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Sample records for two-hour test sequence

  1. A two-hour antibiotic susceptibility test by ATP-bioluminescence.

    Science.gov (United States)

    March Rosselló, Gabriel Alberto; García-Loygorri Jordán de Urries, María Cristina; Gutiérrez Rodríguez, María Purificación; Simarro Grande, María; Orduña Domingo, Antonio; Bratos Pérez, Miguel Ángel

    2016-01-01

    The antibiotic susceptibility test (AST) in Clinical Microbiology laboratories is still time-consuming, and most procedures take 24h to yield results. In this study, a rapid antimicrobial susceptibility test using ATP-bioluminescence has been developed. The design of method was performed using five ATCC collection strains of known susceptibility. This procedure was then validated against standard commercial methods on 10 strains of enterococci, 10 staphylococci, 10 non-fermenting gram negative bacilli, and 13 Enterobacteriaceae from patients. The agreement obtained in the sensitivity between the ATP-bioluminescence method and commercial methods (E-test, MicroScan and VITEK2) was 100%. In summary, the preliminary results obtained in this work show that the ATP-bioluminescence method could provide a fast and reliable AST in two hours. Copyright © 2015 Elsevier España, S.L.U. and Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica. All rights reserved.

  2. 168 Hours Salt Fog Test

    International Nuclear Information System (INIS)

    Nur Ubaidah Saidin; Muhamad Daud; Siti Radiah Mohd Kamarudin

    2011-01-01

    This report explained the test conducted in salt fog chamber to evaluate the effectiveness of mild steel, coated with rust converter, for 168 hours in artificial seawater exposure. The samples were compared with mild steel coated with commercial primer. The tests were conducted followed ASTM B117. Individual pictures were taken of each sample before the tests began, at 24, 48, 72, 96, 120, 144 and 168 hours to see the progression of the corrosion. Results showed that the samples coated with rust converter provide a good significant protection against corrosion phenomenon than the samples coated with commercial primer that available in the market. (author)

  3. Correlation of 2 hour, 4 hour, 8 hour and 12 hour urine protein with 24 hour urinary protein in preeclampsia.

    Directory of Open Access Journals (Sweden)

    Savita Rani Singhal

    2014-09-01

    Full Text Available To find shortest and reliable time period of urine collection for determination of proteinuria.It is a prospective study carried out on 125 pregnant women with preeclampsia after 20 weeks of gestation having urine albumin >1 using dipstick test. Urine was collected in five different time intervals in colors labeled containers with the assistance of nursing staff; the total collection time was 24 hours. Total urine protein of two-hour, four-hour, eight-hour, 12-hour and 24-hour urine was measured and compared with 24-hour collection. Data was analyzed using the Pearson correlation coefficient.There was significant correlation (p value < 0.01 in two, four, eight and 12-hour urine protein with 24-urine protein, with correlation coefficient of 0.97, 0.97, 0.96 and 0.97, respectively. When a cut off value of 25 mg, 50 mg. 100 mg, and 150 mg for urine protein were used for 2-hour, 4-hours, 8-hour and 12-hour urine collection, a sensitivity of 92.45%, 95.28%, 91.51%, and 96.23% and a specificity of 68.42%, 94.74%, 84.21% and 84.21% were obtained, respectively.Two-hour urine proteins can be used for assessment of proteinuria in preeclampsia instead of gold standard 24-hour urine collection for early diagnosis and better patient compliance.

  4. From psychological need satisfaction to intentional behavior: testing a motivational sequence in two behavioral contexts.

    Science.gov (United States)

    Hagger, Martin S; Chatzisarantis, Nikos L D; Harris, Jemma

    2006-02-01

    The present study tested a motivational sequence in which global-level psychological need satisfaction from self-determination theory influenced intentions and behavior directly and indirectly through contextual-level motivation and situational-level decision-making constructs from the theory of planned behavior. Two samples of university students (N = 511) completed measures of global-level psychological need satisfaction, contextual-level autonomous motivation, and situational-level attitudes, subjective norms, perceived behavioral control, intentions, and behavior in two behavioral contexts: exercise and dieting. A structural equation model supported the proposed sequence in both samples. The indirect effect was present for exercise behavior, whereas both direct and indirect effects were found for dieting behavior. Findings independently supported the component theories and provided a comprehensive integrated explanation of volitional behavior.

  5. Change from an 8-hour shift to a 12-hour shift, attitudes, sleep, sleepiness and performance.

    Science.gov (United States)

    Lowden, A; Kecklund, G; Axelsson, J; Akerstedt, T

    1998-01-01

    The present study sought to evaluate the effect of a change from a rotating 3-shift (8-hour) to a 2-shift shift (12 hour) schedule on sleep, sleepiness, performance, perceived health, and well-being. Thirty-two shift workers at a chemical plant (control room operators) responded to a questionnaire a few months before a change was made in their shift schedule and 10 months after the change. Fourteen workers also filled out a diary, carried activity loggers, and carried out reaction-time tests (beginning and end of shift). Fourteen day workers served as a reference group for the questionnaires and 9 were intensively studied during a week with workdays and a free weekend. The questionnaire data showed that the shift change increased satisfaction with workhours, sleep, and time for social activities. Health, perceived accident risk, and reaction-time performance were not negatively affected. Alertness improved and subjective recovery time after night work decreased. The quick changes in the 8-hour schedule greatly increased sleep problems and fatigue. Sleepiness integrated across the entire shift cycle showed that the shift workers were less alert than the day workers, across workdays and days off (although alertness increased with the 12-hour shift). The change from 8-hour to 12-hour shifts was positive in most respects, possibly due to the shorter sequences of the workdays, the longer sequences of consecutive days off, the fewer types of shifts (easier planning), and the elimination of quick changes. The results may differ in groups with a higher work load.

  6. Results of the 1000 Hour Rotary Microfilter Endurance Test

    International Nuclear Information System (INIS)

    Herman, D.

    2010-01-01

    During operation, a primary concern is lifetime of the mechanical seal. Leakage from main shaft mechanical seal is expected to be first indication of wear on rotary filter but will not be the ultimate failure of the filter. Initial clearance inadequate to support thermal expansion resulted in initial scarring of journal. Tolerances adjusted and no journal issues were found during 1000 hour test. Disassembly and inspection of the rotary joint seals showed no unusual wear. No leakage observed during test. Total operation time over 1500 hours. Test summary successfully demonstrated: (1) Filtration of a 'challenging' SRS simulant up to 15 wt % insoluble solids in a 5.6 M salt simulant; (2) Sludge washing; (3) In-situ acid cleaning with dilute acid; (4) Over 1000 hours of operation on new journal material; and (5) Over 1500 hours of operation on all seals. The filter out lasted: 2 air compressors, 2 power outages (one planned), 2 chillers, 1 fire, 1 electrical breaker and 1 feed pump seal.

  7. Production Facility Prototype Blower 1000 Hour Test Results II

    Energy Technology Data Exchange (ETDEWEB)

    Wass, Alexander Joseph [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Woloshun, Keith Albert [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Dale, Gregory E. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Dalmas, Dale Allen [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Romero, Frank Patrick [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2018-01-08

    Long duration tests of the Aerzen GM 12.4 roots style blower in a closed loop configuration provides valuable data and lessons learned for long-term operation at the Mo-99 production facility. The blower was operated in a closed loop configuration with the flow conditions anticipated in plant operation with a Mo-100 target inline. The additional thermal energy generated from beam heating of the Mo-100 disks were not included in these tests. Five 1000 hour tests have been completed since the first test was performed in January of 2016. All five 1000 hour tests have proven successful in exposing preventable issues related to oil and helium leaks. All blower tests to this date have resulted in stable blower performance and consistency. A summary of the results for each test, including a review of the first and second tests, are included in this report.

  8. Two- and 4-hour bright-light exposures differentially effect sleepiness and performance the subsequent night.

    Science.gov (United States)

    Thessing, V C; Anch, A M; Muehlbach, M J; Schweitzer, P K; Walsh, J K

    1994-03-01

    The effect of two durations of bright light upon sleepiness and performance during typical night shift hours was assessed. Thirty normal, healthy young adults participated in a 2-night protocol. On the 1st night subjects were exposed to bright or dim light beginning at 2400 hours, under one of the following three conditions: bright light for 4 hours, dim light for 2 hours followed by bright light for 2 hours or dim light for 4 hours. Following light exposure, subjects remained awake until 0800 hours in a dimly lit room and slept in the laboratory between 0800 and 1600 hours, during which time sleep was estimated with actigraphy. Throughout the 2nd night, the multiple sleep latency test (MSLT), simulated assembly line task (SALT) performance, and subjective sleepiness were recorded. The single, 4-hour exposure to bright light was found to significantly increase MSLT scores and improve SALT performance during the early morning hours on the night following bright-light exposure. No significant effects were noted with a 2-hour exposure. The most likely explanation for these findings is a phase delay in the circadian rhythm of sleepiness-alertness.

  9. Microleakage of two self-adhesive cements in the enamel and dentin after 24 hours and two months.

    Directory of Open Access Journals (Sweden)

    Zahra Jaberi Ansari

    2014-08-01

    Full Text Available Microleakage is a main cause of restorative treatment failure. In this study, we compared occlusal and cervical microleakage of two self-adhesive cements after 24 hours and two months.In this in-vitro experimental study, class II inlay cavities were prepared on 60 sound human third molars. Composite inlays were fabricated with Z100 composite resin. The teeth were randomly assigned to six groups. RelyX-Arc (control, RelyX-Unicem and Maxcem were used for the first three groups and specimens were stored in distilled water at 37°C for 24 hours. The same cements were used for the remaining three groups, but the specimens were stored for 2 months. The teeth were subjected to 500 thermal cycles (5°C and 55°C and immersed in 0.5% basic fuchsin for 24 hours and then sectioned mesiodistally and dye penetration was evaluated in a class II cavity with occlusal and cervical margins using X20 magnification stereomicroscope. Data were analyzed using Kruskal Wallis and Mann-Whitney U tests.After 24 hours, cements had significant differences only in cervical margin microleakage (P=0.0001 and microleakage of RelyX-Unicem and Maxcem was significantly more than that of RelyX-Arc (both P=0.0001. Cervical microleakage in RelyX-Unicem and Maxcem was greater than occlusal (P=0.0001 and P=0.001, respectively. Microleakage was not significantly different between the occlusal and cervical margins after 2 months.Cervical microleakage was greater than occlusal in RelyX-Unicem and Maxcem after 24h. The greatest microleakage was reported for the cervical margin of RelyX-Unicem after 24 hours.

  10. Rapid Multiplex Small DNA Sequencing on the MinION Nanopore Sequencing Platform

    Directory of Open Access Journals (Sweden)

    Shan Wei

    2018-05-01

    Full Text Available Real-time sequencing of short DNA reads has a wide variety of clinical and research applications including screening for mutations, target sequences and aneuploidy. We recently demonstrated that MinION, a nanopore-based DNA sequencing device the size of a USB drive, could be used for short-read DNA sequencing. In this study, an ultra-rapid multiplex library preparation and sequencing method for the MinION is presented and applied to accurately test normal diploid and aneuploidy samples’ genomic DNA in under three hours, including library preparation and sequencing. This novel method shows great promise as a clinical diagnostic test for applications requiring rapid short-read DNA sequencing.

  11. A test matrix sequencer for research test facility automation

    Science.gov (United States)

    Mccartney, Timothy P.; Emery, Edward F.

    1990-01-01

    The hardware and software configuration of a Test Matrix Sequencer, a general purpose test matrix profiler that was developed for research test facility automation at the NASA Lewis Research Center, is described. The system provides set points to controllers and contact closures to data systems during the course of a test. The Test Matrix Sequencer consists of a microprocessor controlled system which is operated from a personal computer. The software program, which is the main element of the overall system is interactive and menu driven with pop-up windows and help screens. Analog and digital input/output channels can be controlled from a personal computer using the software program. The Test Matrix Sequencer provides more efficient use of aeronautics test facilities by automating repetitive tasks that were once done manually.

  12. A Randomized Comparative Study Evaluating Various Cough Stress Tests and 24-Hour Pad Test with Urodynamics in the Diagnosis of Stress Urinary Incontinence.

    Science.gov (United States)

    Henderson, Joseph W; Kane, Sarah M; Mangel, Jeffrey M; Kikano, Elias G; Garibay, Jorge A; Pollard, Robert R; Mahajan, Sangeeta T; Debanne, Sara M; Hijaz, Adonis K

    2018-06-01

    The cough stress test is a common and accepted tool to evaluate stress urinary incontinence but there is no agreement on how the test should be performed. We assessed the diagnostic ability of different cough stress tests performed when varying patient position and bladder volume using urodynamic stress urinary incontinence as the gold standard. The 24-hour pad test was also evaluated. We recruited women who presented to specialty outpatient clinics with the complaint of urinary incontinence and who were recommended to undergo urodynamic testing. A total of 140 patients were randomized to 4 cough stress test groups, including group 1-a comfortably full bladder, group 2-an empty bladder, group 3- a bladder infused with 200 cc saline and group 4-a bladder filled to half functional capacity. The sequence of standing and sitting was randomly assigned. The groups were compared by 1-way ANOVA or the generalized Fisher exact test. The κ statistic was used to evaluate agreement between the sitting and standing positions. The 95% CIs of sensitivity and specificity were calculated using the Wilson method. ROC analysis was done to evaluate the performance of the 24-hour pad test. The cough stress test performed with a bladder filled to half functional capacity was the best performing test with 83% sensitivity and 90% specificity. There was no statistically significant evidence that the sensitivity or specificity of 1 cough stress test differed from that of the others. The pad test had no significant predictive ability to diagnose urodynamic stress urinary incontinence (AUC 0.60, p = 0.08). Cough stress tests were accurate to diagnose urodynamic stress urinary incontinence. The 24-hour pad test was not predictive of urodynamic stress urinary incontinence and not helpful when used in conjunction with the cough stress test. Copyright © 2018 American Urological Association Education and Research, Inc. Published by Elsevier Inc. All rights reserved.

  13. Generation of global hourly radiation sequences using a Transition Markov matrix for Madrid. Generacion de secuencias horarias de radiacion global utilizando matrices de transicion de Markov, para la localidad de Madrid

    Energy Technology Data Exchange (ETDEWEB)

    Mora, Ll

    1989-11-01

    The aim of this work is the generation of sequences of hourly global radiation which have similar statistically characteristics of real sequences for the city of Madrid (Spain). For this generation, a first order Markov model has been proposed. The input parameters of simulation method are the following: The maximum value of hourly radiation and the average monthly value of the transparency normalized index. The maximum value of hourly radiation has been calculated as a function of the solar height by an empirical expression. The transparency normalized index has been defined as the ratio among the measured hourly global radiation to the maximum value for the corresponding solar height. The method is based on the following observations: -The transparency normalized index shows a significant correlation only for two consecutive hours. -The months with the same average transparency normalized indies have similar probability density function. Global solar radiation, time series, simulation, Markov transition matrix, solar energy.

  14. Characterization testing of a 40 ampere hour bipolar nickel-hydrogen battery

    Science.gov (United States)

    Brewer, Jeffrey C.; Manzo, Michelle A.; Gemeiner, Russel P.

    1990-01-01

    Extensive characterization testing has been done on a second 40-ampere hour (A h), 10-cell, bipolar nickel-hydrogen (Ni-H2) battery, to study the effects of operating parameters such as charge and discharge rates, temperature, and pressure on capacity, A h and watt hour (W h) efficiencies, and end-of-charge and midpoint discharge voltages. Testing to date has produced many interesting results, with the battery performing well throughout the test matrix except during the high-rate (5 C and 10 C) discharges, where poorer than expected results were observed. The exact cause of this poor performance is, as yet, unknown. Small scale 2 in. x 2 in. battery tests are to be used in studying this problem. Low earth orbit cycle life testing at a 40-percent depth of discharge and 10 C is scheduled to follow the characterization testing.

  15. Hourly cooling load forecasting using time-indexed ARX models with two-stage weighted least squares regression

    International Nuclear Information System (INIS)

    Guo, Yin; Nazarian, Ehsan; Ko, Jeonghan; Rajurkar, Kamlakar

    2014-01-01

    Highlights: • Developed hourly-indexed ARX models for robust cooling-load forecasting. • Proposed a two-stage weighted least-squares regression approach. • Considered the effect of outliers as well as trend of cooling load and weather patterns. • Included higher order terms and day type patterns in the forecasting models. • Demonstrated better accuracy compared with some ARX and ANN models. - Abstract: This paper presents a robust hourly cooling-load forecasting method based on time-indexed autoregressive with exogenous inputs (ARX) models, in which the coefficients are estimated through a two-stage weighted least squares regression. The prediction method includes a combination of two separate time-indexed ARX models to improve prediction accuracy of the cooling load over different forecasting periods. The two-stage weighted least-squares regression approach in this study is robust to outliers and suitable for fast and adaptive coefficient estimation. The proposed method is tested on a large-scale central cooling system in an academic institution. The numerical case studies show the proposed prediction method performs better than some ANN and ARX forecasting models for the given test data set

  16. Free-piston Stirling engine/linear alternator 1000-hour endurance test

    Science.gov (United States)

    Rauch, J.; Dochat, G.

    1985-01-01

    The Free Piston Stirling Engine (FPSE) has the potential to be a long lived, highly reliable, power conversion device attractive for many product applications such as space, residential or remote site power. The purpose of endurance testing the FPSE was to demonstrate its potential for long life. The endurance program was directed at obtaining 1000 operational hours under various test conditions: low power, full stroke, duty cycle and stop/start. Critical performance parameters were measured to note any change and/or trend. Inspections were conducted to measure and compare critical seal/bearing clearances. The engine performed well throughout the program, completing more than 1100 hours. Hardware inspection, including the critical clearances, showed no significant change in hardware or clearance dimensions. The performance parameters did not exhibit any increasing or decreasing trends. The test program confirms the potential for long life FPSE applications.

  17. Enamel-Caries Prevention Using Two Applications of Fluoride-Laser Sequence.

    Science.gov (United States)

    Noureldin, Amal; Quintanilla, Ines; Kontogiorgos, Elias; Jones, Daniel

    2016-03-01

    Studies demonstrated a significant synergism between fluoride and laser in reduction of enamel solubility. However, minimal research has focused on testing the sequence of their application and no other research investigated the preventive effect of repeated applications of a combined treatment. This study investigated the effect of two applications of fluoride-laser sequence on the resistance of sound enamel to cariogenic challenge compared to one-time application. Sixty enamel slabs were cut from 10 human incisors, ground flat, polished and coated with nail varnish except a 2 x 2 mm window. Specimens were randomly assigned into five groups of 12 specimens; (CON-) negative-control received no treatment, (CON+) positive-control received pH challenge, (FV) treated with M fluoride varnish, (F-L1) one-application fluoride-varnish followed by CO2 laser-treatment (short-pulsed 10.6 µm, 2.4J/ cm2, 10HZ, 10sec), and (F-L2) two-applications of fluoride varnish-laser treatment. Specimens were left in distilled water for one day between applications. Except CON-, all groups were submitted to pH cycling for 9-days (8 demin/ remin + 1 day remineralisation bath) at 37°C. Enamel demineralization was quantitatively evaluated by measurement of Knoop surface-microhardness (SM H) (50-grams/10 seconds). Data were analyzed using one-way ANOVA (p ≤ 0.05) followed by Duncan's Multiple Range Test. Within the limitations of this study, it was found that one or two applications of fluoride-laser sequence significantly improved resistance of the sound enamel surface to acid attack compared to FV-treated group. Although the two applications of fluoride-laser sequence (F-L1 and F-L2) showed higher SMH values, significant resistance to demineralization was only obtained with repeated applications.

  18. Optimized Environmental Test Sequences to Ensure the Sustainability and Reliability of Marine Weapons

    Directory of Open Access Journals (Sweden)

    Jung Ho Yang

    2014-11-01

    Full Text Available In recent years, there has been an increase in the types of marine weapons used in response to diverse hostile threats. However, because marine weapons are only tested under a single set of environmental conditions, failures due to different environmental stresses have been difficult to detect. Hence, this study proposes an environmental test sequence for multi-environment testing. The environmental test sequences for electrical units described in the international standard IEC 60068-1, and for military supply described in the United States national standard MIL-STD-810G were investigated to propose guidelines for the appropriate test sequences. This study demonstrated the need for tests in multiple environments by investigating marine weapon accidents, and evaluated which environmental stresses and test items have the largest impacts on marine weapons using a two-phase quality function deployment (QFD analysis of operational scenarios, environmental stresses, and environmental test items. Integer programming was used to determine the most influential test items and the shortest environmental test time, allowing us to propose optimal test procedures. Based on our analysis, we developed optimal environmental test sequences that could be selected by a test designer.

  19. A likelihood ratio test for species membership based on DNA sequence data

    DEFF Research Database (Denmark)

    Matz, Mikhail V.; Nielsen, Rasmus

    2005-01-01

    DNA barcoding as an approach for species identification is rapidly increasing in popularity. However, it remains unclear which statistical procedures should accompany the technique to provide a measure of uncertainty. Here we describe a likelihood ratio test which can be used to test if a sampled...... sequence is a member of an a priori specified species. We investigate the performance of the test using coalescence simulations, as well as using the real data from butterflies and frogs representing two kinds of challenge for DNA barcoding: extremely low and extremely high levels of sequence variability....

  20. An assessment of time involved in pre-test case review and counseling for a whole genome sequencing clinical research program.

    Science.gov (United States)

    Williams, Janet L; Faucett, W Andrew; Smith-Packard, Bethanny; Wagner, Monisa; Williams, Marc S

    2014-08-01

    Whole genome sequencing (WGS) is being used for evaluation of individuals with undiagnosed disease of suspected genetic origin. Implementing WGS into clinical practice will place an increased burden upon care teams with regard to pre-test patient education and counseling about results. To quantitate the time needed for appropriate pre-test evaluation of participants in WGS testing, we documented the time spent by our clinical research group on various activities related to program preparation, participant screening, and consent prior to WGS. Participants were children or young adults with autism, intellectual or developmental disability, and/or congenital anomalies, who have remained undiagnosed despite previous evaluation, and their biologic parents. Results showed that significant time was spent in securing allocation of clinical research space to counsel participants and families, and in acquisition and review of participant's medical records. Pre-enrollment chart review identified two individuals with existing diagnoses resulting in savings of $30,000 for the genome sequencing alone, as well as saving hours of personnel time for genome interpretation and communication of WGS results. New WGS programs should plan for costs associated with additional pre-test administrative planning and patient evaluation time that will be required to provide high quality care.

  1. The nucleotide sequences of two leghemoglobin genes from soybean

    DEFF Research Database (Denmark)

    Wiborg, O; Hyldig-Nielsen, J J; Jensen, E O

    1982-01-01

    We present the complete nucleotide sequences of two leghemoglobin genes isolated from soybean DNA. Both genes contain three intervening sequences in identical positions. Comparison of the coding sequences with known amino-acid sequences of soybean leghemoglobins suggest that the two genes...

  2. Exome sequencing identifies mutations in ABCD1 and DACH2 in two brothers with a distinct phenotype

    OpenAIRE

    Zhang, Yanliang; Liu, Yanhui; Li, Ya; Duan, Yong; Zhang, Keyun; Wang, Junwang; Dai, Yong

    2014-01-01

    Background We report on two brothers with a distinct syndromic phenotype and explore the potential pathogenic cause. Methods Cytogenetic tests and exome sequencing were performed on the two brothers and their parents. Variants detected by exome sequencing were validated by Sanger sequencing. Results The main phenotype of the two brothers included congenital language disorder, growth retardation, intellectual disability, difficulty in standing and walking, and urinary and fecal incontinence. T...

  3. Comparison of 44-hour and fixed 24-hour ambulatory blood pressure monitoring in dialysis patients.

    Science.gov (United States)

    Liu, Wenjin; Ye, Hong; Tang, Bing; Sun, Zhiping; Wen, Ping; Wu, Wenhui; Bian, Xueqing; Shen, Xia; Yang, Junwei

    2014-01-01

    The two most commonly used strategies to evaluate dialysis patients' blood pressure (BP) level are 44-hour and 24-hour ambulatory blood pressure monitoring (ABPM). The objective of this study was to find an appropriate 24-hour period that correlated well with the 44-hour BP level and determine the differences between these strategies. In a group of 51 dialysis patients, the authors performed 44-hour ABPM and extracted data for a fixed 24-hour ABPM. The fixed 24-hour ABPM started at 6 am on the nondialysis day. A strong correlation was found between all parameters of 44-hour and the fixed 24-hour ABPM, with paired sample t test showing only small magnitude changes in a few parameters. Both 24-hour ABPM and 44-hour ABPM were superior to clinic BP in predicting left ventricular mass index (LVMI) by multiple regression analysis. It was found that 44-hour ambulatory arterial stiffness index (AASI), but not 24-hour AASI, had a positive association with LVMI (r=0.328, P=.021). However, after adjustment for 44-hour systolic blood pressure, this association disappeared. Fixed 24-hour ABPM is a good surrogate of 44-hour ABPM to some extent, while 44-hour ABPM can provide more accurate and detailed information. ©2013 Wiley Periodicals, Inc.

  4. Test results of six-month test of two water electrolysis systems

    Science.gov (United States)

    Mills, E. S.; Wells, G. W.

    1972-01-01

    The two water electrolysis systems used in the NASA space station simulation 90-day manned test of a regenerative life support system were refurbished as required and subjected to 26-weeks of testing. The two electrolysis units are both promising systems for oxygen and hydrogen generation and both needed extensive long-term testing to evaluate the performance of the respective cell design and provide guidance for further development. Testing was conducted to evaluate performance in terms of current, pressure, variable oxygen demands, and orbital simulation. An automatic monitoring system was used to record, monitor and printout performance data at one minute, ten minute or one-hour intervals. Performance data is presented for each day of system operation for each module used during the day. Failures are analyzed, remedial action taken to eliminate problems is discussed and recommendations for redesign for future space applications are stated.

  5. A 34 ampere-hour nickel-cadmium minimum trickle charge testing

    Science.gov (United States)

    Timmerman, P. J.

    1985-01-01

    The current rates used for trickle charging batteries are critical in maintaining a full charge and in preventing an overcharge condition. The importance of the trickle charge rate comes from the design, maintenance and operational requirements of an electrical power system. The results of minimum trickle charge testing performed on six 34 ampere-hour, nickel-cadmium cells manufactured by General Electric are described. The purpose of the testing was to identify the minimum trickle charge rates at temperatures of 15 C and 30 C.

  6. HEURISTIC METHODS FOR TEST SEQUENCING IN TELECOMMUNICATION SATELLITES

    OpenAIRE

    Boche-Sauvan , Ludivine; Cabon , Bertrand; Huguet , Marie-José; Hébrard , Emmanuel

    2014-01-01

    Colloque avec actes et comité de lecture. internationale.; International audience; The increasing complexity in telecommunication satellite payload design demands new test sequencing approaches to face the induced increase of validation complexity. In such a sequencing problem, each test requires specific payload equipment states at a dedicated temperature range. The industrial objectives are both to reduce the total time of tests and to keep the thermal stability of the payload. For solving ...

  7. Studies on the T sub 3 suppression test with reference to the thyrodial sup 123 I uptake in Graves' disease; Comparison of 24-hour and 3-hour uptake

    Energy Technology Data Exchange (ETDEWEB)

    Yamaguchi, Takahiko; Kobayashi, Isao; Yamaguchi, Yoshiyuki; Iwashita, Akira; Inukai, Toshihiko; Ohshima, Kihachi; Shimomura, Yohnosuke; Kobayashi, Setsuo (Gunma Univ., Maebashi (Japan). School of Medicine)

    1990-06-01

    Eighty-three patients with Graves' disease had been treated with methylmercaptoimidazole (MMI). They were prescribed a maintenance dose of antithyroid drug (MMI, 5 mg/day) at the time of a T{sub 3} suppression test. The 3-hour and 24-hour thyroidal {sup 123}I uptake after T{sub 3} administration (75 {mu}g/day, 2 weeks) were measured (post T{sub 3} uptake). In 38 patients whose post T{sub 3} uptake was below 35% in post T{sub 3} 24-hour uptake, treatment was stopped. The T{sub 3} suppression test was then repeated 1 and 3 months later. During a one-year follow up, 26 remained well, while 12 relapsed within 6 to 12 months. We have observed a good correlation between 3-hour uptake and 24-hour uptake of {sup 123}I after T{sub 3} administration (r=0.847, p<0.001). In 38 patients who showed positive T{sub 3} suppression, most patients with MMI withdrawal produced a marked overshoot of post T{sub 3} 3-hour and 24-hour uptake at one month. Retrospective analysis indicated that there was no significant difference in circulating thyroid hormone levels between remission and relapse groups. The present study provides evidence that 3-hour uptake values are able to be substituted for 24-hour uptake values during a T{sub 3} suppression test. In addition, overshoot of thyroidal uptake after antithyroid drug withdrawal was observed in 3-hour values, similar to 24-hour values. (author).

  8. Evaluation of the 12-hour shift schedule at the Fast Flux Test Facility

    International Nuclear Information System (INIS)

    Lewis, P.M.; Swaim, D.J.; Rosa, R.R.; Colligan, M.J.; Booth, R.J.; Swint, M.J.

    1986-09-01

    The objective of this report are to evaluate the effect of the change to the 12-hour/day schedule on operational performance and safety of FFTF; to evaluate the degree to which the change to the 12-hour/day schedule has met its objectives; and to gather information that may be useful to FFTF management and the US Department of Energy (DOE) in evaluating 8- and 12-hour shift schedules at other facilities. The principal conclusion of this report is that the 12-hour/day shift schedule is a reasonable alternative to an 8-hour/day schedule at FFTF. As a result of the scedule change, it seems clear that plant performance improved in two ways. The operator error rate in keeping the Technical Specification Compliance Logs was already very low on the 8-hour shift. On the 12-hour shift, the rate was even lower. Also, the operator interface with craft personnel resulted in an increase in the productivity of the craft personnel

  9. Bioequivalence of two film-coated tablets of imatinib mesylate 400 mg: a randomized, open-label, single-dose, fasting, two-period, two-sequence crossover comparison in healthy male South American volunteers.

    Science.gov (United States)

    Parrillo-Campiglia, Susana; Ercoli, Mónica Cedres; Umpierrez, Ofelia; Rodríguez, Patricia; Márquez, Sara; Guarneri, Carolina; Estevez-Parrillo, Francisco T; Laurenz, Marilena; Estevez-Carrizo, Francisco E

    2009-10-01

    Imatinib is a tyrosine kinase inhibitor that has been established as a highly effective therapy for chronic myelogenous leukemia and gastrointestinal stromal tumors. A new generic, once-daily 400-mg tablet of imatinib has been developed by a pharmaceutical company in Argentina, where the regulatory standard for marketing authorization of an imatinib generic is in vitro dissolution testing. The aim of this study was to assess the bioequivalence of a new generic film-coated test tablet formulation versus a film-coated reference tablet formulation of imatinib 400 mg. The local manufacturer seeks to validate the in vitro performance of this new formulation with a bioequivalence study. A randomized, open-label, single-dose, fasting, 2-period, 2-sequence crossover design with a 2-week washout period was used in this study. The study population consisted of healthy male South American (Uruguayan) volunteers, who were assigned in a 1:1 ratio to a randomized sequence (test-reference or reference-test). In each period, the test or reference formulation was administered after an overnight fast. During the 72-hour follow-up period, participants were monitored for vital signs and symptoms. Blood samples were collected at 15 time points, including baseline, until 72 hours. Physical examination and laboratory tests (blood, urine) were repeated 1 week after study completion. A noncompartmental model was used to determine the pharmacokinetic parameters of imatinib. The 90% CIs of the test/reference ratios for AUC(0-infinity) and C(max) were determined; the test and reference formulations were considered bioequivalent if the 90% CIs were between 0.80 and 1.25. Adverse events were assessed by a nurse who administered a questionnaire while the healthy volunteers were admitted in the unit. The bioequivalence study was conducted in 30 Uruguayan male volunteers. Demographic characteristics (mean [SD]) included age, 27.8 (6.5) years; weight, 71.2 (9.8) kg; height, 1.71 (0.09) m; and body

  10. A Window Into Clinical Next-Generation Sequencing-Based Oncology Testing Practices.

    Science.gov (United States)

    Nagarajan, Rakesh; Bartley, Angela N; Bridge, Julia A; Jennings, Lawrence J; Kamel-Reid, Suzanne; Kim, Annette; Lazar, Alexander J; Lindeman, Neal I; Moncur, Joel; Rai, Alex J; Routbort, Mark J; Vasalos, Patricia; Merker, Jason D

    2017-12-01

    - Detection of acquired variants in cancer is a paradigm of precision medicine, yet little has been reported about clinical laboratory practices across a broad range of laboratories. - To use College of American Pathologists proficiency testing survey results to report on the results from surveys on next-generation sequencing-based oncology testing practices. - College of American Pathologists proficiency testing survey results from more than 250 laboratories currently performing molecular oncology testing were used to determine laboratory trends in next-generation sequencing-based oncology testing. - These presented data provide key information about the number of laboratories that currently offer or are planning to offer next-generation sequencing-based oncology testing. Furthermore, we present data from 60 laboratories performing next-generation sequencing-based oncology testing regarding specimen requirements and assay characteristics. The findings indicate that most laboratories are performing tumor-only targeted sequencing to detect single-nucleotide variants and small insertions and deletions, using desktop sequencers and predesigned commercial kits. Despite these trends, a diversity of approaches to testing exists. - This information should be useful to further inform a variety of topics, including national discussions involving clinical laboratory quality systems, regulation and oversight of next-generation sequencing-based oncology testing, and precision oncology efforts in a data-driven manner.

  11. Optimal choice of word length when comparing two Markov sequences using a χ 2-statistic.

    Science.gov (United States)

    Bai, Xin; Tang, Kujin; Ren, Jie; Waterman, Michael; Sun, Fengzhu

    2017-10-03

    Alignment-free sequence comparison using counts of word patterns (grams, k-tuples) has become an active research topic due to the large amount of sequence data from the new sequencing technologies. Genome sequences are frequently modelled by Markov chains and the likelihood ratio test or the corresponding approximate χ 2 -statistic has been suggested to compare two sequences. However, it is not known how to best choose the word length k in such studies. We develop an optimal strategy to choose k by maximizing the statistical power of detecting differences between two sequences. Let the orders of the Markov chains for the two sequences be r 1 and r 2 , respectively. We show through both simulations and theoretical studies that the optimal k= max(r 1 ,r 2 )+1 for both long sequences and next generation sequencing (NGS) read data. The orders of the Markov chains may be unknown and several methods have been developed to estimate the orders of Markov chains based on both long sequences and NGS reads. We study the power loss of the statistics when the estimated orders are used. It is shown that the power loss is minimal for some of the estimators of the orders of Markov chains. Our studies provide guidelines on choosing the optimal word length for the comparison of Markov sequences.

  12. A functional test of Neandertal and modern human mitochondrial targeting sequences

    International Nuclear Information System (INIS)

    Gralle, Matthias; Schaefer, Ingo; Seibel, Peter; Paeaebo, Svante

    2010-01-01

    Research highlights: → Two mutations in mitochondrial targeting peptides occurred during human evolution, possibly after Neandertals split off from modern human lineage. → The ancestral and modern human versions of these two targeting peptides were tested functionally for their effects on localization and cleavage rate. → In spite of recent evolution, and to the contrary of other mutations in targeting peptides, these mutations had no visible effects. -- Abstract: Targeting of nuclear-encoded proteins to different organelles, such as mitochondria, is a process that can result in the redeployment of proteins to new intracellular destinations during evolution. With the sequencing of the Neandertal genome, it has become possible to identify amino acid substitutions that occurred on the modern human lineage since its separation from the Neandertal lineage. Here we analyze the function of two substitutions in mitochondrial targeting sequences that occurred and rose to high frequency recently during recent human evolution. The ancestral and modern versions of the two targeting sequences do not differ in the efficiency with which they direct a protein to the mitochondria, an observation compatible with the neutral theory of molecular evolution.

  13. A functional test of Neandertal and modern human mitochondrial targeting sequences

    Energy Technology Data Exchange (ETDEWEB)

    Gralle, Matthias, E-mail: gralle@bioqmed.ufrj.br [Instituto de Bioquimica Medica, Universidade Federal do Rio de Janeiro, CCS, Ilha do Fundao, 21941-590 Rio de Janeiro (Brazil); Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig (Germany); Schaefer, Ingo; Seibel, Peter [Department of Molecular Cell Therapy, Leipzig University, Deutscher Platz 5, 04103 Leipzig (Germany); Paeaebo, Svante [Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig (Germany)

    2010-11-26

    Research highlights: {yields} Two mutations in mitochondrial targeting peptides occurred during human evolution, possibly after Neandertals split off from modern human lineage. {yields} The ancestral and modern human versions of these two targeting peptides were tested functionally for their effects on localization and cleavage rate. {yields} In spite of recent evolution, and to the contrary of other mutations in targeting peptides, these mutations had no visible effects. -- Abstract: Targeting of nuclear-encoded proteins to different organelles, such as mitochondria, is a process that can result in the redeployment of proteins to new intracellular destinations during evolution. With the sequencing of the Neandertal genome, it has become possible to identify amino acid substitutions that occurred on the modern human lineage since its separation from the Neandertal lineage. Here we analyze the function of two substitutions in mitochondrial targeting sequences that occurred and rose to high frequency recently during recent human evolution. The ancestral and modern versions of the two targeting sequences do not differ in the efficiency with which they direct a protein to the mitochondria, an observation compatible with the neutral theory of molecular evolution.

  14. Relationship between long working hours and depression in two working populations: a structural equation model approach.

    Science.gov (United States)

    Amagasa, Takashi; Nakayama, Takeo

    2012-07-01

    To test the hypothesis that relationship reported between long working hours and depression was inconsistent in previous studies because job demand was treated as a confounder. Structural equation modeling was used to construct five models, using work-related factors and depressive mood scale obtained from 218 clerical workers, to test for goodness of fit and was externally validated with data obtained from 1160 sales workers. Multiple logistic regression analysis was also performed. The model that showed that long working hours increased depression risk when job demand was regarded as an intermediate variable was the best fitted model (goodness-of-fit index/root-mean-square error of approximation: 0.981 to 0.996/0.042 to 0.044). The odds ratio for depression risk with work that was high demand and 60 hours or more per week was estimated at 2 to 4 versus work that was low demand and less than 60 hours per week. Long working hours increased depression risk, with job demand being an intermediate variable.

  15. tscvh R Package: Computational of the two samples test on microarray-sequencing data

    Science.gov (United States)

    Fajriyah, Rohmatul; Rosadi, Dedi

    2017-12-01

    We present a new R package, a tscvh (two samples cross-variance homogeneity), as we called it. This package is a software of the cross-variance statistical test which has been proposed and introduced by Fajriyah ([3] and [4]), based on the cross-variance concept. The test can be used as an alternative test for the significance difference between two means when sample size is small, the situation which is usually appeared in the bioinformatics research. Based on its statistical distribution, the p-value can be also provided. The package is built under a homogeneity of variance between samples.

  16. PHEBUS on-line aerosol monitor development test program

    International Nuclear Information System (INIS)

    Sprenger, M.H.; Pentecost, C.G.

    1992-03-01

    EG ampersand G Idaho, Inc. developed an on-line aerosol monitor (OLAM) for the French PHEBUS Fission Product Project. Part of the development was to manufacture and test an OLAM prototype. This report presents the results of the testing which determined the mechanical integrity of the monitor at operating temperature and pressure and performed a preliminary test of the optical system. A series of twenty different tests was conducted during the prototype testing sequence. Since no leaks were detected, the OLAM demonstrated that it could provide a pressure boundary at required test conditions. The optical and electrical system also proved its integrity by exceeding the design requirement of less than 105 optical signal drift during an actual two-hour test sequence

  17. cDNA sequences of two apolipoproteins from lamprey

    International Nuclear Information System (INIS)

    Pontes, M.; Xu, X.; Graham, D.; Riley, M.; Doolittle, R.F.

    1987-01-01

    The messages for two small but abundant apolipoproteins found in lamprey blood plasma were cloned with the aid of oligonucleotide probes based on amino-terminal sequences. In both cases, numerous clones were identified in a lamprey liver cDNA library, consistent with the great abundance of these proteins in lamprey blood. One of the cDNAs (LAL1) has a coding region of 105 amino acids that corresponds to a 21-residue signal peptide, a putative 8-residue propeptide, and the 76-residue mature protein found in blood. The other cDNA (LAL2) codes for a total of 191 residues, the first 23 of which constitute a signal peptide. The two proteins, which occur in the high-density lipoprotein fraction of ultracentrifuged plasma, have amino acid compositions similar to those of apolipoproteins found in mammalian blood; computer analysis indicates that the sequences are largely helix-permissive. When the sequences were searched against an amino acid sequence data base, rat apolipoprotein IV was the best matching candidate in both cases. Although a reasonable alignment can be made with that sequence and LAL1, definitive assignment of the two lamprey proteins to typical mammalian classes cannot be made at this point

  18. Automated Testing with Targeted Event Sequence Generation

    DEFF Research Database (Denmark)

    Jensen, Casper Svenning; Prasad, Mukul R.; Møller, Anders

    2013-01-01

    Automated software testing aims to detect errors by producing test inputs that cover as much of the application source code as possible. Applications for mobile devices are typically event-driven, which raises the challenge of automatically producing event sequences that result in high coverage...

  19. Irreducible Tests for Space Mission Sequencing Software

    Science.gov (United States)

    Ferguson, Lisa

    2012-01-01

    As missions extend further into space, the modeling and simulation of their every action and instruction becomes critical. The greater the distance between Earth and the spacecraft, the smaller the window for communication becomes. Therefore, through modeling and simulating the planned operations, the most efficient sequence of commands can be sent to the spacecraft. The Space Mission Sequencing Software is being developed as the next generation of sequencing software to ensure the most efficient communication to interplanetary and deep space mission spacecraft. Aside from efficiency, the software also checks to make sure that communication during a specified time is even possible, meaning that there is not a planet or moon preventing reception of a signal from Earth or that two opposing commands are being given simultaneously. In this way, the software not only models the proposed instructions to the spacecraft, but also validates the commands as well.To ensure that all spacecraft communications are sequenced properly, a timeline is used to structure the data. The created timelines are immutable and once data is as-signed to a timeline, it shall never be deleted nor renamed. This is to prevent the need for storing and filing the timelines for use by other programs. Several types of timelines can be created to accommodate different types of communications (activities, measurements, commands, states, events). Each of these timeline types requires specific parameters and all have options for additional parameters if needed. With so many combinations of parameters available, the robustness and stability of the software is a necessity. Therefore a baseline must be established to ensure the full functionality of the software and it is here where the irreducible tests come into use.

  20. [Results of Training for Personnel Involved in Blood-Transfusion Testing Outside of Regular Work Hours at Saga University Hospital].

    Science.gov (United States)

    Yamada, Marie; Yamada, Naotomo; Higashitani, Takanori; Ohta, Shoichiro; Sueoka, Eisaburo

    2015-11-01

    Laboratory testing prior to blood transfusion outside of regular hours in many hospitals and clinics is frequently conducted by technicians without sufficient experience in such testing work. To obtain consistent test results regardless of the degree of laboratory experience with blood transfusion testing, the number of facilities introducing automated equipment for testing prior to blood transfusion is increasing. Our hospital's blood transfusion department introduced fully automated test equipment in October of 2010 for use when blood transfusions are conducted outside of regular hours. However, excessive dependence on automated testing can lead to an inability to do manual blood typing or cross-match testing when necessitated by breakdowns in the automated test equipment, in the case of abnormal specimen reactions, or other such case. In addition, even outside of normal working hours there are more than a few instances in which transfusion must take place based on urgent communications from clinical staff, with the need for prompt and flexible timing of blood transfusion test and delivery of blood products. To address this situation, in 2010 we began training after-hours laboratory personnel in blood transfusion testing to provide practice using test tubes manually and to achieve greater understanding of blood transfusion test work (especially in cases of critical blood loss). Results of the training and difficulties in its implementation for such after-hours laboratory personnel at our hospital are presented and discussed in this paper. [Original

  1. Two-Stage orders sequencing system for mixed-model assembly

    Science.gov (United States)

    Zemczak, M.; Skolud, B.; Krenczyk, D.

    2015-11-01

    In the paper, the authors focus on the NP-hard problem of orders sequencing, formulated similarly to Car Sequencing Problem (CSP). The object of the research is the assembly line in an automotive industry company, on which few different models of products, each in a certain number of versions, are assembled on the shared resources, set in a line. Such production type is usually determined as a mixed-model production, and arose from the necessity of manufacturing customized products on the basis of very specific orders from single clients. The producers are nowadays obliged to provide each client the possibility to determine a huge amount of the features of the product they are willing to buy, as the competition in the automotive market is large. Due to the previously mentioned nature of the problem (NP-hard), in the given time period only satisfactory solutions are sought, as the optimal solution method has not yet been found. Most of the researchers that implemented inaccurate methods (e.g. evolutionary algorithms) to solving sequencing problems dropped the research after testing phase, as they were not able to obtain reproducible results, and met problems while determining the quality of the received solutions. Therefore a new approach to solving the problem, presented in this paper as a sequencing system is being developed. The sequencing system consists of a set of determined rules, implemented into computer environment. The system itself works in two stages. First of them is connected with the determination of a place in the storage buffer to which certain production orders should be sent. In the second stage of functioning, precise sets of sequences are determined and evaluated for certain parts of the storage buffer under certain criteria.

  2. Testing statistical significance scores of sequence comparison methods with structure similarity

    Directory of Open Access Journals (Sweden)

    Leunissen Jack AM

    2006-10-01

    Full Text Available Abstract Background In the past years the Smith-Waterman sequence comparison algorithm has gained popularity due to improved implementations and rapidly increasing computing power. However, the quality and sensitivity of a database search is not only determined by the algorithm but also by the statistical significance testing for an alignment. The e-value is the most commonly used statistical validation method for sequence database searching. The CluSTr database and the Protein World database have been created using an alternative statistical significance test: a Z-score based on Monte-Carlo statistics. Several papers have described the superiority of the Z-score as compared to the e-value, using simulated data. We were interested if this could be validated when applied to existing, evolutionary related protein sequences. Results All experiments are performed on the ASTRAL SCOP database. The Smith-Waterman sequence comparison algorithm with both e-value and Z-score statistics is evaluated, using ROC, CVE and AP measures. The BLAST and FASTA algorithms are used as reference. We find that two out of three Smith-Waterman implementations with e-value are better at predicting structural similarities between proteins than the Smith-Waterman implementation with Z-score. SSEARCH especially has very high scores. Conclusion The compute intensive Z-score does not have a clear advantage over the e-value. The Smith-Waterman implementations give generally better results than their heuristic counterparts. We recommend using the SSEARCH algorithm combined with e-values for pairwise sequence comparisons.

  3. Fast global sequence alignment technique

    KAUST Repository

    Bonny, Mohamed Talal

    2011-11-01

    Bioinformatics database is growing exponentially in size. Processing these large amount of data may take hours of time even if super computers are used. One of the most important processing tool in Bioinformatics is sequence alignment. We introduce fast alignment algorithm, called \\'Alignment By Scanning\\' (ABS), to provide an approximate alignment of two DNA sequences. We compare our algorithm with the wellknown sequence alignment algorithms, the \\'GAP\\' (which is heuristic) and the \\'Needleman-Wunsch\\' (which is optimal). The proposed algorithm achieves up to 51% enhancement in alignment score when it is compared with the GAP Algorithm. The evaluations are conducted using different lengths of DNA sequences. © 2011 IEEE.

  4. Why the long hours? Job demands and social exchange dynamics.

    Science.gov (United States)

    Genin, Emilie; Haines, Victor Y; Pelletier, David; Rousseau, Vincent; Marchand, Alain

    2016-11-22

    This study investigates the determinants of long working hours from the perspectives of the demand-control model [Karasek, 1979] and social exchange theory [Blau, 1964; Goulder, 1960]. These two theoretical perspectives are tested to understand why individuals work longer (or shorter) hours. The hypotheses are tested with a representative sample of 1,604 employed Canadians. In line with Karasek's model, the results support that high job demands are positively associated with longer work hours. The social exchange perspective would predict a positive association between skill discretion and work hours. This hypothesis was supported for individuals with a higher education degree. Finally, the results support a positive association between active jobs and longer work hours. Our research suggests that job demands and social exchange dynamics need to be considered together in the explanation of longer (or shorter) work hours.

  5. Exome sequencing and genetic testing for MODY.

    Directory of Open Access Journals (Sweden)

    Stefan Johansson

    Full Text Available Genetic testing for monogenic diabetes is important for patient care. Given the extensive genetic and clinical heterogeneity of diabetes, exome sequencing might provide additional diagnostic potential when standard Sanger sequencing-based diagnostics is inconclusive.The aim of the study was to examine the performance of exome sequencing for a molecular diagnosis of MODY in patients who have undergone conventional diagnostic sequencing of candidate genes with negative results.We performed exome enrichment followed by high-throughput sequencing in nine patients with suspected MODY. They were Sanger sequencing-negative for mutations in the HNF1A, HNF4A, GCK, HNF1B and INS genes. We excluded common, non-coding and synonymous gene variants, and performed in-depth analysis on filtered sequence variants in a pre-defined set of 111 genes implicated in glucose metabolism.On average, we obtained 45 X median coverage of the entire targeted exome and found 199 rare coding variants per individual. We identified 0-4 rare non-synonymous and nonsense variants per individual in our a priori list of 111 candidate genes. Three of the variants were considered pathogenic (in ABCC8, HNF4A and PPARG, respectively, thus exome sequencing led to a genetic diagnosis in at least three of the nine patients. Approximately 91% of known heterozygous SNPs in the target exomes were detected, but we also found low coverage in some key diabetes genes using our current exome sequencing approach. Novel variants in the genes ARAP1, GLIS3, MADD, NOTCH2 and WFS1 need further investigation to reveal their possible role in diabetes.Our results demonstrate that exome sequencing can improve molecular diagnostics of MODY when used as a complement to Sanger sequencing. However, improvements will be needed, especially concerning coverage, before the full potential of exome sequencing can be realized.

  6. Two sequence-ready contigs spanning the two copies of a 200-kb duplication on human 21q: partial sequence and polymorphisms.

    Science.gov (United States)

    Potier, M; Dutriaux, A; Orti, R; Groet, J; Gibelin, N; Karadima, G; Lutfalla, G; Lynn, A; Van Broeckhoven, C; Chakravarti, A; Petersen, M; Nizetic, D; Delabar, J; Rossier, J

    1998-08-01

    Physical mapping across a duplication can be a tour de force if the region is larger than the size of a bacterial clone. This was the case of the 170- to 275-kb duplication present on the long arm of chromosome 21 in normal human at 21q11.1 (proximal region) and at 21q22.1 (distal region), which we described previously. We have constructed sequence-ready contigs of the two copies of the duplication of which all the clones are genuine representatives of one copy or the other. This required the identification of four duplicon polymorphisms that are copy-specific and nonallelic variations in the sequence of the STSs. Thirteen STSs were mapped inside the duplicated region and 5 outside but close to the boundaries. Among these STSs 10 were end clones from YACs, PACs, or cosmids, and the average interval between two markers in the duplicated region was 16 kb. Eight PACs and cosmids showing minimal overlaps were selected in both copies of the duplication. Comparative sequence analysis along the duplication showed three single-basepair changes between the two copies over 659 bp sequenced (4 STSs), suggesting that the duplication is recent (less than 4 mya). Two CpG islands were located in the duplication, but no genes were identified after a 36-kb cosmid from the proximal copy of the duplication was sequenced. The homology of this chromosome 21 duplicated region with the pericentromeric regions of chromosomes 13, 2, and 18 suggests that the mechanism involved is probably similar to pericentromeric-directed mechanisms described in interchromosomal duplications. Copyright 1998 Academic Press.

  7. Noninvasive prenatal paternity testing (NIPAT) through maternal plasma DNA sequencing

    DEFF Research Database (Denmark)

    Jiang, Haojun; Xie, Yifan; Li, Xuchao

    2016-01-01

    developed a noninvasive prenatal paternity testing (NIPAT) based on SNP typing with maternal plasma DNA sequencing. We evaluated the influence factors (minor allele frequency (MAF), the number of total SNP, fetal fraction and effective sequencing depth) and designed three different selective SNP panels......Short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs) have been already used to perform noninvasive prenatal paternity testing from maternal plasma DNA. The frequently used technologies were PCR followed by capillary electrophoresis and SNP typing array, respectively. Here, we...... paternity test using STR multiplex system. Our study here proved that the maternal plasma DNA sequencing-based technology is feasible and accurate in determining paternity, which may provide an alternative in forensic application in the future....

  8. Bioequivalence of generic lamotrigine 100-mg tablets in healthy Thai male volunteers: a randomized, single-dose, two-period, two-sequence crossover study.

    Science.gov (United States)

    Srichaiya, Arunee; Longchoopol, Chaowanee; Oo-Puthinan, Sarawut; Sayasathid, Jarun; Sripalakit, Pattana; Viyoch, Jarupa

    2008-10-01

    Lamotrigine is an antiepileptic drug which has been used in the treatment of epilepsy and bipolar disorder. A search of the literature did not find previously published bioequivalence and pharmacokinetic evaluations of lamotrigine in healthy Thai male volunteers. The aim of this study was to compare the pharmacokinetic parameters between 2 brands of lamotrigine in healthy Thai male volunteers. A randomized, single-dose, 2-period, 2-sequence, crossover study design with a 2-week washout period was conducted in healthy Thai males. Subjects were randomized to receive either the test or reference formulation in the first period. All subjects were required to be nonsmokers and without a history of alcohol or drug abuse. Plasma samples were collected over a 120-hour period after 100-mg lamotrigine administration in each period. A validated high-performance liquid chromatography ultraviolet method was used to analyze lamotrigine concentration in plasma. Pharmacokinetic parameters were determined using a noncompartmental method. Bioequivalence between the test and reference products, as defined by the US Food and Drug Administration (FDA), is determined when the ratio for the 90% CIs of the difference in the means of the log-transformed AUC(0-t), AUC(0-infinity), and C(max) of the 2 products are within 0.80 and 1.25. Adverse events were determined by measuring vital signs after dosing. Subjects were also asked if they suffered from undesirable effects such as nausea, vomiting, dizziness, and headache. This bioequivalence study was performed in 24 healthy Thai males (mean [SD] age, 20.5 [1.3] years; range, 19-24 years; weight, 62.5 [7.4] kg; height, 172.8 [6.9] cm; body mass index, 20.9 [2.0] kg/m(2)). The mean (SD) C(max) and T(max) of the test formulation of lamotrigine were 1.7 (0.3) microg/mL and 1.2 (0.9) hours, respectively. The mean (SD) C(max) and T(max) of the reference formulation of lamotrigine were 1.7 (0.3) microg/mL and 1.4 (1.0) hours, respectively. The mean

  9. Hypothesis testing in students: Sequences, stages, and instructional strategies

    Science.gov (United States)

    Moshman, David; Thompson, Pat A.

    Six sequences in the development of hypothesis-testing conceptions are proposed, involving (a) interpretation of the hypothesis; (b) the distinction between using theories and testing theories; (c) the consideration of multiple possibilities; (d) the relation of theory and data; (e) the nature of verification and falsification; and (f) the relation of truth and falsity. An alternative account is then provided involving three global stages: concrete operations, formal operations, and a postformal metaconstructivestage. Relative advantages and difficulties of the stage and sequence conceptualizations are discussed. Finally, three families of teaching strategy are distinguished, which emphasize, respectively: (a) social transmission of knowledge; (b) carefully sequenced empirical experience by the student; and (c) self-regulated cognitive activity of the student. It is argued on the basis of Piaget's theory that the last of these plays a crucial role in the construction of such logical reasoning strategies as those involved in testing hypotheses.

  10. Two tandemly repeated telomere-associated sequences in Nicotiana plumbaginifolia.

    Science.gov (United States)

    Chen, C M; Wang, C T; Wang, C J; Ho, C H; Kao, Y Y; Chen, C C

    1997-12-01

    Two tandemly repeated telomere-associated sequences, NP3R and NP4R, have been isolated from Nicotiana plumbaginifolia. The length of a repeating unit for NP3R and NP4R is 165 and 180 nucleotides respectively. The abundance of NP3R, NP4R and telomeric repeats is, respectively, 8.4 x 10(4), 6 x 10(3) and 1.5 x 10(6) copies per haploid genome of N. plumbaginifolia. Fluorescence in situ hybridization revealed that NP3R is located at the ends and/or in interstitial regions of all 10 chromosomes and NP4R on the terminal regions of three chromosomes in the haploid genome of N. plumbaginifolia. Sequence homology search revealed that not only are NP3R and NP4R homologous to HRS60 and GRS, respectively, two tandem repeats isolated from N. tabacum, but that NP3R and NP4R are also related to each other, suggesting that they originated from a common ancestral sequence. The role of these repeated sequences in chromosome healing is discussed based on the observation that two to three copies of a telomere-similar sequence were present in each repeating unit of NP3R and NP4R.

  11. A comparison of EGFR mutation testing methods in lung carcinoma: direct sequencing, real-time PCR and immunohistochemistry.

    Directory of Open Access Journals (Sweden)

    Bárbara Angulo

    Full Text Available The objective of this study is to compare two EGFR testing methodologies (a commercial real-time PCR kit and a specific EGFR mutant immunohistochemistry, with direct sequencing and to investigate the limit of detection (LOD of both PCR-based methods. We identified EGFR mutations in 21 (16% of the 136 tumours analyzed by direct sequencing. Interestingly, the Therascreen EGFR Mutation Test kit was able to characterize as wild-type one tumour that could not be analyzed by direct sequencing of the PCR product. We then compared the LOD of the kit and that of direct sequencing using the available mutant tumours. The kit was able to detect the presence of a mutation in a 1% dilution of the total DNA in nine of the 18 tumours (50%, which tested positive with the real-time quantitative PCR method. In all cases, EGFR mutation was identified at a dilution of 5%. Where the mutant DNA represented 30% of the total DNA, sequencing was able to detect mutations in 12 out of 19 cases (63%. Additional experiments with genetically defined standards (EGFR ΔE746-A750/+ and EGFR L858R/+ yielded similar results. Immunohistochemistry (IHC staining with exon 19-specific antibody was seen in eight out of nine cases with E746-A750del detected by direct sequencing. Neither of the two tumours with complex deletions were positive. Of the five L858R-mutated tumours detected by the PCR methods, only two were positive for the exon 21-specific antibody. The specificity was 100% for both antibodies. The LOD of the real-time PCR method was lower than that of direct sequencing. The mutation specific IHC produced excellent specificity.

  12. Bioavailability of two single-dose oral formulations of omeprazole 20 mg: an open-label, randomized sequence, two-period crossover comparison in healthy Mexican adult volunteers.

    Science.gov (United States)

    Poo, Jorge Luis; Galán, Juan Francisco; Rosete, Alejandra; de Lago, Alberto; Oliva, Iván; González-de la Parra, Mario; Jiménez, Patricia; Burke-Fraga, Victoria; Namur, Salvador

    2008-04-01

    Omeprazole is a proton-pump inhibitor that acts to reduce acid secretion in the stomach and is used for treating various acid-related gastrointestinal disorders. There are several generic formulations of omeprazole available in Mexico; however, a literature search failed to identify published data concerning the bioavailability of these formulations in the Mexican population. The aim of this study was to compare the bioavailability of 2 oral formulations of omeprazole 20-mg capsules, marketed for use in Mexico, in healthy volunteers: Inhibitron (test formulation) and LosecA 20 mg (reference formulation). This study used a single-dose, open-label, randomized sequence, 2 x 2 crossover (2 administration periods x 2 treatments) design to compare the 2 formulations. Eligible subjects were healthy adult Mexican volunteers of both sexes. Subjects were randomly assigned in a 1:1 ratio to receive a single 20-mg dose of the test formulation followed by the reference formulation, or vice versa, with a 7-day washout period between administration periods. After a 12-hour (overnight) fast, subjects received a single, 20-mg dose of the corresponding formulation. Plasma samples were obtained over a 12-hour period after administration. Plasma omeprazole concentrations were analyzed by a nonstereospecific high-performance liquid chromatography method. For analysis of pharmacokinetic properties, including C(max), AUC from time 0 (baseline) to time t (AUC(0-t)), and AUC from baseline to infinity (AUC(0-infinity)), blood samples were drawn at baseline and 0.17, 0.33, 0.50, 0.75, 1, 1.25, 1.50, 1.75, 2, 2.50, 3, 4, 6, 8, and 12 hours after administration. The formulations were considered bioequivalent if the natural log (ln)-transformed ratios of C(max) and AUC were within the predetermined equivalence range of 80% to 125%, and if P disability, or required intervention to prevent permanent impairment or damage. Thirty-four subjects were enrolled and completed the study (25 men and 9

  13. CANFLEX fuel bundle cross-flow endurance test (test report)

    International Nuclear Information System (INIS)

    Hong, Sung Deok; Chung, C. H.; Chang, S. K.; Kim, B. D.

    1997-04-01

    As part of the normal refuelling sequence of CANDU nuclear reactor, both new and irradiated bundles can be parked in the cross-flow region of the liner tubes. This situation occurs normally for a few minutes. The fuel bundle which is subjected to the cross-flow should be capable of withstanding the consequences of cross flow for normal periods, and maintain its mechanical integrity. The cross-flow endurance test was conducted for CANFLEX bundle, latest developed nuclear fuel, at CANDU-Hot Test Loop. The test was carried out during 4 hours at the inlet cross-flow region. After the test, the bundle successfully met all acceptance criteria after the 4 hours cross-flow test. (author). 2 refs., 3 tabs

  14. CANFLEX fuel bundle cross-flow endurance test (test report)

    Energy Technology Data Exchange (ETDEWEB)

    Hong, Sung Deok; Chung, C. H.; Chang, S. K.; Kim, B. D.

    1997-04-01

    As part of the normal refuelling sequence of CANDU nuclear reactor, both new and irradiated bundles can be parked in the cross-flow region of the liner tubes. This situation occurs normally for a few minutes. The fuel bundle which is subjected to the cross-flow should be capable of withstanding the consequences of cross flow for normal periods, and maintain its mechanical integrity. The cross-flow endurance test was conducted for CANFLEX bundle, latest developed nuclear fuel, at CANDU-Hot Test Loop. The test was carried out during 4 hours at the inlet cross-flow region. After the test, the bundle successfully met all acceptance criteria after the 4 hours cross-flow test. (author). 2 refs., 3 tabs.

  15. 7 positions in 2 hours

    Directory of Open Access Journals (Sweden)

    Jessica Ackerman

    2013-07-01

    Full Text Available 7 positions in 2 hours (2013 is a drawing that documents the process of making the short film Role Reversal Rehearsal. It became quickly apparent that the process of making the work was more dynamic and interesting than the finished piece itself. Relationships between the childcare arrangements of the participants and the collective working process brought about the necessity of collaboration for parent artists. Each participant gave their time, energy and creative insight towards filming a series of birthing positions with roles reversed. The male performer became the central figure in an attempt to prompt empathy, humour, and to embody the importance of the male role in childbirth. There were two hours to choreograph, rehearse, and film the sequence. The drawing by Ackerman encapsulates the 'rhizomatic' approach to producing creative work under the constraints of parenthood. The 'arborescent' structure of hierarchy encouraged in industrial filmmaking is subsumed in favour of a horizontal structure. This new structure allows for the creative input, and flow of collaboration between all people involved - including the 3 and 5 year olds, who contributed ideas for camera and soundtrack in situ.

  16. Comparison between two.magnetic resonance sequences (spin-echo and gradient-echo) in the analysis of lesions of the knee joint meniscus

    International Nuclear Information System (INIS)

    Marti-Bonati, L.; Casillas, C.

    1999-01-01

    To compare the diagnostic reliability, the proportion of common diagnoses and the degree of agreement between the results of two magnetic resonance (MR) sequences in the diagnosis of lesions of the meniscus of the knee. One hundred consecutive patients were studied prospectively by MR (1,5 Teslas). All of them underwent T1-weighted spin-echo and T1 and T2-weighted gradient-echo sequences. The final diagnosis was based on the combined results of four imaging sequences. The sensitivity, specificity, positive predictive value (PPV) and negative predictive (NPV) in terms of the final diagnosis were calculated for each meniscus and MR technique. The chi.squared test and kappa test were employed for the statistical analysis. There were discrepancies between the final diagnosis and the spin-echo sequence in 4 cases and between the final diagnosis and the gradient-echo sequences in 5 Both spin-echo and gradient-echo sequences showed the same diagnostic reliabilities: sensitivity of 0.98, specificity of 0.99, PPV of 0.98 and NPV of 0.99. The correlation between the two sequences was highly significant (chi-squared, p < 0.001) with a very high rate of agreement (kappa=0.84). The two sequences can be considered equally reliable in the study of meniscal lesions. (Author) 7 refs

  17. 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.

  18. Structural and sequence features of two residue turns in beta-hairpins.

    Science.gov (United States)

    Madan, Bharat; Seo, Sung Yong; Lee, Sun-Gu

    2014-09-01

    Beta-turns in beta-hairpins have been implicated as important sites in protein folding. In particular, two residue β-turns, the most abundant connecting elements in beta-hairpins, have been a major target for engineering protein stability and folding. In this study, we attempted to investigate and update the structural and sequence properties of two residue turns in beta-hairpins with a large data set. For this, 3977 beta-turns were extracted from 2394 nonhomologous protein chains and analyzed. First, the distribution, dihedral angles and twists of two residue turn types were determined, and compared with previous data. The trend of turn type occurrence and most structural features of the turn types were similar to previous results, but for the first time Type II turns in beta-hairpins were identified. Second, sequence motifs for the turn types were devised based on amino acid positional potentials of two-residue turns, and their distributions were examined. From this study, we could identify code-like sequence motifs for the two residue beta-turn types. Finally, structural and sequence properties of beta-strands in the beta-hairpins were analyzed, which revealed that the beta-strands showed no specific sequence and structural patterns for turn types. The analytical results in this study are expected to be a reference in the engineering or design of beta-hairpin turn structures and sequences. © 2014 Wiley Periodicals, Inc.

  19. Long-term wireless pH monitoring of the distal esophagus: prolonging the test beyond 48 hours is unnecessary and may be misleading.

    Science.gov (United States)

    Capovilla, G; Salvador, R; Spadotto, L; Voltarel, G; Pesenti, E; Perazzolo, A; Nicoletti, L; Merigliano, S; Costantini, M

    2017-10-01

    Wireless pH monitoring of the esophagus has been widely used to detect GERD for more than a decade. It is generally well tolerated and accepted by patients, but it is still unclear whether prolonging a recording beyond the usual 48 hours can improve the test's diagnostic value. The aim of this study is to examine the diagnostic yield of 96-hour pH monitoring vis-à-vis 24- and 48-hour tests, and to ascertain whether any gain in diagnostic terms was of genuine clinical utility. Patients with suspected GERD underwent 4-day PPI-off wireless pH monitoring of the distal esophagus. The capsule was inserted under endoscopic control, 6 cm above the squamocolumnar junction. Average acid exposure time was calculated after 24, 48, and 96 hours of recording. Ninety-nine patients completed the 96 hour test, and formed the study sample. The wireless test method was used in 42 patients (42.4%) unable to tolerate the traditional pH-monitoring catheter, and in 57 (57.6%) with a previous negative pH study despite symptoms suggestive of GERD. On complete analysis, 47 patients (47.5%) had a pathological test result: 19 patients within the first 24 hours (19.2%, 24 hour group); another 16 after 48 hours (+16.2%, 48 hour group), and a further 12 (+12.1%, 96 hour group) only after 96 hours of monitoring. All 47 patients with an abnormal acid exposure were offered and accepted surgery (10 patients) or medical therapy (37 patients). Clinical follow-up was obtained in all patients with a positive Bravo test result after a median 67 months (IQR: 38-98) using a validated symptom questionnaire. A good outcome after fundoplication or medical therapy was achieved in 73.7% of patients in the 24 hour group, in 62.5% of those in the 48 hour group, and in only 25% of those in the 96 hour group, P = 0.02. Long-term wireless pH monitoring enables an increase in the diagnostic yield over traditional 24- and 48-hour pH studies, but prolonging the test may constitute an unwanted bias and prompt the

  20. Analysis of Hourly Climatic Variables-Meteorological Test Reference Year for Beijing

    DEFF Research Database (Denmark)

    Qin, Lin

    1997-01-01

    The climatic data which was surveyed from 1981 to 1993 in Beijing was analysed to generate a representative year, a Test Reference Year (TRY). This TRY consists of just one year of hourly data that could yield the same simulation results as the long-term data, thereby minimizing the computation...... need to assess long-term system performance. It can be used as input data for the simulation of the performance of solar energy and indoor climate systems. The application of this TRY in the simulation of a solar domestic hot water system is also presented....

  1. Groundwater levels and water quality during a 96-hour aquifer test in Pickaway County, Ohio, 2012

    Science.gov (United States)

    Haefner, Ralph J.; Runkle, Donna L.; Mailot, Brian E.

    2014-01-01

    During October–November 2012, a 96-hour aquifer test was performed at a proposed well field in northern Pickaway County, Ohio, to investigate groundwater with elevated nitrate concentrations. Earlier sampling done by the City of Columbus revealed that some wells had concentrations of nitrate that approached 10 milligrams per liter (mg/L), whereas other wells and the nearby Scioto River had concentrations from 2 to 6 mg/L. The purpose of the current test was to examine potential changes in water quality that may be expected if the site was developed into a public water-supply source; therefore, water-transmitting properties determined during a previous test were not determined a second time. Before and during the test, water-level data and water-quality samples were obtained from observation wells while a test production well was pumped at 1,300 gallons per minute. Before the test, local groundwater levels indicated that groundwater was being discharged to the nearby Scioto River, but during the test, the stream was losing streamflow owing to infiltration. Water levels declined in the pumping well, in adjacent observation wells, and in a nearby streambed piezometer as pumping commenced. The maximum drawdown in the pumping well was 29.75 feet, measured about 95 hours after pumping began. Water-quality data, including analyses for field parameters, major and trace elements, nutrients, and stable isotopes of oxygen and nitrogen in nitrate, demonstrated only small variations before and during the test. Concentrations of nitrate in five samples from the pumping well ranged from about 5.10 to 5.42 mg/L before and during the test, whereas concentrations of nitrate in five samples on or about the same sampling dates and times at a monitoring site on the Scioto River adjacent to the pumping well ranged from 3.46 to 4.97 mg/L. Water from two nearby observation wells had nitrate concentrations approaching 10 mg/L, which is the U.S. Environmental Protection Agency’s Maximum

  2. cDNA sequences of two inducible T-cell genes

    Energy Technology Data Exchange (ETDEWEB)

    Kwon, B.S. (Indiana Univ. School of Medicine, Indianapolis (USA) Guthrie Research Institute, Sayre, PA (USA)); Weissman, S.M. (Yale Univ., New Haven, CT (USA))

    1989-03-01

    The authors have previously described a set of human T-lymphocyte-specific cDNA clones isolated by a modified differential screening procedure. Apparent full-length cDNAs containing the sequences of 14 of the 16 initial isolates were sequenced and were found to represent five different species of mRNA; three of the five species were identical to previously reported cDNA sequences of preproenkephalin, T-cell-replacing factor, and a serine esterase, respectively. The other two species, 4-1BB and L2G25B, were inducible sequences found in mRNA from both a cytolytic T-lymphocyte and a helper T-lymphocyte clone and were not previously described in T-cell mRNA; these mRNA sequences encode peptides of 256 and 92 amino acids, respectively. Both peptides contain putative leader sequences. The protein encoded by 4-1BB also has a potential membrane anchor segment and other features also seen in known receptor proteins.

