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)

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

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)

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)

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

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.

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

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

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...

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...

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.)

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.

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.

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.

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.

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.

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

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)

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)

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.

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.

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)

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

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...

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.

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)

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

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

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.

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

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.

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)

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...

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.

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.

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

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.

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.

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.

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

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...

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.

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

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.

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.

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.

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.

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.

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

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...

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.

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.

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...

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.

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

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

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

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)

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

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.

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.

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.

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 ...

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.

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.

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.

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

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.

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

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

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.

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

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.

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

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.

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

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.

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.

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

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

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

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

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...

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...

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.

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.)

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.

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.

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

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.

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.

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.

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)

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)

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.

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...

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.

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)

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.

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.

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.

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 ...

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.

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.)

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...

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.

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

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...

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.

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)

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.

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.

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.

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.

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

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.

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)

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)

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

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.

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

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)

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

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.

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.

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

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.

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

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.

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.

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...

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

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.

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.

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.

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

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)

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.

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.

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)

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

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.

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

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.

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.

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

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.

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.

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

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...

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.

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)

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.

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.

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.

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.

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...

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.

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)

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.

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

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.

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.

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...

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.

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).

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).

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

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.

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

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....

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

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.

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

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

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.

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.

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.

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.

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...

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

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)

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.

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

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.

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.

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.)

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

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.

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

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 ...

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.

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)

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.

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

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)

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 D_Cs 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 D_Cs 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.

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

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

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.

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.

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

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...

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

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.

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.

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

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

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

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.

Detection of pressure tube leaks relying on moisture beetles only

International Nuclear Information System (INIS)

Kenchington, J.M.; Choi, A.; Jin, Y.

2004-01-01

A major decision was made for Pickering NGS A Annulus Gas System (ACS) that detection of a pressure tube (PT) leak should be achieved by using only moisture beetles and that dew point monitors would provide 'early warning' without status to shut down the reactor. Experience with Unit 3 has shown that dew point monitoring of pressure tube leaks was particularly subject to gas leaks and surface adsorption effects. Unit 4 was the first one to be converted during the full scale pressure tube replacement programme. Because of the fundamental change in design philosophy, moisture injection tests were carried out during commissioning to demonstrate that performance matched design. In particular it was necessary to show that leak before break (LBB) would be achieved if a leak occurred in the limiting string. Units 1 and 3 have since been converted. No decision has been taken to convert Pickering B units as gas leaks are small and no significant adsorption effects are anticipated. Hence dew point monitoring will not be impaired. (author)

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

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.

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)

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.

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.

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

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...

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

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.

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.

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.

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

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

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

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.

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.

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.

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.

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.

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.

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.

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.

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)

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)

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

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)

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 ...

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)

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.

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...

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)

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.

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.

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.

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.)

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

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.

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)

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.

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.

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

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.

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.

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%

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.

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.

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.

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

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.

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.

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.

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.

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.)

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.

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.

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.

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

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

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

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%.

Maintenance of ageing CANDU reactors. A regulatory perspective

International Nuclear Information System (INIS)

Dunstan, T.

1996-01-01

The subject of this paper is, 'requirements for maintenance of ageing reactors from the perspective of a regulator', with a focus on the particular theme of; 'continuing safety assurance'. A major role of maintenance is to ensure the continuing reliability and effectiveness of safety related systems and equipment. Continuing safety assurance is an issue the Atomic Energy Control Board has been wrestling with for some time. From my perspective, much remains to be done before the AECB can be confident that Canadian nuclear plants have the necessary programs in place to achieve continuing safety assurance. To introduce the topic, it would be appropriate to say a few words about the AECB's position with respect to the situation at the Pickering NGS. Why did we blow the whistle last August and, what are we doing about it? (author)

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.

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.

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.

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

A comparison of LOCA analysis using SMOKIN and CERBERUS codes

Energy Technology Data Exchange (ETDEWEB)

Younis, M H [Atomic Energy of Canada Ltd., Mississauga, ON (Canada); Gaboury, G [Ontario Hydro, Toronto, ON (Canada)

1996-12-31

This paper presents the results of a comparison of the analyses of a postulated Loss of Coolant Accident (LOCA) in Pickering NGS A reactors using the two neutron kinetics codes SMOKIN and CERBERUS. Both codes have been used to simulate the space-time neutronic behaviour of CANDU-PHWR reactors. The main objective of the present study is to evaluate the accuracy with which SMOKIN can predict power transients compared to CERBERUS. The comparison shows that the two codes produce similar bulk power and reactivity transients. However, SMOKIN was found to overestimate the power transient (relative to CERBERUS) in some regions of the core, which is indicative of the spatial differences between the two codes. It was demonstrated that part of this overestimate is due to the use of reaction-rate averaged fuel properties in SMOKIN, compared to instantaneous fuel properties in CERBERUS. (author). 5 refs., 3 tabs., 6 figs.

Assessment of the impact of fueling machine failure on the safety of the CANDU-PHWR

International Nuclear Information System (INIS)

Al-Kusayer, T.A.

1982-01-01

A survey of possible LOCA (Loss-of-Coolant Accident) initiating events that might take place for CANDU-PHWRs (Canadian Deuterium Uranium-Pressurized Heavy Water Reactors) has been conducted covering both direct and indirect initiators. Among the 22 initiating events that were surveyed in this study, four direct initiators have been selected and analyzed briefly. Those selected were a pump suction piping break, an isolation valve piping break, a bleed valve failure, and a fueling machine interface failure. These were selected as examples of failures that could take place in the inlet side, outlet side, or PHTS (Primary Heat Transport System) interfaces. The Pickering NGS (Unit-A) was used for this case study. Double failure (failure of the protective devices to operate when the process equipment fault occurs) and a triple failure (failure of the protective devices and the ECCS as well as the process equipment) were found to be highly improbable

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

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.

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...

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

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

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.

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.

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

Development of the environmental qualification safety requirement matrix for the containment system of in-service CANDU reactors

International Nuclear Information System (INIS)

Chun, R.M.; Low, J.; Sobolewski, J.

1994-01-01

Over the last several years, Ontario Hydro Nuclear (OHN) has placed increasing emphasis on environmental qualification (EQ) at its Pickering and Bruce NGS A and B nuclear generating stations (NGSs). The program currently underway (at the time of the conference) builds upon the experience gained from the extensive Darlington NGS EQ experience and from EQ programs conducted by other utilities. Some of the major steps of the OHN EQ program include: defining Safety Requirement Matrices (SRMs), establishing environmental conditions, developing an EQ List, conducting an EQ Assessment and maintaining Operational EQ Assurance during the plant life. The SRM identifies safety related components, their required safety functions and their mission times for each postulated design basis accident (DBA). This is a critical step, as the SRM defines the equipment that requires assurance of EQ and precise requirements must be provided to ensure a cost effective EQ program. This paper describes the development of the SRMs for the containment system of the Bruce stations. The introductory section briefly discusses how the industry has dealt with equipment qualification as it has evolved and the role of the SRMs in the OHN EQ Program. In Section 2, the preparation of the SRM is described along with the applicable ground rules used. The results of the application of the SRM preparation guidelines to the containment system are discussed in Section 3. A summary of the major findings and conclusions is presented. 3 refs., 3 figs

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.

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.

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

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

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.

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

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.

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.

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)

Physical degradation assessment of generator station cables

International Nuclear Information System (INIS)

Stonkus, D.J.

1988-01-01

Preliminary studies of fossil-fired and nuclear generator station cables indicate that the low voltage PVC insulated cables are in relatively good condition. The insulation is flexible and in the case of nuclear cables can withstand a design basis event after nearly 15 years of service. Cables insulated with styrene butadiene rubber have been found embrittled and cables insulated with SBR should be closely inspected in any plant assurance program. Thermal analysis using oxidative induction technique shows promise to indicate cable insulation degradation. Long term reliability assurance and plant life extension studies are being actively pursued at Ontario Hydro. A major study is currently underway to extend the life of the oldest operating fossil-fuel station, the 8-unit, 2400 MW Lakeview TGS in operation since the 1960s. Plant life assurance programs have been initiated at the 2000 MW Lambton TGS in operation since 1969, and for the oldest operating nuclear plant, Pickering NGS A in operation since the early 1970s. As cables are considered one of the critical components in a generator station due to the extreme difficulty and cost of cable replacement, test programs have been initiated to evaluate the physical degradation of the cables and relate the results to electrical diagnostic tests and to chemical changes. The decommissioning of two small nuclear stations, the 20 MW Nuclear Power Demonstration (NPD) and the 200 MW Douglas Point NGS, which were placed in service in 1962 and 1967 respectively, will provide an opportunity to perform destructive electrical and physical evaluation on field aged cables

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.

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.

ANALISIS PERMUKIMAN PEMULUNG SEBAGAI SEBUAH ASSEMBLAGE STUDI KASUS: PERMUKIMAN PEMULUNG DI WILAYAH JURANGMANGU, TANGERANG SELATAN

Directory of Open Access Journals (Sweden)

Eka Permanasari

2017-01-01

There are some research on social and economical condition of informal waste-picker settlements. However, the research on the urban assemblage of informal waste-picker settlements are not very common. Therefore, this research focus on how the social and economical condition shape the informal waste-picker settlements in terms of urban assemblage.   This research investigates the development and transformation of the informal waste-picker settlements in two prime locations in Jurangmangu, South Tangerang. The methods are through observation and interview to key persons (leaders on each settlement. The urban assemblage on these waste-picker settlements is heavily influenced by social and economical condition and activity of their users.   Key words: waste picker settlements, urban assemblage, informality

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

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

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.

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.

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.

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.

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.

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

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.

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.

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

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

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.

PhasePApy: A robust pure Python package for automatic identification of seismic phases

Science.gov (United States)

Chen, Chen; Holland, Austin

2016-01-01

We developed a Python phase identification package: the PhasePApy for earthquake data processing and near‐real‐time monitoring. The package takes advantage of the growing number of Python libraries including Obspy. All the data formats supported by Obspy can be supported within the PhasePApy. The PhasePApy has two subpackages: the PhasePicker and the Associator, aiming to identify phase arrival onsets and associate them to phase types, respectively. The PhasePicker and the Associator can work jointly or separately. Three autopickers are implemented in the PhasePicker subpackage: the frequency‐band picker, the Akaike information criteria function derivative picker, and the kurtosis picker. All three autopickers identify picks with the same processing methods but different characteristic functions. The PhasePicker triggers the pick with a dynamic threshold and can declare a pick with false‐pick filtering. Also, the PhasePicker identifies a pick polarity and uncertainty for further seismological analysis, such as focal mechanism determination. Two associators are included in the Associator subpackage: the 1D Associator and 3D Associator, which assign phase types to picks that can best fit potential earthquakes by minimizing root mean square (rms) residuals of the misfits in distance and time, respectively. The Associator processes multiple picks from all channels at a seismic station and aggregates them to increase computational efficiencies. Both associators use travel‐time look up tables to determine the best estimation of the earthquake location and evaluate the phase type for picks. The PhasePApy package has been used extensively for local and regional earthquakes and can work for active source experiments as well.

Secure and robust cloud computing for high-throughput forensic microsatellite sequence analysis and databasing.

Science.gov (United States)

Bailey, Sarah F; Scheible, Melissa K; Williams, Christopher; Silva, Deborah S B S; Hoggan, Marina; Eichman, Christopher; Faith, Seth A

2017-11-01

Next-generation Sequencing (NGS) is a rapidly evolving technology with demonstrated benefits for forensic genetic applications, and the strategies to analyze and manage the massive NGS datasets are currently in development. Here, the computing, data storage, connectivity, and security resources of the Cloud were evaluated as a model for forensic laboratory systems that produce NGS data. A complete front-to-end Cloud system was developed to upload, process, and interpret raw NGS data using a web browser dashboard. The system was extensible, demonstrating analysis capabilities of autosomal and Y-STRs from a variety of NGS instrumentation (Illumina MiniSeq and MiSeq, and Oxford Nanopore MinION). NGS data for STRs were concordant with standard reference materials previously characterized with capillary electrophoresis and Sanger sequencing. The computing power of the Cloud was implemented with on-demand auto-scaling to allow multiple file analysis in tandem. The system was designed to store resulting data in a relational database, amenable to downstream sample interpretations and databasing applications following the most recent guidelines in nomenclature for sequenced alleles. Lastly, a multi-layered Cloud security architecture was tested and showed that industry standards for securing data and computing resources were readily applied to the NGS system without disadvantageous effects for bioinformatic analysis, connectivity or data storage/retrieval. The results of this study demonstrate the feasibility of using Cloud-based systems for secured NGS data analysis, storage, databasing, and multi-user distributed connectivity. Copyright © 2017 Elsevier B.V. All rights reserved.

Quantitative farm-to-fork human norovirus exposure assessment of individually quick frozen raspberries and raspberry puree.

Science.gov (United States)

Jacxsens, L; Stals, A; De Keuckelaere, A; Deliens, B; Rajkovic, A; Uyttendaele, M

2017-02-02

A quantitative human norovirus (NoV) exposure model describing transmission of NoV during pre-harvest, harvest and further processing of soft red fruits exemplified by raspberries is presented. The outcomes of the model demonstrate the presence of NoV in raspberry puree or individual quick frozen (IQF) raspberry fruits and were generated by Monte Carlo simulations by combining GoldSim® and @Risk® software. Input data were collected from scientific literature, observational studies and assumptions. NoV contamination of soft red fruits is assumed to take place at farms by application of contaminated water for pesticides dilution or by berries' pickers shedding NoV. The model was built simulating that a collection center received berries from ten farms with a total of 245 food handlers picking soft red fruits during a 10-hour day shift. Given 0, 5 and 20 out of 245 berries' pickers were shedding NoV, these conditions were calculated to result in a mean NoV contamination of respectively 0.47, 14.1 and 36.2 NoV particles per kg raspberries in case all raspberries are mixed to one day-batch of 11tons. The NoV contamination of the fruits was mainly driven by the route of NoV shedding food pickers (95.8%) rather than by spraying contaminated pesticide water (4.2%) (baseline scenario with 5 shedding pickers and contaminated pesticide water). Inclusion of appropriate hand washing procedures or hand washing followed by hand disinfection resulted in estimated reductions of the mean NoV levels from 14.1 to 0.16 and 0.17 NoV particles per kg raspberries, respectively, for the baseline scenario with 5 out of 245 food pickers shedding NoV. The use of a mild heat treatment (30s at 75°C) during further processing of berries to purees was noted to reduce mean NoV levels substantially from 14.1 to 0.2 NoV particles per kg raspberry puree. For IQF raspberries, the NoV contamination is heterogeneously distributed and resulted in a mean contamination of 3.1 NoV particles per 250g

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.

Structural social capital and local-level forest governance: Do they inter-relate? A mushroom permit case in Catalonia.

Science.gov (United States)

Gorriz-Mifsud, Elena; Secco, Laura; Da Re, Riccardo; Pisani, Elena; Bonet, José Antonio

2017-03-01

In diffuse forest uses, like non-timber forest products' harvesting, the behavioural alignment of pickers is crucial for avoiding a "tragedy of the commons". Moreover, the introduction of policy tools such as a harvest permit system may help in keeping the activity under control. Besides the official enforcement, pickers' engagement may also derive from the perceived legitimate decision of forest managers and the community pressure to behave according to the shared values. Framed within the social capital theory, this paper examines three types of relations of rural communities in a protected area in Catalonia (Spain) where a system of mushroom picking permits was recently introduced. Through social network analysis, we explore structural changes in relations within the policy network across the policy conception, design and implementation phases. We then test whether social links of the pickers' community relate to influential members of the policy network. Lastly, we assess whether pickers' bonding and bridging structures affect the rate of permit uptake. Our results show that the high degree of acceptance could be explained by an adequate consideration of pickers' preferences within the decision-making group: local pickers show proximity to members of the policy network with medium-high influence during the three policy phases. The policy network also evolves, with some members emerging as key actors during certain phases. Significant differences are found in pickers' relations among and across the involved municipalities following an urban-rural gradient. A preliminary relation is found between social structures and differential pickers' engagement. These results illustrate a case of positive social capital backing policy design and, probably, also implementation. This calls for a meticulous design of forest policy networks with respect to communities of affected forest users. Copyright © 2016 Elsevier Ltd. All rights reserved.

Annual report 1991

International Nuclear Information System (INIS)

1992-01-01

During 1991 Ontario Hydro's activities reflected a company in transition marked by changing customer needs, new social demands and global economic pressures. The nuclear system performed below expectations, although performance improved over 1990. Technical problems prevented the utility from bringing Darlington NGS unit 1 into service. Ontario Hydro has committed about $4 billion to extend the lives of fossil and hydroelectric stations and restore nuclear performance. In September Ontario Hydro's management structure was reorganized again. Policy, planning and strategic efforts were put under the direction of the Chair. All operating functions were to report directly to the President. New Board committees were formed to guide environmental activities and promote a better understanding of aboriginal and northern affairs. The unfavourable economic and operating conditions of 1991 affected financial performance. An 11.8% rate increase was announced for 1992. Electricity demand increased by 1.3%over 1990 to 139.1 million megawatt hours. Major capital additions have been deferred by at least seven years. Uranium contracts were canceled with Rio Algom and Denison Mines. Administrative and support budgets were cut, and executive salaries frozen. A number of quality improvement programs have been implemented with the cooperation of labour groups, reducing the amount of time needed for the retubing of the Pickering-4 reactor. (L.L.)

Pollux: Enhancing the Quality of Service of the Global Information Grid (GIG)

Science.gov (United States)

2009-06-01

and throughput of standard-based and/or COTS-based QoS-enabled pub/sub technologies, including DDS, JMS, Web Services, and CORBA. 2. The DDS QoS...of ser- vice pICKER (QUICKER) model-driven engineering ( MDE ) toolchain shown in Figure 8. QUICKER extends the Platform-Independent Component Modeling

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

The case for new nuclear

International Nuclear Information System (INIS)

Luxat, J.C.

2013-01-01

Over a 22 year period from 1971 to 1993 a total of 20 reactor units were brought into service - an average of approximately one unit per year. Ontario Hydro constructed the four-unit Pickering A station, four units at Bruce A, four units at Pickering B, four units at Bruce B and four units at Darlington during this period. This represents a capacity of nearly 14,000 MW, as shown in Figure 1. During this period there was a large increase in industrial capacity in Ontario, particularly in manufacturing, driven in large measure by the incentives offered by low electricity prices, skilled workers and a good health care system. Subsequently in the mid-1990's the Pickering A and Bruce A units were laid up and maintenance efforts were focused on the Pickering B, Bruce B and Darlington stations. Two of the four units at Pickering A were returned to service in the early 2000's and the four units of Bruce A were returned to service with two units being refurbished. By 2010 nuclear capacity in the province had returned to 12,800 MW. The Ontario Long Term Energy Plan (LTEP) announced at the beginning of December does not include new build nuclear but does include refurbishment of the Darlington station as well as two units at Bruce A and four units at Bruce B. The six units at Pickering will be shut down by 2020. As shown in Figure 1, this will reduce the nuclear capacity from the current 12,800 MW to 8000 MW when the Pickering A and B units are removed from service in 2020 and the refurbishment of Darlington and Bruce units proceeds starting in 2016 and projected to complete by 2031. This will be the lowest nuclear generating capacity in the province since 1985. (author)

Steps to Advanced CANDU 600

International Nuclear Information System (INIS)

Oh, Yongshick; Brooks, G. L.

1988-01-01

The CANDU nuclear power system was developed from merging of AECL heavy water reactor technology with Ontario Hydro electrical power station expertise. The original four units of Ontario Hydro's Pickering Generating Station are the first full-scale commercial application of the CANDU system. AECL and Ontario Hydro then moved to the next evolutionary step, a more advanced larger scale design for four units at the Bruce Generating Station. CANDU 600 followed as a single unit nuclear electric power station design derived from an amalgam of features of the multiple unit Pickering and Bruce designs. The design of the CANDU 600 nuclear steam supply system is based on the Pickering design with improvements derived from the Bruce design. For example, most CANDU 600 auxiliary systems are based on Bruce systems, whereas the fuel handling system is based on the Pickering system. Four CANDU 600 units are in operation, and five are under construction in Romania. For the additional four units at Pickering Generating Station 'B', Ontario Hydro selected a replica of the Pickering 'A' design with limited design changes to maintain a high level of standardization across all eight units. Ontario Hydro applied a similar policy for the additional four units at Bruce Generating Station 'B'. For the four unit Darlington station, Ontario Hydro selected a design based on Bruce with improvements derived from operating experience, the CANDU 600 design and development programs

Corrosion control in CANDU nuclear power reactors

International Nuclear Information System (INIS)

Lesurf, J.E.

1974-01-01

Corrosion control in CANDU reactors which use pressurized heavy water (PHW) and boiling light water (BLW) coolants is discussed. Discussions are included on pressure tubes, primary water chemistry, fuel sheath oxidation and hydriding, and crud transport. It is noted that corrosion has not been a significant problem in CANDU nuclear power reactors which is a tribute to design, material selection, and chemistry control. This is particularly notable at the Pickering Nuclear Generating Station which will have four CANDU-PHW reactors of 540 MWe each. The net capacity factor for Pickering-I from first full power (May 1971) to March 1972 was 79.5 percent, and for Pickering II (first full power November 1971) to March 1972 was 83.5 percent. Pickering III has just reached full power operation (May 1972) and Pickering IV is still under construction. Gentilly CANDU-BLW reached full power operation in May 1972 after extensive commissioning tests at lower power levels with no major corrosion or chemistry problems appearing. Experience and operating data confirm that the value of careful attention to all aspects of corrosion control and augur well for future CANDU reactors. (U.S.)

