occur and suggests probable cause or causes of the sequence errors. Each likely sequence error is presented on a 'card' in Appendix A. Note that it would be impractical to generate a sequence error card file with entries for all possible combinations of faults. Therefore the card file contains sequences with only one fault at a time. Some exceptions have been included however where experience has indicated that several faults can occur simultaneously

  11. Spent fuel bundle counter sequence error manual - KANUPP (125 MW) NGS

    International Nuclear Information System (INIS)

    Nicholson, L.E.

    1992-01-01

    The Spent Fuel Bundle Counter (SFBC) is used to count the number and type of spent fuel transfers that occur into or out of controlled areas at CANDU reactor sites. However if the transfers are executed in a non-standard manner or the SFBC is malfunctioning, the transfers are recorded as sequence errors. Each sequence error message may contain adequate information to determine the cause of the message. This manual provides a guide to interpret the various sequence error messages that can occur and suggests probable cause or causes of the sequence errors. Each likely sequence error is presented on a 'card' in Appendix A. Note that it would be impractical to generate a sequence error card file with entries for all possible combinations of faults. Therefore the card file contains sequences with only one fault at a time. Some exceptions have been included however where experience has indicated that several faults can occur simultaneously

  12. MAAP-CANDU simulations of LOCA/LOECI accidents at Darlington NGS

    International Nuclear Information System (INIS)

    Kwee, M.T.; Choi, M.H.; Leung, R.K.

    1996-01-01

    Severe accidents have been the subject of a great deal of analysis and research, particularly in the light water reactor community. Although severe accident analysis in Canada deuterium-uranium (CANDU) reactors has not been published abundantly, a significant body of research and analysis has been accumulated. This has occurred because CANDU has directly taken into consideration a set of severe accidents [e.g loss-of-coolant accidents (LOCAs) coincident with a loss-of-emergency-coolant injection (LOECI)] in the design basis. These accidents have served to define the design requirements that ensure the integrity of the heat transport system. The CANDU reactor design has inherent heat sinks such as the primary heat transport system, the secondary side, moderator system, and shielding system (shield tank and end shields). These heat sinks are significant and are able to moderate or terminate the progression of severe accidents that go beyond the design base cases. These types of accidents are typically analyzed at Ontario Hydro in conjunction with probabilistic safety analysis (PSA), where the severe accident consequences are analyzed by a series of conservative hand-calculation methods

  13. Service life evaluation of non-metallic containment seals

    International Nuclear Information System (INIS)

    Pringle, T.G.

    1994-01-01

    A Service Life Evaluation Program (SLEP) was successfully completed for expansion joint seals used in the pressure relief duct of Pickering NGS, an eight unit CANDU station. These seals are part of the containment boundary, are difficult to replace and then only during station outages which are scheduled at ten year intervals. The SLEP, consisting of an accelerated aging program and a qualification test, was undertaken to determine the service life of the seals such that they would be capable of remaining functional following a combination of service life, a design basis accident and a subsequent seismic event. The Arrhenius model of aging was used for the accelerated aging program. Samples of seal material were subjected to oven aging at five temperatures, 150, 160, 170, 180 and 190 deg C. Tensile properties and hardness were measured at various aging times and Arrhenius plots constructed. Based on changes in elongation, activation energies of 1.2 eV and 1.1 eV were calculated for the reinforcing fabric and the silicone cover rubber, respectively. Hardness measurements were also taken but as expected, no precise quantitative aging relationship could be determined from material hardness. For the qualification test a representative length of seal was installed and field-spliced in a test frame built to simulate the installed configuration of the seal. It then underwent accelerated aging equivalent to the service life, followed by LOCA irradiation exposure to LOCA conditions of humidity, temperature and pressure and a design-basis seismic event. Finally, a pressure test to approximately five times design pressure was successfully performed to demonstrate the remaining margin of safety. Periodic air leakage tests indicated no deterioration in sealing performance and no physical deterioration was apparent. (author). 11 refs., 2 tabs., 8 figs

  14. Radioactive materials transportation emergency response plan

    International Nuclear Information System (INIS)

    Karmali, N.