  3. 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

  4. The consolidation of implicit sequence memory in obstructive sleep apnea.

    Directory of Open Access Journals (Sweden)

    Eszter Csabi

    Full Text Available Obstructive Sleep Apnea (OSA Syndrome is a relatively frequent sleep disorder characterized by disrupted sleep patterns. It is a well-established fact that sleep has beneficial effect on memory consolidation by enhancing neural plasticity. Implicit sequence learning is a prominent component of skill learning. However, the formation and consolidation of this fundamental learning mechanism remains poorly understood in OSA. In the present study we examined the consolidation of different aspects of implicit sequence learning in patients with OSA. We used the Alternating Serial Reaction Time task to measure general skill learning and sequence-specific learning. There were two sessions: a learning phase and a testing phase, separated by a 10-hour offline period with sleep. Our data showed differences in offline changes of general skill learning between the OSA and control group. The control group demonstrated offline improvement from evening to morning, while the OSA group did not. In contrast, we did not observe differences between the groups in offline changes in sequence-specific learning. Our findings suggest that disrupted sleep in OSA differently affects neural circuits involved in the consolidation of sequence learning.

  5. Exact association test for small size sequencing data.

    Science.gov (United States)

    Lee, Joowon; Lee, Seungyeoun; Jang, Jin-Young; Park, Taesung

    2018-04-20

    Recent statistical methods for next generation sequencing (NGS) data have been successfully applied to identifying rare genetic variants associated with certain diseases. However, most commonly used methods (e.g., burden tests and variance-component tests) rely on large sample sizes. Notwithstanding, due to its-still high cost, NGS data is generally restricted to small sample sizes, that cannot be analyzed by most existing methods. In this work, we propose a new exact association test for sequencing data that does not require a large sample approximation, which is applicable to both common and rare variants. Our method, based on the Generalized Cochran-Mantel-Haenszel (GCMH) statistic, was applied to NGS datasets from intraductal papillary mucinous neoplasm (IPMN) patients. IPMN is a unique pancreatic cancer subtype that can turn into an invasive and hard-to-treat metastatic disease. Application of our method to IPMN data successfully identified susceptible genes associated with progression of IPMN to pancreatic cancer. Our method is expected to identify disease-associated genetic variants more successfully, and corresponding signal pathways, improving our understanding of specific disease's etiology and prognosis.

  6. Sequence Design for a Test Tube of Interacting Nucleic Acid Strands.

    Science.gov (United States)

    Wolfe, Brian R; Pierce, Niles A

    2015-10-16

    We describe an algorithm for designing the equilibrium base-pairing properties of a test tube of interacting nucleic acid strands. A target test tube is specified as a set of desired "on-target" complexes, each with a target secondary structure and target concentration, and a set of undesired "off-target" complexes, each with vanishing target concentration. Sequence design is performed by optimizing the test tube ensemble defect, corresponding to the concentration of incorrectly paired nucleotides at equilibrium evaluated over the ensemble of the test tube. To reduce the computational cost of accepting or rejecting mutations to a random initial sequence, the structural ensemble of each on-target complex is hierarchically decomposed into a tree of conditional subensembles, yielding a forest of decomposition trees. Candidate sequences are evaluated efficiently at the leaf level of the decomposition forest by estimating the test tube ensemble defect from conditional physical properties calculated over the leaf subensembles. As optimized subsequences are merged toward the root level of the forest, any emergent defects are eliminated via ensemble redecomposition and sequence reoptimization. After successfully merging subsequences to the root level, the exact test tube ensemble defect is calculated for the first time, explicitly checking for the effect of the previously neglected off-target complexes. Any off-target complexes that form at appreciable concentration are hierarchically decomposed, added to the decomposition forest, and actively destabilized during subsequent forest reoptimization. For target test tubes representative of design challenges in the molecular programming and synthetic biology communities, our test tube design algorithm typically succeeds in achieving a normalized test tube ensemble defect ≤1% at a design cost within an order of magnitude of the cost of test tube analysis.

  7. Enhanced throughput for infrared automated DNA sequencing

    Science.gov (United States)

    Middendorf, Lyle R.; Gartside, Bill O.; Humphrey, Pat G.; Roemer, Stephen C.; Sorensen, David R.; Steffens, David L.; Sutter, Scott L.

    1995-04-01

    Several enhancements have been developed and applied to infrared automated DNA sequencing resulting in significantly higher throughput. A 41 cm sequencing gel (31 cm well- to-read distance) combines high resolution of DNA sequencing fragments with optimized run times yielding two runs per day of 500 bases per sample. A 66 cm sequencing gel (56 cm well-to-read distance) produces sequence read lengths of up to 1000 bases for ds and ss templates using either T7 polymerase or cycle-sequencing protocols. Using a multichannel syringe to load 64 lanes allows 16 samples (compatible with 96-well format) to be visualized for each run. The 41 cm gel configuration allows 16,000 bases per day (16 samples X 500 bases/sample X 2 ten hour runs/day) to be sequenced with the advantages of infrared technology. Enhancements to internal labeling techniques using an infrared-labeled dATP molecule (Boehringer Mannheim GmbH, Penzberg, Germany; Sequenase (U.S. Biochemical) have also been made. The inclusion of glycerol in the sequencing reactions yields greatly improved results for some primer and template combinations. The inclusion of (alpha) -Thio-dNTP's in the labeling reaction increases signal intensity two- to three-fold.

  8. Testing the Predictive Power of Coulomb Stress on Aftershock Sequences

    Science.gov (United States)

    Woessner, J.; Lombardi, A.; Werner, M. J.; Marzocchi, W.

    2009-12-01

    Empirical and statistical models of clustered seismicity are usually strongly stochastic and perceived to be uninformative in their forecasts, since only marginal distributions are used, such as the Omori-Utsu and Gutenberg-Richter laws. In contrast, so-called physics-based aftershock models, based on seismic rate changes calculated from Coulomb stress changes and rate-and-state friction, make more specific predictions: anisotropic stress shadows and multiplicative rate changes. We test the predictive power of models based on Coulomb stress changes against statistical models, including the popular Short Term Earthquake Probabilities and Epidemic-Type Aftershock Sequences models: We score and compare retrospective forecasts on the aftershock sequences of the 1992 Landers, USA, the 1997 Colfiorito, Italy, and the 2008 Selfoss, Iceland, earthquakes. To quantify predictability, we use likelihood-based metrics that test the consistency of the forecasts with the data, including modified and existing tests used in prospective forecast experiments within the Collaboratory for the Study of Earthquake Predictability (CSEP). Our results indicate that a statistical model performs best. Moreover, two Coulomb model classes seem unable to compete: Models based on deterministic Coulomb stress changes calculated from a given fault-slip model, and those based on fixed receiver faults. One model of Coulomb stress changes does perform well and sometimes outperforms the statistical models, but its predictive information is diluted, because of uncertainties included in the fault-slip model. Our results suggest that models based on Coulomb stress changes need to incorporate stochastic features that represent model and data uncertainty.

  9. CORRELATION OF SPOT URINE ALBUMIN AND 12-HOUR URINE PROTEIN WITH 24-HOUR URINE PROTEIN IN PRE-ECLAMPSIA

    Directory of Open Access Journals (Sweden)

    S. Vinayachandran

    2017-11-01

    Full Text Available BACKGROUND Pre-eclampsia is defined as the development of new-onset hypertension in the second half of pregnancy often accompanied by new-onset proteinuria with other signs and symptoms. Proteinuria is defined by the excretion of 300 mg or more of protein in a 24-hour urine collection. To avoid time consumed in collection of 24-hour urine specimens, efforts have been made to develop faster methods to determine concentration of urine protein. Preliminary studies have suggested that 12-hour urine protein collection maybe adequate for evaluation of pre-eclampsia with advantage of early diagnosis and treatment of pre-eclampsia as well as potential for early hospital discharge and increased compliance with specimen collection. The aim of the study is to evaluate and correlate spot urine albumin and 12-hour urine protein with 24-hour urine protein in pre-eclampsia. MATERIALS AND METHODS A diagnostic evaluation study- a 24-hour urine protein, 12-hour urine protein and spot urine albumin results are analysed. Correlation of 12-hour urine protein and spot urine albumin with 24-hour urine protein is analysed using SPSS software. The strength of correlation was measured by Pearson’s correlation coefficient (r. Student’s t-test and Chi-square tests were used to compare patients with and without 24-hour urine protein ≥300 mg. Probability value of 165 mg with 24-hour urine protein ≥300 mg suggest that this test has role in the evaluation of women with suspected pre-eclampsia and could be substituted for 24-hour urine protein as a simple, faster and cheaper method.

  10. Sequence robust association test for familial data.

    Science.gov (United States)

    Dai, Wei; Yang, Ming; Wang, Chaolong; Cai, Tianxi

    2017-09-01

    Genome-wide association studies (GWAS) and next generation sequencing studies (NGSS) are often performed in family studies to improve power in identifying genetic variants that are associated with clinical phenotypes. Efficient analysis of genome-wide studies with familial data is challenging due to the difficulty in modeling shared but unmeasured genetic and/or environmental factors that cause dependencies among family members. Existing genetic association testing procedures for family studies largely rely on generalized estimating equations (GEE) or linear mixed-effects (LME) models. These procedures may fail to properly control for type I errors when the imposed model assumptions fail. In this article, we propose the Sequence Robust Association Test (SRAT), a fully rank-based, flexible approach that tests for association between a set of genetic variants and an outcome, while accounting for within-family correlation and adjusting for covariates. Comparing to existing methods, SRAT has the advantages of allowing for unknown correlation structures and weaker assumptions about the outcome distribution. We provide theoretical justifications for SRAT and show that SRAT includes the well-known Wilcoxon rank sum test as a special case. Extensive simulation studies suggest that SRAT provides better protection against type I error rate inflation, and could be much more powerful for settings with skewed outcome distribution than existing methods. For illustration, we also apply SRAT to the familial data from the Framingham Heart Study and Offspring Study to examine the association between an inflammatory marker and a few sets of genetic variants. © 2017, The International Biometric Society.

  11. Draft genome sequences of two virulent serotypes of avian Pasteurella multocida

    Science.gov (United States)

    Here we report the draft genome sequences of two virulent avian strains of Pasteurella multocida. Comparative analyses of these genomes were done with the published genome sequence of avirulent Pasteurella multocida strain Pm70....

  12. Draft Genome Sequences of Two Virulent Serotypes of Avian Pasteurella multocida

    OpenAIRE

    Abrahante, Juan E.; Johnson, Timothy J.; Hunter, Samuel S.; Maheswaran, Samuel K.; Hauglund, Melissa J.; Bayles, Darrell O.; Tatum, Fred M.; Briggs, Robert E.

    2013-01-01

    Here we report the draft genome sequences of two virulent avian strains of Pasteurella multocida. Comparative analyses of these genomes were done with the published genome sequence of avirulent P.?multocida strain Pm70.

  13. Deep venous thrombophlebitis: detection with 4-hour versus 24-hour platelet scintigraphy

    International Nuclear Information System (INIS)

    Seabold, J.E.; Conrad, G.R.; Ponto, J.A.; Kimball, D.A.; Frey, E.E.; Ahmed, F.; Coughlan, J.D.; Jensen, K.C.

    1987-01-01

    Thirty-one nonheparinized patients with suspected deep venous thrombophlebitis (DVT) underwent contrast venography and indium-111 platelet scintigraphy (In-111 PS). Venography permitted identification of acute DVT in 12 of 31 cases (39%). One additional patient was considered to have acute DVT despite nonconclusive venography results. In-111 PS results were positive at 4 hours in nine of 13 cases (69%) and at 24 hours in 12 of 13 cases (92%). Two of four patients with false-negative 4-hour In-111 PS studies had received warfarin. Thus, the sensitivity of 4-hour In-111 PS in patients not receiving anticoagulants was 82%. Venography results were negative for acute DVT in 18 cases, and 4-hour In-111 PS studies were negative or equivocal in each. In-111 PS is an alternative to contrast venography for detecting acute DVT. If 4-hour In-111 PS results are positive, anticoagulation can be initiated. Delayed images are necessary if the 4-hour images are negative or equivocal

  14. Recurrent plot analysis of discharge sequences in tracking test of polybutylene polymers

    Energy Technology Data Exchange (ETDEWEB)

    Du, B X; Gu, L; Dong, D S [Key Laboratory of Power System Simulation and Control of Ministry of Education, Department of Electrical Engineering, School of Electrical Engineering and Automation, Tianjin University, Tianjin 300072 (China); Zheng, X L [Henan Electric Power Survey and Design Institute, Henan 450007 (China)], E-mail: duboxue@tju.edu.cn

    2008-10-07

    Polymers are required to use in radiation environments as insulation materials. However, they often suffer from tracking failure. There is an increasing demand to evaluate radiation effects on dielectric performance. This paper presents a recurrence plot (RP) approach to analyse surface discharge sequences of gamma-ray irradiated polymer materials based on tracking test. Studying the non-linear characteristics of discharge sequences can assist in understanding the underlying mechanism of the discharge process. Discharge sequences of the test are extended to m-dimensional phase space by using the phase space reconstructed method. As test samples, polybutylene terephthalate (PBT) and polybutylene naphthalate (PBN) were irradiated to 100 kGy and then up to 1 MGy with a dosage rate of 10 kGy h{sup -1} by using a {sup 60}Co gamma source. The tracking tests were carried out according to the test method described in IEC60112. It is found that the RPs can give visual recurrent patterns of discharge sequences for identification of the effects of gamma-ray radiation dosage on the resistance to tracking of the polymers. The detection of recurrent patterns together with comparative tracking index value results indicate that with the increase in the radiation dosage, the resistance to tracking of PBT decreases, but increases for PBN.

  15. Draft Genome Sequences of Two Virulent Serotypes of Avian Pasteurella multocida

    Science.gov (United States)

    Abrahante, Juan E.; Johnson, Timothy J.; Hunter, Samuel S.; Maheswaran, Samuel K.; Hauglund, Melissa J.; Bayles, Darrell O.; Tatum, Fred M.

    2013-01-01

    Here we report the draft genome sequences of two virulent avian strains of Pasteurella multocida. Comparative analyses of these genomes were done with the published genome sequence of avirulent P. multocida strain Pm70. PMID:23405337

  16. The Persistence of Long Work Hours

    OpenAIRE

    Robert Drago; David Black; Mark Wooden

    2005-01-01

    Previous research hypothesizes that long working hours are related to consumerism, the ideal worker norm, high levels of human capital, and a high cost-of-job-loss. The authors test these hypotheses using panel data on working hours for an Australian sample of full-time employed workers. Analyses include a static cross-sectional model and a persistence model for long hours over time. The results suggest that long hours (50 or more hours in a usual week) are often persistent, and provide stron...

  17. Genomic sequencing in cystic fibrosis newborn screening: what works best, two-tier predefined CFTR mutation panels or second-tier CFTR panel followed by third-tier sequencing?

    Science.gov (United States)

    Currier, Robert J; Sciortino, Stan; Liu, Ruiling; Bishop, Tracey; Alikhani Koupaei, Rasoul; Feuchtbaum, Lisa

    2017-10-01

    PurposeThe purpose of this study was to model the performance of several known two-tier, predefined mutation panels and three-tier algorithms for cystic fibrosis (CF) screening utilizing the ethnically diverse California population.MethodsThe cystic fibrosis transmembrane conductance regulator (CFTR) mutations identified among the 317 CF cases in California screened between 12 August 2008 and 18 December 2012 were used to compare the expected CF detection rates for several two- and three-tier screening approaches, including the current California approach, which consists of a population-specific 40-mutation panel followed by third-tier sequencing when indicated.ResultsThe data show that the strategy of using third-tier sequencing improves CF detection following an initial elevated immunoreactive trypsinogen and detection of only one mutation on a second-tier panel.ConclusionIn a diverse population, the use of a second-tier panel followed by third-tier CFTR gene sequencing provides a better detection rate for CF, compared with the use of a second-tier approach alone, and is an effective way to minimize the referrals of CF carriers for sweat testing. Restricting screening to a second-tier testing to predefined mutation panels, even broad ones, results in some missed CF cases and demonstrates the limited utility of this approach in states that have diverse multiethnic populations.

  18. PHARMACOGENETIC TESTING OPPORTUNITIES IN CARDIOLOGY BASED ON EXOME SEQUENCING

    Directory of Open Access Journals (Sweden)

    N. V. Shcherbakova

    2014-01-01

    Full Text Available Aim. To study what cardiac drugs currently have any comments on biomarkers and what information can be obtained by pharmacogenetic testing using data exome sequencing in patients with cardiac diseases.Material and methods. Exome sequencing in random participant of the ATEROGEN IVANOVO study and bioinformatics analysis of the data were performed. Point mutations were annotated using ANNOVAR program, as well as comparison with a number of specialized databases was done on the basis of user protocols.Results. 11 cardiac drugs and 7 genes which variants can influence cardiac drug metabolism were analyzed. According to exome sequencing of the participant we did not reveal allelic variants that require dose regime correction and careful efficacy control.Conclusion. The exome sequencing application is the next step to a wide range of personalized therapy. Future opportunities for improvement of the risk-benefit ratio in each patient are the main purpose of the collection and analysis of pharmacogenetic data.

  19. Number of 24-hour diet recalls needed to estimate energy intake.

    Science.gov (United States)

    Ma, Yunsheng; Olendzki, Barbara C; Pagoto, Sherry L; Hurley, Thomas G; Magner, Robert P; Ockene, Ira S; Schneider, Kristin L; Merriam, Philip A; Hébert, James R

    2009-08-01

    Twenty-four-hour diet recall interviews (24HRs) are used to assess diet and to validate other diet assessment instruments. Therefore it is important to know how many 24HRs are required to describe an individual's intake. Seventy-nine middle-aged white women completed seven 24HRs over a 14-day period, during which energy expenditure (EE) was determined by the doubly labeled water method (DLW). Mean daily intakes were compared to DLW-derived EE using paired t tests. Linear mixed models were used to evaluate the effect of call sequence and day of the week on 24HR-derived energy intake while adjusting for education, relative body weight, social desirability, and an interaction between call sequence and social desirability. Mean EE from DLW was 2115 kcal/day. Adjusted 24HR-derived energy intake was lowest at call 1 (1501 kcal/day); significantly higher energy intake was observed at calls 2 and 3 (2246 and 2315 kcal/day, respectively). Energy intake on Friday was significantly lower than on Sunday. Averaging energy intake from the first two calls better approximated true energy expenditure than did the first call, and averaging the first three calls further improved the estimate (p=0.02 for both comparisons). Additional calls did not improve estimation. Energy intake is underreported on the first 24HR. Three 24HRs appear optimal for estimating energy intake.

  20. A study of single multiplicative neuron model with nonlinear filters for hourly wind speed prediction

    International Nuclear Information System (INIS)

    Wu, Xuedong; Zhu, Zhiyu; Su, Xunliang; Fan, Shaosheng; Du, Zhaoping; Chang, Yanchao; Zeng, Qingjun

    2015-01-01

    Wind speed prediction is one important methods to guarantee the wind energy integrated into the whole power system smoothly. However, wind power has a non–schedulable nature due to the strong stochastic nature and dynamic uncertainty nature of wind speed. Therefore, wind speed prediction is an indispensable requirement for power system operators. Two new approaches for hourly wind speed prediction are developed in this study by integrating the single multiplicative neuron model and the iterated nonlinear filters for updating the wind speed sequence accurately. In the presented methods, a nonlinear state–space model is first formed based on the single multiplicative neuron model and then the iterated nonlinear filters are employed to perform dynamic state estimation on wind speed sequence with stochastic uncertainty. The suggested approaches are demonstrated using three cases wind speed data and are compared with autoregressive moving average, artificial neural network, kernel ridge regression based residual active learning and single multiplicative neuron model methods. Three types of prediction errors, mean absolute error improvement ratio and running time are employed for different models’ performance comparison. Comparison results from Tables 1–3 indicate that the presented strategies have much better performance for hourly wind speed prediction than other technologies. - Highlights: • Developed two novel hybrid modeling methods for hourly wind speed prediction. • Uncertainty and fluctuations of wind speed can be better explained by novel methods. • Proposed strategies have online adaptive learning ability. • Proposed approaches have shown better performance compared with existed approaches. • Comparison and analysis of two proposed novel models for three cases are provided

  1. Protecting unknown two-qubit entangled states by nesting Uhrig's dynamical decoupling sequences

    International Nuclear Information System (INIS)

    Mukhtar, Musawwadah; Soh, Wee Tee; Saw, Thuan Beng; Gong, Jiangbin

    2010-01-01

    Future quantum technologies rely heavily on good protection of quantum entanglement against environment-induced decoherence. A recent study showed that an extension of Uhrig's dynamical decoupling (UDD) sequence can (in theory) lock an arbitrary but known two-qubit entangled state to the Nth order using a sequence of N control pulses [Mukhtar et al., Phys. Rev. A 81, 012331 (2010)]. By nesting three layers of explicitly constructed UDD sequences, here we first consider the protection of unknown two-qubit states as superposition of two known basis states, without making assumptions of the system-environment coupling. It is found that the obtained decoherence suppression can be highly sensitive to the ordering of the three UDD layers and can be remarkably effective with the correct ordering. The detailed theoretical results are useful for general understanding of the nature of controlled quantum dynamics under nested UDD. As an extension of our three-layer UDD, it is finally pointed out that a completely unknown two-qubit state can be protected by nesting four layers of UDD sequences. This work indicates that when UDD is applicable (e.g., when the environment has a sharp frequency cutoff and when control pulses can be taken as instantaneous pulses), dynamical decoupling using nested UDD sequences is a powerful approach for entanglement protection.

  2. Sequence determination and analysis of the NSs genes of two tospoviruses.

    Science.gov (United States)

    Hallwass, Mariana; Leastro, Mikhail O; Lima, Mirtes F; Inoue-Nagata, Alice K; Resende, Renato O

    2012-03-01

    The tospoviruses groundnut ringspot virus (GRSV) and zucchini lethal chlorosis virus (ZLCV) cause severe losses in many crops, especially in solanaceous and cucurbit species. In this study, the non-structural NSs gene and the 5'UTRs of these two biologically distinct tospoviruses were cloned and sequenced. The NSs sequence of GRSV and ZLCV were both 1,404 nucleotides long. Pairwise comparison showed that the NSs amino acid sequence of GRSV shared 69.6% identity with that of ZLCV and 75.9% identity with that of TSWV, while the NSs sequence of ZLCV and TSWV shared 67.9% identity. Phylogenetic analysis based on NSs sequences confirmed that these viruses cluster in the American clade.

  3. Forecasting Kp from solar wind data: input parameter study using 3-hour averages and 3-hour range values

    Science.gov (United States)

    Wintoft, Peter; Wik, Magnus; Matzka, Jürgen; Shprits, Yuri

    2017-11-01

    We have developed neural network models that predict Kp from upstream solar wind data. We study the importance of various input parameters, starting with the magnetic component Bz, particle density n, and velocity V and then adding total field B and the By component. As we also notice a seasonal and UT variation in average Kp we include functions of day-of-year and UT. Finally, as Kp is a global representation of the maximum range of geomagnetic variation over 3-hour UT intervals we conclude that sudden changes in the solar wind can have a big effect on Kp, even though it is a 3-hour value. Therefore, 3-hour solar wind averages will not always appropriately represent the solar wind condition, and we introduce 3-hour maxima and minima values to some degree address this problem. We find that introducing total field B and 3-hour maxima and minima, derived from 1-minute solar wind data, have a great influence on the performance. Due to the low number of samples for high Kp values there can be considerable variation in predicted Kp for different networks with similar validation errors. We address this issue by using an ensemble of networks from which we use the median predicted Kp. The models (ensemble of networks) provide prediction lead times in the range 20-90 min given by the time it takes a solar wind structure to travel from L1 to Earth. Two models are implemented that can be run with real time data: (1) IRF-Kp-2017-h3 uses the 3-hour averages of the solar wind data and (2) IRF-Kp-2017 uses in addition to the averages, also the minima and maxima values. The IRF-Kp-2017 model has RMS error of 0.55 and linear correlation of 0.92 based on an independent test set with final Kp covering 2 years using ACE Level 2 data. The IRF-Kp-2017-h3 model has RMSE = 0.63 and correlation = 0.89. We also explore the errors when tested on another two-year period with real-time ACE data which gives RMSE = 0.59 for IRF-Kp-2017 and RMSE = 0.73 for IRF-Kp-2017-h3. The errors as function

  4. 20,000-hour stress-corrosion cracking tests on ASTM A36 and A387-9 steels in simulated Hanford groundwater

    International Nuclear Information System (INIS)

    James, L.A.

    1986-03-01

    Modified WOL specimens were employed to evaluate the susceptibility of two candidate container materials, A36 and A387-9 steels, to SCC in simulated groundwater at 250 0 C. The test duration was 20,000 hours. Post-test measurements of specimen compliance were not possible because significant build-up of corrosion products and/or mineral deposits on the fracture faces prevented a linear relationship between load and displacement. Considerable load was ''lost'' due to time-independent plasticity, time-dependent deformation and crack-face wedging, but the amounts lost were comparable to similar short-term tests conducted earlier. A number of direct and indirect observations suggested that no crack extension occurred during the environmental exposure. One indirect observation, the initial pre-test compliance measurements, suggested a possibility of crack extension occurred, but it is believed that these measurements were in error because of the experimental test set-up used in the program

  5. Insights from 20 years of bacterial genome sequencing

    DEFF Research Database (Denmark)

    Land, Miriam; Hauser, Loren; Jun, Se-Ran

    2015-01-01

    Since the first two complete bacterial genome sequences were published in 1995, the science of bacteria has dramatically changed. Using third-generation DNA sequencing, it is possible to completely sequence a bacterial genome in a few hours and identify some types of methylation sites along...... the genome as well. Sequencing of bacterial genome sequences is now a standard procedure, and the information from tens of thousands of bacterial genomes has had a major impact on our views of the bacterial world. In this review, we explore a series of questions to highlight some insights that comparative...... genomics has produced. To date, there are genome sequences available from 50 different bacterial phyla and 11 different archaeal phyla. However, the distribution is quite skewed towards a few phyla that contain model organisms. But the breadth is continuing to improve, with projects dedicated to filling...

  6. Rare variant testing across methods and thresholds using the multi-kernel sequence kernel association test (MK-SKAT).

    Science.gov (United States)

    Urrutia, Eugene; Lee, Seunggeun; Maity, Arnab; Zhao, Ni; Shen, Judong; Li, Yun; Wu, Michael C

    Analysis of rare genetic variants has focused on region-based analysis wherein a subset of the variants within a genomic region is tested for association with a complex trait. Two important practical challenges have emerged. First, it is difficult to choose which test to use. Second, it is unclear which group of variants within a region should be tested. Both depend on the unknown true state of nature. Therefore, we develop the Multi-Kernel SKAT (MK-SKAT) which tests across a range of rare variant tests and groupings. Specifically, we demonstrate that several popular rare variant tests are special cases of the sequence kernel association test which compares pair-wise similarity in trait value to similarity in the rare variant genotypes between subjects as measured through a kernel function. Choosing a particular test is equivalent to choosing a kernel. Similarly, choosing which group of variants to test also reduces to choosing a kernel. Thus, MK-SKAT uses perturbation to test across a range of kernels. Simulations and real data analyses show that our framework controls type I error while maintaining high power across settings: MK-SKAT loses power when compared to the kernel for a particular scenario but has much greater power than poor choices.

  7. Long-Term Recall of Event Sequences in Infancy.

    Science.gov (United States)

    Mandler, Jean M.; McDonough, Laraine

    1995-01-01

    Two experiments demonstrated that 11-month olds can encode novel causal events from a brief period of observational learning and recall much of the information after 24 hours and after 3 months. The infants remembered more individual actions than whole sequences, but reproduced many of the events in their entirety after the long delay. (MDM)

  8. Cloning, sequencing, and sequence analysis of two novel plasmids from the thermophilic anaerobic bacterium Anaerocellum thermophilum

    DEFF Research Database (Denmark)

    Clausen, Anders; Mikkelsen, Marie Just; Schrøder, I.

    2004-01-01

    The nucleotide sequence of two novel plasmids isolated from the extreme thermophilic anaerobic bacterium Anaerocellum thermophilum DSM6725 (A. thermophilum), growing optimally at 70degreesC, has been determined. pBAS2 was found to be a 3653 bp plasmid with a GC content of 43%, and the sequence re...... with highest similarity to DNA repair protein from Campylobacter jejuni (25% aa). Orf34 showed similarity to sigma factors with highest similarity (28% aa) to the sporulation specific Sigma factor, Sigma 28(K) from Bacillus thuringiensis....

  9. Is a sequence of tests during urethral pressure profilometry correlated with symptoms assessment in women?

    Science.gov (United States)

    Valentini, Françoise A; Robain, Gilberte; Marti, Brigitte G

    2012-01-01

    Our purpose was, applying a strictly defined protocol for urethral profilometry, 1) to test the repeatability of same session rest maximum urethral closure pressure (MUCP) and 2) to search for correlation between women complaint and the changes in MUCP value (rest and dynamic tests). A population of 140 consecutive women referred for evaluation of lower urinary tract dysfunction was stratified in 4 groups according with the urinary symptoms: stress, urge, mixed incontinence and continent and in each group in 3 age groups (young, middle age and old). The sequence of tests recorded in supine position was: urethral pressure profile at rest bladder empty, after bladder filling at 250 mL (reference test), stress profile, fatigability (before (rest) and after 10 successive strong coughs), then in standing position. In all groups, there was no significant difference between the two MUCP values at rest bladder filled. In the three incontinent groups, MUCP was higher bladder empty than bladder filled (p rest bladder filled has a good repeatability in individual. However a complex sequence of tests during urethral pressure profilometry remains discussed in middle-age and old age-groups, it allows specifying the stress component of incontinence in young women and the urgency component in all age-groups.

  10. Universal sequence map (USM of arbitrary discrete sequences

    Directory of Open Access Journals (Sweden)

    Almeida Jonas S

    2002-02-01

    Full Text Available Abstract Background For over a decade the idea of representing biological sequences in a continuous coordinate space has maintained its appeal but not been fully realized. The basic idea is that any sequence of symbols may define trajectories in the continuous space conserving all its statistical properties. Ideally, such a representation would allow scale independent sequence analysis – without the context of fixed memory length. A simple example would consist on being able to infer the homology between two sequences solely by comparing the coordinates of any two homologous units. Results We have successfully identified such an iterative function for bijective mappingψ of discrete sequences into objects of continuous state space that enable scale-independent sequence analysis. The technique, named Universal Sequence Mapping (USM, is applicable to sequences with an arbitrary length and arbitrary number of unique units and generates a representation where map distance estimates sequence similarity. The novel USM procedure is based on earlier work by these and other authors on the properties of Chaos Game Representation (CGR. The latter enables the representation of 4 unit type sequences (like DNA as an order free Markov Chain transition table. The properties of USM are illustrated with test data and can be verified for other data by using the accompanying web-based tool:http://bioinformatics.musc.edu/~jonas/usm/. Conclusions USM is shown to enable a statistical mechanics approach to sequence analysis. The scale independent representation frees sequence analysis from the need to assume a memory length in the investigation of syntactic rules.

  11. Operator alertness and performance on 8-hour and 12-hour work shifts

    International Nuclear Information System (INIS)

    Baker, T.L.; Campbell, S.S.; Dawson, D.; Moore-Ede, M.

    1989-01-01

    Recently, much attention has been paid to the alertness and performance problems of rotational shiftworkers in the nuclear power industry. Growing awareness of higher rates of human errors and accidents on night shifts and reports of operations personnel falling asleep on the job have contributed to the heightened interest in this subject. The industry is now considering the effects of different shift rotation systems, including evaluation of the most recent of industry trends in shift scheduling-schedules that include 12 hour work shifts. Surveys show that within the past 5 years about 20% of commercially operational nuclear power plants have instituted schedules that use only 12 hour shifts, or schedules using a combination of 8-hour and 12-hour shifts. Many more plants routinely use 12-hour work shifts during plant outages and refueling operations. In response to this growing trend, the NRC has funded research which is a first attempt to compare alertness, operator performance, and sleep-wake patterns in subjects working simulated 8-hour and 12-hour shifts at the Human Alertness Research Center (HARC), located at the Institute of Circadian Physiology in Boston, MA. This paper will describe in greater detail the design of the study, measurement techniques for alertness and sleep, work routine, work task performance measures, and cognitive performance test protocols. It will review the role of circadian factors in human alertness and performance, and discuss previous research findings in this area. It will discuss other variables that are known to influence human alertness in the workplace, such as caffeine, alcohol, and working environment. The physiological basis for shift worker sleep problems will be explained in the context of the ongoing research project at HARC. Finally, the paper presents previous research on shift work and fatigue which may be relevant to a comparison of 8-hour and 12-hour shifts

  12. ADDRESS SEQUENCES FOR MULTI RUN RAM TESTING

    Directory of Open Access Journals (Sweden)

    V. N. Yarmolik

    2014-01-01

    Full Text Available A universal approach for generation of address sequences with specified properties is proposed and analyzed. A modified version of the Antonov and Saleev algorithm for Sobol sequences genera-tion is chosen as a mathematical description of the proposed method. Within the framework of the proposed universal approach, the Sobol sequences form a subset of the address sequences. Other sub-sets are also formed, which are Gray sequences, anti-Gray sequences, counter sequences and sequenc-es with specified properties.

  13. Two-stage triolein breath test differentiates pancreatic insufficiency from other causes of malabsorption

    International Nuclear Information System (INIS)

    Goff, J.S.

    1982-01-01

    In 24 patients with malabsorption, [ 14 C]triolein breath tests were conducted before and together with the administration of pancreatic enzymes (Pancrease, Johnson and Johnson, Skillman, N.J.). Eleven patients with pancreatic insufficiency had a significant rise in peak percent dose per hour 14 CO 2 excretion after Pancrease, whereas 13 patients with other causes of malabsorption had no increase in 14 CO 2 excretion (2.61 +/- 0.96 vs. 0.15 +/- 0.45, p less than 0.001). The two-stage [ 14 C]triolein breath test appears to be an accurate and simple noninvasive test of fat malabsorption that differentiates steatorrhea secondary to pancreatic insufficiency from other causes of steatorrhea

  14. Does consolidation of visuospatial sequence knowledge depend on eye movements?

    Directory of Open Access Journals (Sweden)

    Daphné Coomans

    Full Text Available In the current study, we assessed whether visuospatial sequence knowledge is retained over 24 hours and whether this retention is dependent on the occurrence of eye movements. Participants performed two sessions of a serial reaction time (SRT task in which they had to manually react to the identity of a target letter pair presented in one of four locations around a fixation cross. When the letter pair 'XO' was presented, a left response had to be given, when the letter pair 'OX' was presented, a right response was required. In the Eye Movements (EM condition, eye movements were necessary to perform the task since the fixation cross and the target were separated by at least 9° visual angle. In the No Eye Movements (NEM condition, on the other hand, eye movements were minimized by keeping the distance from the fixation cross to the target below 1° visual angle and by limiting the stimulus presentation to 100 ms. Since the target identity changed randomly in both conditions, no manual response sequence was present in the task. However, target location was structured according to a deterministic sequence in both the EM and NEM condition. Learning of the target location sequence was determined at the end of the first session and 24 hours after initial learning. Results indicated that the sequence learning effect in the SRT task diminished, yet remained significant, over the 24 hour interval in both conditions. Importantly, the difference in eye movements had no impact on the transfer of sequence knowledge. These results suggest that the retention of visuospatial sequence knowledge occurs alike, irrespective of whether this knowledge is supported by eye movements or not.

  15. Exome sequencing identifies mutations in ABCD1 and DACH2 in two brothers with a distinct phenotype.

    Science.gov (United States)

    Zhang, Yanliang; Liu, Yanhui; Li, Ya; Duan, Yong; Zhang, Keyun; Wang, Junwang; Dai, Yong

    2014-09-19

    We report on two brothers with a distinct syndromic phenotype and explore the potential pathogenic cause. Cytogenetic tests and exome sequencing were performed on the two brothers and their parents. Variants detected by exome sequencing were validated by Sanger sequencing. The main phenotype of the two brothers included congenital language disorder, growth retardation, intellectual disability, difficulty in standing and walking, and urinary and fecal incontinence. To the best of our knowledge, no similar phenotype has been reported previously. No abnormalities were detected by G-banding chromosome analysis or array comparative genomic hybridization. However, exome sequencing revealed novel mutations in the ATP-binding cassette, sub-family D member 1 (ABCD1) and Dachshund homolog 2 (DACH2) genes in both brothers. The ABCD1 mutation was a missense mutation c.1126G > C in exon 3 leading to a p.E376Q substitution. The DACH2 mutation was also a missense mutation c.1069A > T in exon 6, leading to a p.S357C substitution. The mother was an asymptomatic heterozygous carrier. Plasma levels of very-long-chain fatty acids were increased in both brothers, suggesting a diagnosis of adrenoleukodystrophy (ALD); however, their phenotype was not compatible with any reported forms of ALD. DACH2 plays an important role in the regulation of brain and limb development, suggesting that this mutation may be involved in the phenotype of the two brothers. The distinct phenotype demonstrated by these two brothers might represent a new form of ALD or a new syndrome. The combination of mutations in ABCD1 and DACH2 provides a plausible mechanism for this phenotype.

  16. A 205 Hour Krypton Propellant Life Test of the SPT-100 Operating at 3 kW

    Science.gov (United States)

    2013-09-01

    nominal xenon condition (1.35 kW), tests have validated the SPT -100 life time as exceeding 2.71 million N -s (equivalent to approximately 9,000 hours of...condition – If correlation between erosion and energy throughput holds, SPT may be able to endure • Long term life test would be required to validate Kr as...shift (to zero center of SPT at r = 0) • Small rotation to correct for linear stage sag DISTRIBUTION A: Approved for public release; distribution

  17. Improvements of knowledge and perception towards HIV/AIDS among secondary school students after two hours talk.

    Science.gov (United States)

    Jahanfar, S; Lim, A W; Loh, M A; Yeoh, A G; Charles, A

    2008-10-01

    Malaysia is confronted with an increasing incidence of HIV and AIDS among adolescents and young adults. The effectiveness of various programs offered to school going teenagers is unknown. The objective of this study is to measure the effectiveness of two hours talk on sex education offered by a non governmental organization (NGO) in improving youngsters' knowledge and perception towards HIV and AIDS. A cross sectional study was conducted among the adolescent students from a secondary school in Ipoh, Perak, a province of Malaysia. A total of 182 students participated in the study. A standard questionnaire consisting of demographic data, knowledge and perception towards HIV/ADIS were distributed before (pre-test) and after the intervention (post-test). Performance of participants was compared to establish the effectiveness of the intervention. Our findings suggests that there was a significant increase in participants' knowledge and perception after the intervention (p = 0.000). Knowledge improvement was found in both genders however, improvement in perception was higher among female students. Interestingly, 80% of participants disagree that sexual education will encourage sex among youngsters. NGOs are playing a supplementary role in providing sex education programs in schools. This program although of short duration but it is effective in enhancing adolescence awareness about HIV/AIDS.

  18. Clinical Efficiency of Two Sequences of Orthodontic Wires to Correct Crowding of the Lower Anterior Teeth

    Directory of Open Access Journals (Sweden)

    Cláudia Maria de Castro Serafim

    2015-01-01

    Full Text Available This study compared time to correction of mandibular anterior crowding using two arch wire sequences, one with conventional nickel-titanium (NiTi arch wires and the other with conventional and NiTi heat-activated arch wires. Twenty-two boys and girls (mean age: 16.68 ± 2.66 with moderate crowding (3–6 mm were assigned randomly to one of two groups and followed up for five months (six assessments when arch wires were changed. Time to crowding correction was analyzed statistically using the Kaplan-Meier method. Data were collected during the five-month follow-up, and time to correction was compared between groups using the log rank test. At the end of follow-up, mandibular crowding was corrected in 100% of the cases in the group treated with the sequence that included NiTi heat-activated arch wires, whereas about 30% of those treated with NiTi arch wires were not completely corrected. There was a significant difference in time to complete treatment between groups (log rank = 5.996; p<0.05. In the group treated with the sequence that included heat-activated wires, alignment and leveling of mandibular anterior teeth were completed earlier than in the group treated only with conventional NiTi arch wires. Clinical trial registration is found at RBR-7g5zng.

  19. Whole-Genome Sequences of Two Borrelia afzelii and Two Borrelia garinii Lyme Disease Agent Isolates

    Energy Technology Data Exchange (ETDEWEB)

    Casjens, S.R.; Dunn, J.; Mongodin, E. F.; Qiu, W.-G.; Luft, B. J.; Fraser-Liggett, C. M.; Schutzer, S. E.

    2011-12-01

    Human Lyme disease is commonly caused by several species of spirochetes in the Borrelia genus. In Eurasia these species are largely Borrelia afzelii, B. garinii, B. burgdorferi, and B. bavariensis sp. nov. Whole-genome sequencing is an excellent tool for investigating and understanding the influence of bacterial diversity on the pathogenesis and etiology of Lyme disease. We report here the whole-genome sequences of four isolates from two of the Borrelia species that cause human Lyme disease, B. afzelii isolates ACA-1 and PKo and B. garinii isolates PBr and Far04.

  20. Genotypic tropism testing by massively parallel sequencing: qualitative and quantitative analysis

    Directory of Open Access Journals (Sweden)

    Thiele Bernhard

    2011-05-01

    Full Text Available Abstract Background Inferring viral tropism from genotype is a fast and inexpensive alternative to phenotypic testing. While being highly predictive when performed on clonal samples, sensitivity of predicting CXCR4-using (X4 variants drops substantially in clinical isolates. This is mainly attributed to minor variants not detected by standard bulk-sequencing. Massively parallel sequencing (MPS detects single clones thereby being much more sensitive. Using this technology we wanted to improve genotypic prediction of coreceptor usage. Methods Plasma samples from 55 antiretroviral-treated patients tested for coreceptor usage with the Monogram Trofile Assay were sequenced with standard population-based approaches. Fourteen of these samples were selected for further analysis with MPS. Tropism was predicted from each sequence with geno2pheno[coreceptor]. Results Prediction based on bulk-sequencing yielded 59.1% sensitivity and 90.9% specificity compared to the trofile assay. With MPS, 7600 reads were generated on average per isolate. Minorities of sequences with high confidence in CXCR4-usage were found in all samples, irrespective of phenotype. When using the default false-positive-rate of geno2pheno[coreceptor] (10%, and defining a minority cutoff of 5%, the results were concordant in all but one isolate. Conclusions The combination of MPS and coreceptor usage prediction results in a fast and accurate alternative to phenotypic assays. The detection of X4-viruses in all isolates suggests that coreceptor usage as well as fitness of minorities is important for therapy outcome. The high sensitivity of this technology in combination with a quantitative description of the viral population may allow implementing meaningful cutoffs for predicting response to CCR5-antagonists in the presence of X4-minorities.

  1. Genotypic tropism testing by massively parallel sequencing: qualitative and quantitative analysis.

    Science.gov (United States)

    Däumer, Martin; Kaiser, Rolf; Klein, Rolf; Lengauer, Thomas; Thiele, Bernhard; Thielen, Alexander

    2011-05-13

    Inferring viral tropism from genotype is a fast and inexpensive alternative to phenotypic testing. While being highly predictive when performed on clonal samples, sensitivity of predicting CXCR4-using (X4) variants drops substantially in clinical isolates. This is mainly attributed to minor variants not detected by standard bulk-sequencing. Massively parallel sequencing (MPS) detects single clones thereby being much more sensitive. Using this technology we wanted to improve genotypic prediction of coreceptor usage. Plasma samples from 55 antiretroviral-treated patients tested for coreceptor usage with the Monogram Trofile Assay were sequenced with standard population-based approaches. Fourteen of these samples were selected for further analysis with MPS. Tropism was predicted from each sequence with geno2pheno[coreceptor]. Prediction based on bulk-sequencing yielded 59.1% sensitivity and 90.9% specificity compared to the trofile assay. With MPS, 7600 reads were generated on average per isolate. Minorities of sequences with high confidence in CXCR4-usage were found in all samples, irrespective of phenotype. When using the default false-positive-rate of geno2pheno[coreceptor] (10%), and defining a minority cutoff of 5%, the results were concordant in all but one isolate. The combination of MPS and coreceptor usage prediction results in a fast and accurate alternative to phenotypic assays. The detection of X4-viruses in all isolates suggests that coreceptor usage as well as fitness of minorities is important for therapy outcome. The high sensitivity of this technology in combination with a quantitative description of the viral population may allow implementing meaningful cutoffs for predicting response to CCR5-antagonists in the presence of X4-minorities.

  2. Education on Adult Urinary Incontinence in Nursing School Curricula: Can It Be Done in Two Hours?

    Science.gov (United States)

    Morishita, Lynne; And Others

    1994-01-01

    Responses from 339 undergraduate nursing programs (74%) showed that 98% included urinary incontinence content in their curricula. Although most agreed the subject was important and felt their teaching was effective, the didactic component averaged two hours, and clinical experience was not systematic; few faculty are prepared to teach this…

  3. CANFLEX fuel bundle cross-flow endurance test 2 (test procedure)

    Energy Technology Data Exchange (ETDEWEB)

    Hong, Sung Deok; Chung, C. H.; Chang, S. K. [Korea Atomic Energy Research Institute, Taejon (Korea)

    1999-04-01

    This report describes test procedure of cross-flow 2 test for CANFLEX fuel. In October 1996. a cross-flow test was successfully performed in the KAERI Hot Test Loop for four hours at a water flow rate of 31kg/s, temperature of 266 deg C and inlet pressure of 11MPa, but it is requested more extended time periods to determine a realistic operational margin for the CANFLEX bundle during abnormal refuelling operations. The test shall be conducted for twenty two hours under the reactor conditions. After an initial period of ten hours, the test shall be stopped at the intervals of four hours for bundle inspection and inspect the test bundle end-plate to end-cap welds for failure or crack propagation using liquid penetrant examination. 2 refs., 1 fig. (Author)

  4. Association testing for next-generation sequencing data using score statistics

    DEFF Research Database (Denmark)

    Skotte, Line; Korneliussen, Thorfinn Sand; Albrechtsen, Anders

    2012-01-01

    computationally feasible due to the use of score statistics. As part of the joint likelihood, we model the distribution of the phenotypes using a generalized linear model framework, which works for both quantitative and discrete phenotypes. Thus, the method presented here is applicable to case-control studies...... of genotype calls into account have been proposed; most require numerical optimization which for large-scale data is not always computationally feasible. We show that using a score statistic for the joint likelihood of observed phenotypes and observed sequencing data provides an attractive approach...... to association testing for next-generation sequencing data. The joint model accounts for the genotype classification uncertainty via the posterior probabilities of the genotypes given the observed sequencing data, which gives the approach higher power than methods based on called genotypes. This strategy remains...

  5. Generation of synthetic sequences of electricity demand: Application in South Australia

    International Nuclear Information System (INIS)

    Magnano, L.; Boland, J.W.

    2007-01-01

    We have developed a model to generate synthetic sequences of half-hourly electricity demand. The generated sequences represent possible realisations of electricity load that could have occurred. Each of the components included in the model has a physical interpretation. These components are yearly and daily seasonality which were modelled using Fourier series, weekly seasonality modelled with dummy variables, and the relationship with current temperature described by polynomial functions of temperature. Finally the stochastic component was modelled with autoregressive moving average (ARMA) processes. These synthetic sequences were developed for two purposes. The first one is to use them as input data in market simulation software. The second one is to build probability distributions of the outputs to calculate probabilistic forecasts. As an application several summers of half-hourly electricity demand were generated and from them the value of demand that is not expected to be exceeded more than once in 10 years was calculated

  6. Experience of targeted Usher exome sequencing as a clinical test

    Science.gov (United States)

    Besnard, Thomas; García-García, Gema; Baux, David; Vaché, Christel; Faugère, Valérie; Larrieu, Lise; Léonard, Susana; Millan, Jose M; Malcolm, Sue; Claustres, Mireille; Roux, Anne-Françoise

    2014-01-01

    We show that massively parallel targeted sequencing of 19 genes provides a new and reliable strategy for molecular diagnosis of Usher syndrome (USH) and nonsyndromic deafness, particularly appropriate for these disorders characterized by a high clinical and genetic heterogeneity and a complex structure of several of the genes involved. A series of 71 patients including Usher patients previously screened by Sanger sequencing plus newly referred patients was studied. Ninety-eight percent of the variants previously identified by Sanger sequencing were found by next-generation sequencing (NGS). NGS proved to be efficient as it offers analysis of all relevant genes which is laborious to reach with Sanger sequencing. Among the 13 newly referred Usher patients, both mutations in the same gene were identified in 77% of cases (10 patients) and one candidate pathogenic variant in two additional patients. This work can be considered as pilot for implementing NGS for genetically heterogeneous diseases in clinical service. PMID:24498627

  7. Sequence-based prediction of protein-binding sites in DNA: comparative study of two SVM models.

    Science.gov (United States)

    Park, Byungkyu; Im, Jinyong; Tuvshinjargal, Narankhuu; Lee, Wook; Han, Kyungsook

    2014-11-01

    As many structures of protein-DNA complexes have been known in the past years, several computational methods have been developed to predict DNA-binding sites in proteins. However, its inverse problem (i.e., predicting protein-binding sites in DNA) has received much less attention. One of the reasons is that the differences between the interaction propensities of nucleotides are much smaller than those between amino acids. Another reason is that DNA exhibits less diverse sequence patterns than protein. Therefore, predicting protein-binding DNA nucleotides is much harder than predicting DNA-binding amino acids. We computed the interaction propensity (IP) of nucleotide triplets with amino acids using an extensive dataset of protein-DNA complexes, and developed two support vector machine (SVM) models that predict protein-binding nucleotides from sequence data alone. One SVM model predicts protein-binding nucleotides using DNA sequence data alone, and the other SVM model predicts protein-binding nucleotides using both DNA and protein sequences. In a 10-fold cross-validation with 1519 DNA sequences, the SVM model that uses DNA sequence data only predicted protein-binding nucleotides with an accuracy of 67.0%, an F-measure of 67.1%, and a Matthews correlation coefficient (MCC) of 0.340. With an independent dataset of 181 DNAs that were not used in training, it achieved an accuracy of 66.2%, an F-measure 66.3% and a MCC of 0.324. Another SVM model that uses both DNA and protein sequences achieved an accuracy of 69.6%, an F-measure of 69.6%, and a MCC of 0.383 in a 10-fold cross-validation with 1519 DNA sequences and 859 protein sequences. With an independent dataset of 181 DNAs and 143 proteins, it showed an accuracy of 67.3%, an F-measure of 66.5% and a MCC of 0.329. Both in cross-validation and independent testing, the second SVM model that used both DNA and protein sequence data showed better performance than the first model that used DNA sequence data. To the best of

  8. Three-dimensional isotropic T2-weighted cervical MRI at 3 T: Comparison with two-dimensional T2-weighted sequences

    International Nuclear Information System (INIS)

    Kwon, J.W.; Yoon, Y.C.; Choi, S.-H.

    2012-01-01

    Aim: To compare three-dimensional (3D) isotropic T2-weighted magnetic resonance imaging (MRI) sequences and reformation with two-dimensional (2D) T2-weighted sequences regarding image quality of the cervical spine at 3 T. Materials and methods: A phantom study was performed using a water-filled cylinder. The signal-to-noise and image homogeneity were evaluated. Fourteen (n = 14) volunteers were examined at 3 T using 3D isotropic T2-weighted sagittal and conventional 2D T2-weighted sagittal, axial, and oblique sagittal MRI. Multiplanar reformation (MPR) of the 3D T2-weighted sagittal dataset was performed simultaneously with image evaluation. In addition to artefact assessment, the visibility of anatomical structures in the 3D and 2D sequences was qualitatively assessed by two radiologists independently. Cohen’s kappa and Wilcoxon signed rank test were used for the statistical analysis. Result: The 3D isotropic T2-weighted sequence resulted in the highest signal-to-noise ratio (SNR) and lowest non-uniformity (NU) among the sequences in the phantom study. Quantitative evaluation revealed lower NU values of the cerebrospinal fluid (CSF) and muscles in 2D T2-weighted sagittal sequences compared to the 3D volume isotropic turbo spin-echo acquisition (VISTA) sequence. The other NU values revealed no statistically significant difference between the 2D turbo spin-echo (TSE) and 3D VISTA sequences (0.059 < p < 0.959). 3D VISTA images showed significantly fewer CSF flow artefacts (p < 0.001) and better delineated intradural nerve rootlets (p = 0.001) and neural foramina (p = 0.016) compared to 2D sequences. Conclusion: A 3D T2 weighted sequence is superior to conventional 2D sequences for the delineation of intradural nerve rootlets and neural foramina and is less affected by CSF flow artefacts.

  9. No effects of transcranial DLPFC stimulation on implicit task sequence learning and consolidation.

    Science.gov (United States)

    Savic, Branislav; Cazzoli, Dario; Müri, René; Meier, Beat

    2017-08-29

    Neurostimulation of the dorsolateral prefrontal cortex (DLPFC) can modulate performance in cognitive tasks. In a recent study, however, transcranial direct current stimulation (tDCS) of the DLPFC did not affect implicit task sequence learning and consolidation in a paradigm that involved bimanual responses. Because bimanual performance increases the coupling between homologous cortical areas of the hemispheres and left and right DLPFC were stimulated separately the null findings may have been due to the bimanual setup. The aim of the present study was to test the effect of neuro-stimulation on sequence learning in a uni-manual setup. For this purpose two experiments were conducted. In Experiment 1, the DLPFC was stimulated with tDCS. In Experiment 2 the DLPFC was stimulated with transcranial magnetic stimulation (TMS). In both experiments, consolidation was measured 24 hours later. The results showed that sequence learning was present in all conditions and sessions, but it was not influenced by stimulation. Likewise, consolidation of sequence learning was robust across sessions, but it was not influenced by stimulation. These results replicate and extend previous findings. They indicate that established tDCS and TMS protocols on the DLPFC do not influence implicit task sequence learning and consolidation.

  10. Nucleotide sequences of two genomic DNAs encoding peroxidase of Arabidopsis thaliana.

    Science.gov (United States)

    Intapruk, C; Higashimura, N; Yamamoto, K; Okada, N; Shinmyo, A; Takano, M

    1991-02-15

    The peroxidase (EC 1.11.1.7)-encoding gene of Arabidopsis thaliana was screened from a genomic library using a cDNA encoding a neutral isozyme of horseradish, Armoracia rusticana, peroxidase (HRP) as a probe, and two positive clones were isolated. From the comparison with the sequences of the HRP-encoding genes, we concluded that two clones contained peroxidase-encoding genes, and they were named prxCa and prxEa. Both genes consisted of four exons and three introns; the introns had consensus nucleotides, GT and AG, at the 5' and 3' ends, respectively. The lengths of each putative exon of the prxEa gene were the same as those of the HRP-basic-isozyme-encoding gene, prxC3, and coded for 349 amino acids (aa) with a sequence homology of 89% to that encoded by prxC3. The prxCa gene was very close to the HRP-neutral-isozyme-encoding gene, prxC1b, and coded for 354 aa with 91% homology to that encoded by prxC1b. The aa sequence homology was 64% between the two peroxidases encoded by prxCa and prxEa.

  11. A six-hour extrapolated sampling strategy for monitoring mycophenolic acid in renal transplant patients in the Indian subcontinent

    Directory of Open Access Journals (Sweden)

    Fleming D

    2006-01-01

    Full Text Available Background : Therapeutic drug monitoring for mycophenolic acid (MPA is increasingly being advocated. Thepresent therapeutic range relates to the 12-hour area under the serum concentration time profile (AUC.However, this is a cumbersome, tedious, cost restricting procedure. Is it possible to reduce this samplingperiod? Aim : To compare the AUC from a reduced sampling strategy with the full 12-hour profile for MPA. Settings and Design : Clinical Pharmacology Unit of a tertiary care hospital in South India. Retrospective, paireddata. Materials and Methods : Thirty-four 12-hour profiles from post-renal transplant patients on Cellcept ® wereevaluated. Profiles were grouped according to steroid and immunosuppressant co-medication and the timeafter transplant. MPA was estimated by high performance liquid chromatography with UV detection. From the12-hour profiles the AUC up to only six hours was calculated by the trapezoidal rule and a correction factorapplied. These two AUCs were then compared. Statistical Analysis : Linear regression, intra-class correlations (ICC and a two-tailed paired t-test were appliedto the data. Results : Comparing the 12-hour AUC with the paired 6-hour extrapolated AUC, the ICC and linear regression(r2 were very good for all three groups. No statistical difference was found by a two-tailed paired t-test. Nobias was seen with a Bland Altman plot or by calculation. Conclusion : For patients on Cellcept ® with prednisolone ± cyclosporine the 6-hour corrected is an accuratemeasure of the full 12-hour AUC.

  12. Improved PFB operations: 400-hour turbine test results. [coal combustion products and hot corrosion in gas turbines

    Science.gov (United States)

    Rollbuhler, R. J.; Benford, S. M.; Zellars, G. R.

    1980-01-01

    A pressurized fluidized bed (PFB) coal-burning reactor was used to provide hot effluent gases for operation of a small gas turbine. Preliminary tests determined the optimum operating conditions that would result in minimum bed particle carryover in the combustion gases. Solids were removed from the gases before they could be transported into the test turbine by use of a modified two stage cyclone separator. Design changes and refined operation procedures resulted in a significant decrease in particle carryover, from 2800 to 93 ppm (1.5 to 0.05 grains/std cu ft), with minimal drop in gas temperature and pressure. The achievement of stable burn conditions and low solids loadings made possible a 400 hr test of small superalloy rotor, 15 cm (6 in.) in diameter, operating in the effluent. Blades removed and examined metallographically after 200 hr exhibited accelerated oxidation over most of the blade surface, with subsurface alumina penetration to 20 micron m. After 400 hours, average erosion loss was about 25 micron m (1 mil). Sulfide particles, indicating hot corrosion, were present in depletion zones, and their presence corresponded in general to the areas of adherent solids deposit. Sulfidation appears to be a materials problem equal in importance to erosion.

  13. Comparison and evaluation of two exome capture kits and sequencing platforms for variant calling.

    Science.gov (United States)

    Zhang, Guoqiang; Wang, Jianfeng; Yang, Jin; Li, Wenjie; Deng, Yutian; Li, Jing; Huang, Jun; Hu, Songnian; Zhang, Bing

    2015-08-05

    To promote the clinical application of next-generation sequencing, it is important to obtain accurate and consistent variants of target genomic regions at low cost. Ion Proton, the latest updated semiconductor-based sequencing instrument from Life Technologies, is designed to provide investigators with an inexpensive platform for human whole exome sequencing that achieves a rapid turnaround time. However, few studies have comprehensively compared and evaluated the accuracy of variant calling between Ion Proton and Illumina sequencing platforms such as HiSeq 2000, which is the most popular sequencing platform for the human genome. The Ion Proton sequencer combined with the Ion TargetSeq Exome Enrichment Kit together make up TargetSeq-Proton, whereas SureSelect-Hiseq is based on the Agilent SureSelect Human All Exon v4 Kit and the HiSeq 2000 sequencer. Here, we sequenced exonic DNA from four human blood samples using both TargetSeq-Proton and SureSelect-HiSeq. We then called variants in the exonic regions that overlapped between the two exome capture kits (33.6 Mb). The rates of shared variant loci called by two sequencing platforms were from 68.0 to 75.3% in four samples, whereas the concordance of co-detected variant loci reached 99%. Sanger sequencing validation revealed that the validated rate of concordant single nucleotide polymorphisms (SNPs) (91.5%) was higher than the SNPs specific to TargetSeq-Proton (60.0%) or specific to SureSelect-HiSeq (88.3%). With regard to 1-bp small insertions and deletions (InDels), the Sanger sequencing validated rates of concordant variants (100.0%) and SureSelect-HiSeq-specific (89.6%) were higher than those of TargetSeq-Proton-specific (15.8%). In the sequencing of exonic regions, a combination of using of two sequencing strategies (SureSelect-HiSeq and TargetSeq-Proton) increased the variant calling specificity for concordant variant loci and the sensitivity for variant loci called by any one platform. However, for the

  14. The existence and persistence of long work hours

    OpenAIRE

    Drago, Robert William; Black, David; Wooden, Mark

    2005-01-01

    Previous research hypothesizes that long working hours are related to consumerism, the ideal worker norm, high levels of human capital, and a high cost-of-job-loss. The authors test these hypotheses using panel data on working hours for an Australian sample of full-time employed workers. Analyses include a static cross-sectional model and a persistence model for long hours over time. The results suggest that long hours (50 or more hours in a usual week) are often persistent, and provide stron...

  15. Is a sequence of tests during urethral pressure profilometry correlated with symptoms assessment in women?

    Directory of Open Access Journals (Sweden)

    Françoise A. Valentini

    2012-12-01

    Full Text Available Introduction Our purpose was, applying a strictly defined protocol for urethral profilometry, 1 to test the repeatability of same session rest maximum urethral closure pressure (MUCP and 2 to search for correlation between women complaint and the changes in MUCP value (rest and dynamic tests. Materials and Methods A population of 140 consecutive women referred for evaluation of lower urinary tract dysfunction was stratified in 4 groups according with the urinary symptoms: stress, urge, mixed incontinence and continent and in each group in 3 age groups (young, middle age and old. The sequence of tests recorded in supine position was: urethral pressure profile at rest bladder empty, after bladder filling at 250 mL (reference test, stress profile, fatigability (before (rest and after 10 successive strong coughs, then in standing position. Results In all groups, there was no significant difference between the two MUCP values at rest bladder filled. In the three incontinent groups, MUCP was higher bladder empty than bladder filled (p < 0.05 except in the young sub-group. Stress incontinence led to significant decrease of MUCP during dynamic tests in the young group. MUCP was not modified after fatigability test in women with urge complaint whatever age. Conclusion When recorded following a strictly defined protocol, MUCP at rest bladder filled has a good repeatability in individual. However a complex sequence of tests during urethral pressure profilometry remains discussed in middle-age and old age-groups, it allows specifying the stress component of incontinence in young women and the urgency component in all age-groups.

  16. Draft genome sequences of two protease-producing strains of Arsukibacterium, isolated from two cold and alkaline environments

    DEFF Research Database (Denmark)

    Lylloff, Jeanette Eva; Hansen, Lea Benedicte Skov; Jepsen, Morten

    2015-01-01

    Arsukibacterium ikkense GCM72(T) and a close relative, Arsukibacterium sp. MJ3, were isolated from two cold and alkaline environments as producers of extracellular proteolytic enzymes active at high pH and low temperature. This report describes the two draft genome sequences, which may serve...

  17. Sequence specific motor performance gains after memory consolidation in children and adolescents.

    Directory of Open Access Journals (Sweden)

    Shoshi Dorfberger

    Full Text Available Memory consolidation for a trained sequence of finger opposition movements, in 9- and 12-year-old children, was recently found to be significantly less susceptible to interference by a subsequent training experience, compared to that of 17-year-olds. It was suggested that, in children, the experience of training on any sequence of finger movements may affect the performance of the sequence elements, component movements, rather than the sequence as a unit; the latter has been implicated in the learning of the task by adults. This hypothesis implied a possible childhood advantage in the ability to transfer the gains from a trained to the reversed, untrained, sequence of movements. Here we report the results of transfer tests undertaken to test this proposal in 9-, 12-, and 17-year-olds after training in the finger-to-thumb opposition sequence (FOS learning task. Our results show that the performance gains in the trained sequence partially transferred from the left, trained hand, to the untrained hand at 48-hours after a single training session in the three age-groups tested. However, there was very little transfer of the gains from the trained to the untrained, reversed, sequence performed by either hand. The results indicate sequence specific post-training gains in FOS performance, as opposed to a general improvement in performance of the individual, component, movements that comprised both the trained and untrained sequences. These results do not support the proposal that the reduced susceptibility to interference, in children before adolescence, reflects a difference in movement syntax representation after training.

  18. Sequence specific motor performance gains after memory consolidation in children and adolescents.

    Science.gov (United States)

    Dorfberger, Shoshi; Adi-Japha, Esther; Karni, Avi

    2012-01-01

    Memory consolidation for a trained sequence of finger opposition movements, in 9- and 12-year-old children, was recently found to be significantly less susceptible to interference by a subsequent training experience, compared to that of 17-year-olds. It was suggested that, in children, the experience of training on any sequence of finger movements may affect the performance of the sequence elements, component movements, rather than the sequence as a unit; the latter has been implicated in the learning of the task by adults. This hypothesis implied a possible childhood advantage in the ability to transfer the gains from a trained to the reversed, untrained, sequence of movements. Here we report the results of transfer tests undertaken to test this proposal in 9-, 12-, and 17-year-olds after training in the finger-to-thumb opposition sequence (FOS) learning task. Our results show that the performance gains in the trained sequence partially transferred from the left, trained hand, to the untrained hand at 48-hours after a single training session in the three age-groups tested. However, there was very little transfer of the gains from the trained to the untrained, reversed, sequence performed by either hand. The results indicate sequence specific post-training gains in FOS performance, as opposed to a general improvement in performance of the individual, component, movements that comprised both the trained and untrained sequences. These results do not support the proposal that the reduced susceptibility to interference, in children before adolescence, reflects a difference in movement syntax representation after training.

  19. A two-step recognition of signal sequences determines the translocation efficiency of proteins.

    Science.gov (United States)

    Belin, D; Bost, S; Vassalli, J D; Strub, K

    1996-02-01

    The cytosolic and secreted, N-glycosylated, forms of plasminogen activator inhibitor-2 (PAI-2) are generated by facultative translocation. To study the molecular events that result in the bi-topological distribution of proteins, we determined in vitro the capacities of several signal sequences to bind the signal recognition particle (SRP) during targeting, and to promote vectorial transport of murine PAI-2 (mPAI-2). Interestingly, the six signal sequences we compared (mPAI-2 and three mutated derivatives thereof, ovalbumin and preprolactin) were found to have the differential activities in the two events. For example, the mPAI-2 signal sequence first binds SRP with moderate efficiency and secondly promotes the vectorial transport of only a fraction of the SRP-bound nascent chains. Our results provide evidence that the translocation efficiency of proteins can be controlled by the recognition of their signal sequences at two steps: during SRP-mediated targeting and during formation of a committed translocation complex. This second recognition may occur at several time points during the insertion/translocation step. In conclusion, signal sequences have a more complex structure than previously anticipated, allowing for multiple and independent interactions with the translocation machinery.

  20. Probabilistic safety analysis on an SBWR 72 hours after the initiating event

    International Nuclear Information System (INIS)

    Dominguez Bautista, M.T.; Peinador Veira, M.

    1996-01-01

    Passive plants, including SBWRs, are designed to carry out safety functions with passive systems during the first 72 hours after the initiation event with no need for manual actions or external support. After this period, some recovery actions are required to enable the passive systems to continue performing their safety functions. The study was carried out by the INITEC-Empresarios Agrupados Joint Venture within the framework of the international group collaborating with GE on this project. Its purpose has been to assess, by means of probabilistic criteria, the importance to safety of each of these support actions, in order to define possible requirements to be considered in the design in respect of said recovery actions. In brief, the methodology developed for this objective consists of (1) quantifying success event trees from the PSA up to 72 hours, (2) determining the actions required in each sequence to maintain Steady State after 72 hours, (3) identifying available alternative core cooling methods in each sequence, (4) establishing the approximate (order of magnitude) realizability of each alternative method, (5) calculating the frequency of core damage as a function of the failure probability of post-72-hour actions and (6) analysing the importance of post-72-hour actions. The results of this analysis permit the establishment, right from the conceptual design phase, of the requirements that will arise to ensure these actions in the long term, enhancing their reliability and preventing the accident from continuing beyond this period. (Author)

  1. The influence of pH adjustment on kinetics parameters in tapioca wastewater treatment using aerobic sequencing batch reactor system

    Science.gov (United States)

    Mulyani, Happy; Budianto, Gregorius Prima Indra; Margono, Kaavessina, Mujtahid

    2018-02-01

    The present investigation deals with the aerobic sequencing batch reactor system of tapioca wastewater treatment with varying pH influent conditions. This project was carried out to evaluate the effect of pH on kinetics parameters of system. It was done by operating aerobic sequencing batch reactor system during 8 hours in many tapioca wastewater conditions (pH 4.91, pH 7, pH 8). The Chemical Oxygen Demand (COD) and Mixed Liquor Volatile Suspended Solids (MLVSS) of the aerobic sequencing batch reactor system effluent at steady state condition were determined at interval time of two hours to generate data for substrate inhibition kinetics parameters. Values of the kinetics constants were determined using Monod and Andrews models. There was no inhibition constant (Ki) detected in all process variation of aerobic sequencing batch reactor system for tapioca wastewater treatment in this study. Furthermore, pH 8 was selected as the preferred aerobic sequencing batch reactor system condition in those ranging pH investigated due to its achievement of values of kinetics parameters such µmax = 0.010457/hour and Ks = 255.0664 mg/L COD.

  2. Workplace flexibility, work hours, and work-life conflict: finding an extra day or two.

    Science.gov (United States)

    Hill, E Jeffrey; Erickson, Jenet Jacob; Holmes, Erin K; Ferris, Maria

    2010-06-01

    This study explores the influence of workplace flexibility on work-life conflict for a global sample of workers from four groups of countries. Data are from the 2007 International Business Machines Global Work and Life Issues Survey administered in 75 countries (N = 24,436). We specifically examine flexibility in where (work-at-home) and when (perceived schedule flexibility) workers engage in work-related tasks. Multivariate results indicate that work-at-home and perceived schedule flexibility are generally related to less work-life conflict. Break point analyses of sub-groups reveal that employees with workplace flexibility are able to work longer hours (often equivalent to one or two 8-hr days more per week) before reporting work-life conflict. The benefit of work-at-home is increased when combined with schedule flexibility. These findings were generally consistent across all four groups of countries, supporting the case that workplace flexibility is beneficial both to individuals (in the form of reduced work-life conflict) and to businesses (in the form of capacity for longer work hours). However, work-at-home appears less beneficial in countries with collectivist cultures. (c) 2010 APA, all rights reserved.

  3. Comparison of 72-hour fecal fat quantification and the 13C-mixed triglyceride breath test in assessing pancreatic exocrine sufficiency in children with chronic pancreatitis.