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

Monitoring Species of Concern Using Noninvasive Genetic Sampling and Capture-Recapture Methods

Science.gov (United States)

2016-11-01

RC-201205) Monitoring Species of Concern Using Noninvasive Genetic Sampling and Capture- Recapture Methods November 2016 This document has been...From - To) Apr 25 2012-Jan 31 2016 4. TITLE AND SUBTITLE Monitoring Species of Concern Using Noninvasive Genetic Sampling and Capture- Recapture...NGS-CR) modeling to evaluate the status of species of conservation concern . A secondary objective was to demonstrate the combination of NGS with

Aligning Order Picking Methods, Incentive Systems, and Regulatory Focus to Increase Performance

NARCIS (Netherlands)

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

2016-01-01

A controlled field experiment investigates order picking performance in terms of productivity. We examined three manual picker-to-parts order picking methods (parallel, zone, and dynamic zone picking) under two different incentive systems (competition-based vs. cooperation-based) for pickers with

The Ugly Side of The Beautiful Game: The War on Hooliganism Scrutinized

DEFF Research Database (Denmark)

Joern, Lise

2013-01-01

Brett Bebber, Violence and Racism in Football: Politics and Cultural Conflict in British Society, 1968–1998, London: Pickering & Chatto 2012......Brett Bebber, Violence and Racism in Football: Politics and Cultural Conflict in British Society, 1968–1998, London: Pickering & Chatto 2012...

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.

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

Applications and challenges of next-generation sequencing in Brassica species.

Science.gov (United States)

Wei, Lijuan; Xiao, Meili; Hayward, Alice; Fu, Donghui

2013-12-01

Next-generation sequencing (NGS) produces numerous (often millions) short DNA sequence reads, typically varying between 25 and 400 bp in length, at a relatively low cost and in a short time. This revolutionary technology is being increasingly applied in whole-genome, transcriptome, epigenome and small RNA sequencing, molecular marker and gene discovery, comparative and evolutionary genomics, and association studies. The Brassica genus comprises some of the most agro-economically important crops, providing abundant vegetables, condiments, fodder, oil and medicinal products. Many Brassica species have undergone the process of polyploidization, which makes their genomes exceptionally complex and can create difficulties in genomics research. NGS injects new vigor into Brassica research, yet also faces specific challenges in the analysis of complex crop genomes and traits. In this article, we review the advantages and limitations of different NGS technologies and their applications and challenges, using Brassica as an advanced model system for agronomically important, polyploid crops. Specifically, we focus on the use of NGS for genome resequencing, transcriptome sequencing, development of single-nucleotide polymorphism markers, and identification of novel microRNAs and their targets. We present trends and advances in NGS technology in relation to Brassica crop improvement, with wide application for sophisticated genomics research into agronomically important polyploid crops.

Highly sensitive detection of ESR1 mutations in cell-free DNA from patients with metastatic breast cancer using molecular barcode sequencing.

Science.gov (United States)

Masunaga, Nanae; Kagara, Naofumi; Motooka, Daisuke; Nakamura, Shota; Miyake, Tomohiro; Tanei, Tomonori; Naoi, Yasuto; Shimoda, Masafumi; Shimazu, Kenzo; Kim, Seung Jin; Noguchi, Shinzaburo

2018-01-01

We aimed to develop a highly sensitive method to detect ESR1 mutations in cell-free DNA (cfDNA) using next-generation sequencing with molecular barcode (MB-NGS) targeting the hotspot segment (c.1600-1713). The sensitivity of MB-NGS was tested using serially diluted ESR1 mutant DNA and then cfDNA samples from 34 patients with metastatic breast cancer were analyzed with MB-NGS. The results of MB-NGS were validated in comparison with conventional NGS and droplet digital PCR (ddPCR). MB-NGS showed a higher sensitivity (0.1%) than NGS without barcode (1%) by reducing background errors. Of the cfDNA samples from 34 patients with metastatic breast cancer, NGS without barcode revealed seven mutations in six patients (17.6%) and MB-NGS revealed six additional mutations including three mutations not reported in the COSMIC database of breast cancer, resulting in total 13 ESR1 mutations in ten patients (29.4%). Regarding the three hotspot mutations, all the patients with mutations detected by MB-NGS had identical mutations detected by droplet digital PCR (ddPCR), and mutant allele frequency correlated very well between both (r = 0.850, p < 0.01). Moreover, all the patients without these mutations by MB-NGS were found to have no mutations by ddPCR. In conclusion, MB-NGS could successfully detect ESR1 mutations in cfDNA with a higher sensitivity of 0.1% than conventional NGS and was considered as clinically useful as ddPCR.

Canadian nuclear power plant construction cost forecast and analysis

International Nuclear Information System (INIS)

Keng, C.W.K.

1985-01-01

Because of the huge volume of capital required to construct a modern electric power generating station, investment decisions have to be made with as complete an understanding of the consequence of the decision as possible. This understanding must be provided by the evaluation of the situation to take place in the future. This paper attempts to use an econometric method to forecast the construction costs escalation of a standard Canadian nuclear generating station (NGS). A review of the history of Canadian nuclear electric power is provided. The major components of the construction costs of a Canadian NGS are studied and summarized. A data base is built and indexes are prepared. Based on these indexes an econometric forecasting model is constructed using an apparently new econometric methodology of forecasting modelling. Forecasts for a period of forty years are generated and applications of alternative scenario forecasts and range forecasts to uncertainty assessment are demonstrated. The indexes, the model, and the forecasts and their applications, to the best of the author's knowledge, are the very first ever done for Canadian NGS constructions

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.

Plastid: nucleotide-resolution analysis of next-generation sequencing and genomics data.

Science.gov (United States)

Dunn, Joshua G; Weissman, Jonathan S

2016-11-22

Next-generation sequencing (NGS) informs many biological questions with unprecedented depth and nucleotide resolution. These assays have created a need for analytical tools that enable users to manipulate data nucleotide-by-nucleotide robustly and easily. Furthermore, because many NGS assays encode information jointly within multiple properties of read alignments - for example, in ribosome profiling, the locations of ribosomes are jointly encoded in alignment coordinates and length - analytical tools are often required to extract the biological meaning from the alignments before analysis. Many assay-specific pipelines exist for this purpose, but there remains a need for user-friendly, generalized, nucleotide-resolution tools that are not limited to specific experimental regimes or analytical workflows. Plastid is a Python library designed specifically for nucleotide-resolution analysis of genomics and NGS data. As such, Plastid is designed to extract assay-specific information from read alignments while retaining generality and extensibility to novel NGS assays. Plastid represents NGS and other biological data as arrays of values associated with genomic or transcriptomic positions, and contains configurable tools to convert data from a variety of sources to such arrays. Plastid also includes numerous tools to manipulate even discontinuous genomic features, such as spliced transcripts, with nucleotide precision. Plastid automatically handles conversion between genomic and feature-centric coordinates, accounting for splicing and strand, freeing users of burdensome accounting. Finally, Plastid's data models use consistent and familiar biological idioms, enabling even beginners to develop sophisticated analytical workflows with minimal effort. Plastid is a versatile toolkit that has been used to analyze data from multiple NGS assays, including RNA-seq, ribosome profiling, and DMS-seq. It forms the genomic engine of our ORF annotation tool, ORF-RATER, and is readily

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

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.

Effective utilization of maintenance staff in design and implementation of major project work

International Nuclear Information System (INIS)

Wyman, D.; Dingle, J.; Brown, R.

1995-01-01

The reorganization of Pickering Nuclear Division some 2 years ago resulted in the formation of the Projects and Modifications department. This department takes an integrated approach to manage all aspects of large projects at Pickering. The integration of Design, Drafting, Procurement, Construction and Operations functions into project teams represents a fundamental change to project management at Pickering. The development of integrated teams has great potential for reducing both the time and cost associated with project implementation, while at the same time improving the quality, and maintainability of the commissioned in service project. The Pickering Rehab organization 1989-1993, established to perform the rehab / retube of Units 3 and 4 had proven that a team environment will produce effective results. The outcome was astounding, critical categories such as Safety, Quality of Work, and Timeliness, had proven the team's effectiveness. The integration of operations maintenance staff into the project work activities is still evolving, and has probably required the most adaptation to change for both the former Construction and Operations organizations. Maximizing the utilization of the maintenance staff in the design and implementation of major project work will prove to be a key to a long term operating success of these projects. This paper will focus in on the effective usage of Maintenance staff in the design and implementation phases of major project work at Pickering, and on the benefits realized using this approach. It will be divided into 5 sections as indicated. 1. Past Project Shortfalls. 2. Benefits of the inclusion of Maintenance staff in the Calandria Vault Rehab Project. 3. Maintenance involvement in the Pickering 'A' Shutdown System Enhancement (SDSE) Project. 4. Challenges resulting from the inclusion of Maintenance staff project teams. 5. Summary. (author)

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

Chronic Meningitis Investigated via Metagenomic Next-Generation Sequencing

Science.gov (United States)

O’Donovan, Brian D.; Gelfand, Jeffrey M.; Sample, Hannah A.; Chow, Felicia C.; Betjemann, John P.; Shah, Maulik P.; Richie, Megan B.; Gorman, Mark P.; Hajj-Ali, Rula A.; Calabrese, Leonard H.; Zorn, Kelsey C.; Chow, Eric D.; Greenlee, John E.; Blum, Jonathan H.; Green, Gary; Khan, Lillian M.; Banerji, Debarko; Langelier, Charles; Bryson-Cahn, Chloe; Harrington, Whitney; Lingappa, Jairam R.; Shanbhag, Niraj M.; Green, Ari J.; Brew, Bruce J.; Soldatos, Ariane; Strnad, Luke; Doernberg, Sarah B.; Jay, Cheryl A.; Douglas, Vanja; Josephson, S. Andrew; DeRisi, Joseph L.

2018-01-01

Importance Identifying infectious causes of subacute or chronic meningitis can be challenging. Enhanced, unbiased diagnostic approaches are needed. Objective To present a case series of patients with diagnostically challenging subacute or chronic meningitis using metagenomic next-generation sequencing (mNGS) of cerebrospinal fluid (CSF) supported by a statistical framework generated from mNGS of control samples from the environment and from patients who were noninfectious. Design, Setting, and Participants In this case series, mNGS data obtained from the CSF of 94 patients with noninfectious neuroinflammatory disorders and from 24 water and reagent control samples were used to develop and implement a weighted scoring metric based on z scores at the species and genus levels for both nucleotide and protein alignments to prioritize and rank the mNGS results. Total RNA was extracted for mNGS from the CSF of 7 participants with subacute or chronic meningitis who were recruited between September 2013 and March 2017 as part of a multicenter study of mNGS pathogen discovery among patients with suspected neuroinflammatory conditions. The neurologic infections identified by mNGS in these 7 participants represented a diverse array of pathogens. The patients were referred from the University of California, San Francisco Medical Center (n = 2), Zuckerberg San Francisco General Hospital and Trauma Center (n = 2), Cleveland Clinic (n = 1), University of Washington (n = 1), and Kaiser Permanente (n = 1). A weighted z score was used to filter out environmental contaminants and facilitate efficient data triage and analysis. Main Outcomes and Measures Pathogens identified by mNGS and the ability of a statistical model to prioritize, rank, and simplify mNGS results. Results The 7 participants ranged in age from 10 to 55 years, and 3 (43%) were female. A parasitic worm (Taenia solium, in 2 participants), a virus (HIV-1), and 4 fungi (Cryptococcus neoformans

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

Yleaf: Software for Human Y-Chromosomal Haplogroup Inference from Next-Generation Sequencing Data.

Science.gov (United States)

Ralf, Arwin; Montiel González, Diego; Zhong, Kaiyin; Kayser, Manfred

2018-05-01

Next-generation sequencing (NGS) technologies offer immense possibilities given the large genomic data they simultaneously deliver. The human Y-chromosome serves as good example how NGS benefits various applications in evolution, anthropology, genealogy, and forensics. Prior to NGS, the Y-chromosome phylogenetic tree consisted of a few hundred branches, based on NGS data, it now contains many thousands. The complexity of both, Y tree and NGS data provide challenges for haplogroup assignment. For effective analysis and interpretation of Y-chromosome NGS data, we present Yleaf, a publically available, automated, user-friendly software for high-resolution Y-chromosome haplogroup inference independently of library and sequencing methods.

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.

Forecasting Canadian nuclear power station construction costs

International Nuclear Information System (INIS)

Keng, C.W.K.

1985-01-01

Because of the huge volume of capital required to construct a modern electric power generating station, investment decisions have to be made with as complete an understanding of the consequences of the decision as possible. This understanding must be provided by the evaluation of future situations. A key consideration in an evaluation is the financial component. This paper attempts to use an econometric method to forecast the construction costs escalation of a standard Canadian nuclear generating station (NGS). A brief review of the history of Canadian nuclear electric power is provided. The major components of the construction costs of a Canadian NGS are studied and summarized. A database is built and indexes are prepared. Based on these indexes, an econometric forecasting model is constructed using an apparently new econometric methodology of forecasting modelling. Forecasts for a period of 40 years are generated and applications (such as alternative scenario forecasts and range forecasts) to uncertainty assessment and/or decision-making are demonstrated. The indexes, the model, and the forecasts and their applications, to the best of the author's knowledge, are the first for Canadian NGS constructions. (author)

Use of amplicon sequencing to improve sensitivity in PCR-based detection of microbial pathogen in environmental samples.

Science.gov (United States)

Saingam, Prakit; Li, Bo; Yan, Tao

2018-06-01

DNA-based molecular detection of microbial pathogens in complex environments is still plagued by sensitivity, specificity and robustness issues. We propose to address these issues by viewing them as inadvertent consequences of requiring specific and adequate amplification (SAA) of target DNA molecules by current PCR methods. Using the invA gene of Salmonella as the model system, we investigated if next generation sequencing (NGS) can be used to directly detect target sequences in false-negative PCR reaction (PCR-NGS) in order to remove the SAA requirement from PCR. False-negative PCR and qPCR reactions were first created using serial dilutions of laboratory-prepared Salmonella genomic DNA and then analyzed directly by NGS. Target invA sequences were detected in all false-negative PCR and qPCR reactions, which lowered the method detection limits near the theoretical minimum of single gene copy detection. The capability of the PCR-NGS approach in correcting false negativity was further tested and confirmed under more environmentally relevant conditions using Salmonella-spiked stream water and sediment samples. Finally, the PCR-NGS approach was applied to ten urban stream water samples and detected invA sequences in eight samples that would be otherwise deemed Salmonella negative. Analysis of the non-target sequences in the false-negative reactions helped to identify primer dime-like short sequences as the main cause of the false negativity. Together, the results demonstrated that the PCR-NGS approach can significantly improve method sensitivity, correct false-negative detections, and enable sequence-based analysis for failure diagnostics in complex environmental samples. Copyright © 2018 Elsevier B.V. All rights reserved.

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.

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.

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

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

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

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

Building a Robust Tumor Profiling Program: Synergy between Next-Generation Sequencing and Targeted Single-Gene Testing.

Directory of Open Access Journals (Sweden)

Matthew C Hiemenz

Full Text Available Next-generation sequencing (NGS is a powerful platform for identifying cancer mutations. Routine clinical adoption of NGS requires optimized quality control metrics to ensure accurate results. To assess the robustness of our clinical NGS pipeline, we analyzed the results of 304 solid tumor and hematologic malignancy specimens tested simultaneously by NGS and one or more targeted single-gene tests (EGFR, KRAS, BRAF, NPM1, FLT3, and JAK2. For samples that passed our validated tumor percentage and DNA quality and quantity thresholds, there was perfect concordance between NGS and targeted single-gene tests with the exception of two FLT3 internal tandem duplications that fell below the stringent pre-established reporting threshold but were readily detected by manual inspection. In addition, NGS identified clinically significant mutations not covered by single-gene tests. These findings confirm NGS as a reliable platform for routine clinical use when appropriate quality control metrics, such as tumor percentage and DNA quality cutoffs, are in place. Based on our findings, we suggest a simple workflow that should facilitate adoption of clinical oncologic NGS services at other institutions.

Effects of Carbopol® 934 proportion on nanoemulsion gel for topical and transdermal drug delivery: a skin permeation study.

Science.gov (United States)

Zheng, Yin; Ouyang, Wu-Qing; Wei, Yun-Peng; Syed, Shahid Faraz; Hao, Chao-Shuang; Wang, Bo-Zhen; Shang, Yan-Hong

Nanoemulsions (NEs) are used as transdermal drug delivery systems for systematic therapeutic purposes. We hypothesized that the skin permeation profile of an NE could be modulated by incorporating it into a hydrogel containing differing proportions of thickening agent. The objectives of this study were as follows: 1) to determine the stability and skin irritability of NE gels (NGs) containing 1%, 2%, and 3% (w/w) Carbopol ® 934 (CP934) (termed NG1, NG2, and NG3, respectively); 2) to compare the skin permeation profiles and drug deposition patterns of the NGs; and 3) to visualize the drug delivery routes of the NGs. Terbinafine and citral were incorporated into the NGs as model drugs. Ex vivo skin permeation tests indicated that the percutaneous flux rates of terbinafine decreased in the order NE (215 μg/cm 2 ) > NG1 (213 μg/cm 2 ) > NG2 (123 μg/cm 2 ) > NG3 (74.3 μg/cm 2 ). The flux rates of citral decreased in the order NE (1,026 μg/cm 2 ) > NG1 (1,021 μg/cm 2 ) > NG2 (541 μg/cm 2 ) > NG3 (353 μg/cm 2 ). The NGs accumulated greater amounts of the drugs in the stratum corneum and less in the epidermis/dermis than did the NE ( P drug delivery routes from skin appendages to intercellular paths. Histological images suggested that perturbations to the skin structure, specifically the size of the epidermal intercellular spaces and the separation distance of dermal collagen bundles, could be significantly minimized by increasing the proportion of CP934. These results suggest that adjustments of the CP934 proportions can be used to modulate the skin permeation profiles of NGs for specific therapeutic purposes.

Proficiency Testing for Bacterial Whole Genome Sequencing: An End-User Survey of Current Capabilities, Requirements and Priorities

DEFF Research Database (Denmark)

Moran-Gilad, Jacob; Sintchenko, Vitali; Karlsmose Pedersen, Susanne

2015-01-01

The advent of next-generation sequencing (NGS) has revolutionised public health microbiology. Given the potential impact of NGS, it is paramount to ensure standardisation of ‘wet’ laboratory and bioinformatic protocols and promote comparability of methods employed by different laboratories...... and their outputs. Therefore, one of the ambitious goals of the Global Microbial Identifier (GMI) initiative (http://​www.​globalmicrobiali​dentifier.​org/​) has been to establish a mechanism for inter-laboratory NGS proficiency testing (PT). This report presents findings from the survey recently conducted...... by Working Group 4 among GMI members in order to ascertain NGS end-use requirements and attitudes towards NGS PT. The survey identified the high professional diversity of laboratories engaged in NGS-based public health projects and the wide range of capabilities within institutions, at a notable range...

Proficiency testing for bacterial whole genome sequencing: an end-user survey of current capabilities, requirements and priorities

DEFF Research Database (Denmark)

Moran-Gilad, Jacob; Sintchenko, Vitali; Karlsmose Pedersen, Susanne

2015-01-01

The advent of next-generation sequencing (NGS) has revolutionised public health microbiology. Given the potential impact of NGS, it is paramount to ensure standardisation of 'wet' laboratory and bioinformatic protocols and promote comparability of methods employed by different laboratories...... and their outputs. Therefore, one of the ambitious goals of the Global Microbial Identifier (GMI) initiative (http://www.globalmicrobialidentifier.org/) has been to establish a mechanism for inter-laboratory NGS proficiency testing (PT). This report presents findings from the survey recently conducted by Working...... Group 4 among GMI members in order to ascertain NGS end-use requirements and attitudes towards NGS PT. The survey identified the high professional diversity of laboratories engaged in NGS-based public health projects and the wide range of capabilities within institutions, at a notable range of costs...

Impact of operating experience on design of civil structures - An overview

Energy Technology Data Exchange (ETDEWEB)

Tang, J H.K. [Ontario Hydro, Toronto, ON (Canada)

1991-04-01

During the past twenty years, Ontario Hydro has expanded its nuclear power to provide about one third of the electricity used in the province (coal and water powered stations provide the other two thirds). By 1992, the total installed capacity of nuclear generating stations in Ontario will further rise to over 14,000 MW. In common with other power plant design, the layout and structural design of civil facilities for a nuclear generating station are developed from consideration of functional, safety and operational requirements, as well as from past operating experience. Experience on structural performance in the sixteen units of Pickering and Bruce NGS's includes: piping and machinery vibrations, structural fatigue failures, and structural integrity due to extreme loadings not considered in the original design. The operating experience of Ontario Hydro's nuclear stations also indicates that civil structures are subjected to some degree of corrosion or degradation of certain elements similar to other mechanical components in a power station. This category of problems consists of concerns associated with thermal effects on concrete structures due to inoperative cooling system, cracking of concrete, and reliability of elastomeric seal materials at expansion joints of the containment envelop. This paper presents an overview of the operating problems and issues regarding changes in the licensing requirements related to civil structures and supporting systems of major mechanical components. The impact of these generic experience on the design of retrofits and new generating stations is also described in the paper.

Impact of operating experience on design of civil structures - An overview

International Nuclear Information System (INIS)

Tang, J.H.K.