    1987-05-01

    Ontario Hydro transports radioactive material between its nuclear facilities, Atomic Energy of Canada Limited at Chalk River Laboratories and Radiochemical Company in Kanata, on a regular basis. Ontario Hydro also occasionally transports to Whiteshell Laboratories, Hydro-Quebec and New Brunswick Electric Power Commission. Although there are stringent packaging and procedural requirements for these shipments, Ontario Hydro has developed a Radioactive Materials Transportation Emergency Response Plan in the event that there is an accident. The Transportation Emergency Response plan is based on six concepts: 1) the Province id divided into three response areas with each station (Pickering, Darlington, Bruce) having identified response areas; 2) response is activated via a toll-free number. A shift supervisor at Pickering will answer the call, determine the hazards involved from the central shipment log and provide on-line advice to the emergency worker. At the same time he will notify the nearest Ontario Hydro area office to provide initial corporate response, and will request the nearest nuclear station to provide response assistance; 3) all stations have capability in terms of trained personnel and equipment to respond to an accident; 4) all Ontario Hydro shipments are logged with Pickering NGS. Present capability is based on computerized logging with the computer located in the shift office at Pickering to allow quick access to information on the shipment; 5) there is a three tier structure for emergency public information. The local Area Manager is the first Ontario Hydro person at the scene of the accident. The responding facility technical spokesperson is the second line of Corporate presence and the Ontario Hydro Corporate spokesperson is notified in case the accident is a media event; and 6) Ontario Hydro will respond to non-Hydro shipments of radioactive materials in terms of providing assistance, guidance and capability. However, the shipper is responsible

  15. Topobathymetric model of Mobile Bay, Alabama

    Science.gov (United States)

    Danielson, Jeffrey J.; Brock, John C.; Howard, Daniel M.; Gesch, Dean B.; Bonisteel-Cormier, Jamie M.; Travers, Laurinda J.

    2013-01-01

    were made to these input data. The NGDC hydrographic, multibeam, and trackline surveys were transformed from mean low water (MLW) or mean lower low water (MLLW) to NAVD 88 using VDatum (http://vdatum.noaa.gov). VDatum is a tool developed by the National Geodetic Survey (NGS) that performs transformations among tidal, ellipsoid-based, geoid-based, and orthometric datums using calibrated hydrodynamic models. The vertical accuracy of the input topographic data varied depending on the input source. Because the input elevation data were derived primarily from lidar, the vertical accuracy ranges from 6 to 20 centimeters in root mean square error (RMSE). he horizontal datum of the Mobile Bay topobathymetric model is the North American Datum of 1983 (NAD 83), geographic coordinates. All the topographic and bathymetric datasets were originally referenced to NAD 83, and no transformations were made to the input data. The bathymetric surveys were downloaded referenced to NAD 83 geographic, and therefore no horizontal transformations were required. The topbathymetric model of Mobile Bay and detailed metadata can be obtained from the USGS Web sites: http://nationalmap.gov/.

  16. Genome-wide ENU mutagenesis in combination with high density SNP analysis and exome sequencing provides rapid identification of novel mouse models of developmental disease.

    Directory of Open Access Journals (Sweden)

    Georgina Caruana

    Full Text Available Mice harbouring gene mutations that cause phenotypic abnormalities during organogenesis are invaluable tools for linking gene function to normal development and human disorders. To generate mouse models harbouring novel alleles that are involved in organogenesis we conducted a phenotype-driven, genome-wide mutagenesis screen in mice using the mutagen N-ethyl-N-nitrosourea (ENU.ENU was injected into male C57BL/6 mice and the mutations transmitted through the germ-line. ENU-induced mutations were bred to homozygosity and G3 embryos screened at embryonic day (E 13.5 and E18.5 for abnormalities in limb and craniofacial structures, skin, blood, vasculature, lungs, gut, kidneys, ureters and gonads. From 52 pedigrees screened 15 were detected with anomalies in one or more of the structures/organs screened. Using single nucleotide polymorphism (SNP-based linkage analysis in conjunction with candidate gene or next-generation sequencing (NGS we identified novel recessive alleles for Fras1, Ift140 and Lig1.In this study we have generated mouse models in which the anomalies closely mimic those seen in human disorders. The association between novel mutant alleles and phenotypes will lead to a better understanding of gene function in normal development and establish how their dysfunction causes human anomalies and disease.