    Science.gov (United States)

    Wejnarska, Karolina; Kołodziejczyk, Elwira; Ryżko, Józef; Oracz, Grzegorz

    Chronic pancreatitis (CP) in children is still a rare, although increasingly recognized entity. Over the duration of the disease several complications can be observed, two of which are major ones: endo- and exocrine insufficiency. In the medical care of children with CP it is crucial to diagnose the decreased endo- and exocrine function of the pancreas, in order to preserve patients from malnutrition and the failure to thrive. The aim of the study was to compare the usefulness of two indirect methods of assessing the pancreas exocrine function in children with CP. Ninety one patients with CP were enrolled in the study (41 boys, 50 girls, aged 2-17.8 years). Only Patients who had had both the 72-hour fecal fat quantification and the 13C-mixed triglyceride breath test (13C -MTBT) performed were selected. We compared the results of both tests for sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) in detecting exocrine pancreatic insufficiency. Out of 91 patients, 12 were diagnosed with exocrine pancreatic insufficiency (EPI). The sensitivity of the fecal fat quantification was 50%, the specificity for the test was 100%. PPV and NPV were 100% and 93%, respectively. 13C-MTBT had the sensitivity of 42% and the specificity of 99%. PPV and NPV for the breath test were of 83% and 92%, respectively. No statistically significant discrepancy between the values obtained was found. Although the 72-hour fecal fat quantification remains the gold standard in detecting EPI, both of the methods that had been investigated were shown to be comparable regarding sensitivity, specificity, PPV and NPV in assessing pancreas exocrine sufficiency in children with CP. Due to the easier execution of the breath test, both for the patient and for medical personnel, its importance may increase.

  4. Effects of tonal language background on tests of temporal sequencing in children.

    Science.gov (United States)

    Mukari, Siti Zamratol-Mai S; Yu, Xuan; Ishak, Wan Syafira; Mazlan, Rafidah

    2015-01-01

    The aims of the present study were to determine the effects of language background on the performance of the pitch pattern sequence test (PPST) and duration pattern sequence test (DPST). As temporal order sequencing may be affected by age and working memory, these factors were also studied. Performance of tonal and non-tonal language speakers on PPST and DPST were compared. Twenty-eight native Mandarin (tonal language) speakers and twenty-nine native Malay (non-tonal language) speakers between seven to nine years old participated in this study. The results revealed that relative to native Malay speakers, native Mandarin speakers demonstrated better scores on the PPST in both humming and verbal labeling responses. However, a similar language effect was not apparent in the DPST. An age effect was only significant in the PPST (verbal labeling). Finally, no significant effect of working memory was found on the PPST and the DPST. These findings suggest that the PPST is affected by tonal language background, and highlight the importance of developing different normative values for tonal and non-tonal language speakers.

  5. Two cases of a fetus with sirenomelia sequence.

    Science.gov (United States)

    Horikoshi, Tsuguhiro; Kikuchi, Akihiko; Tatematsu, Mikiko; Matsumoto, Yasuhiro; Hayashi, Akiko; Unno, Nobuya

    2005-09-01

    We report two cases of a fetus with sirenomelia sequence which showed oligohydramnios and a single umbilical artery. The first case was of a single fetus with symelia apus and only one leg. Prenatal diagnosis of this case was possible. The second case was of a dichorionic-diamniotic twin pregnancy in which one fetus had symelia dipus with two fused lower extremities. Prenatal diagnosis of the condition was not made. In both cases, the fetuses died shortly after birth from respiratory distress due to severe pulmonary hypoplasia. Absence of urinary tract, imperforate anus, and spine deformity were confirmed in both cases. Although prenatal diagnosis of symelia dipus seems difficult, this condition must be considered in a fetus with severe oligohydramnios.

  6. Space Suit Portable Life Support System (PLSS) 2.0 Unmanned Vacuum Environment Testing

    Science.gov (United States)

    Watts, Carly; Vogel, Matthew

    2016-01-01

    For the first time in more than 30 years, an advanced space suit Portable Life Support System (PLSS) design was operated inside a vacuum chamber representative of the flight operating environment. The test article, PLSS 2.0, was the second system-level integrated prototype of the advanced PLSS design, following the PLSS 1.0 Breadboard that was developed and tested throughout 2011. Whereas PLSS 1.0 included five technology development components with the balance the system simulated using commercial-off-the-shelf items, PLSS 2.0 featured first generation or later prototypes for all components less instrumentation, tubing and fittings. Developed throughout 2012, PLSS 2.0 was the first attempt to package the system into a flight-like representative volume. PLSS 2.0 testing included an extensive functional evaluation known as Pre-Installation Acceptance (PIA) testing, Human-in-the-Loop testing in which the PLSS 2.0 prototype was integrated via umbilicals to a manned prototype space suit for 19 two-hour simulated EVAs, and unmanned vacuum environment testing. Unmanned vacuum environment testing took place from 1/9/15-7/9/15 with PLSS 2.0 located inside a vacuum chamber. Test sequences included performance mapping of several components, carbon dioxide removal evaluations at simulated intravehicular activity (IVA) conditions, a regulator pressure schedule assessment, and culminated with 25 simulated extravehicular activities (EVAs). During the unmanned vacuum environment test series, PLSS 2.0 accumulated 378 hours of integrated testing including 291 hours of operation in a vacuum environment and 199 hours of simulated EVA time. The PLSS prototype performed nominally throughout the test series, with two notable exceptions including a pump failure and a Spacesuit Water Membrane Evaporator (SWME) leak, for which post-test failure investigations were performed. In addition to generating an extensive database of PLSS 2.0 performance data, achievements included requirements and

  7. Draft genome sequences of two commensal Enterococcus cecorum strains isolated from chickens in Belgium

    DEFF Research Database (Denmark)

    Dolka, Beata; Boyen, Filip; Butaye, Patrick

    2015-01-01

    Here, we report the draft genome sequences of two commensal Enterococcus cecorum strains (1710s23 and 1711s24), cultivated from the ceca of healthy laying hens originating from different farms in Belgium.......Here, we report the draft genome sequences of two commensal Enterococcus cecorum strains (1710s23 and 1711s24), cultivated from the ceca of healthy laying hens originating from different farms in Belgium....

  8. Genome Sequences of Two Copper-Resistant Escherichia coli Strains Isolated from Copper-Fed Pigs

    DEFF Research Database (Denmark)

    Lüthje, Freja L.; Hasman, Henrik; Aarestrup, Frank Møller

    2014-01-01

    The draft genome sequences of two copper-resistant Escherichia coli strains were determined. These had been isolated from copper-fed pigs and contained additional putative operons conferring copper and other metal and metalloid resistances.......The draft genome sequences of two copper-resistant Escherichia coli strains were determined. These had been isolated from copper-fed pigs and contained additional putative operons conferring copper and other metal and metalloid resistances....

  9. Eight- and twelve-hour shifts in Austrian rail traffic controllers: a psychophysiological comparison

    Directory of Open Access Journals (Sweden)

    K. WOLFGANG KALLUS

    2009-09-01

    Full Text Available The present study compared a 12-hour and an 8-hour shift system in 18 Austrian rail traffic controllers. To gain objective indicators for arousal and fatigue induced by the whole workrest sequence, we recorded heart rate during the last night shift, in addition to subjective measures that included physical symptoms. A higher increase of monotony, fatigue and saturation emerged during the 8-hour compared to the 12-hour regime, together with a heart rate decrease during the last 8-hour night shift. In line with other researchers, we conclude that flexible working conditions in specific occupational groups may compensate for disadvantages of prolonged working periods, giving way to advantages of longer shifts such as longer pauses and extra days off for social and other personal activities.

  10. Enhanced muscle strength with carbohydrate supplement two hours before open cholecystectomy: a randomized, double-blind study

    Directory of Open Access Journals (Sweden)

    Marcella Giovana Gava

    Full Text Available Objective: to investigate the effects of preoperative fasting abbreviation with oral supplementation with carbohydrate in the evolution of grip strength in patients undergoing cholecystectomy by laparotomy. Methods : we conducted a clinical, randomizeddouble blind study with adult female patients, aged 18-60 years. Patients were divided into two groups: Control Group, with fasting prescription 6-8h until the time of operation; and Intervention Group, which received prescription of fasting for solids 6-8h before surgery, but ingested an oral supplement containing 12.5% carbohydrate, six (400ml and two (200ml hours before theprocedure. The handgrip strength was measured in both hands in both groups, at patient's admission (6h before surgery, the immediate pre-operative time (1h before surgery and 12-18h postoperatively. Results : we analyzed 27 patients, 14 in the intervention group and 13 in the control group. There was no mortality. The handgrip strength (mean [standard deviation] was significantly higher in the intervention group in the three periods studied, in at least one hand: preoperatively in the dominant hand (27.8 [2.6] vs 24.1 [3.7] kg; p=0.04, in the immediate preoperative in both hands, and postoperatively in the non-dominant hand (28.5 [3.0] vs 21.3 [5.9] kg; p=0.01. Conclusion : the abbreviation of preoperative fasting to two hours with drink containing carbohydrate improves muscle function in the perioperative period.

  11. Whole-exome sequencing revealed two novel mutations in Usher syndrome.

    Science.gov (United States)

    Koparir, Asuman; Karatas, Omer Faruk; Atayoglu, Ali Timucin; Yuksel, Bayram; Sagiroglu, Mahmut Samil; Seven, Mehmet; Ulucan, Hakan; Yuksel, Adnan; Ozen, Mustafa

    2015-06-01

    Usher syndrome is a clinically and genetically heterogeneous autosomal recessive inherited disorder accompanied by hearing loss and retinitis pigmentosa (RP). Since the associated genes are various and quite large, we utilized whole-exome sequencing (WES) as a diagnostic tool to identify the molecular basis of Usher syndrome. DNA from a 12-year-old male diagnosed with Usher syndrome was analyzed by WES. Mutations detected were confirmed by Sanger sequencing. The pathogenicity of these mutations was determined by in silico analysis. A maternally inherited deleterious frameshift mutation, c.14439_14454del in exon 66 and a paternally inherited non-sense c.10830G>A stop-gain SNV in exon 55 of USH2A were found as two novel compound heterozygous mutations. Both of these mutations disrupt the C terminal of USH2A protein. As a result, WES revealed two novel compound heterozygous mutations in a Turkish USH2A patient. This approach gave us an opportunity to have an appropriate diagnosis and provide genetic counseling to the family within a reasonable time. Copyright © 2015 Elsevier B.V. All rights reserved.

  12. Tests of two convection theories for red giant and red supergiant envelopes

    Science.gov (United States)

    Stothers, Richard B.; Chin, Chao-Wen

    1995-01-01

    Two theories of stellar envelope convection are considered here in the context of red giants and red supergiants of intermediate to high mass: Boehm-Vitense's standard mixing-length theory (MLT) and Canuto & Mazzitelli's new theory incorporating the full spectrum of turbulence (FST). Both theories assume incompressible convection. Two formulations of the convective mixing length are also evaluated: l proportional to the local pressure scale height (H(sub P)) and l proportional to the distance from the upper boundary of the convection zone (z). Applications to test both theories are made by calculating stellar evolutionary sequences into the red zone (z). Applications to test both theories are made by calculating stellar evolutionary sequences into the red phase of core helium burning. Since the theoretically predicted effective temperatures for cool stars are known to be sensitive to the assigned value of the mixing length, this quantity has been individually calibrated for each evolutionary sequence. The calibration is done in a composite Hertzsprung-Russell diagram for the red giant and red supergiant members of well-observed Galactic open clusters. The MLT model requires the constant of proportionality for the convective mixing length to vary by a small but statistically significant amount with stellar mass, whereas the FST model succeeds in all cases with the mixing lenghth simply set equal to z. The structure of the deep stellar interior, however, remains very nearly unaffected by the choices of convection theory and mixing lenghth. Inside the convective envelope itself, a density inversion always occurs, but is somewhat smaller for the convectively more efficient MLT model. On physical grounds the FST model is preferable, and seems to alleviate the problem of finding the proper mixing length.

  13. Whole genome sequencing and bioinformatics analysis of two Egyptian genomes.

    Science.gov (United States)

    ElHefnawi, Mahmoud; Jeon, Sungwon; Bhak, Youngjune; ElFiky, Asmaa; Horaiz, Ahmed; Jun, JeHoon; Kim, Hyunho; Bhak, Jong

    2018-05-15

    We report two Egyptian male genomes (EGP1 and EGP2) sequenced at ~ 30× sequencing depths. EGP1 had 4.7 million variants, where 198,877 were novel variants while EGP2 had 209,109 novel variants out of 4.8 million variants. The mitochondrial haplogroup of the two individuals were identified to be H7b1 and L2a1c, respectively. We also identified the Y haplogroup of EGP1 (R1b) and EGP2 (J1a2a1a2 > P58 > FGC11). EGP1 had a mutation in the NADH gene of the mitochondrial genome ND4 (m.11778 G > A) that causes Leber's hereditary optic neuropathy. Some SNPs shared by the two genomes were associated with an increased level of cholesterol and triglycerides, probably related with Egyptians obesity. Comparison of these genomes with African and Western-Asian genomes can provide insights on Egyptian ancestry and genetic history. This resource can be used to further understand genomic diversity and functional classification of variants as well as human migration and evolution across Africa and Western-Asia. Copyright © 2017. Published by Elsevier B.V.

  14. Automated methods for single-stranded DNA isolation and dideoxynucleotide DNA sequencing reactions on a robotic workstation

    International Nuclear Information System (INIS)

    Mardis, E.R.; Roe, B.A.

    1989-01-01

    Automated procedures have been developed for both the simultaneous isolation of 96 single-stranded M13 chimeric template DNAs in less than two hours, and for simultaneously pipetting 24 dideoxynucleotide sequencing reactions on a commercially available laboratory workstation. The DNA sequencing results obtained by either radiolabeled or fluorescent methods are consistent with the premise that automation of these portions of DNA sequencing projects will improve the reproducibility of the DNA isolation and the procedures for these normally labor-intensive steps provides an approach for rapid acquisition of large amounts of high quality, reproducible DNA sequence data

  15. New Approach To Hour-By-Hour Weather Forecast

    Science.gov (United States)

    Liao, Q. Q.; Wang, B.

    2017-12-01

    Fine hourly forecast in single station weather forecast is required in many human production and life application situations. Most previous MOS (Model Output Statistics) which used a linear regression model are hard to solve nonlinear natures of the weather prediction and forecast accuracy has not been sufficient at high temporal resolution. This study is to predict the future meteorological elements including temperature, precipitation, relative humidity and wind speed in a local region over a relatively short period of time at hourly level. By means of hour-to-hour NWP (Numeral Weather Prediction)meteorological field from Forcastio (https://darksky.net/dev/docs/forecast) and real-time instrumental observation including 29 stations in Yunnan and 3 stations in Tianjin of China from June to October 2016, predictions are made of the 24-hour hour-by-hour ahead. This study presents an ensemble approach to combine the information of instrumental observation itself and NWP. Use autoregressive-moving-average (ARMA) model to predict future values of the observation time series. Put newest NWP products into the equations derived from the multiple linear regression MOS technique. Handle residual series of MOS outputs with autoregressive (AR) model for the linear property presented in time series. Due to the complexity of non-linear property of atmospheric flow, support vector machine (SVM) is also introduced . Therefore basic data quality control and cross validation makes it able to optimize the model function parameters , and do 24 hours ahead residual reduction with AR/SVM model. Results show that AR model technique is better than corresponding multi-variant MOS regression method especially at the early 4 hours when the predictor is temperature. MOS-AR combined model which is comparable to MOS-SVM model outperform than MOS. Both of their root mean square error and correlation coefficients for 2 m temperature are reduced to 1.6 degree Celsius and 0.91 respectively. The

  16. A Method to Select Software Test Cases in Consideration of Past Input Sequence

    International Nuclear Information System (INIS)

    Kim, Hee Eun; Kim, Bo Gyung; Kang, Hyun Gook

    2015-01-01

    In the Korea Nuclear I and C Systems (KNICS) project, the software for the fully-digitalized reactor protection system (RPS) was developed under a strict procedure. Even though the behavior of the software is deterministic, the randomness of input sequence produces probabilistic behavior of software. A software failure occurs when some inputs to the software occur and interact with the internal state of the digital system to trigger a fault that was introduced into the software during the software lifecycle. In this paper, the method to select test set for software failure probability estimation is suggested. This test set reflects past input sequence of software, which covers all possible cases. In this study, the method to select test cases for software failure probability quantification was suggested. To obtain profile of paired state variables, relationships of the variables need to be considered. The effect of input from human operator also have to be considered. As an example, test set of PZR-PR-Lo-Trip logic was examined. This method provides framework for selecting test cases of safety-critical software

  17. Verification of two simple meteorological models at large travel distances using ten-hour 85Kr measurements

    International Nuclear Information System (INIS)

    Pendergast, M.M.

    1978-01-01

    This report evaluates the wind-rose model and a trajectory model for calculating air concentrations averaged over 10 hours at distances greater than 100 km. Ten-hour averaged 85 Kr air concentrations from 13 sites located withing 143 km of the Savannah River Plant (SRP) were used to evaluate two simple models: a wind-rose model, and a trajectory model. The wind-rose model has previously been shown to estimate annual average concentrations to within a factor of four for travel distances of about 100 km. When 85 Kr concentrations were observed (80 cases), the wind-rose model predicted above background for only 36 percent of the cases, while the trajectory model predicted above background for 56 percent of the cases. The wind-rose model tended to overpredict air concentration by a factor of 4 while the trajectory model tended to underpredict by a factor of 3 for those occasions where observations and calculations were above background

  18. Relative bioavailability of two oral formulations of risperidone 2 mg: A single-dose, randomized-sequence, open-label, two-period crossover comparison in healthy Brazilian volunteers.

    Science.gov (United States)

    Belotto, Karisa Cristina Rodrigues; Raposo, Nádia Rezende Barbosa; Ferreira, Aline Siqueira; Gattaz, Wagner Farid

    2010-11-01

    Risperidone (RSP) is a benzisoxazole antipsychotic agent used to treat schizophrenia and other psychiatric illnesses in adults and children (including those with autism). After oral administration, RSP is completely absorbed from the gastrointestinal tract and undergoes hydroxylation to yield 9-hydroxyrisperidone (9-OH-RSP), an active metabolite that has a pharmacologic profile and potency similar to RSP. The aims of this study were to compare the relative bioavailability of a pharmaceutical-equivalent (test) formulation with a reference formulation of oral RSP 2 mg, both available commercially on the Brazilian pharmaceutical market, and to generate data regarding the oral bioavailability of the tested drug in healthy Brazilian volunteers. This single-dose, randomized-sequence, open-label, 2-period crossover study was conducted in healthy Brazilian volunteers from August to December 2008. Subjects were randomly assigned to receive the test formulation followed by the reference formulation or vice versa, with a 30-day washout period between doses. Study drugs were administered after a 12-hour overnight fast. For pharmacokinetic analysis, blood samples were drawn at 0 (baseline), 0.25, 0.5, 1, 1.5, 3, 5, 8, 12, 24, 48, 72, 96, and 120 hours after administration. Plasma concentrations of RSP and 9-OH-RSP were determined using LC-MS/MS. The test and reference formulations were to be considered bioequivalent if the 90% CIs for the geometric mean test/reference ratios were within a predetermined range of 80% to 125%, in accordance with the policies of the Brazilian Sanitary Surveillance Agency and the US Food and Drug Administration. Tolerability was determined using clinical assessments, monitoring of vital signs, analysis of laboratory test results, and subject interviews regarding adverse events. A total of 22 subjects were enrolled (11 men, 11 women; mean [SD] age, 32 [12] years [range, 1858 years]; weight, 70.4 [11.9] kg [range, 50-103 kg]; height, 1.67 [0.08] m

  19. Comparative bioavailability and tolerability of a single 20-mg dose of two fluoxetine hydrochloride dispersible tablet formulations in fasting, healthy Chinese male volunteers: an open-label, randomized-sequence, two-period crossover study.

    Science.gov (United States)

    Shi, Shaojun; Liu, Yani; Wu, Jianhong; Li, Zhongfang; Zhao, Yan; Zhong, Dafang; Zeng, Fandian

    2010-10-01

    The proprietary formulation of fluoxetine hydrochloride is an antidepressant of the selective serotonin reuptake inhibitor class. Pharmacokinetic studies investigating the bioequivalence of generic and branded formulations are needed to market generic fluoxetine in China. The aim of this study was to compare the bioavailability and tolerability of the proposed generic formulation with the established reference formulation of fluoxetine hydrochloride 20 mg in a fasting, healthy Chinese male population. This 10-week, open-label, randomized-sequence, single-dose, 2-period crossover study was conducted in healthy native Han Chinese male volunteers. Eligible subjects were randomly assigned in a 1:1 ratio to receive a single 20-mg dose of the test or reference formulation, followed by a 35-day washout period and administration of the alternate formulation. Doses were administered after a 12-hour overnight fast. For analysis of pharmacokinetic properties (including C(max), T(max), AUC(0-t), AUC(0-∞), and t(½)), blood samples were obtained over a 672-hour period after dosing. Plasma concentrations of fluoxetine and its active metabolite, norfluoxetine, were analyzed using a validated LC-MS/MS method. The formulations were to be considered bioequivalent if the ln-transformed ratios (test/ reference) of C(max) and AUC were within the predetermined bioequivalence range of 80% to 125%, as established by the US Food and Drug Administration, and if the P values were fasting, healthy Chinese male volunteers. Both formulations appeared to be well tolerated. Copyright © 2010 Excerpta Medica Inc. All rights reserved.

  20. Living hours under pressure

    DEFF Research Database (Denmark)

    Ilsøe, Anna; Larsen, Trine Pernille; Felbo-Kolding, Jonas

    2017-01-01

    Purpose The purpose of this paper is to investigate the effect of part-time work on absolute wages. The empirical focus is wages and working hours in three selected sectors within private services in the Danish labour market – industrial cleaning, retail, hotels and restaurants – and their agreem......Purpose The purpose of this paper is to investigate the effect of part-time work on absolute wages. The empirical focus is wages and working hours in three selected sectors within private services in the Danish labour market – industrial cleaning, retail, hotels and restaurants...... in industrial cleaning includes a minimum floor of 15 weekly working hours – this is not the case in retail, hotels and restaurants. This creates a loophole in the latter two sectors that can be exploited by employers to gain wage flexibility through part-time work. Originality/value The living wage literature...

  1. Long working hours and emotional well-being in korean manufacturing industry employees.

    Science.gov (United States)

    Lee, Kyoung-Hye; Kim, Jong-Eun; Kim, Young-Ki; Kang, Dong-Mug; Yun, Myeong-Ja; Park, Shin-Goo; Song, Jae-Seok; Lee, Sang-Gil

    2013-12-05

    Korea is well known for its long work hours amongst employees. Because workers of the manufacturing industry are constantly exposed to extended work hours, this study was based on how long work hours affect their emotional well-being. The analysis was done using the secondary Korean Working Condition Survey (KWCS). Long work hours were defined to be more than 48 hours, and they were subcategorized into units of 52 hours and 60 hours. Based on the WHO (five) well-being index, emotional state was subdivided into three groups - reference group, low-mood group, and possible depression group- where 28 points and 50 points were division points, and two groups were compared at a time. Association between long work hours and emotional state was analyzed using binary and multinomial logistic regression analysis. Working for extended working hours in the manufacturing industry showed a statistically significant increase (t test p work-related characteristics were fixed as controlled variables, as work hours increased the odds ratio of the possible depression group increased compared to the reference group, and especially the odds ratio was 2.73 times increased for work hours between 48-52 and 4.09 times increased for 60 hours or more and both were statistically significant. In comparing the low-mood group and possible depression group, as work hours increased the odds ratio increased to 1.73, 2.39, and 4.16 times, and all work hours from working 48-52 hours, 53-60 hours, and 60 hours or more were statistically significant. Multinomial logistic regression analysis also showed that among the reference group and possible group, the possible depression group was statistically significant as odds ratio increased to 2.94 times in working 53-60 hours, and 4.35 times in 60 hours or more. Long work hours have an adverse effect on emotional well-being. A more diversified research towards variables that affect long work hours and emotional well-being and how they interact with each

  2. Sequencing of bovine herpesvirus 4 v.test strain reveals important genome features

    Directory of Open Access Journals (Sweden)

    Gillet Laurent

    2011-08-01

    Full Text Available Abstract Background Bovine herpesvirus 4 (BoHV-4 is a useful model for the human pathogenic gammaherpesviruses Epstein-Barr virus and Kaposi's Sarcoma-associated Herpesvirus. Although genome manipulations of this virus have been greatly facilitated by the cloning of the BoHV-4 V.test strain as a Bacterial Artificial Chromosome (BAC, the lack of a complete genome sequence for this strain limits its experimental use. Methods In this study, we have determined the complete sequence of BoHV-4 V.test strain by a pyrosequencing approach. Results The long unique coding region (LUR consists of 108,241 bp encoding at least 79 open reading frames and is flanked by several polyrepetitive DNA units (prDNA. As previously suggested, we showed that the prDNA unit located at the left prDNA-LUR junction (prDNA-G differs from the other prDNA units (prDNA-inner. Namely, the prDNA-G unit lacks the conserved pac-2 cleavage and packaging signal in its right terminal region. Based on the mechanisms of cleavage and packaging of herpesvirus genomes, this feature implies that only genomes bearing left and right end prDNA units are encapsulated into virions. Conclusions In this study, we have determined the complete genome sequence of the BAC-cloned BoHV-4 V.test strain and identified genome organization features that could be important in other herpesviruses.

  3. The Effects of Four-Hour Delay of PUnishment under Two Conditions of Verbal Instruction

    Science.gov (United States)

    Verna, Gary B.

    1977-01-01

    The effects of 4-hour delay of punishment (withdrawal of reward) on response inhibition was studied with 24 fourth-grade children. Results showed that verbal expression of the punishment contingency allows the 10-year-old child to profit from 4-hour delayed punishment as much as immediate punishment. (Author/JMB)

  4. Comparative analyses of two Geraniaceae transcriptomes using next-generation sequencing.

    Science.gov (United States)

    Zhang, Jin; Ruhlman, Tracey A; Mower, Jeffrey P; Jansen, Robert K

    2013-12-29

    Organelle genomes of Geraniaceae exhibit several unusual evolutionary phenomena compared to other angiosperm families including accelerated nucleotide substitution rates, widespread gene loss, reduced RNA editing, and extensive genomic rearrangements. Since most organelle-encoded proteins function in multi-subunit complexes that also contain nuclear-encoded proteins, it is likely that the atypical organellar phenomena affect the evolution of nuclear genes encoding organellar proteins. To begin to unravel the complex co-evolutionary interplay between organellar and nuclear genomes in this family, we sequenced nuclear transcriptomes of two species, Geranium maderense and Pelargonium x hortorum. Normalized cDNA libraries of G. maderense and P. x hortorum were used for transcriptome sequencing. Five assemblers (MIRA, Newbler, SOAPdenovo, SOAPdenovo-trans [SOAPtrans], Trinity) and two next-generation technologies (454 and Illumina) were compared to determine the optimal transcriptome sequencing approach. Trinity provided the highest quality assembly of Illumina data with the deepest transcriptome coverage. An analysis to determine the amount of sequencing needed for de novo assembly revealed diminishing returns of coverage and quality with data sets larger than sixty million Illumina paired end reads for both species. The G. maderense and P. x hortorum transcriptomes contained fewer transcripts encoding the PLS subclass of PPR proteins relative to other angiosperms, consistent with reduced mitochondrial RNA editing activity in Geraniaceae. In addition, transcripts for all six plastid targeted sigma factors were identified in both transcriptomes, suggesting that one of the highly divergent rpoA-like ORFs in the P. x hortorum plastid genome is functional. The findings support the use of the Illumina platform and assemblers optimized for transcriptome assembly, such as Trinity or SOAPtrans, to generate high-quality de novo transcriptomes with broad coverage. In addition

  5. Some AFLP amplicons are highly conserved DNA sequences mapping to the same linkage groups in two F2 populations of carrot

    Directory of Open Access Journals (Sweden)

    Santos Carlos A.F.

    2002-01-01

    Full Text Available Amplified fragment length polymorphism (AFLP is a fast and reliable tool to generate a large number of DNA markers. In two unrelated F2 populations of carrot (Daucus carota L., Brasilia x HCM and B493 x QAL (wild carrot, it was hypothesized that DNA 1 digested with the same restriction endonuclease enzymes and amplified with the same primer combination and 2 sharing the same position in polyacrylamide gels should be conserved sequences. To test this hypothesis AFLP fragments from polyacrylamide gels were eluted, reamplified, separated in agarose gels, purified, cloned and sequenced. Among thirty-one paired fragments from each F2 population, twenty-six had identity greater than 91% and five presented identity of 24% to 44%. Among the twenty-six conserved AFLPs only one mapped to different linkage groups in the two populations while four of the five less-conserved bands mapped to different linkage groups. Of eight SCAR (sequence characterized amplified regions primers tested, one conserved AFLP resulted in co-dominant markers in both populations. Screening among 14 carrot inbreds or cultivars with three AFLP-SCAR primers revealed clear and polymorphic PCR products, with similar molecular sizes on agarose gels. The development of co-dominant markers based on conserved AFLP fragments will be useful to detect seed mixtures among hybrids, to improve and to merge linkage maps and to study diversity and phylogenetic relationships.

  6. An evaluation of Comparative Genome Sequencing (CGS by comparing two previously-sequenced bacterial genomes

    Directory of Open Access Journals (Sweden)

    Herring Christopher D

    2007-08-01

    Full Text Available Abstract Background With the development of new technology, it has recently become practical to resequence the genome of a bacterium after experimental manipulation. It is critical though to know the accuracy of the technique used, and to establish confidence that all of the mutations were detected. Results In order to evaluate the accuracy of genome resequencing using the microarray-based Comparative Genome Sequencing service provided by Nimblegen Systems Inc., we resequenced the E. coli strain W3110 Kohara using MG1655 as a reference, both of which have been completely sequenced using traditional sequencing methods. CGS detected 7 of 8 small sequence differences, one large deletion, and 9 of 12 IS element insertions present in W3110, but did not detect a large chromosomal inversion. In addition, we confirmed that CGS also detected 2 SNPs, one deletion and 7 IS element insertions that are not present in the genome sequence, which we attribute to changes that occurred after the creation of the W3110 lambda clone library. The false positive rate for SNPs was one per 244 Kb of genome sequence. Conclusion CGS is an effective way to detect multiple mutations present in one bacterium relative to another, and while highly cost-effective, is prone to certain errors. Mutations occurring in repeated sequences or in sequences with a high degree of secondary structure may go undetected. It is also critical to follow up on regions of interest in which SNPs were not called because they often indicate deletions or IS element insertions.

  7. Safety considerations for continuous hydrogen production test apparatus with capacity of 50 N-litter hydrogen per hour

    International Nuclear Information System (INIS)

    Onuki, Kaoru; Akino, Norio; Shimizu, Saburo; Nakajima, Hayato; Higashi, Shunichi; Kubo, Shinji

    2001-03-01

    Since the thermochemical hydrogen production Iodine-Sulfur process decomposes water into hydrogen and oxygen using toxic chemicals such as sulfuric acid, iodine and hydriodic acid, safety considerations are very important in its research and development. Therefore, before construction of continuous hydrogen production test apparatus with capacity of 50 N-litter hydrogen per hour, comprehensive safety considerations were carried out to examine the design and construction works of the test apparatus, and the experimental plans using the apparatus. Emphasis was given on the safety considerations on prevention of breakage of glasswares and presumable abnormalities, accidents and their countermeasures. This report summarizes the results of the considerations. (author)

  8. Meeting the Canadian 24-Hour Movement Guidelines for Children and Youth.

    Science.gov (United States)

    Roberts, Karen C; Yao, Xiaoquan; Carson, Valerie; Chaput, Jean-Philippe; Janssen, Ian; Tremblay, Mark S

    2017-10-18

    The Canadian 24-Hour Movement Guidelines for Children and Youth: An Integration of Physical Activity, Sedentary Behaviour, and Sleep , provide specific recommendations on the amount of time over a typical 24-hour day that children and youth aged 5 to 17 should spend in moderate-to-vigorous physical activity (at least 60 minutes), recreational screen time (no more than 2 hours), and sleep (9 to 11 hours for 5- to 13-year-olds; 8 to 10 hours for 14- to 17-year-olds). Based on combined results of cycles 2 (2009-to-2011) and 3 (2012-to-2013) of the Canadian Health Measures Survey, this analysis examines average daily moderate-to-vigorous physical activity, screen time and sleep duration of 5- to 11-year-olds and 12- to 17-year-olds, and the percentages meeting the 24-Hour Guidelines' recommendations. Findings are presented overall and by age group and sex. Differences in average daily times between groups were tested for statistical significance, as weredifferences between groups in the percentages meeting each recommendation and combination of recommendations. Overall, 17.5% of children and youth met the 24-Hour Guidelines' specific time recommendations. Higher percentages of children than youth (29.6% versus 5.5%) and boys than girls (22.9% versus 11.8%) met the recommendations. About a third (36.3%) met two of the three recommendations. Recommendations for moderate-to-vigorous physical activity, sedentary behaviour, and sleep have higher levels of adherence among children than youth.

  9. Bioequivalence and pharmacokinetic evaluation of two formulations of risperidone 2 mg : an open-label, single-dose, fasting, randomized-sequence, two-way crossover study in healthy male Chinese volunteers.

    Science.gov (United States)

    Liu, Yun; Zhang, Meng-qi; Jia, Jing-ying; Liu, Yan-mei; Liu, Gang-yi; Li, Shui-jun; Wang, Wei; Weng, Li-ping; Yu, Chen

    2013-03-01

    Risperidone is a benzisoxazole derivate and is effective in the treatment of schizophrenia and other psychiatric illnesses in adults and children. Although there are a few reports in the literature regarding the pharmacokinetic characteristics of risperidone, insufficient data on its pharmacokinetic properties in a Chinese population are available. To meet the requirements for marketing a new generic product, this study was designed to compare the pharmacokinetic properties and bioequivalence of two 2 mg tablet formulations of risperidone: a newly developed generic formulation (test) and a branded formulation (reference) in healthy adult male Chinese volunteers. A single-dose, open-label, randomized-sequence, 2 × 2 crossover study was conducted in fasted healthy male Chinese volunteers. Eligible participants were randomly assigned in a 1:1 ratio to receive 1 tablet (2 mg each) of the test formulation (Risperidone tablet; Dr. Reddy's Laboratories Ltd., Hyderabad, India) or the reference formulation (Risperdal(®) tablet; Xian-Janssen Pharmaceutical Ltd., Xi-an, China), followed by a 2-week washout period and subsequent administration of the alternate formulation. The study drugs were administered after a 10-hour overnight fast. Plasma samples were collected over 96 hours. Plasma concentrations of the parent drug, risperidone, and its active metabolite, 9-hydroxy-risperidone, were analyzed by a liquid chromatography-tandem mass spectrometry method. The formulations would be considered bioequivalent if the 90% confidence intervals (CIs) of the natural log-transformed values were within the predetermined 80-125% equivalence range for the maximum plasma drug concentration (Cmax) and the area under the plasma concentration-time curve (AUC), in accordance with guidelines issued by the US Food and Drug Administration. Assessment of tolerability was based on recording of adverse events (AEs), monitoring of vital signs, electrocardiograms, and laboratory tests at baseline

  10. Evaluation of a twelve-hour/day shift schedule

    International Nuclear Information System (INIS)

    Lewis, P.M.; Swaim, D.J.

    1986-01-01

    In April 1985, the operating crews at the Fast Flux Test Facility near Richland, Washington, changed their rotating shift schedule from an 8-hour to a 12-hour a day work schedule. The primary purpose of the change was to reduce the attrition of operators by increasing their job satisfaction. Eighty-four percent of the operators favored the change. A program was established to evaluate the effects on plant performance, operator alertness, attrition, sleep, health, job satisfaction, and off-the-job satisfaction. Preliminary results from that evaluation program indicate that the 12-hour shift schedule is a reasonable alternative to an 8-hour schedule at this facility

  11. Clinical pharmacogenomics testing in the era of next generation sequencing: challenges and opportunities for precision medicine.

    Science.gov (United States)

    Ji, Yuan; Si, Yue; McMillin, Gwendolyn A; Lyon, Elaine

    2018-04-23

    The rapid development and dramatic decrease in cost of sequencing techniques have ushered the implementation of genomic testing in patient care. Next generation DNA sequencing (NGS) techniques have been used increasingly in clinical laboratories to scan the whole or part of the human genome in order to facilitate diagnosis and/or prognostics of genetic disease. Despite many hurdles and debates, pharmacogenomics (PGx) is believed to be an area of genomic medicine where precision medicine could have immediate impact in the near future. Areas covered: This review focuses on lessons learned through early attempts of clinically implementing PGx testing; the challenges and opportunities that PGx testing brings to precision medicine in the era of NGS. Expert commentary: Replacing targeted analysis approach with NGS for PGx testing is neither technically feasible nor necessary currently due to several technical limitations and uncertainty involved in interpreting variants of uncertain significance for PGx variants. However, reporting PGx variants out of clinical whole exome or whole genome sequencing (WES/WGS) might represent additional benefits for patients who are tested by WES/WGS.

  12. Detection of vancomycin resistances in enterococci within 3 1/2 hours

    Science.gov (United States)

    Schröder, U. -Ch.; Beleites, C.; Assmann, C.; Glaser, U.; Hübner, U.; Pfister, W.; Fritzsche, W.; Popp, J.; Neugebauer, U.

    2015-02-01

    Vancomycin resistant enterococci (VRE) constitute a challenging problem in health care institutions worldwide. Novel methods to rapidly identify resistances are highly required to ensure an early start of tailored therapy and to prevent further spread of the bacteria. Here, a spectroscopy-based rapid test is presented that reveals resistances of enterococci towards vancomycin within 3.5 hours. Without any specific knowledge on the strain, VRE can be recognized with high accuracy in two different enterococci species. By means of dielectrophoresis, bacteria are directly captured from dilute suspensions, making sample preparation very easy. Raman spectroscopic analysis of the trapped bacteria over a time span of two hours in absence and presence of antibiotics reveals characteristic differences in the molecular response of sensitive as well as resistant Enterococcus faecalis and Enterococcus faecium. Furthermore, the spectroscopic fingerprints provide an indication on the mechanisms of induced resistance in VRE.

  13. Parallel Sequencing of Expressed Sequence Tags from Two Complementary DNA Libraries for High and Low Phosphorus Adaptation in Common Beans

    Directory of Open Access Journals (Sweden)

    Matthew W. Blair

    2011-11-01

    Full Text Available Expressed sequence tags (ESTs have proven useful for gene discovery in many crops. In this work, our objective was to construct complementary DNA (cDNA libraries from root tissues of common beans ( L. grown under low and high P hydroponic conditions and to conduct EST sequencing and comparative analyses of the libraries. Expressed sequence tag analysis of 3648 clones identified 2372 unigenes, of which 1591 were annotated as known genes while a total of 465 unigenes were not associated with any known gene. Unigenes with hits were categorized according to biological processes, molecular function, and cellular compartmentalization. Given the young tissue used to make the root libraries, genes for catalytic activity and binding were highly expressed. Comparisons with previous root EST sequencing and between the two libraries made here resulted in a set of genes to study further for differential gene expression and adaptation to low P, such as a 14 kDa praline-rich protein, a metallopeptidase, tonoplast intrinsic protein, adenosine triphosphate (ATP citrate synthase, and cell proliferation genes expressed in the low P treated plants. Given that common beans are often grown on acid soils of the tropics and subtropics that are usually low in P these genes and the two parallel libraries will be useful for selection for better uptake of this essential macronutrient. The importance of EST generation for common bean root tissues under low P and other abiotic soil stresses is also discussed.

  14. Job search, hours restrictions, and desired hours of work

    NARCIS (Netherlands)

    Bloemen, H.G.

    2008-01-01

    A structural empirical job search model is presented that incorporates the labor supply decision of individuals. The arrival of a job offer is modeled as a random draw from a wage-hours offer distribution. Subjective information is used on desired working hours to identify optimal hours from offered

  15. Whole-genome sequencing reveals mutational landscape underlying phenotypic differences between two widespread Chinese cattle breeds

    OpenAIRE

    Xu, Yao; Jiang, Yu; Shi, Tao; Cai, Hanfang; Lan, Xianyong; Zhao, Xin; Plath, Martin; Chen, Hong

    2017-01-01

    Whole-genome sequencing provides a powerful tool to obtain more genetic variability that could produce a range of benefits for cattle breeding industry. Nanyang (Bos indicus) and Qinchuan (Bos taurus) are two important Chinese indigenous cattle breeds with distinct phenotypes. To identify the genetic characteristics responsible for variation in phenotypes between the two breeds, in the present study, we for the first time sequenced the genomes of four Nanyang and four Qinchuan cattle with 10 ...

  16. X-38 Drop Model: Landing Sequence Collage from Cessna Drop Test

    Science.gov (United States)

    1995-01-01

    make them more durable than those used on the space shuttles. The X-38 itself was an unpiloted lifting body designed at 80 percent of the size of a projected emergency crew return vehicle for the International Space Station, although two later versions were planned at 100 percent of the CRV size. The X-38 and the actual CRV are patterned after a lifting-body shape first employed in the Air Force-NASA X-24 lifting-body project in the early to mid-1970s. The current vehicle design is base lined with life support supplies for about nine hours of orbital free flight from the space station. It's landing will be fully automated with backup systems which allow the crew to control orientation in orbit, select a deorbit site, and steer the parafoil, if necessary. The X-38 vehicles (designated V131, V132, and V-131R) are 28.5 feet long, 14.5 feet wide, and weigh approximately 16,000 pounds on average. The vehicles have a nitrogen-gas-operated attitude control system and a bank of batteries for internal power. The actual CRV to be flown in space was expected to be 30 feet long. The X-38 project is a joint effort between the Johnson Space Center, Houston, Texas (JSC), Langley Research Center, Hampton, Virginia (LaRC) and Dryden Flight Research Center, Edwards, California (DFRC) with the program office located at JSC. A contract was awarded to Scaled Composites, Inc., Mojave, California, for construction of the X-38 test airframes. The first vehicle was delivered to the JSC in September 1996. The vehicle was fitted with avionics, computer systems and other hardware at Johnson. A second vehicle was delivered to JSC in December 1996. Flight research with the X-38 at Dryden began with an unpiloted captive-carry flight in which the vehicle remained attached to its future launch vehicle, Dryden's B-52 008. There were four captive flights in 1997 and three in 1998, plus the first drop test on March 12, 1998, using the parachutes and parafoil. Further captive and drop tests occurred in

  17. Network clustering coefficient approach to DNA sequence analysis

    Energy Technology Data Exchange (ETDEWEB)

    Gerhardt, Guenther J.L. [Universidade Federal do Rio Grande do Sul-Hospital de Clinicas de Porto Alegre, Rua Ramiro Barcelos 2350/sala 2040/90035-003 Porto Alegre (Brazil); Departamento de Fisica e Quimica da Universidade de Caxias do Sul, Rua Francisco Getulio Vargas 1130, 95001-970 Caxias do Sul (Brazil); Lemke, Ney [Programa Interdisciplinar em Computacao Aplicada, Unisinos, Av. Unisinos, 950, 93022-000 Sao Leopoldo, RS (Brazil); Corso, Gilberto [Departamento de Biofisica e Farmacologia, Centro de Biociencias, Universidade Federal do Rio Grande do Norte, Campus Universitario, 59072 970 Natal, RN (Brazil)]. E-mail: corso@dfte.ufrn.br

    2006-05-15

    In this work we propose an alternative DNA sequence analysis tool based on graph theoretical concepts. The methodology investigates the path topology of an organism genome through a triplet network. In this network, triplets in DNA sequence are vertices and two vertices are connected if they occur juxtaposed on the genome. We characterize this network topology by measuring the clustering coefficient. We test our methodology against two main bias: the guanine-cytosine (GC) content and 3-bp (base pairs) periodicity of DNA sequence. We perform the test constructing random networks with variable GC content and imposed 3-bp periodicity. A test group of some organisms is constructed and we investigate the methodology in the light of the constructed random networks. We conclude that the clustering coefficient is a valuable tool since it gives information that is not trivially contained in 3-bp periodicity neither in the variable GC content.

  18. Can DNA-Based Ecosystem Assessments Quantify Species Abundance? Testing Primer Bias and Biomass--Sequence Relationships with an Innovative Metabarcoding Protocol.

    Directory of Open Access Journals (Sweden)

    Vasco Elbrecht

    Full Text Available Metabarcoding is an emerging genetic tool to rapidly assess biodiversity in ecosystems. It involves high-throughput sequencing of a standard gene from an environmental sample and comparison to a reference database. However, no consensus has emerged regarding laboratory pipelines to screen species diversity and infer species abundances from environmental samples. In particular, the effect of primer bias and the detection limit for specimens with a low biomass has not been systematically examined, when processing samples in bulk. We developed and tested a DNA metabarcoding protocol that utilises the standard cytochrome c oxidase subunit I (COI barcoding fragment to detect freshwater macroinvertebrate taxa. DNA was extracted in bulk, amplified in a single PCR step, and purified, and the libraries were directly sequenced in two independent MiSeq runs (300-bp paired-end reads. Specifically, we assessed the influence of specimen biomass on sequence read abundance by sequencing 31 specimens of a stonefly species with known haplotypes spanning three orders of magnitude in biomass (experiment I. Then, we tested the recovery of 52 different freshwater invertebrate taxa of similar biomass using the same standard barcoding primers (experiment II. Each experiment was replicated ten times to maximise statistical power. The results of both experiments were consistent across replicates. We found a distinct positive correlation between species biomass and resulting numbers of MiSeq reads. Furthermore, we reliably recovered 83% of the 52 taxa used to test primer bias. However, sequence abundance varied by four orders of magnitudes between taxa despite the use of similar amounts of biomass. Our metabarcoding approach yielded reliable results for high-throughput assessments. However, the results indicated that primer efficiency is highly species-specific, which would prevent straightforward assessments of species abundance and biomass in a sample. Thus, PCR

  19. Antimicrobial susceptibility determined by the E test, Löwenstein-Jensen proportion, and DNA sequencing methods among Mycobacterium tuberculosis isolates discrepancies, preliminary results

    Directory of Open Access Journals (Sweden)

    Maria Inês Moura Freixo

    2004-02-01

    Full Text Available Mycobacterium tuberculosis strains resistant to streptomycin (SM, isoniazid (INH, and/or rifampin (RIF as determined by the conventional Löwenstein-Jensen proportion method (LJPM were compared with the E test, a minimum inhibitory concentration susceptibility method. Discrepant isolates were further evaluated by BACTEC and by DNA sequence analyses for mutations in genes most often associated with resistance to these drugs (rpsL, katG, inhA, and rpoB. Preliminary discordant E test results were seen in 75% of isolates resistant to SM and in 11% to INH. Discordance improved for these two drugs (63% for SM and none for INH when isolates were re-tested but worsened for RIF (30%. Despite good agreement between phenotypic results and sequencing analyses, wild type profiles were detected on resistant strains mainly for SM and INH. It should be aware that susceptible isolates according to molecular methods might contain other mechanisms of resistance. Although reproducibility of the LJPM susceptibility method has been established, variable E test results for some M. tuberculosis isolates poses questions regarding its reproducibility particularly the impact of E test performance which may vary among laboratories despite adherence to recommended protocols. Further studies must be done to enlarge the evaluated samples and looked possible mutations outside of the hot spot sequenced gene among discrepant strains.

  20. MODELS OF HOURLY DRY BULB TEMPERATURE AND ...

    African Journals Online (AJOL)

    Hourly meteorological data of both dry bulb temperature and relative humidity for 18 locations in Nigeria for the period 1995 to 2009 were analysed to obtain the mean monthly average and monthly hourly average of each of the two meteorological variables for each month for each location. The difference between the ...

  1. Giardia telomeric sequence d(TAGGG)4 forms two intramolecular G-quadruplexes in K+ solution: effect of loop length and sequence on the folding topology.

    Science.gov (United States)

    Hu, Lanying; Lim, Kah Wai; Bouaziz, Serge; Phan, Anh Tuân

    2009-11-25

    Recently, it has been shown that in K(+) solution the human telomeric sequence d[TAGGG(TTAGGG)(3)] forms a (3 + 1) intramolecular G-quadruplex, while the Bombyx mori telomeric sequence d[TAGG(TTAGG)(3)], which differs from the human counterpart only by one G deletion in each repeat, forms a chair-type intramolecular G-quadruplex, indicating an effect of G-tract length on the folding topology of G-quadruplexes. To explore the effect of loop length and sequence on the folding topology of G-quadruplexes, here we examine the structure of the four-repeat Giardia telomeric sequence d[TAGGG(TAGGG)(3)], which differs from the human counterpart only by one T deletion within the non-G linker in each repeat. We show by NMR that this sequence forms two different intramolecular G-quadruplexes in K(+) solution. The first one is a novel basket-type antiparallel-stranded G-quadruplex containing two G-tetrads, a G x (A-G) triad, and two A x T base pairs; the three loops are consecutively edgewise-diagonal-edgewise. The second one is a propeller-type parallel-stranded G-quadruplex involving three G-tetrads; the three loops are all double-chain-reversal. Recurrence of several structural elements in the observed structures suggests a "cut and paste" principle for the design and prediction of G-quadruplex topologies, for which different elements could be extracted from one G-quadruplex and inserted into another.

  2. Hourly cooling load prediction of a vehicle in the southern region of Turkey by Artificial Neural Network

    International Nuclear Information System (INIS)

    Solmaz, Ozgur; Ozgoren, Muammer; Aksoy, Muharrem Hilmi

    2014-01-01

    Highlights: • An ANN model was developed to predict hourly cooling load of a vehicle. • Hourly meteorological data of 5 different provinces was used. • The agreement of the cooling load values between the calculations and predictions was fairly promising. • The ANN model could be successfully used to design automotive air conditioning systems. - Abstract: In this study, Artificial Neural Networks (ANNs) method for prediction hourly cooling load of a vehicle was implemented. The cooling load of the vehicle was calculated along the cooling season (1 May–30 September) for Antalya, Konya, Mersin, Mugla and Sanliurfa provinces in Turkey. For ANN model, seven neurons determinated as input signals of latitude, longitude, altitude, day of the year, hour of the day, hourly mean ambient air temperature and hourly solar radiation were used for the input layer of the network. One neuron producing an output signal of the hourly cooling load was utilized in the output layer. All data were divided into two categories for training and testing of the ANN. The 80% of the data was reserved to training and the remaining was used for testing of the model. Neuron numbers in the hidden layer from 7 to 40 were tested step by step to find the best matching ANN structure. The obtained results for different numbers of neurons were compared in terms of root mean squared error (RMSE), coefficient of determination (R 2 ) and mean absolute error (MAE). The best matching results for the training and testing were obtained as 8 neurons for the minimum testing RMSE value for the prediction of cooling load by the ANN model on the 23rd day of each month along the cooling season. For the model with 8 neurons RMSE, R 2 and MAE (Training/Testing) were found to be 0.0128/0.0259, 0.9959/0.9818 and 78.81/174.71 W/m 2 , respectively. It is shown that the cooling load of a vehicle can be successfully predicted by means of the ANNs from geographical characteristics and meteorological data

  3. Testing two novel stump-lifting heads in a final felling Norway spruce stand

    Energy Technology Data Exchange (ETDEWEB)

    Kaerhae, K. (Metsaeteho Oy, Helsinki (Finland)), Email: kalle.karha@metsateho.fi; Mutikainen, A. (TTS Research, Rajamaeki (Finland)), Email: arto.mutikainen@tts.fi

    2009-07-01

    The use of stump and root wood chips has increased very rapidly in the 21st century in Finland: in the year 2000, the total consumption of stump wood chips for energy generation was 10 GWh, while in 2008 it was around 1.2 TWh. Metsaeteho Oy and TTS Research tested two new stump-lifting devices for lifting stumps in a final felling Norway spruce (picea abies) stand. In the time study with the Vaekevae Stump Processor lifting head, the productivity of stump lifting was 7,5 m3 / E{sub 0}-hour when lifting spruce stumps with a diameter of 30 cm from clayey soil, and 8.3 m3 /E{sub 0}-hour when lifting spruce stumps from sandy soil. When lifting stumps with a diameter of 40 cm, the stump-lifting productivity was 9.0 m3 /E{sub 0}-h (clay) and 10,5 m3 / E{sub 0}-h (sand). The results of this relatively restricted test indicated that the Vaekevae Stump Processor is s reliable and effective stump-lifting head that enables the harvesting of high-quality stump raw material for energy generation. The stump lifting productivity of the other lifting head (Jaervinen) was lower than that of the Vaekevae Strump Processor. Some development suggestions for the Jaervinen lifting head were presented and discussed. (orig.)

  4. Quantification of loading in biomechanical testing: the influence of dissection sequence.

    Science.gov (United States)

    Funabashi, Martha; El-Rich, Marwan; Prasad, Narasimha; Kawchuk, Gregory N

    2015-09-18

    Sequential dissection is a technique used to investigate loads experienced by articular tissues. When the joint of interest is tested in an unconstrained manner, its kinematics change with each tissue removal. To address this limitation, sufficiently rigid robots are used to constrain joint kinematics. While this approach can quantify loads experienced by each tissue, it does not assure similar results when removal order is changed. Specifically, structure loading is assumed to be independent of removal order if the structure behaves linearly (i.e. principle of superposition applies), but dependent on removal order when response is affected by material and/or geometry nonlinearities and/or viscoelasticiy (e.g. biological tissues). Therefore, this experiment was conducted to evaluate if structure loading created through robotic testing is dependent on the order in which connectors are removed. Six identical models were 3D printed. Each model was composed of 2 rigid bodies and 3 connecting structures with nonlinear time-dependent behavior. To these models, pure rotations were applied about a predefined static center of rotation using a parallel robot. A unique dissection sequence was used for each of the six models and the same movements applied robotically after each dissection. When comparing the moments experienced by each structure between different removal sequences, a statistically significant difference (probotic testing are specific to removal order. Copyright © 2015 Elsevier Ltd. All rights reserved.

  5. Neighborhood walkability, income, and hour-by-hour physical activity patterns.

    Science.gov (United States)

    Arvidsson, Daniel; Eriksson, Ulf; Lönn, Sara Larsson; Sundquist, Kristina

    2013-04-01

    This study aimed to investigate both the mean daily physical activity and the hour-by-hour physical activity patterns across the day using accelerometry and how they are associated with neighborhood walkability and individual income. Moderate physical activity (MPA) was assessed by accelerometry in 2252 adults in the city of Stockholm, Sweden. Neighborhood walkability (residential density, street connectivity, and land use mix) was objectively assessed within 1000m network buffers around the participants' residence and individual income was self-reported. Living in a high walkability neighborhood was associated with more mean daily MPA compared with living in a low walkability neighborhood on weekdays and weekend days. Hour-by-hour analyses showed that this association appeared mainly in the afternoon/early evening during weekdays, whereas it appeared across the middle of the day during weekend days. Individual income was associated with mean daily MPA on weekend days. On weekdays, the hour-by-hour analyses showed that high income was associated with more MPA around noon and in late afternoon/early evening, whereas low income was associated with more MPA at the hours before noon and in the early afternoon. During the weekend, high income was more consistently associated with higher MPA. Hour-by-hour accelerometry physical activity patterns provides a more comprehensive picture of the associations between neighborhood walkability and individual income and physical activity and the variability of these associations across the day.

  6. Duty Hour Reporting: Conflicting Values in Professionalism.

    Science.gov (United States)

    Byrne, John M; Loo, Lawrence K; Giang, Dan W

    2015-09-01

    Duty hour limits challenge professional values, sometimes forcing residents to choose between patient care and regulatory compliance. This may affect truthfulness in duty hour reporting. We assessed residents' reasons for falsifying duty hour reports. We surveyed residents in 1 sponsoring institution to explore the reasons for noncompliance, frequency of violations, falsification of reports, and the residents' awareness of the option to extend hours to care for a single patient. The analysis used descriptive statistics. Linear regression was used to explore falsification of duty hour reports by year of training. The response rate was 88% (572 of 650). Primary reasons for duty hour violations were number of patients (19%) and individual patient acuity/complexity (19%). Junior residents were significantly more likely to falsify duty hours (R = -0.966). Of 124 residents who acknowledged falsification, 51 (41%) identified the primary reason as concern that the program will be in jeopardy of violating the Accreditation Council for Graduate Medical Education (ACGME) duty hour limits followed by fear of punishment (34, 27%). This accounted for more than two-thirds of the primary reasons for falsification. Residents' falsification of duty hour data appears to be motivated by concerns about adverse actions from the ACGME, and fear they might be punished. To foster professionalism, we recommend that sponsoring institutions educate residents about professionalism in duty hour reporting. The ACGME should also convey the message that duty hour limits be applied in a no-blame systems-based approach, and allow junior residents to extend duty hours for the care of individual patients.

  7. Reproducibility of two, three, four and five 24-hour recalls in peri ...

    African Journals Online (AJOL)

    2011-06-10

    Jun 10, 2011 ... participants' ability to accurately record or recall food consumption, describe food .... used.16 The accuracy of food item and portion size data captured for ..... Four 24-hour recalls are more practical and cost-effective, and carry.

  8. Evaluation program for secondary spacecraft cells: Initial evaluation tests of General Electric Company 40.0 ampere-hour nickel-cadmium spacecraft cells for the tracking data relay satellite system

    Science.gov (United States)

    Harkness, J. D.

    1978-01-01

    Five cells provided by NASA's Goddard Space Flight Center were evaluated at room temperature and pressure (25 C plus or minus 2 C) with discharges at the 2 hour rate. Measurements of the cell containers following test, indicated an average increase of .006 inches at the plate thickness. Average end of charge voltages and pressures, and capacity output in ampere hours were determined. Three cells exceeded the voltage requirements of 1.52 volts during both c/10 charges at 20 C. All cells exceeded the voltage requirement of 1.52 volts during the 0 C overcharge test, although their end charges were below 1.50 volts. The pressure requirement of 65 psia was exceeded by both pressure transducer cells during c/10 charges at 25 C and 20 C and also during the 0 C overcharge test. The cells with pressure transducers reached a pressure of 20 psia before reaching the voltage limit of 1.550 volts during the pressure versus capacity test, and exhibited a pressure decay of 2 psia during the last 30 minutes of the 1 hour open circuit stand. Average capacity was 51.3 ampere hours.

  9. No Correlation Between Work-Hours and Operative Volumes

    DEFF Research Database (Denmark)

    Kjærgaard, Jane; Sillesen, Martin; Beier-Holgersen, Randi

    2016-01-01

    OBJECTIVE: Since 2003, United States residents have been limited to an 80-hour workweek. This has prompted concerns of reduced educational quality, especially inadequate operating exposure. In contrast, the Danish surgical specialty-training program mandates a cap on working hours of 37 per week....... We hypothesize that there is no direct correlation between work-hours and operative volume achieved during surgical residency. To test the hypothesis, we compare Danish and US operative volumes achieved during surgical residency training. DESIGN: Retrospective comparative study. PARTICIPANTS...... find no difference in overall surgical volumes between Danes and US residents during their surgical training. When time in training was accounted for, differences between weekly surgical volumes achieved were minor, indicating a lack of direct correlation between weekly work-hours and operative volumes...

  10. Human liver phosphatase 2A: cDNA and amino acid sequence of two catalytic subunit isotypes

    International Nuclear Information System (INIS)

    Arino, J.; Woon, Chee Wai; Brautigan, D.L.; Miller, T.B. Jr.; Johnson, G.L.

    1988-01-01

    Two cDNA clones were isolated from a human liver library that encode two phosphatase 2A catalytic subunits. The two cDNAs differed in eight amino acids (97% identity) with three nonconservative substitutions. All of the amino acid substitutions were clustered in the amino-terminal domain of the protein. Amino acid sequence of one human liver clone (HL-14) was identical to the rabbit skeletal muscle phosphatase 2A cDNA (with 97% nucleotide identity). The second human liver clone (HL-1) is encoded by a separate gene, and RNA gel blot analysis indicates that both mRNAs are expressed similarly in several human clonal cell lines. Sequence comparison with phosphatase 1 and 2A indicates highly divergent amino acid sequences at the amino and carboxyl termini of the proteins and identifies six highly conserved regions between the two proteins that are predicted to be important for phosphatase enzymatic activity

  11. Multimodal sequence learning.

    Science.gov (United States)

    Kemény, Ferenc; Meier, Beat

    2016-02-01

    While sequence learning research models complex phenomena, previous studies have mostly focused on unimodal sequences. The goal of the current experiment is to put implicit sequence learning into a multimodal context: to test whether it can operate across different modalities. We used the Task Sequence Learning paradigm to test whether sequence learning varies across modalities, and whether participants are able to learn multimodal sequences. Our results show that implicit sequence learning is very similar regardless of the source modality. However, the presence of correlated task and response sequences was required for learning to take place. The experiment provides new evidence for implicit sequence learning of abstract conceptual representations. In general, the results suggest that correlated sequences are necessary for implicit sequence learning to occur. Moreover, they show that elements from different modalities can be automatically integrated into one unitary multimodal sequence. Copyright © 2015 Elsevier B.V. All rights reserved.

  12. Comparison of two Next Generation sequencing platforms for full genome sequencing of Classical Swine Fever Virus

    DEFF Research Database (Denmark)

    Fahnøe, Ulrik; Pedersen, Anders Gorm; Höper, Dirk

    2013-01-01

    to the consensus sequence. Additionally, we got an average sequence depth for the genome of 4000 for the Iontorrent PGM and 400 for the FLX platform making the mapping suitable for single nucleotide variant (SNV) detection. The analysis revealed a single non-silent SNV A10665G leading to the amino acid change D......Next Generation Sequencing (NGS) is becoming more adopted into viral research and will be the preferred technology in the years to come. We have recently sequenced several strains of Classical Swine Fever Virus (CSFV) by NGS on both Genome Sequencer FLX (GS FLX) and Iontorrent PGM platforms...

  13. Accurate clinical genetic testing for autoinflammatory diseases using the next-generation sequencing platform MiSeq.

    Science.gov (United States)

    Nakayama, Manabu; Oda, Hirotsugu; Nakagawa, Kenji; Yasumi, Takahiro; Kawai, Tomoki; Izawa, Kazushi; Nishikomori, Ryuta; Heike, Toshio; Ohara, Osamu

    2017-03-01

    Autoinflammatory diseases occupy one of a group of primary immunodeficiency diseases that are generally thought to be caused by mutation of genes responsible for innate immunity, rather than by acquired immunity. Mutations related to autoinflammatory diseases occur in 12 genes. For example, low-level somatic mosaic NLRP3 mutations underlie chronic infantile neurologic, cutaneous, articular syndrome (CINCA), also known as neonatal-onset multisystem inflammatory disease (NOMID). In current clinical practice, clinical genetic testing plays an important role in providing patients with quick, definite diagnoses. To increase the availability of such testing, low-cost high-throughput gene-analysis systems are required, ones that not only have the sensitivity to detect even low-level somatic mosaic mutations, but also can operate simply in a clinical setting. To this end, we developed a simple method that employs two-step tailed PCR and an NGS system, MiSeq platform, to detect mutations in all coding exons of the 12 genes responsible for autoinflammatory diseases. Using this amplicon sequencing system, we amplified a total of 234 amplicons derived from the 12 genes with multiplex PCR. This was done simultaneously and in one test tube. Each sample was distinguished by an index sequence of second PCR primers following PCR amplification. With our procedure and tips for reducing PCR amplification bias, we were able to analyze 12 genes from 25 clinical samples in one MiSeq run. Moreover, with the certified primers designed by our short program-which detects and avoids common SNPs in gene-specific PCR primers-we used this system for routine genetic testing. Our optimized procedure uses a simple protocol, which can easily be followed by virtually any office medical staff. Because of the small PCR amplification bias, we can analyze simultaneously several clinical DNA samples with low cost and can obtain sufficient read numbers to detect a low level of somatic mosaic mutations.

  14. 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

  15. Niobium 1 percent zirconium/potassium and titanium/potassium life-test heat pipe design and testing

    Science.gov (United States)

    Sena, J. Tom; Merrigan, Michael A.

    Experimental lifetime performance studies currently in progress use Niobium 1 percent Zirconium (Nb-1Zr) and Titanium (Ti) heat pipes with potassium (K) as the working fluid. A heat pipe life test matrix was developed for testing the heat pipes. Because the corrosion rates in alkali metal heat pipes are affected by temperature and working fluid evaporation flux, the variable parameters of the experimental matrix are established as steady operating temperature and input heat flux density. Total impurity inventory is a factor in corrosion rate so impurity levels are being evaluated in the heat pipe materials before and after testing. Eight Nb-1Zr/K heat pipes were designed, fabricated, and tested. Two of the heat pipes have completed testing whereas the other six are currently in test. These are gravity assist heat pipes operating in a reflux mode. The heat pipes are tested by sets, one set of two and two sets of three heat pipes. Three Ti/K heat pipes are also in life test. These heat pipes are tested as a set in a horizontal position in a capillary pumped annular flow mode. Each of the heat pipes is encapsulated in a quartz vacuum container with a water calorimeter over the vacuum container for power throughput measurements. Thermocouples are attached to the heat pipes for measuring temperature. Heat input to the heat pipes is via an RF coil. The heat pipes are operating at between 800 and 900 K, with heat input fluxes of 13.8 to 30 W/sq cm. Of the Nb-1Zr/K heat pipes, two of the heat pipes have been in operation for 14,000 hours, three over 10,000 hours, and three over 7,000 hours. The Ti/K heat pipes have been in operation for 1,266 hours.

  16. Migration plans and hours of work in Malaysia.

    Science.gov (United States)

    Gillin, E D; Sumner, D A

    1985-01-01

    "This article describes characteristics of prospective migrants in the Malaysian Family Life Survey and investigates how planning to move affects hours of work. [The authors] use ideas about intertemporal substitution...to discuss the response to temporary and permanent wage expectations on the part of potential migrants. [An] econometric section presents reduced-form estimates for wage rates and planned migration equations and two-stage least squares estimates for hours of work. Men currently planning a move were found to work fewer hours. Those originally planning only a temporary stay at their current location work more hours." excerpt

  17. Duty hours and incidents in flight among commercial airline pilots.

    Science.gov (United States)

    O'Hagan, Anna Donnla; Issartel, Johann; Fletcher, Richard; Warrington, Giles

    2016-01-01

    Working long duty hours has often been associated with increased risk of incidents and accidents in transport industries. Despite this, information regarding the intermediate relationship between duty hours and incident risk is limited. This study aimed to test a work hours/incident model to identify the interplay of factors contributing to incidents within the aviation industry. Nine hundred and fifty-four European-registered commercial airline pilots completed a 30-item survey investigating self-report attitudes and experiences of fatigue. Path analysis was used to test the proposed model. The fit indices indicated this to be a good fit model (χ(2) = 11.066, df = 5, p = 0.05; Comparative Fit Index = 0.991; Normed Fit Index = 0.984; Tucker-Lewis Index = 0.962; Root Mean Square of Approximation = 0.036). Highly significant relationships were identified between duty hours and sleep disturbance (r = 0.18, p hours through to self-reported incidents in flight was identified. Further investigation employing both objective and subjective measures of sleep and fatigue is needed.

  18. How extreme is extreme hourly precipitation?

    Science.gov (United States)

    Papalexiou, Simon Michael; Dialynas, Yannis G.; Pappas, Christoforos

    2016-04-01

    The importance of accurate representation of precipitation at fine time scales (e.g., hourly), directly associated with flash flood events, is crucial in hydrological design and prediction. The upper part of a probability distribution, known as the distribution tail, determines the behavior of extreme events. In general, and loosely speaking, tails can be categorized in two families: the subexponential and the hyperexponential family, with the first generating more intense and more frequent extremes compared to the latter. In past studies, the focus has been mainly on daily precipitation, with the Gamma distribution being the most popular model. Here, we investigate the behaviour of tails of hourly precipitation by comparing the upper part of empirical distributions of thousands of records with three general types of tails corresponding to the Pareto, Lognormal, and Weibull distributions. Specifically, we use thousands of hourly rainfall records from all over the USA. The analysis indicates that heavier-tailed distributions describe better the observed hourly rainfall extremes in comparison to lighter tails. Traditional representations of the marginal distribution of hourly rainfall may significantly deviate from observed behaviours of extremes, with direct implications on hydroclimatic variables modelling and engineering design.

  19. Lower wages for less hours? A simultaneous wage-hours model for Germany

    OpenAIRE

    Wolf, Elke

    2000-01-01

    In this paper the impact of working hours on the gross hourly wage rate of West German women is analyzed. We use a simultaneous wage-hours model which takes into account the participation decision. First, our estimates show that the hourly wage rate is strongly a¤ected by the working hours. In order to avoid any assumptions about the functional form, we estimate linear spline functions. Second, we detect di¤erent wage-hours profiles for specific groups of individuals. Despite these di¤erences...

  20. Statistical tests to compare motif count exceptionalities

    Directory of Open Access Journals (Sweden)

    Vandewalle Vincent

    2007-03-01

    Full Text Available Abstract Background Finding over- or under-represented motifs in biological sequences is now a common task in genomics. Thanks to p-value calculation for motif counts, exceptional motifs are identified and represent candidate functional motifs. The present work addresses the related question of comparing the exceptionality of one motif in two different sequences. Just comparing the motif count p-values in each sequence is indeed not sufficient to decide if this motif is significantly more exceptional in one sequence compared to the other one. A statistical test is required. Results We develop and analyze two statistical tests, an exact binomial one and an asymptotic likelihood ratio test, to decide whether the exceptionality of a given motif is equivalent or significantly different in two sequences of interest. For that purpose, motif occurrences are modeled by Poisson processes, with a special care for overlapping motifs. Both tests can take the sequence compositions into account. As an illustration, we compare the octamer exceptionalities in the Escherichia coli K-12 backbone versus variable strain-specific loops. Conclusion The exact binomial test is particularly adapted for small counts. For large counts, we advise to use the likelihood ratio test which is asymptotic but strongly correlated with the exact binomial test and very simple to use.

  1. Sensitive analysis of low-flow parameters using the hourly hydrological model for two mountainous basins in Japan

    Science.gov (United States)

    Fujimura, Kazumasa; Iseri, Yoshihiko; Kanae, Shinjiro; Murakami, Masahiro

    2014-05-01

    Accurate estimation of low flow can contribute to better water resources management and also lead to more reliable evaluation of climate change impacts on water resources. In the early study, the nonlinearity of low flow related to the storage in the basin was suggested by Horton (1937) as the exponential function of Q=KSN, where Q is the discharge, S is the storage, K is a constant and N is the exponent value. In the recent study by Ding (2011) showed the general storage-discharge equation of Q = KNSN. Since the constant K is defined as the fractional recession constant and symbolized as Au by Ando et al. (1983), in this study, we rewrite this equation as Qg=AuNSgN, where Qg is the groundwater runoff and Sg is the groundwater storage. Although this equation was applied to a short-term runoff event of less than 14 hours using the unit hydrograph method by Ding, it was not yet applied for a long-term runoff event including low flow more than 10 years. This study performed a sensitive analysis of two parameters of the constant Au and exponent value N by using the hourly hydrological model for two mountainous basins in Japan. The hourly hydrological model used in this study was presented by Fujimura et al. (2012), which comprise the Diskin-Nazimov infiltration model, groundwater recharge and groundwater runoff calculations, and a direct runoff component. The study basins are the Sameura Dam basin (SAME basin) (472 km2) located in the western Japan which has variability of rainfall, and the Shirakawa Dam basin (SIRA basin) (205km2) located in a region of heavy snowfall in the eastern Japan, that are different conditions of climate and geology. The period of available hourly data for the SAME basin is 20 years from 1 January 1991 to 31 December 2010, and for the SIRA basin is 10 years from 1 October 2003 to 30 September 2013. In the sensitive analysis, we prepared 19900 sets of the two parameters of Au and N, the Au value ranges from 0.0001 to 0.0100 in steps of 0

  2. Determination of maximum physiologic thyroid uptake and correlation with 24-hour RAI uptake value

    International Nuclear Information System (INIS)

    Duldulao, M.; Obaldo, J.