1991-01-01

During the past twenty years, Ontario Hydro has expanded its nuclear power to provide about one third of the electricity used in the province (coal and water powered stations provide the other two thirds). By 1992, the total installed capacity of nuclear generating stations in Ontario will further rise to over 14,000 MW. In common with other power plant design, the layout and structural design of civil facilities for a nuclear generating station are developed from consideration of functional, safety and operational requirements, as well as from past operating experience. Experience on structural performance in the sixteen units of Pickering and Bruce NGS's includes: piping and machinery vibrations, structural fatigue failures, and structural integrity due to extreme loadings not considered in the original design. The operating experience of Ontario Hydro's nuclear stations also indicates that civil structures are subjected to some degree of corrosion or degradation of certain elements similar to other mechanical components in a power station. This category of problems consists of concerns associated with thermal effects on concrete structures due to inoperative cooling system, cracking of concrete, and reliability of elastomeric seal materials at expansion joints of the containment envelop. This paper presents an overview of the operating problems and issues regarding changes in the licensing requirements related to civil structures and supporting systems of major mechanical components. The impact of these generic experience on the design of retrofits and new generating stations is also described in the paper

Tuning the wettability of calcite cubes by varying the sizes of the polystyrene nanoparticles attached to their surfaces

International Nuclear Information System (INIS)

He Yongjun; Li Tanliang; Yu Xiangyang; Zhao Shiyong; Lu Jianhua; He Jia

2007-01-01

The wettability of calcite cubes was tuned by varying the sizes of the polystyrene nanoparticles attached to their surfaces via a dispersion polymerization. The products were characterized by scanning electron microscopy (SEM), X-ray diffraction (XRD), energy dispersion spectrum (EDS) and Fourier transformation infrared spectrum (FTIR). The results showed that the hydrophobicity of the calcite cubes was enhanced with the increase of the size of the polystyrene nanoparticles attached. Using polystyrene nanoparticle-attached calcite cubes (PNACC) as emulsifiers, stable water-in-tricaprylin Pickering emulsions were produced. By gelling the water droplets of the Pickering emulsions, the hierarchical structures of polystyrene nanoparticle-attached calcite cube-armored microspheres were obtained. The polystyrene nanoparticle-attached calcite cubes were expected to have novel surface properties similar neither to traditional Pickering particles, nor to macroscopically asymmetrical Janus particles

Spotlight on GME/GHSE Supported Research

Science.gov (United States)

2017-12-07

hour per response, including the time for reviewing instructions, searching existing data sources, gathering and maintaining the data needed, and...utilize Pyrosequencing for their Protocol. Genetic Status of Genes via PCR & NGS ... 3.000.000.000bp 1 __ ____ _ 0_ .. -··. _ Ll...Construct Exome library for NGS . Sequence Exome via NGS . Store Exome data for future studies 1 bp 30,000,000 bp PCR DATA NGS DATA C

How next-generation sequencing and multiscale data analysis will transform infectious disease management.

Science.gov (United States)

Pak, Theodore R; Kasarskis, Andrew

2015-12-01

Recent reviews have examined the extent to which routine next-generation sequencing (NGS) on clinical specimens will improve the capabilities of clinical microbiology laboratories in the short term, but do not explore integrating NGS with clinical data from electronic medical records (EMRs), immune profiling data, and other rich datasets to create multiscale predictive models. This review introduces a range of "omics" and patient data sources relevant to managing infections and proposes 3 potentially disruptive applications for these data in the clinical workflow. The combined threats of healthcare-associated infections and multidrug-resistant organisms may be addressed by multiscale analysis of NGS and EMR data that is ideally updated and refined over time within each healthcare organization. Such data and analysis should form the cornerstone of future learning health systems for infectious disease. © The Author 2015. Published by Oxford University Press on behalf of the Infectious Diseases Society of America.

Nondissipative gravitational turbulence

International Nuclear Information System (INIS)

Gurevich, A.V.; Zybin, K.P.

1988-01-01

The nonlinear stage of development of the Jeans instability in a cold nondissipative gravitating gas is considered. It is shown that for a time exceeding the Jeans time a nondissipative gravitational singularity (NGS) is formed in the vicinity of a local density maximum. The NGS is a stationary dynamic structure, the basis of which is the singularity. The density of the gas at the center of the NGS (for r → 0) tends to infinity, and the field potential and the mean velocity of the trapped gas, possess a power singularity. The turbulent state arises as the result of development of the instability in the case of an irregular initial density distribution. It is an hierarchic structure consisting of nested moving NGS of various sizes, the NGS of smaller dimensions being trapped in the field of a NGS of larger dimensions. The scaling relations for each given NGS in this case hold for both the gas density and density of smaller size trapped NGS. A brief comparison with the observational data shows that the real hierarchic structure of the Universe ranging from scales pertaining to spherical stellar clusters up to those of rich galaxy clusters is apparently a developed gravitational turbulence

Characterization of Protein and Peptide Binding to Nanogels Formed by Differently Charged Chitosan Derivatives

Directory of Open Access Journals (Sweden)

Anastasia Zubareva

2013-07-01

Full Text Available Chitosan (Chi is a natural biodegradable cationic polymer with remarkable potency as a vehicle for drug or vaccine delivery. Chi possesses multiple groups, which can be used both for Chi derivatization and for particle formation. The aim of this work was to produce stable nanosized range Chi gels (nanogels, NGs with different charge and to study the driving forces of complex formation between Chi NGs and proteins or peptides. Positively charged NGs of 150 nm in diameter were prepared from hexanoyl chitosan (HC by the ionotropic gelation method while negatively charged NGs of 190 nm were obtained from succinoyl Chi (SC by a Ca2+ coacervation approach. NGs were loaded with a panel of proteins or peptides with different weights and charges. We show that NGs preferentially formed complexes with oppositely charged molecules, especially peptides, as was demonstrated by gel-electrophoresis, confocal microscopy and HPLC. Complex formation was accompanied by a change in zeta-potential and decrease in size. We concluded that complex formation between Chi NGs and peptide/proteins is mediated mostly by electrostatic interactions.

High-energy radiation processing, a smart approach to obtain PVP-graft-AA nanogels

International Nuclear Information System (INIS)

Grimaldi, N.; Sabatino, M.A.; Przybytniak, G.; Kaluska, I.; Bondì, M.L.; Bulone, D.; Alessi, S.; Spadaro, G.; Dispenza, C.

2014-01-01

Poly(N-vinylpyrrolidone)-grafted-acrylic acid biocompatible nanogels (NGs) were prepared using an exiting industrial-type electron accelerator and setups, starting from semi-dilute aqueous solutions of a commercial PVP and the acrylic acid monomer. As a result, NGs with tunable size and structure can be obtained quantitatively. Sterility was also imparted at the integrated dose absorbed. The chemical structure of the NGs produced was confirmed through Fourier Transformer Infrared Spectroscopy (FT-IR). The molecular and physico-chemical properties of NGs, such as the hydrodynamic dimensions and surface charge densities, for various polymer and monomer concentrations in the irradiated solutions, are discussed here. - Highlights: • Aqueous solutions of PVP and AA were irradiated by industrial electron accelerator. • NGs with different physico-chemical and molecular properties can be obtained. • Carboxyl-functionalized NGs produced are promising building blocks for bio-devices

Next generation sequencing and its applications in forensic genetics

DEFF Research Database (Denmark)

Børsting, Claus; Morling, Niels

2015-01-01

articles and presentations at conferences with forensic aspects of NGS. These contributions have demonstrated that NGS offers new possibilities for forensic genetic case work. More information may be obtained from unique samples in a single experiment by analyzing combinations of markers (STRs, SNPs......It has been almost a decade since the first next generation sequencing (NGS) technologies emerged and quickly changed the way genetic research is conducted. Today, full genomes are mapped and published almost weekly and with ever increasing speed and decreasing costs. NGS methods and platforms have...... matured during the last 10 years, and the quality of the sequences has reached a level where NGS is used in clinical diagnostics of humans. Forensic genetic laboratories have also explored NGS technologies and especially in the last year, there has been a small explosion in the number of scientific...

Best practice guidelines for the use of next-generation sequencing applications in genome diagnostics: a national collaborative study of dutch genome diagnostic laboratories

NARCIS (Netherlands)

Weiss, Marjan M.; van der Zwaag, Bert; Jongbloed, Jan D. H.; Vogel, Maartje J.; Brüggenwirth, Hennie T.; Lekanne Deprez, Ronald H.; Mook, Olaf; Ruivenkamp, Claudia A. L.; van Slegtenhorst, Marjon A.; van den Wijngaard, Arthur; Waisfisz, Quinten; Nelen, Marcel R.; van der Stoep, Nienke

2013-01-01

Next-generation sequencing (NGS) methods are being adopted by genome diagnostics laboratories worldwide. However, implementing NGS-based tests according to diagnostic standards is a challenge for individual laboratories. To facilitate the implementation of NGS in Dutch laboratories, the Dutch

Single-variant and multi-variant trend tests for genetic association with next-generation sequencing that are robust to sequencing error.

Science.gov (United States)

Kim, Wonkuk; Londono, Douglas; Zhou, Lisheng; Xing, Jinchuan; Nato, Alejandro Q; Musolf, Anthony; Matise, Tara C; Finch, Stephen J; Gordon, Derek

2012-01-01

As with any new technology, next-generation sequencing (NGS) has potential advantages and potential challenges. One advantage is the identification of multiple causal variants for disease that might otherwise be missed by SNP-chip technology. One potential challenge is misclassification error (as with any emerging technology) and the issue of power loss due to multiple testing. Here, we develop an extension of the linear trend test for association that incorporates differential misclassification error and may be applied to any number of SNPs. We call the statistic the linear trend test allowing for error, applied to NGS, or LTTae,NGS. This statistic allows for differential misclassification. The observed data are phenotypes for unrelated cases and controls, coverage, and the number of putative causal variants for every individual at all SNPs. We simulate data considering multiple factors (disease mode of inheritance, genotype relative risk, causal variant frequency, sequence error rate in cases, sequence error rate in controls, number of loci, and others) and evaluate type I error rate and power for each vector of factor settings. We compare our results with two recently published NGS statistics. Also, we create a fictitious disease model based on downloaded 1000 Genomes data for 5 SNPs and 388 individuals, and apply our statistic to those data. We find that the LTTae,NGS maintains the correct type I error rate in all simulations (differential and non-differential error), while the other statistics show large inflation in type I error for lower coverage. Power for all three methods is approximately the same for all three statistics in the presence of non-differential error. Application of our statistic to the 1000 Genomes data suggests that, for the data downloaded, there is a 1.5% sequence misclassification rate over all SNPs. Finally, application of the multi-variant form of LTTae,NGS shows high power for a number of simulation settings, although it can have

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.

Web-based bioinformatics workflows for end-to-end RNA-seq data computation and analysis in agricultural animal species

Science.gov (United States)

Remarkable advances in next-generation sequencing (NGS) technologies, bioinformatics algorithms, and computational technologies have significantly accelerated genomic research. However, complicated NGS data analysis still remains as a major bottleneck. RNA-seq, as one of the major area in the NGS fi...

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease.

Science.gov (United States)

Dilliott, Allison A; Farhan, Sali M K; Ghani, Mahdi; Sato, Christine; Liang, Eric; Zhang, Ming; McIntyre, Adam D; Cao, Henian; Racacho, Lemuel; Robinson, John F; Strong, Michael J; Masellis, Mario; Bulman, Dennis E; Rogaeva, Ekaterina; Lang, Anthony; Tartaglia, Carmela; Finger, Elizabeth; Zinman, Lorne; Turnbull, John; Freedman, Morris; Swartz, Rick; Black, Sandra E; Hegele, Robert A

2018-04-04

Next-generation sequencing (NGS) is quickly revolutionizing how research into the genetic determinants of constitutional disease is performed. The technique is highly efficient with millions of sequencing reads being produced in a short time span and at relatively low cost. Specifically, targeted NGS is able to focus investigations to genomic regions of particular interest based on the disease of study. Not only does this further reduce costs and increase the speed of the process, but it lessens the computational burden that often accompanies NGS. Although targeted NGS is restricted to certain regions of the genome, preventing identification of potential novel loci of interest, it can be an excellent technique when faced with a phenotypically and genetically heterogeneous disease, for which there are previously known genetic associations. Because of the complex nature of the sequencing technique, it is important to closely adhere to protocols and methodologies in order to achieve sequencing reads of high coverage and quality. Further, once sequencing reads are obtained, a sophisticated bioinformatics workflow is utilized to accurately map reads to a reference genome, to call variants, and to ensure the variants pass quality metrics. Variants must also be annotated and curated based on their clinical significance, which can be standardized by applying the American College of Medical Genetics and Genomics Pathogenicity Guidelines. The methods presented herein will display the steps involved in generating and analyzing NGS data from a targeted sequencing panel, using the ONDRISeq neurodegenerative disease panel as a model, to identify variants that may be of clinical significance.

Use of ergonomic principles in manual order picking systems

Directory of Open Access Journals (Sweden)

Labus Nina

2018-02-01

Full Text Available Successful companies are continually striving to streamline costs and optimize processes, enabling them to grow progress, develop and ensure competitiveness on the market. A large part of the costs arises in warehouses, where up to 55% of total costs are generated by order-picking, which makes it important and interesting in terms of research. The paper explores “picker to part” order-picking concept, which enables flexible work and is the optimal choice for most companies. The concept is associated with a high level of work-related injuries and work-related illnesses. Work requires physical efforts resulting from handling heavy goods, performing repetitive movements and using manipulative means. Human as the main actor of the concept affects the costs caused by picking and the quality of work done, which depends on technological support, physically and psychologically capable and motivated people. Due to the high costs of service, the focus on time planning and productivity increases. Contrary, the lack of attention is paid to the working conditions and the health status of the pickers. To overcome this gab, a review of scientific and professional literature on ergonomic principles in picking concept »picker to part« was carried out, followed by a quantitative survey of ergonomic properties in warehousing activities. Results revealed that more than 60% of the surveyed order-pickers associate problems with health with the characteristics of work, about 24% of them associate health problems with the use of a particular means of transport, and all agree that provided measures to reduce physical effort and greater support of technologies influence on increased speed of work and better health status of order-pickers.

Management of design support for nuclear plant modifications

International Nuclear Information System (INIS)

Doyle, F.W.

1991-01-01

The paper will present an overview of the Ontario Hydro organization and processes for providing design support to the operating nuclear power plants. Examples of design support for Pickering GS will be highlighted. The process is described from identification of projects through the design, procurement, construction, commissioning and in-service phases. The practices for managing engineering deliverables are discussed in the context of how these integrate into the overall change control process. The interaction of Engineering with Operations, Construction, Supply and the regulatory bodies is discussed both for major retro-fit programs and for ongoing design support to the nuclear power plants. Recent experiences during the 1990 Pickering Station Outage and during the Unit 3 fuel channel replacement program are highlighted and an integrated 5 year plan for upgrading the safety related systems for the Pickering Nuclear Power Plant is presented. (author)

Reference Ranges in [(99m)Tc]Mercaptoacetyltriglycerine Renography

DEFF Research Database (Denmark)

Rewers, Kate I; Hvidsten, Svend; Gerke, Oke

2015-01-01

PURPOSE: The purpose of the study was to define reference ranges for quantitative parameters in [(99m)Tc]mercaptoacetyltriglycerine ([(99m)Tc]MAG3) renography to assist interpretation in a semi-automated (Xeleris, GE) compared to a manual (Picker, Odyssey) software package. PROCEDURES: Forty......-eight subjects approved for renal donation were evaluated with [(99m)Tc]MAG3 renography using both the Xeleris and the Picker software. RESULTS: Reference ranges for the two software were comparable regarding the relative function of the two kidneys (the split function, SF) and the residual activities (RA......). The time to peak whole-kidney activities (T max whole-kidney) was more dependent on the type of software. Using Bland-Altman limits, we found good and acceptable agreement between the two methods. CONCLUSIONS: We found good correlation between renography results using the Xeleris and Picker software...

Visual programming for next-generation sequencing data analytics.

Science.gov (United States)

Milicchio, Franco; Rose, Rebecca; Bian, Jiang; Min, Jae; Prosperi, Mattia

2016-01-01

High-throughput or next-generation sequencing (NGS) technologies have become an established and affordable experimental framework in biological and medical sciences for all basic and translational research. Processing and analyzing NGS data is challenging. NGS data are big, heterogeneous, sparse, and error prone. Although a plethora of tools for NGS data analysis has emerged in the past decade, (i) software development is still lagging behind data generation capabilities, and (ii) there is a 'cultural' gap between the end user and the developer. Generic software template libraries specifically developed for NGS can help in dealing with the former problem, whilst coupling template libraries with visual programming may help with the latter. Here we scrutinize the state-of-the-art low-level software libraries implemented specifically for NGS and graphical tools for NGS analytics. An ideal developing environment for NGS should be modular (with a native library interface), scalable in computational methods (i.e. serial, multithread, distributed), transparent (platform-independent), interoperable (with external software interface), and usable (via an intuitive graphical user interface). These characteristics should facilitate both the run of standardized NGS pipelines and the development of new workflows based on technological advancements or users' needs. We discuss in detail the potential of a computational framework blending generic template programming and visual programming that addresses all of the current limitations. In the long term, a proper, well-developed (although not necessarily unique) software framework will bridge the current gap between data generation and hypothesis testing. This will eventually facilitate the development of novel diagnostic tools embedded in routine healthcare.

Creative Destruction: Next Generation Sequencing in Drug Development, Formulary Evaluations and Pricing

Directory of Open Access Journals (Sweden)

Paul C Langley

2016-11-01

Full Text Available Next generation sequencing (NGS has the potential to disrupt not only the accepted process of drug development but also the hurdles a drug manufacturer would be expected to face in securing formulary approval and a possible premium price for the new compound. The purpose of this commentary is to consider the role of NGS in this process, one which is characterized as a process of creative destruction, where adoption of NGS in personalized medicine sets in train a mechanism of incessant product and process review. A mechanism driven by continuing modifications and extensions to NGS platforms as our understanding of the role of mutations and mutation load in therapy choice expands. At the same time this mechanism has significant implications for the continued revision of treatment guidelines and their adoption of NGS as integral parts of the treatment pathway. There are, however, a number of unresolved issues which have to be addressed. These include the choice of NGS platform, barriers to integrating evidence to support NGS-based therapy choices in treatment guidelines, the implications of NGS for drug development and the modification or rejection of current trial structures, the integration of comorbid disease states and the standards that formulary committees should adopt to evaluate NGS claims. The overarching theme, however, is the need to invest in a robust and credible evidence base. While we are a long way from achieving this, the focus must be on putting claims for therapy choice forward that are credible, evaluable and replicable.   Type: Commentary

Next-generation sequencing in NSCLC and melanoma patients: a cost and budget impact analysis

Science.gov (United States)

van Amerongen, Rosa A; Retèl, Valesca P; Coupé, Veerle MH; Nederlof, Petra M; Vogel, Maartje J; van Harten, Wim H

2016-01-01

Next-generation sequencing (NGS) has reached the molecular diagnostic laboratories. Although the NGS technology aims to improve the effectiveness of therapies by selecting the most promising therapy, concerns are that NGS testing is expensive and that the ‘benefits’ are not yet in relation to these costs. In this study, we give an estimation of the costs and an institutional and national budget impact of various types of NGS tests in non-small-cell lung cancer (NSCLC) and melanoma patients within The Netherlands. First, an activity-based costing (ABC) analysis has been conducted on the costs of two examples of NGS panels (small- and medium-targeted gene panel (TGP)) based on data of The Netherlands Cancer Institute (NKI). Second, we performed a budget impact analysis (BIA) to estimate the current (2015) and future (2020) budget impact of NGS on molecular diagnostics for NSCLC and melanoma patients in The Netherlands. Literature, expert opinions, and a data set of patients within the NKI (n = 172) have been included in the BIA. Based on our analysis, we expect that the NGS test cost concerns will be limited. In the current situation, NGS can indeed result in higher diagnostic test costs, which is mainly related to required additional tests besides the small TGP. However, in the future, we expect that the use of whole-genome sequencing (WGS) will increase, for which it is expected that additional tests can be (partly) avoided. Although the current clinical benefits are expected to be limited, the research potentials of NGS are already an important advantage. PMID:27899957

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

Next-generation sequencing in NSCLC and melanoma patients : A cost and budget impact analysis

NARCIS (Netherlands)

Van Amerongen, Rosa A.; Retèl, Valesca P.; Coupé, Veerle M.H.; Nederlof, Petra M.; Vogel, Maartje J.; Van Harten, Wim H.

2016-01-01

Next-generation sequencing (NGS) has reached the molecular diagnostic laboratories. Although the NGS technology aims to improve the effectiveness of therapies by selecting the most promising therapy, concerns are that NGS testing is expensive and that the 'benefits' are not yet in relation to these

Next generation sequencing and its applications in forensic genetics.

Science.gov (United States)

Børsting, Claus; Morling, Niels

2015-09-01

It has been almost a decade since the first next generation sequencing (NGS) technologies emerged and quickly changed the way genetic research is conducted. Today, full genomes are mapped and published almost weekly and with ever increasing speed and decreasing costs. NGS methods and platforms have matured during the last 10 years, and the quality of the sequences has reached a level where NGS is used in clinical diagnostics of humans. Forensic genetic laboratories have also explored NGS technologies and especially in the last year, there has been a small explosion in the number of scientific articles and presentations at conferences with forensic aspects of NGS. These contributions have demonstrated that NGS offers new possibilities for forensic genetic case work. More information may be obtained from unique samples in a single experiment by analyzing combinations of markers (STRs, SNPs, insertion/deletions, mRNA) that cannot be analyzed simultaneously with the standard PCR-CE methods used today. The true variation in core forensic STR loci has been uncovered, and previously unknown STR alleles have been discovered. The detailed sequence information may aid mixture interpretation and will increase the statistical weight of the evidence. In this review, we will give an introduction to NGS and single-molecule sequencing, and we will discuss the possible applications of NGS in forensic genetics. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

H/He ratios for WN stars in the LMC and the galaxy

International Nuclear Information System (INIS)

Perry, D.N.; Conti, P.S.

1982-01-01

In the visible, most of the He II lines of WR stars are due to the Pickering series (n-4). Though there are significant problems with using the Pickering decrement the authors have utilized it to find H/He ratios for 21 WN stars in the LMC, and 38 stars in the Galaxy. They have additionally extended the analysis to include the derivation of the H/He ratio if the lines are optically thick. (Auth.)

Synthesis of a novel thermo/pH sensitive nanogel based on salep modified graphene oxide for drug release

Energy Technology Data Exchange (ETDEWEB)

Bardajee, Ghasem Rezanejade, E-mail: rezanejad@pnu.ac.ir; Hooshyar, Zari; Farsi, Maryam; Mobini, Akram; Sang, Golnaz

2017-03-01

Nanogels (NGs) are three-dimensional water soluble cross-linked hydrogel materials in the nanoscale size range with a high loading capacity for guest molecules and act as drug carrier systems. In the present work, a new type of thermo/pH sensitive NG comprising salep modified graphene oxide (SMGO) with branched N-isopropylacrylamide (NIPAM) and acrylic acid (AA) was prepared. The SMGO/P(NIPAM-co-AA) NGs exhibited nanoporous structure and spherical particles with diameters about 82 nm as characterized by scanning electron microscopy (SEM), transmission electron microscopy (TEM), and dynamic light scattering (DLS). The samples were also characterized by Fourier transform infrared spectroscopy (FT-IR) and thermo gravimetric analysis (TGA) to further confirm about the formation of NGs. Doxorubicin (DOX) loaded SMGO/P(NIPAM-co-AA) NGs showed thermo/pH dependent releasing behavior: slow drug release at neutral pH and lower temperature but increased significantly in acidic pH and higher temperature, without any burst release. In addition, the NGs exhibited no effect on the cell viability in the tested concentration range up to 410 μg/mL and drug release systems enhanced toxicity to HeLa cells when compared to the equivalent dose of the free drug. Overall, our results put forth NGs as potential candidates in the development of a new nanocarrier for anti-cancer drug delivery. - Highlights: • A novel thermo/pH sensitive nanogels (NGs) was successfully synthesized. • NGs showed high loading capacity for DOX drug and slow drug release at neutral pH. • NGs exhibited no effect on the cell viability in the tested concentration range.