  17. A novel procedure on next generation sequencing data analysis using text mining algorithm.

    Science.gov (United States)

    Zhao, Weizhong; Chen, James J; Perkins, Roger; Wang, Yuping; Liu, Zhichao; Hong, Huixiao; Tong, Weida; Zou, Wen

    2016-05-13

    Next-generation sequencing (NGS) technologies have provided researchers with vast possibilities in various biological and biomedical research areas. Efficient data mining strategies are in high demand for large scale comparative and evolutional studies to be performed on the large amounts of data derived from NGS projects. Topic modeling is an active research field in machine learning and has been mainly used as an analytical tool to structure large textual corpora for data mining. We report a novel procedure to analyse NGS data using topic modeling. It consists of four major procedures: NGS data retrieval, preprocessing, topic modeling, and data mining using Latent Dirichlet Allocation (LDA) topic outputs. The NGS data set of the Salmonella enterica strains were used as a case study to show the workflow of this procedure. The perplexity measurement of the topic numbers and the convergence efficiencies of Gibbs sampling were calculated and discussed for achieving the best result from the proposed procedure. The output topics by LDA algorithms could be treated as features of Salmonella strains to accurately describe the genetic diversity of fliC gene in various serotypes. The results of a two-way hierarchical clustering and data matrix analysis on LDA-derived matrices successfully classified Salmonella serotypes based on the NGS data. The implementation of topic modeling in NGS data analysis procedure provides a new way to elucidate genetic information from NGS data, and identify the gene-phenotype relationships and biomarkers, especially in the era of biological and medical big data. The implementation of topic modeling in NGS data analysis provides a new way to elucidate genetic information from NGS data, and identify the gene-phenotype relationships and biomarkers, especially in the era of biological and medical big data.

  18. Modelling Practice

    DEFF Research Database (Denmark)

    Cameron, Ian; Gani, Rafiqul

    2011-01-01

    This chapter deals with the practicalities of building, testing, deploying and maintaining models. It gives specific advice for each phase of the modelling cycle. To do this, a modelling framework is introduced which covers: problem and model definition; model conceptualization; model data...... requirements; model construction; model solution; model verification; model validation and finally model deployment and maintenance. Within the adopted methodology, each step is discussedthrough the consideration of key issues and questions relevant to the modelling activity. Practical advice, based on many...

  19. Leadership Models.

    Science.gov (United States)

    Freeman, Thomas J.

    This paper discusses six different models of organizational structure and leadership, including the scalar chain or pyramid model, the continuum model, the grid model, the linking pin model, the contingency model, and the circle or democratic model. Each model is examined in a separate section that describes the model and its development, lists…

  20. Models and role models.

    Science.gov (United States)

    ten Cate, Jacob M

    2015-01-01

    Developing experimental models to understand dental caries has been the theme in our research group. Our first, the pH-cycling model, was developed to investigate the chemical reactions in enamel or dentine, which lead to dental caries. It aimed to leverage our understanding of the fluoride mode of action and was also utilized for the formulation of oral care products. In addition, we made use of intra-oral (in situ) models to study other features of the oral environment that drive the de/remineralization balance in individual patients. This model addressed basic questions, such as how enamel and dentine are affected by challenges in the oral cavity, as well as practical issues related to fluoride toothpaste efficacy. The observation that perhaps fluoride is not sufficiently potent to reduce dental caries in the present-day society triggered us to expand our knowledge in the bacterial aetiology of dental caries. For this we developed the Amsterdam Active Attachment biofilm model. Different from studies on planktonic ('single') bacteria, this biofilm model captures bacteria in a habitat similar to dental plaque. With data from the combination of these models, it should be possible to study separate processes which together may lead to dental caries. Also products and novel agents could be evaluated that interfere with either of the processes. Having these separate models in place, a suggestion is made to design computer models to encompass the available information. Models but also role models are of the utmost importance in bringing and guiding research and researchers. 2015 S. Karger AG, Basel