    2007-01-01

    Full text: In hyperthyroid patients, thyroid uptake values are overestimated, sometimes approaching or exceeding 100%. This is physiologically and mathematically impossible. This study was undertaken to determine the maximum physiologic thyroid uptake value through a proposed simple method using a gamma camera. Methodology: Twenty-two patients (17 females and 5 males), with ages ranging from 19-61 y/o (mean age ± SD; 41 ± 12), with 24-hour uptake value of >50%, clinically hyperthyroid and referred for subsequent radioactive iodine therapy were studied. The computed maximum physiologic thyroid uptake was compared with the 24-hour uptake using the paired Student t-test and evaluated using linear regression analysis. Results: The computed physiologic uptake correlated poorly with the 24-hour uptake value. However, in the male subgroup, there was no statistically significant difference between the two (p=0.77). Linear regression analysis gives the following relationship: physiologic uptake (%) = 77.76 - 0.284 (24-hour RAI uptake value). Conclusion: Provided that proper regions of interest are applied with correct attenuation and background subtraction, determination of physiologic thyroid uptake may be obtained using the proposed method. This simple method may be useful prior to I-131 therapy for hyperthyroidism especially when a single uptake determination is performed. (author)

  3. Comparison of pause predictions of two sequence-dependent transcription models

    International Nuclear Information System (INIS)

    Bai, Lu; Wang, Michelle D

    2010-01-01

    Two recent theoretical models, Bai et al (2004, 2007) and Tadigotla et al (2006), formulated thermodynamic explanations of sequence-dependent transcription pausing by RNA polymerase (RNAP). The two models differ in some basic assumptions and therefore make different yet overlapping predictions for pause locations, and different predictions on pause kinetics and mechanisms. Here we present a comprehensive comparison of the two models. We show that while they have comparable predictive power of pause locations at low NTP concentrations, the Bai et al model is more accurate than Tadigotla et al at higher NTP concentrations. The pausing kinetics predicted by Bai et al is also consistent with time-course transcription reactions, while Tadigotla et al is unsuited for this type of kinetic prediction. More importantly, the two models in general predict different pausing mechanisms even for the same pausing sites, and the Bai et al model provides an explanation more consistent with recent single molecule observations

  4. A Comparison of the First Two Sequenced Chloroplast Genomes in Asteraceae: Lettuce and Sunflower

    Energy Technology Data Exchange (ETDEWEB)

    Timme, Ruth E.; Kuehl, Jennifer V.; Boore, Jeffrey L.; Jansen, Robert K.

    2006-01-20

    Asteraceae is the second largest family of plants, with over 20,000 species. For the past few decades, numerous phylogenetic studies have contributed to our understanding of the evolutionary relationships within this family, including comparisons of the fast evolving chloroplast gene, ndhF, rbcL, as well as non-coding DNA from the trnL intron plus the trnLtrnF intergenic spacer, matK, and, with lesser resolution, psbA-trnH. This culminated in a study by Panero and Funk in 2002 that used over 13,000 bp per taxon for the largest taxonomic revision of Asteraceae in over a hundred years. Still, some uncertainties remain, and it would be very useful to have more information on the relative rates of sequence evolution among various genes and on genome structure as a potential set of phylogenetic characters to help guide future phylogenetic structures. By way of contributing to this, we report the first two complete chloroplast genome sequences from members of the Asteraceae, those of Helianthus annuus and Lactuca sativa. These plants belong to two distantly related subfamilies, Asteroideae and Cichorioideae, respectively. In addition to these, there is only one other published chloroplast genome sequence for any plant within the larger group called Eusterids II, that of Panax ginseng (Araliaceae, 156,318 bps, AY582139). Early chloroplast genome mapping studies demonstrated that H. annuus and L. sativa share a 22 kb inversion relative to members of the subfamily Barnadesioideae. By comparison to outgroups, this inversion was shown to be derived, indicating that the Asteroideae and Cichorioideae are more closely related than either is to the Barnadesioideae. Later sequencing study found that taxa that share this 22 kb inversion also contain within this region a second, smaller, 3.3 kb inversion. These sequences also enable an analysis of patterns of shared repeats in the genomes at fine level and of RNA editing by comparison to available EST sequences. In addition, since

  5. Metagenome sequencing of the microbial community of two Brazilian anthropogenic Amazon dark earth sites, Brazil.

    Science.gov (United States)

    Lemos, Leandro Nascimento; de Souza, Rosineide Cardoso; de Souza Cannavan, Fabiana; Patricio, André; Pylro, Victor Satler; Hanada, Rogério Eiji; Mui, Tsai Siu

    2016-12-01

    The Anthropogenic Amazon Dark Earth soil is considered one of the world's most fertile soils. These soils differs from conventional Amazon soils because its higher organic content concentration. Here we describe the metagenome sequencing of microbial communities of two sites of Anthropogenic Amazon Dark Earth soils from Amazon Rainforest, Brazil. The raw sequence data are stored under Short Read Accession number: PRJNA344917.

  6. Multipass mining sequence room closures: In situ data report

    International Nuclear Information System (INIS)

    Munson, D.E.; Jones, R.L.; Northrop-Salazar, C.L.; Woerner, S.J.

    1992-12-01

    During the construction of the Thermal/Structural In Situ Test Rooms at the Waste Isolation Pilot Plant (WIPP) facility, measurements of the salt displacements were obtained at very early times, essentially concurrent with the mining activity. This was accomplished by emplacing manually read closure gage stations directly at the mining face, actually between the face and the mining machine, immediately upon mining of the intended gage location. Typically, these mining sequence closure measurements were taken within one hour of mining of the location and within one meter of the mining face. Readings were taken at these gage stations as the multipass mining continued, with the gage station reestablished as each successive mining pass destroyed the earlier gage points. Data reduction yields the displacement history during the mining operation. These early mining sequence closure data, when combined with the later data of the permanently emplaced closure gages, gives the total time-dependent closure displacements of the test rooms. This complete closure history is an essential part of assuring that the in situ test databases will provide an adequate basis for validation of the predictive technology of salt creep behavior, as required by the WIPP technology development program for disposal of radioactive waste in bedded salt

  7. Job mobility and hours of work: the effect of Dutch legislation

    OpenAIRE

    Fouarge, D.; Baaijens, F P.

    2009-01-01

    Previous research has pointed to the existence of hours constraints on the labour market: not all employees’ preferences with respect to the length of the working week seem to be fulfilled, and changes in the number of working hours often coincide with job mobility. In this paper, we test whether or not a recently introduced Dutch legislation providing employees with the right to adjust working hours within their job has reduced the correlation between changes in working hours and job mobilit...

  8. Separation of the Components of a Commercial Analgesic Tablet: A Two-Week Sequence Comparing Purification by Two-Base Extraction and Column Chromatography

    Science.gov (United States)

    Revell, Kevin D.

    2011-01-01

    A new laboratory experiment is described in which students compare two benchtop separation methods to isolate the three active components of the commercial analgesic Excedrin. In the two-week sequence, aspirin, acetaminophen, and caffeine are separated using either a two-base liquid-liquid extraction or silica column chromatography. Students then…

  9. THE EFFECTS OF 30 HOURS SLEEP DEPRIVATION ON BASIC FOOTBALL SKILLS OF SOCCER PLAYERS

    Directory of Open Access Journals (Sweden)

    Mehrdad Hefzollesan

    2012-08-01

    Full Text Available The aim of this study is to determine the effect of sleep deprivation on the passing and shooting skills of football players. To this end, 18 students of Sahand University, with age range 20 to 24 years performed basic soccer skills (shoot and pass in the pre-test and post test stages. In this study to assess these skills, the test "Mor - Christian" has been used. In the first step, subjects conducted the shoot and pass test as pre-test after 8 hours sleep a night. 10 days later, to ensure the validity of tests and test results on the learning effect, subjects did the same test again after 8 hours sleep a night. In the third stage, 30 hours of sleep deprivation as an independent variable imposed on the subjects and then the test was repeated and experimental test results were compared as recorded using paired t-test. The findings showed that 30 hour sleep deprivation decreases passing and shooting skills implementation skills (p <0.001. Therefore, the findings showed that sleep deprivation can be a devastating effect on basic football skills.

  10. Quality Control Test for Sequence-Phenotype Assignments

    Science.gov (United States)

    Ortiz, Maria Teresa Lara; Rosario, Pablo Benjamín Leon; Luna-Nevarez, Pablo; Gamez, Alba Savin; Martínez-del Campo, Ana; Del Rio, Gabriel

    2015-01-01

    Relating a gene mutation to a phenotype is a common task in different disciplines such as protein biochemistry. In this endeavour, it is common to find false relationships arising from mutations introduced by cells that may be depurated using a phenotypic assay; yet, such phenotypic assays may introduce additional false relationships arising from experimental errors. Here we introduce the use of high-throughput DNA sequencers and statistical analysis aimed to identify incorrect DNA sequence-phenotype assignments and observed that 10–20% of these false assignments are expected in large screenings aimed to identify critical residues for protein function. We further show that this level of incorrect DNA sequence-phenotype assignments may significantly alter our understanding about the structure-function relationship of proteins. We have made available an implementation of our method at http://bis.ifc.unam.mx/en/software/chispas. PMID:25700273

  11. Genome sequences of two Leuconostoc pseudomesenteroides strains isolated from Danish dairy starter cultures

    DEFF Research Database (Denmark)

    Pedersen, Thomas Bæk; Kot, Witold Piotr; Hansen, L.H.

    2014-01-01

    The lactic acid bacterium Leuconostoc pseudomesenteroides can be found in mesophilic cheese starters, where it produces aromatic compounds from, e.g., citrate. Here, we present the draft genome sequences of two L. pseudomesenteroides strains isolated from traditional Danish cheese starters....

  12. Source terms associated with two severe accident sequences in a 900 MWe PWR

    International Nuclear Information System (INIS)

    Fermandjian, J.; Evrard, J.M.; Berthion, Y.; Lhiaubet, G.; Lucas, M.

    1983-12-01

    Hypothetical accidents taken into account in PWR risk assessment result in fission product release from the fuel, transfer through the primary circuit, transfer into the reactor containment building (RCB) and finally release to the environment. The objective of this paper is to define the characteristics of the source term (noble gases, particles and volatile iodine forms) released from the reactor containment building during two dominant core-melt accident sequences: S 2 CD and TLB according to the ''Reactor Safety Study'' terminology. The reactor chosen for this study is a French 900 MWe PWR unit. The reactor building is a prestressed concrete containment with an internal liner. The first core-melt accident sequence is a 2-break loss-of-coolant accident on the cold leg, with failure of both system and the containment spray system. The second one is a transient initiated by a loss of offsite and onsite power supply and auxiliary feedwater system. These two sequences have been chosen because they are representative of risk dominant scenarios. Source terms associated with hypothetical core-melt accidents S 2 CD and TLB in a French PWR -900 MWe- have been performed using French computer codes (in particular, JERICHO Code for containment response analysis and AEROSOLS/31 for aerosol behavior in the containment)

  13. Processing and Characterization of Thousand-Hour 500 C Durable 4H-SiC JFET Integrated Circuits

    Science.gov (United States)

    Spry, David J.; Neudeck, Philip G.; Chen, Liangyu; Lukco, Dorothy; Chang, Carl W.; Beheim, Glenn M.; Krasowski, Michael J.; Prokop, Norman F.

    2016-01-01

    This work reports fabrication and testing of integrated circuits (ICs) with two levels of interconnect that consistently achieve greater than 1000 hours of stable electrical operation at 500 C in air ambient. These ICs are based on 4H-SiC junction field effect transistor (JFET) technology that integrates hafnium ohmic contacts with TaSi2 interconnects and SiO2 and Si3N4 dielectric layers over 1-m scale vertical topology. Following initial burn-in, important circuit parameters remain stable for more than 1000 hours of 500 C operational testing. These results advance the technology foundation for realizing long-term durable 500 C ICs with increased functional capability for sensing and control combustion engine, planetary, deep-well drilling, and other harsh-environment applications.

  14. 24 Hours of Sleep, Sedentary Behavior, and Physical Activity with Nine Wearable Devices

    Science.gov (United States)

    Rosenberger, Mary E.; Buman, Matthew P.; Haskell, William L.; McConnell, Michael V.; Carstensen, Laura L.

    2015-01-01

    Getting enough sleep, exercising and limiting sedentary activities can greatly contribute to disease prevention and overall health and longevity. Measuring the full 24-hour activity cycle - sleep, sedentary behavior (SED), light intensity physical activity (LPA) and moderate-to-vigorous physical activity (MVPA) - may now be feasible using small wearable devices. PURPOSE This study compares nine devices for accuracy in 24-hour activity measurement. METHODS Adults (N=40, 47% male) wore nine devices for 24-hours: Actigraph GT3X+, activPAL, Fitbit One, GENEactiv, Jawbone Up, LUMOback, Nike Fuelband, Omron pedometer, and Z-Machine. Comparisons (to standards) were made for total sleep time (Z-machine), time spent in SED (activPAL), LPA (GT3x+), MVPA (GT3x+), and steps (Omron). Analysis included mean absolute percent error, equivalence testing, and Bland-Altman plots. RESULTS Error rates ranged from 8.1–16.9% for sleep; 9.5–65.8% for SED; 19.7–28.0% for LPA; 51.8–92% for MVPA; and 14.1–29.9% for steps. Equivalence testing indicated only two comparisons were significantly equivalent to standards: the LUMOback for sedentary behavior and the GT3X+ for sleep. Bland-Altman plots indicated GT3X+ had the closest measurement for sleep, LUMOback for sedentary behavior, GENEactiv for LPA, Fitbit for MVPA and GT3X+ for steps. CONCLUSIONS Currently, no device accurately captures activity data across the entire 24-hour day, but the future of activity measurement should aim for accurate 24-hour measurement as a goal. Researchers should continue to select measurement devices based on their primary outcomes of interest. PMID:26484953

  15. Humans can consciously generate random number sequences: a possible test for artificial intelligence.

    Science.gov (United States)

    Persaud, Navindra

    2005-01-01

    Computer algorithms can only produce seemingly random or pseudorandom numbers whereas certain natural phenomena, such as the decay of radioactive particles, can be utilized to produce truly random numbers. In this study, the ability of humans to generate random numbers was tested in healthy adults. Subjects were simply asked to generate and dictate random numbers. Generated numbers were tested for uniformity, independence and information density. The results suggest that humans can generate random numbers that are uniformly distributed, independent of one another and unpredictable. If humans can generate sequences of random numbers then neural networks or forms of artificial intelligence, which are purported to function in ways essentially the same as the human brain, should also be able to generate sequences of random numbers. Elucidating the precise mechanism by which humans generate random number sequences and the underlying neural substrates may have implications in the cognitive science of decision-making. It is possible that humans use their random-generating neural machinery to make difficult decisions in which all expected outcomes are similar. It is also possible that certain people, perhaps those with neurological or psychiatric impairments, are less able or unable to generate random numbers. If the random-generating neural machinery is employed in decision making its impairment would have profound implications in matters of agency and free will.

  16. Identification and characterization of two novel bla(KLUC resistance genes through large-scale resistance plasmids sequencing.

    Directory of Open Access Journals (Sweden)

    Teng Xu

    Full Text Available Plasmids are important antibiotic resistance determinant carriers that can disseminate various drug resistance genes among species or genera. By using a high throughput sequencing approach, two groups of plasmids of Escherichia coli (named E1 and E2, each consisting of 160 clinical E. coli strains isolated from different periods of time were sequenced and analyzed. A total of 20 million reads were obtained and mapped onto the known resistance gene sequences. As a result, a total of 9 classes, including 36 types of antibiotic resistant genes, were identified. Among these genes, 25 and 27 single nucleotide polymorphisms (SNPs appeared, of which 9 and 12 SNPs are nonsynonymous substitutions in the E1 and E2 samples. It is interesting to find that a novel genotype of bla(KLUC, whose close relatives, bla(KLUC-1 and bla(KLUC-2, have been previously reported as carried on the Kluyvera cryocrescens chromosome and Enterobacter cloacae plasmid, was identified. It shares 99% and 98% amino acid identities with Kluc-1 and Kluc-2, respectively. Further PCR screening of 608 Enterobacteriaceae family isolates yielded a second variant (named bla(KLUC-4. It was interesting to find that Kluc-3 showed resistance to several cephalosporins including cefotaxime, whereas bla(KLUC-4 did not show any resistance to the antibiotics tested. This may be due to a positively charged residue, Arg, replaced by a neutral residue, Leu, at position 167, which is located within an omega-loop. This work represents large-scale studies on resistance gene distribution, diversification and genetic variation in pooled multi-drug resistance plasmids, and provides insight into the use of high throughput sequencing technology for microbial resistance gene detection.

  17. Immunoglobulin variable region sequences of two human monoclonal antibodies directed to an onco-developmental carbohydrate antigen, lactotetraosylceramide (LcOse4Cer).

    Science.gov (United States)

    Yago, K; Zenita, K; Ohwaki, I; Harada, R; Nozawa, S; Tsukazaki, K; Iwamori, M; Endo, N; Yasuda, N; Okuma, M

    1993-11-01

    A human monoclonal antibody, 11-50, was generated and was shown to recognize an onco-developmental carbohydrate antigen, LcOse4Cer. The isotype of this antibody was IgM, lambda, similar to the previously known human anti-LcOse4 antibodies, such as IgMWOO and HMST-1. We raised a murine anti-idiotypic antibody G3 (IgG1, kappa) against 11-50, and tested its reactivity towards the affinity purified human polyclonal anti-LcOse4 antibodies prepared from pooled human sera using a Gal beta 1-->3GlcNAc beta-immobilized column. The results indicated that at least a part of the human polyclonal anti-LcOse4 antibodies shared the G3 idiotype with 11-50. We further analyzed the sequence of variable regions of the two anti-LcOse4 antibodies, 11-50 and HMST-1. Sequence analysis of the heavy chain variable regions indicated that the VH regions of these two antibodies were highly homologous to each other (93.5% at the nucleic acid level), and these antibodies utilized the germline genes VH1.9III and hv3005f3 as the VH segments, which are closely related germline genes of the VHIII family. It was noted that these germline VH genes are frequently utilized in fetal B cells. The JH region of both antibodies was encoded by the JH4 gene. For the light chain, the V lambda segments of the two antibodies were 96.3% homologous to each other at the nucleic acid level. The V lambda segments of both antibodies showed the highest homology to the rearranged V lambda gene called V lambda II.DS among reported V lambda genes, while the exact germline V lambda genes encoding the two antibodies were not yet registered in available sequence databanks. The amino acid sequences of the J lambda segments of both antibodies were identical. These results indicate that the two human antibodies recognizing the onco-developmental carbohydrate antigen Lc4 are encoded by the same or very homologous germline genes.

  18. Statistical approaches to use a model organism for regulatory sequences annotation of newly sequenced species.

    Directory of Open Access Journals (Sweden)

    Pietro Liò

    Full Text Available A major goal of bioinformatics is the characterization of transcription factors and the transcriptional programs they regulate. Given the speed of genome sequencing, we would like to quickly annotate regulatory sequences in newly-sequenced genomes. In such cases, it would be helpful to predict sequence motifs by using experimental data from closely related model organism. Here we present a general algorithm that allow to identify transcription factor binding sites in one newly sequenced species by performing Bayesian regression on the annotated species. First we set the rationale of our method by applying it within the same species, then we extend it to use data available in closely related species. Finally, we generalise the method to handle the case when a certain number of experiments, from several species close to the species on which to make inference, are available. In order to show the performance of the method, we analyse three functionally related networks in the Ascomycota. Two gene network case studies are related to the G2/M phase of the Ascomycota cell cycle; the third is related to morphogenesis. We also compared the method with MatrixReduce and discuss other types of validation and tests. The first network is well known and provides a biological validation test of the method. The two cell cycle case studies, where the gene network size is conserved, demonstrate an effective utility in annotating new species sequences using all the available replicas from model species. The third case, where the gene network size varies among species, shows that the combination of information is less powerful but is still informative. Our methodology is quite general and could be extended to integrate other high-throughput data from model organisms.

  19. Purification of infectious adenovirus in two hours by ultracentrifugation and tangential flow filtration

    International Nuclear Information System (INIS)

    Ugai, Hideyo; Yamasaki, Takahito; Hirose, Megumi; Inabe, Kumiko; Kujime, Yukari; Terashima, Miho; Liu, Bingbing; Tang, Hong; Zhao, Mujun; Murata, Takehide; Kimura, Makoto; Pan, Jianzhi; Obata, Yuichi; Hamada, Hirofumi; Yokoyama, Kazunari K.

    2005-01-01

    Adenoviruses are excellent vectors for gene transfer and are used extensively for high-level expression of the products of transgenes in living cells. The development of simple and rapid methods for the purification of stable infectious recombinant adenoviruses (rAds) remains a challenge. We report here a method for the purification of infectious adenovirus type 5 (Ad5) that involves ultracentrifugation on a cesium chloride gradient at 604,000g for 15 min at 4 deg C and tangential flow filtration. The entire procedure requires less than two hours and infectious Ad5 can be recovered at levels higher than 64% of the number of plaque-forming units (pfu) in the initial crude preparation of viruses. We have obtained titers of infectious purified Ad5 of 1.35 x 10 10 pfu/ml and a ratio of particle titer to infectious titer of seven. The method described here allows the rapid purification of rAds for studies of gene function in vivo and in vitro, as well as the rapid purification of Ad5

  20. Two different groups of signal sequence in M-superfamily conotoxins.

    Science.gov (United States)

    Wang, Qi; Jiang, Hui; Han, Yu-Hong; Yuan, Duo-Duo; Chi, Cheng-Wu

    2008-04-01

    M-superfamily conotoxins can be divided into four branches (M-1, M-2, M-3 and M-4) according to the number of amino acid residues in the third Cys loop. In general, it is widely accepted that the conotoxin signal peptides of each superfamily are strictly conserved. Recently, we cloned six cDNAs of novel M-superfamily conotoxins from Conus leopardus, Conus marmoreus and Conus quercinus, belonging to either M-1 or M-3 branch. These conotoxins, judging from the putative peptide sequences deducted from cDNAs, are rich in acidic residues and share highly conserved signal and pro-peptide region. However, they are quite different from the reported conotoxins of M-2 and M-4 branches even in their signal peptides, which in general are considered highly conserved for each superfamily of conotoxins. The signal sequences of M-1 and M-3 conotoxins composed of 24 residues start with MLKMGVVL-, while those of M-2 and M-4 conotoxins composed of 25 residues start with MMSKLGVL-. It is another example that different types of signal peptides can exist within a superfamily besides the I-conotoxin superfamily. In addition to the different disulfide connectivity of M-1 conotoxins from that of M-4 or M-2 conotoxins, the sequence alignment, preferential Cys codon usage and phylogenetic tree analysis suggest that M-1 and M-3 conotoxins have much closer relationship, being different from the conotoxins of other two branches (M-4 and M-2) of M-superfamily.

  1. Towards Point-of-Care Diagnosis of Pulmonary Tuberculosis and Drug Susceptibility Testing by Whole Genome Sequencing of DNA Isolated from Sputum

    Directory of Open Access Journals (Sweden)

    Kayzad S. Nilgiriwala

    2017-12-01

    Full Text Available Preliminary screening of pulmonary tuberculosis (TB in India still relies on sputum microscopy, which has low sensitivity leading to high rate of false negatives. Moreover, conventional phenotypic drug susceptibility testing (DST is conducted over a period of weeks leading to delays in correct treatment. Next generation sequencing technologies (Illumina and Oxford Nanopore have made it possible to sequence miniscule amount of DNA and generate enough data within a day for detecting specific microbes and their DST profile. Sputum samples from two pulmonary TB patients were processed by decontamination and DNA was isolated from the decontaminated sputum sediments. The isolated DNA was used for sequencing by Illumina and by MinION (Oxford Nanopore Technologies. The sequence data was used to diagnose TB and to determine the DST profiles for the first- and second-line drugs by Mykrobe Predictor. Validation was conducted by sequencing DNA (by Illumina isolated from pure growth culture from both the samples individually. DNA sequencing data (for both, Ilumina and MinION from one of the sputum samples indicated the presence of Mycobacterium tuberculosis (M. tb resistant to streptomycin, isoniazid, rifampicin and ethambutol and its lineage was predicted to be Beijing East Asia. The second sample indicated the presence of M. tb sensitive to the first- and second-line drugs by MinION and showed minor resistance call only to rifampicin by Illumina. Lineage of the second sample was predicted to be East Africa Indian Ocean, whereas Illumina data indicated it to be Delhi Central Asia. The two samples were correctly diagnosed for the presence of M. tb in the sputum DNA. Their DST profiles and lineage were also successfully determined from both the sequencing platforms (with minor discrepancies paving the way towards diagnosis and DST of TB from DNA isolated from sputum samples at point-of-care. Nanopore sequencing currently requires skilled personnel for DNA

  2. Two sequence motifs from HIF-1α bind to the DNA-binding site of p53

    OpenAIRE

    Hansson, Lars O.; Friedler, Assaf; Freund, Stefan; Rüdiger, Stefan; Fersht, Alan R.

    2002-01-01

    There is evidence that hypoxia-inducible factor-1α (HIF-1α) interacts with the tumor suppressor p53. To characterize the putative interaction, we mapped the binding of the core domain of p53 (p53c) to an array of immobilized HIF-1α-derived peptides and found two peptide-sequence motifs that bound to p53c with micromolar affinity in solution. One sequence was adjacent to and the other coincided with the two proline residues of the oxygen-dependent degradation domain (P402 and P564) that act as...

  3. Molecular diagnosis of Usher syndrome: application of two different next generation sequencing-based procedures.

    Directory of Open Access Journals (Sweden)

    Danilo Licastro

    Full Text Available Usher syndrome (USH is a clinically and genetically heterogeneous disorder characterized by visual and hearing impairments. Clinically, it is subdivided into three subclasses with nine genes identified so far. In the present study, we investigated whether the currently available Next Generation Sequencing (NGS technologies are already suitable for molecular diagnostics of USH. We analyzed a total of 12 patients, most of which were negative for previously described mutations in known USH genes upon primer extension-based microarray genotyping. We enriched the NGS template either by whole exome capture or by Long-PCR of the known USH genes. The main NGS sequencing platforms were used: SOLiD for whole exome sequencing, Illumina (Genome Analyzer II and Roche 454 (GS FLX for the Long-PCR sequencing. Long-PCR targeting was more efficient with up to 94% of USH gene regions displaying an overall coverage higher than 25×, whereas whole exome sequencing yielded a similar coverage for only 50% of those regions. Overall this integrated analysis led to the identification of 11 novel sequence variations in USH genes (2 homozygous and 9 heterozygous out of 18 detected. However, at least two cases were not genetically solved. Our result highlights the current limitations in the diagnostic use of NGS for USH patients. The limit for whole exome sequencing is linked to the need of a strong coverage and to the correct interpretation of sequence variations with a non obvious, pathogenic role, whereas the targeted approach suffers from the high genetic heterogeneity of USH that may be also caused by the presence of additional causative genes yet to be identified.

  4. Molecular Diagnosis of Usher Syndrome: Application of Two Different Next Generation Sequencing-Based Procedures

    Science.gov (United States)

    Licastro, Danilo; Mutarelli, Margherita; Peluso, Ivana; Neveling, Kornelia; Wieskamp, Nienke; Rispoli, Rossella; Vozzi, Diego; Athanasakis, Emmanouil; D'Eustacchio, Angela; Pizzo, Mariateresa; D'Amico, Francesca; Ziviello, Carmela; Simonelli, Francesca; Fabretto, Antonella; Scheffer, Hans; Gasparini, Paolo; Banfi, Sandro; Nigro, Vincenzo

    2012-01-01

    Usher syndrome (USH) is a clinically and genetically heterogeneous disorder characterized by visual and hearing impairments. Clinically, it is subdivided into three subclasses with nine genes identified so far. In the present study, we investigated whether the currently available Next Generation Sequencing (NGS) technologies are already suitable for molecular diagnostics of USH. We analyzed a total of 12 patients, most of which were negative for previously described mutations in known USH genes upon primer extension-based microarray genotyping. We enriched the NGS template either by whole exome capture or by Long-PCR of the known USH genes. The main NGS sequencing platforms were used: SOLiD for whole exome sequencing, Illumina (Genome Analyzer II) and Roche 454 (GS FLX) for the Long-PCR sequencing. Long-PCR targeting was more efficient with up to 94% of USH gene regions displaying an overall coverage higher than 25×, whereas whole exome sequencing yielded a similar coverage for only 50% of those regions. Overall this integrated analysis led to the identification of 11 novel sequence variations in USH genes (2 homozygous and 9 heterozygous) out of 18 detected. However, at least two cases were not genetically solved. Our result highlights the current limitations in the diagnostic use of NGS for USH patients. The limit for whole exome sequencing is linked to the need of a strong coverage and to the correct interpretation of sequence variations with a non obvious, pathogenic role, whereas the targeted approach suffers from the high genetic heterogeneity of USH that may be also caused by the presence of additional causative genes yet to be identified. PMID:22952768

  5. Long working hours and physical activity.

    Science.gov (United States)

    Angrave, David; Charlwood, Andy; Wooden, Mark

    2015-08-01

    It is widely believed that persons employed in jobs demanding long working hours are at greater risk of physical inactivity than other workers, primarily because they have less leisure time available to undertake physical activity. The aim of this study was to test this hypothesis using prospective data obtained from a nationally representative sample of employed persons. Longitudinal data from the Household, Income and Labour Dynamics in Australia Survey (93,367 observations from 17,893 individuals) were used to estimate conditional fixed effects logistic regression models of the likelihood of moderate or vigorous physical exercise for at least 30 min, at least four times a week. No significant associations between long working hours and the incidence of healthy levels of physical activity were uncovered once other exogenous influences on activity levels were controlled for. The odds of men or women who usually work 60 or more hours per week exercising at healthy levels were 6% and 11% less, respectively, than those of comparable persons working a more standard 35-40 h/week; however, neither estimate was significantly different from 0 at 95% CI. The findings suggest that there is no trade-off between long working hours and physical activity in Australia. It is argued that these findings are broadly consistent with previous research studies from Anglo-Saxon countries (where long working hours are pervasive) that employed large nationally representative samples. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

  6. Quantitation of 24-Hour Moisturization by Electrical Measurements of Skin Hydration.

    Science.gov (United States)

    Wickett, R Randall; Damjanovic, Bronson

    The purpose of this study was to quantify the effects of several moisturizers on hydration of the stratum corneum by measuring their effect on electrical conductance over a 24-hour period. Double-blind, randomized controlled trial. Twenty-five healthy female volunteers aged 18 to 65 years with dry skin on the lower legs and no other known dermatologic pathology participated in the study. Additional exclusion criteria were pregnant or taking anti-inflammatory steroids. The study was carried out in a clinical research facility in Winnipeg, Manitoba, Canada. Subjects underwent a 3-day conditioning period using a natural soap bar on the lower legs and no application of moisturizer to the skin. Participants then came to the test site and equilibrated for at least 30 minutes under controlled conditions of temperature and humidity. After baseline hydration measurements on test sites on the lower legs of each subject, a single application of each of 5 test products at a dose of 2 mg/cm was made. Skin hydration was assessed by electrical conductance measurements with a specialized probe. The probe was briefly placed on the skin surface with light pressure, and the measurement recorded in units of microsiemens (μS). Conductance was measured at 2, 4, 6, 8, and 24 hours after product applications. Although all but 1 of the test products increased conductance at 2 hours, only 2 moisturizers containing high levels of glycerin (products C and E) maintained increased conductance relative to baseline at 24 hours, +37.8 (P skin conductance for at least 24 hours after a single application.

  7. Accurate clinical genetic testing for autoinflammatory diseases using the next-generation sequencing platform MiSeq

    Directory of Open Access Journals (Sweden)

    Manabu Nakayama

    2017-03-01

    Full Text Available Autoinflammatory diseases occupy one of a group of primary immunodeficiency diseases that are generally thought to be caused by mutation of genes responsible for innate immunity, rather than by acquired immunity. Mutations related to autoinflammatory diseases occur in 12 genes. For example, low-level somatic mosaic NLRP3 mutations underlie chronic infantile neurologic, cutaneous, articular syndrome (CINCA, also known as neonatal-onset multisystem inflammatory disease (NOMID. In current clinical practice, clinical genetic testing plays an important role in providing patients with quick, definite diagnoses. To increase the availability of such testing, low-cost high-throughput gene-analysis systems are required, ones that not only have the sensitivity to detect even low-level somatic mosaic mutations, but also can operate simply in a clinical setting. To this end, we developed a simple method that employs two-step tailed PCR and an NGS system, MiSeq platform, to detect mutations in all coding exons of the 12 genes responsible for autoinflammatory diseases. Using this amplicon sequencing system, we amplified a total of 234 amplicons derived from the 12 genes with multiplex PCR. This was done simultaneously and in one test tube. Each sample was distinguished by an index sequence of second PCR primers following PCR amplification. With our procedure and tips for reducing PCR amplification bias, we were able to analyze 12 genes from 25 clinical samples in one MiSeq run. Moreover, with the certified primers designed by our short program—which detects and avoids common SNPs in gene-specific PCR primers—we used this system for routine genetic testing. Our optimized procedure uses a simple protocol, which can easily be followed by virtually any office medical staff. Because of the small PCR amplification bias, we can analyze simultaneously several clinical DNA samples with low cost and can obtain sufficient read numbers to detect a low level of

  8. 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.

  9. Complete genome sequences of two strains of the meat spoilage bacterium Brochothrix thermosphacta isolated from ground chicken

    Science.gov (United States)

    Brochothrix thermosphacta is an important meat spoilage bacterium. Here we report the genome sequences of two strains of B. thermosphacta isolated from ground chicken. The genome sequences were determined using long-read PacBio single-molecule real-time (SMRT©) technology and are the first complete ...

  10. Pharmacokinetic equivalence study of two formulations of the anticonvulsant pregabalin

    Directory of Open Access Journals (Sweden)

    Tjandrawinata RR

    2015-04-01

    Full Text Available Raymond R Tjandrawinata,1 Effi Setiawati,2 Ratih Sofia Ika Putri,2 Vincent Angga Gunawan,2 Fenny Ong,1 Liana W Susanto,1 Dwi Nofiarny11Dexa Laboratories of Biomolecular Sciences, Cikarang, West Java, Indonesia; 2PT Equilab International Bioavailability and Bioequivalence Laboratory, Jakarta, IndonesiaPurpose: The present study was conducted to evaluate whether the bioavailability of pregabalin capsules 150 mg manufactured by PT Dexa Medica was equivalent to the reference formulation.Methods: This was a randomized, open-label, two-period, two-sequence, and crossover study under fasting condition, with a 1-week washout period. Plasma concentrations of pregabalin from 20 subjects were determined by using a validated liquid chromatography with tandem mass spectrometry (LC-MS/MS detection method. Pharmacokinetic parameters assessed in this study were: area under the plasma concentration–time curve from time zero to last observed quantifiable concentration (AUC0–t, area under the plasma concentration–time curve from time zero to infinity (AUC0–∞, maximum plasma concentration (Cmax, time to maximum plasma concentration (tmax, and terminal half-life (t1/2. The 90% confidence intervals (CIs for the geometric mean ratios of test formulation/reference formulation were calculated for the AUC and Cmax parameters; while tmax difference was analyzed nonparametrically on the original data using the Wilcoxon matched-pairs test, and t1/2 difference was analyzed using Student's paired t-test.Results: The mean (standard deviation [SD] AUC0–t, AUC0–∞, Cmax, and t1/2 of pregabalin from the test formulation were 27,845.86 (4,508.27 ng·h/mL, 28,311.70 (4,790.55 ng·h/mL, 3,999.71 (801.52 ng/mL, and 5.66 (1.20 hours, respectively; while the mean (SD AUC0–t, AUC0–∞, Cmax, and t1/2 of pregabalin from the reference formulation were 27,398.12 (4,266.28 ng·h/mL, 27,904.24 (4,507.31 ng·h/mL, 3,849.50 (814.50 ng/mL, and 5.87 (1.25 hours, respectively

  11. Working Hours and Productivity

    OpenAIRE

    Collewet, Marion; Sauermann, Jan

    2017-01-01

    This paper studies the link between working hours and productivity using daily information on working hours and performance of a sample of call centre agents. We exploit variation in the number of hours worked by the same employee across days and weeks due to central scheduling, enabling us to estimate the effect of working hours on productivity. We find that as the number of hours worked increases, the average handling time for a call increases, meaning that agents become less productive. Th...

  12. Random-effects linear modeling and sample size tables for two special crossover designs of average bioequivalence studies: the four-period, two-sequence, two-formulation and six-period, three-sequence, three-formulation designs.

    Science.gov (United States)

    Diaz, Francisco J; Berg, Michel J; Krebill, Ron; Welty, Timothy; Gidal, Barry E; Alloway, Rita; Privitera, Michael

    2013-12-01

    Due to concern and debate in the epilepsy medical community and to the current interest of the US Food and Drug Administration (FDA) in revising approaches to the approval of generic drugs, the FDA is currently supporting ongoing bioequivalence studies of antiepileptic drugs, the EQUIGEN studies. During the design of these crossover studies, the researchers could not find commercial or non-commercial statistical software that quickly allowed computation of sample sizes for their designs, particularly software implementing the FDA requirement of using random-effects linear models for the analyses of bioequivalence studies. This article presents tables for sample-size evaluations of average bioequivalence studies based on the two crossover designs used in the EQUIGEN studies: the four-period, two-sequence, two-formulation design, and the six-period, three-sequence, three-formulation design. Sample-size computations assume that random-effects linear models are used in bioequivalence analyses with crossover designs. Random-effects linear models have been traditionally viewed by many pharmacologists and clinical researchers as just mathematical devices to analyze repeated-measures data. In contrast, a modern view of these models attributes an important mathematical role in theoretical formulations in personalized medicine to them, because these models not only have parameters that represent average patients, but also have parameters that represent individual patients. Moreover, the notation and language of random-effects linear models have evolved over the years. Thus, another goal of this article is to provide a presentation of the statistical modeling of data from bioequivalence studies that highlights the modern view of these models, with special emphasis on power analyses and sample-size computations.

  13. Molecular diet analysis of two African free-tailed bats (Molossidae) using high throughput sequencing

    DEFF Research Database (Denmark)

    Bohmann, Kristine; Monadjem, Ara; Noer, Christina Lehmkuhl

    2011-01-01

    Given the diversity of prey consumed by insectivorous bats, it is difficult to discern the composition of their diet using morphological or conventional PCR-based analyses of their faeces. We demonstrate the use of a powerful alternate tool, the use of the Roche FLX sequencing platform to deep......-sequence uniquely 5′ tagged insect-generic barcode cytochrome c oxidase I (COI) fragments, that were PCR amplified from faecal pellets of two free-tailed bat species Chaerephon pumilus and Mops condylurus (family: Molossidae). Although the analyses were challenged by the paucity of southern African insect COI...

  14. Assignment of casein kinase 2 alpha sequences to two different human chromosomes

    DEFF Research Database (Denmark)

    Boldyreff, B; Klett, C; Göttert, E

    1992-01-01

    Human casein kinase 2 alpha gene (CK-2-alpha) sequences have been localized within the human genome by in situ hybridization and somatic cell hybrid analysis using a CK-2 alpha cDNA as a probe. By in situ hybridization, the CK-2 alpha cDNA could be assigned to two different loci, one on 11p15.1-ter...

  15. An exponential combination procedure for set-based association tests in sequencing studies.

    Science.gov (United States)

    Chen, Lin S; Hsu, Li; Gamazon, Eric R; Cox, Nancy J; Nicolae, Dan L

    2012-12-07

    State-of-the-art next-generation-sequencing technologies can facilitate in-depth explorations of the human genome by investigating both common and rare variants. For the identification of genetic factors that are associated with disease risk or other complex phenotypes, methods have been proposed for jointly analyzing variants in a set (e.g., all coding SNPs in a gene). Variants in a properly defined set could be associated with risk or phenotype in a concerted fashion, and by accumulating information from them, one can improve power to detect genetic risk factors. Many set-based methods in the literature are based on statistics that can be written as the summation of variant statistics. Here, we propose taking the summation of the exponential of variant statistics as the set summary for association testing. From both Bayesian and frequentist perspectives, we provide theoretical justification for taking the sum of the exponential of variant statistics because it is particularly powerful for sparse alternatives-that is, compared with the large number of variants being tested in a set, only relatively few variants are associated with disease risk-a distinctive feature of genetic data. We applied the exponential combination gene-based test to a sequencing study in anticancer pharmacogenomics and uncovered mechanistic insights into genes and pathways related to chemotherapeutic susceptibility for an important class of oncologic drugs. Copyright © 2012 The American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

  16. Nucleotide sequences of two cellulase genes from alkalophilic Bacillus sp. strain N-4 and their strong homology.

    OpenAIRE

    Fukumori, F; Sashihara, N; Kudo, T; Horikoshi, K

    1986-01-01

    Two genes for cellulases of alkalophilic Bacillus sp. strain N-4 (ATCC 21833) have been sequenced. From the DNA sequences the cellulases encoded in the plasmids pNK1 and pNK2 consist of 488 and 409 amino acids, respectively. The DNA and protein sequences of the pNK1-encoded cellulase are related to those of the pNK2-encoded cellulase. The pNK2-encoded cellulase lacks the direct repeat sequence of a stretch of 60 amino acids near the C-terminal end of the pNK1-encoded cellulase. The duplicatio...

  17. Quantitative diffusion characteristics of the human brain depend on MRI sequence parameters

    International Nuclear Information System (INIS)

    Wilson, M.; Blumhardt, L.D.; Morgan, P.S.

    2002-01-01

    Quantitative diffusion-weighted MRI has been applied to the study of neurological diseases, including multiple sclerosis, where the molecular self-diffusion coefficient D has been measured in both lesions and normal-appearing white matter. Histograms of D have been used as a novel measure of the ''lesion load'', with potential applications that include the monitoring of efficacy in new treatment trials. However different ways of measuring D may affect its value, making comparison between different centres and research groups impossible. We aimed to assess the effect, if any, of using two different MRI sequences on the value of D. We studied 13 healthy volunteers, using two different quantitative diffusion sequences (including different b max values and gradient applications). Maps of D were analysed using both regions of interest (ROI) in white matter and ''whole brain'' histograms, and compared between the two sequences. In addition, we studied three standardised test liquids (with known values of D) using both sequences. Histograms from the two sequences had different distributions, with a greater spread and higher peak position from the sequence with lower b max . This greater spread of D was also evident in the white matter and test liquid ROI. ''Limits of agreement'' analysis demonstrated that the differences could be clinically relevant, despite significant correlations between the sequences obtained using simple rank methods. We conclude that different quantitative diffusion sequences are unlikely to produce directly comparable values of D, particularly if different b max values are used. In addition, the use of inappropriate statistical tests may give false impressions of close agreement. Standardisation of methods for the measurement of D are required if these techniques are to become useful tools, for example in monitoring changes in the disease burden of multiple sclerosis. (orig.)

  18. Quantitative diffusion characteristics of the human brain depend on MRI sequence parameters

    Energy Technology Data Exchange (ETDEWEB)

    Wilson, M.; Blumhardt, L.D. [University of Nottingham, Department of Neurology, Royal Preston Hospital, Preston (United Kingdom); Morgan, P.S. [Division of Academic Radiology, Queens Medical Centre, Nottingham (United Kingdom)

    2002-07-01

    Quantitative diffusion-weighted MRI has been applied to the study of neurological diseases, including multiple sclerosis, where the molecular self-diffusion coefficient D has been measured in both lesions and normal-appearing white matter. Histograms of D have been used as a novel measure of the ''lesion load'', with potential applications that include the monitoring of efficacy in new treatment trials. However different ways of measuring D may affect its value, making comparison between different centres and research groups impossible. We aimed to assess the effect, if any, of using two different MRI sequences on the value of D. We studied 13 healthy volunteers, using two different quantitative diffusion sequences (including different b{sub max} values and gradient applications). Maps of D were analysed using both regions of interest (ROI) in white matter and ''whole brain'' histograms, and compared between the two sequences. In addition, we studied three standardised test liquids (with known values of D) using both sequences. Histograms from the two sequences had different distributions, with a greater spread and higher peak position from the sequence with lower b{sub max}. This greater spread of D was also evident in the white matter and test liquid ROI. ''Limits of agreement'' analysis demonstrated that the differences could be clinically relevant, despite significant correlations between the sequences obtained using simple rank methods. We conclude that different quantitative diffusion sequences are unlikely to produce directly comparable values of D, particularly if different b{sub max} values are used. In addition, the use of inappropriate statistical tests may give false impressions of close agreement. Standardisation of methods for the measurement of D are required if these techniques are to become useful tools, for example in monitoring changes in the disease burden of multiple sclerosis. (orig.)

  19. Effect of a 12-hour/day shift on performance

    International Nuclear Information System (INIS)

    Lewis, P.M.; Swaim, D.J.

    1988-06-01

    The operating crews at the Fast Flux Facility near Richland, Washington, changed their rotating shift schedule from an 8- to 12- hour/day work schedule. The primary reason for the change was to reduce the attrition of operators by increasing their job satisfaction. Eighty-four percent of the operators favored the change. Plant performance and safety were not adversely affected. A statistical analysis of 53 operator-related, off-normal events in 28 months concluded that there was no significant difference in either the number or the severity of off-normal events on the 12-hour shift. A statistical analysis of 200,000 log entries concluded that the error rate in completing logs actually declined by 25 percent on the 12-hour shift. Alertness, which was measured using computerized tests of mathematics and logical reasoning, reach a nadir on the first night shift for the 8- and 12-hour schedules alike, which indicates that the primary cause of fatigue was sleep disruption, not cumulative hours of work. All supervisors and 52 percent of the operators believe their crews work more effectively on the 12-hour shift; only 12 percent of the operators believe that their crews work less effectively. The evaluation indicated that the 12-hour shift scheduled is a reasonable alternative to an 8-hour schedule at this facility. 2 refs

  20. Spatio-temporal alignment of pedobarographic image sequences.

    Science.gov (United States)

    Oliveira, Francisco P M; Sousa, Andreia; Santos, Rubim; Tavares, João Manuel R S

    2011-07-01

    This article presents a methodology to align plantar pressure image sequences simultaneously in time and space. The spatial position and orientation of a foot in a sequence are changed to match the foot represented in a second sequence. Simultaneously with the spatial alignment, the temporal scale of the first sequence is transformed with the aim of synchronizing the two input footsteps. Consequently, the spatial correspondence of the foot regions along the sequences as well as the temporal synchronizing is automatically attained, making the study easier and more straightforward. In terms of spatial alignment, the methodology can use one of four possible geometric transformation models: rigid, similarity, affine, or projective. In the temporal alignment, a polynomial transformation up to the 4th degree can be adopted in order to model linear and curved time behaviors. Suitable geometric and temporal transformations are found by minimizing the mean squared error (MSE) between the input sequences. The methodology was tested on a set of real image sequences acquired from a common pedobarographic device. When used in experimental cases generated by applying geometric and temporal control transformations, the methodology revealed high accuracy. In addition, the intra-subject alignment tests from real plantar pressure image sequences showed that the curved temporal models produced better MSE results (P alignment of pedobarographic image data, since previous methods can only be applied on static images.

  1. 40 CFR Table C-2 to Subpart C of... - Sequence of Test Measurements

    Science.gov (United States)

    2010-07-01

    ... 40 Protection of Environment 5 2010-07-01 2010-07-01 false Sequence of Test Measurements C Table C-2 to Subpart C of Part 53 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR... Medium. 2 High High. 3 Medium Low. 4 High High. 5 Low Medium. 6 Medium Low. 7 Low Medium. 8 Medium Low. 9...

  2. A prospective evaluation of whole-exome sequencing as a first-tier molecular test in infants with suspected monogenic disorders.

    Science.gov (United States)

    Stark, Zornitza; Tan, Tiong Y; Chong, Belinda; Brett, Gemma R; Yap, Patrick; Walsh, Maie; Yeung, Alison; Peters, Heidi; Mordaunt, Dylan; Cowie, Shannon; Amor, David J; Savarirayan, Ravi; McGillivray, George; Downie, Lilian; Ekert, Paul G; Theda, Christiane; James, Paul A; Yaplito-Lee, Joy; Ryan, Monique M; Leventer, Richard J; Creed, Emma; Macciocca, Ivan; Bell, Katrina M; Oshlack, Alicia; Sadedin, Simon; Georgeson, Peter; Anderson, Charlotte; Thorne, Natalie; Melbourne Genomics Health Alliance; Gaff, Clara; White, Susan M

    2016-11-01

    To prospectively evaluate the diagnostic and clinical utility of singleton whole-exome sequencing (WES) as a first-tier test in infants with suspected monogenic disease. Singleton WES was performed as a first-tier sequencing test in infants recruited from a single pediatric tertiary center. This occurred in parallel with standard investigations, including single- or multigene panel sequencing when clinically indicated. The diagnosis rate, clinical utility, and impact on management of singleton WES were evaluated. Of 80 enrolled infants, 46 received a molecular genetic diagnosis through singleton WES (57.5%) compared with 11 (13.75%) who underwent standard investigations in the same patient group. Clinical management changed following exome diagnosis in 15 of 46 diagnosed participants (32.6%). Twelve relatives received a genetic diagnosis following cascade testing, and 28 couples were identified as being at high risk of recurrence in future pregnancies. This prospective study provides strong evidence for increased diagnostic and clinical utility of singleton WES as a first-tier sequencing test for infants with a suspected monogenic disorder. Singleton WES outperformed standard care in terms of diagnosis rate and the benefits of a diagnosis, namely, impact on management of the child and clarification of reproductive risks for the extended family in a timely manner.Genet Med 18 11, 1090-1096.

  3. Genetic Association Analysis of Fasting and 1- and 2-Hour Glucose Tolerance Test Data Using a Generalized Index of Dissimilarity Measure for the Korean Population

    Directory of Open Access Journals (Sweden)

    Jaeyong Yee

    2016-12-01

    Full Text Available Glucose tolerance tests have been devised to determine the speed of blood glucose clearance. Diabetes is often tested with the standard oral glucose tolerance test (OGTT, along with fasting glucose level. However, no single test may be sufficient for the diagnosis, and the World Health Organization (WHO/International Diabetes Federation (IDF has suggested composite criteria. Accordingly, a single multi-class trait was constructed with three of the fasting phenotypes and 1- and 2-hour OGTT phenotypes from the Korean Association Resource (KARE project, and the genetic association was investigated. All of the 18 possible combinations made out of the 3 sets of classification for the individual phenotypes were taken into our analysis. These were possible due to a method that was recently developed by us for estimating genomic associations using a generalized index of dissimilarity. Eight single-nucleotide polymorphisms (SNPs that were found to have the strongest main effect are reported with the corresponding genes. Four of them conform to previous reports, located in the CDKAL1 gene, while the other 4 SNPs are new findings. Two-order interacting SNP pairs of are also presented. One pair (rs2328549 and rs6486740 has a prominent association, where the two single-nucleotide polymorphism locations are CDKAL1 and GLT1D1. The latter has not been found to have a strong main effect. New findings may result from the proper construction and analysis of a composite trait.

  4. Persistence Probabilities of Two-Sided (Integrated) Sums of Correlated Stationary Gaussian Sequences

    Science.gov (United States)

    Aurzada, Frank; Buck, Micha

    2018-02-01

    We study the persistence probability for some two-sided, discrete-time Gaussian sequences that are discrete-time analogues of fractional Brownian motion and integrated fractional Brownian motion, respectively. Our results extend the corresponding ones in continuous time in Molchan (Commun Math Phys 205(1):97-111, 1999) and Molchan (J Stat Phys 167(6):1546-1554, 2017) to a wide class of discrete-time processes.

  5. Two Hour Vocational Classes at the Laurel County Area Vocational School. Final Report.

    Science.gov (United States)

    Moore, James E.

    This developmental project with a research component was initiated at the Laurel County Vocational School with the major objective of determining if 2-hour instructional blocks could be operated in programs enrolling only secondary students. Subobjectives involved data gathering and statistical analyses on (1) student achievement, (2) ratings of…

  6. Development and preliminary evaluation of a multiplexed amplification and next generation sequencing method for viral hemorrhagic fever diagnostics.

    Directory of Open Access Journals (Sweden)

    Annika Brinkmann

    2017-11-01

    Full Text Available We describe the development and evaluation of a novel method for targeted amplification and Next Generation Sequencing (NGS-based identification of viral hemorrhagic fever (VHF agents and assess the feasibility of this approach in diagnostics.An ultrahigh-multiplex panel was designed with primers to amplify all known variants of VHF-associated viruses and relevant controls. The performance of the panel was evaluated via serially quantified nucleic acids from Yellow fever virus, Rift Valley fever virus, Crimean-Congo hemorrhagic fever (CCHF virus, Ebola virus, Junin virus and Chikungunya virus in a semiconductor-based sequencing platform. A comparison of direct NGS and targeted amplification-NGS was performed. The panel was further tested via a real-time nanopore sequencing-based platform, using clinical specimens from CCHF patients.The multiplex primer panel comprises two pools of 285 and 256 primer pairs for the identification of 46 virus species causing hemorrhagic fevers, encompassing 6,130 genetic variants of the strains involved. In silico validation revealed that the panel detected over 97% of all known genetic variants of the targeted virus species. High levels of specificity and sensitivity were observed for the tested virus strains. Targeted amplification ensured viral read detection in specimens with the lowest virus concentration (1-10 genome equivalents and enabled significant increases in specific reads over background for all viruses investigated. In clinical specimens, the panel enabled detection of the causative agent and its characterization within 10 minutes of sequencing, with sample-to-result time of less than 3.5 hours.Virus enrichment via targeted amplification followed by NGS is an applicable strategy for the diagnosis of VHFs which can be adapted for high-throughput or nanopore sequencing platforms and employed for surveillance or outbreak monitoring.

  7. Development and preliminary evaluation of a multiplexed amplification and next generation sequencing method for viral hemorrhagic fever diagnostics.

    Science.gov (United States)

    Brinkmann, Annika; Ergünay, Koray; Radonić, Aleksandar; Kocak Tufan, Zeliha; Domingo, Cristina; Nitsche, Andreas

    2017-11-01

    We describe the development and evaluation of a novel method for targeted amplification and Next Generation Sequencing (NGS)-based identification of viral hemorrhagic fever (VHF) agents and assess the feasibility of this approach in diagnostics. An ultrahigh-multiplex panel was designed with primers to amplify all known variants of VHF-associated viruses and relevant controls. The performance of the panel was evaluated via serially quantified nucleic acids from Yellow fever virus, Rift Valley fever virus, Crimean-Congo hemorrhagic fever (CCHF) virus, Ebola virus, Junin virus and Chikungunya virus in a semiconductor-based sequencing platform. A comparison of direct NGS and targeted amplification-NGS was performed. The panel was further tested via a real-time nanopore sequencing-based platform, using clinical specimens from CCHF patients. The multiplex primer panel comprises two pools of 285 and 256 primer pairs for the identification of 46 virus species causing hemorrhagic fevers, encompassing 6,130 genetic variants of the strains involved. In silico validation revealed that the panel detected over 97% of all known genetic variants of the targeted virus species. High levels of specificity and sensitivity were observed for the tested virus strains. Targeted amplification ensured viral read detection in specimens with the lowest virus concentration (1-10 genome equivalents) and enabled significant increases in specific reads over background for all viruses investigated. In clinical specimens, the panel enabled detection of the causative agent and its characterization within 10 minutes of sequencing, with sample-to-result time of less than 3.5 hours. Virus enrichment via targeted amplification followed by NGS is an applicable strategy for the diagnosis of VHFs which can be adapted for high-throughput or nanopore sequencing platforms and employed for surveillance or outbreak monitoring.

  8. Two complete chloroplast genome sequences of Cannabis sativa varieties.

    Science.gov (United States)

    Oh, Hyehyun; Seo, Boyoung; Lee, Seunghwan; Ahn, Dong-Ha; Jo, Euna; Park, Jin-Kyoung; Min, Gi-Sik

    2016-07-01

    In this study, we determined the complete chloroplast (cp) genomes from two varieties of Cannabis sativa. The genome sizes were 153,848 bp (the Korean non-drug variety, Cheungsam) and 153,854 bp (the African variety, Yoruba Nigeria). The genome structures were identical with 131 individual genes [86 protein-coding genes (PCGs), eight rRNA, and 37 tRNA genes]. Further, except for the presence of an intron in the rps3 genes of two C. sativa varieties, the cp genomes of C. sativa had conservative features similar to that of all known species in the order Rosales. To verify the position of C. sativa within the order Rosales, we conducted phylogenetic analysis by using concatenated sequences of all PCGs from 17 complete cp genomes. The resulting tree strongly supported monophyly of Rosales. Further, the family Cannabaceae, represented by C. sativa, showed close relationship with the family Moraceae. The phylogenetic relationship outlined in our study is well congruent with those previously shown for the order Rosales.

  9. First full-length genome sequence of the polerovirus luffa aphid-borne yellows virus (LABYV) reveals the presence of at least two consensus sequences in an isolate from Thailand.

    Science.gov (United States)

    Knierim, Dennis; Maiss, Edgar; Kenyon, Lawrence; Winter, Stephan; Menzel, Wulf

    2015-10-01

    Luffa aphid-borne yellows virus (LABYV) was proposed as the name for a previously undescribed polerovirus based on partial genome sequences obtained from samples of cucurbit plants collected in Thailand between 2008 and 2013. In this study, we determined the first full-length genome sequence of LABYV. Based on phylogenetic analysis and genome properties, it is clear that this virus represents a distinct species in the genus Polerovirus. Analysis of sequences from sample TH24, which was collected in 2010 from a luffa plant in Thailand, reveals the presence of two different full-length genome consensus sequences.

  10. 12-hour-shift plant schedule improves operator productivity

    International Nuclear Information System (INIS)

    Gould, S.

    1989-01-01

    Twelve-hour scheduling has been a mainstay of the petrochemical industry, is common in the papermill industry, and is relatively new to the nuclear utility industry. A review of industry experiences, research, and a federal Nuclear Regulatory Commission (NRC) study of the 12-hour shift (NUREG/CR-4248) demonstrate that the advantages outweigh the disadvantages. The primary advantages are greater job satisfaction, fewer errors, and the better communications inherent in two shift turnovers versus three. Several companies that implemented the 12-hour shift found an increase in employee morale, no adverse effect on worker health, and no decline in safety. They experienced greater productivity, fewer operator errors, and better communication

  11. High-throughput genome sequencing of two Listeria monocytogenes clinical isolates during a large foodborne outbreak

    Directory of Open Access Journals (Sweden)

    Trout-Yakel Keri M

    2010-02-01

    Full Text Available Abstract Background A large, multi-province outbreak of listeriosis associated with ready-to-eat meat products contaminated with Listeria monocytogenes serotype 1/2a occurred in Canada in 2008. Subtyping of outbreak-associated isolates using pulsed-field gel electrophoresis (PFGE revealed two similar but distinct AscI PFGE patterns. High-throughput pyrosequencing of two L. monocytogenes isolates was used to rapidly provide the genome sequence of the primary outbreak strain and to investigate the extent of genetic diversity associated with a change of a single restriction enzyme fragment during PFGE. Results The chromosomes were collinear, but differences included 28 single nucleotide polymorphisms (SNPs and three indels, including a 33 kbp prophage that accounted for the observed difference in AscI PFGE patterns. The distribution of these traits was assessed within further clinical, environmental and food isolates associated with the outbreak, and this comparison indicated that three distinct, but highly related strains may have been involved in this nationwide outbreak. Notably, these two isolates were found to harbor a 50 kbp putative mobile genomic island encoding translocation and efflux functions that has not been observed in other Listeria genomes. Conclusions High-throughput genome sequencing provided a more detailed real-time assessment of genetic traits characteristic of the outbreak strains than could be achieved with routine subtyping methods. This study confirms that the latest generation of DNA sequencing technologies can be applied during high priority public health events, and laboratories need to prepare for this inevitability and assess how to properly analyze and interpret whole genome sequences in the context of molecular epidemiology.

  12. Variable depth recursion algorithm for leaf sequencing

    International Nuclear Information System (INIS)

    Siochi, R. Alfredo C.

    2007-01-01

    The processes of extraction and sweep are basic segmentation steps that are used in leaf sequencing algorithms. A modified version of a commercial leaf sequencer changed the way that the extracts are selected and expanded the search space, but the modification maintained the basic search paradigm of evaluating multiple solutions, each one consisting of up to 12 extracts and a sweep sequence. While it generated the best solutions compared to other published algorithms, it used more computation time. A new, faster algorithm selects one extract at a time but calls itself as an evaluation function a user-specified number of times, after which it uses the bidirectional sweeping window algorithm as the final evaluation function. To achieve a performance comparable to that of the modified commercial leaf sequencer, 2-3 calls were needed, and in all test cases, there were only slight improvements beyond two calls. For the 13 clinical test maps, computation speeds improved by a factor between 12 and 43, depending on the constraints, namely the ability to interdigitate and the avoidance of the tongue-and-groove under dose. The new algorithm was compared to the original and modified versions of the commercial leaf sequencer. It was also compared to other published algorithms for 1400, random, 15x15, test maps with 3-16 intensity levels. In every single case the new algorithm provided the best solution

  13. Genetic control of environmental variation of two quantitative traits of Drosophila melanogaster revealed by whole-genome sequencing

    DEFF Research Database (Denmark)

    Sørensen, Peter; de los Campos, Gustavo; Morgante, Fabio

    2015-01-01

    and others more volatile performance. Understanding the mechanisms responsible for environmental variability not only informs medical questions but is relevant in evolution and in agricultural science. In this work fully sequenced inbred lines of Drosophila melanogaster were analyzed to study the nature...... of genetic control of environmental variance for two quantitative traits: starvation resistance (SR) and startle response (SL). The evidence for genetic control of environmental variance is compelling for both traits. Sequence information is incorporated in random regression models to study the underlying...... genetic signals, which are shown to be different in the two traits. Genomic variance in sexual dimorphism was found for SR but not for SL. Indeed, the proportion of variance captured by sequence information and the contribution to this variance from four chromosome segments differ between sexes in SR...

  14. 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.

  15. A two-locus DNA sequence database for typing plant and human pathogens within the Fusarium oxysporum species complex

    DEFF Research Database (Denmark)

    O'Donnell, Kerry; Gueidan, C; Sink, S

    2009-01-01

    We constructed a two-locus database, comprising partial translation elongation factor (EF-1alpha) gene sequences and nearly full-length sequences of the nuclear ribosomal intergenic spacer region (IGS rDNA) for 850 isolates spanning the phylogenetic breadth of the Fusarium oxysporum species compl...... of the IGS rDNA sequences may be non-orthologous. We also evaluated enniatin, fumonisin and moniliformin mycotoxin production in vitro within a phylogenetic framework....

  16. Hourly awakening vs continuous contact lens sensor measurements of 24-hour intraocular pressure: effect on sleep macrostructure and intraocular pressure rhythm.

    Science.gov (United States)

    Aptel, Florent; Tamisier, Renaud; Pépin, Jean-Louis; Mottet, Benjamin; Hubanova, Ralitsa; Romanet, Jean-Paul; Chiquet, Christophe

    2014-10-01

    All studies of 24-hour intraocular pressure (IOP) rhythm conducted to date have used repeated IOP measurements requiring nocturnal awakenings, potentially disturbing sleep macrostructure. To evaluate the effects on sleep architecture and IOP rhythm of hourly awakening vs a contact lens sensor (CLS) to continuously monitor IOP without awakening. Cross-sectional study at a referral center of chronobiology among 12 young healthy volunteers, with a mean (SD) age of 22.3 (2.3) years. Volunteers underwent two 24-hour IOP measurement sessions during a 2-month period. The eye order and session order were randomized. During one session, the IOP of the first eye was continuously monitored using a CLS, and the IOP of the fellow eye was measured hourly using a portable noncontact tonometer (session with nocturnal hourly awakening). During the other session, the IOP of the first eye was continuously monitored using a CLS, and the IOP of the fellow eye was not measured (session without nocturnal awakening). Overnight polysomnography was performed during the 2 sessions. A nonlinear least squares, dual-harmonic regression analysis was used to model the 24-hour IOP rhythm from the CLS data. Comparisons of acrophase, bathyphase, amplitude, and the midline estimating statistic of rhythm were used to evaluate the effect of hourly awakening on IOP rhythm. To evaluate the effects of hourly awakening on sleep architecture, comparisons of sleep structure were used, including total sleep period, rapid eye movement, wake after sleep onset, absolute and relative total sleep time, and non-rapid eye movement sleep (N1, N2, and N3). A 24-hour IOP rhythm was found in all individuals for the sessions with and without awakening (P  .30). Hourly awakening during noncontact tonometer IOP measurements did not seem to alter the mean variables of the 24-hour IOP pattern evaluated using CLS, including signal, maximum signal, minimum signal, acrophase, and bathyphase (P > .15). The 24-hour IOP

  17. Pad-weighing test performed with standardized bladder volume

    DEFF Research Database (Denmark)

    Lose, G; Rosenkilde, P; Gammelgaard, J

    1988-01-01

    The result of the one-hour pad-weighing test proposed by the International Continence Society has been demonstrated to depend on the urine load during the test. To increase reproducibility of the pad-weighing test by minimizing the influence of variation in urine load the test was done with a sta...... to +/- 24 g between two tests. It is concluded that this setup (i.e., standardized bladder volume) of the one-hour pad-weighing test allows for a more reliable assessment of urinary incontinence for quantitative purposes....... with a standardized bladder volume (50% of the cystometric bladder capacity). Twenty-five female patients with stress or mixed incontinence underwent two separate tests. Test-retest results were highly correlated (r = 0.97, p less than 0.001). Nonetheless, analysis of test-retest differences revealed a variation up...

  18. Genome Sequences of the Oxytetracycline Production Strain Streptomyces rimosus R6-500 and Two Mutants with Chromosomal Rearrangements

    KAUST Repository

    Baranasic, Damir

    2014-07-17

    The genome sequence of Streptomyces rimosus R6-500, an industrially improved strain which produces high titers of the important antibiotic oxytetracycline, is reported, as well as the genome sequences of two derivatives arising due to the genetic instability of the strain.

  19. Genome Sequences of the Oxytetracycline Production Strain Streptomyces rimosus R6-500 and Two Mutants with Chromosomal Rearrangements

    KAUST Repository

    Baranasic, Damir; Zucko, Jurica; Nair, Mridul; Pain, Arnab; Long, Paul F.; Hranueli, Daslav; Cullum, John; Starcevic, Antonio

    2014-01-01

    The genome sequence of Streptomyces rimosus R6-500, an industrially improved strain which produces high titers of the important antibiotic oxytetracycline, is reported, as well as the genome sequences of two derivatives arising due to the genetic instability of the strain.

  20. Impact of new duty-hour rules on residency training.

    Science.gov (United States)

    Duran-Nelson, Alisa; Van Camp, Joan; Ling, Louis

    2010-11-01

    On the surface, changing the rules related to the number of hours residents work per day and per week sounds like a good idea. Theoretically, residents who work fewer hours would be less tired and provide better patient care. But even small changes in residency training programs have implications for the quality of the educational experience and the cost of training, as well as patient care. This article highlights the challenges that two Minnesota residency programs are facing as they adapt to the new rules around residents' work hours.

  1. Chromosome-scale comparative sequence analysis unravels molecular mechanisms of genome evolution between two wheat cultivars

    KAUST Repository

    Thind, Anupriya Kaur

    2018-02-08

    Background: Recent improvements in DNA sequencing and genome scaffolding have paved the way to generate high-quality de novo assemblies of pseudomolecules representing complete chromosomes of wheat and its wild relatives. These assemblies form the basis to compare the evolutionary dynamics of wheat genomes on a megabase-scale. Results: Here, we provide a comparative sequence analysis of the 700-megabase chromosome 2D between two bread wheat genotypes, the old landrace Chinese Spring and the elite Swiss spring wheat line CH Campala Lr22a. There was a high degree of sequence conservation between the two chromosomes. Analysis of large structural variations revealed four large insertions/deletions (InDels) of >100 kb. Based on the molecular signatures at the breakpoints, unequal crossing over and double-strand break repair were identified as the evolutionary mechanisms that caused these InDels. Three of the large InDels affected copy number of NLRs, a gene family involved in plant immunity. Analysis of single nucleotide polymorphism (SNP) density revealed three haploblocks of 8 Mb, 9 Mb and 48 Mb with a 35-fold increased SNP density compared to the rest of the chromosome. Conclusions: This comparative analysis of two high-quality chromosome assemblies enabled a comprehensive assessment of large structural variations. The insight obtained from this analysis will form the basis of future wheat pan-genome studies.

  2. Haematobia irritans dataset of raw sequence reads from Illumina-based transcriptome sequencing of specific tissues and life stages

    Science.gov (United States)

    Illumina HiSeq technology was used to sequence the transcriptome from various dissected tissues and life stages from the horn fly, Haematobia irritans. These samples include eggs (0, 2, 4, and 9 hours post-oviposition), adult fly gut, adult fly legs, adult fly malpighian tubule, adult fly ovary, adu...

  3. Which is more useful in predicting hospital mortality--dichotomised blood test results or actual test values? A retrospective study in two hospitals.

    Science.gov (United States)

    Mohammed, Mohammed A; Rudge, Gavin; Wood, Gordon; Smith, Gary; Nangalia, Vishal; Prytherch, David; Holder, Roger; Briggs, Jim

    2012-01-01

    Routine blood tests are an integral part of clinical medicine and in interpreting blood test results clinicians have two broad options. (1) Dichotomise the blood tests into normal/abnormal or (2) use the actual values and overlook the reference values. We refer to these as the "binary" and the "non-binary" strategy respectively. We investigate which strategy is better at predicting the risk of death in hospital based on seven routinely undertaken blood tests (albumin, creatinine, haemoglobin, potassium, sodium, urea, and white blood cell count) using tree models to implement the two strategies. A retrospective database study of emergency admissions to an acute hospital during April 2009 to March 2010, involving 10,050 emergency admissions with routine blood tests undertaken within 24 hours of admission. We compared the area under the Receiver Operating Characteristics (ROC) curve for predicting in-hospital mortality using the binary and non-binary strategy. The mortality rate was 6.98% (701/10050). The mean predicted risk of death in those who died was significantly (p-value non-binary strategy (risk = 0.222 95%CI: 0.194 to 0.251), representing a risk difference of 28.74 deaths in the deceased patients (n = 701). The binary strategy had a significantly (p-value non-binary strategy (0.853 95% CI: 0.840 to 0.867). Similar results were obtained using data from another hospital. Dichotomising routine blood test results is less accurate in predicting in-hospital mortality than using actual test values because it underestimates the risk of death in patients who died. Further research into the use of actual blood test values in clinical decision making is required especially as the infrastructure to implement this potentially promising strategy already exists in most hospitals.