Synthesis of a novel thermo/pH sensitive nanogel based on salep modified graphene oxide for drug release

International Nuclear Information System (INIS)

Bardajee, Ghasem Rezanejade; Hooshyar, Zari; Farsi, Maryam; Mobini, Akram; Sang, Golnaz

2017-01-01

Nanogels (NGs) are three-dimensional water soluble cross-linked hydrogel materials in the nanoscale size range with a high loading capacity for guest molecules and act as drug carrier systems. In the present work, a new type of thermo/pH sensitive NG comprising salep modified graphene oxide (SMGO) with branched N-isopropylacrylamide (NIPAM) and acrylic acid (AA) was prepared. The SMGO/P(NIPAM-co-AA) NGs exhibited nanoporous structure and spherical particles with diameters about 82 nm as characterized by scanning electron microscopy (SEM), transmission electron microscopy (TEM), and dynamic light scattering (DLS). The samples were also characterized by Fourier transform infrared spectroscopy (FT-IR) and thermo gravimetric analysis (TGA) to further confirm about the formation of NGs. Doxorubicin (DOX) loaded SMGO/P(NIPAM-co-AA) NGs showed thermo/pH dependent releasing behavior: slow drug release at neutral pH and lower temperature but increased significantly in acidic pH and higher temperature, without any burst release. In addition, the NGs exhibited no effect on the cell viability in the tested concentration range up to 410 μg/mL and drug release systems enhanced toxicity to HeLa cells when compared to the equivalent dose of the free drug. Overall, our results put forth NGs as potential candidates in the development of a new nanocarrier for anti-cancer drug delivery. - Highlights: • A novel thermo/pH sensitive nanogels (NGs) was successfully synthesized. • NGs showed high loading capacity for DOX drug and slow drug release at neutral pH. • NGs exhibited no effect on the cell viability in the tested concentration range.

A Nuclear Dilemma--Korean War Deja Vu

Science.gov (United States)

2006-03-08

USAWC STRATEGY RESEARCH PROJECT A NUCLEAR DILEMMA—KOREAN WAR DEJA VU by Lieutenant Colonel Trent A. Pickering United States Air Force Colonel William...Lieutenant Colonel Trent A. Pickering TITLE: A Nuclear Dilemma—Korean War Deja Vu FORMAT: Strategy Research Project DATE: 8 March 2006 WORD COUNT: 19,270...1. REPORT DATE 15 MAR 2006 2. REPORT TYPE 3. DATES COVERED 00-00-2005 to 00-00-2006 4. TITLE AND SUBTITLE Nuclear Dilemma--Korean War Deja

Comparison of three human papillomavirus DNA detection methods: Next generation sequencing, multiplex-PCR and nested-PCR followed by Sanger based sequencing.

Science.gov (United States)

da Fonseca, Allex Jardim; Galvão, Renata Silva; Miranda, Angelica Espinosa; Ferreira, Luiz Carlos de Lima; Chen, Zigui

2016-05-01

To compare the diagnostic performance for HPV infection using three laboratorial techniques. Ninty-five cervicovaginal samples were randomly selected; each was tested for HPV DNA and genotypes using 3 methods in parallel: Multiplex-PCR, the Nested PCR followed by Sanger sequencing, and the Next_Gen Sequencing (NGS) with two assays (NGS-A1, NGS-A2). The study was approved by the Brazilian National IRB (CONEP protocol 16,800). The prevalence of HPV by the NGS assays was higher than that using the Multiplex-PCR (64.2% vs. 45.2%, respectively; P = 0.001) and the Nested-PCR (64.2% vs. 49.5%, respectively; P = 0.003). NGS also showed better performance in detecting high-risk HPV (HR-HPV) and HPV16. There was a weak interobservers agreement between the results of Multiplex-PCR and Nested-PCR in relation to NGS for the diagnosis of HPV infection, and a moderate correlation for HR-HPV detection. Both NGS assays showed a strong correlation for detection of HPVs (k = 0.86), HR-HPVs (k = 0.91), HPV16 (k = 0.92) and HPV18 (k = 0.91). NGS is more sensitive than the traditional Sanger sequencing and the Multiplex PCR to genotype HPVs, with promising ability to detect multiple infections, and may have the potential to establish an alternative method for the diagnosis and genotyping of HPV. © 2015 Wiley Periodicals, Inc.

National Earthquake Information Center Seismic Event Detections on Multiple Scales

Science.gov (United States)

Patton, J.; Yeck, W. L.; Benz, H.; Earle, P. S.; Soto-Cordero, L.; Johnson, C. E.

2017-12-01

The U.S. Geological Survey National Earthquake Information Center (NEIC) monitors seismicity on local, regional, and global scales using automatic picks from more than 2,000 near-real time seismic stations. This presents unique challenges in automated event detection due to the high variability in data quality, network geometries and density, and distance-dependent variability in observed seismic signals. To lower the overall detection threshold while minimizing false detection rates, NEIC has begun to test the incorporation of new detection and picking algorithms, including multiband (Lomax et al., 2012) and kurtosis (Baillard et al., 2014) pickers, and a new bayesian associator (Glass 3.0). The Glass 3.0 associator allows for simultaneous processing of variably scaled detection grids, each with a unique set of nucleation criteria (e.g., nucleation threshold, minimum associated picks, nucleation phases) to meet specific monitoring goals. We test the efficacy of these new tools on event detection in networks of various scales and geometries, compare our results with previous catalogs, and discuss lessons learned. For example, we find that on local and regional scales, rapid nucleation of small events may require event nucleation with both P and higher-amplitude secondary phases (e.g., S or Lg). We provide examples of the implementation of a scale-independent associator for an induced seismicity sequence (local-scale), a large aftershock sequence (regional-scale), and for monitoring global seismicity. Baillard, C., Crawford, W. C., Ballu, V., Hibert, C., & Mangeney, A. (2014). An automatic kurtosis-based P-and S-phase picker designed for local seismic networks. Bulletin of the Seismological Society of America, 104(1), 394-409. Lomax, A., Satriano, C., & Vassallo, M. (2012). Automatic picker developments and optimization: FilterPicker - a robust, broadband picker for real-time seismic monitoring and earthquake early-warning, Seism. Res. Lett. , 83, 531-540, doi: 10

Particle self-assembly at ionic liquid-based interfaces.

Science.gov (United States)

Frost, Denzil S; Nofen, Elizabeth M; Dai, Lenore L

2014-04-01

This review presents an overview of the nature of ionic liquid (IL)-based interfaces and self-assembled particle morphologies of IL-in-water, oil- and water-in-IL, and novel IL-in-IL Pickering emulsions with emphasis on their unique phenomena, by means of experimental and computational studies. In IL-in-water Pickering emulsions, particles formed monolayers at ionic liquid-water interfaces and were close-packed on fully covered emulsion droplets or aggregated on partially covered droplets. Interestingly, other than equilibrating at the ionic liquid-water interfaces, microparticles with certain surface chemistries were extracted into the ionic liquid phase with a high efficiency. These experimental findings were supported by potential of mean force calculations, which showed large energy drops as hydrophobic particles crossed the interface into the IL phase. In the oil- and water-in-IL Pickering emulsions, microparticles with acidic surface chemistries formed monolayer bridges between the internal phase droplets rather than residing at the oil/water-ionic liquid interfaces, a significant deviation from traditional Pickering emulsion morphology. Molecular dynamics simulations revealed aspects of the mechanism behind this bridging phenomenon, including the role of the droplet phase, surface chemistry, and inter-particle film. Novel IL-in-IL Pickering emulsions exhibited an array of self-assembled morphologies including the previously observed particle absorption and bridging phenomena. The appearance of these morphologies depended on the particle surface chemistry as well as the ILs used. The incorporation of particle self-assembly with ionic liquid science allows for new applications at the intersection of these two fields, and have the potential to be numerous due to the tunability of the ionic liquids and particles incorporated, as well as the particle morphology by combining certain groups of particle surface chemistry, IL type (protic or aprotic), and whether oil

Networks of recyclable material waste-picker’s cooperatives: An alternative for the solid waste management in the city of Rio de Janeiro

International Nuclear Information System (INIS)

Tirado-Soto, Magda Martina; Zamberlan, Fabio Luiz

2013-01-01

Highlights: ► In the marketing of recyclable materials, the waste-pickers are the least wins. ► It is proposed creating a network of recycling cooperatives to achieve viability. ► The waste-pickers contribute to waste management to the city. - Abstract: 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

Networks of recyclable material waste-picker’s cooperatives: An alternative for the solid waste management in the city of Rio de Janeiro

Energy Technology Data Exchange (ETDEWEB)

Tirado-Soto, Magda Martina, E-mail: magda@pep.ufrj.br [Program of Production Engineering, School and Research in Engineering, Federal University of Rio de Janeiro (Brazil); Zamberlan, Fabio Luiz, E-mail: fabio@pep.ufrj.br [Program of Production Engineering, School and Research in Engineering, Federal University of Rio de Janeiro (Brazil)

2013-04-15

Highlights: ► In the marketing of recyclable materials, the waste-pickers are the least wins. ► It is proposed creating a network of recycling cooperatives to achieve viability. ► The waste-pickers contribute to waste management to the city. - Abstract: 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.

Assuring the Quality of Next-Generation Sequencing in Clinical Microbiology and Public Health Laboratories.

Science.gov (United States)

Gargis, Amy S; Kalman, Lisa; Lubin, Ira M

2016-12-01

Clinical microbiology and public health laboratories are beginning to utilize next-generation sequencing (NGS) for a range of applications. This technology has the potential to transform the field by providing approaches that will complement, or even replace, many conventional laboratory tests. While the benefits of NGS are significant, the complexities of these assays require an evolving set of standards to ensure testing quality. Regulatory and accreditation requirements, professional guidelines, and best practices that help ensure the quality of NGS-based tests are emerging. This review highlights currently available standards and guidelines for the implementation of NGS in the clinical and public health laboratory setting, and it includes considerations for NGS test validation, quality control procedures, proficiency testing, and reference materials. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Application of Next-generation Sequencing in Clinical Molecular Diagnostics

Directory of Open Access Journals (Sweden)

Morteza Seifi

2017-05-01

Full Text Available ABSTRACT Next-generation sequencing (NGS is the catch all terms that used to explain several different modern sequencing technologies which let us to sequence nucleic acids much more rapidly and cheaply than the formerly used Sanger sequencing, and as such have revolutionized the study of molecular biology and genomics with excellent resolution and accuracy. Over the past years, many academic companies and institutions have continued technological advances to expand NGS applications from research to the clinic. In this review, the performance and technical features of current NGS platforms were described. Furthermore, advances in the applying of NGS technologies towards the progress of clinical molecular diagnostics were emphasized. General advantages and disadvantages of each sequencing system are summarized and compared to guide the selection of NGS platforms for specific research aims.

Highly multiplexed and quantitative cell-surface protein profiling using genetically barcoded antibodies.

Science.gov (United States)

Pollock, Samuel B; Hu, Amy; Mou, Yun; Martinko, Alexander J; Julien, Olivier; Hornsby, Michael; Ploder, Lynda; Adams, Jarrett J; Geng, Huimin; Müschen, Markus; Sidhu, Sachdev S; Moffat, Jason; Wells, James A

2018-03-13

Human cells express thousands of different surface proteins that can be used for cell classification, or to distinguish healthy and disease conditions. A method capable of profiling a substantial fraction of the surface proteome simultaneously and inexpensively would enable more accurate and complete classification of cell states. We present a highly multiplexed and quantitative surface proteomic method using genetically barcoded antibodies called phage-antibody next-generation sequencing (PhaNGS). Using 144 preselected antibodies displayed on filamentous phage (Fab-phage) against 44 receptor targets, we assess changes in B cell surface proteins after the development of drug resistance in a patient with acute lymphoblastic leukemia (ALL) and in adaptation to oncogene expression in a Myc-inducible Burkitt lymphoma model. We further show PhaNGS can be applied at the single-cell level. Our results reveal that a common set of proteins including FLT3, NCR3LG1, and ROR1 dominate the response to similar oncogenic perturbations in B cells. Linking high-affinity, selective, genetically encoded binders to NGS enables direct and highly multiplexed protein detection, comparable to RNA-sequencing for mRNA. PhaNGS has the potential to profile a substantial fraction of the surface proteome simultaneously and inexpensively to enable more accurate and complete classification of cell states. Copyright © 2018 the Author(s). Published by PNAS.

Needs Assessment for Research Use of High-Throughput Sequencing at a Large Academic Medical Center.

Directory of Open Access Journals (Sweden)

Albert Geskin

Full Text Available Next Generation Sequencing (NGS methods are driving profound changes in biomedical research, with a growing impact on patient care. Many academic medical centers are evaluating potential models to prepare for the rapid increase in NGS information needs. This study sought to investigate (1 how and where sequencing data is generated and analyzed, (2 research objectives and goals for NGS, (3 workforce capacity and unmet needs, (4 storage capacity and unmet needs, (5 available and anticipated funding resources, and (6 future challenges. As a precursor to informed decision making at our institution, we undertook a systematic needs assessment of investigators using survey methods. We recruited 331 investigators from over 60 departments and divisions at the University of Pittsburgh Schools of Health Sciences and had 140 respondents, or a 42% response rate. Results suggest that both sequencing and analysis bottlenecks currently exist. Significant educational needs were identified, including both investigator-focused needs, such as selection of NGS methods suitable for specific research objectives, and program-focused needs, such as support for training an analytic workforce. The absence of centralized infrastructure was identified as an important institutional gap. Key principles for organizations managing this change were formulated based on the survey responses. This needs assessment provides an in-depth case study which may be useful to other academic medical centers as they identify and plan for future needs.

Heap: a highly sensitive and accurate SNP detection tool for low-coverage high-throughput sequencing data

KAUST Repository

Kobayashi, Masaaki

2017-04-20

Recent availability of large-scale genomic resources enables us to conduct so called genome-wide association studies (GWAS) and genomic prediction (GP) studies, particularly with next-generation sequencing (NGS) data. The effectiveness of GWAS and GP depends on not only their mathematical models, but the quality and quantity of variants employed in the analysis. In NGS single nucleotide polymorphism (SNP) calling, conventional tools ideally require more reads for higher SNP sensitivity and accuracy. In this study, we aimed to develop a tool, Heap, that enables robustly sensitive and accurate calling of SNPs, particularly with a low coverage NGS data, which must be aligned to the reference genome sequences in advance. To reduce false positive SNPs, Heap determines genotypes and calls SNPs at each site except for sites at the both ends of reads or containing a minor allele supported by only one read. Performance comparison with existing tools showed that Heap achieved the highest F-scores with low coverage (7X) restriction-site associated DNA sequencing reads of sorghum and rice individuals. This will facilitate cost-effective GWAS and GP studies in this NGS era. Code and documentation of Heap are freely available from https://github.com/meiji-bioinf/heap (29 March 2017, date last accessed) and our web site (http://bioinf.mind.meiji.ac.jp/lab/en/tools.html (29 March 2017, date last accessed)).

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

Distinct neutrophil subpopulations phenotype by flow cytometry in myelodysplastic syndromes.

Science.gov (United States)

Vikentiou, Myrofora; Psarra, Katerina; Kapsimali, Violetta; Liapis, Konstantinos; Michael, Michalis; Tsionos, Konstantinos; Lianidou, Evi; Papasteriades, Chryssa

2009-03-01

The cardinal feature of myelodysplastic syndromes (MDS) is dysplasia involving one or more myeloid cell lineages. In the present study, we used 4-color flow cytometric analysis to investigate dysgranulopoiesis in bone marrow specimens from 65 patients with MDS. The antigen expression patterns of total neutrophil granulocytes (TNG) and of the two distinct neutrophil granulocytic subpopulations (NGSs), NGS-1 (dimmer CD45 expression) and NGS-2 (stronger CD45 expression) identified on the side scatter (SS) vs. CD45-intensity plot, were studied. The neutrophil granulocytes from patients with MDS showed characteristic antigen expression aberrancies which were more pronounced in NGS-2 subpopulation. Studying separately the NGS-2 subpopulation with the CD16/MPO/LF combination, the low CD16(+)/MPO(+) and low CD16(+)/LF(+) percentages seemed to discriminate between lower-risk and higher-risk patients with MDS in most occasions. Furthermore, a detailed assessment of the NGS-1 and NGS-2 immunophenotypic patterns revealed early dysplastic changes, not otherwise observed by standard TNG analysis, especially in cases of lower-risk MDS.

Analysis of Pre-Analytic Factors Affecting the Success of Clinical Next-Generation Sequencing of Solid Organ Malignancies

International Nuclear Information System (INIS)

Chen, Hui; Luthra, Rajyalakshmi; Goswami, Rashmi S.; Singh, Rajesh R.; Roy-Chowdhuri, Sinchita

2015-01-01

Application of next-generation sequencing (NGS) technology to routine clinical practice has enabled characterization of personalized cancer genomes to identify patients likely to have a response to targeted therapy. The proper selection of tumor sample for downstream NGS based mutational analysis is critical to generate accurate results and to guide therapeutic intervention. However, multiple pre-analytic factors come into play in determining the success of NGS testing. In this review, we discuss pre-analytic requirements for AmpliSeq PCR-based sequencing using Ion Torrent Personal Genome Machine (PGM) (Life Technologies), a NGS sequencing platform that is often used by clinical laboratories for sequencing solid tumors because of its low input DNA requirement from formalin fixed and paraffin embedded tissue. The success of NGS mutational analysis is affected not only by the input DNA quantity but also by several other factors, including the specimen type, the DNA quality, and the tumor cellularity. Here, we review tissue requirements for solid tumor NGS based mutational analysis, including procedure types, tissue types, tumor volume and fraction, decalcification, and treatment effects

Analysis of Pre-Analytic Factors Affecting the Success of Clinical Next-Generation Sequencing of Solid Organ Malignancies

Energy Technology Data Exchange (ETDEWEB)

Chen, Hui [Department of Pathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030 (United States); Luthra, Rajyalakshmi, E-mail: rluthra@mdanderson.org; Goswami, Rashmi S.; Singh, Rajesh R. [Department of Hematopathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030 (United States); Roy-Chowdhuri, Sinchita [Department of Pathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030 (United States)

2015-08-28

Application of next-generation sequencing (NGS) technology to routine clinical practice has enabled characterization of personalized cancer genomes to identify patients likely to have a response to targeted therapy. The proper selection of tumor sample for downstream NGS based mutational analysis is critical to generate accurate results and to guide therapeutic intervention. However, multiple pre-analytic factors come into play in determining the success of NGS testing. In this review, we discuss pre-analytic requirements for AmpliSeq PCR-based sequencing using Ion Torrent Personal Genome Machine (PGM) (Life Technologies), a NGS sequencing platform that is often used by clinical laboratories for sequencing solid tumors because of its low input DNA requirement from formalin fixed and paraffin embedded tissue. The success of NGS mutational analysis is affected not only by the input DNA quantity but also by several other factors, including the specimen type, the DNA quality, and the tumor cellularity. Here, we review tissue requirements for solid tumor NGS based mutational analysis, including procedure types, tissue types, tumor volume and fraction, decalcification, and treatment effects.

Analysis of Pre-Analytic Factors Affecting the Success of Clinical Next-Generation Sequencing of Solid Organ Malignancies

Directory of Open Access Journals (Sweden)

Hui Chen

2015-08-01

Full Text Available Application of next-generation sequencing (NGS technology to routine clinical practice has enabled characterization of personalized cancer genomes to identify patients likely to have a response to targeted therapy. The proper selection of tumor sample for downstream NGS based mutational analysis is critical to generate accurate results and to guide therapeutic intervention. However, multiple pre-analytic factors come into play in determining the success of NGS testing. In this review, we discuss pre-analytic requirements for AmpliSeq PCR-based sequencing using Ion Torrent Personal Genome Machine (PGM (Life Technologies, a NGS sequencing platform that is often used by clinical laboratories for sequencing solid tumors because of its low input DNA requirement from formalin fixed and paraffin embedded tissue. The success of NGS mutational analysis is affected not only by the input DNA quantity but also by several other factors, including the specimen type, the DNA quality, and the tumor cellularity. Here, we review tissue requirements for solid tumor NGS based mutational analysis, including procedure types, tissue types, tumor volume and fraction, decalcification, and treatment effects.

Applying Ancestry and Sex Computation as a Quality Control Tool in Targeted Next-Generation Sequencing.

Science.gov (United States)

Mathias, Patrick C; Turner, Emily H; Scroggins, Sheena M; Salipante, Stephen J; Hoffman, Noah G; Pritchard, Colin C; Shirts, Brian H

2016-03-01

To apply techniques for ancestry and sex computation from next-generation sequencing (NGS) data as an approach to confirm sample identity and detect sample processing errors. We combined a principal component analysis method with k-nearest neighbors classification to compute the ancestry of patients undergoing NGS testing. By combining this calculation with X chromosome copy number data, we determined the sex and ancestry of patients for comparison with self-report. We also modeled the sensitivity of this technique in detecting sample processing errors. We applied this technique to 859 patient samples with reliable self-report data. Our k-nearest neighbors ancestry screen had an accuracy of 98.7% for patients reporting a single ancestry. Visual inspection of principal component plots was consistent with self-report in 99.6% of single-ancestry and mixed-ancestry patients. Our model demonstrates that approximately two-thirds of potential sample swaps could be detected in our patient population using this technique. Patient ancestry can be estimated from NGS data incidentally sequenced in targeted panels, enabling an inexpensive quality control method when coupled with patient self-report. © American Society for Clinical Pathology, 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

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...

Public Space, Public Waste, and the Right to the City.

Science.gov (United States)

Chikarmane, Poornima

2016-08-01

I draw on my experiences as an organizer with a waste-pickers collective, Kagad Kach Patra Kashtakari Panchayat in Pune, India, to reflect on the power dynamics in control of public space. The Pune Municipal Corporation (PMC), a public body, has used public resources to facilitate and enable accumulation by private companies, who have not been able to produce what they had committed to in the processing of waste. The waste pickers, in alliance with affected village-based land agitation committees, have mobilized against the dumping that is ruining their way of life, environments, and health, and are fighting for their own integration into waste value chains. The article uses the frame of David Harvey's(1) "right to the city"; a key part of the mobilizing work with waste pickers has been Freirean conscientization methods to spread awareness of the economic importance, to the city and to the planet, of waste recycling. © The Author(s) 2016.

Quantifying low-frequency revertants in oral poliovirus vaccine using next generation sequencing.

Science.gov (United States)

Sarcey, Eric; Serres, Aurélie; Tindy, Fabrice; Chareyre, Audrey; Ng, Siemon; Nicolas, Marine; Vetter, Emmanuelle; Bonnevay, Thierry; Abachin, Eric; Mallet, Laurent

2017-08-01

Spontaneous reversion to neurovirulence of live attenuated oral poliovirus vaccine (OPV) serotype 3 (chiefly involving the n.472U>C mutation), must be monitored during production to ensure vaccine safety and consistency. Mutant analysis by polymerase chain reaction and restriction enzyme cleavage (MAPREC) has long been endorsed by the World Health Organization as the preferred in vitro test for this purpose; however, it requires radiolabeling, which is no longer supported by many laboratories. We evaluated the performance and suitability of next generation sequencing (NGS) as an alternative to MAPREC. The linearity of NGS was demonstrated at revertant concentrations equivalent to the study range of 0.25%-1.5%. NGS repeatability and intermediate precision were comparable across all tested samples, and NGS was highly reproducible, irrespective of sequencing platform or analysis software used. NGS was performed on OPV serotype 3 working seed lots and monovalent bulks (n=21) that were previously tested using MAPREC, and which covered the representative range of vaccine production. Percentages of 472-C revertants identified by NGS and MAPREC were comparable and highly correlated (r≥0.80), with a Pearson correlation coefficient of 0.95585 (p<0.0001). NGS demonstrated statistically equivalent performance to that of MAPREC for quantifying low-frequency OPV serotype 3 revertants, and offers a valid alternative to MAPREC. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

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.

Heap: a highly sensitive and accurate SNP detection tool for low-coverage high-throughput sequencing data

KAUST Repository

Kobayashi, Masaaki; Ohyanagi, Hajime; Takanashi, Hideki; Asano, Satomi; Kudo, Toru; Kajiya-Kanegae, Hiromi; Nagano, Atsushi J.; Tainaka, Hitoshi; Tokunaga, Tsuyoshi; Sazuka, Takashi; Iwata, Hiroyoshi; Tsutsumi, Nobuhiro; Yano, Kentaro

2017-01-01

and GP depends on not only their mathematical models, but the quality and quantity of variants employed in the analysis. In NGS single nucleotide polymorphism (SNP) calling, conventional tools ideally require more reads for higher SNP sensitivity

Next-Generation Sequencing in Clinical Molecular Diagnostics of Cancer: Advantages and Challenges

Directory of Open Access Journals (Sweden)

Rajyalakshmi Luthra

2015-10-01

Full Text Available The application of next-generation sequencing (NGS to characterize cancer genomes has resulted in the discovery of numerous genetic markers. Consequently, the number of markers that warrant routine screening in molecular diagnostic laboratories, often from limited tumor material, has increased. This increased demand has been difficult to manage by traditional low- and/or medium-throughput sequencing platforms. Massively parallel sequencing capabilities of NGS provide a much-needed alternative for mutation screening in multiple genes with a single low investment of DNA. However, implementation of NGS technologies, most of which are for research use only (RUO, in a diagnostic laboratory, needs extensive validation in order to establish Clinical Laboratory Improvement Amendments (CLIA and College of American Pathologists (CAP-compliant performance characteristics. Here, we have reviewed approaches for validation of NGS technology for routine screening of tumors. We discuss the criteria for selecting gene markers to include in the NGS panel and the deciding factors for selecting target capture approaches and sequencing platforms. We also discuss challenges in result reporting, storage and retrieval of the voluminous sequencing data and the future potential of clinical NGS.

Non-invasive prenatal diagnosis of achondroplasia and thanatophoric dysplasia: next-generation sequencing allows for a safer, more accurate, and comprehensive approach.

Science.gov (United States)

Chitty, Lyn S; Mason, Sarah; Barrett, Angela N; McKay, Fiona; Lench, Nicholas; Daley, Rebecca; Jenkins, Lucy A

2015-07-01

Accurate prenatal diagnosis of genetic conditions can be challenging and usually requires invasive testing. Here, we demonstrate the potential of next-generation sequencing (NGS) for the analysis of cell-free DNA in maternal blood to transform prenatal diagnosis of monogenic disorders. Analysis of cell-free DNA using a PCR and restriction enzyme digest (PCR-RED) was compared with a novel NGS assay in pregnancies at risk of achondroplasia and thanatophoric dysplasia. PCR-RED was performed in 72 cases and was correct in 88.6%, inconclusive in 7% with one false negative. NGS was performed in 47 cases and was accurate in 96.2% with no inconclusives. Both approaches were used in 27 cases, with NGS giving the correct result in the two cases inconclusive with PCR-RED. NGS provides an accurate, flexible approach to non-invasive prenatal diagnosis of de novo and paternally inherited mutations. It is more sensitive than PCR-RED and is ideal when screening a gene with multiple potential pathogenic mutations. These findings highlight the value of NGS in the development of non-invasive prenatal diagnosis for other monogenic disorders. © 2015 John Wiley & Sons, Ltd.

Prescreening of microbial populations for the assessment of sequencing potential.

Science.gov (United States)

Hanning, Irene B; Ricke, Steven C

2011-01-01

Next-generation sequencing (NGS) is a powerful tool that can be utilized to profile and compare microbial populations. By amplifying a target gene present in all bacteria and subsequently sequencing amplicons, the bacteria genera present in the populations can be identified and compared. In some scenarios, little to no difference may exist among microbial populations being compared in which case a prescreening method would be practical to determine which microbial populations would be suitable for further analysis by NGS. Denaturing density-gradient electrophoresis (DGGE) is relatively cheaper than NGS and the data comparing microbial populations are ready to be viewed immediately after electrophoresis. DGGE follows essentially the same initial methodology as NGS by targeting and amplifying the 16S rRNA gene. However, as opposed to sequencing amplicons, DGGE amplicons are analyzed by electrophoresis. By prescreening microbial populations with DGGE, more efficient use of NGS methods can be accomplished. In this chapter, we outline the protocol for DGGE targeting the same gene (16S rRNA) that would be targeted for NGS to compare and determine differences in microbial populations from a wide range of ecosystems.

Targeted next-generation sequencing in monogenic dyslipidemias.

Science.gov (United States)

Hegele, Robert A; Ban, Matthew R; Cao, Henian; McIntyre, Adam D; Robinson, John F; Wang, Jian

2015-04-01

To evaluate the potential clinical translation of high-throughput next-generation sequencing (NGS) methods in diagnosis and management of dyslipidemia. Recent NGS experiments indicate that most causative genes for monogenic dyslipidemias are already known. Thus, monogenic dyslipidemias can now be diagnosed using targeted NGS. Targeting of dyslipidemia genes can be achieved by either: designing custom reagents for a dyslipidemia-specific NGS panel; or performing genome-wide NGS and focusing on genes of interest. Advantages of the former approach are lower cost and limited potential to detect incidental pathogenic variants unrelated to dyslipidemia. However, the latter approach is more flexible because masking criteria can be altered as knowledge advances, with no need for re-design of reagents or follow-up sequencing runs. Also, the cost of genome-wide analysis is decreasing and ethical concerns can likely be mitigated. DNA-based diagnosis is already part of the clinical diagnostic algorithms for familial hypercholesterolemia. Furthermore, DNA-based diagnosis is supplanting traditional biochemical methods to diagnose chylomicronemia caused by deficiency of lipoprotein lipase or its co-factors. The increasing availability and decreasing cost of clinical NGS for dyslipidemia means that its potential benefits can now be evaluated on a larger scale.

Applications of Next-Generation Sequencing Technologies to Diagnostic Virology

Directory of Open Access Journals (Sweden)

Giorgio Palù

2011-11-01

Full Text Available Novel DNA sequencing techniques, referred to as “next-generation” sequencing (NGS, provide high speed and throughput that can produce an enormous volume of sequences with many possible applications in research and diagnostic settings. In this article, we provide an overview of the many applications of NGS in diagnostic virology. NGS techniques have been used for high-throughput whole viral genome sequencing, such as sequencing of new influenza viruses, for detection of viral genome variability and evolution within the host, such as investigation of human immunodeficiency virus and human hepatitis C virus quasispecies, and monitoring of low-abundance antiviral drug-resistance mutations. NGS techniques have been applied to metagenomics-based strategies for the detection of unexpected disease-associated viruses and for the discovery of novel human viruses, including cancer-related viruses. Finally, the human virome in healthy and disease conditions has been described by NGS-based metagenomics.

Statistical analysis of next generation sequencing data

CERN Document Server

Nettleton, Dan

2014-01-01

Next Generation Sequencing (NGS) is the latest high throughput technology to revolutionize genomic research. NGS generates massive genomic datasets that play a key role in the big data phenomenon that surrounds us today. To extract signals from high-dimensional NGS data and make valid statistical inferences and predictions, novel data analytic and statistical techniques are needed. This book contains 20 chapters written by prominent statisticians working with NGS data. The topics range from basic preprocessing and analysis with NGS data to more complex genomic applications such as copy number variation and isoform expression detection. Research statisticians who want to learn about this growing and exciting area will find this book useful. In addition, many chapters from this book could be included in graduate-level classes in statistical bioinformatics for training future biostatisticians who will be expected to deal with genomic data in basic biomedical research, genomic clinical trials and personalized med...

Next-generation sequencing library preparation method for identification of RNA viruses on the Ion Torrent Sequencing Platform.

Science.gov (United States)

Chen, Guiqian; Qiu, Yuan; Zhuang, Qingye; Wang, Suchun; Wang, Tong; Chen, Jiming; Wang, Kaicheng

2018-05-09

Next generation sequencing (NGS) is a powerful tool for the characterization, discovery, and molecular identification of RNA viruses. There were multiple NGS library preparation methods published for strand-specific RNA-seq, but some methods are not suitable for identifying and characterizing RNA viruses. In this study, we report a NGS library preparation method to identify RNA viruses using the Ion Torrent PGM platform. The NGS sequencing adapters were directly inserted into the sequencing library through reverse transcription and polymerase chain reaction, without fragmentation and ligation of nucleic acids. The results show that this method is simple to perform, able to identify multiple species of RNA viruses in clinical samples.

Anti-tumor Study of Chondroitin Sulfate-Methotrexate Nanogels

Science.gov (United States)

Wang, Jinyu; Zhao, Weibo; Chen, Haixiao; Qin, An; Zhu, Peizhi

2017-10-01

Self-assembly nanogels (NGs) were formed by bioconjugating methotrexate (MTX) with chondroitin sulfate (CS). MTX-CS NGs can greatly enhance the solubility and improve the delivery efficacy of MTX due to the CD44 binding property of CS. Vivo experiments revealed that MTX-CS NGs showed less toxicity than MTX. MTX-CS NGs can improve the anti-tumor effect while reducing the side effects of MTX. Due to their CD44 binding property, chondroitin sulfate-drug conjugates could be a promising and efficient platform for improving the solubility of sparingly soluble drug molecules as well as targeted delivery to cancer cells and tumor tissues.

Evolution of CANDU reactor design

International Nuclear Information System (INIS)

Pon, G.A.

1978-08-01

The CANDU (CANada Deuterium Uranium) design had its begin-ings in the early 1950's with the preliminary engineering studies that led to the 20 MW(e) NPD (Nuclear Power Demonstration) and the 200 MW(e) Douglas Point station . The next decade saw the first operation of both these stations and the commitment of the 2000 MW(e) Pickering and 3000 MW(e) Bruce plants. The present decade has witnessed the excellent performance of Pickering and Bruce and commitments to construct Gentilly-2, Cordoba, Pt. Lepreau, Wolsung, Pickering B, Bruce B and Darlington. In most cases, successive CANDU designs have meant an increase in plant output. Evolutionary developments have been made to fit the requirements of higher ratings and sizes, new regulations, better reliability and maintainability and lower costs. These changes, which are described system by system, have been introduced in the course of engineering parallel reactor projects with overlapping construction schedules -circumstances which ensure close contact with the practical realities of economics, manufacturing functions, construction activities and performance in commissioning. Features for one project furnished alternative concepts for others still on the drawing board and the experience gained in the first application yielded a sound basis for its re-use in succeeding projects. Thus the experiences gained in NPD, Douglas Point, Gentilly-1 and KANUPP have contributed to Pickering and Bruce, which in turn have contributed to the design of Gentilly-2. (author)

gCUP: rapid GPU-based HIV-1 co-receptor usage prediction for next-generation sequencing.

Science.gov (United States)

Olejnik, Michael; Steuwer, Michel; Gorlatch, Sergei; Heider, Dominik

2014-11-15

Next-generation sequencing (NGS) has a large potential in HIV diagnostics, and genotypic prediction models have been developed and successfully tested in the recent years. However, albeit being highly accurate, these computational models lack computational efficiency to reach their full potential. In this study, we demonstrate the use of graphics processing units (GPUs) in combination with a computational prediction model for HIV tropism. Our new model named gCUP, parallelized and optimized for GPU, is highly accurate and can classify >175 000 sequences per second on an NVIDIA GeForce GTX 460. The computational efficiency of our new model is the next step to enable NGS technologies to reach clinical significance in HIV diagnostics. Moreover, our approach is not limited to HIV tropism prediction, but can also be easily adapted to other settings, e.g. drug resistance prediction. The source code can be downloaded at http://www.heiderlab.de d.heider@wz-straubing.de. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Light-weight reference-based compression of FASTQ data.

Science.gov (United States)

Zhang, Yongpeng; Li, Linsen; Yang, Yanli; Yang, Xiao; He, Shan; Zhu, Zexuan

2015-06-09

The exponential growth of next generation sequencing (NGS) data has posed big challenges to data storage, management and archive. Data compression is one of the effective solutions, where reference-based compression strategies can typically achieve superior compression ratios compared to the ones not relying on any reference. This paper presents a lossless light-weight reference-based compression algorithm namely LW-FQZip to compress FASTQ data. The three components of any given input, i.e., metadata, short reads and quality score strings, are first parsed into three data streams in which the redundancy information are identified and eliminated independently. Particularly, well-designed incremental and run-length-limited encoding schemes are utilized to compress the metadata and quality score streams, respectively. To handle the short reads, LW-FQZip uses a novel light-weight mapping model to fast map them against external reference sequence(s) and produce concise alignment results for storage. The three processed data streams are then packed together with some general purpose compression algorithms like LZMA. LW-FQZip was evaluated on eight real-world NGS data sets and achieved compression ratios in the range of 0.111-0.201. This is comparable or superior to other state-of-the-art lossless NGS data compression algorithms. LW-FQZip is a program that enables efficient lossless FASTQ data compression. It contributes to the state of art applications for NGS data storage and transmission. LW-FQZip is freely available online at: http://csse.szu.edu.cn/staff/zhuzx/LWFQZip.

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.

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

Exploring the Mechanisms of Gastrointestinal Cancer Development Using Deep Sequencing Analysis

International Nuclear Information System (INIS)

Matsumoto, Tomonori; Shimizu, Takahiro; Takai, Atsushi; Marusawa, Hiroyuki

2015-01-01

Next-generation sequencing (NGS) technologies have revolutionized cancer genomics due to their high throughput sequencing capacity. Reports of the gene mutation profiles of various cancers by many researchers, including international cancer genome research consortia, have increased over recent years. In addition to detecting somatic mutations in tumor cells, NGS technologies enable us to approach the subject of carcinogenic mechanisms from new perspectives. Deep sequencing, a method of optimizing the high throughput capacity of NGS technologies, allows for the detection of genetic aberrations in small subsets of premalignant and/or tumor cells in noncancerous chronically inflamed tissues. Genome-wide NGS data also make it possible to clarify the mutational signatures of each cancer tissue by identifying the precise pattern of nucleotide alterations in the cancer genome, providing new information regarding the mechanisms of tumorigenesis. In this review, we highlight these new methods taking advantage of NGS technologies, and discuss our current understanding of carcinogenic mechanisms elucidated from such approaches

Next-generation sequencing and culture-based techniques offer complementary insights into fungi and prokaryotes in beach sands.

Science.gov (United States)

Romão, Daniela; Staley, Christopher; Ferreira, Filipa; Rodrigues, Raquel; Sabino, Raquel; Veríssimo, Cristina; Wang, Ping; Sadowsky, Michael; Brandão, João

2017-06-15

A next-generation sequencing (NGS) approach, in conjunction with culture-based methods, was used to examine fungal and prokaryotic communities for the presence of potential pathogens in beach sands throughout Portugal. Culture-based fungal enumeration revealed low and variable concentrations of the species targeted (yeasts and dermatophytes), which were underrepresented in the community characterized by NGS targeting the ITS1 region. Conversely, NGS indicated that the potentially pathogenic species Purpureocillium liliacinum comprised nearly the entire fungal community. Culturable fecal indicator bacterial concentrations were low throughout the study and unrelated to communities characterized by NGS. Notably, the prokaryotic communities characterized revealed a considerable abundance of archaea. Results highlight differences in communities between methods in beach sand monitoring but indicate the techniques offer complementary insights. Thus, there is a need to leverage culture-based methods with NGS methods, using a toolbox approach, to determine appropriate targets and metrics for beach sand monitoring to adequately protect public health. Copyright © 2017. Published by Elsevier Ltd.

Exploring the Mechanisms of Gastrointestinal Cancer Development Using Deep Sequencing Analysis

Energy Technology Data Exchange (ETDEWEB)

Matsumoto, Tomonori; Shimizu, Takahiro; Takai, Atsushi; Marusawa, Hiroyuki, E-mail: maru@kuhp.kyoto-u.ac.jp [Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, 54 Shogoin-Kawahara-cho, Sakyo-ku, Kyoto 606-8507 (Japan)

2015-06-15

Next-generation sequencing (NGS) technologies have revolutionized cancer genomics due to their high throughput sequencing capacity. Reports of the gene mutation profiles of various cancers by many researchers, including international cancer genome research consortia, have increased over recent years. In addition to detecting somatic mutations in tumor cells, NGS technologies enable us to approach the subject of carcinogenic mechanisms from new perspectives. Deep sequencing, a method of optimizing the high throughput capacity of NGS technologies, allows for the detection of genetic aberrations in small subsets of premalignant and/or tumor cells in noncancerous chronically inflamed tissues. Genome-wide NGS data also make it possible to clarify the mutational signatures of each cancer tissue by identifying the precise pattern of nucleotide alterations in the cancer genome, providing new information regarding the mechanisms of tumorigenesis. In this review, we highlight these new methods taking advantage of NGS technologies, and discuss our current understanding of carcinogenic mechanisms elucidated from such approaches.

Next-Generation Mitogenomics: A Comparison of Approaches Applied to Caecilian Amphibian Phylogeny

OpenAIRE

Maddock, Simon T.; Briscoe, Andrew G.; Wilkinson, Mark; Waeschenbach, Andrea; San Mauro, Diego; Day, Julia J.; Littlewood, D. Tim J.; Foster, Peter G.; Nussbaum, Ronald A.; Gower, David J.

2016-01-01

Mitochondrial genome (mitogenome) sequences are being generated with increasing speed due to the advances of next-generation sequencing (NGS) technology and associated analytical tools. However, detailed comparisons to explore the utility of alternative NGS approaches applied to the same taxa have not been undertaken. We compared a ‘traditional’ Sanger sequencing method with two NGS approaches (shotgun sequencing and non-indexed, multiplex amplicon sequencing) on four different sequencing pla...

Nispero: a cloud-computing based Scala tool specially suited for bioinformatics data processing

OpenAIRE

Evdokim Kovach; Alexey Alekhin; Eduardo Pareja Tobes; Raquel Tobes; Eduardo Pareja; Marina Manrique

2014-01-01

Nowadays it is widely accepted that the bioinformatics data analysis is a real bottleneck in many research activities related to life sciences. High-throughput technologies like Next Generation Sequencing (NGS) have completely reshaped the biology and bioinformatics landscape. Undoubtedly NGS has allowed important progress in many life-sciences related fields but has also presented interesting challenges in terms of computation capabilities and algorithms. Many kinds of tasks related with NGS...

Novel Tools for Conservation Genomics: Comparing Two High-Throughput Approaches for SNP Discovery in the Transcriptome of the European Hake

DEFF Research Database (Denmark)

Milano, Ilaria; Babbucci, Massimiliano; Panitz, Frank

2011-01-01

The growing accessibility to genomic resources using next-generation sequencing (NGS) technologies has revolutionized the application of molecular genetic tools to ecology and evolutionary studies in non-model organisms. Here we present the case study of the European hake (Merluccius merluccius),...

Routine use of next-generation sequencing for preimplantation genetic diagnosis of blastomeres obtained from embryos on day 3 in fresh in vitro fertilization cycles.