  4. Which Is More Useful in Predicting Hospital Mortality -Dichotomised Blood Test Results or Actual Test Values? A Retrospective Study in Two Hospitals

    Science.gov (United States)

    Mohammed, Mohammed A.; Rudge, Gavin; Wood, Gordon; Smith, Gary; Nangalia, Vishal; Prytherch, David; Holder, Roger; Briggs, Jim

    2012-01-01

    Background Routine blood tests are an integral part of clinical medicine and in interpreting blood test results clinicians have two broad options. (1) Dichotomise the blood tests into normal/abnormal or (2) use the actual values and overlook the reference values. We refer to these as the “binary” and the “non-binary” strategy respectively. We investigate which strategy is better at predicting the risk of death in hospital based on seven routinely undertaken blood tests (albumin, creatinine, haemoglobin, potassium, sodium, urea, and white blood cell count) using tree models to implement the two strategies. Methodology A retrospective database study of emergency admissions to an acute hospital during April 2009 to March 2010, involving 10,050 emergency admissions with routine blood tests undertaken within 24 hours of admission. We compared the area under the Receiver Operating Characteristics (ROC) curve for predicting in-hospital mortality using the binary and non-binary strategy. Results The mortality rate was 6.98% (701/10050). The mean predicted risk of death in those who died was significantly (p-value non-binary strategy (risk = 0.222 95%CI: 0.194 to 0.251), representing a risk difference of 28.74 deaths in the deceased patients (n = 701). The binary strategy had a significantly (p-value non-binary strategy (0.853 95% CI: 0.840 to 0.867). Similar results were obtained using data from another hospital. Conclusions Dichotomising routine blood test results is less accurate in predicting in-hospital mortality than using actual test values because it underestimates the risk of death in patients who died. Further research into the use of actual blood test values in clinical decision making is required especially as the infrastructure to implement this potentially promising strategy already exists in most hospitals. PMID:23077528

  5. A case study of cost-efficient staffing under annualized hours.

    Science.gov (United States)

    van der Veen, Egbert; Hans, Erwin W; Veltman, Bart; Berrevoets, Leo M; Berden, Hubert J J M

    2015-09-01

    We propose a mathematical programming formulation that incorporates annualized hours and shows to be very flexible with regard to modeling various contract types. The objective of our model is to minimize salary cost, thereby covering workforce demand, and using annualized hours. Our model is able to address various business questions regarding tactical workforce planning problems, e.g., with regard to annualized hours, subcontracting, and vacation planning. In a case study for a Dutch hospital two of these business questions are addressed, and we demonstrate that applying annualized hours potentially saves up to 5.2% in personnel wages annually.

  6. Microbial Contaminants of Cord Blood Units Identified by 16S rRNA Sequencing and by API Test System, and Antibiotic Sensitivity Profiling.

    Directory of Open Access Journals (Sweden)

    Luís França

    Full Text Available Over a period of ten months a total of 5618 cord blood units (CBU were screened for microbial contamination under routine conditions. The antibiotic resistance profile for all isolates was also examined using ATB strips. The detection rate for culture positive units was 7.5%, corresponding to 422 samples.16S rRNA sequence analysis and identification with API test system were used to identify the culturable aerobic, microaerophilic and anaerobic bacteria from CBUs. From these samples we recovered 485 isolates (84 operational taxonomic units, OTUs assigned to the classes Bacteroidia, Actinobacteria, Clostridia, Bacilli, Betaproteobacteria and primarily to the Gammaproteobacteria. Sixty-nine OTUs, corresponding to 447 isolates, showed 16S rRNA sequence similarities above 99.0% with known cultured bacteria. However, 14 OTUs had 16S rRNA sequence similarities between 95 and 99% in support of genus level identification and one OTU with 16S rRNA sequence similarity of 90.3% supporting a family level identification only. The phenotypic identification formed 29 OTUs that could be identified to the species level and 9 OTUs that could be identified to the genus level by API test system. We failed to obtain identification for 14 OTUs, while 32 OTUs comprised organisms producing mixed identifications. Forty-two OTUs covered species not included in the API system databases. The API test system Rapid ID 32 Strep and Rapid ID 32 E showed the highest proportion of identifications to the species level, the lowest ratio of unidentified results and the highest agreement to the results of 16S rRNA assignments. Isolates affiliated to the Bacilli and Bacteroidia showed the highest antibiotic multi-resistance indices and microorganisms of the Clostridia displayed the most antibiotic sensitive phenotypes.

  7. Microbial Contaminants of Cord Blood Units Identified by 16S rRNA Sequencing and by API Test System, and Antibiotic Sensitivity Profiling.

    Science.gov (United States)

    França, Luís; Simões, Catarina; Taborda, Marco; Diogo, Catarina; da Costa, Milton S

    2015-01-01

    Over a period of ten months a total of 5618 cord blood units (CBU) were screened for microbial contamination under routine conditions. The antibiotic resistance profile for all isolates was also examined using ATB strips. The detection rate for culture positive units was 7.5%, corresponding to 422 samples.16S rRNA sequence analysis and identification with API test system were used to identify the culturable aerobic, microaerophilic and anaerobic bacteria from CBUs. From these samples we recovered 485 isolates (84 operational taxonomic units, OTUs) assigned to the classes Bacteroidia, Actinobacteria, Clostridia, Bacilli, Betaproteobacteria and primarily to the Gammaproteobacteria. Sixty-nine OTUs, corresponding to 447 isolates, showed 16S rRNA sequence similarities above 99.0% with known cultured bacteria. However, 14 OTUs had 16S rRNA sequence similarities between 95 and 99% in support of genus level identification and one OTU with 16S rRNA sequence similarity of 90.3% supporting a family level identification only. The phenotypic identification formed 29 OTUs that could be identified to the species level and 9 OTUs that could be identified to the genus level by API test system. We failed to obtain identification for 14 OTUs, while 32 OTUs comprised organisms producing mixed identifications. Forty-two OTUs covered species not included in the API system databases. The API test system Rapid ID 32 Strep and Rapid ID 32 E showed the highest proportion of identifications to the species level, the lowest ratio of unidentified results and the highest agreement to the results of 16S rRNA assignments. Isolates affiliated to the Bacilli and Bacteroidia showed the highest antibiotic multi-resistance indices and microorganisms of the Clostridia displayed the most antibiotic sensitive phenotypes.

  8. More hours, more jobs? The employment effects of longer working hours

    OpenAIRE

    Martyn Andrews; Hans-Dieter Gerner; Thorsten Schank; Richard Upward

    2015-01-01

    Increases in standard hours of work have been a contentious policy issue in Germany. Whilst this might directly lead to a substitution of workers by hours, there may also be a positive employment effect due to reduced costs. Moreover, the response of firms may differ between firms that offer overtime and those that do not. For a panel of German plants (2001–2006) drawn from the IAB Establishment Panel, we are the first to analyse the effect of increased standard hours on employment. Using dif...

  9. 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

  10. An hour of bright white light in the early morning improves performance and advances sleep and circadian phase during the Antarctic winter.

    Science.gov (United States)

    Corbett, R W; Middleton, B; Arendt, J

    2012-09-13

    Previous work has demonstrated that exposure to an hour of bright light in the morning and the evening during the Polar winter has beneficial effects on circadian phase. This study investigated the effect of a single hour of bright white morning light on circadian phase, sleep, alertness and cognitive performance. Nine individuals (eight male, one female, median age 30 years), wintering at Halley Research Station (75°S), Antarctica from 7th May until 6th August 2007, were exposed to bright white light for a fortnight from 08:30 to 09:30 h, with two fortnight control periods on either side. This sequence was performed twice, before and following Midwinter. Light exposure, sleep and alertness were assessed daily by actigraphy, sleep diaries and subjective visual analogue scales. Circadian phase (assessed by urinary 6-sulphatoxymelatonin rhythm) and cognitive performance were evaluated at the end of each fortnight. During light exposure circadian phase was advanced from 4.97 ± 0.96 decimal hours (dh) (mean ± SD) to 4.08 ± 0.68 dh (p = 0.003). Wake-up time was shifted by a similar margin from 8.45 ± 1.83 dh to 7.59 ± 0.78 dh (p < 0.001). Sleep start time was also advanced (p = 0.047) but by a lesser amount, consequently, actual sleep time was slightly reduced. There was no change in objective or subjective measures of sleep quality or subjective measures of alertness. An improvement in cognitive performance was found with both the Single Letter Cancellation Test (p < 0.001) and the Digit Symbol Substitution Test (p = 0.026) with preserved circadian variation. These beneficial effects of a single short duration light treatment may have implications not only for the Antarctic but other remote environments where access to natural light and delayed circadian phase, is problematic. These results require validation in larger studies at varying locations. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

  11. Successful treatment of two cases of urorectal septum malformation sequence with oligohydramnios and severe respiratory failure

    Directory of Open Access Journals (Sweden)

    Sekiguchi K

    2013-03-01

    Full Text Available Kazuhito Sekiguchi, Daijiro Takahashi, Takehiko Hiroma, Tomohiko Nakamura Division of Neonatology, Nagano Children's Hospital, Nagano, Japan Abstract: Urorectal septum malformation sequence can be diagnosed prenatally. We report herein the successful treatment of severe respiratory failure in two patients with urorectal septum malformation sequence and prenatally diagnosed oligohydramnios. The patients showed significant hypoxic deterioration and persistent pulmonary artery hypertension soon after birth. We used high-frequency ventilation (HFO, nitric oxide (NO, and extracorporeal membrane oxygenation (ECMO. The patients were successfully weaned from ECMO and artificial ventilation and discharged to home. Although termination of the pregnancy has often been selected for fetuses with oligohydramnios-related urorectal septum malformation sequence, our results suggest the opportunity for these fetuses to be treated using respiratory supports including HFO, NO, and ECMO after birth. Keywords: urorectal septum malformation sequence, oligohydramnios, pulmonary hypoplasia

  12. Working hours and productivity

    NARCIS (Netherlands)

    Collewet, Marion; Sauermann, Jan

    2017-01-01

    This paper studies the link between working hours and productivity using daily information on working hours and performance of a sample of call centre agents. We exploit variation in the number of hours worked by the same employee across days and weeks due to central scheduling, enabling us to

  13. 29 CFR 778.320 - Hours that would not be hours worked if not paid for.

    Science.gov (United States)

    2010-07-01

    ... working hours fall in this category. The agreement of the parties to provide compensation for such hours... regular rate of an employee if the hours are compensated at the same rate as other working hours. The.... Activities of this type include eating meals between working hours. Where it appears from all the pertinent...

  14. Quick regional centroid moment tensor solutions for the Emilia 2012 (northern Italy seismic sequence

    Directory of Open Access Journals (Sweden)

    Silvia Pondrelli

    2012-10-01

    Full Text Available In May 2012, a seismic sequence struck the Emilia region (northern Italy. The mainshock, of Ml 5.9, occurred on May 20, 2012, at 02:03 UTC. This was preceded by a smaller Ml 4.1 foreshock some hours before (23:13 UTC on May 19, 2012 and followed by more than 2,500 earthquakes in the magnitude range from Ml 0.7 to 5.2. In addition, on May 29, 2012, three further strong earthquakes occurred, all with magnitude Ml ≥5.2: a Ml 5.8 earthquake in the morning (07:00 UTC, followed by two events within just 5 min of each other, one at 10:55 UTC (Ml 5.3 and the second at 11:00 UTC (Ml 5.2. For all of the Ml ≥4.0 earthquakes in Italy and for all of the Ml ≥4.5 in the Mediterranean area, an automatic procedure for the computation of a regional centroid moment tensor (RCMT is triggered by an email alert. Within 1 h of the event, a manually revised quick RCMT (QRCMT can be published on the website if the solution is considered stable. In particular, for the Emilia seismic sequence, 13 QRCMTs were determined and for three of them, those with M >5.5, the automatically computed QRCMTs fitted the criteria for publication without manual revision. Using this seismic sequence as a test, we can then identify the magnitude threshold for automatic publication of our QRCMTs.

  15. Follow-up of coeliac disease with the novel one-hour 13C-sorbitol breath test versus the H2-sorbitol breath test.

    Science.gov (United States)

    Tveito, Kari; Hetta, Anne Kristine; Askedal, Mia; Brunborg, Cathrine; Sandvik, Leiv; Løberg, Else Marit; Skar, Viggo

    2011-07-01

    We recently developed a (13)C-sorbitol breath test ((13)C-SBT) as an alternative to the H(2)-sorbitol breath test (H(2)-SBT) for coeliac disease. In this study we compared the diagnostic properties of the H(2)-SBT and the (13)C-SBT in follow-up of coeliac disease. Twenty-seven coeliac patients on a gluten-free diet (GFD) performed the breath tests. All had been tested before treatment in the initial study of the (13)C-SBT, in which 39 untreated coeliac patients, 40 patient controls, and 26 healthy volunteers participated. Five gram sorbitol and 100 mg (13)C-sorbitol were dissolved in 250 ml tap water and given orally. H(2), CH(4) and (13)CO(2) were measured in end-expiratory breath samples every 30 min for 4 h. Increased H(2) concentration ≥20 ppm from basal values was used as cut-off for the H(2)-SBT. Sixty minutes values were used as diagnostic index in the (13)C-SBT. (13)CO(2) levels at 60 min increased in 20/26 treated coeliac patients (77%) after GFD, but were significantly lower than in control groups. Out of 20 patients who had a positive H(2)-SBT before GFD, 12 had a negative H(2)-SBT after GFD. Peak H(2) concentrations were not correlated with (13)C-SBT results. The study confirms the sensitivity of a one-hour (13)C-SBT for small intestinal malabsorption. The (13)C-SBT has superior diagnostic properties compared with the H(2)-SBT in follow-up of coeliac disease.

  16. Working hours and common mental disorders in English police officers

    OpenAIRE

    Houdmont, Jonathan; Randall, Raymond

    2016-01-01

    Background: There is a paucity of evidence on working hours and their psychological correlates in police officers of the federated ranks in England.\\ud Aims: An exploratory study to establish the extent to which a sample of English police officers worked long hours and the association between long working hours and common mental disorder (CMD).\\ud Methods: Officers of the federated ranks (constable, sergeant, inspector) from two English county forces completed a questionnaire to report their ...

  17. Epidemiology of hyperbilirubinemia in the first 24 hours after birth

    Directory of Open Access Journals (Sweden)

    Zarrinkoub F

    2007-09-01

    Full Text Available   Background: Jaundice is one of the most frequent problems observed in newborns. Our purpose was to investigate the incidence and the risk factors on jaundice noted in the first 24 hours after birth.Methods: All newborns observed to have jaundice within the first 24 hours after birth were enrolled prospectively in this study. Laboratory evaluations included blood group typing of mother and newborn, hemoglobin and hematocrit, complete blood count, peripheral blood smear, reticulocyte count, G6PD activity, maternal indirect and neonatal direct Coombs test, and serum total, conjugated, and unconjugated bilirubin. In all cases, gender, birth weight, Apgar scores, gestational age, mode of delivery, birth trauma, cephalhematoma, maternal age, parity, or any siblings with neonatal jaundice were recorded. Data were analyzed using one-way ANOVA, Student's t-, and chi-square tests.Results: Of a total of 2096 newborns delivered in one year, 122 (5.8% developed jaundice within the first 24 hours after birth. Risk factors for hyperbilirubinemia were ABO incompatibility, prematurity, infection, G6PD deficiency, cephalhematoma, asphyxia, and Rh disease. There were no statistically significant relationships between jaundice and maternal age, parity, mode of delivery, neonatal gender or previous siblings with jaundice (p>0.05.Conclusions: Jaundice observed in the initial 24 hours after birth was infrequent, but clinically significant. All newborns should be followed by repeated exams within the first 24 hours after birth and before discharge, especially if the maternal blood group is O.

  18. Reliability of two social cognition tests: The combined stories test and the social knowledge test.

    Science.gov (United States)

    Thibaudeau, Élisabeth; Cellard, Caroline; Legendre, Maxime; Villeneuve, Karèle; Achim, Amélie M

    2018-04-01

    Deficits in social cognition are common in psychiatric disorders. Validated social cognition measures with good psychometric properties are necessary to assess and target social cognitive deficits. Two recent social cognition tests, the Combined Stories Test (COST) and the Social Knowledge Test (SKT), respectively assess theory of mind and social knowledge. Previous studies have shown good psychometric properties for these tests, but the test-retest reliability has never been documented. The aim of this study was to evaluate the test-retest reliability and the inter-rater reliability of the COST and the SKT. The COST and the SKT were administered twice to a group of forty-two healthy adults, with a delay of approximately four weeks between the assessments. Excellent test-retest reliability was observed for the COST, and a good test-retest reliability was observed for the SKT. There was no evidence of practice effect. Furthermore, an excellent inter-rater reliability was observed for both tests. This study shows a good reliability of the COST and the SKT that adds to the good validity previously reported for these two tests. These good psychometrics properties thus support that the COST and the SKT are adequate measures for the assessment of social cognition. Copyright © 2018. Published by Elsevier B.V.

  19. Comparison between two motor tests used for muscular strength/endurance analysis

    Directory of Open Access Journals (Sweden)

    Matheus Amarante do Nascimento

    2013-04-01

    Full Text Available The aim of this study was to compare motor performance in modified pull-up (MPUand flexed knee push-up (FKPU tests in young women. Thirty-five apparently healthy women (20.1±2.2 years were submitted to each one of the tests at an interval of48 hours in a random balanced design. Most individuals performed between 0 an d 10 repetitions (86% of the MPU test, and approximately 17% did not perform even one repetitions. On the other hand, the highest prevalence of outcomes for the FKPUtest was between 16 and 35 repetitions (71%. The Wilcoxon test identified statistically significant differences (p MPU. A moderate agreement (kappa =0.40 was found between the performance in both tests. Negative correlations of low magnitude (r=-0.23 to 0.46 were found between morphological variables (body weight,height, fat mass, and lean body mass and motor performance in both tests. The results suggest that the FKPU test is presented as a better indicator ofmuscular endurance levels, where as the MPU test seems to better discriminate muscular strength in young women.

  20. Working hours

    OpenAIRE

    Fialová, Lenka

    2012-01-01

    Working hours The aim of this thesis that I set was a comprehensive analysis of the working hours issue. The main purpose was to summarize this area of labor law while taking into account the Labour Code amendment which came into force on 1st January 2012. The changes in the related legal terms were also included into this thesis because of the mentioned changes. The thesis is composed of three chapters. Chapter One deals briefly with history of Labour Law and regulatory development. Author`s...

  1. Impact of states' nurse work hour regulations on overtime practices and work hours among registered nurses.

    Science.gov (United States)

    Bae, Sung-Heui; Yoon, Jangho

    2014-10-01

    To examine the degree to which states' work hour regulations for nurses-policies regarding mandatory overtime and consecutive work hours-decrease mandatory overtime practice and hours of work among registered nurses. We analyzed a nationally representative sample of registered nurses from the National Sample Survey of Registered Nurses for years 2004 and 2008. We obtained difference-in-differences estimates of the effect of the nurse work hour policies on the likelihood of working mandatory overtime, working more than 40 hours per week, and working more than 60 hours per week for all staff nurses working in hospitals and nursing homes. The mandatory overtime and consecutive work hour regulations were significantly associated with 3.9 percentage-point decreases in the likelihood of working overtime mandatorily and 11.5 percentage-point decreases in the likelihood of working more than 40 hours per week, respectively. State mandatory overtime and consecutive work hour policies are effective in reducing nurse work hours. The consecutive work hour policy appears to be a better regulatory tool for reducing long work hours for nurses. © Health Research and Educational Trust.

  2. Interspecific Comparison and annotation of two complete mitochondrial genome sequences from the plant pathogenic fungus Mycosphaerella graminicola

    Energy Technology Data Exchange (ETDEWEB)

    Millenbaugh, Bonnie A; Pangilinan, Jasmyn L.; Torriani, Stefano F.F.; Goodwin, Stephen B.; Kema, Gert H.J.; McDonald, Bruce A.

    2007-12-07

    The mitochondrial genomes of two isolates of the wheat pathogen Mycosphaerella graminicola were sequenced completely and compared to identify polymorphic regions. This organism is of interest because it is phylogenetically distant from other fungi with sequenced mitochondrial genomes and it has shown discordant patterns of nuclear and mitochondrial diversity. The mitochondrial genome of M. graminicola is a circular molecule of approximately 43,960 bp containing the typical genes coding for 14 proteins related to oxidative phosphorylation, one RNA polymerase, two rRNA genes and a set of 27 tRNAs. The mitochondrial DNA of M. graminicola lacks the gene encoding the putative ribosomal protein (rps5-like), commonly found in fungal mitochondrial genomes. Most of the tRNA genes were clustered with a gene order conserved with many other ascomycetes. A sample of thirty-five additional strains representing the known global mt diversity was partially sequenced to measure overall mitochondrial variability within the species. Little variation was found, confirming previous RFLP-based findings of low mitochondrial diversity. The mitochondrial sequence of M. graminicola is the first reported from the family Mycosphaerellaceae or the order Capnodiales. The sequence also provides a tool to better understand the development of fungicide resistance and the conflicting pattern of high nuclear and low mitochondrial diversity in global populations of this fungus.

  3. Fact retrieval and memory consolidation for a movement sequence: bidirectional effects of 'unrelated' cognitive tasks on procedural memory.

    Directory of Open Access Journals (Sweden)

    Rachel Tibi

    Full Text Available The generation of long-term memory for motor skills can be modulated by subsequent motor experiences that interfere with the consolidation process. Recent studies suggest that even a non-motor task may adversely affect some aspects of motor sequence memory. Here we show that motor sequence memory can be either enhanced or reduced, by different cognitive tasks. Participants were trained in performing finger movement sequences. Fully explicit instructions about the target sequence were given before practice. The buildup of procedural knowledge was tested at three time-points: immediately before training (T1, after practice (T2, and 24 hours later (T3. Each participant performed the task on two separate occasions; training on a different movement sequence on each occasion. In one condition, interference, participants performed a non-motor task immediately after T2. Half the participants solved simple math problems and half performed a simple semantic judgment task. In the baseline condition there was no additional task. All participants improved significantly between T1 and T2 (within-session gains. In addition, in the baseline condition, performance significantly improved between T2 and T3 (delayed 'off-line' gains. Solving math problems significantly enhanced these delayed gains in motor performance, whereas performing semantic decisions significantly reduced delayed gains compared to baseline. Thus, procedural motor memory consolidation can be either enhanced or inhibited by subsequent cognitive experiences. These effects do not require explicit or implicit new learning. The retrieval of unrelated, non-motor, well established knowledge can modulate procedural memory.

  4. Protecting genomic sequence anonymity with generalization lattices.

    Science.gov (United States)

    Malin, B A

    2005-01-01

    Current genomic privacy technologies assume the identity of genomic sequence data is protected if personal information, such as demographics, are obscured, removed, or encrypted. While demographic features can directly compromise an individual's identity, recent research demonstrates such protections are insufficient because sequence data itself is susceptible to re-identification. To counteract this problem, we introduce an algorithm for anonymizing a collection of person-specific DNA sequences. The technique is termed DNA lattice anonymization (DNALA), and is based upon the formal privacy protection schema of k -anonymity. Under this model, it is impossible to observe or learn features that distinguish one genetic sequence from k-1 other entries in a collection. To maximize information retained in protected sequences, we incorporate a concept generalization lattice to learn the distance between two residues in a single nucleotide region. The lattice provides the most similar generalized concept for two residues (e.g. adenine and guanine are both purines). The method is tested and evaluated with several publicly available human population datasets ranging in size from 30 to 400 sequences. Our findings imply the anonymization schema is feasible for the protection of sequences privacy. The DNALA method is the first computational disclosure control technique for general DNA sequences. Given the computational nature of the method, guarantees of anonymity can be formally proven. There is room for improvement and validation, though this research provides the groundwork from which future researchers can construct genomics anonymization schemas tailored to specific datasharing scenarios.

  5. Development and Implementation of a Two-Semester Introductory Organic-Bioorganic Chemistry Sequence: Conclusions from the First Six Years

    Science.gov (United States)

    Goess, Brian C.

    2014-01-01

    A two-semester second-year introductory organic chemistry sequence featuring one semester of accelerated organic chemistry followed by one semester of bioorganic chemistry is described. Assessment data collected over a six-year period reveal that such a course sequence can facilitate student mastery of fundamental organic chemistry in the first…

  6. De novo sequencing of two novel peptides homologous to calcitonin-like peptides, from skin secretion of the Chinese Frog, Odorrana schmackeri

    NARCIS (Netherlands)

    Evaristo, Geisa P C; Pinkse, Martijn W H; Chen, Tianbao; Wang, Lei; Mohammed, Shabaz; Heck, Albert J R; Mathes, Isabella; Lottspeich, Friedrich; Shaw, Chris; Albar, Juan Pablo; Verhaert, Peter D E M

    2015-01-01

    An MS/MS based analytical strategy was followed to solve the complete sequence of two new peptides from frog (Odorrana schmackeri) skin secretion. This involved reduction and alkylation with two different alkylating agents followed by high resolution tandem mass spectrometry. De novo sequencing was

  7. Automated two-point dixon screening for the evaluation of hepatic steatosis and siderosis: comparison with R2*-relaxometry and chemical shift-based sequences

    Energy Technology Data Exchange (ETDEWEB)

    Henninger, B.; Rauch, S.; Schocke, M.; Jaschke, W.; Kremser, C. [Medical University of Innsbruck, Department of Radiology, Innsbruck (Austria); Zoller, H. [Medical University of Innsbruck, Department of Internal Medicine, Innsbruck (Austria); Kannengiesser, S. [Siemens AG, Healthcare Sector, MR Applications Development, Erlangen (Germany); Zhong, X. [Siemens Healthcare, MR R and D Collaborations, Atlanta, GA (United States); Reiter, G. [Siemens AG, Healthcare Sector, MR R and D Collaborations, Graz (Austria)

    2015-05-01

    To evaluate the automated two-point Dixon screening sequence for the detection and estimated quantification of hepatic iron and fat compared with standard sequences as a reference. One hundred and two patients with suspected diffuse liver disease were included in this prospective study. The following MRI protocol was used: 3D-T1-weighted opposed- and in-phase gradient echo with two-point Dixon reconstruction and dual-ratio signal discrimination algorithm (''screening'' sequence); fat-saturated, multi-gradient-echo sequence with 12 echoes; gradient-echo T1 FLASH opposed- and in-phase. Bland-Altman plots were generated and correlation coefficients were calculated to compare the sequences. The screening sequence diagnosed fat in 33, iron in 35 and a combination of both in 4 patients. Correlation between R2* values of the screening sequence and the standard relaxometry was excellent (r = 0.988). A slightly lower correlation (r = 0.978) was found between the fat fraction of the screening sequence and the standard sequence. Bland-Altman revealed systematically lower R2* values obtained from the screening sequence and higher fat fraction values obtained with the standard sequence with a rather high variability in agreement. The screening sequence is a promising method with fast diagnosis of the predominant liver disease. It is capable of estimating the amount of hepatic fat and iron comparable to standard methods. (orig.)

  8. Automated two-point dixon screening for the evaluation of hepatic steatosis and siderosis: comparison with R2*-relaxometry and chemical shift-based sequences

    International Nuclear Information System (INIS)

    Henninger, B.; Rauch, S.; Schocke, M.; Jaschke, W.; Kremser, C.; Zoller, H.; Kannengiesser, S.; Zhong, X.; Reiter, G.

    2015-01-01

    To evaluate the automated two-point Dixon screening sequence for the detection and estimated quantification of hepatic iron and fat compared with standard sequences as a reference. One hundred and two patients with suspected diffuse liver disease were included in this prospective study. The following MRI protocol was used: 3D-T1-weighted opposed- and in-phase gradient echo with two-point Dixon reconstruction and dual-ratio signal discrimination algorithm (''screening'' sequence); fat-saturated, multi-gradient-echo sequence with 12 echoes; gradient-echo T1 FLASH opposed- and in-phase. Bland-Altman plots were generated and correlation coefficients were calculated to compare the sequences. The screening sequence diagnosed fat in 33, iron in 35 and a combination of both in 4 patients. Correlation between R2* values of the screening sequence and the standard relaxometry was excellent (r = 0.988). A slightly lower correlation (r = 0.978) was found between the fat fraction of the screening sequence and the standard sequence. Bland-Altman revealed systematically lower R2* values obtained from the screening sequence and higher fat fraction values obtained with the standard sequence with a rather high variability in agreement. The screening sequence is a promising method with fast diagnosis of the predominant liver disease. It is capable of estimating the amount of hepatic fat and iron comparable to standard methods. (orig.)

  9. Operation test for 200-kW class internally improved MCFC stacks having achieved 5000 hours; 200kW kyu naibu kaishitsu gata MCFC sutakku unten shiken 5,000 jikan tassei

    Energy Technology Data Exchange (ETDEWEB)

    Hashino, K. [Kansai Electric Power Co. Inc., Osaka (Japan)

    2000-03-10

    The operation test for 200-kW class internally improved MCFC stacks being performed at the Amagasaki fuel cell power generation testing plant of Kansai Electric Power Co., Inc. has achieved on January 22, 2000 five thousand hours, the original test time target. Temperature raising has begun on June 18 last year, and the first power generation was carried out on June 30. Since then the operation has continued smoothly at near rated output, and the test was completed nearly as planned without experiencing any trouble caused by Y2K problem. This research is being carried out as the research work shared by the Molten Carbonate Fuel Cell Power Generation System Technology Research Association (MCFC Research Association) based on the research commissioning from NEDO as part of the New Sunshine Project. After the confirmation of the initial performance, verification of the carbon dioxide self-sustaining operation, and the property evaluation test of every 500 hours are going smoothly. The intention hereafter is to achieve 5,000 hours as the power generation time, with the schedule to reduce the stack temperature in the middle of February, and cease the operation. As of January 25, the amount of power generated reached 1,089 MWh. (NEDO)

  10. Capturing Neutrinos from a Star's Final Hours

    Science.gov (United States)

    Hensley, Kerry

    2018-04-01

    Patton (University of Washington) and collaborators first used a stellar evolution model to explore neutrino production in massive stars. They modeled the evolution of two massive stars 15 and 30 times the mass of our Sun from the onset of nuclear fusion to the moment of collapse.The authors found that in the last few hours before collapse, during which the material in the stars cores is rapidly upcycled into heavier elements, the flux from beta-process neutrinos rivals that of thermal neutrinos and even exceeds it at high energies. So now we know there are many beta-process neutrinos but can we spot them?Neutrino and antineutrino fluxes at Earth from the last 2 hours of a 30-solar-mass stars life compared to the flux from background sources. The rows represent calculations using two different neutrino mass hierarchies. Click to enlarge. [Patton et al. 2017]Observing Elusive NeutrinosFor an imminent supernova at a distance of 1 kiloparsec, the authors find that the presupernova electron neutrino flux rises above the background noise from the Sun, nuclear reactors, and radioactive decay within the Earth in the final two hours before collapse.Based on these calculations, current and future neutrino observatories should be able to detect tens of neutrinos from a supernova within 1 kiloparsec, about 30% of which would be beta-process neutrinos. As the distance to the star increases, the time and energy window within which neutrinos can be observed gradually narrows, until it closes for stars at a distance of about 30 kiloparsecs.Are there any nearby supergiants soon to go supernova so these predictions can be tested? At a distance of only 650 light-years, the red supergiant star Betelgeuse should produce detectable neutrinos when it explodes an exciting opportunity for astronomers in the far future!CitationKelly M. Patton et al 2017ApJ8516. doi:10.3847/1538-4357/aa95c4

  11. The nucleotide sequences of 5S rRNAs from a rotifer, Brachionus plicatilis, and two nematodes, Rhabditis tokai and Caenorhabditis elegans.

    Science.gov (United States)

    Kumazaki, T; Hori, H; Osawa, S; Ishii, N; Suzuki, K

    1982-11-11

    The nucleotide sequences of 5S rRNAs from a rotifer, Brachionus plicatilis, and two nematodes, Rhabditis tokai and Caenorhabditis elegans have been determined. The rotifer has two 5S rRNA species that are composed of 120 and 121 nucleotides, respectively. The sequences of these two 5S rRNAs are the same except that the latter has an additional base at its 3'-terminus. The 5S rRNAs from the two nematode species are both 119 nucleotides long. The sequence similarity percents are 79% (Brachionus/Rhabditis), 80% (Brachionus/Caenorhabditis), and 95% (Rhabditis/Caenorhabditis) among these three species. Brachionus revealed the highest similarity to Lingula (89%), but not to the nematodes (79%).

  12. The Productivity Of Working Hours

    OpenAIRE

    John Pencavel

    2013-01-01

    Observations on munition workers, most of them women, are organized to examine the relationship between their output and their working hours. The relationship is nonlinear: below an hours threshold, output is proportional to hours; above a threshold, output rises at a decreasing rate as hours increase. Implications of these results for the estimation of labor supply functions are taken up. The findings also link up with current research on the effects of long working hours on accidents and in...

  13. Shortened preoperative fasting time to allow oral rehydration solution clear liquid up to two hours before elective major surgery in adults

    International Nuclear Information System (INIS)

    Shah, J.N.; Maharjan, S.; Curung, R.

    2018-01-01

    To generate evidence of feasibility to allow clear liquid 2 hours before elective surgery. Study Design: Cross-sectional observational study. Place and Duration of Study: The Department of Surgery, Patan Hospital, Patan Academy of Health Sciences, Nepal, from October to December 2016. Methodology: One hundred consecutive adult elective major surgery patients of American Society of Anesthesiologist criteria 1 or 2 were enrolled. The protocol was discussed with patients, nurses, anesthetists and surgeons to allow 500 ml clear liquid (ORS) up to 0600 hours on the day of surgery to maintain minimum of 2 hours (h) nil per os (NPO) before surgery. Compliance, discomfort, nausea and vomiting were observed. Institutional review committee approved the study. Microsoft excel was used for descriptive analysis. Results: All 100 patients completed the protocol of shortened fasting time. Two patients had incomplete records and were excluded from analysis. Among the 98 patients analysed, age was 48 +-12.38 years with 74 females (75.51% of 98). There were 68 gastrointestinal, 20 urosurgery and 10 others surgeries. There was no discomfort, nausea or vomiting reported due to ORS 2-h before elective surgery. Conclusion: Preoperative clear liquid up to 2-h before elective surgery in adults is feasible and safe in our set-up to shorten the fasting time. (author)

  14. Benefits resulting from 1- and 6-hour parathyroid hormone and calcium levels after thyroidectomy.

    Science.gov (United States)

    Payne, Richard J; Tewfik, Marc A; Hier, Michael P; Tamilia, Michael; Mac Namara, Elizabeth; Young, Jonathan; Black, Martin J

    2005-09-01

    Previous studies have established the efficacy of post-thyroidectomy hypocalcemia monitoring using parathyroid hormone (PTH) and corrected calcium levels at 1 and 6 hours. The goal of this study was to measure the impact of managing patients based on the above findings with respect to: duration of hospital stays, rates of transient hypocalcemia, number of blood tests, cost savings, and discharge from the hospital as early as 8 hours post-thyroidectomy without compromising safety. This is a prospective study involving 95 total thyroidectomy patients using historical data as controls. The previous protocol was modified in that all blood tests ceased for patients meeting the 6-hour critical level of PTH > or = 28 ng/L and simultaneous corrected calcium > or = 2.14 mmol/L (8.56 mg/dL). Furthermore, patients with 1-hour PTH levels cost savings of 766 Canadian dollars per patient. The new algorithm resulting from PTH and corrected calcium monitoring at 1 and 6 hours post-thyroidectomy has led to significant cost savings for our institution. It has also translated into greater patient satisfaction as a result of fewer blood tests, a lower incidence of transient hypocalcemia, and significantly shorter hospital stays.

  15. Nurses' extended work hours: Patient, nurse and organizational outcomes.

    Science.gov (United States)

    Kunaviktikul, W; Wichaikhum, O; Nantsupawat, A; Nantsupawat, R; Chontawan, R; Klunklin, A; Roongruangsri, S; Nantachaipan, P; Supamanee, T; Chitpakdee, B; Akkadechanunt, T; Sirakamon, S

    2015-09-01

    Nursing shortages have been associated with increased nurse workloads that may result in work errors, thus impacting patient, nurse and organizational outcomes. To examine for the first time in Thailand nurses' extended work hours (working more than 40 h per week) and its relationship to patient, nurse and organizational outcomes. Using multistage sampling, 1524 registered nurses working in 90 hospitals across Thailand completed demographic forms: the Nurses' Extended Work Hours Form; the Patient, Nurse, Organizational Outcomes Form; the Organizational Productivity Questionnaire and the Maslach Burnout Inventory. The data were analysed using descriptive statistics, Spearman's rank correlation and logistic regression. The average extended work hour of respondents was 18.82 h per week. About 80% worked two consecutive shifts. The extended work hours had a positive correlation with patient outcomes, such as patient identification errors, pressure ulcers, communication errors and patient complaints and with nurse outcomes of emotional exhaustion and depersonalization. Furthermore, we found a negative correlation between extended work hours and job satisfaction as a whole, intent to stay and organizational productivity. Nurses who had extended work hours of >16 h per week were significantly more likely to perceive all four adverse patient outcomes than participants working an extended ≤8 h per week. Patient outcomes were measured by respondents' self-reports. This may not always reflect the real occurrence of adverse events. Associations between extended work hours and outcomes for patients, nurses and the organization were found. The findings demonstrate that working two shifts (16 h) more than the regular work hours lead to negative outcomes for patients, nurses and the organization. Our findings add to increasing international evidence that nurses' poor working conditions result in negative outcomes for professionals, patients and health systems

  16. Work shift duration: a review comparing eight hour and 12 hour shift systems.

    Science.gov (United States)

    Smith, L; Folkard, S; Tucker, P; Macdonald, I

    1998-04-01

    Shiftwork is now a major feature of working life across a broad range of industries. The features of the shift systems operated can impact on the wellbeing, performance, and sleep of shiftworkers. This paper reviews the current state of knowledge on one major characteristic of shift rotas-namely, shift duration. Evidence comparing the relative effects of eight hour and 12 hour shifts on fatigue and job performance, safety, sleep, and physical and psychological health are considered. At the organisational level, factors such as the mode of system implementation, attitudes towards shift rotas, sickness absence and turnover, overtime, and moonlighting are discussed. Manual and electronic searches of the shiftwork research literature were conducted to obtain information on comparisons between eight hour and 12 hour shifts. The research findings are largely equivocal. The bulk of the evidence suggests few differences between eight and 12 hour shifts in the way they affect people. There may even be advantages to 12 hour shifts in terms of lower stress levels, better physical and psychological wellbeing, improved durations and quality of off duty sleep as well as improvements in family relations. On the negative side, the main concerns are fatigue and safety. It is noted that a 12 hour shift does not equate with being active for only 12 hours. There can be considerable extension of the person's time awake either side of the shift. However, the effects of longer term exposure to extended work days have been relatively uncharted in any systematic way. Longitudinal comparative research into the chronic impact of the compressed working week is needed.

  17. DNA hypomethylation, transient neonatal diabetes, and prune belly sequence in one of two identical twins.

    Science.gov (United States)

    Laborie, Lene Bjerke; Mackay, Deborah J G; Temple, I Karen; Molven, Anders; Søvik, Oddmund; Njølstad, Pål Rasmus

    2010-02-01

    One known genetic mechanism for transient neonatal diabetes is loss of methylation at 6q24. The etiology of prune belly sequence is unknown but a genetic defect, affecting the mesoderm from which the triad abdominal muscle hypoplasia, urinary tract abnormalities, and cryptorchidism develop, has been suggested. We investigated a family, including one twin, with transient neonatal diabetes and prune belly sequence. Autoantibody tests excluded type 1 diabetes. Microsatellite marker analysis confirmed the twins being monozygotic. We identified no mutations in ZFP57, KCNJ11, ABCC8, GCK, HNF1A, HNF1B, HNF3B, IPF1, PAX4, or ZIC3. The proband had loss of methylation at the 6q24 locus TNDM and also at the loci IGF2R, DIRAS3, and PEG1, while the other family members, including the healthy monozygotic twin, had normal findings. The loss of methylation on chromosome 6q24 and elsewhere may indicate a generalized maternal hypomethylation syndrome, which accounts for both transient neonatal diabetes and prune belly sequence.

  18. Health and psychosocial effects of flexible working hours.

    Science.gov (United States)

    Janssen, Daniela; Nachreiner, Friedhelm

    2004-12-01

    To examine whether any impairments in health and social lives can be found under different kinds of flexible working hours, and whether such effects are related to specific characteristics of these working hours. Two studies -- a company based survey (N=660) and an internet survey (N=528) -- have been conducted. The first one was a questionnaire study (paper and pencil) on employees working under some 'typical' kinds of different flexible working time arrangements in different companies and different occupational fields (health care, manufacturing, retail, administration, call centres). The second study was an internet-based survey, using an adaptation of the questionnaire from the first study. The results of both studies consistently show that high variability of working hours is associated with increased impairments in health and well-being and this is especially true if this variability is company controlled. These effects are less pronounced if variability is self-controlled; however, autonomy does not compensate the effects of variability. Recommendations for an appropriate design of flexible working hours should be developed in order to minimize any impairing effects on health and psychosocial well-being; these recommendations should include -- besides allowing for discretion in controlling one's (flexible) working hours -- that variability in flexible working hours should be kept low (or at least moderate), even if this variability is self-controlled.

  19. Measuring fit of sequence data to phylogenetic model: gain of power using marginal tests.

    Science.gov (United States)

    Waddell, Peter J; Ota, Rissa; Penny, David

    2009-10-01

    Testing fit of data to model is fundamentally important to any science, but publications in the field of phylogenetics rarely do this. Such analyses discard fundamental aspects of science as prescribed by Karl Popper. Indeed, not without cause, Popper (Unended quest: an intellectual autobiography. Fontana, London, 1976) once argued that evolutionary biology was unscientific as its hypotheses were untestable. Here we trace developments in assessing fit from Penny et al. (Nature 297:197-200, 1982) to the present. We compare the general log-likelihood ratio (the G or G (2) statistic) statistic between the evolutionary tree model and the multinomial model with that of marginalized tests applied to an alignment (using placental mammal coding sequence data). It is seen that the most general test does not reject the fit of data to model (P approximately 0.5), but the marginalized tests do. Tests on pairwise frequency (F) matrices, strongly (P < 0.001) reject the most general phylogenetic (GTR) models commonly in use. It is also clear (P < 0.01) that the sequences are not stationary in their nucleotide composition. Deviations from stationarity and homogeneity seem to be unevenly distributed amongst taxa; not necessarily those expected from examining other regions of the genome. By marginalizing the 4( t ) patterns of the i.i.d. model to observed and expected parsimony counts, that is, from constant sites, to singletons, to parsimony informative characters of a minimum possible length, then the likelihood ratio test regains power, and it too rejects the evolutionary model with P < 0.001. Given such behavior over relatively recent evolutionary time, readers in general should maintain a healthy skepticism of results, as the scale of the systematic errors in published trees may really be far larger than the analytical methods (e.g., bootstrap) report.

  20. Complex programmable logic device based alarm sequencer for nuclear power plants

    International Nuclear Information System (INIS)

    Khedkar, Ravindra; Solomon, J. Selva; KrishnaKumar, B.

    2001-01-01

    Complex Programmable Logic Device based Alarm Sequencer is an instrument, which detects alarms, memorizes them and displays the sequences of occurrence of alarms. It caters to sixteen alarm signals and distinguishes the sequence among any two alarms with a time resolution of 1 ms. The system described has been designed for continuous operation in process plants, nuclear power plants etc. The system has been tested and found to be working satisfactorily. (author)

  1. Fixed Costs and Hours Constraints

    Science.gov (United States)

    Johnson, William R.

    2011-01-01

    Hours constraints are typically identified by worker responses to questions asking whether they would prefer a job with more hours and more pay or fewer hours and less pay. Because jobs with different hours but the same rate of pay may be infeasible when there are fixed costs of employment or mandatory overtime premia, the constraint in those…

  2. Relative bioavailability of generic and branded acetylcysteine effervescent tablets: A single-dose, open-label, randomized-sequence, two-period crossover study in fasting healthy Chinese male volunteers.

    Science.gov (United States)

    Liu, Yan-Mei; Liu, Yun; Lu, Chuan; Jia, Jing-Ying; Liu, Gang-Yi; Weng, Li-Ping; Wang, Jia-Yan; Li, Guo-Xiu; Wang, Wei; Li, Shui-Jun; Yu, Chen

    2010-11-01

    Acetylcysteine may be used as a muco- lytic agent for the treatment of chronic bronchitis, chronic obstructive pulmonary disease, and other pulmonary diseases complicated by the production of viscous mucus. However, little is known of its pharmacokinetic properties when given orally in healthy volunteers, particularly in a Chinese Han population. This study was conducted to provide support for the marketing of a generic product in China. The purpose of this study was to compare the pharmacokinetics and relative bioavailability of a generic test formulation and a branded reference formulation of acetylcysteine in fasting healthy Chinese male volunteers. A single-dose, open-label, randomized-sequence, 2-period crossover design with a 7-day washout period between doses was used in this study. Healthy Chinese male nonsmokers aged 18 to 40 years with a body mass index (BMI) of 19 to 25 kg/m(2) were selected. Eligible volunteers were randomly assigned to receive acetylcysteine 600 mg PO as either the test formulation (3 tablets of 200 mg each) or reference formulation (1 tablet of 600 mg) under fasting conditions. A total of 15 serial blood samples were collected over a 24-hour interval, and total plasma acetylcysteine concentrations were analyzed by a validated liquid chromatography-isotopic dilution mass spectrometry method. Pharmacokinetic parameters (C(max), T(max), t(½) AUC(0-t), and AUC(0-∞) were calculated and analyzed statistically. The 2 formulations were considered bioequivalent if the 90% CIs of the log-transformed ratios (test/reference) of C(max) and AUC were within the predetermined bioequivalence ranges (70%-143% for C(max); 80%-125% for AUC), as established by the State Food and Drug Administration of China. Tolerability was determined by vital signs, clinical laboratory tests, 12-lead ECGs, physical examinations, and interviews with the subjects about adverse events (AEs). A total of 24 healthy Chinese Han male volunteers were enrolled in and

  3. The 2016 Kumamoto earthquake sequence.

    Science.gov (United States)

    Kato, Aitaro; Nakamura, Kouji; Hiyama, Yohei

    2016-01-01

    Beginning in April 2016, a series of shallow, moderate to large earthquakes with associated strong aftershocks struck the Kumamoto area of Kyushu, SW Japan. An M j 7.3 mainshock occurred on 16 April 2016, close to the epicenter of an M j 6.5 foreshock that occurred about 28 hours earlier. The intense seismicity released the accumulated elastic energy by right-lateral strike slip, mainly along two known, active faults. The mainshock rupture propagated along multiple fault segments with different geometries. The faulting style is reasonably consistent with regional deformation observed on geologic timescales and with the stress field estimated from seismic observations. One striking feature of this sequence is intense seismic activity, including a dynamically triggered earthquake in the Oita region. Following the mainshock rupture, postseismic deformation has been observed, as well as expansion of the seismicity front toward the southwest and northwest.

  4. The 2016 Kumamoto earthquake sequence

    Science.gov (United States)

    KATO, Aitaro; NAKAMURA, Kouji; HIYAMA, Yohei

    2016-01-01

    Beginning in April 2016, a series of shallow, moderate to large earthquakes with associated strong aftershocks struck the Kumamoto area of Kyushu, SW Japan. An Mj 7.3 mainshock occurred on 16 April 2016, close to the epicenter of an Mj 6.5 foreshock that occurred about 28 hours earlier. The intense seismicity released the accumulated elastic energy by right-lateral strike slip, mainly along two known, active faults. The mainshock rupture propagated along multiple fault segments with different geometries. The faulting style is reasonably consistent with regional deformation observed on geologic timescales and with the stress field estimated from seismic observations. One striking feature of this sequence is intense seismic activity, including a dynamically triggered earthquake in the Oita region. Following the mainshock rupture, postseismic deformation has been observed, as well as expansion of the seismicity front toward the southwest and northwest. PMID:27725474

  5. Integrated sequence analysis. Final report

    International Nuclear Information System (INIS)

    Andersson, K.; Pyy, P.

    1998-02-01

    The NKS/RAK subprojet 3 'integrated sequence analysis' (ISA) was formulated with the overall objective to develop and to test integrated methodologies in order to evaluate event sequences with significant human action contribution. The term 'methodology' denotes not only technical tools but also methods for integration of different scientific disciplines. In this report, we first discuss the background of ISA and the surveys made to map methods in different application fields, such as man machine system simulation software, human reliability analysis (HRA) and expert judgement. Specific event sequences were, after the surveys, selected for application and testing of a number of ISA methods. The event sequences discussed in the report were cold overpressure of BWR, shutdown LOCA of BWR, steam generator tube rupture of a PWR and BWR disturbed signal view in the control room after an external event. Different teams analysed these sequences by using different ISA and HRA methods. Two kinds of results were obtained from the ISA project: sequence specific and more general findings. The sequence specific results are discussed together with each sequence description. The general lessons are discussed under a separate chapter by using comparisons of different case studies. These lessons include areas ranging from plant safety management (design, procedures, instrumentation, operations, maintenance and safety practices) to methodological findings (ISA methodology, PSA,HRA, physical analyses, behavioural analyses and uncertainty assessment). Finally follows a discussion about the project and conclusions are presented. An interdisciplinary study of complex phenomena is a natural way to produce valuable and innovative results. This project came up with structured ways to perform ISA and managed to apply the in practice. The project also highlighted some areas where more work is needed. In the HRA work, development is required for the use of simulators and expert judgement as

  6. Integrated sequence analysis. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Andersson, K.; Pyy, P

    1998-02-01

    The NKS/RAK subprojet 3 `integrated sequence analysis` (ISA) was formulated with the overall objective to develop and to test integrated methodologies in order to evaluate event sequences with significant human action contribution. The term `methodology` denotes not only technical tools but also methods for integration of different scientific disciplines. In this report, we first discuss the background of ISA and the surveys made to map methods in different application fields, such as man machine system simulation software, human reliability analysis (HRA) and expert judgement. Specific event sequences were, after the surveys, selected for application and testing of a number of ISA methods. The event sequences discussed in the report were cold overpressure of BWR, shutdown LOCA of BWR, steam generator tube rupture of a PWR and BWR disturbed signal view in the control room after an external event. Different teams analysed these sequences by using different ISA and HRA methods. Two kinds of results were obtained from the ISA project: sequence specific and more general findings. The sequence specific results are discussed together with each sequence description. The general lessons are discussed under a separate chapter by using comparisons of different case studies. These lessons include areas ranging from plant safety management (design, procedures, instrumentation, operations, maintenance and safety practices) to methodological findings (ISA methodology, PSA,HRA, physical analyses, behavioural analyses and uncertainty assessment). Finally follows a discussion about the project and conclusions are presented. An interdisciplinary study of complex phenomena is a natural way to produce valuable and innovative results. This project came up with structured ways to perform ISA and managed to apply the in practice. The project also highlighted some areas where more work is needed. In the HRA work, development is required for the use of simulators and expert judgement as

  7. Colleges Are Slashing Adjuncts' Hours to Skirt New Rules on Health-Insurance Eligibility

    Science.gov (United States)

    Dunn, Sydni

    2013-01-01

    Allison G. Armentrout, an adjunct instructor at Stark State College, does not get paid by the hour. She earns $4,600 to teach two English composition courses. But now she carefully tracks how many hours she works on an electronic time sheet. During a recent week, she spent three hours preparing for her lectures, close to six hours in the…

  8. Long working hours and use of psychotropic medicine: a follow-up study with register linkage.

    Science.gov (United States)

    Hannerz, Harald; Albertsen, Karen

    2016-03-01

    This study aimed to investigate the possibility of a prospective association between long working hours and use of psychotropic medicine. Survey data drawn from random samples of the general working population of Denmark in the time period 1995-2010 were linked to national registers covering all inhabitants. The participants were followed for first occurrence of redeemed prescriptions for psychotropic medicine. The primary analysis included 25,959 observations (19,259 persons) and yielded a total of 2914 new cases of psychotropic drug use in 99,018 person-years at risk. Poisson regression was used to model incidence rates of redeemed prescriptions for psychotropic medicine as a function of working hours (32-40, 41-48, >48 hours/week). The analysis was controlled for gender, age, sample, shift work, and socioeconomic status. A likelihood ratio test was used to test the null hypothesis, which stated that the incidence rates were independent of weekly working hours. The likelihood ratio test did not reject the null hypothesis (P=0.085). The rate ratio (RR) was 1.04 [95% confidence interval (95% CI) 0.94-1.15] for the contrast 41-48 versus 32-40 work hours/week and 1.15 (95% CI 1.02-1.30) for >48 versus 32-40 hours/week. None of the rate ratios that were estimated in the present study were statistically significant after adjustment for multiple testing. However, stratified analyses, in which 30 RR were estimated, generated the hypothesis that overtime work (>48 hours/week) might be associated with an increased risk among night or shift workers (RR=1.51, 95% CI 1.15-1.98). The present study did not find a statistically significant association between long working hours and incidence of psychotropic drug usage among Danish employees.

  9. 46 CFR 160.041-5 - Inspections and tests.

    Science.gov (United States)

    2010-10-01

    ... temperature of 150 °F. for one hour and then to a temperature of 30 °F. below zero for one hour. There shall... one foot of water for a period of two hours. At the end of this period the container shall be removed.... Four cartons from each container tested shall be submerged under a head of one foot of water for a...

  10. Application of genotyping-by-sequencing on semiconductor sequencing platforms: a comparison of genetic and reference-based marker ordering in barley.

    Directory of Open Access Journals (Sweden)

    Martin Mascher

    Full Text Available The rapid development of next-generation sequencing platforms has enabled the use of sequencing for routine genotyping across a range of genetics studies and breeding applications. Genotyping-by-sequencing (GBS, a low-cost, reduced representation sequencing method, is becoming a common approach for whole-genome marker profiling in many species. With quickly developing sequencing technologies, adapting current GBS methodologies to new platforms will leverage these advancements for future studies. To test new semiconductor sequencing platforms for GBS, we genotyped a barley recombinant inbred line (RIL population. Based on a previous GBS approach, we designed bar code and adapter sets for the Ion Torrent platforms. Four sets of 24-plex libraries were constructed consisting of 94 RILs and the two parents and sequenced on two Ion platforms. In parallel, a 96-plex library of the same RILs was sequenced on the Illumina HiSeq 2000. We applied two different computational pipelines to analyze sequencing data; the reference-independent TASSEL pipeline and a reference-based pipeline using SAMtools. Sequence contigs positioned on the integrated physical and genetic map were used for read mapping and variant calling. We found high agreement in genotype calls between the different platforms and high concordance between genetic and reference-based marker order. There was, however, paucity in the number of SNP that were jointly discovered by the different pipelines indicating a strong effect of alignment and filtering parameters on SNP discovery. We show the utility of the current barley genome assembly as a framework for developing very low-cost genetic maps, facilitating high resolution genetic mapping and negating the need for developing de novo genetic maps for future studies in barley. Through demonstration of GBS on semiconductor sequencing platforms, we conclude that the GBS approach is amenable to a range of platforms and can easily be modified as new

  11. Draft genome sequencing of giardia intestinalis assemblage B isolate GS: is human giardiasis caused by two different species?

    Directory of Open Access Journals (Sweden)

    Oscar Franzén

    2009-08-01

    Full Text Available Giardia intestinalis is a major cause of diarrheal disease worldwide and two major Giardia genotypes, assemblages A and B, infect humans. The genome of assemblage A parasite WB was recently sequenced, and the structurally compact 11.7 Mbp genome contains simplified basic cellular machineries and metabolism. We here performed 454 sequencing to 16x coverage of the assemblage B isolate GS, the only Giardia isolate successfully used to experimentally infect animals and humans. The two genomes show 77% nucleotide and 78% amino-acid identity in protein coding regions. Comparative analysis identified 28 unique GS and 3 unique WB protein coding genes, and the variable surface protein (VSP repertoires of the two isolates are completely different. The promoters of several enzymes involved in the synthesis of the cyst-wall lack binding sites for encystation-specific transcription factors in GS. Several synteny-breaks were detected and verified. The tetraploid GS genome shows higher levels of overall allelic sequence polymorphism (0.5 versus <0.01% in WB. The genomic differences between WB and GS may explain some of the observed biological and clinical differences between the two isolates, and it suggests that assemblage A and B Giardia can be two different species.

  12. Improved PFB operations - 400-hour turbine test results

    Science.gov (United States)

    Rollbuhler, R. J.; Benford, S. M.; Zellars, G. R.

    1980-04-01

    The paper deals with a 400-hr small turbine test in the effluent of a pressurized fluidized bed (PFB) at an average temperature of 770 C, an average relative gas velocity of 300 m/sec, and average solid loadings of 200 ppm. Consideration is given to combustion parameters and operating procedure as well as to the turbine system and turbine test operating procedures. Emphasis is placed on erosion/corrosion results.

  13. Thirty-two phase sequences design with good autocorrelation ...

    Indian Academy of Sciences (India)

    mum peak aperiodic autocorrelation sidelobe level one are called Barker Sequences. ... the generation and processing of polyphase signals have now become easy ..... Cook C E, Bernfield M 1967 An introduction to theory and application.

  14. CERN restaurants: opening hours during summer

    CERN Document Server

    2016-01-01

    In the summer, the three CERN restaurants remain open during their usual hours. On Monday 1st August and Thursday 8 September, the Restaurant 1 will be open from 7:00 a.m. to 10:00 p.m.   The satellites will be open as follows: Building 6: normal hours Building 13: normal hours Building 30: normal hours Building 40: closing at 4:30 p.m. instead of 5:00 pm Building 54: normal hours in July, closed in August Building 864: normal hours Building 865: normal hours Building 774: normal hours

  15. elPrep: High-Performance Preparation of Sequence Alignment/Map Files for Variant Calling.

    Directory of Open Access Journals (Sweden)

    Charlotte Herzeel

    Full Text Available elPrep is a high-performance tool for preparing sequence alignment/map files for variant calling in sequencing pipelines. It can be used as a replacement for SAMtools and Picard for preparation steps such as filtering, sorting, marking duplicates, reordering contigs, and so on, while producing identical results. What sets elPrep apart is its software architecture that allows executing preparation pipelines by making only a single pass through the data, no matter how many preparation steps are used in the pipeline. elPrep is designed as a multithreaded application that runs entirely in memory, avoids repeated file I/O, and merges the computation of several preparation steps to significantly speed up the execution time. For example, for a preparation pipeline of five steps on a whole-exome BAM file (NA12878, we reduce the execution time from about 1:40 hours, when using a combination of SAMtools and Picard, to about 15 minutes when using elPrep, while utilising the same server resources, here 48 threads and 23GB of RAM. For the same pipeline on whole-genome data (NA12878, elPrep reduces the runtime from 24 hours to less than 5 hours. As a typical clinical study may contain sequencing data for hundreds of patients, elPrep can remove several hundreds of hours of computing time, and thus substantially reduce analysis time and cost.

  16. A space-time hybrid hourly rainfall model for derived flood frequency analysis

    Directory of Open Access Journals (Sweden)

    U. Haberlandt

    2008-12-01

    Full Text Available For derived flood frequency analysis based on hydrological modelling long continuous precipitation time series with high temporal resolution are needed. Often, the observation network with recording rainfall gauges is poor, especially regarding the limited length of the available rainfall time series. Stochastic precipitation synthesis is a good alternative either to extend or to regionalise rainfall series to provide adequate input for long-term rainfall-runoff modelling with subsequent estimation of design floods. Here, a new two step procedure for stochastic synthesis of continuous hourly space-time rainfall is proposed and tested for the extension of short observed precipitation time series.

    First, a single-site alternating renewal model is presented to simulate independent hourly precipitation time series for several locations. The alternating renewal model describes wet spell durations, dry spell durations and wet spell intensities using univariate frequency distributions separately for two seasons. The dependence between wet spell intensity and duration is accounted for by 2-copulas. For disaggregation of the wet spells into hourly intensities a predefined profile is used. In the second step a multi-site resampling procedure is applied on the synthetic point rainfall event series to reproduce the spatial dependence structure of rainfall. Resampling is carried out successively on all synthetic event series using simulated annealing with an objective function considering three bivariate spatial rainfall characteristics. In a case study synthetic precipitation is generated for some locations with short observation records in two mesoscale catchments of the Bode river basin located in northern Germany. The synthetic rainfall data are then applied for derived flood frequency analysis using the hydrological model HEC-HMS. The results show good performance in reproducing average and extreme rainfall characteristics as well as in

  17. Thirteen- and Sixteen-Month-Olds' Long-Term Recall of Event Sequences.

    Science.gov (United States)

    Hertsgaard, L.; Bauer, P. J.

    In two experiments, the ability of children younger than 20 months to engage in delayed ordered recall was investigated. In the first experiment, 13- and 16-month-old children were presented with 2-step event sequences and tested for recall, first, immediately following the event and second, after a one-week delay. Sequences were novel-causal,…

  18. Draft Genome Sequences of Two Novel Acidimicrobiaceae Members from an Acid Mine Drainage Biofilm Metagenome

    OpenAIRE

    Pinto, Ameet J.; Sharp, Jonathan O.; Yoder, Michael J.; Almstrand, Robert

    2016-01-01

    Bacteria belonging to the family Acidimicrobiaceae are frequently encountered in heavy metal-contaminated acidic environments. However, their phylogenetic and metabolic diversity is poorly resolved. We present draft genome sequences of two novel and phylogenetically distinct Acidimicrobiaceae members assembled from an acid mine drainage biofilm metagenome.

  19. Long working hours and sickness absence-a fixed effects design.

    Science.gov (United States)

    Bernstrøm, Vilde Hoff

    2018-05-02

    While long working hours seem to lead to impaired health, several studies have also shown that long working hours are related to lower levels of sickness absence. Previous studies on the relationship between long working hours and sickness absence have compared those who work long hours to those who do not, looking only at between-individual correlations. Those results might therefore reflect relatively stable differences between employees who typically work long hours and employees who typically do not. The aim of the present study is to examine within-individual correlations between long working hours and sickness absence. Records from the Human Resources department in a large Norwegian hospital from 2012 to 2015 provided objective data on both working hours and sickness absence. Two analyses were performed: a prospective cohort analysis to replicate the results from previous between-individual analyses and a second analysis of within-individual correlations using a fixed effect design. In line with existing research, both between-individual and within-individual analyses showed a negative relationship between long working hours (> 48 h/week) and short-term sickness absence (1-8 days) and no significant difference in incidence of long-term sickness absence (> 8 days). The results indicate that the negative relationship between long working hours and sickness absence is not due only to relatively stable individual differences between those who typically work long hours and those who do not. The results from both analyses therefore still contrast with previous research showing a negative relationship between long working hours and other health indicators.

  20. Validation and optimization of the Ion Torrent S5 XL sequencer and Oncomine workflow for BRCA1 and BRCA2 genetic testing.

    Science.gov (United States)

    Shin, Saeam; Kim, Yoonjung; Chul Oh, Seoung; Yu, Nae; Lee, Seung-Tae; Rak Choi, Jong; Lee, Kyung-A

    2017-05-23

    In this study, we validated the analytical performance of BRCA1/2 sequencing using Ion Torrent's new bench-top sequencer with amplicon panel with optimized bioinformatics pipelines. Using 43 samples that were previously validated by Illumina's MiSeq platform and/or by Sanger sequencing/multiplex ligation-dependent probe amplification, we amplified the target with the Oncomine™ BRCA Research Assay and sequenced on Ion Torrent S5 XL (Thermo Fisher Scientific, Waltham, MA, USA). We compared two bioinformatics pipelines for optimal processing of S5 XL sequence data: the Torrent Suite with a plug-in Torrent Variant Caller (Thermo Fisher Scientific), and commercial NextGENe software (Softgenetics, State College, PA, USA). All expected 681 single nucleotide variants, 15 small indels, and three copy number variants were correctly called, except one common variant adjacent to a rare variant on the primer-binding site. The sensitivity, specificity, false positive rate, and accuracy for detection of single nucleotide variant and small indels of S5 XL sequencing were 99.85%, 100%, 0%, and 99.99% for the Torrent Variant Caller and 99.85%, 99.99%, 0.14%, and 99.99% for NextGENe, respectively. The reproducibility of variant calling was 100%, and the precision of variant frequency also showed good performance with coefficients of variation between 0.32 and 5.29%. We obtained highly accurate data through uniform and sufficient coverage depth over all target regions and through optimization of the bioinformatics pipeline. We confirmed that our platform is accurate and practical for diagnostic BRCA1/2 testing in a clinical laboratory.

  1. Memory and learning with rapid audiovisual sequences

    Science.gov (United States)

    Keller, Arielle S.; Sekuler, Robert

    2015-01-01

    We examined short-term memory for sequences of visual stimuli embedded in varying multisensory contexts. In two experiments, subjects judged the structure of the visual sequences while disregarding concurrent, but task-irrelevant auditory sequences. Stimuli were eight-item sequences in which varying luminances and frequencies were presented concurrently and rapidly (at 8 Hz). Subjects judged whether the final four items in a visual sequence identically replicated the first four items. Luminances and frequencies in each sequence were either perceptually correlated (Congruent) or were unrelated to one another (Incongruent). Experiment 1 showed that, despite encouragement to ignore the auditory stream, subjects' categorization of visual sequences was strongly influenced by the accompanying auditory sequences. Moreover, this influence tracked the similarity between a stimulus's separate audio and visual sequences, demonstrating that task-irrelevant auditory sequences underwent a considerable degree of processing. Using a variant of Hebb's repetition design, Experiment 2 compared musically trained subjects and subjects who had little or no musical training on the same task as used in Experiment 1. Test sequences included some that intermittently and randomly recurred, which produced better performance than sequences that were generated anew for each trial. The auditory component of a recurring audiovisual sequence influenced musically trained subjects more than it did other subjects. This result demonstrates that stimulus-selective, task-irrelevant learning of sequences can occur even when such learning is an incidental by-product of the task being performed. PMID:26575193

  2. Memory and learning with rapid audiovisual sequences.

    Science.gov (United States)

    Keller, Arielle S; Sekuler, Robert

    2015-01-01

    We examined short-term memory for sequences of visual stimuli embedded in varying multisensory contexts. In two experiments, subjects judged the structure of the visual sequences while disregarding concurrent, but task-irrelevant auditory sequences. Stimuli were eight-item sequences in which varying luminances and frequencies were presented concurrently and rapidly (at 8 Hz). Subjects judged whether the final four items in a visual sequence identically replicated the first four items. Luminances and frequencies in each sequence were either perceptually correlated (Congruent) or were unrelated to one another (Incongruent). Experiment 1 showed that, despite encouragement to ignore the auditory stream, subjects' categorization of visual sequences was strongly influenced by the accompanying auditory sequences. Moreover, this influence tracked the similarity between a stimulus's separate audio and visual sequences, demonstrating that task-irrelevant auditory sequences underwent a considerable degree of processing. Using a variant of Hebb's repetition design, Experiment 2 compared musically trained subjects and subjects who had little or no musical training on the same task as used in Experiment 1. Test sequences included some that intermittently and randomly recurred, which produced better performance than sequences that were generated anew for each trial. The auditory component of a recurring audiovisual sequence influenced musically trained subjects more than it did other subjects. This result demonstrates that stimulus-selective, task-irrelevant learning of sequences can occur even when such learning is an incidental by-product of the task being performed.

  3. Forward selection two sample binomial test

    Science.gov (United States)

    Wong, Kam-Fai; Wong, Weng-Kee; Lin, Miao-Shan

    2016-01-01

    Fisher’s exact test (FET) is a conditional method that is frequently used to analyze data in a 2 × 2 table for small samples. This test is conservative and attempts have been made to modify the test to make it less conservative. For example, Crans and Shuster (2008) proposed adding more points in the rejection region to make the test more powerful. We provide another way to modify the test to make it less conservative by using two independent binomial distributions as the reference distribution for the test statistic. We compare our new test with several methods and show that our test has advantages over existing methods in terms of control of the type 1 and type 2 errors. We reanalyze results from an oncology trial using our proposed method and our software which is freely available to the reader. PMID:27335577

  4. Surface Weather Observations Hourly

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Standard hourly observations taken at Weather Bureau/National Weather Service offices and airports throughout the United States. Hourly observations began during the...

  5. Comparison of lipid and calorie loss from donor human milk among 3 methods of simulated gavage feeding: one-hour, 2-hour, and intermittent gravity feedings.

    Science.gov (United States)

    Brooks, Christine; Vickers, Amy Manning; Aryal, Subhash

    2013-04-01

    The objective of this study was to compare the differences in lipid loss from 24 samples of banked donor human milk (DHM) among 3 feeding methods: DHM given by syringe pump over 1 hour, 2 hours, and by bolus/gravity gavage. Comparative, descriptive. There were no human subjects. Twenty-four samples of 8 oz of DHM were divided into four 60-mL aliquots. Timed feedings were given by Medfusion 2001 syringe pumps with syringes connected to narrow-lumened extension sets designed for enteral feedings and connected to standard silastic enteral feeding tubes. Gravity feedings were given using the identical syringes connected to the same silastic feeding tubes. All aliquots were analyzed with the York Dairy Analyzer. Univariate repeated-measures analyses of variance were used for the omnibus testing for overall differences between the feeding methods. Lipid content expressed as grams per deciliter at the end of each feeding method was compared with the prefed control samples using the Dunnett's test. The Tukey correction was used for other pairwise multiple comparisons. The univariate repeated-measures analysis of variance conducted to test for overall differences between feeding methods showed a significant difference between the methods (F = 58.57, df = 3, 69, P gravity feeding methods (P = .3296). Pairwise comparison using the Tukey correction revealed a significant difference between both gravity and 1-hour feeding methods (P gravity and 2-hour feeding method (P gravity feedings, the timed feedings resulted in a statistically significant loss of fat as compared with their controls. These findings should raise questions about how those infants in the neonatal intensive care unit are routinely gavage fed.

  6. Multiplexed microsatellite recovery using massively parallel sequencing

    Science.gov (United States)

    Jennings, T.N.; Knaus, B.J.; Mullins, T.D.; Haig, S.M.; Cronn, R.C.

    2011-01-01

    Conservation and management of natural populations requires accurate and inexpensive genotyping methods. Traditional microsatellite, or simple sequence repeat (SSR), marker analysis remains a popular genotyping method because of the comparatively low cost of marker development, ease of analysis and high power of genotype discrimination. With the availability of massively parallel sequencing (MPS), it is now possible to sequence microsatellite-enriched genomic libraries in multiplex pools. To test this approach, we prepared seven microsatellite-enriched, barcoded genomic libraries from diverse taxa (two conifer trees, five birds) and sequenced these on one lane of the Illumina Genome Analyzer using paired-end 80-bp reads. In this experiment, we screened 6.1 million sequences and identified 356958 unique microreads that contained di- or trinucleotide microsatellites. Examination of four species shows that our conversion rate from raw sequences to polymorphic markers compares favourably to Sanger- and 454-based methods. The advantage of multiplexed MPS is that the staggering capacity of modern microread sequencing is spread across many libraries; this reduces sample preparation and sequencing costs to less than $400 (USD) per species. This price is sufficiently low that microsatellite libraries could be prepared and sequenced for all 1373 organisms listed as 'threatened' and 'endangered' in the United States for under $0.5M (USD).