Science.gov (United States)

Łukaszuk, Krzysztof; Pukszta, Sebastian; Wells, Dagan; Cybulska, Celina; Liss, Joanna; Płóciennik, Łukasz; Kuczyński, Waldemar; Zabielska, Judyta

2015-04-01

To determine the usefulness of semiconductor-based next-generation sequencing (NGS) for cleavage-stage preimplantation genetic diagnosis (PGD) of aneuploidy. Prospective case-control study. A private center for reproductive medicine. A total of 45 patients underwent day-3 embryo biopsy with PGD and fresh cycle transfer. Additionally, 53 patients, matched according to age, anti-Müllerian hormone levels, antral follicles count, and infertility duration were selected as controls. Choice of embryos for transfer was based on the PGD NGS results. Clinical pregnancy rate (PR) per embryo transfer (ET) was the primary outcome. Secondary outcomes were implantation and miscarriage rates. The PR per transfer was higher in the NGS group (84.4% vs. 41.5%). The implantation rate (61.5% vs. 34.8%) was higher in the NGS group. The miscarriage rate was similar in the 2 groups (2.8% vs. 4.6%). We demonstrate the technical feasibility of NGS-based PGD involving cleavage-stage biopsy and fresh ETs. Encouraging data were obtained from a prospective trial using this approach, arguing that cleavage-stage NGS may represent a valuable addition to current aneuploidy screening methods. These findings require further validation in a well-designed randomized controlled trial. ACTRN12614001035617. Copyright © 2015 American Society for Reproductive Medicine. Published by Elsevier Inc. All rights reserved.

Histoimmunogenetics Markup Language 1.0: Reporting next generation sequencing-based HLA and KIR genotyping.

Science.gov (United States)

Milius, Robert P; Heuer, Michael; Valiga, Daniel; Doroschak, Kathryn J; Kennedy, Caleb J; Bolon, Yung-Tsi; Schneider, Joel; Pollack, Jane; Kim, Hwa Ran; Cereb, Nezih; Hollenbach, Jill A; Mack, Steven J; Maiers, Martin

2015-12-01

We present an electronic format for exchanging data for HLA and KIR genotyping with extensions for next-generation sequencing (NGS). This format addresses NGS data exchange by refining the Histoimmunogenetics Markup Language (HML) to conform to the proposed Minimum Information for Reporting Immunogenomic NGS Genotyping (MIRING) reporting guidelines (miring.immunogenomics.org). Our refinements of HML include two major additions. First, NGS is supported by new XML structures to capture additional NGS data and metadata required to produce a genotyping result, including analysis-dependent (dynamic) and method-dependent (static) components. A full genotype, consensus sequence, and the surrounding metadata are included directly, while the raw sequence reads and platform documentation are externally referenced. Second, genotype ambiguity is fully represented by integrating Genotype List Strings, which use a hierarchical set of delimiters to represent allele and genotype ambiguity in a complete and accurate fashion. HML also continues to enable the transmission of legacy methods (e.g. site-specific oligonucleotide, sequence-specific priming, and Sequence Based Typing (SBT)), adding features such as allowing multiple group-specific sequencing primers, and fully leveraging techniques that combine multiple methods to obtain a single result, such as SBT integrated with NGS. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

Orientation of cotton growers of multan district about heal hazards and pesticide use

International Nuclear Information System (INIS)

Haq, Q.U.; Hussain, R.; Ali, T.; Ahmad, M.

2008-01-01

Cotton growing farmers and cotton pickers are the twin pillars of cotton growing community. Cotton growing farmers (male) are involved in monitoring of quality and quantity of cotton crops by handsome usage of pesticides for better marketing of cotton crops. Whereas, cotton pickers (female) are involved in picking of cotton mainly. To assess their knowledge and source of knowledge about pesticides related health problems, the study was designed and conducted in 20 villages of district Multan selected by multistage random sampling technique. From the selected 20 villages, from the list bearing the villages, mouzas and union councils of district Multan, 220 cotton growers and 150 cotton pickers were selected by simple random sampling technique and interviewed through a reliable and validated interview schedule. The data collected were processed through Statistical Package for Social Sciences (SPSS). The results showed that 75% of cotton growing farmers were having orientation about side effects of pesticides whereas, almost 8% of cotton growers were having no knowledge about side effects of pesticides. (author)

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

AlignerBoost: A Generalized Software Toolkit for Boosting Next-Gen Sequencing Mapping Accuracy Using a Bayesian-Based Mapping Quality Framework.

Directory of Open Access Journals (Sweden)

Qi Zheng

2016-10-01

Full Text Available Accurate mapping of next-generation sequencing (NGS reads to reference genomes is crucial for almost all NGS applications and downstream analyses. Various repetitive elements in human and other higher eukaryotic genomes contribute in large part to ambiguously (non-uniquely mapped reads. Most available NGS aligners attempt to address this by either removing all non-uniquely mapping reads, or reporting one random or "best" hit based on simple heuristics. Accurate estimation of the mapping quality of NGS reads is therefore critical albeit completely lacking at present. Here we developed a generalized software toolkit "AlignerBoost", which utilizes a Bayesian-based framework to accurately estimate mapping quality of ambiguously mapped NGS reads. We tested AlignerBoost with both simulated and real DNA-seq and RNA-seq datasets at various thresholds. In most cases, but especially for reads falling within repetitive regions, AlignerBoost dramatically increases the mapping precision of modern NGS aligners without significantly compromising the sensitivity even without mapping quality filters. When using higher mapping quality cutoffs, AlignerBoost achieves a much lower false mapping rate while exhibiting comparable or higher sensitivity compared to the aligner default modes, therefore significantly boosting the detection power of NGS aligners even using extreme thresholds. AlignerBoost is also SNP-aware, and higher quality alignments can be achieved if provided with known SNPs. AlignerBoost's algorithm is computationally efficient, and can process one million alignments within 30 seconds on a typical desktop computer. AlignerBoost is implemented as a uniform Java application and is freely available at https://github.com/Grice-Lab/AlignerBoost.

Validation of the digital PCR system in tyrosine kinase inhibitor-resistant EGFR mutant non-small-cell lung cancer.

Science.gov (United States)

Masago, Katsuhiro; Fujita, Shiro; Hata, Akito; Okuda, Chiyuki; Yoshizumi, Yuko; Kaji, Reiko; Katakami, Nobuyuki; Hirata, Yukio; Yatabe, Yasushi

2018-03-01

The aim of this study was to compare the accuracy of the QuantStudio 3D Digital polymerase chain reaction (dPCR) system and a PCR-based next generation sequencing (NGS) system for detecting a secondary mutation in the epidermal growth factor receptor (EGFR) gene T790M in non-small cell lung cancer (NSCLC) patients previously diagnosed with EGFR-activating mutations. Twenty-five patients with NSCLC previously treated with EGFR-TKIs were examined. The patients were treated daily with either erlotinib or gefitinib. New biopsies, followed by DNA sequencing on an Ion Torrent systems using the Ion Torrent AmpliSeq Cancer Hotspot Panel and dPCR were performed. A comparison of NGS, sensitive PCR, and dPCR revealed that the sensitivities of NGS and dPCR were similar in this study. As well, T790M was detected in as low as about 5% of mutant allelic frequencies, which represented 5% of the total reads on site mapped reads in NGS and greater than 5% of the dPCR reads, which represented mutant and wild type copies. The strategy in which NGS sequencing is followed by revealed acquired mutation with dPCR may be a reasonable one. We demonstrated the utility of combining NGS and dPCR as a tool for monitoring T790M. NGS and dPCR with formalin-fixed paraffin-embedded (FFPE) specimens might become a standard genomic test for exploring acquired resistance to targeted molecular medicines. © 2018 Japanese Society of Pathology and John Wiley & Sons Australia, Ltd.

AlignerBoost: A Generalized Software Toolkit for Boosting Next-Gen Sequencing Mapping Accuracy Using a Bayesian-Based Mapping Quality Framework.

Science.gov (United States)

Zheng, Qi; Grice, Elizabeth A

2016-10-01

Accurate mapping of next-generation sequencing (NGS) reads to reference genomes is crucial for almost all NGS applications and downstream analyses. Various repetitive elements in human and other higher eukaryotic genomes contribute in large part to ambiguously (non-uniquely) mapped reads. Most available NGS aligners attempt to address this by either removing all non-uniquely mapping reads, or reporting one random or "best" hit based on simple heuristics. Accurate estimation of the mapping quality of NGS reads is therefore critical albeit completely lacking at present. Here we developed a generalized software toolkit "AlignerBoost", which utilizes a Bayesian-based framework to accurately estimate mapping quality of ambiguously mapped NGS reads. We tested AlignerBoost with both simulated and real DNA-seq and RNA-seq datasets at various thresholds. In most cases, but especially for reads falling within repetitive regions, AlignerBoost dramatically increases the mapping precision of modern NGS aligners without significantly compromising the sensitivity even without mapping quality filters. When using higher mapping quality cutoffs, AlignerBoost achieves a much lower false mapping rate while exhibiting comparable or higher sensitivity compared to the aligner default modes, therefore significantly boosting the detection power of NGS aligners even using extreme thresholds. AlignerBoost is also SNP-aware, and higher quality alignments can be achieved if provided with known SNPs. AlignerBoost's algorithm is computationally efficient, and can process one million alignments within 30 seconds on a typical desktop computer. AlignerBoost is implemented as a uniform Java application and is freely available at https://github.com/Grice-Lab/AlignerBoost.

Performance of next-generation sequencing on small tumor specimens and/or low tumor content samples using a commercially available platform.

Directory of Open Access Journals (Sweden)

Scott Morris

Full Text Available Next generation sequencing tests (NGS are usually performed on relatively small core biopsy or fine needle aspiration (FNA samples. Data is limited on what amount of tumor by volume or minimum number of FNA passes are needed to yield sufficient material for running NGS. We sought to identify the amount of tumor for running the PCDx NGS platform.2,723 consecutive tumor tissues of all cancer types were queried and reviewed for inclusion. Information on tumor volume, success of performing NGS, and results of NGS were compiled. Assessment of sequence analysis, mutation calling and sensitivity, quality control, drug associations, and data aggregation and analysis were performed.6.4% of samples were rejected from all testing due to insufficient tumor quantity. The number of genes with insufficient sensitivity make definitive mutation calls increased as the percentage of tumor decreased, reaching statistical significance below 5% tumor content. The number of drug associations also decreased with a lower percentage of tumor, but this difference only became significant between 1-3%. The number of drug associations did decrease with smaller tissue size as expected. Neither specimen size or percentage of tumor affected the ability to pass mRNA quality control. A tumor area of 10 mm2 provides a good margin of error for specimens to yield adequate drug association results.Specimen suitability remains a major obstacle to clinical NGS testing. We determined that PCR-based library creation methods allow the use of smaller specimens, and those with a lower percentage of tumor cells to be run on the PCDx NGS platform.

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

Effects of Carbopol® 934 proportion on nanoemulsion gel for topical and transdermal drug delivery: a skin permeation study

Directory of Open Access Journals (Sweden)

Zheng Y

2016-11-01

Full Text Available Yin Zheng,1 Wu-Qing Ouyang,1 Yun-Peng Wei,1 Shahid Faraz Syed,2,3 Chao-Shuang Hao,1 Bo-Zhen Wang,4 Yan-Hong Shang1,5 1Department of Basic Veterinary Sciences, College of Veterinary Medicine, 2Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi; 3Faculty of Veterinary and Animal Sciences, Lasbella University of Agriculture Water and Marine Sciences, Uthal Baluchistan, Pakistan; 4College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang, 5College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China Abstract: Nanoemulsions (NEs are used as transdermal drug delivery systems for systematic therapeutic purposes. We hypothesized that the skin permeation profile of an NE could be modulated by incorporating it into a hydrogel containing differing proportions of thickening agent. The objectives of this study were as follows: 1 to determine the stability and skin irritability of NE gels (NGs containing 1%, 2%, and 3% (w/w Carbopol® 934 (CP934 (termed NG1, NG2, and NG3, respectively; 2 to compare the skin permeation profiles and drug deposition patterns of the NGs; and 3 to visualize the drug delivery routes of the NGs. Terbinafine and citral were incorporated into the NGs as model drugs. Ex vivo skin permeation tests indicated that the percutaneous flux rates of terbinafine decreased in the order NE (215 µg/cm2 > NG1 (213 µg/cm2 > NG2 (123 µg/cm2 > NG3 (74.3 µg/cm2. The flux rates of citral decreased in the order NE (1,026 µg/cm2 > NG1 (1,021 µg/cm2 > NG2 (541 µg/cm2 > NG3 (353 µg/cm2. The NGs accumulated greater amounts of the drugs in the stratum corneum and less in the epidermis/dermis than did the NE (P<0.05 over a period of 12 h. Laser scanning confocal microscopy indicated that the NGs altered the main drug delivery routes from skin appendages to intercellular paths. Histological images suggested

Get your high-quality low-cost genome sequence

NARCIS (Netherlands)

Faino, L.; Thomma, B.P.H.J.

2014-01-01

The study of whole-genome sequences has become essential for almost all branches of biological research. Next-generation sequencing (NGS) has revolutionized the scalability, speed, and resolution of sequencing and brought genomic science within reach of academic laboratories that study non-model

Recent fuel handling experience in Canada

International Nuclear Information System (INIS)

Welch, A.C.

1991-01-01

For many years, good operation of the fuel handling system at Ontario Hydro's nuclear stations has been taken for granted with the unavailability of the station arising from fuel handling system-related problems usually contributing less than one percent of the total unavailability of the stations. While the situation at the newer Hydro stations continues generally to be good (with the specific exception of some units at Pickering B) some specific and some general problems have caused significant loss of availability at the older plants (Pickering A and Bruce A). Generally the experience at the 600 MWe units in Canada has also continued to be good with Point Lepreau leading the world in availability. As a result of working to correct identified deficiencies, there were some changes for the better as some items of equipment that were a chronic source of trouble were replaced with improved components. In addition, the fuel handling system has been used three times as a delivery system for large-scale non destructive examination of the pressure tubes, twice at Bruce and once at Pickering and performing these inspections this way has saved many days of reactor downtime. Under COG there are several programs to develop improved versions of some of the main assemblies of the fuelling machine head. This paper will generally cover the events relating to Pickering in more detail but will describe the problems with the Bruce Fuelling Machine Bridges since the 600 MW 1P stations have a bridge drive arrangement that is somewhat similar to Bruce

Nanographenes as electron-deficient cores of donor-acceptor systems.

Science.gov (United States)

Liu, Yu-Min; Hou, Hao; Zhou, Yan-Zhen; Zhao, Xin-Jing; Tang, Chun; Tan, Yuan-Zhi; Müllen, Klaus

2018-05-15

Conjugation of nanographenes (NGs) with electro-active molecules can establish donor-acceptor π-systems in which the former generally serve as the electron-donating moieties due to their electronic-rich nature. In contrast, here we report a series of reversed donor-acceptor structures are obtained by C-N coupling of electron-deficient perchlorinated NGs with electron-rich anilines. Selective amination at the vertexes of the NGs is unambiguously shown through X-ray crystallography. By varying the donating ability of the anilino groups, the optical and assembly properties of donor-acceptor NGs can be finely modulated. The electron-deficient concave core of the resulting conjugates can host electron-rich guest molecules by intermolecular donor-acceptor interactions and gives rise to charge-transfer supramolecular architectures.

Next-generation sequencing for genetic testing of familial colorectal cancer syndromes.

Science.gov (United States)

Simbolo, Michele; Mafficini, Andrea; Agostini, Marco; Pedrazzani, Corrado; Bedin, Chiara; Urso, Emanuele D; Nitti, Donato; Turri, Giona; Scardoni, Maria; Fassan, Matteo; Scarpa, Aldo

2015-01-01

Genetic screening in families with high risk to develop colorectal cancer (CRC) prevents incurable disease and permits personalized therapeutic and follow-up strategies. The advancement of next-generation sequencing (NGS) technologies has revolutionized the throughput of DNA sequencing. A series of 16 probands for either familial adenomatous polyposis (FAP; 8 cases) or hereditary nonpolyposis colorectal cancer (HNPCC; 8 cases) were investigated for intragenic mutations in five CRC familial syndromes-associated genes (APC, MUTYH, MLH1, MSH2, MSH6) applying both a custom multigene Ion AmpliSeq NGS panel and conventional Sanger sequencing. Fourteen pathogenic variants were detected in 13/16 FAP/HNPCC probands (81.3 %); one FAP proband presented two co-existing pathogenic variants, one in APC and one in MUTYH. Thirteen of these 14 pathogenic variants were detected by both NGS and Sanger, while one MSH2 mutation (L280FfsX3) was identified only by Sanger sequencing. This is due to a limitation of the NGS approach in resolving sequences close or within homopolymeric stretches of DNA. To evaluate the performance of our NGS custom panel we assessed its capability to resolve the DNA sequences corresponding to 2225 pathogenic variants reported in the COSMIC database for APC, MUTYH, MLH1, MSH2, MSH6. Our NGS custom panel resolves the sequences where 2108 (94.7 %) of these variants occur. The remaining 117 mutations reside inside or in close proximity to homopolymer stretches; of these 27 (1.2 %) are imprecisely identified by the software but can be resolved by visual inspection of the region, while the remaining 90 variants (4.0 %) are blind spots. In summary, our custom panel would miss 4 % (90/2225) of pathogenic variants that would need a small set of Sanger sequencing reactions to be solved. The multiplex NGS approach has the advantage of analyzing multiple genes in multiple samples simultaneously, requiring only a reduced number of Sanger sequences to resolve

Next-Generation Sequencing of Antibody Display Repertoires

Directory of Open Access Journals (Sweden)

Romain Rouet

2018-02-01

Full Text Available In vitro selection technology has transformed the development of therapeutic monoclonal antibodies. Using methods such as phage, ribosome, and yeast display, high affinity binders can be selected from diverse repertoires. Here, we review strategies for the next-generation sequencing (NGS of phage- and other antibody-display libraries, as well as NGS platforms and analysis tools. Moreover, we discuss recent examples relating to the use of NGS to assess library diversity, clonal enrichment, and affinity maturation.

What can next generation sequencing do for you? Next generation sequencing as a valuable tool in plant research

OpenAIRE

Bräutigam, Andrea; Gowik, Udo

2010-01-01

Next generation sequencing (NGS) technologies have opened fascinating opportunities for the analysis of plants with and without a sequenced genome on a genomic scale. During the last few years, NGS methods have become widely available and cost effective. They can be applied to a wide variety of biological questions, from the sequencing of complete eukaryotic genomes and transcriptomes, to the genome-scale analysis of DNA-protein interactions. In this review, we focus on the use of NGS for pla...

Digital computer control on Canadian nuclear power plants -experience to date and the future outlook

International Nuclear Information System (INIS)

Pearson, A.

1977-10-01

This paper discusses the performance of the digital computer control system at Pickering through the years 1973 to 1976. This evaluation is based on a study of the Pickering Generating Station operating records. The paper goes on to explore future computer architectures and the advantages that could accrue from a distributed system approach. Also outlined are the steps being taken to develop these ideas further in the context of two Chalk River projects - REDNET, an advanced data acquisition system being installed to process information from engineering experiments in NRX and NRU reactors, and CRIP, a prototype communications network using cable television technology. (author)

The Experiment as Act

DEFF Research Database (Denmark)

Søndergaard, Morten

In December 1965, an experiment took place at The Independent Art Space in Copenhagen (Den Frie Kunstbygning). Short named POEX65, it was looking to create and activate POetry EXperiments across artistic genres and formats (thus, in essence, making a POetry EXposition). The POEX65 event framed many...... to be able to analyse the phenomena found at POEX65. Here I will use the notion of the ‘ontological theatre’ (Pickering), which, according to Pickering, is acted out in experimental art productions. The experiment could thus be seen as an ‘agency-realism’ – as an ‘act’ of relations across the aesthetics...

Electron-beam rocket acceleration of hydrogen pellets

International Nuclear Information System (INIS)

Tsai, C.C.; Foster, C.A.; Milora, S.L.; Schechter, D.E.; Whealton, J.H.

1992-01-01

A proof-of-principle device for characterizing electron-beam rocket pellet acceleration has been developed and operated during the last few years. Experimental data have been collected for thousands of accelerated hydrogen pellets under a variety of beam conditions. One intact hydrogen pellet was accelerated to a speed of 578 m/s by an electron beam of 10 kV, 0.8 A, and I ms. The collected data reveal the significant finding that the measured bum velocity of bare hydrogen pellets increases with the square of the beam voltage in a way that is qualitatively consistent with the theoretical prediction based on the neutral gas shielding (NGS) model. The measured bum velocity increases with the beam current or power and then saturates at values two to three times greater than that predicted by the NGS model. The discrepancy may result from low pellet strength and large beam-pellet interaction areas. Moreover, this feature may be the cause of the low measured exhaust velocity, which often exceeds the sonic velocity of the ablated gas. Consistent with the NGS model, the measured exhaust velocity increases in direct proportion to the beam current and in inverse proportion to the beam voltage. To alleviate the pellet strength problem, experiments have been performed with the hydrogen ice contained in a lightweight rocket casing or shell. Pellets in such sabots have the potential to withstand higher beam powers and achieve higher thrust-coupling efficiency. Some experimental results are reported and ways of accelerating pellets to higher velocity are discussed

The quest for rare variants: pooled multiplexed next generation sequencing in plants.

Science.gov (United States)

Marroni, Fabio; Pinosio, Sara; Morgante, Michele

2012-01-01

Next generation sequencing (NGS) instruments produce an unprecedented amount of sequence data at contained costs. This gives researchers the possibility of designing studies with adequate power to identify rare variants at a fraction of the economic and labor resources required by individual Sanger sequencing. As of today, few research groups working in plant sciences have exploited this potentiality, showing that pooled NGS provides results in excellent agreement with those obtained by individual Sanger sequencing. The aim of this review is to convey to the reader the general ideas underlying the use of pooled NGS for the identification of rare variants. To facilitate a thorough understanding of the possibilities of the method, we will explain in detail the possible experimental and analytical approaches and discuss their advantages and disadvantages. We will show that information on allele frequency obtained by pooled NGS can be used to accurately compute basic population genetics indexes such as allele frequency, nucleotide diversity, and Tajima's D. Finally, we will discuss applications and future perspectives of the multiplexed NGS approach.

Streaming support for data intensive cloud-based sequence analysis.