  7. Is it acceptable to use coagulation plasma samples stored at room temperature and 4°C for 24 hours for additional prothrombin time, activated partial thromboplastin time, fibrinogen, antithrombin, and D-dimer testing?

    Science.gov (United States)

    Rimac, V; Coen Herak, D

    2017-10-01

    Coagulation laboratories are faced on daily basis with requests for additional testing in already analyzed fresh plasma samples. This prompted us to examine whether plasma samples stored at room temperature (RT), and 4°C for 24 hours can be accepted for additional prothrombin time (PT), activated partial thromboplastin time (aPTT), fibrinogen (Fbg), antithrombin (AT), and D-dimer testing. We measured PT, aPTT, Fbg in 50 and AT in 30 plasma samples with normal and pathological values, within 4 hours of blood collection (baseline results) and after 24-hours storage at RT (primary tubes), and 4°C (aliquots). D-dimer stability was investigated in 20 samples stored in primary tubes at 4°C. No statistically significant difference between baseline results and results in samples stored at RT and 4°C was observed for PT (P=.938), aPTT (P=.186), Fbg (P=.962), AT (P=.713), and D-dimers (P=.169). The highest median percentage changes were found for aPTT, being more pronounced for samples stored at 4°C (13.0%) than at RT (8.7%). Plasma samples stored both at RT and 4°C for 24 hours are acceptable for additional PT, Fbg, and AT testing. Plasma samples stored 24 hours in primary tubes at 4°C are suitable for D-dimer testing. © 2017 John Wiley & Sons Ltd.

  8. Human thyroid peroxidase: complete cDNA and protein sequence, chromosome mapping, and identification of two alternately spliced mRNAs

    International Nuclear Information System (INIS)

    Kimura, S.; Kotani, T.; McBride, O.W.; Umeki, K.; Hirai, K.; Nakayama, T.; Ohtaki, S.

    1987-01-01

    Two forms of human thyroid peroxidase cDNAs were isolated from a λgt11 cDNA library, prepared from Graves disease thyroid tissue mRNA, by use of oligonucleotides. The longest complete cDNA, designated phTPO-1, has 3048 nucleotides and an open reading frame consisting of 933 amino acids, which would encode a protein with a molecular weight of 103,026. Five potential asparagine-linked glycosylation sites are found in the deduced amino acid sequence. The second peroxidase cDNA, designated phTPO-2, is almost identical to phTPO-1 beginning 605 base pairs downstream except that it contains 1-base-pair difference and lacks 171 base pairs in the middle of the sequence. This results in a loss of 57 amino acids corresponding to a molecular weight of 6282. Interestingly, this 171-nucleotide sequence has GT and AG at its 5' and 3' boundaries, respectively, that are in good agreement with donor and acceptor splice site consensus sequences. Using specific oligonucleotide probes for the mRNAs derived from the cDNA sequences hTOP-1 and hTOP-2, the authors show that both are expressed in all thyroid tissues examined and the relative level of two mRNAs is different in each sample. The results suggest that two thyroid peroxidase proteins might be generated through alternate splicing of the same gene. By using somatic cell hybrid lines, the thyroid peroxidase gene was mapped to the short arm of human chromosome 2

  9. Effects of para-aminobenzoic acid (PABA) form and administration mode on PABA recovery in 24-hour urine collections.

    Science.gov (United States)

    Sharma, Rashmi S; Joy, Raechel C; Boushey, Carol J; Ferruzzi, Mario G; Leonov, Alexei P; McCrory, Megan A

    2014-03-01

    Para-aminobenzoic acid (PABA) has long been used as an objective measure to assess completeness of 24-hour urine collections. However, pharmaceutical-grade PABA for human ingestion is not available in the United States. An alternative, the potassium salt of PABA, aminobenzoate potassium, can be obtained for clinical use, although it has not yet been validated in this role. Both PABA and aminobenzoate potassium can be directly ingested in their tablet or capsule forms or added to food before consumption. Our aim was to investigate the effect of form (PABA vs aminobenzoate potassium) and administration mode (directly ingested as a tablet/capsule vs added to food) on urinary PABA recovery levels. Twenty healthy participants underwent 3 test days separated by two 24-hour wash-out periods. Three test conditions, one on each test day, were investigated in randomized order: PABA tablet, aminobenzoate potassium capsule, and PABA or aminobenzoate potassium in food. Ingestion of each dose was supervised and participants performed the 24-hour urine collections while free-living. The 24-hour urine collections were analyzed for PABA recovery (%R) levels using a colorimetric assay. Recoveries 85% to 110% were deemed complete and those >110% were reanalyzed by high pressure liquid chromatography and mass spectrometry. Only complete collections (>85%R) were included in analyses. The recovery for the PABA tablet, aminobenzoate potassium capsule, and PABA/aminobenzoate potassium in food were similar at 98.8%R±2.0%R, 95.1%R±2.3%R, and 93.2%R±2.1%R, respectively, and did not differ significantly. These results suggest that aminobenzoate potassium may be used as an alternative to PABA for assessing the completeness of 24-hour urine collections and to track compliance with consuming provided diets in community-dwelling studies. Copyright © 2014 Academy of Nutrition and Dietetics. Published by Elsevier Inc. All rights reserved.

  10. Validation Test Report for the BioCast Optical Forecast Model Version 1.0

    Science.gov (United States)

    2015-04-09

    hour forecast sequence have been established for ten months of continuous daily forecasting sequence trails in the northern Gulf of Mexico and the...beam-c field) is combined with today’s NCOM hourly forecast currents to predict the turbidity distribution (c)1 in 24 hours. The following day’s...proxy for turbidity ) coupled with the currents derived from the NCOM, BioCast enables the currents to advect the turbidity pixel information

  11. Identifying Corneal Infections in Formalin-Fixed Specimens Using Next Generation Sequencing.

    Science.gov (United States)

    Li, Zhigang; Breitwieser, Florian P; Lu, Jennifer; Jun, Albert S; Asnaghi, Laura; Salzberg, Steven L; Eberhart, Charles G

    2018-01-01

    We test the ability of next-generation sequencing, combined with computational analysis, to identify a range of organisms causing infectious keratitis. This retrospective study evaluated 16 cases of infectious keratitis and four control corneas in formalin-fixed tissues from the pathology laboratory. Infectious cases also were analyzed in the microbiology laboratory using culture, polymerase chain reaction, and direct staining. Classified sequence reads were analyzed with two different metagenomics classification engines, Kraken and Centrifuge, and visualized using the Pavian software tool. Sequencing generated 20 to 46 million reads per sample. On average, 96% of the reads were classified as human, 0.3% corresponded to known vectors or contaminant sequences, 1.7% represented microbial sequences, and 2.4% could not be classified. The two computational strategies successfully identified the fungal, bacterial, and amoebal pathogens in most patients, including all four bacterial and mycobacterial cases, five of six fungal cases, three of three Acanthamoeba cases, and one of three herpetic keratitis cases. In several cases, additional potential pathogens also were identified. In one case with cytomegalovirus identified by Kraken and Centrifuge, the virus was confirmed by direct testing, while two where Staphylococcus aureus or cytomegalovirus were identified by Centrifuge but not Kraken could not be confirmed. Confirmation was not attempted for an additional three potential pathogens identified by Kraken and 11 identified by Centrifuge. Next generation sequencing combined with computational analysis can identify a wide range of pathogens in formalin-fixed corneal specimens, with potential applications in clinical diagnostics and research.

  12. Complete genomic sequences of two salmonella enterica subsp. enterica serogroup C2 (O:6,8) strains from central California

    Science.gov (United States)

    Salmonella enteric subsp. enterica strains RM11060, serotype 6,8:d:-, and RM11065, serotype 6,8:-:e,n,z15, were isolated from environmental sampling in Central California in 2009. We report the complete genome sequences and annotation of these two strains. These genomic sequences are distinct and wi...

  13. Robust and rapid algorithms facilitate large-scale whole genome sequencing downstream analysis in an integrative framework.

    Science.gov (United States)

    Li, Miaoxin; Li, Jiang; Li, Mulin Jun; Pan, Zhicheng; Hsu, Jacob Shujui; Liu, Dajiang J; Zhan, Xiaowei; Wang, Junwen; Song, Youqiang; Sham, Pak Chung

    2017-05-19

    Whole genome sequencing (WGS) is a promising strategy to unravel variants or genes responsible for human diseases and traits. However, there is a lack of robust platforms for a comprehensive downstream analysis. In the present study, we first proposed three novel algorithms, sequence gap-filled gene feature annotation, bit-block encoded genotypes and sectional fast access to text lines to address three fundamental problems. The three algorithms then formed the infrastructure of a robust parallel computing framework, KGGSeq, for integrating downstream analysis functions for whole genome sequencing data. KGGSeq has been equipped with a comprehensive set of analysis functions for quality control, filtration, annotation, pathogenic prediction and statistical tests. In the tests with whole genome sequencing data from 1000 Genomes Project, KGGSeq annotated several thousand more reliable non-synonymous variants than other widely used tools (e.g. ANNOVAR and SNPEff). It took only around half an hour on a small server with 10 CPUs to access genotypes of ∼60 million variants of 2504 subjects, while a popular alternative tool required around one day. KGGSeq's bit-block genotype format used 1.5% or less space to flexibly represent phased or unphased genotypes with multiple alleles and achieved a speed of over 1000 times faster to calculate genotypic correlation. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  14. Genotypic Resistance Tests Sequences Reveal the Role of Marginalized Populations in HIV-1 Transmission in Switzerland.

    Science.gov (United States)

    Shilaih, Mohaned; Marzel, Alex; Yang, Wan Lin; Scherrer, Alexandra U; Schüpbach, Jörg; Böni, Jürg; Yerly, Sabine; Hirsch, Hans H; Aubert, Vincent; Cavassini, Matthias; Klimkait, Thomas; Vernazza, Pietro L; Bernasconi, Enos; Furrer, Hansjakob; Günthard, Huldrych F; Kouyos, Roger

    2016-06-14

    Targeting hard-to-reach/marginalized populations is essential for preventing HIV-transmission. A unique opportunity to identify such populations in Switzerland is provided by a database of all genotypic-resistance-tests from Switzerland, including both sequences from the Swiss HIV Cohort Study (SHCS) and non-cohort sequences. A phylogenetic tree was built using 11,127 SHCS and 2,875 Swiss non-SHCS sequences. Demographics were imputed for non-SHCS patients using a phylogenetic proximity approach. Factors associated with non-cohort outbreaks were determined using logistic regression. Non-B subtype (univariable odds-ratio (OR): 1.9; 95% confidence interval (CI): 1.8-2.1), female gender (OR: 1.6; 95% CI: 1.4-1.7), black ethnicity (OR: 1.9; 95% CI: 1.7-2.1) and heterosexual transmission group (OR:1.8; 95% CI: 1.6-2.0), were all associated with underrepresentation in the SHCS. We found 344 purely non-SHCS transmission clusters, however, these outbreaks were small (median 2, maximum 7 patients) with a strong overlap with the SHCS'. 65% of non-SHCS sequences were part of clusters composed of >= 50% SHCS sequences. Our data suggests that marginalized-populations are underrepresented in the SHCS. However, the limited size of outbreaks among non-SHCS patients in-care implies that no major HIV outbreak in Switzerland was missed by the SHCS surveillance. This study demonstrates the potential of sequence data to assess and extend the scope of infectious-disease surveillance.

  15. On Wasserstein Two-Sample Testing and Related Families of Nonparametric Tests

    Directory of Open Access Journals (Sweden)

    Aaditya Ramdas

    2017-01-01

    Full Text Available Nonparametric two-sample or homogeneity testing is a decision theoretic problem that involves identifying differences between two random variables without making parametric assumptions about their underlying distributions. The literature is old and rich, with a wide variety of statistics having being designed and analyzed, both for the unidimensional and the multivariate setting. Inthisshortsurvey,wefocusonteststatisticsthatinvolvetheWassersteindistance. Usingan entropic smoothing of the Wasserstein distance, we connect these to very different tests including multivariate methods involving energy statistics and kernel based maximum mean discrepancy and univariate methods like the Kolmogorov–Smirnov test, probability or quantile (PP/QQ plots and receiver operating characteristic or ordinal dominance (ROC/ODC curves. Some observations are implicit in the literature, while others seem to have not been noticed thus far. Given nonparametric two-sample testing’s classical and continued importance, we aim to provide useful connections for theorists and practitioners familiar with one subset of methods but not others.

  16. Effects on employees of controlling working hours and working schedules.

    Science.gov (United States)

    Kubo, T; Takahashi, M; Togo, F; Liu, X; Shimazu, A; Tanaka, K; Takaya, M

    2013-03-01

    High levels of control over working time and low variability in working hours have been associated with improved health-related outcomes. The potential mechanisms for this association remain unclear. To examine how work-time control and variability of working times are associated with fatigue recovery, sleep quality, work-life balance, and 'near misses' at work. Manufacturing sector employees completed a questionnaire that assessed work-time control, work-time variability, fatigue recovery, sleep quality, work-life balance and the frequency of near misses in the past 6 months. Mixed model analysis of covariance and multiple logistic regression analysis tested the main effects of work-time control and variability and their interaction, while adjusting for age, sex, work schedules, and overtime work in the past month. Subscales of work-time control were also investigated (control over daily working hours and over days off). One thousand three hundred and seventy-two completed questionnaires were returned, a response rate of 69%. A significantly higher quality of sleep and better work-life balance were found in the 'high control with low variability' reference group than in the other groups. Significantly better recovery of fatigue was also observed in the group having control over days off with low variability. While near misses were more frequent in the group with high control over daily working hours coupled with high variability compared with the reference group this was not significant. High work-time control and low variability were associated with favourable outcomes of health and work-life balance. This combined effect was not observed for the safety outcome addressed here.

  17. Elevation or Suppression? The Resolved Star Formation Main Sequence of Galaxies with Two Different Assembly Modes

    Science.gov (United States)

    Liu, Qing; Wang, Enci; Lin, Zesen; Gao, Yulong; Liu, Haiyang; Berhane Teklu, Berzaf; Kong, Xu

    2018-04-01

    We investigate the spatially resolved star formation main sequence in star-forming galaxies using Integral Field Spectroscopic observations from the Mapping Nearby Galaxies at the Apache Point Observatory survey. We demonstrate that the correlation between the stellar mass surface density (Σ*) and star formation rate surface density (ΣSFR) holds down to the sub-galactic scale, leading to the sub-galactic main sequence (SGMS). By dividing galaxies into two populations based on their recent mass assembly modes, we find the resolved main sequence in galaxies with the “outside-in” mode is steeper than that in galaxies with the “inside-out” mode. This is also confirmed on a galaxy-by-galaxy level, where we find the distributions of SGMS slopes for individual galaxies are clearly separated for the two populations. When normalizing and stacking the SGMS of individual galaxies on one panel for the two populations, we find that the inner regions of galaxies with the “inside-out” mode statistically exhibit a suppression in star formation, with a less significant trend in the outer regions of galaxies with the “outside-in” mode. In contrast, the inner regions of galaxies with “outside-in” mode and the outer regions of galaxies with “inside-out” mode follow a slightly sublinear scaling relation with a slope ∼0.9, which is in good agreement with previous findings, suggesting that they are experiencing a universal regulation without influences of additional physical processes.

  18. De novo sequencing of two novel peptides homologous to calcitonin-like peptides, from skin secretion of the Chinese Frog, Odorrana schmackeri

    Directory of Open Access Journals (Sweden)

    Geisa P.C. Evaristo

    2015-09-01

    Full Text Available An MS/MS based analytical strategy was followed to solve the complete sequence of two new peptides from frog (Odorrana schmackeri skin secretion. This involved reduction and alkylation with two different alkylating agents followed by high resolution tandem mass spectrometry. De novo sequencing was achieved by complementary CID and ETD fragmentations of full-length peptides and of selected tryptic fragments. Heavy and light isotope dimethyl labeling assisted with annotation of sequence ion series. The identified primary structures are GCD[I/L]STCATHN[I/L]VNE[I/L]NKFDKSKPSSGGVGPESP-NH2 and SCNLSTCATHNLVNELNKFDKSKPSSGGVGPESF-NH2, i.e. two carboxyamidated 34 residue peptides with an aminoterminal intramolecular ring structure formed by a disulfide bridge between Cys2 and Cys7. Edman degradation analysis of the second peptide positively confirmed the exact sequence, resolving I/L discriminations. Both peptide sequences are novel and share homology with calcitonin, calcitonin gene related peptide (CGRP and adrenomedullin from other vertebrates. Detailed sequence analysis as well as the 34 residue length of both O. schmackeri peptides, suggest they do not fully qualify as either calcitonins (32 residues or CGRPs (37 amino acids and may justify their classification in a novel peptide family within the calcitonin gene related peptide superfamily. Smooth muscle contractility assays with synthetic replicas of the S–S linked peptides on rat tail artery, uterus, bladder and ileum did not reveal myotropic activity.

  19. Automated two-point dixon screening for the evaluation of hepatic steatosis and siderosis: comparison with R2-relaxometry and chemical shift-based sequences.

    Science.gov (United States)

    Henninger, B; Zoller, H; Rauch, S; Schocke, M; Kannengiesser, S; Zhong, X; Reiter, G; Jaschke, W; Kremser, C

    2015-05-01

    To evaluate the automated two-point Dixon screening sequence for the detection and estimated quantification of hepatic iron and fat compared with standard sequences as a reference. One hundred and two patients with suspected diffuse liver disease were included in this prospective study. The following MRI protocol was used: 3D-T1-weighted opposed- and in-phase gradient echo with two-point Dixon reconstruction and dual-ratio signal discrimination algorithm ("screening" sequence); fat-saturated, multi-gradient-echo sequence with 12 echoes; gradient-echo T1 FLASH opposed- and in-phase. Bland-Altman plots were generated and correlation coefficients were calculated to compare the sequences. The screening sequence diagnosed fat in 33, iron in 35 and a combination of both in 4 patients. Correlation between R2* values of the screening sequence and the standard relaxometry was excellent (r = 0.988). A slightly lower correlation (r = 0.978) was found between the fat fraction of the screening sequence and the standard sequence. Bland-Altman revealed systematically lower R2* values obtained from the screening sequence and higher fat fraction values obtained with the standard sequence with a rather high variability in agreement. The screening sequence is a promising method with fast diagnosis of the predominant liver disease. It is capable of estimating the amount of hepatic fat and iron comparable to standard methods. • MRI plays a major role in the clarification of diffuse liver disease. • The screening sequence was introduced for the assessment of diffuse liver disease. • It is a fast and automated algorithm for the evaluation of hepatic iron and fat. • It is capable of estimating the amount of hepatic fat and iron.

  20. Sequence and structural analysis of the chitinase insertion domain reveals two conserved motifs involved in chitin-binding.

    Directory of Open Access Journals (Sweden)

    Hai Li

    2010-01-01

    Full Text Available Chitinases are prevalent in life and are found in species including archaea, bacteria, fungi, plants, and animals. They break down chitin, which is the second most abundant carbohydrate in nature after cellulose. Hence, they are important for maintaining a balance between carbon and nitrogen trapped as insoluble chitin in biomass. Chitinases are classified into two families, 18 and 19 glycoside hydrolases. In addition to a catalytic domain, which is a triosephosphate isomerase barrel, many family 18 chitinases contain another module, i.e., chitinase insertion domain. While numerous studies focus on the biological role of the catalytic domain in chitinase activity, the function of the chitinase insertion domain is not completely understood. Bioinformatics offers an important avenue in which to facilitate understanding the role of residues within the chitinase insertion domain in chitinase function.Twenty-seven chitinase insertion domain sequences, which include four experimentally determined structures and span five kingdoms, were aligned and analyzed using a modified sequence entropy parameter. Thirty-two positions with conserved residues were identified. The role of these conserved residues was explored by conducting a structural analysis of a number of holo-enzymes. Hydrogen bonding and van der Waals calculations revealed a distinct subset of four conserved residues constituting two sequence motifs that interact with oligosaccharides. The other conserved residues may be key to the structure, folding, and stability of this domain.Sequence and structural studies of the chitinase insertion domains conducted within the framework of evolution identified four conserved residues which clearly interact with the substrates. Furthermore, evolutionary studies propose a link between the appearance of the chitinase insertion domain and the function of family 18 chitinases in the subfamily A.

  1. Council tax valuation bands and contacts with a GP out-of-hours service.

    Science.gov (United States)

    Beale, Norman; Taylor, Gordon; Gwynne, Mark; Peart, Carole

    2006-04-01

    UK GPs are no longer responsible for the organisation of out-of-hours care for their patients, but resources remains capitation-based. This cross-sectional study tests whether council tax valuation bands can predict the demand for such services. All out-of-hours contacts made by patients in North Wiltshire over 4 months were classified by council tax band; frequencies compared with official population statistics. Council tax band predicts out-of-hours GP workload irrespective of age and sex: the more modest the home, the higher the GP contact rate. It may prove more difficult to sustain out-of-hours services in deprived parts of the UK.

  2. Amino-acid sequence of two trypsin isoinhibitors, ITD I and ITD III from squash seeds (Cucurbita maxima).

    Science.gov (United States)

    Wilusz, T; Wieczorek, M; Polanowski, A; Denton, A; Cook, J; Laskowski, M

    1983-01-01

    The amino-acid sequences of two trypsin isoinhibitors, ITD I and ITD III, from squash seeds (Cucurbita maxima) were determined. Both isoinhibitors contain 29 amino-acid residues, including 6 half cystine residues. They differ only by one amino acid. Lysine in position 9 of ITD III is substituted by glutamic acid in ITD I. Arginine in position 5 is present at the reactive site of both isoinhibitors. The previously published sequence of ITD III has been shown to be incorrect.

  3. HIV drug resistance testing among patients failing second line antiretroviral therapy. Comparison of in-house and commercial sequencing.

    Science.gov (United States)

    Chimukangara, Benjamin; Varyani, Bhavini; Shamu, Tinei; Mutsvangwa, Junior; Manasa, Justen; White, Elizabeth; Chimbetete, Cleophas; Luethy, Ruedi; Katzenstein, David

    2017-05-01

    HIV genotyping is often unavailable in low and middle-income countries due to infrastructure requirements and cost. We compared genotype resistance testing in patients with virologic failure, by amplification of HIV pol gene, followed by "in-house" sequencing and commercial sequencing. Remnant plasma samples from adults and children failing second-line ART were amplified and sequenced using in-house and commercial di-deoxysequencing, and analyzed in Harare, Zimbabwe and at Stanford, U.S.A, respectively. HIV drug resistance mutations were determined using the Stanford HIV drug resistance database. Twenty-six of 28 samples were amplified and 25 were successfully genotyped. Comparison of average percent nucleotide and amino acid identities between 23 pairs sequenced in both laboratories were 99.51 (±0.56) and 99.11 (±0.95), respectively. All pairs clustered together in phylogenetic analysis. Sequencing analysis identified 6/23 pairs with mutation discordances resulting in differences in phenotype, but these did not impact future regimens. The results demonstrate our ability to produce good quality drug resistance data in-house. Despite discordant mutations in some sequence pairs, the phenotypic predictions were not clinically significant. Copyright © 2016 Elsevier B.V. All rights reserved.

  4. Hour of Code”: Can It Change Students’ Attitudes toward Programming?

    Directory of Open Access Journals (Sweden)

    Hayden Wimmer

    2016-03-01

    Full Text Available The Hour of Code is a one-hour introduction to computer science organized by Code.org, a non-profit dedicated to expanding participation in computer science. This study investigated the impact of the Hour of Code on students’ attitudes towards computer programming and their knowledge of programming. A sample of undergraduate students from two universities was selected to participate. Participants completed an Hour of Code tutorial as part of an undergraduate course. An electronic questionnaire was implemented in a pre-survey and post-survey format to gauge the change in student attitudes toward programming and their programming ability. The findings indicated the positive impact of the Hour of Code tutorial on students’ attitude toward programming. However, the students’ programming skills did not significantly change. The authors suggest that a deeper alignment of marketing, teaching, and content would help sustain the type of initiative exemplified by the Hour of Code.

  5. Simultaneous analysis of all SNPs in genome-wide and re-sequencing association studies.

    Directory of Open Access Journals (Sweden)

    Clive J Hoggart

    2008-07-01

    Full Text Available Testing one SNP at a time does not fully realise the potential of genome-wide association studies to identify multiple causal variants, which is a plausible scenario for many complex diseases. We show that simultaneous analysis of the entire set of SNPs from a genome-wide study to identify the subset that best predicts disease outcome is now feasible, thanks to developments in stochastic search methods. We used a Bayesian-inspired penalised maximum likelihood approach in which every SNP can be considered for additive, dominant, and recessive contributions to disease risk. Posterior mode estimates were obtained for regression coefficients that were each assigned a prior with a sharp mode at zero. A non-zero coefficient estimate was interpreted as corresponding to a significant SNP. We investigated two prior distributions and show that the normal-exponential-gamma prior leads to improved SNP selection in comparison with single-SNP tests. We also derived an explicit approximation for type-I error that avoids the need to use permutation procedures. As well as genome-wide analyses, our method is well-suited to fine mapping with very dense SNP sets obtained from re-sequencing and/or imputation. It can accommodate quantitative as well as case-control phenotypes, covariate adjustment, and can be extended to search for interactions. Here, we demonstrate the power and empirical type-I error of our approach using simulated case-control data sets of up to 500 K SNPs, a real genome-wide data set of 300 K SNPs, and a sequence-based dataset, each of which can be analysed in a few hours on a desktop workstation.

  6. Working hours in a period of low economic growth

    OpenAIRE

    Walterskirchen, Ewald

    2016-01-01

    Collectively agreed reductions of working hours phased out in Europe in the 1990s. During the last two decades, working time became more flexible and heterogeneous. Working hours of full-time employees in the EU hardly changed. The strong increase in part-time work was the outstanding phenomenon. Today, one third of female employees and almost ten percent of male employees work part-time. In a period of slow growth, productivity gains will be squeezed by subdued investment and low capacity ut...

  7. Design of horizontal test cryostat for testing two 650 MHz cavities: cryogenic considerations

    Science.gov (United States)

    Khare, P.; Gilankar, S.; Kush, P. K.; Lakshminarayanan, A.; Choubey, R.; Ghosh, R.; Jain, A.; Patel, H.; Gupta, P. D.; Hocker, A.; Ozelis, J. P.; Geynisman, M.; Reid, C.; Poloubotko, V.; Mitchell, D.; Peterson, T. J.; Nicol, T. H.

    2017-02-01

    Horizontal Test Cryostat has been designed for testing two 650 MHz "dressed" Superconducting Radio Frequency (SCRF) cavities in a single testing cycle at Raja Ramanna Centre for Advanced Technology, India (RRCAT) in collaboration with Fermi National Accelerator Laboratory, USA (FNAL). This cryostat will facilitate testing of two 5-cell 650 MHz SCRF cavities, in CW or pulsed regime, for upcoming High Intensity Superconducting Proton Accelerator projects at both countries. Two such HTS facilities are planned, one at RRCAT for Indian Spallation Neutron Source project (ISNS), which is on the horizon, and the other at FNAL, USA. A test cryostat, a part of horizontal test stand-2 (HTS-2) will be set up at RRCAT for Indian project. In order to maximize the utility of this facility, it can also be used to test two dressed 9-cell 1.3 GHz cavities and other similarly-sized devices. The facility assumes, as an input, the availability of liquid nitrogen at 80 K and liquid helium at 4.5 K and 2 K, with a refrigeration capacity of approximately 50 W at 2 K. Design work of cryostat has been completed and now procurement process is in progress. This paper discusses salient features of the cryostat. It also describes different design calculations and ANSYS analysis for cool down of few subsystems like cavity support system and liquid nitrogen cooled thermal radiation shield of horizontal test cryostat..

  8. Impact of Age and Hearing Impairment on Work Performance during Long Working Hours

    Directory of Open Access Journals (Sweden)

    Verena Wagner-Hartl

    2018-01-01

    Full Text Available Based on demographic prognoses, it must be assumed that a greater number of older workers will be found in the future labor market. How to deal with their possible age-related impairments of sensory functions, like hearing impairment and work performance during extended working time, has not been addressed explicitly until now. The study addresses this interplay. The study was performed on two consecutive days after normal working hours. The 55 participants had to “work” in the study at least three additional hours to simulate a situation of long working hours. The tested measures for (job performance were: general attention, long-term selective attention, concentration, and reaction time. All of the investigated variables were taken at both days of the study (2 × 2 × 2 repeated measurement design. The results show effects for age, the interaction of hearing impairment and time of measurement, and effects of the measurement time. Older participants reacted slower than younger participants did. Furthermore, younger participants reacted more frequently in a correct way. Hearing impairment seems to have a negative impact especially on measures of false reactions, and therefore especially on measurement time 1. The results can be interpreted in a way that hearing-impaired participants are able to compensate their deficits over time.

  9. Impact of Age and Hearing Impairment on Work Performance during Long Working Hours.

    Science.gov (United States)

    Wagner-Hartl, Verena; Grossi, Nina R; Kallus, K Wolfgang

    2018-01-09

    Based on demographic prognoses, it must be assumed that a greater number of older workers will be found in the future labor market. How to deal with their possible age-related impairments of sensory functions, like hearing impairment and work performance during extended working time, has not been addressed explicitly until now. The study addresses this interplay. The study was performed on two consecutive days after normal working hours. The 55 participants had to "work" in the study at least three additional hours to simulate a situation of long working hours. The tested measures for (job) performance were: general attention, long-term selective attention, concentration, and reaction time. All of the investigated variables were taken at both days of the study (2 × 2 × 2 repeated measurement design). The results show effects for age, the interaction of hearing impairment and time of measurement, and effects of the measurement time. Older participants reacted slower than younger participants did. Furthermore, younger participants reacted more frequently in a correct way. Hearing impairment seems to have a negative impact especially on measures of false reactions, and therefore especially on measurement time 1. The results can be interpreted in a way that hearing-impaired participants are able to compensate their deficits over time.

  10. Is sequence awareness mandatory for perceptual sequence learning: An assessment using a pure perceptual sequence learning design.

    Science.gov (United States)

    Deroost, Natacha; Coomans, Daphné

    2018-02-01

    We examined the role of sequence awareness in a pure perceptual sequence learning design. Participants had to react to the target's colour that changed according to a perceptual sequence. By varying the mapping of the target's colour onto the response keys, motor responses changed randomly. The effect of sequence awareness on perceptual sequence learning was determined by manipulating the learning instructions (explicit versus implicit) and assessing the amount of sequence awareness after the experiment. In the explicit instruction condition (n = 15), participants were instructed to intentionally search for the colour sequence, whereas in the implicit instruction condition (n = 15), they were left uninformed about the sequenced nature of the task. Sequence awareness after the sequence learning task was tested by means of a questionnaire and the process-dissociation-procedure. The results showed that the instruction manipulation had no effect on the amount of perceptual sequence learning. Based on their report to have actively applied their sequence knowledge during the experiment, participants were subsequently regrouped in a sequence strategy group (n = 14, of which 4 participants from the implicit instruction condition and 10 participants from the explicit instruction condition) and a no-sequence strategy group (n = 16, of which 11 participants from the implicit instruction condition and 5 participants from the explicit instruction condition). Only participants of the sequence strategy group showed reliable perceptual sequence learning and sequence awareness. These results indicate that perceptual sequence learning depends upon the continuous employment of strategic cognitive control processes on sequence knowledge. Sequence awareness is suggested to be a necessary but not sufficient condition for perceptual learning to take place. Copyright © 2018 Elsevier B.V. All rights reserved.

  11. Long sequence correlation coprocessor

    Science.gov (United States)

    Gage, Douglas W.

    1994-09-01

    A long sequence correlation coprocessor (LSCC) accelerates the bitwise correlation of arbitrarily long digital sequences by calculating in parallel the correlation score for 16, for example, adjacent bit alignments between two binary sequences. The LSCC integrated circuit is incorporated into a computer system with memory storage buffers and a separate general purpose computer processor which serves as its controller. Each of the LSCC's set of sequential counters simultaneously tallies a separate correlation coefficient. During each LSCC clock cycle, computer enable logic associated with each counter compares one bit of a first sequence with one bit of a second sequence to increment the counter if the bits are the same. A shift register assures that the same bit of the first sequence is simultaneously compared to different bits of the second sequence to simultaneously calculate the correlation coefficient by the different counters to represent different alignments of the two sequences.

  12. In vivo capsular switch in Streptococcus pneumoniae--analysis by whole genome sequencing.

    Directory of Open Access Journals (Sweden)

    Fen Z Hu

    Full Text Available Two multidrug resistant strains of Streptococcus pneumoniae - SV35-T23 (capsular type 23F and SV36-T3 (capsular type 3 were recovered from the nasopharynx of two adult patients during an outbreak of pneumococcal disease in a New York hospital in 1996. Both strains belonged to the pandemic lineage PMEN1 but they differed strikingly in virulence when tested in the mouse model of IP infection: as few as 1000 CFU of SV36 killed all mice within 24 hours after inoculation while SV35-T23 was avirulent.Whole genome sequencing (WGS of the two isolates was performed (i to test if these two isolates belonging to the same clonal type and recovered from an identical epidemiological scenario only differed in their capsular genes? and (ii to test if the vast difference in virulence between the strains was mostly - or exclusively - due to the type III capsule. WGS demonstrated extensive differences between the two isolates including over 2500 single nucleotide polymorphisms in core genes and also differences in 36 genetic determinants: 25 of which were unique to SV35-T23 and 11 unique to strain SV36-T3. Nineteen of these differences were capsular genes and 9 bacteriocin genes.Using genetic transformation in the laboratory, the capsular region of SV35-T23 was replaced by the type 3 capsular genes from SV36-T3 to generate the recombinant SV35-T3* which was as virulent as the parental strain SV36-T3* in the murine model and the type 3 capsule was the major virulence factor in the chinchilla model as well. On the other hand, a careful comparison of strains SV36-T3 and the laboratory constructed SV35-T3* in the chinchilla model suggested that some additional determinants present in SV36 but not in the laboratory recombinant may also contribute to the progression of middle ear disease. The nature of this determinants remains to be identified.

  13. Reconstruction of ancestral RNA sequences under multiple structural constraints.

    Science.gov (United States)

    Tremblay-Savard, Olivier; Reinharz, Vladimir; Waldispühl, Jérôme

    2016-11-11

    Secondary structures form the scaffold of multiple sequence alignment of non-coding RNA (ncRNA) families. An accurate reconstruction of ancestral ncRNAs must use this structural signal. However, the inference of ancestors of a single ncRNA family with a single consensus structure may bias the results towards sequences with high affinity to this structure, which are far from the true ancestors. In this paper, we introduce achARNement, a maximum parsimony approach that, given two alignments of homologous ncRNA families with consensus secondary structures and a phylogenetic tree, simultaneously calculates ancestral RNA sequences for these two families. We test our methodology on simulated data sets, and show that achARNement outperforms classical maximum parsimony approaches in terms of accuracy, but also reduces by several orders of magnitude the number of candidate sequences. To conclude this study, we apply our algorithms on the Glm clan and the FinP-traJ clan from the Rfam database. Our results show that our methods reconstruct small sets of high-quality candidate ancestors with better agreement to the two target structures than with classical approaches. Our program is freely available at: http://csb.cs.mcgill.ca/acharnement .

  14. The usefulness of DNA sequencing after extraction by Whatman FTA filter matrix technology and phenotypic tests for differentiation of Candida albicans and Candida dubliniensis.

    Science.gov (United States)

    Kiraz, Nuri; Oz, Yasemin; Aslan, Huseyin; Muslumanoglu, Hamza

    2014-02-01

    Since C. dubliniensis is similar to C. albicans phenotypically, it can be misidentified as C. albicans. We aimed to investigate the prevalence of C. dubliniensis among isolates previously identified as C. albicans in our stocks and to compare the phenotypic methods and DNA sequencing of D1/D2 region on the ribosomal large subunit (rLSU) gene. A total of 850 isolates included in this study. Phenotypic identification was performed based on germ tube formation, chlamydospore production, colony colors on chromogenic agar, inability of growth at 45 °C and growth on hypertonic Sabouraud dextrose agar. Eighty isolates compatible with C. dubliniensis by at least one phenotypic test were included in the sequence analysis. Nested PCR amplification of D1/D2 region of the rLSU gene was performed after the fungal DNA extraction by Whatman FTA filter paper technology. The sequencing analysis of PCR products carried out by an automated capillary gel electrophoresis device. The rate of C. dubliniensis was 2.35 % (n = 20) among isolates previously described as C. albicans. Consequently, none of the phenotypic tests provided satisfactory performance alone in our study, and molecular methods required special equipment and high cost. Thus, at least two phenotypic methods can be used for identification of C. dubliniensis, and molecular methods can be used for confirmation.

  15. Deregulating Overtime Hours Restrictions on Women and its Effects on Female Employment

    DEFF Research Database (Denmark)

    Kato, Takao; Kodama, Naomi

    2017-01-01

    This paper provides novel evidence on the effect of deregulating overtime hours restrictions on women by using the 1985 Amendments to the Labour Standards Act (LSA) in Japan as a natural experiment. The original LSA of 1947 prohibited women from working overtime exceeding two hours a day; six hours...... a week; and 150 hours a year. The 1985 Amendments exempted a variety of occupations and industries from such an overtime restriction on women. Applying a difference-in-difference model to census data, we find causal evidence pointing to the positive effect of this particular piece of labour market...

  16. Analysis of Office/Laboratory Staying Hour and Home Working Hour of Japanese Scientists and Engineers

    Science.gov (United States)

    Ejiri, A.

    The second questionnaire for scientists and engineers was carried out in 2007, and status of Japanese scientists and engineers were analyzed and reported. A part of the data was reanalyzed from the viewpoint of work life balance. In particular, office/laboratory staying hour and home working hour were analyzed and dependences on various factors were investigated. It was found that these hours depend on gender, marital status, number of child, employment status and age. In addition, the total hours tend to be kept constant regardless of various factors.

  17. Impact of working hours on sleep and mental health.

    Science.gov (United States)

    Afonso, P; Fonseca, M; Pires, J F

    2017-07-01

    The number of hours people are required to work has a pervasive influence on both physical and mental health. Excessive working hours can also negatively affect sleep quality. The impact at work of mental health problems can have serious consequences for individuals' as well as for organizations' productivity. To evaluate differences in sleep quality and anxiety and depression symptoms between longer working hours group (LWHG) and regular working hours group (RWHG). To examine factors influencing weekly working hours, sleep quality and anxiety and depressive symptoms. Participants were divided into two groups, RWHG and LWHG, based on working hours, with a cut-off of 48 h per week. We used the Hospital Anxiety and Depression Scale (HADS) to assess anxiety and depression symptoms and the Pittsburgh Sleep Quality Index (PSQI) to measure the quality and patterns of sleep. The response rate was 23%. Among the 429 study participants, those in the LWHG group (n = 256, 53%) had significantly more depressive and anxiety symptoms and worse sleep quality than those in RWHG (n = 223, 47%). Working time was significantly positively correlated with higher corporate position and HADS scores. Moreover, HADS scores were positively correlated with PSQI scores and negatively correlated with age. This study suggests that longer working hours are associated with poorer mental health status and increasing levels of anxiety and depression symptoms. There was a positive correlation between these symptoms and sleep disturbances. © The Author 2017. Published by Oxford University Press on behalf of the Society of Occupational Medicine. All rights reserved. For Permissions, please email: journals.permissions@oup.com

  18. Library Design-Facilitated High-Throughput Sequencing of Synthetic Peptide Libraries.

    Science.gov (United States)

    Vinogradov, Alexander A; Gates, Zachary P; Zhang, Chi; Quartararo, Anthony J; Halloran, Kathryn H; Pentelute, Bradley L

    2017-11-13

    A methodology to achieve high-throughput de novo sequencing of synthetic peptide mixtures is reported. The approach leverages shotgun nanoliquid chromatography coupled with tandem mass spectrometry-based de novo sequencing of library mixtures (up to 2000 peptides) as well as automated data analysis protocols to filter away incorrect assignments, noise, and synthetic side-products. For increasing the confidence in the sequencing results, mass spectrometry-friendly library designs were developed that enabled unambiguous decoding of up to 600 peptide sequences per hour while maintaining greater than 85% sequence identification rates in most cases. The reliability of the reported decoding strategy was additionally confirmed by matching fragmentation spectra for select authentic peptides identified from library sequencing samples. The methods reported here are directly applicable to screening techniques that yield mixtures of active compounds, including particle sorting of one-bead one-compound libraries and affinity enrichment of synthetic library mixtures performed in solution.

  19. Estimation of clear sky hourly global solar radiation in Iraq

    Energy Technology Data Exchange (ETDEWEB)

    Al-Jumaily, Kais J.; Al-Zuhairi, Munya F.; Mahdi, Zahraa S. [Department of Atmospheric Sciences, College of Science, Al-Mustansiriyah University, Baghdad (Iraq)

    2012-07-01

    The availability of hourly solar radiation data is very important for applications utilizing solar energy and for climate and environmental aspects. The aim of this work is to use a simple model for estimating hourly global solar radiation under clear sky condition in Iraq. Calculations were compared with measurements obtained from local station in Baghdad city and from Meteosat satellite data for different locations in Iraq. The statistical test methods of the mean bias error (MBE), root mean square error (RMSE) and t-test were used to evaluate the performance of the model. Results indicated that a fairly good agreement exists between calculated and measured values for all locations in Iraq. Since the model is independent of any meteorological variable, it would be of a practical use for rural areas where no meteorological data are available.

  20. Complete genome sequences of two strains of Treponema pallidum subsp. pertenue from Ghana, Africa: Identical genome sequences in samples isolated more than 7 years apart.

    Directory of Open Access Journals (Sweden)

    Michal Strouhal

    2017-09-01

    Full Text Available Treponema pallidum subsp. pertenue (TPE is the causative agent of yaws, a multi-stage disease, endemic in tropical regions of Africa, Asia, Oceania, and South America. To date, four TPE strains have been completely sequenced including three TPE strains of human origin (Samoa D, CDC-2, and Gauthier and one TPE strain (Fribourg-Blanc isolated from a baboon. All TPE strains are highly similar to T. pallidum subsp. pallidum (TPA strains. The mutation rate in syphilis and related treponemes has not been experimentally determined yet.Complete genomes of two TPE strains, CDC 2575 and Ghana-051, that infected patients in Ghana and were isolated in 1980 and 1988, respectively, were sequenced and analyzed. Both strains had identical consensus genome nucleotide sequences raising the question whether TPE CDC 2575 and Ghana-051 represent two different strains. Several lines of evidence support the fact that both strains represent independent samples including regions showing intrastrain heterogeneity (13 and 5 intrastrain heterogeneous sites in TPE Ghana-051 and TPE CDC 2575, respectively. Four of these heterogeneous sites were found in both genomes but the frequency of alternative alleles differed. The identical consensus genome sequences were used to estimate the upper limit of the yaws treponeme evolution rate, which was 4.1 x 10-10 nucleotide changes per site per generation.The estimated upper limit for the mutation rate of TPE was slightly lower than the mutation rate of E. coli, which was determined during a long-term experiment. Given the known diversity between TPA and TPE genomes and the assumption that both TPA and TPE have a similar mutation rate, the most recent common ancestor of syphilis and yaws treponemes appears to be more than ten thousand years old and likely even older.

  1. Disambiguate: An open-source application for disambiguating two species in next generation sequencing data from grafted samples.

    Science.gov (United States)

    Ahdesmäki, Miika J; Gray, Simon R; Johnson, Justin H; Lai, Zhongwu

    2016-01-01

    Grafting of cell lines and primary tumours is a crucial step in the drug development process between cell line studies and clinical trials. Disambiguate is a program for computationally separating the sequencing reads of two species derived from grafted samples. Disambiguate operates on DNA or RNA-seq alignments to the two species and separates the components at very high sensitivity and specificity as illustrated in artificially mixed human-mouse samples. This allows for maximum recovery of data from target tumours for more accurate variant calling and gene expression quantification. Given that no general use open source algorithm accessible to the bioinformatics community exists for the purposes of separating the two species data, the proposed Disambiguate tool presents a novel approach and improvement to performing sequence analysis of grafted samples. Both Python and C++ implementations are available and they are integrated into several open and closed source pipelines. Disambiguate is open source and is freely available at https://github.com/AstraZeneca-NGS/disambiguate.

  2. Genome sequencing and comparison of two nonhuman primate animal models, the cynomolgus and Chinese rhesus macaques

    DEFF Research Database (Denmark)

    Yan, Guangmei; Zhang, Guojie; Fang, Xiaodong

    2011-01-01

    The nonhuman primates most commonly used in medical research are from the genus Macaca. To better understand the genetic differences between these animal models, we present high-quality draft genome sequences from two macaque species, the cynomolgus/crab-eating macaque and the Chinese rhesus...

  3. CANFLEX fuel bundle cross-flow endurance test 2 (Test report)

    Energy Technology Data Exchange (ETDEWEB)

    Hong, Sung Deok; Chung, C. H.; Chang, S. K.; Kim, B. D. [Korea Atomic Energy Research Institute, Taejeon (Korea)

    2000-02-01

    This report describes cross-flow endurance test 2 that was conducted at the CANDU-Hot Test Loop. The test was completed on March 30, 1999 using a new CANFLEX bundle, built by KAERI. It was carried out for a total of 22 hours. After an initial period of ten hours, the test was stopped at the intervals of four hours for bundle inspection and inter-element gap measurement[7]. The test bundle end-plate to end-cap welds were inspected carefully for failure or crack propagation using liquid penetrant examination especially at the heat-affected zones. 12 refs., 4 figs., 10 tabs. (Author)

  4. Chromosomal localization of two novel repetitive sequences isolated from the Chenopodium quinoa Willd. genome.

    Science.gov (United States)

    Kolano, B; Gardunia, B W; Michalska, M; Bonifacio, A; Fairbanks, D; Maughan, P J; Coleman, C E; Stevens, M R; Jellen, E N; Maluszynska, J

    2011-09-01

    The chromosomal organization of two novel repetitive DNA sequences isolated from the Chenopodium quinoa Willd. genome was analyzed across the genomes of selected Chenopodium species. Fluorescence in situ hybridization (FISH) analysis with the repetitive DNA clone 18-24J in the closely related allotetraploids C. quinoa and Chenopodium berlandieri Moq. (2n = 4x = 36) evidenced hybridization signals that were mainly present on 18 chromosomes; however, in the allohexaploid Chenopodium album L. (2n = 6x = 54), cross-hybridization was observed on all of the chromosomes. In situ hybridization with rRNA gene probes indicated that during the evolution of polyploidy, the chenopods lost some of their rDNA loci. Reprobing with rDNA indicated that in the subgenome labeled with 18-24J, one 35S rRNA locus and at least half of the 5S rDNA loci were present. A second analyzed sequence, 12-13P, localized exclusively in pericentromeric regions of each chromosome of C. quinoa and related species. The intensity of the FISH signals differed considerably among chromosomes. The pattern observed on C. quinoa chromosomes after FISH with 12-13P was very similar to GISH results, suggesting that the 12-13P sequence constitutes a major part of the repetitive DNA of C. quinoa.

  5. 10 CFR 26.205 - Work hours.

    Science.gov (United States)

    2010-01-01

    ... an 8-hour break between successive work periods when a break of less than 10 hours is necessary to...) Individuals who are working 8-hour shift schedules shall have at least 1 day off per week, averaged over the shift cycle; (ii) Individuals who are working 10-hour shift schedules shall have at least 2 days off per...

  6. Working hours and common mental disorders in English police officers.

    Science.gov (United States)

    Houdmont, J; Randall, R

    2016-12-01

    There is a paucity of evidence on working hours and their psychological correlates in police officers of the federated ranks in England. An exploratory study to establish the extent to which a sample of English police officers worked long hours and the association between long working hours and common mental disorder (CMD). Officers of the federated ranks (constable, sergeant, inspector) from two English county forces completed a questionnaire to report their typical weekly working hours and symptoms of CMD. We also collected socio- and occupational-demographic data. We defined long working hours as ≥49 h in a typical week in accordance with 48-h weekly limit specified in the 1993 European Directive on the Organisation of Working Time. We established associations between long working hours and self-reported CMDs using binary logistic regression to generate odds ratios (ORs) and 95% confidence intervals (CIs) adjusted for potential confounding variables. Twenty-seven per cent (n = 327/1226) of respondents reported long working hours. The ORs for psychological distress (OR 2.05, 95% CI 1.57-2.68), emotional exhaustion (OR 1.99, 95% CI 1.52-2.59), and depersonalization (OR 1.30, 95% CI 1.00-1.71) were significantly increased for long working hours after adjustment for socio- and occupational-demographic characteristics. More than one quarter of sampled police officers reported working long hours and were significantly more likely to report CMD. National and longitudinal research is required to confirm these findings, which suggest management of working hours may effectively promote psychological well-being. © The Author 2016. Published by Oxford University Press on behalf of the Society of Occupational Medicine. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  7. Complete sequence analysis reveals two distinct poleroviruses infecting cucurbits in China.

    Science.gov (United States)

    Xiang, Hai-ying; Shang, Qiao-xia; Han, Cheng-gui; Li, Da-wei; Yu, Jia-lin

    2008-01-01

    The complete RNA genomes of a Chinese isolate of cucurbit aphid-borne yellows virus (CABYV-CHN) and a new polerovirus tentatively referred to as melon aphid-borne yellows virus (MABYV) were determined. The entire genome of CABYV-CHN shared 89.0% nucleotide sequence identity with the French CABYV isolate. In contrast, nucleotide sequence identities between MABYV and CABYV and other poleroviruses were in the range of 50.7-74.2%, with amino acid sequence identities ranging from 24.8 to 82.9% for individual gene products. We propose that CABYV-CHN is a strain of CABYV and that MABYV is a member of a tentative distinct species within the genus Polerovirus.

  8. Two-dimensional goodness-of-fit testing in astronomy

    International Nuclear Information System (INIS)

    Peacock, J.A

    1983-01-01

    This paper deals with the techniques available to test for consistency between the empirical distribution of data points on a plane and a hypothetical density law. Two new statistical tests are developed. The first is a two-dimensional version of the Kolmogorov-Smirnov test, for which the distribution of the test statistic is investigated using a Monte Carlo method. This test is found in practice to be very nearly distribution-free, and empirical formulae for the confidence levels are given. Secondly, the method of power-spectrum analysis is extended to deal with cases in which the null hypothesis is not a uniform distribution. These methods are illustrated by application to the distribution of quasar candidates found on an objective-prism plate of the Virgo Cluster. (author)

  9. Single-base resolution and long-coverage sequencing based on single-molecule nanomanipulation

    International Nuclear Information System (INIS)

    An Hongjie; Huang Jiehuan; Lue Ming; Li Xueling; Lue Junhong; Li Haikuo; Zhang Yi; Li Minqian; Hu Jun

    2007-01-01

    We show new approaches towards a novel single-molecule sequencing strategy which consists of high-resolution positioning isolation of overlapping DNA fragments with atomic force microscopy (AFM), subsequent single-molecule PCR amplification and conventional Sanger sequencing. In this study, a DNA labelling technique was used to guarantee the accuracy in positioning the target DNA. Single-molecule multiplex PCR was carried out to test the contamination. The results showed that the two overlapping DNA fragments isolated by AFM could be successfully sequenced with high quality and perfect contiguity, indicating that single-base resolution and long-coverage sequencing have been achieved simultaneously

  10. Three Mile Island - The hour-by-hour account of what really happened

    International Nuclear Information System (INIS)

    Stephens, M.

    1980-01-01

    An hour-by-hour account is given of the progression of events leading up to and during the accident at the Three Mile Island Unit 2 reactor. The emergency procedures followed, the evacuation of local residents and the decisions taken as the possibility of a meltdown became apparent are recorded in detail together with aspects of the media coverage and the problems of communication. (U.K.)

  11. The early printed Books of Hours in the Grey Collection in Cape Town: evidence of an information revolution

    Directory of Open Access Journals (Sweden)

    F C Steyn

    2014-11-01

    Full Text Available Printed books of hours, the best-seller of the late medieval trade in books, provide evidence of an information revolution equal to that occasioned by the Internet today. The Grey Collection of the National Library in Cape Town possesses eight books of hours, printed between 1498 and 1530, and they are almost completely unknown. Yet these valuable incunabula, all of them printed on vellum with hand-painted initials, and some of them with hand-painted miniatures, are of importance to anybody interested in books, the history of the book, the dissemination of information, the art of the late 15th to the early 16th centuries and early printing. They are also religious books, and of value to people interested in that discipline. The books are therefore eminently suitable as subjects for transdisciplinary research through which the subjects of history, sociology, art and religion can be drawn together. Two of these books, printed by Thielman Kerver in Paris, are discussed in detail in this article. The books are especially remarkable for their many illustrations that include pictures around the borders of each page as well as full-page illustrations. The pictures are neither metal cuts nor woodcuts, as were usual in that period, but relief prints. The most important part of the texts is a sequence of prayers to the Virgin Mary. Soon after these books were printed , in 1571, Pope Pius V prohibited the use of all existing books of hours.

  12. Genomic DNA Enrichment Using Sequence Capture Microarrays: a Novel Approach to Discover Sequence Nucleotide Polymorphisms (SNP) in Brassica napus L

    Science.gov (United States)

    Clarke, Wayne E.; Parkin, Isobel A.; Gajardo, Humberto A.; Gerhardt, Daniel J.; Higgins, Erin; Sidebottom, Christine; Sharpe, Andrew G.; Snowdon, Rod J.; Federico, Maria L.; Iniguez-Luy, Federico L.

    2013-01-01

    Targeted genomic selection methodologies, or sequence capture, allow for DNA enrichment and large-scale resequencing and characterization of natural genetic variation in species with complex genomes, such as rapeseed canola (Brassica napus L., AACC, 2n=38). The main goal of this project was to combine sequence capture with next generation sequencing (NGS) to discover single nucleotide polymorphisms (SNPs) in specific areas of the B. napus genome historically associated (via quantitative trait loci –QTL– analysis) to traits of agronomical and nutritional importance. A 2.1 million feature sequence capture platform was designed to interrogate DNA sequence variation across 47 specific genomic regions, representing 51.2 Mb of the Brassica A and C genomes, in ten diverse rapeseed genotypes. All ten genotypes were sequenced using the 454 Life Sciences chemistry and to assess the effect of increased sequence depth, two genotypes were also sequenced using Illumina HiSeq chemistry. As a result, 589,367 potentially useful SNPs were identified. Analysis of sequence coverage indicated a four-fold increased representation of target regions, with 57% of the filtered SNPs falling within these regions. Sixty percent of discovered SNPs corresponded to transitions while 40% were transversions. Interestingly, fifty eight percent of the SNPs were found in genic regions while 42% were found in intergenic regions. Further, a high percentage of genic SNPs was found in exons (65% and 64% for the A and C genomes, respectively). Two different genotyping assays were used to validate the discovered SNPs. Validation rates ranged from 61.5% to 84% of tested SNPs, underpinning the effectiveness of this SNP discovery approach. Most importantly, the discovered SNPs were associated with agronomically important regions of the B. napus genome generating a novel data resource for research and breeding this crop species. PMID:24312619

  13. Feasibility of ambulatory, continuous 24-hour finger arterial pressure recording

    NARCIS (Netherlands)

    Imholz, B. P.; Langewouters, G. J.; van Montfrans, G. A.; Parati, G.; van Goudoever, J.; Wesseling, K. H.; Wieling, W.; Mancia, G.

    1993-01-01

    We tested Portapres, an innovative portable, battery-operated device for the continuous, noninvasive, 24-hour ambulatory measurement of blood pressure in the finger. Portapres is based on Finapres, a stationary device for the measurement of finger arterial pressure. Systems were added to record

  14. Two estrogen response element sequences near the PCNA gene are not responsible for its estrogen-enhanced expression in MCF7 cells.

    Science.gov (United States)

    Wang, Cheng; Yu, Jie; Kallen, Caleb B

    2008-01-01

    The proliferating cell nuclear antigen (PCNA) is an essential component of DNA replication, cell cycle regulation, and epigenetic inheritance. High expression of PCNA is associated with poor prognosis in patients with breast cancer. The 5'-region of the PCNA gene contains two computationally-detected estrogen response element (ERE) sequences, one of which is evolutionarily conserved. Both of these sequences are of undocumented cis-regulatory function. We recently demonstrated that estradiol (E2) enhances PCNA mRNA expression in MCF7 breast cancer cells. MCF7 cells proliferate in response to E2. Here, we demonstrate that E2 rapidly enhanced PCNA mRNA and protein expression in a process that requires ERalpha as well as de novo protein synthesis. One of the two upstream ERE sequences was specifically bound by ERalpha-containing protein complexes, in vitro, in gel shift analysis. Yet, each ERE sequence, when cloned as a single copy, or when engineered as two tandem copies of the ERE-containing sequence, was not capable of activating a luciferase reporter construct in response to E2. In MCF7 cells, neither ERE-containing genomic region demonstrated E2-dependent recruitment of ERalpha by sensitive ChIP-PCR assays. We conclude that E2 enhances PCNA gene expression by an indirect process and that computational detection of EREs, even when evolutionarily conserved and when near E2-responsive genes, requires biochemical validation.

  15. Resident duty hours in Canada: a survey and national statement.

    Science.gov (United States)

    Masterson, Mark F; Shrichand, Pankaj; Maniate, Jerry M

    2014-01-01

    Physicians in general, and residents in particular, are adapting to duty schedules in which they have fewer continuous work hours; however, there are no Canadian guidelines on duty hours restrictions. To better inform resident duty hour policy in Canada, we set out to prepare a set of recommendations that would draw upon evidence reported in the literature and reflect the experiences of resident members of the Canadian Association of Internes and Residents (CAIR). A survey was prepared and distributed electronically to all resident members of CAIR. A total of 1796 eligible residents participated in the survey. Of those who responded, 38% (601) reported that they felt they could safely provide care for up to 16 continuous hours, and 20% (315) said that 12 continuous hours was the maximum period during which they could safely provide care (n=1592). Eighty-two percent (1316) reported their perception that the quality of care they had provided suffered because of the number of consecutive hours worked (n=1598). Only 52% (830) had received training in handover (n=1594); those who had received such training reported that it was commonly provided through informal modelling. On the basis of these data and the existing literature, CAIR recommends that resident duty hours be managed in a way that does not endanger the health of residents or patients; does not impair education; is flexible; and does not violate ethical or legal standards. Further, residents should be formally trained in handover skills and alternative duty hour models.

  16. Evaluation of two main RNA-seq approaches for gene quantification in clinical RNA sequencing: polyA+ selection versus rRNA depletion.

    Science.gov (United States)

    Zhao, Shanrong; Zhang, Ying; Gamini, Ramya; Zhang, Baohong; von Schack, David

    2018-03-19

    To allow efficient transcript/gene detection, highly abundant ribosomal RNAs (rRNA) are generally removed from total RNA either by positive polyA+ selection or by rRNA depletion (negative selection) before sequencing. Comparisons between the two methods have been carried out by various groups, but the assessments have relied largely on non-clinical samples. In this study, we evaluated these two RNA sequencing approaches using human blood and colon tissue samples. Our analyses showed that rRNA depletion captured more unique transcriptome features, whereas polyA+ selection outperformed rRNA depletion with higher exonic coverage and better accuracy of gene quantification. For blood- and colon-derived RNAs, we found that 220% and 50% more reads, respectively, would have to be sequenced to achieve the same level of exonic coverage in the rRNA depletion method compared with the polyA+ selection method. Therefore, in most cases we strongly recommend polyA+ selection over rRNA depletion for gene quantification in clinical RNA sequencing. Our evaluation revealed that a small number of lncRNAs and small RNAs made up a large fraction of the reads in the rRNA depletion RNA sequencing data. Thus, we recommend that these RNAs are specifically depleted to improve the sequencing depth of the remaining RNAs.

  17. Analysis of a native whitefly transcriptome and its sequence divergence with two invasive whitefly species

    Directory of Open Access Journals (Sweden)

    Wang Xiao-Wei

    2012-10-01

    Full Text Available Abstract Background Genomic divergence between invasive and native species may provide insight into the molecular basis underlying specific characteristics that drive the invasion and displacement of closely related species. In this study, we sequenced the transcriptome of an indigenous species, Asia II 3, of the Bemisia tabaci complex and compared its genetic divergence with the transcriptomes of two invasive whiteflies species, Middle East Asia Minor 1 (MEAM1 and Mediterranean (MED, respectively. Results More than 16 million reads of 74 base pairs in length were obtained for the Asia II 3 species using the Illumina sequencing platform. These reads were assembled into 52,535 distinct sequences (mean size: 466 bp and 16,596 sequences were annotated with an E-value above 10-5. Protein family comparisons revealed obvious diversification among the transcriptomes of these species suggesting species-specific adaptations during whitefly evolution. On the contrary, substantial conservation of the whitefly transcriptomes was also evident, despite their differences. The overall divergence of coding sequences between the orthologous gene pairs of Asia II 3 and MEAM1 is 1.73%, which is comparable to the average divergence of Asia II 3 and MED transcriptomes (1.84% and much higher than that of MEAM1 and MED (0.83%. This is consistent with the previous phylogenetic analyses and crossing experiments suggesting these are distinct species. We also identified hundreds of highly diverged genes and compiled sequence identify data into gene functional groups and found the most divergent gene classes are Cytochrome P450, Glutathione metabolism and Oxidative phosphorylation. These results strongly suggest that the divergence of genes related to metabolism might be the driving force of the MEAM1 and Asia II 3 differentiation. We also analyzed single nucleotide polymorphisms within the orthologous gene pairs of indigenous and invasive whiteflies which are helpful for

  18. Flexible work in call centres: Working hours, work-life conflict & health.

    Science.gov (United States)

    Bohle, Philip; Willaby, Harold; Quinlan, Michael; McNamara, Maria

    2011-01-01

    Call-centre workers encounter major psychosocial pressures, including high work intensity and undesirable working hours. Little is known, however, about whether these pressures vary with employment status and how they affect work-life conflict and health. Questionnaire data were collected from 179 telephone operators in Sydney, Australia, of whom 124 (69.3%) were female and 54 (30.2%) were male. Ninety-three (52%) were permanent full-time workers, 37 (20.7%) were permanent part-time, and 49 (27.4%) were casual employees. Hypothesised structural relationships between employment status, working hours and work organisation, work-life conflict and health were tested using partial least squares modelling in PLS (Chin, 1998). The final model demonstrated satisfactory fit. It supported important elements of the hypothesised structure, although four of the proposed paths failed to reach significance and the fit was enhanced by adding a path. The final model indicated that casual workers reported more variable working hours which were relatively weakly associated with greater dissatisfaction with hours. The interaction of schedule control and variability of hours also predicted dissatisfaction with hours. Conversely, permanent workers reported greater work intensity, which was associated with both lower work schedule control and greater work-life conflict. Greater work-life conflict was associated with more fatigue and psychological symptoms. Labour market factors and the undesirability of longer hours in a stressful, high-intensity work environment appear to have contributed to the results. Copyright © 2010 Elsevier Ltd and The Ergonomics Society. All rights reserved.

  19. RANDNA: a random DNA sequence generator.

    Science.gov (United States)

    Piva, Francesco; Principato, Giovanni

    2006-01-01

    Monte Carlo simulations are useful to verify the significance of data. Genomic regularities, such as the nucleotide correlations or the not uniform distribution of the motifs throughout genomic or mature mRNA sequences, exist and their significance can be checked by means of the Monte Carlo test. The test needs good quality random sequences in order to work, moreover they should have the same nucleotide distribution as the sequences in which the regularities have been found. Random DNA sequences are also useful to estimate the background score of an alignment, that is a threshold below which the resulting score is merely due to chance. We have developed RANDNA, a free software which allows to produce random DNA or RNA sequences setting both their length and the percentage of nucleotide composition. Sequences having the same nucleotide distribution of exonic, intronic or intergenic sequences can be generated. Its graphic interface makes it possible to easily set the parameters that characterize the sequences being produced and saved in a text format file. The pseudo-random number generator function of Borland Delphi 6 is used, since it guarantees a good randomness, a long cycle length and a high speed. We have checked the quality of sequences generated by the software, by means of well-known tests, both by themselves and versus genuine random sequences. We show the good quality of the generated sequences. The software, complete with examples and documentation, is freely available to users from: http://www.introni.it/en/software.

  20. Complete sequences of the mitochondrial DNA of the wild Gracilariopsis lemaneiformis and two mutagenic cultivated breeds (Gracilariaceae, Rhodophyta.

    Directory of Open Access Journals (Sweden)

    Lei Zhang

    Full Text Available The complete mitochondrial DNA (mtDNA of Gracilariopsis lemaneiformis was sequenced (25883 bp and mapped to a circular model. The A+T composition was 72.5%. Forty six genes and two potentially functional open reading frames were identified. They include 24 protein-coding genes, 2 rRNA genes, 20 tRNA genes and 2 ORFs (orf60, orf142. There is considerable sequence synteny across the five red algal mtDNAs falling into Florideophyceae including Gr. lemaneiformis in this study and previously sequenced species. A long stem-loop and a hairpin structure were identified in intergenic regions of mt genome of Gr. lemaneiformis, which are believed to be involved with transcription and replication. In addition, the mtDNAs of two mutagenic cultivated breeds ("981" and "07-2" were also sequenced. Compared with the mtDNA of wild Gr. lemaneiformis, the genome size and gene length and order of three strains were completely identical except nine base mutations including eight in the protein-coding genes and one in the tRNA gene. None of the base mutations caused frameshift or a premature stop codon in the mtDNA genes. Phylogenetic analyses based on mitochondrial protein-coding genes and rRNA genes demonstrated Gracilariopsis andersonii had closer phylogenetic relationship with its parasite Gracilariophila oryzoides than Gracilariopsis lemaneiformis which was from the same genus of Gracilariopsis.

  1. Complete sequences of the mitochondrial DNA of the wild Gracilariopsis lemaneiformis and two mutagenic cultivated breeds (Gracilariaceae, Rhodophyta).

    Science.gov (United States)

    Zhang, Lei; Wang, Xumin; Qian, Hao; Chi, Shan; Liu, Cui; Liu, Tao

    2012-01-01

    The complete mitochondrial DNA (mtDNA) of Gracilariopsis lemaneiformis was sequenced (25883 bp) and mapped to a circular model. The A+T composition was 72.5%. Forty six genes and two potentially functional open reading frames were identified. They include 24 protein-coding genes, 2 rRNA genes, 20 tRNA genes and 2 ORFs (orf60, orf142). There is considerable sequence synteny across the five red algal mtDNAs falling into Florideophyceae including Gr. lemaneiformis in this study and previously sequenced species. A long stem-loop and a hairpin structure were identified in intergenic regions of mt genome of Gr. lemaneiformis, which are believed to be involved with transcription and replication. In addition, the mtDNAs of two mutagenic cultivated breeds ("981" and "07-2") were also sequenced. Compared with the mtDNA of wild Gr. lemaneiformis, the genome size and gene length and order of three strains were completely identical except nine base mutations including eight in the protein-coding genes and one in the tRNA gene. None of the base mutations caused frameshift or a premature stop codon in the mtDNA genes. Phylogenetic analyses based on mitochondrial protein-coding genes and rRNA genes demonstrated Gracilariopsis andersonii had closer phylogenetic relationship with its parasite Gracilariophila oryzoides than Gracilariopsis lemaneiformis which was from the same genus of Gracilariopsis.

  2. Is there an added value of T1-weighted contrast-enhanced fat-suppressed spin-echo MR sequences compared to STIR sequences in MRI of the foot and ankle?

    Energy Technology Data Exchange (ETDEWEB)

    Zubler, Veronika; Zanetti, Marco; Dietrich, Tobias J.; Pfirrmann, Christian W.; Mamisch-Saupe, Nadja [University of Zurich, Faculty of Medicine, Zurich (Switzerland); Orthopedic University Hospital Balgrist, Department of Radiology, Zurich (Switzerland); Espinosa, Norman [University of Zurich, Faculty of Medicine, Zurich (Switzerland); Orthopedic University Hospital Balgrist, Orthopedic Surgery, Zurich (Switzerland)

    2017-08-15

    To prospectively compare T1-weighted fat-suppressed spin-echo magnetic resonance (MR) sequences after gadolinium application (T1wGdFS) to STIR sequences in patients with acute and chronic foot pain. In 51 patients referred for MRI of the foot and ankle, additional transverse and sagittal T1wGdFS sequences were obtained. Two sets of MR images (standard protocol with STIR or T1wGdFS) were analysed. Diagnosis, diagnostic confidence, and localization of the abnormality were noted. Standard of reference was established by an expert panel of two experienced MSK radiologists and one experienced foot surgeon based on MR images, clinical charts and surgical reports. Patients reported prospectively localization of pain. Descriptive statistics, McNemar test and Kappa test were used. Diagnostic accuracy with STIR protocol was 80% for reader 1, 67% for reader 2, with contrast-protocol 84%, both readers. Significance was found for reader 2. Diagnostic confidence for reader 1 was 1.7 with STIR, 1.3 with contrast-protocol; reader 2: 2.1/1.7. Significance was found for reader 1. Pain location correlated with STIR sequences in 64% and 52%, with gadolinium sequences in 70% and 71%. T1-weighted contrast material-enhanced fat-suppressed spin-echo magnetic resonance sequences improve diagnostic accuracy, diagnostic confidence and correlation of MR abnormalities with pain location in MRI of the foot and ankle. However, the additional value is small. (orig.)

  3. Is there an added value of T1-weighted contrast-enhanced fat-suppressed spin-echo MR sequences compared to STIR sequences in MRI of the foot and ankle?

    International Nuclear Information System (INIS)

    Zubler, Veronika; Zanetti, Marco; Dietrich, Tobias J.; Pfirrmann, Christian W.; Mamisch-Saupe, Nadja; Espinosa, Norman

    2017-01-01

    To prospectively compare T1-weighted fat-suppressed spin-echo magnetic resonance (MR) sequences after gadolinium application (T1wGdFS) to STIR sequences in patients with acute and chronic foot pain. In 51 patients referred for MRI of the foot and ankle, additional transverse and sagittal T1wGdFS sequences were obtained. Two sets of MR images (standard protocol with STIR or T1wGdFS) were analysed. Diagnosis, diagnostic confidence, and localization of the abnormality were noted. Standard of reference was established by an expert panel of two experienced MSK radiologists and one experienced foot surgeon based on MR images, clinical charts and surgical reports. Patients reported prospectively localization of pain. Descriptive statistics, McNemar test and Kappa test were used. Diagnostic accuracy with STIR protocol was 80% for reader 1, 67% for reader 2, with contrast-protocol 84%, both readers. Significance was found for reader 2. Diagnostic confidence for reader 1 was 1.7 with STIR, 1.3 with contrast-protocol; reader 2: 2.1/1.7. Significance was found for reader 1. Pain location correlated with STIR sequences in 64% and 52%, with gadolinium sequences in 70% and 71%. T1-weighted contrast material-enhanced fat-suppressed spin-echo magnetic resonance sequences improve diagnostic accuracy, diagnostic confidence and correlation of MR abnormalities with pain location in MRI of the foot and ankle. However, the additional value is small. (orig.)

  4. Two-stage clustering (TSC: a pipeline for selecting operational taxonomic units for the high-throughput sequencing of PCR amplicons.

    Directory of Open Access Journals (Sweden)

    Xiao-Tao Jiang

    Full Text Available Clustering 16S/18S rRNA amplicon sequences into operational taxonomic units (OTUs is a critical step for the bioinformatic analysis of microbial diversity. Here, we report a pipeline for selecting OTUs with a relatively low computational demand and a high degree of accuracy. This pipeline is referred to as two-stage clustering (TSC because it divides tags into two groups according to their abundance and clusters them sequentially. The more abundant group is clustered using a hierarchical algorithm similar to that in ESPRIT, which has a high degree of accuracy but is computationally costly for large datasets. The rarer group, which includes the majority of tags, is then heuristically clustered to improve efficiency. To further improve the computational efficiency and accuracy, two preclustering steps are implemented. To maintain clustering accuracy, all tags are grouped into an OTU depending on their pairwise Needleman-Wunsch distance. This method not only improved the computational efficiency but also mitigated the spurious OTU estimation from 'noise' sequences. In addition, OTUs clustered using TSC showed comparable or improved performance in beta-diversity comparisons compared to existing OTU selection methods. This study suggests that the distribution of sequencing datasets is a useful property for improving the computational efficiency and increasing the clustering accuracy of the high-throughput sequencing of PCR amplicons. The software and user guide are freely available at http://hwzhoulab.smu.edu.cn/paperdata/.

  5. Hours Lost to Planned and Unplanned Dental Visits Among US Adults.

    Science.gov (United States)

    Kelekar, Uma; Naavaal, Shillpa

    2018-01-11

    Poor oral health is associated with lost hours at work or school, which may affect a person's productivity. The objective of our study was to estimate work or school hours lost to dental visits among adults aged 18 and older by the types of visits (emergency or unplanned; routine, planned, or orthodontic; or cosmetic) and to determine the factors associated with hours lost. We used the most recent Oral Health Supplement data, from the 2008 National Health Interview Survey (NHIS), to estimate the total hours lost at work or school for dental visits among adults in the United States. The associations of the hours lost in unplanned and planned dental visits with socioeconomic characteristics, oral health status, and affordability were calculated. We used χ 2 tests and logistic regression to determine associations at P work or school hours were lost annually for dental care in the United States, of which 92.4 million hours were for emergency (unplanned) care (0.99 h/adult), 159.8 million for routine (planned) care or orthodontic care (1.71 h/adult), and 68.6 million for cosmetic care (0.73 h/adult). Adults with poor oral health were more likely to lose one or more hours in unplanned dental visits (OR = 5.60; 95% confidence interval [CI], 3.25-9.63) than those who reported very good oral health. Not being able to afford dental care was positively associated with more work hours lost in unplanned care (odds ratio [OR] = 2.56; 95% CI, 1.76-3.73). Compared with Hispanic adults, non-Hispanic white adults (OR = 2.09; 95% CI, 1.40-3.11) and non-Hispanic Asian adults and adults of other races/ethnicities (OR =1.91; 95% CI, 1.06-3.47) were more likely to lose any hours for planned care. Consistently, those with more than a high school education were more likely to lose any hours in planned care (OR = 1.39; 95% CI, 1.06-1.83) than those with a high school education or less. Dental problems result in hours lost from work and may adversely affect a person's productivity. There is

  6. Characteristics and outcomes for women physicians who work reduced hours.

    Science.gov (United States)

    Carr, Phyllis L; Gareis, Karen C; Barnett, Rosalind C

    2003-05-01

    To understand the characteristics of women physicians who work reduced hours in dual-earner couples and how such work schedules affect the quality of the marital role, parental role, and job role, as well as indicators of psychological distress, burnout, career satisfaction, and life satisfaction. Survey of a random sample of female physicians between 25 and 50 years of age, working within 25 miles of Boston, whose names were obtained from the Registry of Board Certification in Medicine in Massachusetts. Interviewers conducted a 60-minute face-to-face close-ended interview after a 20-minute mailed questionnaire had been completed. Fifty-one full-time physicians and 47 reduced-hours physicians completed the study, for a completion rate of 49.5%. There was no difference in age, number of years as a physician, mean household income, number of children, or presence of an infant in the home between reduced-hours and full-time physicians. Reduced-hours physicians, however, were more likely to be in a generalist specialty (40% vs. 12%, p = 0.001) and to spend a greater portion of their time in patient care (64.5% vs. 50.1%, p = 0.003) and less time in research (4.9% vs. 18.0%, p = 0.002) than full-time physicians. In addition, there was no difference between the two groups in the perception of work interfering with family life (1.8 vs. 1.7, p = 0.17; scale 1-7 with 7 high) or family life interfering with work (1.4 vs. 1.5, p = 0.62). Physicians who worked their preferred number of hours (25% of full-time and 57% of reduced-hours physicians), regardless of full-time (self-reported hours 35-90 hours per week) or reduced-hours (20-60 hours per week) status, reported better job role quality (r = 0.35, p = 0.001), schedule fit (r = 0.41, p Women physicians who work their preferred number of hours achieve the best balance of work and family outcomes.

  7. The relevance of 7-day patch test reading.

    Science.gov (United States)

    Higgins, Eleanor; Collins, Paul

    2013-01-01

    Patch test readings are usually performed on day 2 (48 hours) and day 4 (96 hours). However, reports in the literature identify delayed allergy to metals, corticosteroids, antibiotics, some preservatives, acrylic and methacrylic monomers and p-phenylenediamine. The aim of our study was to identify the benefit of performing a day 7 (168 hours) reading to identify relevant late positive reactions. Two hundred three consecutive patients were patch tested to the British Society for Cutaneous Allergy standard series with additional test series selected according to clinical history and applied at the same time. Twenty-six patients (12.8%) had new positive reactions on day 7 (168 hours), with 28 relevant positive reactions to 21 allergens. These included mercury 0.5% (2/26); cobalt chloride 1% (2/26); colophony 20% (2/26); disperse blue mix 106/124 1% (2/26); preservatives (4/26) that included Methylchloroisothiazolinone/methylisothiazolinone, sodium metabisulfite, and diazolidinyl urea; fragrances (7/26); and gentamycin sulfate 20% (1/26). These results confirm findings in the literature and support the argument for performing a day 7 reading (168 hours) to identify relevant late positive reactions.

  8. Irradiation Effects Test Series: Test IE-2. Test results report

    International Nuclear Information System (INIS)

    Allison, C.M.; Croucher, D.W.; Ploger, S.A.; Mehner, A.S.

    1977-08-01

    The report describes the results of a test using four 0.97-m long PWR-type fuel rods with differences in diametral gap and cladding irradiation. The objective of this test was to provide information about the effects of these differences on fuel rod behavior during quasi-equilibrium and film boiling operation. The fuel rods were subjected to a series of preconditioning power cycles of less than 30 kW/m. Rod powers were then increased to 68 kW/m at a coolant mass flux of 4900 kg/s-m 2 . After one hour at 68 kW/m, a power-cooling-mismatch sequence was initiated by a flow reduction at constant power. At a flow of 2550 kg/s-m 2 , the onset of film boiling occurred on one rod, Rod IE-011. An additional flow reduction to 2245 kg/s-m 2 caused the onset of film boiling on the remaining three rods. Data are presented on the behavior of fuel rods during quasiequilibrium and during film boiling operation. The effects of initial gap size, cladding irradiation, rod power cycling, a rapid power increase, and sustained film boiling are discussed. These discussions are based on measured test data, preliminary postirradiation examination results, and comparisons of results with FRAP-T3 computer model calculations

  9. Averaging and sampling for magnetic-observatory hourly data

    Directory of Open Access Journals (Sweden)

    J. J. Love

    2010-11-01

    Full Text Available A time and frequency-domain analysis is made of the effects of averaging and sampling methods used for constructing magnetic-observatory hourly data values. Using 1-min data as a proxy for continuous, geomagnetic variation, we construct synthetic hourly values of two standard types: instantaneous "spot" measurements and simple 1-h "boxcar" averages. We compare these average-sample types with others: 2-h average, Gaussian, and "brick-wall" low-frequency-pass. Hourly spot measurements provide a statistically unbiased representation of the amplitude range of geomagnetic-field variation, but as a representation of continuous field variation over time, they are significantly affected by aliasing, especially at high latitudes. The 1-h, 2-h, and Gaussian average-samples are affected by a combination of amplitude distortion and aliasing. Brick-wall values are not affected by either amplitude distortion or aliasing, but constructing them is, in an operational setting, relatively more difficult than it is for other average-sample types. It is noteworthy that 1-h average-samples, the present standard for observatory hourly data, have properties similar to Gaussian average-samples that have been optimized for a minimum residual sum of amplitude distortion and aliasing. For 1-h average-samples from medium and low-latitude observatories, the average of the combination of amplitude distortion and aliasing is less than the 5.0 nT accuracy standard established by Intermagnet for modern 1-min data. For medium and low-latitude observatories, average differences between monthly means constructed from 1-min data and monthly means constructed from any of the hourly average-sample types considered here are less than the 1.0 nT resolution of standard databases. We recommend that observatories and World Data Centers continue the standard practice of reporting simple 1-h-average hourly values.

  10. Identification of two invasive Cacopsylla chinensis (Hemiptera: Psyllidae) lineages based on two mitochondrial sequences and restriction fragment length polymorphism of cytochrome oxidase I amplicon.

    Science.gov (United States)

    Lee, Hsien-Chung; Yang, Man-Miao; Yeh, Wen-Bin

    2008-08-01

    The occurrence of pear decline, a disease found in some pear (Pyrus spp.) orchards of Taiwan in recent years, is accompanied by an outbreak of Cacopsylla chinensis (Yang & Li). Two major morphological forms (summer and winter forms) with a variety of intermediate body color and two phylogenetic lineages of this psyllid have been described. The work herein used sequences of mitochondrial cytochrome oxidase I (COI) and 16S rDNA regions to delineate the genetic differentiation of this color-variable insect and to elucidate their relationship. Sequence divergence and phylogenetic analysis have shown that C. chinensis individuals could be divided into two lineages with 3.3 and 2.3% divergence of COI and 16S rDNA, respectively. All specimens from China were found to belong to lineage I. Restriction fragment length polymorphism analysis of COI with restriction enzymes AcuI, AseI, BccI, and FokI on 263 specimens of six populations from Taiwan produced two digestion patterns, which are in agreement with the two lineages described above. Both patterns could be found in each population, with most individuals belonging to lineage I and 5-21% of the individuals belonging to lineage II. Because these two lineages included summer as well as winter morphological forms, the lineage differentiation is apparently not related to morphological characters of this psyllid. Because the invasive records are not in favor of a sympatric differentiation, this psyllid is more likely introduced as different populations from countries in temperate regions.

  11. Preliminary Validation of a New Measure of Negative Response Bias: The Temporal Memory Sequence Test.

    Science.gov (United States)

    Hegedish, Omer; Kivilis, Naama; Hoofien, Dan

    2015-01-01

    The Temporal Memory Sequence Test (TMST) is a new measure of negative response bias (NRB) that was developed to enrich the forced-choice paradigm. The TMST does not resemble the common structure of forced-choice tests and is presented as a temporal recall memory test. The validation sample consisted of 81 participants: 21 healthy control participants, 20 coached simulators, and 40 patients with acquired brain injury (ABI). The TMST had high reliability and significantly high positive correlations with the Test of Memory Malingering and Word Memory Test effort scales. Moreover, the TMST effort scales exhibited high negative correlations with the Glasgow Coma Scale, thus validating the previously reported association between probable malingering and mild traumatic brain injury. A suggested cutoff score yielded acceptable classification rates in the ABI group as well as in the simulator and control groups. The TMST appears to be a promising measure of NRB detection, with respectable rates of reliability and construct and criterion validity.

  12. Mutation Detection in Patients With Advanced Cancer by Universal Sequencing of Cancer-Related Genes in Tumor and Normal DNA vs Guideline-Based Germline Testing.

    Science.gov (United States)

    Mandelker, Diana; Zhang, Liying; Kemel, Yelena; Stadler, Zsofia K; Joseph, Vijai; Zehir, Ahmet; Pradhan, Nisha; Arnold, Angela; Walsh, Michael F; Li, Yirong; Balakrishnan, Anoop R; Syed, Aijazuddin; Prasad, Meera; Nafa, Khedoudja; Carlo, Maria I; Cadoo, Karen A; Sheehan, Meg; Fleischut, Megan H; Salo-Mullen, Erin; Trottier, Magan; Lipkin, Steven M; Lincoln, Anne; Mukherjee, Semanti; Ravichandran, Vignesh; Cambria, Roy; Galle, Jesse; Abida, Wassim; Arcila, Marcia E; Benayed, Ryma; Shah, Ronak; Yu, Kenneth; Bajorin, Dean F; Coleman, Jonathan A; Leach, Steven D; Lowery, Maeve A; Garcia-Aguilar, Julio; Kantoff, Philip W; Sawyers, Charles L; Dickler, Maura N; Saltz, Leonard; Motzer, Robert J; O'Reilly, Eileen M; Scher, Howard I; Baselga, Jose; Klimstra, David S; Solit, David B; Hyman, David M; Berger, Michael F; Ladanyi, Marc; Robson, Mark E; Offit, Kenneth

    2017-09-05

    Guidelines for cancer genetic testing based on family history may miss clinically actionable genetic changes with established implications for cancer screening or prevention. To determine the proportion and potential clinical implications of inherited variants detected using simultaneous sequencing of the tumor and normal tissue ("tumor-normal sequencing") compared with genetic test results based on current guidelines. From January 2014 until May 2016 at Memorial Sloan Kettering Cancer Center, 10 336 patients consented to tumor DNA sequencing. Since May 2015, 1040 of these patients with advanced cancer were referred by their oncologists for germline analysis of 76 cancer predisposition genes. Patients with clinically actionable inherited mutations whose genetic test results would not have been predicted by published decision rules were identified. Follow-up for potential clinical implications of mutation detection was through May 2017. Tumor and germline sequencing compared with the predicted yield of targeted germline sequencing based on clinical guidelines. Proportion of clinically actionable germline mutations detected by universal tumor-normal sequencing that would not have been detected by guideline-directed testing. Of 1040 patients, the median age was 58 years (interquartile range, 50.5-66 years), 65.3% were male, and 81.3% had stage IV disease at the time of genomic analysis, with prostate, renal, pancreatic, breast, and colon cancer as the most common diagnoses. Of the 1040 patients, 182 (17.5%; 95% CI, 15.3%-19.9%) had clinically actionable mutations conferring cancer susceptibility, including 149 with moderate- to high-penetrance mutations; 101 patients tested (9.7%; 95% CI, 8.1%-11.7%) would not have had these mutations detected using clinical guidelines, including 65 with moderate- to high-penetrance mutations. Frequency of inherited mutations was related to case mix, stage, and founder mutations. Germline findings led to discussion or initiation of

  13. Clinical Use of Next-Generation Sequencing in the Diagnosis of Wilson’s Disease

    Directory of Open Access Journals (Sweden)

    Dániel Németh

    2016-01-01

    Full Text Available Objective. Wilson’s disease is a disorder of copper metabolism which is fatal without treatment. The great number of disease-causing ATP7B gene mutations and the variable clinical presentation of WD may cause a real diagnostic challenge. The emergence of next-generation sequencing provides a time-saving, cost-effective method for full sequencing of the whole ATP7B gene compared to the traditional Sanger sequencing. This is the first report on the clinical use of NGS to examine ATP7B gene. Materials and Methods. We used Ion Torrent Personal Genome Machine in four heterozygous patients for the identification of the other mutations and also in two patients with no known mutation. One patient with acute on chronic liver failure was a candidate for acute liver transplantation. The results were validated by Sanger sequencing. Results. In each case, the diagnosis of Wilson’s disease was confirmed by identifying the mutations in both alleles within 48 hours. One novel mutation (p.Ala1270Ile was found beyond the eight other known ones. The rapid detection of the mutations made possible the prompt diagnosis of WD in a patient with acute liver failure. Conclusions. According to our results we found next-generation sequencing a very useful, reliable, time-saving, and cost-effective method for diagnosing Wilson’s disease in selected cases.

  14. Complete nucleotide sequences and virion particle association of two satellite RNAs of panicum mosaic virus.

    Science.gov (United States)

    Pyle, Jesse D; Monis, Judit; Scholthof, Karen-Beth

    2017-08-15

    Over six decades ago, panicum mosaic virus (PMV) was identified as the first viral pathogen of cultivated switchgrass (Panicum virgatum). Subsequently, PMV was demonstrated to support the replication of both a satellite RNA virus (SPMV) and satellite RNA (satRNA) agents during natural infections of host grasses. In this study, we report the isolation and full-length sequences of two PMV satRNAs identified in 1988 from St. Augustinegrass (Stenotaphrum secundatum) and centipedegrass (Eremochloa ophiuroides) hosts. Each of these satellites have sequence relatedness at their 5'- and 3'-ends. In addition, satC has a region of ∼100 nt complementary to the 3'-end of the PMV genome. These agents are associated with purified virions of SPMV infections. Additionally, satS and satC RNAs contain conserved in-frame open reading frames in the complementary-sense sequences that could potentially generate 6.6- and 7.9-kDa proteins, respectively. In protoplasts and plants satS is infectious, when co-inoculated with the PMV RNA alone or PMV+SPMV RNAs, and negatively affects their accumulation. Copyright © 2017 Elsevier B.V. All rights reserved.

  15. On Linear Combinations of Two Orthogonal Polynomial Sequences on the Unit Circle

    Directory of Open Access Journals (Sweden)

    Suárez C

    2010-01-01

    Full Text Available Let be a monic orthogonal polynomial sequence on the unit circle. We define recursively a new sequence of polynomials by the following linear combination: , , . In this paper, we give necessary and sufficient conditions in order to make be an orthogonal polynomial sequence too. Moreover, we obtain an explicit representation for the Verblunsky coefficients and in terms of and . Finally, we show the relation between their corresponding Carathéodory functions and their associated linear functionals.

  16. Small scale heater tests in argillite of the Eleana Formation at the Nevada Test Site

    International Nuclear Information System (INIS)

    McVey, D.F.; Thomas, R.K.; Lappin, A.R.

    1979-11-01

    Near-surface heater tests were run in the Eleana Formation at the Nevada Test Site, in an effort to evaluate argillaceous rock for nuclear waste storage. The main test, which employed a full-scale heater with a thermal output approximating commercial borosilicate waste, was designed to operate for several months. Two smaller, scaled tests were run prior to the full-scale test. This report develops the thermal scaling laws, describes the pretest thermal and thermomechanical analysis conducted for these two tests, and discusses the material properties data used in the analyses. In the first test, scaled to a large heater of 3.5 kW power, computed heater temperatures were within 7% of measured values for the entire 96-hour test run. The second test, scaled to a large heater having 5.0 kW power, experienced periodic water in-flow onto the heater, which tended to damp the temperature. For the second test, the computed temperatures were within 7% of measured for the first 20 hours. After this time, the water effect became significant and the measured temperatures were 15 to 20% below those predicted. On the second test, rock surface spallation was noted in the bore hole above the heater, as predicted. The scaled tests indicated that in-situ argillite would not undergo major thermostructural failure during the follow-on, 3.5 kW, full-scale test. 24 figures, 6 tables

  17. Earthquake Tests of Reinforced Concrete Frames

    DEFF Research Database (Denmark)

    Skjærbæk, P. S.; Nielsen, Søren R.K.; Kirkegaard, Poul Henning

    1997-01-01

    the equilibrium state. Afterwards the test structure is subjected to the three strong ground motion oscillations where the two first sequences are followed by a free decay test. No free decay test was performed after the third earthquake due to collapse of the test structure during the third strong motion...

  18. Earthquake Tests of Reinforced Concrete Frames

    DEFF Research Database (Denmark)

    Skjærbæk, P. S.; Nielsen, Søren R.K.; Kirkegaard, Poul Henning

    1996-01-01

    the equilibrium state. Afterwards the test structure is subjected to the three strong ground motion oscillations where the two first sequences are followed by a free decay test. No free decay test was performed after the third earthquake due to collapse of the test structure during the third strong motion...

  19. The sequence specificity of UV-induced DNA damage in a systematically altered DNA sequence.

    Science.gov (United States)

    Khoe, Clairine V; Chung, Long H; Murray, Vincent

    2018-06-01

    The sequence specificity of UV-induced DNA damage was investigated in a specifically designed DNA plasmid using two procedures: end-labelling and linear amplification. Absorption of UV photons by DNA leads to dimerisation of pyrimidine bases and produces two major photoproducts, cyclobutane pyrimidine dimers (CPDs) and pyrimidine(6-4)pyrimidone photoproducts (6-4PPs). A previous study had determined that two hexanucleotide sequences, 5'-GCTC*AC and 5'-TATT*AA, were high intensity UV-induced DNA damage sites. The UV clone plasmid was constructed by systematically altering each nucleotide of these two hexanucleotide sequences. One of the main goals of this study was to determine the influence of single nucleotide alterations on the intensity of UV-induced DNA damage. The sequence 5'-GCTC*AC was designed to examine the sequence specificity of 6-4PPs and the highest intensity 6-4PP damage sites were found at 5'-GTTC*CC nucleotides. The sequence 5'-TATT*AA was devised to investigate the sequence specificity of CPDs and the highest intensity CPD damage sites were found at 5'-TTTT*CG nucleotides. It was proposed that the tetranucleotide DNA sequence, 5'-YTC*Y (where Y is T or C), was the consensus sequence for the highest intensity UV-induced 6-4PP adduct sites; while it was 5'-YTT*C for the highest intensity UV-induced CPD damage sites. These consensus tetranucleotides are composed entirely of consecutive pyrimidines and must have a DNA conformation that is highly productive for the absorption of UV photons. Crown Copyright © 2018. Published by Elsevier B.V. All rights reserved.

  20. Long Working Hours and Coronary Heart Disease: A Systematic Review and Meta-Analysis

    Science.gov (United States)

    Virtanen, Marianna; Heikkilä, Katriina; Jokela, Markus; Ferrie, Jane E.; Batty, G. David; Vahtera, Jussi; Kivimäki, Mika

    2012-01-01

    The authors aggregated the results of observational studies examining the association between long working hours and coronary heart disease (CHD). Data sources used were MEDLINE (through January 19, 2011) and Web of Science (through March 14, 2011). Two investigators independently extracted results from eligible studies. Heterogeneity between the studies was assessed using the I2 statistic, and the possibility of publication bias was assessed using the funnel plot and Egger's test for small-study effects. Twelve studies were identified (7 case-control, 4 prospective, and 1 cross-sectional). For a total of 22,518 participants (2,313 CHD cases), the minimally adjusted relative risk of CHD for long working hours was 1.80 (95% confidence interval (CI): 1.42, 2.29), and in the maximally (multivariate-) adjusted analysis the relative risk was 1.59 (95% CI: 1.23, 2.07). The 4 prospective studies produced a relative risk of 1.39 (95% CI: 1.12, 1.72), while the corresponding relative risk in the 7 case-control studies was 2.43 (95% CI: 1.81, 3.26). Little evidence of publication bias but relatively large heterogeneity was observed. Studies varied in size, design, measurement of exposure and outcome, and adjustments. In conclusion, results from prospective observational studies suggest an approximately 40% excess risk of CHD in employees working long hours. PMID:22952309

  1. Hourly Precipitation Data (HPD) Publication

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Hourly Precipitation Data (HPD) Publication is archived and available from the National Climatic Data Center (NCDC). This publication contains hourly precipitation...

  2. Quantitative and qualitative perceptions of the 2011 residency duty hour restrictions: a multicenter, multispecialty cross-sectional study.

    Science.gov (United States)

    Tierney, William S; Elkin, Rachel L; Nielsen, Craig D

    2015-03-25

    July 2011 saw the implementation of the newest duty hour restrictions, further limiting the working hours of first year residents and necessitating a variety of adaptations on the part of residency programs. The present study sought to characterize the perceived impact of these restrictions on residency program personnel using a multi-specialty and multi-site approach. We developed and administered a survey to internal medicine and general surgery residency programs at three academic medical centers within an urban region. The survey combined quantitative and qualitative components to gain a broader understanding of the impact of the newest regulations. Quantitative responses were compared between Internal Medicine and General Surgery programs with Student t-tests. Other comparisons were performed using ANOVA or Kruskal-Wallis testing as appropriate. For all comparisons, the threshold for significance was set at 0.01. Two independent reviewers coded all qualitative data and assigned one or more themes based on content. Descriptive statistics were calculated and the diversity of themes identified. No between-group comparisons were conducted with the qualitative data. We found significant differences in the overall perceptions of duty hour restrictions across specialty (internal medicine more positive than general surgery) and across position (first year residents more positive than senior residents and faculty). Notably, individuals who trained at osteopathic medical schools reported significantly more negative views of the duty hour restrictions than those who had trained at allopathic or international medical schools, suggesting an influence of undergraduate medical training. The complementary qualitative data offered insights into the perceived strengths and weaknesses of the duty hour restrictions, as well as actionable suggestions that could help to improve residency program function. This study characterizes responses to the new duty hour restrictions from a

  3. Long working hours and cancer risk

    DEFF Research Database (Denmark)

    Heikkila, Katriina; Nyberg, Solja T.; Madsen, Ida E. H.

    2016-01-01

    in 116 462 men and women who were free of cancer at baseline. Incident cancers were ascertained from national cancer, hospitalisation and death registers; weekly working hours were self-reported. Results: During median follow-up of 10.8 years, 4371 participants developed cancer (n colorectal cancer: 393......Background: Working longer than the maximum recommended hours is associated with an increased risk of cardiovascular disease, but the relationship of excess working hours with incident cancer is unclear. Methods: This multi-cohort study examined the association between working hours and cancer risk......; n lung cancer: 247; n breast cancer: 833; and n prostate cancer: 534). We found no clear evidence for an association between working hours and the overall cancer risk. Working hours were also unrelated the risk of incident colorectal, lung or prostate cancers. Working greater than or equal to55 h...

  4. Sensitivity of BWR shutdown margin tests to local reactivity anomalies

    International Nuclear Information System (INIS)

    Cokinos, D.M.; Carew, J.F.

    1987-01-01

    Successful shutdown margin (SDM) demonstration is a required procedure in the startup of a newly configured boiling water reactor (BWR) core. In its most reactive condition throughout a cycle, a BWR core must be capable of being made subcritical by a specified margin with the highest worth control rod fully withdrawn and all other rods at their fully inserted positions. Two different methods are used to demonstrate SDM: (a) the adjacent-rod test and (b) the in-sequence test. In the adjacent-rod test, the strongest rod is fully withdrawn and an adjacent rod is withdrawn to reach criticality. In the in-sequence test, control rods spread throughout the core are withdrawn in a predetermined sequence of withdrawals. Larger than expected core k/sub eff/ values have been observed during the performance of BWR SDM tests. The purpose of the work summarized in this paper has been to investigated and quantify the sensitivity of both the adjacent-rod and in-sequence SDM tests to local reactivity anomalies. This was accomplished by introducing reactivity perturbations at selected four-bundle cell locations and by evaluating their effect on core reactivity in each of the two tests

  5. Reconstruction of ancestral RNA sequences under multiple structural constraints

    Directory of Open Access Journals (Sweden)

    Olivier Tremblay-Savard

    2016-11-01

    Full Text Available Abstract Background Secondary structures form the scaffold of multiple sequence alignment of non-coding RNA (ncRNA families. An accurate reconstruction of ancestral ncRNAs must use this structural signal. However, the inference of ancestors of a single ncRNA family with a single consensus structure may bias the results towards sequences with high affinity to this structure, which are far from the true ancestors. Methods In this paper, we introduce achARNement, a maximum parsimony approach that, given two alignments of homologous ncRNA families with consensus secondary structures and a phylogenetic tree, simultaneously calculates ancestral RNA sequences for these two families. Results We test our methodology on simulated data sets, and show that achARNement outperforms classical maximum parsimony approaches in terms of accuracy, but also reduces by several orders of magnitude the number of candidate sequences. To conclude this study, we apply our algorithms on the Glm clan and the FinP-traJ clan from the Rfam database. Conclusions Our results show that our methods reconstruct small sets of high-quality candidate ancestors with better agreement to the two target structures than with classical approaches. Our program is freely available at: http://csb.cs.mcgill.ca/acharnement .

  6. Next-generation Sequencing-based genomic profiling: Fostering innovation in cancer care?

    Directory of Open Access Journals (Sweden)

    Gustavo S. Fernandes

    Full Text Available OBJECTIVES: With the development of next-generation sequencing (NGS technologies, DNA sequencing has been increasingly utilized in clinical practice. Our goal was to investigate the impact of genomic evaluation on treatment decisions for heavily pretreated patients with metastatic cancer. METHODS: We analyzed metastatic cancer patients from a single institution whose cancers had progressed after all available standard-of-care therapies and whose tumors underwent next-generation sequencing analysis. We determined the percentage of patients who received any therapy directed by the test, and its efficacy. RESULTS: From July 2013 to December 2015, 185 consecutive patients were tested using a commercially available next-generation sequencing-based test, and 157 patients were eligible. Sixty-six patients (42.0% were female, and 91 (58.0% were male. The mean age at diagnosis was 52.2 years, and the mean number of pre-test lines of systemic treatment was 2.7. One hundred and seventy-seven patients (95.6% had at least one identified gene alteration. Twenty-four patients (15.2% underwent systemic treatment directed by the test result. Of these, one patient had a complete response, four (16.7% had partial responses, two (8.3% had stable disease, and 17 (70.8% had disease progression as the best result. The median progression-free survival time with matched therapy was 1.6 months, and the median overall survival was 10 months. CONCLUSION: We identified a high prevalence of gene alterations using an next-generation sequencing test. Although some benefit was associated with the matched therapy, most of the patients had disease progression as the best response, indicating the limited biological potential and unclear clinical relevance of this practice.

  7. Validity and reproducibility of self-reported working hours among Japanese male employees.

    Science.gov (United States)

    Imai, Teppei; Kuwahara, Keisuke; Miyamoto, Toshiaki; Okazaki, Hiroko; Nishihara, Akiko; Kabe, Isamu; Mizoue, Tetsuya; Dohi, Seitaro

    2016-07-22

    Working long hours is a potential health hazard. Although self-reporting of working hours in various time frames has been used in epidemiologic studies, its validity is unclear. The objective of this study was to examine the validity and reproducibility of self-reported working hours among Japanese male employees. The participants were 164 male employees of four large-scale companies in Japan. For validity, the Spearman correlation between self-reported working hours in the second survey and the working hours recorded by the company was calculated for the following four time frames: daily working hours, monthly overtime working hours in the last month, average overtime working hours in the last 3 months, and the frequency of long working months (≥45 h/month) within the last 12 months. For reproducibility, the intraclass correlation between the first (September 2013) and second surveys (December 2013) was calculated for each of the four time frames. The Spearman correlations between self-reported working hours and those based on company records were 0.74, 0.81, 0.85, and 0.89 for daily, monthly, 3-monthly, and yearly time periods, respectively. The intraclass correlations for self-reported working hours between the two questionnaire surveys were 0.63, 0.66, 0.73, and 0.87 for the respective time frames. The results of the present study among Japanese male employees suggest that the validity of self-reported working hours is high for all four time frames, whereas the reproducibility is moderate to high.

  8. Timing and sequencing of events marking the transition to adulthood in two informal settlements in Nairobi, Kenya.

    Science.gov (United States)

    Beguy, Donatien; Kabiru, Caroline W; Zulu, Eliya M; Ezeh, Alex C

    2011-06-01

    Young people living in poor urban informal settlements face unique challenges as they transition to adulthood. This exploratory paper uses retrospective information from the baseline survey of a 3-year prospective study to examine the timing and sequencing of four key markers (first sex, marriage, birth, and independent housing) of the transition to adulthood among 3,944 adolescents in two informal settlements in Nairobi city, Kenya. Event history analysis techniques are employed to examine the timing of the events. Results indicate that there is no significant gender difference with regard to first sexual debut among adolescents. For many boys and girls, the first sexual experience occurs outside of marriage or other union. For males, the sequencing of entry begins with entry into first sex, followed by independent housing. Conversely, for females, the sequencing begins with first sex and then parenthood. Apart from sexual debut, the patterns of entry into union and parenthood do not differ much from what was observed for Nairobi as a whole. The space constraints that typify the two slums may have influenced the pattern of leaving home observed. We discuss these and other findings in light of their implications for young people's health and well-being in resource-poor settings in urban areas.

  9. The Two-Tier Fecal Occult Blood Test: Cost-Effective Screening

    Directory of Open Access Journals (Sweden)

    Andrew J Rae

    1994-01-01

    Full Text Available The two-tier test represents a strategy combining HO Sensa and Hemeselect fecal occult blood tests (FOBTs with the aim of greater specificity and consequent economic advantages. If patients register a positive result on any HO Sensa guaiac test, they are once again tested by a hemoglobin-specific Hemeselect test. This concept was applied to a multicentre study involving persons 40 years or older. One component of the study enrolled 573 high risk patients while the second arm recruited an additional 1301 patients (52% asymptomatic/48% symptomatic stratified according to personal history and symptoms. The two-tier test produced fewer false positives than traditional tests in both groups evaluated in the study. In the high risk group, specificity (88.7% for two-tier versus 80.6% for Hemoccult and 69.5% for HO Sensa was higher and false positive rates were lower (11.3% for two-tier versus 19.5% for Hemoccultand 30.5% for HO Sensa for the two-tier test versus Hemoccult and HO Sensa FOBTs (95% CI for all colorectal cancers [CRCs] and polyps greater than 1 cm, α=0.05 . No significant differences in sensitivity were observed between tests in the same group. Also, in the high risk group, benefits of the two-tier test outweighed the costs. Due to the small number of cancers and polyps in the second arm of the study, presentation of data is meant to be descriptive and representative of trends in a ‘normal’ population. Nevertheless, specificity of the two-tier test was higher (96.8% for two-tier versus 87.2% for Hemoccult and 69.5% for HO Sensa and false positive rate lower (3.2% for two-tier versus 12.8% for Hemoccult and 22.3% for HO Sensa than either the Hemoccult or HO Sensa FOBT (95% CI for all CRCs and polyps greater than 1 cm. This initial study, focusing on the cost-benefit relationship of increased specificity, represents a new way of economically evaluating existing FOBTs.

  10. Hypothesis testing on the fractal structure of behavioral sequences: the Bayesian assessment of scaling methodology.

    Science.gov (United States)

    Moscoso del Prado Martín, Fermín

    2013-12-01

    I introduce the Bayesian assessment of scaling (BAS), a simple but powerful Bayesian hypothesis contrast methodology that can be used to test hypotheses on the scaling regime exhibited by a sequence of behavioral data. Rather than comparing parametric models, as typically done in previous approaches, the BAS offers a direct, nonparametric way to test whether a time series exhibits fractal scaling. The BAS provides a simpler and faster test than do previous methods, and the code for making the required computations is provided. The method also enables testing of finely specified hypotheses on the scaling indices, something that was not possible with the previously available methods. I then present 4 simulation studies showing that the BAS methodology outperforms the other methods used in the psychological literature. I conclude with a discussion of methodological issues on fractal analyses in experimental psychology. PsycINFO Database Record (c) 2014 APA, all rights reserved.

  11. Sequencing of chloroplast genome using whole cellular DNA and Solexa sequencing technology

    Directory of Open Access Journals (Sweden)

    Jian eWu

    2012-11-01

    Full Text Available Sequencing of the chloroplast genome using traditional sequencing methods has been difficult because of its size (>120 kb and the complicated procedures required to prepare templates. To explore the feasibility of sequencing the chloroplast genome using DNA extracted from whole cells and Solexa sequencing technology, we sequenced whole cellular DNA isolated from leaves of three Brassica rapa accessions with one lane per accession. In total, 246 Mb, 362Mb, 361 Mb sequence data were generated for the three accessions Chiifu-401-42, Z16 and FT, respectively. Microreads were assembled by reference-guided assembly using the cpDNA sequences of B. rapa, Arabidopsis thaliana, and Nicotiana tabacum. We achieved coverage of more than 99.96% of the cp genome in the three tested accessions using the B. rapa sequence as the reference. When A. thaliana or N. tabacum sequences were used as references, 99.7–99.8% or 95.5–99.7% of the B. rapa chloroplast genome was covered, respectively. These results demonstrated that sequencing of whole cellular DNA isolated from young leaves using the Illumina Genome Analyzer is an efficient method for high-throughput sequencing of chloroplast genome.

  12. Cortisol secretion after adrenocorticotrophin (ACTH and Dexamethasone tests in healthy female and male dogs

    Directory of Open Access Journals (Sweden)

    Castillo Victor

    2009-08-01

    Full Text Available Abstract Background For the conclusive diagnosis of Cushing's Syndrome, a stimulating ACTH test or a low suppressive Dexamethasone test is used. Reports in other species than the dog indicate that plasma cortisol concentration after ACTH administration is affected by gender. We investigated the effect of gender on the cortisol response to ACTH and Dexamethasone tests in dogs. Methods Seven healthy adult Cocker Spaniels (4 females and 3 males were assigned to a two by two factorial design: 4 dogs (2 females and 2 males received IV Dexamethasone 0.01 mg/kg, while the other 3 dogs received an IV saline solution (control group. Two weeks later the treatments were reversed. After one month, ACTH was given IV (250 μg/animal to 4 dogs (2 female and 2 males while the rest was treated with saline solution (control group. Cortisol concentrations were determined by a direct solid-phase radioimmunoassay and cholesterol and triglycerides by commercial kits. Results and Discussion No effect of treatment was observed in metabolite concentrations, but females presented higher cholesterol concentrations. ACTH-treated dogs showed an increase in cortisol levels in the first hour after sampling until 3 hours post injection. Cortisol concentrations in Dexamethasone-treated dogs decreased one hour post injection and remained low for 3 hours, thereafter cortisol concentrations increased. The increase in cortisol levels from one to two hours post ACTH injection was significantly higher in females than males. In Dexamethasone-treated males cortisol levels decreased one hour post injection up to 3 hours; in females the decrease was more pronounced and prolonged, up to 5 hours post injection. Conclusion We have demonstrated that cortisol response to ACTH and Dexamethasone treatment in dogs differs according to sex.

  13. US Naval Observatory Hourly Observations

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Hourly observations journal from the National Observatory in Washington DC. The observatory is the first station in the United States to produce hourly observations...

  14. Hours Constraints Within and Between Jobs

    OpenAIRE

    Euwals, R.W.

    1997-01-01

    In the empirical literature on labour supply, several models are developed to incorporate constraints on working hours. These models do not address the question to which extent working hours are constrained within and between jobs. In this paper I investigate the effect of individual changes in labour supply preferences on actual working hours. The availability of subjective information on the individual’s preferred working hours gives direct measures on the degree of adjustment of working ho...

  15. Strategies for managing work/life interaction among women and men with variable and unpredictable work hours in retail sales in Québec, Canada.

    Science.gov (United States)

    Messing, Karen; Tissot, France; Couture, Vanessa; Bernstein, Stephanie

    2014-01-01

    Increasingly, work schedules in retail sales are generated by software that takes into account variations in predicted sales. The resulting variable and unpredictable schedules require employees to be available, unpaid, over extended periods. At the request of a union, we studied schedule preferences in a retail chain in Québec using observations, interviews, and questionnaires. Shift start times had varied on average by four hours over the previous week; 83 percent had worked at least one day the previous weekend. Difficulties with work/life balance were associated with schedules and, among women, with family responsibilities. Most workers wanted: more advance notice; early shifts; regular schedules; two days off in sequence; and weekends off. Choices varied, so software could be adapted to take preferences into account. Also, employers could give better advance notice and establish systems for shift exchanges. Governments could limit store hours and schedule variability while prolonging the minimum sequential duration of leave per week.

  16. The two capsid proteins of maize rayado fino virus contain common peptide sequences.

    Science.gov (United States)

    Falk, B W; Tsai, J H

    1986-01-01

    Virions of maize rayado fino virus (MRFV) were purified and two major capsid proteins (ca. Mr 29,000 and 22,000) were resolved by SDS-PAGE. When the two major capsid proteins were isolated from gels and compared by one-dimensional peptide mapping after digestion with Staphylococcus aureus V-8 protease, indistinguishable peptide maps were obtained, suggesting that these two proteins contain common peptide sequences. Some preparations also showed minor protein components that were intermediate between the Mr 22,000 and Mr 29,000 capsid proteins. One of the minor proteins, ca. Mr 27,000, gave a peptide map indistinguishable from the major capsid proteins. In vitro ageing of partially purified preparations or virion treatment with proteolytic enzymes failed to show conversion of the Mr 29,000 protein to a Mr 22,000. Protease inhibitors added to the buffers used for virion purification did not affect the apparent 1:3 ratio of 29,000 to 22,000 proteins in the purified preparations.

  17. Determination of Functional Capabilities, the Level of Physical Performance and the State of Main Physiological Body Systems in the First Hours after the Accomplishment of Long-term Space Flights ("Field Test")

    Science.gov (United States)

    Kozlovskaya, Inesa; Tomilovskaya, Elena; Rukavishnikov, Ilya; Kitov, Vladimir; Reschke, Millard; Kofman, Igor

    2014-01-01

    Long-term stay in weightlessness is accompanied by alterations in the activity of main physiological body systems including sensory-motor, skeletal-muscular disturbances and cardiovascular deconditioning. However, up to now, there are no data on the state and level of functional performance of cosmonauts/astronauts directly after flight, nor are there data to help define the dynamic recovery of functional characteristics and work efficiency which are greatly needed to provide the safety and planning of their activity once they reach space objects. The Russian and American scientists are currently engaged in a joint experiment known as the "Field Test" with the goal of studying the functional performance and the state of main physiological body systems directly after landing and their temporal recovery dynamics. The functional performance is identified during the test by temporal characteristics of the movements of spatial translation, the stability of the vertical stance for 3.5 min, and the kinematic characteristics of walking - non-complicated and complicated. The following characteristics are identified as physiological characteristics of the test: a) orthostatic tolerance during stand test, b) back muscle tone; c) vertical stability - by characteristics of the correction responses to unexpected perturbations of the vertical stance, and d) support reactions during the performance of the full battery of tests. To date, a pilot version of the "Field Test" has been conducted with participation from four Russian cosmonauts. The results of studies have shown that in 1 - 5 hours after landing the functional abilities of the cosmonauts are considerably reduced. All the test movements at this time are considerably slower than preflight and the more complicated the task is, the greater significant reduction in orthostatic tolerance: during the first test that occurs 1 - 5 hours after landing. two of four cosmonauts declined to continue the task after the orthostatic test

  18. Evaluation program for secondary spacecraft cells: Initial evaluation tests of General Electric Company 40.0 ampere hour nickel cadmium spacecraft cells for the tracking data relay satellite system

    Science.gov (United States)

    Hall, S. W.

    1980-01-01

    Average end of charge voltages and pressures, and capacity output in ampere hours are presented. Test limits specify those values at which a cell is to be terminated from charge or discharge. Requirements are based on past cell performance data. The requirement does not constitute a limit for discontinuance from testing. The nickel cadmium batteries were screened for internal shorts, low capacity, electrolyte leakage, or inability of any cell to recover its open circuit voltage above 1.150 volts during the internal short test.

  19. Genome and Transcriptome Sequencing of the Ostreid herpesvirus 1 From Tomales Bay, California

    Science.gov (United States)

    Burge, C. A.; Langevin, S.; Closek, C. J.; Roberts, S. B.; Friedman, C. S.

    2016-02-01

    Mass mortalities of larval and seed bivalve molluscs attributed to the Ostreid herpesvirus 1 (OsHV-1) occur globally. OsHV-1 was fully sequenced and characterized as a member of the Family Malacoherpesviridae. Multiple strains of OsHV-1 exist and may vary in virulence, i.e. OsHV-1 µvar. For most global variants of OsHV-1, sequence data is limited to PCR-based sequencing of segments, including two recent genomes. In the United States, OsHV-1 is limited to detection in adjacent embayments in California, Tomales and Drakes bays. Limited DNA sequence data of OsHV-1 infecting oysters in Tomales Bay indicates the virus detected in Tomales Bay is similar but not identical to any one global variant of OsHV-1. In order to better understand both strain variation and virulence of OsHV-1 infecting oysters in Tomales Bay, we used genomic and transcriptomic sequencing. Meta-genomic sequencing (Illumina MiSeq) was conducted from infected oysters (n=4 per year) collected in 2003, 2007, and 2014, where full OsHV-1 genome sequences and low overall microbial diversity were achieved from highly infected oysters. Increased microbial diversity was detected in three of four samples sequenced from 2003, where qPCR based genome copy numbers of OsHV-1 were lower. Expression analysis (SOLiD RNA sequencing) of OsHV-1 genes expressed in oyster larvae at 24 hours post exposure revealed a nearly complete transcriptome, with several highly expressed genes, which are similar to recent transcriptomic analyses of other OsHV-1 variants. Taken together, our results indicate that genome and transcriptome sequencing may be powerful tools in understanding both strain variation and virulence of non-culturable marine viruses.

  20. Two estrogen response element sequences near the PCNA gene are not responsible for its estrogen-enhanced expression in MCF7 cells.

    Directory of Open Access Journals (Sweden)

    Cheng Wang

    Full Text Available The proliferating cell nuclear antigen (PCNA is an essential component of DNA replication, cell cycle regulation, and epigenetic inheritance. High expression of PCNA is associated with poor prognosis in patients with breast cancer. The 5'-region of the PCNA gene contains two computationally-detected estrogen response element (ERE sequences, one of which is evolutionarily conserved. Both of these sequences are of undocumented cis-regulatory function. We recently demonstrated that estradiol (E2 enhances PCNA mRNA expression in MCF7 breast cancer cells. MCF7 cells proliferate in response to E2.Here, we demonstrate that E2 rapidly enhanced PCNA mRNA and protein expression in a process that requires ERalpha as well as de novo protein synthesis. One of the two upstream ERE sequences was specifically bound by ERalpha-containing protein complexes, in vitro, in gel shift analysis. Yet, each ERE sequence, when cloned as a single copy, or when engineered as two tandem copies of the ERE-containing sequence, was not capable of activating a luciferase reporter construct in response to E2. In MCF7 cells, neither ERE-containing genomic region demonstrated E2-dependent recruitment of ERalpha by sensitive ChIP-PCR assays.We conclude that E2 enhances PCNA gene expression by an indirect process and that computational detection of EREs, even when evolutionarily conserved and when near E2-responsive genes, requires biochemical validation.

  1. Testing Two Tools for Multimodal Navigation

    Directory of Open Access Journals (Sweden)

    Mats Liljedahl

    2012-01-01

    Full Text Available The latest smartphones with GPS, electronic compasses, directional audio, touch screens, and so forth, hold a potential for location-based services that are easier to use and that let users focus on their activities and the environment around them. Rather than interpreting maps, users can search for information by pointing in a direction and database queries can be created from GPS location and compass data. Users can also get guidance to locations through point and sweep gestures, spatial sound, and simple graphics. This paper describes two studies testing two applications with multimodal user interfaces for navigation and information retrieval. The applications allow users to search for information and get navigation support using combinations of point and sweep gestures, nonspeech audio, graphics, and text. Tests show that users appreciated both applications for their ease of use and for allowing users to interact directly with the surrounding environment.

  2. Portuguese Lexical Clusters and CVC Sequences in Speech Perception and Production.

    Science.gov (United States)

    Cunha, Conceição

    2015-01-01

    This paper investigates similarities between lexical consonant clusters and CVC sequences differing in the presence or absence of a lexical vowel in speech perception and production in two Portuguese varieties. The frequent high vowel deletion in the European variety (EP) and the realization of intervening vocalic elements between lexical clusters in Brazilian Portuguese (BP) may minimize the contrast between lexical clusters and CVC sequences in the two Portuguese varieties. In order to test this hypothesis we present a perception experiment with 72 participants and a physiological analysis of 3-dimensional movement data from 5 EP and 4 BP speakers. The perceptual results confirmed a gradual confusion of lexical clusters and CVC sequences in EP, which corresponded roughly to the gradient consonantal overlap found in production. © 2015 S. Karger AG, Basel.

  3. Genome Sequences of Two Pseudomonas syringae pv. tomato Race 1 Strains, Isolated from Tomato Fields in California

    OpenAIRE

    Thapa, Shree P.; Coaker, Gitta

    2016-01-01

    Pseudomonas syringae pv. tomato race 1 strains have evolved to overcome genetic resistance in tomato. Here, we present the draft genome sequences of two race 1 P.?syringae pv. tomato strains, A9 and 407, isolated from diseased tomato plants in California.

  4. Long hours in paid and domestic work and subsequent sickness absence: does control over daily working hours matter?

    Science.gov (United States)

    Ala-Mursula, L; Vahtera, J; Kouvonen, A; Väänänen, A; Linna, A; Pentti, J; Kivimäki, M

    2006-09-01

    To explore the associations of working hours (paid, domestic, commuting, and total) with sickness absence, and to examine whether these associations vary according to the level of employee control over daily working hours. Prospective cohort study among 25 703 full-time public sector employees in 10 towns in Finland. A survey of working hours and control over working hours was carried out in 2000-01. The survey responses were linked with register data on the number of self-certified (3 days) sickness absences until the end of 2003. Poisson regression analyses with generalised estimating equations were used to take into account the fact that the employees were nested within work units. Adjustments were made for work and family characteristics and health behaviour. The mean follow-up period was 28.1 (SD 8.1) months. Long domestic and total working hours were associated with higher rates of medically certified sickness absences among both genders. In contrast, long paid working hours were associated with lower rates of subsequent self-certified sickness absences. Long commuting hours were related to increased rates of sickness absence of both types. Low control over daily working hours predicted medically certified sickness absences for both the women and men and self-certified absences for the men. In combinations, high control over working hours reduced the adverse associations of long domestic and total working hours with medically certified absences. Employee control over daily working hours may protect health and help workers successfully combine a full-time job with the demands of domestic work.

  5. Physicians' attentional performance following a 24-hour observation period: do we need to regulate sleep prior to work?

    Science.gov (United States)

    Smyth, P; Maximova, K; Jirsch, J D

    2017-08-01

    The tradition of physicians working while sleep deprived is increasingly criticised. Medical regulatory bodies have restricted resident physician duty-hours, not addressing the greater population of physicians. We aimed to assess factors such as sleep duration prior to a 24-hour observation period on physicians' attention. We studied 70 physicians (mean age 38 years old (SD 10.8 years)): 36 residents and 34 faculty from call rosters at the University of Alberta. Among 70 physicians, 52 (74%) performed overnight call; 18 did not perform overnight call and were recruited to control for the learning effect of repetitive neuropsychological testing. Attentional Network Test (ANT) measured physicians' attention at the beginning and end of the 24-hour observation period. Participants self-reported ideal sleep needs, sleep duration in the 24 hours prior to (ie, baseline) and during the 24-hour observation period (ie, follow-up). Median regression models examined effects on ANT parameters. Sleep deprivation at follow-up was associated with reduced attentional accuracy following the 24-hour observation period, but only for physicians more sleep deprived at baseline. Other components of attention were not associated with sleep deprivation after adjusting for repetitive testing. Age, years since medical school and caffeine use did not impact changes in ANT parameters. Our study suggests that baseline sleep before 24 hours of observation impacts the accuracy of physicians' attentional testing at 24 hours. Further study is required to determine if optimising physician sleep prior to overnight call shifts is a sustainable strategy to mitigate the effects of sleep deprivation. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

  6. Modelling hourly rates of evaporation from small lakes

    Directory of Open Access Journals (Sweden)

    R. J. Granger

    2011-01-01

    Full Text Available The paper presents the results of a field study of open water evaporation carried out on three small lakes in Western and Northern Canada. In this case small lakes are defined as those for which the temperature above the water surface is governed by the upwind land surface conditions; that is, a continuous boundary layer exists over the lake, and large-scale atmospheric effects such as entrainment do not come into play. Lake evaporation was measured directly using eddy covariance equipment; profiles of wind speed, air temperature and humidity were also obtained over the water surfaces. Observations were made as well over the upwind land surface.

    The major factors controlling open water evaporation were examined. The study showed that for time periods shorter than daily, the open water evaporation bears no relationship to the net radiation; the wind speed is the most significant factor governing the evaporation rates, followed by the land-water temperature contrast and the land-water vapour pressure contrast. The effect of the stability on the wind field was demonstrated; relationships were developed relating the land-water wind speed contrast to the land-water temperature contrast. The open water period can be separated into two distinct evaporative regimes: the warming period in the Spring, when the land is warmer than the water, the turbulent fluxes over water are suppressed; and the cooling period, when the water is warmer than the land, the turbulent fluxes over water are enhanced.

    Relationships were developed between the hourly rates of lake evaporation and the following significant variables and parameters (wind speed, land-lake temperature and humidity contrasts, and the downwind distance from shore. The result is a relatively simple versatile model for estimating the hourly lake evaporation rates. The model was tested using two independent data sets. Results show that the modelled evaporation follows the observed values

  7. [Organization of socially acceptable working hours in nursing].

    Science.gov (United States)

    Büssing, A; Glaser, J

    1994-05-01

    Three dimensions in the structure of the working hour system of nurses, rendering them socially acceptable, are becoming important: duration of the working day, the time of day which is being worked and the distribution of working hours. The latter two are of particular importance because flexible shift is becoming the dominant pattern in nursing. Six indicators are discussed as criteria for social acceptability: security of employment which includes access to the labour-market, level of income, health, opportunity for social relationships, social participation, and autonomy. Responses of 297 nurses in one General Hospital taking part in a study, were analysed to examine empirically the concept of 'socially acceptable structure of the working hours'. Ideal and factual patterns are considered first. Secondly aspects of autonomy are considered and the way this depends on time, thirdly the criteria used to define 'social acceptability' are examined for validity. Results show firstly the cross contrast between the hospital's expectation and the nurses' wishes with regard to working hours. Furthermore, inspite of the demand for flexibility, staff have very little choice and there is little sign of joint decision making. Thirdly results show that health, interpersonal and social aspects are of special importance and that, correspondingly, in the view of nurses, financial and practical problems are of lesser importance in their every day life.

  8. Heart Rate Variability in Obstetricians Working 14-Hour Call Compared to 24-Hour Call in Labour and Delivery.

    Science.gov (United States)

    Thurman, Robin H; Yoon, Eugene; Murphy, Kellie E; Windrim, Rory; Farrugia, M Michéle

    2017-12-01

    Obstetricians have stressful and demanding jobs that may impact their health. A physiological measurement of cardiac function which varies with stress is heart rate variability (HRV). By measuring the cyclic variations in R-R intervals, or beat-to-beat differences, HRV reflects the continuous interplay of the controlling forces in the autonomic nervous system. Studies have shown HRV to be reduced during periods of work-induced stress, including 24-hour shifts. Our study aimed to determine if there was a correlation between length of shift worked and HRV. We hypothesised that working for a full 24-hour period is more stressful than a shorter, nighttime-only period, and HRV analyses were used to measure this objectively. Obstetricians wore an HRV monitor for 24 hours during both a regular day followed by a 14-hour night shift and a continuous 24-hour shift in labour and delivery. The 24-hour samples were analysed using standard HRV measurements. HRV measurements obtained from each physician were then compared according to shift type, with each physician acting as his or her own comparator. There were no statistically significant differences in the most important measures of HRV between 24-hour periods which included either a 14-hour overnight shift or a continuous 24-hour shift on labour and delivery. We found no significant differences in key HRV measures in obstetricians working 14 hours versus 24 hours in labour and delivery. An anecdotal increase in physician awareness of his/her own health related to working conditions was noted during the study. Future studies should attempt to control for the hours prior to a night shift, assess associated endocrine variations, and focus upon HRV in the post-shift period. Crown Copyright © 2017. Published by Elsevier Inc. All rights reserved.

  9. Polyfluorophore Labels on DNA: Dramatic Sequence Dependence of Quenching

    Science.gov (United States)

    Teo, Yin Nah; Wilson, James N.

    2010-01-01

    We describe studies carried out in the DNA context to test how a common fluorescence quencher, dabcyl, interacts with oligodeoxynu-cleoside fluorophores (ODFs)—a system of stacked, electronically interacting fluorophores built on a DNA scaffold. We tested twenty different tetrameric ODF sequences containing varied combinations and orderings of pyrene (Y), benzopyrene (B), perylene (E), dimethylaminostilbene (D), and spacer (S) monomers conjugated to the 3′ end of a DNA oligomer. Hybridization of this probe sequence to a dabcyl-labeled complementary strand resulted in strong quenching of fluorescence in 85% of the twenty ODF sequences. The high efficiency of quenching was also established by their large Stern–Volmer constants (KSV) of between 2.1 × 104 and 4.3 × 105M−1, measured with a free dabcyl quencher. Interestingly, quenching of ODFs displayed strong sequence dependence. This was particularly evident in anagrams of ODF sequences; for example, the sequence BYDS had a KSV that was approximately two orders of magnitude greater than that of BSDY, which has the same dye composition. Other anagrams, for example EDSY and ESYD, also displayed different responses upon quenching by dabcyl. Analysis of spectra showed that apparent excimer and exciplex emission bands were quenched with much greater efficiency compared to monomer emission bands by at least an order of magnitude. This suggests an important role played by delocalized excited states of the π stack of fluorophores in the amplified quenching of fluorescence. PMID:19780115

  10. Draft genome sequences of two opportunistic pathogenic strains of Staphylococcus cohnii isolated from human patients.

    Science.gov (United States)

    Mendoza-Olazarán, Soraya; Garcia-Mazcorro, José F; Morfín-Otero, Rayo; Villarreal-Treviño, Licet; Camacho-Ortiz, Adrián; Rodríguez-Noriega, Eduardo; Bocanegra-Ibarias, Paola; Maldonado-Garza, Héctor J; Dowd, Scot E; Garza-González, Elvira

    2017-01-01

    Herein, we report the draft-genome sequences and annotation of two opportunistic pathogenic strains of Staphylococcus cohnii isolated from humans. One strain (SC-57) was isolated from blood from a male patient in May 2006 and the other (SC-532) from a catheter from a male patient in June 2006. Similar to other genomes of Staphylococcus species, most genes (42%) of both strains are involved in metabolism of amino acids and derivatives, carbohydrates and proteins. Eighty (4%) genes are involved in virulence, disease, and defense and both species show phenotypic low biofilm production and evidence of increased antibiotic resistance associated to biofilm production. From both isolates, a new Staphylococcal Cassette Chromosome mec was detected: mec class A, ccr type 1. This is the first report of whole genome sequences of opportunistic S. cohnii isolated from human patients.

  11. CLUSTOM-CLOUD: In-Memory Data Grid-Based Software for Clustering 16S rRNA Sequence Data in the Cloud Environment.

    Directory of Open Access Journals (Sweden)

    Jeongsu Oh

    Full Text Available High-throughput sequencing can produce hundreds of thousands of 16S rRNA sequence reads corresponding to different organisms present in the environmental samples. Typically, analysis of microbial diversity in bioinformatics starts from pre-processing followed by clustering 16S rRNA reads into relatively fewer operational taxonomic units (OTUs. The OTUs are reliable indicators of microbial diversity and greatly accelerate the downstream analysis time. However, existing hierarchical clustering algorithms that are generally more accurate than greedy heuristic algorithms struggle with large sequence datasets. To keep pace with the rapid rise in sequencing data, we present CLUSTOM-CLOUD, which is the first distributed sequence clustering program based on In-Memory Data Grid (IMDG technology-a distributed data structure to store all data in the main memory of multiple computing nodes. The IMDG technology helps CLUSTOM-CLOUD to enhance both its capability of handling larger datasets and its computational scalability better than its ancestor, CLUSTOM, while maintaining high accuracy. Clustering speed of CLUSTOM-CLOUD was evaluated on published 16S rRNA human microbiome sequence datasets using the small laboratory cluster (10 nodes and under the Amazon EC2 cloud-computing environments. Under the laboratory environment, it required only ~3 hours to process dataset of size 200 K reads regardless of the complexity of the human microbiome data. In turn, one million reads were processed in approximately 20, 14, and 11 hours when utilizing 20, 30, and 40 nodes on the Amazon EC2 cloud-computing environment. The running time evaluation indicates that CLUSTOM-CLOUD can handle much larger sequence datasets than CLUSTOM and is also a scalable distributed processing system. The comparative accuracy test using 16S rRNA pyrosequences of a mock community shows that CLUSTOM-CLOUD achieves higher accuracy than DOTUR, mothur, ESPRIT-Tree, UCLUST and Swarm. CLUSTOM

  12. CLUSTOM-CLOUD: In-Memory Data Grid-Based Software for Clustering 16S rRNA Sequence Data in the Cloud Environment.

    Science.gov (United States)

    Oh, Jeongsu; Choi, Chi-Hwan; Park, Min-Kyu; Kim, Byung Kwon; Hwang, Kyuin; Lee, Sang-Heon; Hong, Soon Gyu; Nasir, Arshan; Cho, Wan-Sup; Kim, Kyung Mo

    2016-01-01

    High-throughput sequencing can produce hundreds of thousands of 16S rRNA sequence reads corresponding to different organisms present in the environmental samples. Typically, analysis of microbial diversity in bioinformatics starts from pre-processing followed by clustering 16S rRNA reads into relatively fewer operational taxonomic units (OTUs). The OTUs are reliable indicators of microbial diversity and greatly accelerate the downstream analysis time. However, existing hierarchical clustering algorithms that are generally more accurate than greedy heuristic algorithms struggle with large sequence datasets. To keep pace with the rapid rise in sequencing data, we present CLUSTOM-CLOUD, which is the first distributed sequence clustering program based on In-Memory Data Grid (IMDG) technology-a distributed data structure to store all data in the main memory of multiple computing nodes. The IMDG technology helps CLUSTOM-CLOUD to enhance both its capability of handling larger datasets and its computational scalability better than its ancestor, CLUSTOM, while maintaining high accuracy. Clustering speed of CLUSTOM-CLOUD was evaluated on published 16S rRNA human microbiome sequence datasets using the small laboratory cluster (10 nodes) and under the Amazon EC2 cloud-computing environments. Under the laboratory environment, it required only ~3 hours to process dataset of size 200 K reads regardless of the complexity of the human microbiome data. In turn, one million reads were processed in approximately 20, 14, and 11 hours when utilizing 20, 30, and 40 nodes on the Amazon EC2 cloud-computing environment. The running time evaluation indicates that CLUSTOM-CLOUD can handle much larger sequence datasets than CLUSTOM and is also a scalable distributed processing system. The comparative accuracy test using 16S rRNA pyrosequences of a mock community shows that CLUSTOM-CLOUD achieves higher accuracy than DOTUR, mothur, ESPRIT-Tree, UCLUST and Swarm. CLUSTOM-CLOUD is written in JAVA

  13. CLUSTOM-CLOUD: In-Memory Data Grid-Based Software for Clustering 16S rRNA Sequence Data in the Cloud Environment

    Science.gov (United States)

    Park, Min-Kyu; Kim, Byung Kwon; Hwang, Kyuin; Lee, Sang-Heon; Hong, Soon Gyu; Nasir, Arshan; Cho, Wan-Sup; Kim, Kyung Mo

    2016-01-01

    High-throughput sequencing can produce hundreds of thousands of 16S rRNA sequence reads corresponding to different organisms present in the environmental samples. Typically, analysis of microbial diversity in bioinformatics starts from pre-processing followed by clustering 16S rRNA reads into relatively fewer operational taxonomic units (OTUs). The OTUs are reliable indicators of microbial diversity and greatly accelerate the downstream analysis time. However, existing hierarchical clustering algorithms that are generally more accurate than greedy heuristic algorithms struggle with large sequence datasets. To keep pace with the rapid rise in sequencing data, we present CLUSTOM-CLOUD, which is the first distributed sequence clustering program based on In-Memory Data Grid (IMDG) technology–a distributed data structure to store all data in the main memory of multiple computing nodes. The IMDG technology helps CLUSTOM-CLOUD to enhance both its capability of handling larger datasets and its computational scalability better than its ancestor, CLUSTOM, while maintaining high accuracy. Clustering speed of CLUSTOM-CLOUD was evaluated on published 16S rRNA human microbiome sequence datasets using the small laboratory cluster (10 nodes) and under the Amazon EC2 cloud-computing environments. Under the laboratory environment, it required only ~3 hours to process dataset of size 200 K reads regardless of the complexity of the human microbiome data. In turn, one million reads were processed in approximately 20, 14, and 11 hours when utilizing 20, 30, and 40 nodes on the Amazon EC2 cloud-computing environment. The running time evaluation indicates that CLUSTOM-CLOUD can handle much larger sequence datasets than CLUSTOM and is also a scalable distributed processing system. The comparative accuracy test using 16S rRNA pyrosequences of a mock community shows that CLUSTOM-CLOUD achieves higher accuracy than DOTUR, mothur, ESPRIT-Tree, UCLUST and Swarm. CLUSTOM-CLOUD is written in

  14. Rapid and Deep Proteomes by Faster Sequencing on a Benchtop Quadrupole Ultra-High-Field Orbitrap Mass Spectrometer

    DEFF Research Database (Denmark)

    Kelstrup, Christian D; Jersie-Christensen, Rosa R; Batth, Tanveer Singh

    2014-01-01

    per second or up to 600 new peptides sequenced per gradient minute. We identify 4400 proteins from one microgram of HeLa digest using a one hour gradient, which is an approximately 30% improvement compared to previous instrumentation. In addition, we show very deep proteome coverage can be achieved...... in less than 24 hours of analysis time by offline high pH reversed-phase peptide fractionation from which we identify more than 140,000 unique peptide sequences. This is comparable to state-of-the-art multi-day, multi-enzyme efforts. Finally the acquisition methods are evaluated for single...

  15. Complete sequence and analysis of plastid genomes of two economically important red algae: Pyropia haitanensis and Pyropia yezoensis.

    Directory of Open Access Journals (Sweden)

    Li Wang

    Full Text Available Pyropia haitanensis and P. yezoensis are two economically important marine crops that are also considered to be research models to study the physiological ecology of intertidal seaweed communities, evolutionary biology of plastids, and the origins of sexual reproduction. This plastid genome information will facilitate study of breeding, population genetics and phylogenetics.We have fully sequenced using next-generation sequencing the circular plastid genomes of P. hatanensis (195,597 bp and P. yezoensis (191,975 bp, the largest of all the plastid genomes of the red lineage sequenced to date. Organization and gene contents of the two plastids were similar, with 211-213 protein-coding genes (including 29-31 unknown-function ORFs, 37 tRNA genes, and 6 ribosomal RNA genes, suggesting a largest coding capacity in the red lineage. In each genome, 14 protein genes overlapped and no interrupted genes were found, indicating a high degree of genomic condensation. Pyropia maintain an ancient gene content and conserved gene clusters in their plastid genomes, containing nearly complete repertoires of the plastid genes known in photosynthetic eukaryotes. Similarity analysis based on the whole plastid genome sequences showed the distance between P. haitanensis and P. yezoensis (0.146 was much smaller than that of Porphyra purpurea and P. haitanensis (0.250, and P. yezoensis (0.251; this supports re-grouping the two species in a resurrected genus Pyropia while maintaining P. purpurea in genus Porphyra. Phylogenetic analysis supports a sister relationship between Bangiophyceae and Florideophyceae, though precise phylogenetic relationships between multicellular red alage and chromists were not fully resolved.These results indicate that Pyropia have compact plastid genomes. Large coding capacity and long intergenic regions contribute to the size of the largest plastid genomes reported for the red lineage. Possessing the largest coding capacity and ancient gene

  16. Testing of the IMRA Wattlite Laser

    International Nuclear Information System (INIS)

    Biswal, S; Erbert, G

    2000-01-01

    Long term testing of the IMRA Wattlite oscillator began this month. The oscillator was operated for over 250 hours while monitoring the output power, the center wavelength and the pointing stability. Due to safety requirements, data was only collected during normal working hours. At night, the external shutter was closed so no data was collected, however, the laser continued to operate. In this mode of operation, approximately 80 hours of data was taken during the 250 hours of operation. The laser was turned off during the two weekend periods of this test series and restarted the following Monday. The warm-up period of the oscillator is most evident in the wavelength data shown in Figure 1. During the two cold start periods, the laser required about two hours for the wavelength to stabilize. Excluding the warm-up periods, the wavelength drift was approximately ± 0.1nm over the 250 hours of operation. The output power was monitored with a large area photo-diode. A plot of the output power as a function of time is shown in Figure 2. The two cold start periods are also evident in this data showing the same two-hour warm-up period for the power to stabilize. Once the laser was stable, the output power varied by only a few percent. It is also important to note that there is no degradation in the output power over the 250 hours of operation. The pointing error from the oscillator was monitored by focusing the output beam onto a video camera. The data acquisition program finds the centroid of the focused spot to the nearest pixel on the CCD array. The resolution of the system was 42 micro-radians/pixel in the horizontal axis and 49 micro-radians/pixel in the vertical axis. A plot of the pointing error as a function of time is shown in Figures 3 and 4. The pointing errors recorded are very small and are near the resolution of the diagnostic system. This is not surprising considering the output beam is from a single mode fiber. The pointing stability should only be related

  17. Development and validation of a direct-comparison method for cardiac {sup 123}I-metaiodobenzylguanidine washout rates derived from late 3-hour and 4-hour imaging

    Energy Technology Data Exchange (ETDEWEB)

    Okuda, Koichi; Hashimoto, Mitsumasa [Kanazawa Medical University, Department of Physics, Kahoku, Ishikawa (Japan); Nakajima, Kenichi; Matsuo, Shinro; Taki, Junichi; Kinuya, Seigo [Kanazawa University Hospital, Department of Nuclear Medicine, Kanazawa, Ishikawa (Japan); Sugino, Shuichi [Okayama Kyokuto Hospital, Department of Radiology, Okayama, Okayama (Japan); Kirihara, Yumiko [FUJIFILM RI Pharma Co., Ltd., Chuo-Ku, Tokyo (Japan)

    2016-02-15

    The washout rate (WR) has been used in {sup 123}I-metaiodobenzylguanidine (MIBG) imaging to evaluate cardiac sympathetic innervation. However, WR varies depending on the time between the early and late MIBG scans. Late scans are performed at either 3 or 4 hours after injection of MIBG. The aim of this study was to directly compare the WR at 3 hours (WR{sub 3h}) with the WR at 4 hours (WR{sub 4h}). We hypothesized that the cardiac count would reduce linearly between the 3-hour and 4-hour scans. A linear regression model for cardiac counts at two time-points was generated. We enrolled a total of 96 patients who underwent planar {sup 123}I-MIBG scintigraphy early (15 min) and during the late phase at both 3 and 4 hours. Patients were randomly divided into two groups: a model-creation group (group 1) and a clinical validation group (group 2). Cardiac counts at 15 minutes (count{sub early}), 3 hours (count{sub 3h}) and 4 hours (count{sub 4h}) were measured. Cardiac count{sub 4h} was mathematically estimated using the linear regression model from count{sub early} and count{sub 3h}. In group 1, the actual cardiac count{sub 4h}/count{sub early} was highly significantly correlated with count{sub 3h}/count{sub early} (r = 0.979). In group 2, the average estimated count{sub 4h} was 92.8 ± 31.9, and there was no significant difference between this value and the actual count{sub 4h} (91.9 ± 31.9). Bland-Altman analysis revealed a small bias of -0.9 with 95 % limits of agreement of -6.2 and +4.3. WR{sub 4h} calculated using the estimated cardiac count{sub 4h} was comparable to the actual WR{sub 4h} (24.3 ± 9.6 % vs. 25.1 ± 9.7 %, p = ns). Bland-Altman analysis and the intraclass correlation coefficient showed that there was excellent agreement between the estimated and actual WR{sub 4h}. The linear regression model that we used accurately estimated cardiac count{sub 4h} using count{sub early} and count{sub 3h}. Moreover, WR{sub 4h} that was mathematically calculated using

  18. Binning sequences using very sparse labels within a metagenome

    Directory of Open Access Journals (Sweden)

    Halgamuge Saman K

    2008-04-01

    Full Text Available Abstract Background In metagenomic studies, a process called binning is necessary to assign contigs that belong to multiple species to their respective phylogenetic groups. Most of the current methods of binning, such as BLAST, k-mer and PhyloPythia, involve assigning sequence fragments by comparing sequence similarity or sequence composition with already-sequenced genomes that are still far from comprehensive. We propose a semi-supervised seeding method for binning that does not depend on knowledge of completed genomes. Instead, it extracts the flanking sequences of highly conserved 16S rRNA from the metagenome and uses them as seeds (labels to assign other reads based on their compositional similarity. Results The proposed seeding method is implemented on an unsupervised Growing Self-Organising Map (GSOM, and called Seeded GSOM (S-GSOM. We compared it with four well-known semi-supervised learning methods in a preliminary test, separating random-length prokaryotic sequence fragments sampled from the NCBI genome database. We identified the flanking sequences of the highly conserved 16S rRNA as suitable seeds that could be used to group the sequence fragments according to their species. S-GSOM showed superior performance compared to the semi-supervised methods tested. Additionally, S-GSOM may also be used to visually identify some species that do not have seeds. The proposed method was then applied to simulated metagenomic datasets using two different confidence threshold settings and compared with PhyloPythia, k-mer and BLAST. At the reference taxonomic level Order, S-GSOM outperformed all k-mer and BLAST results and showed comparable results with PhyloPythia for each of the corresponding confidence settings, where S-GSOM performed better than PhyloPythia in the ≥ 10 reads datasets and comparable in the ≥ 8 kb benchmark tests. Conclusion In the task of binning using semi-supervised learning methods, results indicate S-GSOM to be the best of

  19. Changes in serial laboratory test results in snakebite patients: when can we safely exclude envenoming?

    Science.gov (United States)

    Ireland, Graham; Brown, Simon G A; Buckley, Nicholas A; Stormer, Jeff; Currie, Bart J; White, Julian; Spain, David; Isbister, Geoffrey K

    2010-09-06

    To determine which laboratory tests are first associated with severe envenoming after a snakebite, when (ie, how long after the bite) the test results become abnormal, and whether this can determine a safe observation period after suspected snakebite. Prospective cohort study of 478 patients with suspected or confirmed snakebite recruited to the Australian Snakebite Project from January 2002 to April 2009, who had at least three sets of laboratory test results and at least 12 hours of observation in hospital after the bite. Severe envenoming was defined as venom-induced consumption coagulopathy (VICC), myotoxicity, neurotoxicity or thrombotic microangiopathy. International normalised ratio (INR), activated partial thromboplastin time (aPTT), creatine kinase (CK) level, and neurological examination. There were 240 patients with severe envenoming, 75 with minor envenoming and 163 non-envenomed patients. Of 206 patients with VICC, 178 had an INR > 1.2 (abnormal) on admission, and the remaining 28 had an INR > 1.2 within 12 hours of the bite. Of 33 patients with myotoxicity, a combination of CK > 250 U/L and an abnormal aPTT identified all but two cases by 12 hours; one of these two was identified within 12 hours by leukocytosis. Nine cases of isolated neurotoxicity had a median time of onset after the bite of 4 hours (range, 35 min - 12 h). The combination of serial INR, aPTT and CK tests and repeated neurological examination identified 213 of 222 severe envenoming cases (96%) by 6 hours and 238 of 240 (99%) by 12 hours. Laboratory parameters (INR, aPTT and CK) and neurological reassessments identified nearly all severe envenoming cases within 12 hours of the bite, even in this conservative analysis that assumed normal test results if the test was not done.