Science.gov (United States)

Issa, Shadi A; Kienzler, Romeo; El-Kalioby, Mohamed; Tonellato, Peter J; Wall, Dennis; Bruggmann, Rémy; Abouelhoda, Mohamed

2013-01-01

Cloud computing provides a promising solution to the genomics data deluge problem resulting from the advent of next-generation sequencing (NGS) technology. Based on the concepts of "resources-on-demand" and "pay-as-you-go", scientists with no or limited infrastructure can have access to scalable and cost-effective computational resources. However, the large size of NGS data causes a significant data transfer latency from the client's site to the cloud, which presents a bottleneck for using cloud computing services. In this paper, we provide a streaming-based scheme to overcome this problem, where the NGS data is processed while being transferred to the cloud. Our scheme targets the wide class of NGS data analysis tasks, where the NGS sequences can be processed independently from one another. We also provide the elastream package that supports the use of this scheme with individual analysis programs or with workflow systems. Experiments presented in this paper show that our solution mitigates the effect of data transfer latency and saves both time and cost of computation.

Streaming Support for Data Intensive Cloud-Based Sequence Analysis

Directory of Open Access Journals (Sweden)

Shadi A. Issa

2013-01-01

Full Text Available Cloud computing provides a promising solution to the genomics data deluge problem resulting from the advent of next-generation sequencing (NGS technology. Based on the concepts of “resources-on-demand” and “pay-as-you-go”, scientists with no or limited infrastructure can have access to scalable and cost-effective computational resources. However, the large size of NGS data causes a significant data transfer latency from the client’s site to the cloud, which presents a bottleneck for using cloud computing services. In this paper, we provide a streaming-based scheme to overcome this problem, where the NGS data is processed while being transferred to the cloud. Our scheme targets the wide class of NGS data analysis tasks, where the NGS sequences can be processed independently from one another. We also provide the elastream package that supports the use of this scheme with individual analysis programs or with workflow systems. Experiments presented in this paper show that our solution mitigates the effect of data transfer latency and saves both time and cost of computation.

Structural variation discovery in the cancer genome using next generation sequencing: Computational solutions and perspectives

Science.gov (United States)

Liu, Biao; Conroy, Jeffrey M.; Morrison, Carl D.; Odunsi, Adekunle O.; Qin, Maochun; Wei, Lei; Trump, Donald L.; Johnson, Candace S.; Liu, Song; Wang, Jianmin

2015-01-01

Somatic Structural Variations (SVs) are a complex collection of chromosomal mutations that could directly contribute to carcinogenesis. Next Generation Sequencing (NGS) technology has emerged as the primary means of interrogating the SVs of the cancer genome in recent investigations. Sophisticated computational methods are required to accurately identify the SV events and delineate their breakpoints from the massive amounts of reads generated by a NGS experiment. In this review, we provide an overview of current analytic tools used for SV detection in NGS-based cancer studies. We summarize the features of common SV groups and the primary types of NGS signatures that can be used in SV detection methods. We discuss the principles and key similarities and differences of existing computational programs and comment on unresolved issues related to this research field. The aim of this article is to provide a practical guide of relevant concepts, computational methods, software tools and important factors for analyzing and interpreting NGS data for the detection of SVs in the cancer genome. PMID:25849937

Streaming Support for Data Intensive Cloud-Based Sequence Analysis

Science.gov (United States)

Issa, Shadi A.; Kienzler, Romeo; El-Kalioby, Mohamed; Tonellato, Peter J.; Wall, Dennis; Bruggmann, Rémy; Abouelhoda, Mohamed

2013-01-01

Cloud computing provides a promising solution to the genomics data deluge problem resulting from the advent of next-generation sequencing (NGS) technology. Based on the concepts of “resources-on-demand” and “pay-as-you-go”, scientists with no or limited infrastructure can have access to scalable and cost-effective computational resources. However, the large size of NGS data causes a significant data transfer latency from the client's site to the cloud, which presents a bottleneck for using cloud computing services. In this paper, we provide a streaming-based scheme to overcome this problem, where the NGS data is processed while being transferred to the cloud. Our scheme targets the wide class of NGS data analysis tasks, where the NGS sequences can be processed independently from one another. We also provide the elastream package that supports the use of this scheme with individual analysis programs or with workflow systems. Experiments presented in this paper show that our solution mitigates the effect of data transfer latency and saves both time and cost of computation. PMID:23710461

Application of next generation sequencing in clinical microbiology and infection prevention.

Science.gov (United States)

Deurenberg, Ruud H; Bathoorn, Erik; Chlebowicz, Monika A; Couto, Natacha; Ferdous, Mithila; García-Cobos, Silvia; Kooistra-Smid, Anna M D; Raangs, Erwin C; Rosema, Sigrid; Veloo, Alida C M; Zhou, Kai; Friedrich, Alexander W; Rossen, John W A

2017-02-10

Current molecular diagnostics of human pathogens provide limited information that is often not sufficient for outbreak and transmission investigation. Next generation sequencing (NGS) determines the DNA sequence of a complete bacterial genome in a single sequence run, and from these data, information on resistance and virulence, as well as information for typing is obtained, useful for outbreak investigation. The obtained genome data can be further used for the development of an outbreak-specific screening test. In this review, a general introduction to NGS is presented, including the library preparation and the major characteristics of the most common NGS platforms, such as the MiSeq (Illumina) and the Ion PGM™ (ThermoFisher). An overview of the software used for NGS data analyses used at the medical microbiology diagnostic laboratory in the University Medical Center Groningen in The Netherlands is given. Furthermore, applications of NGS in the clinical setting are described, such as outbreak management, molecular case finding, characterization and surveillance of pathogens, rapid identification of bacteria using the 16S-23S rRNA region, taxonomy, metagenomics approaches on clinical samples, and the determination of the transmission of zoonotic micro-organisms from animals to humans. Finally, we share our vision on the use of NGS in personalised microbiology in the near future, pointing out specific requirements. Copyright © 2016 The Author(s). Published by Elsevier B.V. All rights reserved.

Reprint of "Application of next generation sequencing in clinical microbiology and infection prevention".

Science.gov (United States)

Deurenberg, Ruud H; Bathoorn, Erik; Chlebowicz, Monika A; Couto, Natacha; Ferdous, Mithila; García-Cobos, Silvia; Kooistra-Smid, Anna M D; Raangs, Erwin C; Rosema, Sigrid; Veloo, Alida C M; Zhou, Kai; Friedrich, Alexander W; Rossen, John W A

2017-05-20

Current molecular diagnostics of human pathogens provide limited information that is often not sufficient for outbreak and transmission investigation. Next generation sequencing (NGS) determines the DNA sequence of a complete bacterial genome in a single sequence run, and from these data, information on resistance and virulence, as well as information for typing is obtained, useful for outbreak investigation. The obtained genome data can be further used for the development of an outbreak-specific screening test. In this review, a general introduction to NGS is presented, including the library preparation and the major characteristics of the most common NGS platforms, such as the MiSeq (Illumina) and the Ion PGM™ (ThermoFisher). An overview of the software used for NGS data analyses used at the medical microbiology diagnostic laboratory in the University Medical Center Groningen in The Netherlands is given. Furthermore, applications of NGS in the clinical setting are described, such as outbreak management, molecular case finding, characterization and surveillance of pathogens, rapid identification of bacteria using the 16S-23S rRNA region, taxonomy, metagenomics approaches on clinical samples, and the determination of the transmission of zoonotic micro-organisms from animals to humans. Finally, we share our vision on the use of NGS in personalised microbiology in the near future, pointing out specific requirements. Copyright © 2017. Published by Elsevier B.V.

Oxidation and deuterium uptake of Zr-2.5Nb pressure tubes in CANDU-PHW reactors

International Nuclear Information System (INIS)

Urbanic, V.F.; Warr, B.D.; Manolescu, A.; Chow, C.K.; Shanahan, M.W.

1989-01-01

Oxidation and deuterium uptake in Zr-2.5Nb pressure tubes are being monitored by destructive examination of tubes removed from commercial Canadian deuterium uranium pressurized heavy-water (CANDU-PHW) stations and by analyses of microsamples, obtained in-situ, from the inside surface of tubes in the reactor. Unlike Zircaloy-2, there is no evidence for any acceleration in the oxidation rate for exposures up to about 4500 effective full power days. Changes towards a more equilibrium microstructure during irradiation may be partly responsible for maintaining the low oxidation rate, since thermal aging treatments, producing similar microstructural changes in initially cold worked tubes, were found to improve out-reactor corrosion resistance in 589 K water. With one exception, the deuterium uptake in Zr-2.5Nb tubes has been remarkably low and no greater than 3-mg/kg deuterium per year (0.39 mg/dm 2 hydrogen per year) . The exception is the most recent surveillance tube removed from Pickering (NGS) Unit 3, which had a deuterium content near the outlet end about five times higher than that seen in the previous tube examined. Current investigations suggest that most of the uptake in that tube may have come from the gas annulus surrounding the tube where deuterium exists as an impurity, and oxidation has been insufficient to maintain a protective oxide film. Results from weight gain measurements, chemical analyses, metallography, scanning electron microscopy, and transmission electron microscopy of irradiated pressure tubes and of small coupons exposed out reactor are presented and discussed with respect to the observed corrosion and hydriding behavior of CANDU-PHW pressure tubes. (author)

Results of Analyses of the Next Generation Solvent for Parsons

International Nuclear Information System (INIS)

Peters, T.; Washington, A.; Fink, S.

2012-01-01

Savannah River National Laboratory (SRNL) prepared a nominal 150 gallon batch of Next Generation Solvent (NGS) for Parsons. This material was then analyzed and tested for cesium mass transfer efficiency. The bulk of the results indicate that the solvent is qualified as acceptable for use in the upcoming pilot-scale testing at Parsons Technology Center. This report describes the analysis and testing of a batch of Next Generation Solvent (NGS) prepared in support of pilot-scale testing in the Parsons Technology Center. A total of ∼150 gallons of NGS solvent was prepared in late November of 2011. Details for the work are contained in a controlled laboratory notebook. Analysis of the Parsons NGS solvent indicates that the material is acceptable for use. SRNL is continuing to improve the analytical method for the guanidine.

Discovery and validation of Barrett's esophagus microRNA transcriptome by next generation sequencing.

Directory of Open Access Journals (Sweden)

Ajay Bansal

Full Text Available Barrett's esophagus (BE is transition from squamous to columnar mucosa as a result of gastroesophageal reflux disease (GERD. The role of microRNA during this transition has not been systematically studied.For initial screening, total RNA from 5 GERD and 6 BE patients was size fractionated. RNA <70 nucleotides was subjected to SOLiD 3 library preparation and next generation sequencing (NGS. Bioinformatics analysis was performed using R package "DEseq". A p value<0.05 adjusted for a false discovery rate of 5% was considered significant. NGS-identified miRNA were validated using qRT-PCR in an independent group of 40 GERD and 27 BE patients. MicroRNA expression of human BE tissues was also compared with three BE cell lines.NGS detected 19.6 million raw reads per sample. 53.1% of filtered reads mapped to miRBase version 18. NGS analysis followed by qRT-PCR validation found 10 differentially expressed miRNA; several are novel (-708-5p, -944, -224-5p and -3065-5p. Up- or down- regulation predicted by NGS was matched by qRT-PCR in every case. Human BE tissues and BE cell lines showed a high degree of concordance (70-80% in miRNA expression. Prediction analysis identified targets that mapped to developmental signaling pathways such as TGFβ and Notch and inflammatory pathways such as toll-like receptor signaling and TGFβ. Cluster analysis found similarly regulated (up or down miRNA to share common targets suggesting coordination between miRNA.Using highly sensitive next-generation sequencing, we have performed a comprehensive genome wide analysis of microRNA in BE and GERD patients. Differentially expressed miRNA between BE and GERD have been further validated. Expression of miRNA between BE human tissues and BE cell lines are highly correlated. These miRNA should be studied in biological models to further understand BE development.

National Geodetic Survey's Airport Aerial Photography

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — The National Geodetic Survey (NGS), formerly part of the U.S. Coast and Geodetic Survey, has been performing Aeronautical surveys since the 1920's. NGS, in...

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.

Next generation sequencing in clinical medicine: Challenges and lessons for pathology and biomedical informatics

Directory of Open Access Journals (Sweden)

Rama R Gullapalli

2012-01-01

Full Text Available The Human Genome Project (HGP provided the initial draft of mankind′s DNA sequence in 2001. The HGP was produced by 23 collaborating laboratories using Sanger sequencing of mapped regions as well as shotgun sequencing techniques in a process that occupied 13 years at a cost of ~$3 billion. Today, Next Generation Sequencing (NGS techniques represent the next phase in the evolution of DNA sequencing technology at dramatically reduced cost compared to traditional Sanger sequencing. A single laboratory today can sequence the entire human genome in a few days for a few thousand dollars in reagents and staff time. Routine whole exome or even whole genome sequencing of clinical patients is well within the realm of affordability for many academic institutions across the country. This paper reviews current sequencing technology methods and upcoming advancements in sequencing technology as well as challenges associated with data generation, data manipulation and data storage. Implementation of routine NGS data in cancer genomics is discussed along with potential pitfalls in the interpretation of the NGS data. The overarching importance of bioinformatics in the clinical implementation of NGS is emphasized. [7] We also review the issue of physician education which also is an important consideration for the successful implementation of NGS in the clinical workplace. NGS technologies represent a golden opportunity for the next generation of pathologists to be at the leading edge of the personalized medicine approaches coming our way. Often under-emphasized issues of data access and control as well as potential ethical implications of whole genome NGS sequencing are also discussed. Despite some challenges, it′s hard not to be optimistic about the future of personalized genome sequencing and its potential impact on patient care and the advancement of knowledge of human biology and disease in the near future.

Single Stage Contactor Testing Of The Next Generation Solvent Blend

Energy Technology Data Exchange (ETDEWEB)

Herman, D. T.; Peters, T. B.; Duignan, M. R.; Williams, M. R.; Poirier, M. R.; Brass, E. A.; Garrison, A. G.; Ketusky, E. T.

2014-01-06

The Modular Caustic Side Solvent Extraction (CSSX) Unit (MCU) facility at the Savannah River Site (SRS) is actively pursuing the transition from the current BOBCalixC6 based solvent to the Next Generation Solvent (NGS)-MCU solvent to increase the cesium decontamination factor. To support this integration of NGS into the MCU facility the Savannah River National Laboratory (SRNL) performed testing of a blend of the NGS (MaxCalix based solvent) with the current solvent (BOBCalixC6 based solvent) for the removal of cesium (Cs) from the liquid salt waste stream. This testing utilized a blend of BOBCalixC6 based solvent and the NGS with the new extractant, MaxCalix, as well as a new suppressor, tris(3,7dimethyloctyl) guanidine. Single stage tests were conducted using the full size V-05 and V-10 liquid-to-liquid centrifugal contactors installed at SRNL. These tests were designed to determine the mass transfer and hydraulic characteristics with the NGS solvent blended with the projected heel of the BOBCalixC6 based solvent that will exist in MCU at time of transition. The test program evaluated the amount of organic carryover and the droplet size of the organic carryover phases using several analytical methods. The results indicate that hydraulically, the NGS solvent performed hydraulically similar to the current solvent which was expected. For the organic carryover 93% of the solvent is predicted to be recovered from the stripping operation and 96% from the extraction operation. As for the mass transfer, the NGS solvent significantly improved the cesium DF by at least an order of magnitude when extrapolating the One-stage results to actual Seven-stage extraction operation with a stage efficiency of 95%.

MicroRNA Profiling in Aqueous Humor of Individual Human Eyes by Next-Generation Sequencing.

Science.gov (United States)

Wecker, Thomas; Hoffmeier, Klaus; Plötner, Anne; Grüning, Björn Andreas; Horres, Ralf; Backofen, Rolf; Reinhard, Thomas; Schlunck, Günther

2016-04-01

Extracellular microRNAs (miRNAs) in aqueous humor were suggested to have a role in transcellular signaling and may serve as disease biomarkers. The authors adopted next-generation sequencing (NGS) techniques to further characterize the miRNA profile in single samples of 60 to 80 μL human aqueous humor. Samples were obtained at the outset of cataract surgery in nine independent, otherwise healthy eyes. Four samples were used to extract RNA and generate sequencing libraries, followed by an adapter-driven amplification step, electrophoretic size selection, sequencing, and data analysis. Five samples were used for quantitative PCR (qPCR) validation of NGS results. Published NGS data on circulating miRNAs in blood were analyzed in comparison. One hundred fifty-eight miRNAs were consistently detected by NGS in all four samples; an additional 59 miRNAs were present in at least three samples. The aqueous humor miRNA profile shows some overlap with published NGS-derived inventories of circulating miRNAs in blood plasma with high prevalence of human miR-451a, -21, and -16. In contrast to blood, miR-184, -4448, -30a, -29a, -29c, -19a, -30d, -205, -24, -22, and -3074 were detected among the 20 most prevalent miRNAs in aqueous humor. Relative expression patterns of miR-451a, -202, and -144 suggested by NGS were confirmed by qPCR. Our data illustrate the feasibility of miRNA analysis by NGS in small individual aqueous humor samples. Intraocular cells as well as blood plasma contribute to the extracellular aqueous humor miRNome. The data suggest possible roles of miRNA in intraocular cell adhesion and signaling by TGF-β and Wnt, which are important in intraocular pressure regulation and glaucoma.

Genomic and transcriptomic approaches to study immunology in cyprinids: What is next?

Science.gov (United States)

Petit, Jules; David, Lior; Dirks, Ron; Wiegertjes, Geert F

2017-10-01

Accelerated by the introduction of Next-Generation Sequencing (NGS), a number of genomes of cyprinid fish species have been drafted, leading to a highly valuable collective resource of comparative genome information on cyprinids (Cyprinidae). In addition, NGS-based transcriptome analyses of different developmental stages, organs, or cell types, increasingly contribute to the understanding of complex physiological processes, including immune responses. Cyprinids are a highly interesting family because they comprise one of the most-diversified families of teleosts and because of their variation in ploidy level, with diploid, triploid, tetraploid, hexaploid and sometimes even octoploid species. The wealth of data obtained from NGS technologies provides both challenges and opportunities for immunological research, which will be discussed here. Correct interpretation of ploidy effects on immune responses requires knowledge of the degree of functional divergence between duplicated genes, which can differ even between closely-related cyprinid fish species. We summarize NGS-based progress in analysing immune responses and discuss the importance of respecting the presence of (multiple) duplicated gene sequences when performing transcriptome analyses for detailed understanding of complex physiological processes. Progressively, advances in NGS technology are providing workable methods to further elucidate the implications of gene duplication events and functional divergence of duplicates genes and proteins involved in immune responses in cyprinids. We conclude with discussing how future applications of NGS technologies and analysis methods could enhance immunological research and understanding. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Biofilm-Growing Bacteria Involved in the Corrosion of Concrete Wastewater Pipes: Protocols for Comparative Metagenomic Analyses

Science.gov (United States)

Advances in high-throughput next-generation sequencing (NGS) technology for direct sequencing of environmental DNA (i.e. shotgun metagenomics) is transforming the field of microbiology. NGS technologies are now regularly being applied in comparative metagenomic studies, which pr...

Ontario Power Generation Nuclear: results and opportunities

International Nuclear Information System (INIS)

Dermarkar, F.

2006-01-01

This paper describes the accomplishments of Ontario Power Generation (OPG) Nuclear and outlines future opportunities. OPG's mandate is to cost effectively produce electricity, while operating in a safe, open and environmentally responsible manner. OPG's nuclear production has been increasing over the past three years - partly from the addition of newly refurbished Pickering A Units 1 and 4, and partly from the increased production from Darlington and Pickering B. OPG will demonstrate its proficiency and capability in nuclear by continuing to enhance the performance and cost effectiveness of its existing operations. Its priorities are to focus on performance excellence, commercial success, openness, accountability and transparency

The Potential of Stimuli-Responsive Nanogels in Drug and Active Molecule Delivery for Targeted Therapy

Directory of Open Access Journals (Sweden)

Marta Vicario-de-la-Torre

2017-05-01

Full Text Available Nanogels (NGs are currently under extensive investigation due to their unique properties, such as small particle size, high encapsulation efficiency and protection of active agents from degradation, which make them ideal candidates as drug delivery systems (DDS. Stimuli-responsive NGs are cross-linked nanoparticles (NPs, composed of polymers, natural, synthetic, or a combination thereof that can swell by absorption (uptake of large amounts of solvent, but not dissolve due to the constituent structure of the polymeric network. NGs can undergo change from a polymeric solution (swell form to a hard particle (collapsed form in response to (i physical stimuli such as temperature, ionic strength, magnetic or electric fields; (ii chemical stimuli such as pH, ions, specific molecules or (iii biochemical stimuli such as enzymatic substrates or affinity ligands. The interest in NGs comes from their multi-stimuli nature involving reversible phase transitions in response to changes in the external media in a faster way than macroscopic gels or hydrogels due to their nanometric size. NGs have a porous structure able to encapsulate small molecules such as drugs and genes, then releasing them by changing their volume when external stimuli are applied.

Validation of Metagenomic Next-Generation Sequencing Tests for Universal Pathogen Detection.

Science.gov (United States)

Schlaberg, Robert; Chiu, Charles Y; Miller, Steve; Procop, Gary W; Weinstock, George

2017-06-01

- Metagenomic sequencing can be used for detection of any pathogens using unbiased, shotgun next-generation sequencing (NGS), without the need for sequence-specific amplification. Proof-of-concept has been demonstrated in infectious disease outbreaks of unknown causes and in patients with suspected infections but negative results for conventional tests. Metagenomic NGS tests hold great promise to improve infectious disease diagnostics, especially in immunocompromised and critically ill patients. - To discuss challenges and provide example solutions for validating metagenomic pathogen detection tests in clinical laboratories. A summary of current regulatory requirements, largely based on prior guidance for NGS testing in constitutional genetics and oncology, is provided. - Examples from 2 separate validation studies are provided for steps from assay design, and validation of wet bench and bioinformatics protocols, to quality control and assurance. - Although laboratory and data analysis workflows are still complex, metagenomic NGS tests for infectious diseases are increasingly being validated in clinical laboratories. Many parallels exist to NGS tests in other fields. Nevertheless, specimen preparation, rapidly evolving data analysis algorithms, and incomplete reference sequence databases are idiosyncratic to the field of microbiology and often overlooked.

The first FDA marketing authorizations of next-generation sequencing technology and tests: challenges, solutions and impact for future assays.

Science.gov (United States)

Bijwaard, Karen; Dickey, Jennifer S; Kelm, Kellie; Težak, Živana

2015-01-01

The rapid emergence and clinical translation of novel high-throughput sequencing technologies created a need to clarify the regulatory pathway for the evaluation and authorization of these unique technologies. Recently, the US FDA authorized for marketing four next generation sequencing (NGS)-based diagnostic devices which consisted of two heritable disease-specific assays, library preparation reagents and a NGS platform that are intended for human germline targeted sequencing from whole blood. These first authorizations can serve as a case study in how different types of NGS-based technology are reviewed by the FDA. In this manuscript we describe challenges associated with the evaluation of these novel technologies and provide an overview of what was reviewed. Besides making validated NGS-based devices available for in vitro diagnostic use, these first authorizations create a regulatory path for similar future instruments and assays.

High-performance integrated virtual environment (HIVE): a robust infrastructure for next-generation sequence data analysis.

Science.gov (United States)

Simonyan, Vahan; Chumakov, Konstantin; Dingerdissen, Hayley; Faison, William; Goldweber, Scott; Golikov, Anton; Gulzar, Naila; Karagiannis, Konstantinos; Vinh Nguyen Lam, Phuc; Maudru, Thomas; Muravitskaja, Olesja; Osipova, Ekaterina; Pan, Yang; Pschenichnov, Alexey; Rostovtsev, Alexandre; Santana-Quintero, Luis; Smith, Krista; Thompson, Elaine E; Tkachenko, Valery; Torcivia-Rodriguez, John; Voskanian, Alin; Wan, Quan; Wang, Jing; Wu, Tsung-Jung; Wilson, Carolyn; Mazumder, Raja

2016-01-01

The High-performance Integrated Virtual Environment (HIVE) is a distributed storage and compute environment designed primarily to handle next-generation sequencing (NGS) data. This multicomponent cloud infrastructure provides secure web access for authorized users to deposit, retrieve, annotate and compute on NGS data, and to analyse the outcomes using web interface visual environments appropriately built in collaboration with research and regulatory scientists and other end users. Unlike many massively parallel computing environments, HIVE uses a cloud control server which virtualizes services, not processes. It is both very robust and flexible due to the abstraction layer introduced between computational requests and operating system processes. The novel paradigm of moving computations to the data, instead of moving data to computational nodes, has proven to be significantly less taxing for both hardware and network infrastructure.The honeycomb data model developed for HIVE integrates metadata into an object-oriented model. Its distinction from other object-oriented databases is in the additional implementation of a unified application program interface to search, view and manipulate data of all types. This model simplifies the introduction of new data types, thereby minimizing the need for database restructuring and streamlining the development of new integrated information systems. The honeycomb model employs a highly secure hierarchical access control and permission system, allowing determination of data access privileges in a finely granular manner without flooding the security subsystem with a multiplicity of rules. HIVE infrastructure will allow engineers and scientists to perform NGS analysis in a manner that is both efficient and secure. HIVE is actively supported in public and private domains, and project collaborations are welcomed. Database URL: https://hive.biochemistry.gwu.edu. © The Author(s) 2016. Published by Oxford University Press.

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.

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.

Practical issues in implementing whole-genome-sequencing in routine diagnostic microbiology

NARCIS (Netherlands)

Rossen, J. W. A.; Friedrich, A. W.; Moran-Gilad, J.

Background: Next generation sequencing (NGS) is increasingly being used in clinical microbiology. Like every new technology adopted in microbiology, the integration of NGS into clinical and routine workflows must be carefully managed. Aim: To review the practical aspects of implementing bacterial

Is the $1000 Genome as Near as We Think? A Cost Analysis of Next-Generation Sequencing

NARCIS (Netherlands)

Nimwegen, K.J.M. van; Soest, R.A.; Veltman, J.A.; Nelen, M.R.; Wilt, G.J. van der; Peart-Vissers, L.E.L.M.; Grutters, J.P.C.

2016-01-01

BACKGROUND: The substantial technological advancements in next-generation sequencing (NGS), combined with dropping costs, have allowed for a swift diffusion of NGS applications in clinical settings. Although several commercial parties report to have broken the $1000 barrier for sequencing an entire

Semirelativity in semiconductors: a review.

Science.gov (United States)

Zawadzki, Wlodek

2017-09-20

An analogy between behavior of electrons in narrow-gap semiconductors (NGS) and relativistic electrons in vacuum is reviewed. Energy band structures [Formula: see text] are considered for various NGS materials and their correspondence to the energy-momentum relation in special relativity is emphasized. It is indicated that special relativity for vacuum is analogous to a two-band [Formula: see text] description for NGS. The maximum electron velocity in NGS is [Formula: see text], which corresponds to the light velocity in vacuum. An effective mass of charge carriers in semiconductors is introduced, relating their velocity to quasimomentum and it is shown that this mass depends on electron energy (or velocity) in a way similar to the mass of free relativistic electrons. In [Formula: see text] alloys one can reach vanishing energy gap at which electrons and light holes become three-dimensional massless Dirac fermions. A wavelength [Formula: see text] is defined for NGS, in analogy to the Compton wavelength in relativistic quantum mechanics. It is estimated that [Formula: see text] is on the order of tens of Angstroms in typical semiconducting materials which is experimentally confirmed in tunneling experiments on energy dispersion in the forbidden gap. Statistical properties of the electron gas in NGS are calculated and their similarity is demonstrated to those of the Juttner gas of relativistic particles. Interband electron tunneling in NGS is described and shown to be in close analogy to the predicted but unobserved tunneling between negative and positive energies resulting from the Dirac equation for free electrons. It is demonstrated that the relativistic analogy holds for orbital and spin properties of electrons in the presence of an external magnetic field. In particular, it is shown that the spin magnetic moment of both NGS electrons and relativistic electrons approaches zero with increasing energy. This conclusion is confirmed experimentally for NGS. Electrons

Semirelativity in semiconductors: a review

Science.gov (United States)

Zawadzki, Wlodek

2017-09-01

An analogy between behavior of electrons in narrow-gap semiconductors (NGS) and relativistic electrons in vacuum is reviewed. Energy band structures \\varepsilon ≤ft(\\mathbf{k}\\right) are considered for various NGS materials and their correspondence to the energy-momentum relation in special relativity is emphasized. It is indicated that special relativity for vacuum is analogous to a two-band \\mathbf{k}\\centerdot \\mathbf{p} description for NGS. The maximum electron velocity in NGS is u≃ 1× {{10}8}~\\text{cm}~{{\\text{s}}-1} , which corresponds to the light velocity in vacuum. An effective mass of charge carriers in semiconductors is introduced, relating their velocity to quasimomentum and it is shown that this mass depends on electron energy (or velocity) in a way similar to the mass of free relativistic electrons. In \\text{H}{{\\text{g}}1-x}\\text{C}{{\\text{d}}x}\\text{Te} alloys one can reach vanishing energy gap at which electrons and light holes become three-dimensional massless Dirac fermions. A wavelength {λz} is defined for NGS, in analogy to the Compton wavelength in relativistic quantum mechanics. It is estimated that {λz} is on the order of tens of Angstroms in typical semiconducting materials which is experimentally confirmed in tunneling experiments on energy dispersion in the forbidden gap. Statistical properties of the electron gas in NGS are calculated and their similarity is demonstrated to those of the Juttner gas of relativistic particles. Interband electron tunneling in NGS is described and shown to be in close analogy to the predicted but unobserved tunneling between negative and positive energies resulting from the Dirac equation for free electrons. It is demonstrated that the relativistic analogy holds for orbital and spin properties of electrons in the presence of an external magnetic field. In particular, it is shown that the spin magnetic moment of both NGS electrons and relativistic electrons approaches zero with increasing

TagDust2: a generic method to extract reads from sequencing data.

Science.gov (United States)

Lassmann, Timo

2015-01-28

Arguably the most basic step in the analysis of next generation sequencing data (NGS) involves the extraction of mappable reads from the raw reads produced by sequencing instruments. The presence of barcodes, adaptors and artifacts subject to sequencing errors makes this step non-trivial. Here I present TagDust2, a generic approach utilizing a library of hidden Markov models (HMM) to accurately extract reads from a wide array of possible read architectures. TagDust2 extracts more reads of higher quality compared to other approaches. Processing of multiplexed single, paired end and libraries containing unique molecular identifiers is fully supported. Two additional post processing steps are included to exclude known contaminants and filter out low complexity sequences. Finally, TagDust2 can automatically detect the library type of sequenced data from a predefined selection. Taken together TagDust2 is a feature rich, flexible and adaptive solution to go from raw to mappable NGS reads in a single step. The ability to recognize and record the contents of raw reads will help to automate and demystify the initial, and often poorly documented, steps in NGS data analysis pipelines. TagDust2 is freely available at: http://tagdust.sourceforge.net .

Generation of artificial FASTQ files to evaluate the performance of next-generation sequencing pipelines.

Directory of Open Access Journals (Sweden)

Matthew Frampton

Full Text Available Pipelines for the analysis of Next-Generation Sequencing (NGS data are generally composed of a set of different publicly available software, configured together in order to map short reads of a genome and call variants. The fidelity of pipelines is variable. We have developed ArtificialFastqGenerator, which takes a reference genome sequence as input and outputs artificial paired-end FASTQ files containing Phred quality scores. Since these artificial FASTQs are derived from the reference genome, it provides a gold-standard for read-alignment and variant-calling, thereby enabling the performance of any NGS pipeline to be evaluated. The user can customise DNA template/read length, the modelling of coverage based on GC content, whether to use real Phred base quality scores taken from existing FASTQ files, and whether to simulate sequencing errors. Detailed coverage and error summary statistics are outputted. Here we describe ArtificialFastqGenerator and illustrate its implementation in evaluating a typical bespoke NGS analysis pipeline under different experimental conditions. ArtificialFastqGenerator was released in January 2012. Source code, example files and binaries are freely available under the terms of the GNU General Public License v3.0. from https://sourceforge.net/projects/artfastqgen/.

Generic Amplicon Deep Sequencing to Determine Ilarvirus Species Diversity in Australian Prunus.

Science.gov (United States)

Kinoti, Wycliff M; Constable, Fiona E; Nancarrow, Narelle; Plummer, Kim M; Rodoni, Brendan

2017-01-01

The distribution of Ilarvirus species populations amongst 61 Australian Prunus trees was determined by next generation sequencing (NGS) of amplicons generated using a genus-based generic RT-PCR targeting a conserved region of the Ilarvirus RNA2 component that encodes the RNA dependent RNA polymerase (RdRp) gene. Presence of Ilarvirus sequences in each positive sample was further validated by Sanger sequencing of cloned amplicons of regions of each of RNA1, RNA2 and/or RNA3 that were generated by species specific PCRs and by metagenomic NGS. Prunus necrotic ringspot virus (PNRSV) was the most frequently detected Ilarvirus , occurring in 48 of the 61 Ilarvirus -positive trees and Prune dwarf virus (PDV) and Apple mosaic virus (ApMV) were detected in three trees and one tree, respectively. American plum line pattern virus (APLPV) was detected in three trees and represents the first report of APLPV detection in Australia. Two novel and distinct groups of Ilarvirus -like RNA2 amplicon sequences were also identified in several trees by the generic amplicon NGS approach. The high read depth from the amplicon NGS of the generic PCR products allowed the detection of distinct RNA2 RdRp sequence variant populations of PNRSV, PDV, ApMV, APLPV and the two novel Ilarvirus -like sequences. Mixed infections of ilarviruses were also detected in seven Prunus trees. Sanger sequencing of specific RNA1, RNA2, and/or RNA3 genome segments of each virus and total nucleic acid metagenomics NGS confirmed the presence of PNRSV, PDV, ApMV and APLPV detected by RNA2 generic amplicon NGS. However, the two novel groups of Ilarvirus -like RNA2 amplicon sequences detected by the generic amplicon NGS could not be associated to the presence of sequence from RNA1 or RNA3 genome segments or full Ilarvirus genomes, and their origin is unclear. This work highlights the sensitivity of genus-specific amplicon NGS in detection of virus sequences and their distinct populations in multiple samples, and the

Generic Amplicon Deep Sequencing to Determine Ilarvirus Species Diversity in Australian Prunus

Directory of Open Access Journals (Sweden)

Wycliff M. Kinoti

2017-06-01

Full Text Available The distribution of Ilarvirus species populations amongst 61 Australian Prunus trees was determined by next generation sequencing (NGS of amplicons generated using a genus-based generic RT-PCR targeting a conserved region of the Ilarvirus RNA2 component that encodes the RNA dependent RNA polymerase (RdRp gene. Presence of Ilarvirus sequences in each positive sample was further validated by Sanger sequencing of cloned amplicons of regions of each of RNA1, RNA2 and/or RNA3 that were generated by species specific PCRs and by metagenomic NGS. Prunus necrotic ringspot virus (PNRSV was the most frequently detected Ilarvirus, occurring in 48 of the 61 Ilarvirus-positive trees and Prune dwarf virus (PDV and Apple mosaic virus (ApMV were detected in three trees and one tree, respectively. American plum line pattern virus (APLPV was detected in three trees and represents the first report of APLPV detection in Australia. Two novel and distinct groups of Ilarvirus-like RNA2 amplicon sequences were also identified in several trees by the generic amplicon NGS approach. The high read depth from the amplicon NGS of the generic PCR products allowed the detection of distinct RNA2 RdRp sequence variant populations of PNRSV, PDV, ApMV, APLPV and the two novel Ilarvirus-like sequences. Mixed infections of ilarviruses were also detected in seven Prunus trees. Sanger sequencing of specific RNA1, RNA2, and/or RNA3 genome segments of each virus and total nucleic acid metagenomics NGS confirmed the presence of PNRSV, PDV, ApMV and APLPV detected by RNA2 generic amplicon NGS. However, the two novel groups of Ilarvirus-like RNA2 amplicon sequences detected by the generic amplicon NGS could not be associated to the presence of sequence from RNA1 or RNA3 genome segments or full Ilarvirus genomes, and their origin is unclear. This work highlights the sensitivity of genus-specific amplicon NGS in detection of virus sequences and their distinct populations in multiple samples

PIK3CA-associated developmental disorders exhibit distinct classes of mutations with variable expression and tissue distribution

NARCIS (Netherlands)

Mirzaa, Ghayda; Timms, Andrew E.; Conti, Valerio; Boyle, Evan August; Girisha, Katta M.; Martin, Beth; Kircher, Martin; Olds, Carissa; Juusola, Jane; Collins, Sarah; Park, Kaylee; Carter, Melissa; Glass, Ian; Krägeloh-Mann, Inge; Chitayat, David; Parikh, Aditi Shah; Bradshaw, Rachael; Torti, Erin; Braddock, Stephen; Burke, Leah; Ghedia, Sondhya; Stephan, Mark; Stewart, Fiona; Prasad, Chitra; Napier, Melanie; Saitta, Sulagna; Straussberg, Rachel; Gabbett, Michael; O'Connor, Bridget C.; Keegan, Catherine E.; Yin, Lim Jiin; Lai, Angeline Hwei Meeng; Martin, Nicole; McKinnon, Margaret; Addor, Marie-Claude; Boccuto, Luigi; Schwartz, Charles E.; Lanoel, Agustina; Conway, Robert L.; Devriendt, Koenraad; Tatton-Brown, Katrina; Pierpont, Mary Ella; Painter, Michael; Worgan, Lisa; Reggin, James; Hennekam, Raoul; Tsuchiya, Karen; Pritchard, Colin C.; Aracena, Mariana; Gripp, Karen W.; Cordisco, Maria; Esch, Hilde Van; Garavelli, Livia; Curry, Cynthia; Goriely, Anne; Kayserilli, Hulya; Shendure, Jay; Graham, John; Guerrini, Renzo; Dobyns, William B.

2016-01-01

Mosaicism is increasingly recognized as a cause of developmental disorders with the advent of next-generation sequencing (NGS). Mosaic mutations of PIK3CA have been associated with the widest spectrum of phenotypes associated with overgrowth and vascular malformations. We performed targeted NGS

Practical Issues in Implementing Whole-Genome-Sequencing in Routine Diagnostic Microbiology

NARCIS (Netherlands)

Rossen, John W A; Friedrich, Alexander W; Moran-Gilad, Jacob

BACKGROUND: next generation sequencing (NGS) is increasingly being used in clinical microbiology. Like every new technology that is being adopted in microbiology, the integration of NGS into clinical and routine workflows needs to be carefully managed. AIM: to review the practical aspects of

Using next-generation sequencing to develop molecular diagnostics for Pseudoperonospora cubensis, the cucurbit downy mildew pathogen

Science.gov (United States)

Advances in Next Generation Sequencing (NGS) allow for rapid development of genomics resources needed to generate molecular diagnostics assays for infectious agents. NGS approaches are particularly helpful for organisms that cannot be cultured, such as the downy mildew pathogens, a group of biotrop...

HLA typing: Conventional techniques v.next-generation sequencing

African Journals Online (AJOL)

The existing techniques have contributed significantly to our current knowledge of allelic diversity. At present, sequence-based typing (SBT) methods, in particular next-generation sequencing. (NGS), provide the highest possible resolution. NGS platforms were initially only used for genomic sequencing, but also showed.

Comparison of Four Human Papillomavirus Genotyping Methods: Next-generation Sequencing, INNO-LiPA, Electrochemical DNA Chip, and Nested-PCR.

Science.gov (United States)

Nilyanimit, Pornjarim; Chansaenroj, Jira; Poomipak, Witthaya; Praianantathavorn, Kesmanee; Payungporn, Sunchai; Poovorawan, Yong

2018-03-01

Human papillomavirus (HPV) infection causes cervical cancer, thus necessitating early detection by screening. Rapid and accurate HPV genotyping is crucial both for the assessment of patients with HPV infection and for surveillance studies. Fifty-eight cervicovaginal samples were tested for HPV genotypes using four methods in parallel: nested-PCR followed by conventional sequencing, INNO-LiPA, electrochemical DNA chip, and next-generation sequencing (NGS). Seven HPV genotypes (16, 18, 31, 33, 45, 56, and 58) were identified by all four methods. Nineteen HPV genotypes were detected by NGS, but not by nested-PCR, INNO-LiPA, or electrochemical DNA chip. Although NGS is relatively expensive and complex, it may serve as a sensitive HPV genotyping method. Because of its highly sensitive detection of multiple HPV genotypes, NGS may serve as an alternative for diagnostic HPV genotyping in certain situations. © The Korean Society for Laboratory Medicine

A prospective pilot study of genome-wide exome and transcriptome profiling in patients with small cell lung cancer progressing after first-line therapy.

Directory of Open Access Journals (Sweden)

Glen J Weiss

Full Text Available Small cell lung cancer (SCLC that has progressed after first-line therapy is an aggressive disease with few effective therapeutic strategies. In this prospective study, we employed next-generation sequencing (NGS to identify therapeutically actionable alterations to guide treatment for advanced SCLC patients.Twelve patients with SCLC were enrolled after failing platinum-based chemotherapy. Following informed consent, genome-wide exome and RNA-sequencing was performed in a CLIA-certified, CAP-accredited environment. Actionable targets were identified and therapeutic recommendations made from a pharmacopeia of FDA-approved drugs. Clinical response to genomically-guided treatment was evaluated by Response Evaluation Criteria in Solid Tumors (RECIST 1.1.The study completed its accrual goal of 12 evaluable patients. The minimum tumor content for successful NGS was 20%, with a median turnaround time from sample collection to genomics-based treatment recommendation of 27 days. At least two clinically actionable targets were identified in each patient, and six patients (50% received treatment identified by NGS. Two had partial responses by RECIST 1.1 on a clinical trial involving a PD-1 inhibitor + irinotecan (indicated by MLH1 alteration. The remaining patients had clinical deterioration before NGS recommended therapy could be initiated.Comprehensive genomic profiling using NGS identified clinically-actionable alterations in SCLC patients who progressed on initial therapy. Recommended PD-1 therapy generated partial responses in two patients. Earlier access to NGS guided therapy, along with improved understanding of those SCLC patients likely to respond to immune-based therapies, should help to extend survival in these cases with poor outcomes.

A prospective pilot study of genome-wide exome and transcriptome profiling in patients with small cell lung cancer progressing after first-line therapy.

Science.gov (United States)

Weiss, Glen J; Byron, Sara A; Aldrich, Jessica; Sangal, Ashish; Barilla, Heather; Kiefer, Jeffrey A; Carpten, John D; Craig, David W; Whitsett, Timothy G

2017-01-01

Small cell lung cancer (SCLC) that has progressed after first-line therapy is an aggressive disease with few effective therapeutic strategies. In this prospective study, we employed next-generation sequencing (NGS) to identify therapeutically actionable alterations to guide treatment for advanced SCLC patients. Twelve patients with SCLC were enrolled after failing platinum-based chemotherapy. Following informed consent, genome-wide exome and RNA-sequencing was performed in a CLIA-certified, CAP-accredited environment. Actionable targets were identified and therapeutic recommendations made from a pharmacopeia of FDA-approved drugs. Clinical response to genomically-guided treatment was evaluated by Response Evaluation Criteria in Solid Tumors (RECIST) 1.1. The study completed its accrual goal of 12 evaluable patients. The minimum tumor content for successful NGS was 20%, with a median turnaround time from sample collection to genomics-based treatment recommendation of 27 days. At least two clinically actionable targets were identified in each patient, and six patients (50%) received treatment identified by NGS. Two had partial responses by RECIST 1.1 on a clinical trial involving a PD-1 inhibitor + irinotecan (indicated by MLH1 alteration). The remaining patients had clinical deterioration before NGS recommended therapy could be initiated. Comprehensive genomic profiling using NGS identified clinically-actionable alterations in SCLC patients who progressed on initial therapy. Recommended PD-1 therapy generated partial responses in two patients. Earlier access to NGS guided therapy, along with improved understanding of those SCLC patients likely to respond to immune-based therapies, should help to extend survival in these cases with poor outcomes.