  20. 46 CFR 15.710 - Working hours.

    Science.gov (United States)

    2010-10-01

    ... 46 Shipping 1 2010-10-01 2010-10-01 false Working hours. 15.710 Section 15.710 Shipping COAST... Limitations and Qualifying Factors § 15.710 Working hours. In addition to prescribing watch requirements, 46 U.S.C. 8104 sets limitations on the working hours of credentialed officers and crew members...

  1. 75 FR 285 - Hours of Service

    Science.gov (United States)

    2010-01-05

    ... flexibility would not increase safety risks or adversely impact driver health? 3. How many hours per day and... period long enough to provide restorative sleep regardless of the number of hours worked prior to the... No. FMCSA-2004-19608] RIN 2126-AB26 Hours of Service AGENCY: Federal Motor Carrier Safety...

  2. Context-dependent motor skill: perceptual processing in memory-based sequence production.

    Science.gov (United States)

    Ruitenberg, Marit F L; Abrahamse, Elger L; De Kleine, Elian; Verwey, Willem B

    2012-10-01

    Previous studies have shown that motor sequencing skill can benefit from the reinstatement of the learning context-even with respect to features that are formally not required for appropriate task performance. The present study explored whether such context-dependence develops when sequence execution is fully memory-based-and thus no longer assisted by stimulus-response translations. Specifically, we aimed to distinguish between preparation and execution processes. Participants performed two keying sequences in a go/no-go version of the discrete sequence production task in which the context consisted of the color in which the target keys of a particular sequence were displayed. In a subsequent test phase, these colors either were the same as during practice, were reversed for the two sequences or were novel. Results showed that, irrespective of the amount of practice, performance across all key presses in the reversed context condition was impaired relative to performance in the same and novel contexts. This suggests that the online preparation and/or execution of single key presses of the sequence is context-dependent. We propose that a cognitive processor is responsible both for these online processes and for advance sequence preparation and that combined findings from the current and previous studies build toward the notion that the cognitive processor is highly sensitive to changes in context across the various roles that it performs.

  3. [Comparison of rDNA internal transcribed spacer sequences in asparagus].

    Science.gov (United States)

    Ou, Li-Jun; Ye, Wei; Zeng, Gui-Ping; Jiang, Xiang-Hui; She, Chao-Wen; Xu, Dong; Yang, Jia-Qiang

    2010-10-01

    Using ITS sequence of nine species to identify counterfeiting medicine and analyse phylogenetic of Asparagus. Analysing ITS sequences by amplification, cloning,sequencing and alignment. The length range of ITS sequence of nine species was from 711 to 748 bp, the percentage of G + C content was about 60%. The phylogenetic tree constructed on the basis of the ITS sequences showed that nine species were divided into two branches: Asparagus cochinchinensis, Asparagus officinalis, Asparagus densiflorus, Asparagus densiflorus cv. Myers and Asparagus densiflorus cv. Sprengeri were a branch and the others were a branch. Asparagus densiflorus and Asparagus densflorus cv. Myers those were from Africa had priority to clustering and then clustering with Asparagus densiflorus cv. Sprengeri that was a variant of Asparagus densiflorus in the first branch. Asparagus setaceus had relatively distant genetic relationship with the others three materials in another branch. The ITS sequences could distinguish species of Asparagus to test the counterfeit. Division status in phylogenetic tree of some species were debatable and ITS sequence was combined with others analytical tools to analyze the realistic phylogeny.

  4. Comparative study of alertness and performance on 8-hour and 12-hour evening and night shifts for nuclear power plant operators

    International Nuclear Information System (INIS)

    Baker, T.L.

    1990-01-01

    Twenty males aged 25-40 years, many with extensive shiftwork and/or power plant operations experience, volunteered for a laboratory study to compare 8-hour and 12-hour shift schedules. Experiments were conducted in workplace simulation laboratories of the Human Alertness Research Center (HARC) at the Institute for Circadian Physiology in Boston, MA. This unique facility includes a simulated control room with process control simulator, control panels, and self-contained residential apartments where subjects sleep and spend off-duty hours. The design of the study is described. Subjects learn the operation of the process control simulator in multiple practice sessions prior to the experiment. They also practice computer-based performance tests, learn work shift protocols and assignments, and procedures for keeping subjective rating scales for alertness, mood and performance. By the time the first experimental shift begins, all subjects are prepared to perform their simulated work shift duties. These duties include monitoring of four video display terminals for silent (visual cues only) and auditory (visual and auditory) alarms, acknowledging the alarms with computer controls, and keeping log records of alarm activity. The process control simulator simultaneously keeps records of subject performance of these tasks by recording storing all times of alarm activity and alarm acknowledgement by the subject

  5. Sequence embedding for fast construction of guide trees for multiple sequence alignment

    LENUS (Irish Health Repository)

    Blackshields, Gordon

    2010-05-14

    Abstract Background The most widely used multiple sequence alignment methods require sequences to be clustered as an initial step. Most sequence clustering methods require a full distance matrix to be computed between all pairs of sequences. This requires memory and time proportional to N 2 for N sequences. When N grows larger than 10,000 or so, this becomes increasingly prohibitive and can form a significant barrier to carrying out very large multiple alignments. Results In this paper, we have tested variations on a class of embedding methods that have been designed for clustering large numbers of complex objects where the individual distance calculations are expensive. These methods involve embedding the sequences in a space where the similarities within a set of sequences can be closely approximated without having to compute all pair-wise distances. Conclusions We show how this approach greatly reduces computation time and memory requirements for clustering large numbers of sequences and demonstrate the quality of the clusterings by benchmarking them as guide trees for multiple alignment. Source code is available for download from http:\\/\\/www.clustal.org\\/mbed.tgz.

  6. Poorer Health – Shorter Hours? Health and Flexibility of Hours of Work

    OpenAIRE

    Geyer, Johannes; Myck, Michal

    2010-01-01

    We analyse the role of health in determining the difference between desired and actual hours of work in a sample of German men using the Socio-Economic Panel Data for years 1996-2007. The effects of both self-assessed health and legal disability status are examined. About 60% of employees report working more than they would wish with the mean difference of -3.9 hours/week. We estimate static and dynamic model specifications allowing for auto-regressive nature of the dependent variable and tes...

  7. Comparison of 24-hour urinary protein and protein-to-creatinine ratio in the assessment of proteinuria

    International Nuclear Information System (INIS)

    Wahbeh, Ayman M; Ewais, Mohammad H; Elsharif, Mahamed E

    2009-01-01

    To determine the correlation between protein-to-creatinine ratio (PCR) and 24-hour urinary protein (UP), we measured proteinuria in 68 patients attending the nephrology clinic at Jordan University Hospital by 24-hour urine protein excretion and protein-to-creatinine ratio. The cutoff values for spot urine protein-to-creatinine ratio in predicting 24-hour protein 'threshold' excretion of 0.5, 1.0 and 3.5 g/day were determined using receiver operating characteristic curves. A very good correlation (r= 0.832, P< 0.0001) was found between spot urine protein-to-creatinine ratio and 24-hour urine protein excretion. Bland-Altman plot showed the two tests had reasonable limits of agreement at low level of protein excretion but the limits became wider as the protein excretion increased. For protein excretion < 2.0 g/day, the limits of agreement of spot urine (PCR) and (UP) were +1.48 and -1.2 g/day. The spot urine protein-to-creatinine ratios of 0.72 (sensitivity 0.97; specificity 1.0), 1.2 (0.97; 0.89) and 3.23 (1.0; 0.86) mg/mg reliably predicted 24-hour urine total protein equivalent 'thresholds' of 0.5, 1.0 and 3.5 g/day, respectively. We conclude that the protein-to-creatinine ratio in spot urine specimens is an accurate, convenient, and reliable method to estimate the protein excretion in urine. However, the protein-to-creatinine ratio will likely be within clinically acceptable limits only when proteinuria is at reasonably low levels. (author)

  8. [Spanish normative studies in a young adult population (NEURONORMA young adults Project): norms for the verbal span, visuospatial span, Letter-Number Sequencing, Trail Making Test and Symbol Digit Modalities Test].

    Science.gov (United States)

    Tamayo, F; Casals-Coll, M; Sánchez-Benavides, G; Quintana, M; Manero, R M; Rognoni, T; Calvo, L; Palomo, R; Aranciva, F; Peña-Casanova, J

    2012-01-01

    Verbal and visuospatial span, Letter-Number Sequencing, Trail Making Test, and Symbol Digit Modalities Test are frequently used in clinical practice to assess attention, executive functions and memory. In the present study, as part of the Spanish normative studies of NEURONORMA young adults Project, normative data adjusted by age and education are provided for digits, Corsi Block-Tapping Task, Letter-Number Sequencing, Trail Making Test, and Symbol Digit Modalities Test. The sample consisted of 179 participants from 18 to 49 years old, who were cognitively normal. Tables to convert raw scores to scaled scores are provided. Age and education adjusted scores are provided by applying linear regressions. Education affected scores in most of the attention tests; age was found to be related to the visuospatial span and to speed of visuomotor tracking, and there was no relationship as regards sex. The data obtained will be useful in the clinical evaluation of young Spanish adults. Copyright © 2011 Sociedad Española de Neurología. Published by Elsevier Espana. All rights reserved.

  9. Investigations on the two-dimensional aperiodic plasma photonic crystals with fractal Fibonacci sequence

    Directory of Open Access Journals (Sweden)

    Hai-Feng Zhang

    2017-07-01

    Full Text Available In this paper, the properties of photonic band gaps (PBGs and defect modes of two-dimensional (2D fractal plasma photonic crystals (PPCs under a transverse-magnetic (TM wave are theoretically investigated by a modified plane wave expansion (PWE method. The configuration of 2D PPCs is the square lattices with the iteration rule of the Fibonacci sequence whose constituents are homogeneous and isotropic. The proposed 2D PPCs is filled with the dielectric cylinders in the plasma background. The accuracy and convergence of the present modified PWE method also are validated by a numerical example. The calculated results illustrate that the enough accuracy and good convergence can be achieved compared to the conventional PWE method, if the number of meshed grids is large enough. The dispersion curves of the proposed PPCs and 2D PPCs with a conventional square lattice are theoretically computed to study the properties of PBGs and defect modes. The simulated results demonstrate that the advantaged properties can be obtained in the proposed PPCs compared to the 2D conventional PPCs with similar lattices. If the Fibonacci sequence is introduced into the 2D PPCs, the larger PBGs and higher cutoff frequency can be achieved. The lower edges of PBGs are flat, which are originated from the Mie resonances. The defect modes can be considered as the quasi-localized states since the Fibonacci sequence has the self-similarity and non-periodicity at the same time. The effects of configurational parameters on the characters of the present PPCs are investigated. The results show that the PBGs and defect modes can be easily manipulated by tuning those parameters.

  10. [Relationships between walking hours, sleeping hours, meaningfulness of life (ikigai) and mortality in the elderly: prospective cohort study].

    Science.gov (United States)

    Seki, N

    2001-07-01

    The purpose of this study was to determine lifestyle factors in the elderly that affected longevity, using a population-based prospective study. The participants were 440 men and 625 women aged 60 to 74 living in a rural Japanese community. The baseline data such as age, sex, present illness, walking hours per day, sleeping hours per day, alcohol consumption, a history of smoking, and "ikigai" (meaningfulness of life) were collected in July 1990. During 90 months of follow-up from July 1990 to December 31 1997, there were 123 deaths. By Cox's multivariate hazard model adjusted age, sex, and medical histories, walking > or = 1 hour/day (HR = 0.63, 95% CI 0.44-0.91) and an "ikigai" (HR = 0.66, 95% CI 0.44-0.99) lowered the risk for all-cause mortality independently. In regard to hours of sleep, the cumulative survival curve showed that 7 hours/day was the border and sleeping > or = 7 hours/day lowered the risk (HR = 0.49 95% CI 0.33-0.74). Based on the findings in this study, walking > or = 1 hour/day, sleeping > or = 7 hours/day, and "ikigai" are important factors for longevity in the elderly.

  11. Atrial Fibrillation Detection During 24-Hour Ambulatory Blood Pressure Monitoring: Comparison With 24-Hour Electrocardiography.

    Science.gov (United States)

    Kollias, Anastasios; Destounis, Antonios; Kalogeropoulos, Petros; Kyriakoulis, Konstantinos G; Ntineri, Angeliki; Stergiou, George S

    2018-07-01

    This study assessed the diagnostic accuracy of a novel 24-hour ambulatory blood pressure (ABP) monitor (Microlife WatchBP O3 Afib) with implemented algorithm for automated atrial fibrillation (AF) detection during each ABP measurement. One hundred subjects (mean age 70.6±8.2 [SD] years; men 53%; hypertensives 85%; 17 with permanent AF; 4 paroxysmal AF; and 79 non-AF) had simultaneous 24-hour ABP monitoring and 24-hour Holter monitoring. Among a total of 6410 valid ABP readings, 1091 (17%) were taken in ECG AF rhythm. In reading-to-reading ABP analysis, the sensitivity, specificity, and accuracy of ABP monitoring in detecting AF were 93%, 87%, and 88%, respectively. In non-AF subjects, 12.8% of the 24-hour ABP readings indicated false-positive AF, of whom 27% were taken during supraventricular premature beats. There was a strong association between the proportion of false-positive AF readings and that of supraventricular premature beats ( r =0.67; P ABP monitoring had 100%/85% sensitivity/specificity (area under the curve 0.91; P ABP monitor with AF detector has high sensitivity and moderate specificity for AF screening during routine ABP monitoring. Thus, in elderly hypertensives, a 24-hour ABP recording with at least 26% of the readings suggesting AF indicates a high probability for AF diagnosis and should be regarded as an indication for performing 24-hour Holter monitoring. © 2018 American Heart Association, Inc.

  12. Basic design of the test facility for the two-phase critical flow with non-condensable gas

    International Nuclear Information System (INIS)

    Chang, Seok Kyu; Kim, Chang Hwe; Chung, Chang Hwan

    2000-12-01

    The two-phase critical flow test with non-condensible gas is for the simulation of the critical flow phenomena which can be occurred during SB-LOCA on SMART reactor. The basic design of the test facility for the actual installation is performed from the basis of the previous conceptual design according to the test requirements. The 1.3m 3 pressure vessel has the circulation pipeline which contains pump(5m 3 /hr), main heater(150KW) and cooler for heating the working fluid to the test temperature within 6 hours. The N2 gas, water supply line are attached to the upper part and test section, flowmeter and various sensors are installed at the lower part of the pressure vessel. The suppression tank is for the storage and cooling of the discharged water. The N2 gas storage tank provides the system pressure to the pressure vessel during the test. The 0.7m 3 N2 gas injection tank supplies the required N2 gas to the entrance of the test section. Since these N2 supply systems require much amount of gas during short period, multistage valve systems and optimal control logics are needed and applied. For the filling of the N2 gas to the N2 storage tank, 5m 3 LN2 tank and related gas converting system were designed. The operating mode of the test facility can be classified to the starting, steady, main test and cooling modes and the proper monitoring and control logics are developed for each operating mode. The operation of the test facility is performed through the PLC and the acquisition of the test data is done with DAS

  13. TOUR CONSTRUCTION HEURISTICS FOR AN ORDER SEQUENCING PROBLEM

    Directory of Open Access Journals (Sweden)

    De Villiers, A. P.

    2012-11-01

    Full Text Available An order picking system that requires pickers to move in a clockwise direction around a picking line with fixed locations is considered. The problem is divided into three tiers. The tier in which orders must be sequenced is addressed. Eight tour construction heuristics are developed and implemented for an order picking system operating in unidirectional picking lines. Two classes of tour construction heuristics the tour construction starting position ( and the tour construction ending position ( are developed to sequence orders in a picking line. All algorithms are tested and compared using real life data sets. The best solution quality was obtained by a heuristic with adaptations.

  14. Prenylcoumarins in One or Two Steps by a Microwave-Promoted Tandem Claisen Rearrangement/Wittig Olefination/Cyclization Sequence.

    Science.gov (United States)

    Schultze, Christiane; Schmidt, Bernd

    2018-05-04

    The one-pot synthesis of 8-prenylcoumarins from 1,1-dimethylallylated salicylaldehydes and the stabilized ylide [(ethoxycarbonyl)methylene]triphenylphosphorane under microwave conditions was found to have a limited scope. The sequence suffers from a difficult and sometimes low-yielding synthesis of the precursors and from a competing deprenylation upon microwave irradiation. This side reaction occurs in particular with electron rich arenes with two or more alkoxy groups at adjacent positions, a prominent substitution pattern in naturally occurring 8-prenylcoumarins. Both limitations of this one-step sequence were overcome by a two-step synthesis consisting of a microwave-promoted tandem allyl ether Claisen rearrangement/Wittig olefination and a subsequent olefin cross metathesis with 2-methyl-2-butene. The cross metathesis step proceeds with a high selectivity and yields exclusively the desired prenyl, rather than the alternative crotyl substituent. Several naturally occurring 8-prenylcoumarins that were previously inaccessible have been synthesized in good overall yields along this route.

  15. Highly conserved non-coding sequences are associated with vertebrate development.

    Directory of Open Access Journals (Sweden)

    Adam Woolfe

    2005-01-01

    Full Text Available In addition to protein coding sequence, the human genome contains a significant amount of regulatory DNA, the identification of which is proving somewhat recalcitrant to both in silico and functional methods. An approach that has been used with some success is comparative sequence analysis, whereby equivalent genomic regions from different organisms are compared in order to identify both similarities and differences. In general, similarities in sequence between highly divergent organisms imply functional constraint. We have used a whole-genome comparison between humans and the pufferfish, Fugu rubripes, to identify nearly 1,400 highly conserved non-coding sequences. Given the evolutionary divergence between these species, it is likely that these sequences are found in, and furthermore are essential to, all vertebrates. Most, and possibly all, of these sequences are located in and around genes that act as developmental regulators. Some of these sequences are over 90% identical across more than 500 bases, being more highly conserved than coding sequence between these two species. Despite this, we cannot find any similar sequences in invertebrate genomes. In order to begin to functionally test this set of sequences, we have used a rapid in vivo assay system using zebrafish embryos that allows tissue-specific enhancer activity to be identified. Functional data is presented for highly conserved non-coding sequences associated with four unrelated developmental regulators (SOX21, PAX6, HLXB9, and SHH, in order to demonstrate the suitability of this screen to a wide range of genes and expression patterns. Of 25 sequence elements tested around these four genes, 23 show significant enhancer activity in one or more tissues. We have identified a set of non-coding sequences that are highly conserved throughout vertebrates. They are found in clusters across the human genome, principally around genes that are implicated in the regulation of development

  16. A Multi-Proxy Analysis of two Loess-Paleosol Sequences in the Northern Harz Foreland

    Science.gov (United States)

    Krauss, Lydia; Zens, Joerg; Zeeden, Christian; Schulte, Philipp; Eckmeier, Eileen; Lehmkuhl, Frank

    2016-04-01

    Within the second phase of the "Collaborative Research Centre 806 (CRC806) - Our Way to Europe - Culture-Environment Interaction and Human Mobility in the Late Quaternary" two loess-paleosol sections in the northern Harz foreland are being investigated. The region is part of the Northern European loess belt. The northern edge of the loess distribution is characterized by an interlocking of Weichselian silt and sand sized aeolian sediments. To the south the Northern European loess belt is limited by the central German uplands (Mittelgebirge). Here the continuous loess cover disperses into separated loess basins. In comparison to relatively long, continuous and intensively studied sections, e.g. along the Rhine river, investigations on loess-paleosol sequences in the northern Harz foreland have been sparse so far. In 2006 REINECKE created an overview of Pleistocene landscape developments by investigating terrace sequences and loess sections in this area. Due to improvements of research methods over the last ten years, the two loess-paleosol sequences Hecklingen and Zilly are being reinvestigated. Aiming towards a better understanding of the paleoenvironmental conditions during the Weichselian in an area close to the Scandinavian ice sheet, results from grain size, geochemical (XRF, CNS) and color measurements are combined. The results show an increased input of aeolian material during the last glacial maximum and the last cover loess period, supporting the theory of dryer and colder conditions during this time frame. Further, we can see a stronger short distant input within the recent soil and during the last glacial maximum in both profiles. In Hecklingen this is also observed within the MIS 3 soil material. Since soil material dating to the MIS 3 is present, we can assume that surface processes where less intrusive during the MIS 3 and 2 as in e.g. the Lower Rhine Embayment. REINECKE, V. (2006): Untersuchungen zur mittel- und jungpleistozänen Reliefentwicklung und

  17. Log-balanced combinatorial sequences

    Directory of Open Access Journals (Sweden)

    Tomislav Došlic

    2005-01-01

    Full Text Available We consider log-convex sequences that satisfy an additional constraint imposed on their rate of growth. We call such sequences log-balanced. It is shown that all such sequences satisfy a pair of double inequalities. Sufficient conditions for log-balancedness are given for the case when the sequence satisfies a two- (or more- term linear recurrence. It is shown that many combinatorially interesting sequences belong to this class, and, as a consequence, that the above-mentioned double inequalities are valid for all of them.

  18. A comparative analysis of double inversion recovery TFE and TSE sequences on carotid artery wall imaging

    International Nuclear Information System (INIS)

    Chen Jun; Di Yujin; Bu Chunqing; Zhang Yanfeng; Li Shuhua

    2012-01-01

    Objective: To analyze the characteristics of double inversion recovery (DIR) turbo field echo (TFE) and turbo spin echo (TSE) sequences and explore the value of double inversion recovery TFE sequence on carotid artery wall imaging. Patients and methods: 56 patients (32 males and 24 females, aged 31–76 years with a mean age of 53 years) were performed with DIR TFE and DIR TSE T1 weighted imaging (T1WI) sequences on carotid artery bifurcations. Image quality acquired by different techniques were evaluated and scored by two physicians. Whether there is significant difference is determined by SPSS 11.0 software. Paired-samples t test was used for statistics. Results: There was no significant difference in the image quality scores between two sequences (t = 0.880, P = 0.383 > 0.05). Conclusions: DIR TFE sequence has short scanning time and high spatial resolution. DIR TFE sequence can be used as the preferred sequence for screening carotid atherosclerotic plaque compared with DIR TSE sequence.

  19. Finite element simulations of two rock mechanics tests

    International Nuclear Information System (INIS)

    Dahlke, H.J.; Lott, S.A.

    1986-04-01

    Rock mechanics tests are performed to determine in situ stress conditions and material properties of an underground rock mass. To design stable underground facilities for the permanent storage of high-level nuclear waste, determination of these properties and conditions is a necessary first step. However, before a test and its associated equipment can be designed, the engineer needs to know the range of expected values to be measured by the instruments. Sensitivity studies by means of finite element simulations are employed in this preliminary design phase to evaluate the pertinent parameters and their effects on the proposed measurements. The simulations, of two typical rock mechanics tests, the plate bearing test and the flat-jack test, by means of the finite element analysis, are described. The plate bearing test is used to determine the rock mass deformation modulus. The flat-jack test is used to determine the in situ stress conditions of the host rock. For the plate bearing test, two finite element models are used to simulate the classic problem of a load on an elastic half space and the actual problem of a plate bearing test in an underground tunnel of circular cross section. For the flat-jack simulation, a single finite element model is used to simulate both horizontal and vertical slots. Results will be compared to closed-form solutions available in the literature

  20. Whole-Genome Sequences of Two Carbapenem-Resistant Klebsiella quasipneumoniae Strains Isolated from a Tertiary Hospital in Johor, Malaysia.

    Science.gov (United States)

    Gan, Han Ming; Rajasekaram, Ganeswrie; Eng, Wilhelm Wei Han; Kaniappan, Priyatharisni; Dhanoa, Amreeta

    2017-08-10

    We report the whole-genome sequences of two carbapenem-resistant clinical isolates of Klebsiella quasipneumoniae subsp. similipneumoniae obtained from two different patients. Both strains contained three different extended-spectrum β-lactamase genes and showed strikingly high pairwise average nucleotide identity of 99.99% despite being isolated 3 years apart from the same hospital. Copyright © 2017 Gan et al.

  1. Construction of the two-phase critical flow test facility

    International Nuclear Information System (INIS)

    Chung, C. H.; Chang, S. K.; Park, H. S.; Min, K. H.; Choi, N. H.; Kim, C. H.; Lee, S. H.; Kim, H. C.; Chang, M. H.

    2002-03-01

    The two-phase critical test loop facility has been constructed in the KAERI engineering laboratory for the simulation of small break loss of coolant accident entrained with non-condensible gas of SMART. The test facility can operate at 12 MPa of pressure and 0 to 60 C of sub-cooling with 0.5 kg/s of non- condensible gas injection into break flow, and simulate up to 20 mm of pipe break. Main components of the test facility were arranged such that the pressure vessel containing coolant, a test section simulating break and a suppression tank inter-connected with pipings were installed vertically. As quick opening valve opens, high pressure/temperature coolant flows through the test section forming critical two-phase flow into the suppression tank. The pressure vessel was connected to two high pressure N2 gas tanks through a control valve to control pressure in the pressure vessel. Another N2 gas tank was also connected to the test section for the non-condensible gas injection. The test facility operation was performed on computers supported with PLC systems installed in the control room, and test data such as temperature, break flow rate, pressure drop across test section, gas injection flow rate were all together gathered in the data acquisition system for further data analysis. This test facility was classified as a safety related high pressure gas facility in law. Thus the loop design documentation was reviewed, and inspected during construction of the test loop by the regulatory body. And the regulatory body issued permission for the operation of the test facility

  2. Scientific activity and working hours of physicians in university hospitals: results from the Innsbruck and Salzburg physician lifestyle assessment (TISPLA).

    Science.gov (United States)

    Steger, Bernhard; Colvin, Hans Peter; Rieder, Josef

    2009-01-01

    Controllable lifestyle has become an important factor influencing career decision-making among physicians. In academic medicine, doctors are required to combine both patient care and research in their daily routine. Insufficient release of clinicians for research during contracted work hours may lead to increased weekly working hours in academic medical centers and deter medical graduates from academia. We tested for an association between numbers of scientific publications and an increased hourly workload among physicians. This was a cross-sectional online survey among all salaried physicians working in the university hospitals of Innsbruck and Salzburg, Austria. The main outcome measures were the self-reported total number of scientific papers published in peer-reviewed medical journals over the past two years and self-reported working hours. Of 590 returned surveys, 393 were fully completed and included in the study. The sample was stratified into three groups according to scientific output in the past two years: Group A, >/= 6 publications; Group B, 1-5 publications; Group C, no publications. Men were more likely than women to have a scientific publication: in Group A there was a male predominance of 75%, whereas in Group C only 48% were men (P = 0.0034). A total of 59% (n = 232) of all participants had not published a scientific article in the past two years (Group C) and worked a mean of 58.3 +/- 12 h/week. Physicians in Group B (n = 113) had published 2.4 +/- 1.4 papers and worked 62.8 +/- 12.9 h/week; those in Group A (n = 48) had published 11.5 +/- 6.6 papers and worked 73 +/- 13.1 h/week (P work time but for 60% of overtime hours, reflecting the fact that research was mainly performed during overtime. Research activity among clinicians in academic medical centers is associated with significantly increased overtime hours. Measures need to be taken to allow medical graduates an academic career at reasonable impairment of personal lifestyle.

  3. Processing and Prolonged 500 C Testing of 4H-SiC JFET Integrated Circuits with Two Levels of Metal Interconnect

    Science.gov (United States)

    Spry, David J.; Neudeck, Philip G.; Chen, Liangyu; Lukco, Dorothy; Chang, Carl W.; Beheim, Glenn M.; Krasowski, Michael J.; Prokop, Norman F.

    2015-01-01

    Complex integrated circuit (IC) chips rely on more than one level of interconnect metallization for routing of electrical power and signals. This work reports the processing and testing of 4H-SiC junction field effect transistor (JFET) prototype IC's with two levels of metal interconnect capable of prolonged operation at 500 C. Packaged functional circuits including 3- and 11-stage ring oscillators, a 4-bit digital to analog converter, and a 4-bit address decoder and random access memory cell have been demonstrated at 500 C. A 3-stage oscillator functioned for over 3000 hours at 500 C in air ambient. Improved reproducibility remains to be accomplished.

  4. 48 CFR 552.236-74 - Working Hours.

    Science.gov (United States)

    2010-10-01

    ... 48 Federal Acquisition Regulations System 4 2010-10-01 2010-10-01 false Working Hours. 552.236-74... Hours. As prescribed in 536.570-5, insert the following clause: Working Hours (APR 1984) (a) It is contemplated that all work will be performed during the customary working hours of the trades involved unless...

  5. Comparative analysis of sequences from PT 2013

    DEFF Research Database (Denmark)

    Mikkelsen, Susie Sommer

    Sheatfish and not EHNV. Generally, mistakes occurred at the ends of the sequences. This can be due to several factors. One is that the sequence has not been trimmed of the sequence primer sites. Another is the lack of quality control of the chromatogram. Finally, sequencing in just one direction can result...... diseases in Europe. As part of the EURL proficiency test for fish diseases it is required to sequence any RANA virus isolates found in any of the samples. It is also highly recommended to sequence the ISA virus to determine whether it be HPRΔ or HPR0. Furthermore, it is recommended that any VHSV and IHNV...... isolates be genotyped. As part of the evaluation of the proficiency results it was decided this year to look into the quality and similarity of the sequence results for selected viruses. Ampoule III in the proficiency test 2013 contained an EHNV isolate. The EURL received 43 sequences from 41 laboratories...

  6. Psychosocial factors at work, long work hours, and obesity: a systematic review.

    Science.gov (United States)

    Solovieva, Svetlana; Lallukka, Tea; Virtanen, Marianna; Viikari-Juntura, Eira

    2013-05-01

    Associations between psychosocial work environment and excess weight have not been systematically addressed. The aim of this systematic review was to summarize the published evidence for the associations of psychosocial factors at work and long work hours with weight-related outcomes . Methods We conducted a search of Medline and Embase for all original articles published up to September 2012 using predefined keywords. After excluding studies with a definite selection bias, we included 39 articles. About 60% of the studies reported at least one positive association between psychosocial factors at work and a weight-related outcome. However, 76% of the tested associations were found to be non-significant. Furthermore, the associations were rather weak. Studies of higher quality tended to observe associations more often than those of lower quality. Positive associations were found more frequently (i) among women versus men, (ii) in cross-sectional versus longitudinal studies, and (iii) for overweight or obesity versus other outcomes. About 70% of the studies reported positive associations between long work hours and weight-related outcomes. All four studies that evaluated the association between working overtime and weight gain (three longitudinal and one cross-sectional), showed a positive association among men and two of them also observed associations among women. We found evidence for weak associations between psychosocial factors at work and excess weight. Associations were observed between long work hours, working overtime, and weight gain, especially among men. More cohort studies among non-obese baseline participants using appropriate analytical methods based on an elaborated hypothetical model are needed.

  7. In-111 platelet scintigraphy for detection of lower-extremity deep venous thrombophlebitis: Are 4-hour delayed images sufficient

    International Nuclear Information System (INIS)

    Seabold, J.E.; Conrad, G.R.; Ponto, J.A.; Kimball, D.A.; Frey, E.E.; Coughlan, J.D.; Ahmed, F.; Jensen, K.C.

    1986-01-01

    Twenty-one nonheparinized patients suspected of having lower-extremity deep venous thrombosis underwent 4- and 24-hour In-111-labeled platelet scintigraphy (PS) and lower-extremity contrast venography (CV). Eleven of the 21 patients (52%) had one or more intraluminal filling defects on CV, indicating active thrombophlebitis. In seven of these 11 patients (64%) In-PS was abnormal at 4 hours, and in ten (91%) at 24 hours. All patients with abnormal studies at 4 hours showed greater uptake of more abnormal sites at 24 hours. Of the ten patients with CV-negative studies, two had abnormal bilateral lower pelvis/upper thigh uptake in In-PS at 24 hours. These two In-PS studies were considered to be false positive. Twenty-four-hour In-PS images are necessary if 4-hour images show faint focal uptake of asymmetric blood pool activity, or are normal

  8. Exposure to bright light for several hours during the daytime lowers tympanic temperature

    Science.gov (United States)

    Aizawa, Seika; Tokura, H.

    The present study investigates the effect on thympanic temperature of exposure to different light intensities for several hours during the daytime. Nine healthy young adult volunteers (two male, seven female) were exposed to bright light of 4000 lx or dim light of 100 lx during the daytime from 0930 to 1800 hours; the light condition was then kept at 100 lx for a further hour. Tympanic temperature was measured continuously at a neutral condition (28° C, 60% relative humidity) from 1000 to 1800 hours. Urinary samples were collected from 1100 to 1900 hours every 2 h, and melatonin excretion rate was measured by enzyme immunoassay. Of nine subjects, six showed clearly lower tympanic temperatures in the bright compared with the dim condition from 1400 to 1800 hours. Average tympanic temperatures were significantly lower in the bright than in the dim condition from 1645 to 1800 hours. Melatonin excretion rate tended to be higher in the bright than in the dim condition. It was concluded that exposure to bright light of 4000 lx during the daytime for several hours could reduce tympanic temperature, compared with that measured in dim light of 100 lx.

  9. Exposure to bright light for several hours during the daytime lowers tympanic temperature.

    Science.gov (United States)

    Aizawa, S; Tokura, H

    1997-11-01

    The present study investigates the effect on thympanic temperature of exposure to different light intensities for several hours during the daytime. Nine healthy young adult volunteers (two male, seven female) were exposed to bright light of 4000 lx or dim light of 100 lx during the daytime from 0930 to 1800 hours; the light condition was then kept at 100 lx for a further hour. Tympanic temperature was measured continuously at a neutral condition (28 degrees C, 60% relative humidity) from 1000 to 1800 hours. Urinary samples were collected from 1100 to 1900 hours every 2 h, and melatonin excretion rate was measured by enzyme immunoassay. Of nine subjects, six showed clearly lower tympanic temperatures in the bright compared with the dim condition from 1400 to 1800 hours. Average tympanic temperatures were significantly lower in the bright than in the dim condition from 1645 to 1800 hours. Melatonin excretion rate tended to be higher in the bright than in the dim condition. It was concluded that exposure to bright light of 4000 lx during the daytime for several hours could reduce tympanic temperature, compared with that measured in dim light of 100 lx.

  10. Magnetic resonance cholangiography: comparison of two- and three-dimensional sequences for assessment of malignant biliary obstruction

    International Nuclear Information System (INIS)

    Choi, Jin-Young; Kim, Myeong-Jin; Lee, Jeong Min; Lee, Jae Young; Kim, Se Hyung; Han, Joon Koo; Choi, Byung Ihn; Kim, Ki Whang

    2008-01-01

    The purpose was to retrospectively compare two-dimensional (2D) magnetic resonance cholangiography (MRC) including breath-hold single-shot rapid acquisition with relaxation enhancement (RARE) and multislice half-Fourier RARE versus navigator-triggered 3D-RARE MRC in the evaluation of biliary malignancy. MRC findings were evaluated in 31 patients with malignant biliary obstruction, including biliary malignancy, gallbladder carcinoma, and ampullary cancer. Two observers independently reviewed the images to assess the overall image quality, artifacts, ductal conspicuity, extent of disease, diagnostic confidence of tumor extent, and origin of tumor. The results were compared with surgical and histopathologic findings. Studies obtained with 3D-MRC were of significantly higher technical quality than those obtained with 2D-MRC. However, the accuracy between two sequences for classification of tumor showed no statistical significance. There was no significant difference between the Az values of 2D- and 3D-MRC for overall tumor extent in bilateral second order branch, intrapancreatic common bile duct (CBD) involvement (Az = 0.889, 0.881 for 2D and Az = 0.903, 0.864 for 3D). Nor was there a significant difference between two sequences in the assessment of the origin of tumor. Although 3D-MRC has superior image quality over 2D-MRC, 3D-MRC showed no statistically significant difference in accuracy compared with 2D-MRC for evaluating the extent of disease in malignant biliary obstructions. (orig.)

  11. Characterization of microflora in Latin-style cheeses by next-generation sequencing technology

    Directory of Open Access Journals (Sweden)

    Lusk Tina S

    2012-11-01

    Full Text Available Abstract Background Cheese contamination can occur at numerous stages in the manufacturing process including the use of improperly pasteurized or raw milk. Of concern is the potential contamination by Listeria monocytogenes and other pathogenic bacteria that find the high moisture levels and moderate pH of popular Latin-style cheeses like queso fresco a hospitable environment. In the investigation of a foodborne outbreak, samples typically undergo enrichment in broth for 24 hours followed by selective agar plating to isolate bacterial colonies for confirmatory testing. The broth enrichment step may also enable background microflora to proliferate, which can confound subsequent analysis if not inhibited by effective broth or agar additives. We used 16S rRNA gene sequencing to provide a preliminary survey of bacterial species associated with three brands of Latin-style cheeses after 24-hour broth enrichment. Results Brand A showed a greater diversity than the other two cheese brands (Brands B and C at nearly every taxonomic level except phylum. Brand B showed the least diversity and was dominated by a single bacterial taxon, Exiguobacterium, not previously reported in cheese. This genus was also found in Brand C, although Lactococcus was prominent, an expected finding since this bacteria belongs to the group of lactic acid bacteria (LAB commonly found in fermented foods. Conclusions The contrasting diversity observed in Latin-style cheese was surprising, demonstrating that despite similarity of cheese type, raw materials and cheese making conditions appear to play a critical role in the microflora composition of the final product. The high bacterial diversity associated with Brand A suggests it may have been prepared with raw materials of high bacterial diversity or influenced by the ecology of the processing environment. Additionally, the presence of Exiguobacterium in high proportions (96% in Brand B and, to a lesser extent, Brand C (46%, may

  12. Sequence and RT-PCR expression analysis of two peroxidases from Arabidopsis thaliana belonging to a novel evolutionary branch of plant peroxidases.

    Science.gov (United States)

    Kjaersgård, I V; Jespersen, H M; Rasmussen, S K; Welinder, K G

    1997-03-01

    cDNA clones encoding two new Arabidopsis thaliana peroxidases, ATP 1a and ATP 2a, have been identified by searching the Arabidopsis database of expressed sequence tags (dbEST). They represent a novel branch of hitherto uncharacterized plant peroxidases which is only 35% identical in amino acid sequence to the well characterized group of basic plant peroxidases represented by the horseradish (Armoracia rusticana) isoperoxidases HRP C, HRP E5 and the similar Arabidopsis isoperoxidases ATP Ca, ATP Cb, and ATP Ea. However ATP 1a is 87% identical in amino acid sequence to a peroxidase encoded by an mRNA isolated from cotton (Gossypium hirsutum). As cotton and Arabidopsis belong to rather diverse families (Malvaceae and Crucifereae, respectively), in contrast with Arabidopsis and horseradish (both Crucifereae), the high degree of sequence identity indicates that this novel type of peroxidase, albeit of unknown function, is likely to be widespread in plant species. The atp 1 and atp 2 types of cDNA sequences were the most redundant among the 28 different isoperoxidases identified among about 200 peroxidase encoding ESTs. Interestingly, 8 out of totally 38 EST sequences coding for ATP 1 showed three identical nucleotide substitutions. This variant form is designated ATP 1b. Similarly, six out of totally 16 EST sequences coding for ATP 2 showed a number of deletions and nucleotide changes. This variant form is designated ATP 2b. The selected EST clones are full-length and contain coding regions of 993 nucleotides for atp 1a, and 984 nucleotides for atp 2a. These regions show 61% DNA sequence identity. The predicted mature proteins ATP 1a, and ATP 2a are 57% identical in sequence and contain the structurally and functionally important residues, characteristic of the plant peroxidase superfamily. However, they do show two differences of importance to peroxidase catalysis: (1) the asparagine residue linked with the active site distal histidine via hydrogen bonding is absent

  13. A tale of two sequences: microRNA-target chimeric reads.

    Science.gov (United States)

    Broughton, James P; Pasquinelli, Amy E

    2016-04-04

    In animals, a functional interaction between a microRNA (miRNA) and its target RNA requires only partial base pairing. The limited number of base pair interactions required for miRNA targeting provides miRNAs with broad regulatory potential and also makes target prediction challenging. Computational approaches to target prediction have focused on identifying miRNA target sites based on known sequence features that are important for canonical targeting and may miss non-canonical targets. Current state-of-the-art experimental approaches, such as CLIP-seq (cross-linking immunoprecipitation with sequencing), PAR-CLIP (photoactivatable-ribonucleoside-enhanced CLIP), and iCLIP (individual-nucleotide resolution CLIP), require inference of which miRNA is bound at each site. Recently, the development of methods to ligate miRNAs to their target RNAs during the preparation of sequencing libraries has provided a new tool for the identification of miRNA target sites. The chimeric, or hybrid, miRNA-target reads that are produced by these methods unambiguously identify the miRNA bound at a specific target site. The information provided by these chimeric reads has revealed extensive non-canonical interactions between miRNAs and their target mRNAs, and identified many novel interactions between miRNAs and noncoding RNAs.

  14. Genotyping using whole-genome sequencing is a realistic alternative to surveillance based on phenotypic antimicrobial susceptibility testing

    DEFF Research Database (Denmark)

    Zankari, Ea; Hasman, Henrik; Kaas, Rolf Sommer

    2013-01-01

    -genome sequencing (WGS) may soon be within reach even for routine surveillance and clinical diagnostics. The aim of this study was to evaluate WGS as a routine tool for surveillance of antimicrobial resistance compared with current phenotypic procedures. Methods: Antimicrobial susceptibility tests were performed...... to the categorizing of isolates as resistant and 2569 as susceptible. Seven cases of disagreement between tested and predicted susceptibility were observed, six of which were related to spectinomycin resistance in Escherichia coli. Correlation between MLST type and resistance profiles was only observed in Salmonella...

  15. Procedural Memory Consolidation in the Performance of Brief Keyboard Sequences

    Science.gov (United States)

    Duke, Robert A.; Davis, Carla M.

    2006-01-01

    Using two sequential key press sequences, we tested the extent to which subjects' performance on a digital piano keyboard changed between the end of training and retest on subsequent days. We found consistent, significant improvements attributable to sleep-based consolidation effects, indicating that learning continued after the cessation of…

  16. Extended working hours: Impacts on workers

    Science.gov (United States)

    D. Mitchell; T. Gallagher

    2010-01-01

    Some logging business owners are trying to manage their equipment assets by increasing the scheduled machine hours. The intent is to maximize the total tons produced by a set of equipment. This practice is referred to as multi-shifting, double-shifting, or extended working hours. One area often overlooked is the impact that working non-traditional hours can have on...

  17. Using the Δ3 statistic to test for missed levels in mixed sequence neutron resonance data

    International Nuclear Information System (INIS)

    Mulhall, Declan

    2009-01-01

    The Δ 3 (L) statistic is studied as a tool to detect missing levels in the neutron resonance data where two sequences are present. These systems are problematic because there is no level repulsion, and the resonances can be too close to resolve. Δ 3 (L) is a measure of the fluctuations in the number of levels in an interval of length L on the energy axis. The method used is tested on ensembles of mixed Gaussian orthogonal ensemble spectra, with a known fraction of levels (x%) randomly depleted, and can accurately return x. The accuracy of the method as a function of spectrum size is established. The method is used on neutron resonance data for 11 isotopes with either s-wave neutrons on odd-A isotopes, or p-wave neutrons on even-A isotopes. The method compares favorably with a maximum likelihood method applied to the level spacing distribution. Nuclear data ensembles were made from 20 isotopes in total, and their Δ 3 (L) statistics are discussed in the context of random matrix theory.

  18. Allelic Tests and Sequence Analysis of Three Genes for Resistance to Xanthomonas perforans Race T3 in Tomato

    Institute of Scientific and Technical Information of China (English)

    ZHAO Baimei; CAO Haipeng; DUAN Junjie; YANG Wencai

    2015-01-01

    Three crosses,Hawaii7981×PI128216,Hawaii7981×LA1589,and PI128216×LA1589,were made to develop F2 populations for testing allelism among three genes Xv3,Rx4,and RxLA1589 conferring resistance to bacterial spot caused by Xanthomonas perforans race T3 in tomato. Each population consisted of 535–1 655 individuals. An infiltration method was used to inoculate the leaves of the parental and F2 plants as well as the susceptible control OH88119 for detecting hypersensitive resistance(HR). The results showed that all the tomato plants except OH88119 had HR to race T3,indicating that Xv3,Rx4,and RxLA1589 were allelic genes. Genomic DNA fragments of the Rx4 alleles from Hawaii7981,PI128216,and LA1589 were amplified using gene-specific primers and sequenced. No sequence variation was observed in the coding region of Rx4 in the three resistant lines. Based on the published map positions of these loci as well as the allelic tests and sequence data obtained in this study,we speculated that Xv3,Rx4,and RxLA1589 were the same gene. The results will provide useful information for understanding the mechanism of resistance to race T3 and developing resistant tomato varieties.

  19. Whole Genome Sequencing Increases Molecular Diagnostic Yield Compared with Current Diagnostic Testing for Inherited Retinal Disease.

    Science.gov (United States)

    Ellingford, Jamie M; Barton, Stephanie; Bhaskar, Sanjeev; Williams, Simon G; Sergouniotis, Panagiotis I; O'Sullivan, James; Lamb, Janine A; Perveen, Rahat; Hall, Georgina; Newman, William G; Bishop, Paul N; Roberts, Stephen A; Leach, Rick; Tearle, Rick; Bayliss, Stuart; Ramsden, Simon C; Nemeth, Andrea H; Black, Graeme C M

    2016-05-01

    To compare the efficacy of whole genome sequencing (WGS) with targeted next-generation sequencing (NGS) in the diagnosis of inherited retinal disease (IRD). Case series. A total of 562 patients diagnosed with IRD. We performed a direct comparative analysis of current molecular diagnostics with WGS. We retrospectively reviewed the findings from a diagnostic NGS DNA test for 562 patients with IRD. A subset of 46 of 562 patients (encompassing potential clinical outcomes of diagnostic analysis) also underwent WGS, and we compared mutation detection rates and molecular diagnostic yields. In addition, we compared the sensitivity and specificity of the 2 techniques to identify known single nucleotide variants (SNVs) using 6 control samples with publically available genotype data. Diagnostic yield of genomic testing. Across known disease-causing genes, targeted NGS and WGS achieved similar levels of sensitivity and specificity for SNV detection. However, WGS also identified 14 clinically relevant genetic variants through WGS that had not been identified by NGS diagnostic testing for the 46 individuals with IRD. These variants included large deletions and variants in noncoding regions of the genome. Identification of these variants confirmed a molecular diagnosis of IRD for 11 of the 33 individuals referred for WGS who had not obtained a molecular diagnosis through targeted NGS testing. Weighted estimates, accounting for population structure, suggest that WGS methods could result in an overall 29% (95% confidence interval, 15-45) uplift in diagnostic yield. We show that WGS methods can detect disease-causing genetic variants missed by current NGS diagnostic methodologies for IRD and thereby demonstrate the clinical utility and additional value of WGS. Copyright © 2016 American Academy of Ophthalmology. Published by Elsevier Inc. All rights reserved.

  20. Device-independent parallel self-testing of two singlets

    Science.gov (United States)

    Wu, Xingyao; Bancal, Jean-Daniel; McKague, Matthew; Scarani, Valerio

    2016-06-01

    Device-independent self-testing offers the possibility of certifying the quantum state and measurements, up to local isometries, using only the statistics observed by querying uncharacterized local devices. In this paper we study parallel self-testing of two maximally entangled pairs of qubits; in particular, the local tensor product structure is not assumed but derived. We prove two criteria that achieve the desired result: a double use of the Clauser-Horne-Shimony-Holt inequality and the 3 ×3 magic square game. This demonstrate that the magic square game can only be perfectly won by measuring a two-singlet state. The tolerance to noise is well within reach of state-of-the-art experiments.

  1. Overlapping genomic sequences: a treasure trove of single-nucleotide polymorphisms.

    Science.gov (United States)

    Taillon-Miller, P; Gu, Z; Li, Q; Hillier, L; Kwok, P Y

    1998-07-01

    An efficient strategy to develop a dense set of single-nucleotide polymorphism (SNP) markers is to take advantage of the human genome sequencing effort currently under way. Our approach is based on the fact that bacterial artificial chromosomes (BACs) and P1-based artificial chromosomes (PACs) used in long-range sequencing projects come from diploid libraries. If the overlapping clones sequenced are from different lineages, one is comparing the sequences from 2 homologous chromosomes in the overlapping region. We have analyzed in detail every SNP identified while sequencing three sets of overlapping clones found on chromosome 5p15.2, 7q21-7q22, and 13q12-13q13. In the 200.6 kb of DNA sequence analyzed in these overlaps, 153 SNPs were identified. Computer analysis for repetitive elements and suitability for STS development yielded 44 STSs containing 68 SNPs for further study. All 68 SNPs were confirmed to be present in at least one of the three (Caucasian, African-American, Hispanic) populations studied. Furthermore, 42 of the SNPs tested (62%) were informative in at least one population, 32 (47%) were informative in two or more populations, and 23 (34%) were informative in all three populations. These results clearly indicate that developing SNP markers from overlapping genomic sequence is highly efficient and cost effective, requiring only the two simple steps of developing STSs around the known SNPs and characterizing them in the appropriate populations.

  2. Sleep and memory consolidation: motor performance and proactive interference effects in sequence learning.

    Science.gov (United States)

    Borragán, Guillermo; Urbain, Charline; Schmitz, Rémy; Mary, Alison; Peigneux, Philippe

    2015-04-01

    That post-training sleep supports the consolidation of sequential motor skills remains debated. Performance improvement and sensitivity to proactive interference are both putative measures of long-term memory consolidation. We tested sleep-dependent memory consolidation for visuo-motor sequence learning using a proactive interference paradigm. Thirty-three young adults were trained on sequence A on Day 1, then had Regular Sleep (RS) or were Sleep Deprived (SD) on the night after learning. After two recovery nights, they were tested on the same sequence A, then had to learn a novel, potentially competing sequence B. We hypothesized that proactive interference effects on sequence B due to the prior learning of sequence A would be higher in the RS condition, considering that proactive interference is an indirect marker of the robustness of sequence A, which should be better consolidated over post-training sleep. Results highlighted sleep-dependent improvement for sequence A, with faster RTs overnight for RS participants only. Moreover, the beneficial impact of sleep was specific to the consolidation of motor but not sequential skills. Proactive interference effects on learning a new material at Day 4 were similar between RS and SD participants. These results suggest that post-training sleep contributes to optimizing motor but not sequential components of performance in visuo-motor sequence learning. Copyright © 2015 Elsevier Inc. All rights reserved.

  3. Changing the formula of residents' work hours in internal medicine: moving from "years in training" to "hours in training".

    Science.gov (United States)

    Mansi, Ishak A

    2011-03-01

    In a recent report, the Institute of Medicine recommended more restrictions on residents' working hours. Several problems exist with a system that places a weekly limit on resident duty hours: (1) it assumes the presence of a linear relationship between hours of work and patient safety; (2) it fails to consider differences in intensity among programs; and (3) it does not address increases in the scientific content of medicine, and it places the burden of enforcing the duty hour limits on the Accreditation Council for Graduate Medical Education. An innovative method of calculating credit hours for graduate medical education would shift the focus from "years of residency" to "hours of residency." For example, internal medicine residents would be requested to spend 8640 hours of total training hours (assuming 60 hours per week for 48 weeks annually) instead of the traditional 3 years. This method of counting training hours is used by other professions, such as the Intern Development Program of the National Council of Architectural Registration Boards. The proposed approach would allow residents and program directors to pace training based on individual capabilities. Standards for resident education should include the average number of patients treated in each setting (inpatient or outpatient). A possible set of "multipliers" based on these parameters, and possibly others such as resident evaluation, is devised to calculate the "final adjusted accredited hours" that count toward graduation. Substituting "years of training" with "hours of training" may resolve many of the concerns with the current residency education model, as well as adapt to the demands of residents' personal lives. It also may allow residents to pace their training according to their capabilities and learning styles, and contribute to reflective learning and better quality education.

  4. Some reasoning on the improvement of the ETAS modeling at the occurrence of the 2016 central Italy seismic sequence

    Directory of Open Access Journals (Sweden)

    Anna Maria Lombardi

    2016-12-01

    Full Text Available This study presents an application of the ETAS model to the first 20 days of the 2016 central Italy sequence. Despite of the provisional nature of data, the model is able to describe the occurrence rate, but for the first hours after the mainshock occurrence. A sensitivity analysis of the model to two uncertainty sources, the model parameters and the occurrence history, shows that the second has a main role in controlling the performance of the ETAS model, more than the uncertainty on parameters. Previous results, together with the clear inability of ETAS to forecast the occurrence of a sequence before its starting time, give important suggestions about possible improvements. Here, a very preliminary attempt in this sense is presented.

  5. Draft Genome Sequences of Two Propionibacterium acnes Strains Isolated from Progressive Macular Hypomelanosis Lesions of Human Skin

    DEFF Research Database (Denmark)

    Petersen, Rolf; Lomholt, Hans B.; Scholz, Christian F. P.

    2015-01-01

    Propionibacterium acnes is a Gram-positive bacterium that is prevalent on human skin. It has been associated with skin disorders such as acne vulgaris and progressive macular hypomelanosis (PMH). Here, we report draft genome sequences of two type III P. acnes strains, PMH5 and PMH7, isolated from...

  6. Only Two Hours? A Qualitative Study of the Challenges Parents Perceive in Restricting Child Television Time

    Science.gov (United States)

    Evans, Cortney A.; Jordan, Amy B.; Horner, Jennifer

    2011-01-01

    This study examines parents' and children's reaction to the American Academy of Pediatrics recommendation to limit children's television (TV) viewing to 2 hours a day or less. To better understand the challenges faced by parents who would seek to adhere to the guidelines, we conducted qualitative small group interviews with 60 parent/child dyads…

  7. Can hospital-based doctors change their working hours? Evidence from Australia.

    Science.gov (United States)

    Norman, R; Hall, J

    2014-07-01

    To explore factors predicting hospital-based doctors' desire to work less, and then their success in making that change. Consecutive waves of an Australian longitudinal survey of doctors (Medicine in Australia-Balancing Employment and Life). There were 6285 and 6337 hospital-based completers in the two waves, consisting of specialists, hospital-based non-specialists and specialist registrars. Forty-eight per cent stated a preference to reduce hours. Predictive characteristics were being female and working more than 40 h/week (both P less likely to state the preference. Factors associated with not wanting to reduce working hours were being in excellent health and being satisfied with work (both P working hours, only 32% successfully managed to do so in the subsequent year (defined by a reduction of at least 5 h/week). Predictors of successfully reducing hours were being older, female and working more than 40 h/week (all P hours and then their subsequent success in doing so. Designing policies that seek to reduce attrition may alleviate some of the ongoing pressures in the Australian hospital system. © 2014 The Authors; Internal Medicine Journal © 2014 Royal Australasian College of Physicians.

  8. Analysis of expressed sequence tags from Prunus mume flower and fruit and development of simple sequence repeat markers

    Directory of Open Access Journals (Sweden)

    Gao Zhihong

    2010-07-01

    Full Text Available Abstract Background Expressed Sequence Tag (EST has been a cost-effective tool in molecular biology and represents an abundant valuable resource for genome annotation, gene expression, and comparative genomics in plants. Results In this study, we constructed a cDNA library of Prunus mume flower and fruit, sequenced 10,123 clones of the library, and obtained 8,656 expressed sequence tag (EST sequences with high quality. The ESTs were assembled into 4,473 unigenes composed of 1,492 contigs and 2,981 singletons and that have been deposited in NCBI (accession IDs: GW868575 - GW873047, among which 1,294 unique ESTs were with known or putative functions. Furthermore, we found 1,233 putative simple sequence repeats (SSRs in the P. mume unigene dataset. We randomly tested 42 pairs of PCR primers flanking potential SSRs, and 14 pairs were identified as true-to-type SSR loci and could amplify polymorphic bands from 20 individual plants of P. mume. We further used the 14 EST-SSR primer pairs to test the transferability on peach and plum. The result showed that nearly 89% of the primer pairs produced target PCR bands in the two species. A high level of marker polymorphism was observed in the plum species (65% and low in the peach (46%, and the clustering analysis of the three species indicated that these SSR markers were useful in the evaluation of genetic relationships and diversity between and within the Prunus species. Conclusions We have constructed the first cDNA library of P. mume flower and fruit, and our data provide sets of molecular biology resources for P. mume and other Prunus species. These resources will be useful for further study such as genome annotation, new gene discovery, gene functional analysis, molecular breeding, evolution and comparative genomics between Prunus species.

  9. Dog Y chromosomal DNA sequence: identification, sequencing and SNP discovery

    Directory of Open Access Journals (Sweden)

    Kirkness Ewen

    2006-10-01

    Full Text Available Abstract Background Population genetic studies of dogs have so far mainly been based on analysis of mitochondrial DNA, describing only the history of female dogs. To get a picture of the male history, as well as a second independent marker, there is a need for studies of biallelic Y-chromosome polymorphisms. However, there are no biallelic polymorphisms reported, and only 3200 bp of non-repetitive dog Y-chromosome sequence deposited in GenBank, necessitating the identification of dog Y chromosome sequence and the search for polymorphisms therein. The genome has been only partially sequenced for one male dog, disallowing mapping of the sequence into specific chromosomes. However, by comparing the male genome sequence to the complete female dog genome sequence, candidate Y-chromosome sequence may be identified by exclusion. Results The male dog genome sequence was analysed by Blast search against the human genome to identify sequences with a best match to the human Y chromosome and to the female dog genome to identify those absent in the female genome. Candidate sequences were then tested for male specificity by PCR of five male and five female dogs. 32 sequences from the male genome, with a total length of 24 kbp, were identified as male specific, based on a match to the human Y chromosome, absence in the female dog genome and male specific PCR results. 14437 bp were then sequenced for 10 male dogs originating from Europe, Southwest Asia, Siberia, East Asia, Africa and America. Nine haplotypes were found, which were defined by 14 substitutions. The genetic distance between the haplotypes indicates that they originate from at least five wolf haplotypes. There was no obvious trend in the geographic distribution of the haplotypes. Conclusion We have identified 24159 bp of dog Y-chromosome sequence to be used for population genetic studies. We sequenced 14437 bp in a worldwide collection of dogs, identifying 14 SNPs for future SNP analyses, and

  10. Static multiplicities in heterogeneous azeotropic distillation sequences

    DEFF Research Database (Denmark)

    Esbjerg, Klavs; Andersen, Torben Ravn; Jørgensen, Sten Bay

    1998-01-01

    In this paper the results of a bifurcation analysis on heterogeneous azeotropic distillation sequences are given. Two sequences suitable for ethanol dehydration are compared: The 'direct' and the 'indirect' sequence. It is shown, that the two sequences, despite their similarities, exhibit very...... different static behavior. The method of Petlyuk and Avet'yan (1971), Bekiaris et al. (1993), which assumes infinite reflux and infinite number of stages, is extended to and applied on heterogeneous azeotropic distillation sequences. The predictions are substantiated through simulations. The static sequence...

  11. Volatility of fragrance chemicals: patch testing implications.

    Science.gov (United States)

    Gilpin, Sarah J; Hui, Xiaoying; Maibach, Howard I

    2009-01-01

    Diagnostic and predictive patch testing to determine contact allergy due to fragrance materials requires applying a fixed dose of material to the skin. This dose can be affected by the volatile nature of fragrances; little data exist on how the loss of fragrance dose due to volatility affects patch testing. (1) To evaluate pH dependence and evaporation rates of two fragrance chemicals, geraniol, citronellol, and a common fragrance solvent, diethyl phthalate (DEP) and (2) Assess implications for predictive patch-testing methods for fragrances. pH analysis of each material at 1% for three values (4.0, 5.0, 7.0) was done over 40 hours. Volatility experiments for each material, nonradiolabeled and radiolabeled, were conducted over a 24-hour period, taking readings at six time points (5 minutes, 15 minutes, 40 minutes, 1 hour, 3 hours, and 24 hours). Evaporation rates were not sensitive to pH shifts from 4.0 to 7.0. Evaporation rates for nonradiolabeled materials were low: after 24 hours, geraniol lost 8.9%, citronellol 27.0% and DEP 14.5%. The volatility data for radiolabeled materials demonstrated that geraniol loses up to 39% of its dose, citronellol loses up to 26%, and DEP up to 14% within 40 minutes. The tendency of fragrance materials to evaporate can impact the dose being applied to the patch and therefore the result of the patch and ultimately the decision-making process regarding that fragrance material's safety. These data, developed with DEP, utilized in a predictive sensitization assay cannot be generalized.

  12. Executive Functions are not Affected by 24 Hours of Sleep Deprivation: A Color-Word Stroop Task Study.

    Science.gov (United States)

    Dixit, Abhinav; Mittal, Tushar

    2015-01-01

    Sleep is an important factor affecting cognitive performance. Sleep deprivation results in fatigue, lack of concentration, confusion and sleepiness along with anxiety, depression and irritability. Sleep deprivation can have serious consequences in professions like armed forces and medicine where quick decisions and actions need to be taken. Color-Word Stroop task is one of the reliable tests to assess attention and it analyzes the processing of information in two dimensions i.e., reading of words and naming of colour. The evidence regarding the effect of sleep deprivation on Stroop interference is conflicting. The present study evaluated the effect of 24 hours of sleep deprivation on reaction time and interference in Stroop task. The present study was done on 30 healthy male medical student volunteers in the age group of 18-25 years after taking their consent and clearance from Institute Ethics Committee. Recordings of Stroop task were at three times: baseline (between 7-9 am), after 12 hours (7-9 pm) and after 24 hours (7-9 am, next day). The subjects were allowed to perform normal daily activities. The study revealed a significant increase in reaction time after 24 hours of sleep deprivation in comparison to baseline and after 12 hours of sleep deprivation. There was no significant change in interference and facilitation after sleep deprivation in comparison to baseline. The number of errors also did not show any significant change after sleep deprivation. The study indicated that there was slowing of responses without change in executive functions after 24 hours of sleep deprivation. It is probable that 24 hours of sleep deprivation does not bring about change in areas of brain affecting executive functions in healthy individuals who have normal sleep cycle. The present study indicated that in professions like armed forces and medicine working 24 hours at a stretch can lead to decrease in motor responses without affecting information processing and judgment

  13. Genome Sequence Databases (Overview): Sequencing and Assembly

    Energy Technology Data Exchange (ETDEWEB)

    Lapidus, Alla L.

    2009-01-01

    From the date its role in heredity was discovered, DNA has been generating interest among scientists from different fields of knowledge: physicists have studied the three dimensional structure of the DNA molecule, biologists tried to decode the secrets of life hidden within these long molecules, and technologists invent and improve methods of DNA analysis. The analysis of the nucleotide sequence of DNA occupies a special place among the methods developed. Thanks to the variety of sequencing technologies available, the process of decoding the sequence of genomic DNA (or whole genome sequencing) has become robust and inexpensive. Meanwhile the assembly of whole genome sequences remains a challenging task. In addition to the need to assemble millions of DNA fragments of different length (from 35 bp (Solexa) to 800 bp (Sanger)), great interest in analysis of microbial communities (metagenomes) of different complexities raises new problems and pushes some new requirements for sequence assembly tools to the forefront. The genome assembly process can be divided into two steps: draft assembly and assembly improvement (finishing). Despite the fact that automatically performed assembly (or draft assembly) is capable of covering up to 98% of the genome, in most cases, it still contains incorrectly assembled reads. The error rate of the consensus sequence produced at this stage is about 1/2000 bp. A finished genome represents the genome assembly of much higher accuracy (with no gaps or incorrectly assembled areas) and quality ({approx}1 error/10,000 bp), validated through a number of computer and laboratory experiments.

  14. Resolution of two native monomeric 90 kDa nitrate reductase active proteins from Shewanella gelidimarina and the sequence of two napA genes

    International Nuclear Information System (INIS)

    Simpson, Philippa J.L.; McKinzie, Audra A.; Codd, Rachel

    2010-01-01

    Research highlights: → Two monomeric 90 kDa nitrate reductase active proteins from Shewanella gelidimarina. → Sequence of napA from napEDABC-type operon and napA from NapDAGHB-type operon. → Isolation of NAP as NapA or NapAB correlated with NapA P47E amino acid substitution. -- Abstract: The reduction of nitrate to nitrite in the bacterial periplasm occurs in the 90 kDa NapA subunit of the periplasmic nitrate reductase (NAP) system. Most Shewanella genomes contain two nap operons: napEDABC and napDAGHB, which is an unusual feature of this genus. Two native, monomeric, 90 kDa nitrate reductase active proteins were resolved by hydrophobic interaction chromatography from aerobic cultures of Shewanella gelidimarina replete with reduced nitrogen compounds. The 90 kDa protein obtained in higher yield was characterized as NapA by electronic absorption and electron paramagnetic resonance spectroscopies and was identified by LC/MS/MS and MALDI-TOF/TOF MS as NapA from the napEDABC-type operon. The other 90 kDa protein, which was unstable and produced in low yields, was posited as NapA from the napDAGHB-type operon. Two napA genes have been sequenced from the napEDABC-type and napDAGHB-type operons of S. gelidimarina. Native NAP from S. putrefaciens was resolved as one NapA monomer and one NapAB heterodimer. Two amino acid substitutions in NapA correlated with the isolation of NAP as a NapA monomer or a NapAB heterodimer. The resolution of native, redox-active NapA isoforms in Shewanella provides new insight into the respiratory versatility of this genus, which has implications in bioremediation and the assembly of microbial fuel cells.

  15. Long working hours and depressive symptoms

    DEFF Research Database (Denmark)

    Virtanen, Marianna; Jokela, Markus; Madsen, Ida Eh

    2018-01-01

    Objectives This systematic review and meta-analysis combined published study-level data and unpublished individual-participant data with the aim of quantifying the relation between long working hours and the onset of depressive symptoms. Methods We searched PubMed and Embase for published....... In the majority of cohorts, long working hours was defined as working ≥55 hours per week. In multivariable-adjusted meta-analyses of 189 729 participants from 35 countries [96 275 men, 93 454 women, follow-up ranging from 1-5 years, 21 747 new-onset cases), there was an overall association of 1.14 (95% confidence...... interval (CI) 1.03-1.25] between long working hours and the onset of depressive symptoms, with significant evidence of heterogeneity (I 2=45.1%, P=0.004). A moderate association between working hours and depressive symptoms was found in Asian countries (1.50, 95% CI 1.13-2.01), a weaker association...

  16. Long working hours and depressive symptoms

    DEFF Research Database (Denmark)

    Virtanen, Marianna; Jokela, Markus; Madsen, Ida Eh

    2018-01-01

    . In the majority of cohorts, long working hours was defined as working ≥55 hours per week. In multivariable-adjusted meta-analyses of 189 729 participants from 35 countries [96 275 men, 93 454 women, follow-up ranging from 1-5 years, 21 747 new-onset cases), there was an overall association of 1.14 (95% confidence......Objectives This systematic review and meta-analysis combined published study-level data and unpublished individual-participant data with the aim of quantifying the relation between long working hours and the onset of depressive symptoms. Methods We searched PubMed and Embase for published...... interval (CI) 1.03-1.25] between long working hours and the onset of depressive symptoms, with significant evidence of heterogeneity (I 2=45.1%, P=0.004). A moderate association between working hours and depressive symptoms was found in Asian countries (1.50, 95% CI 1.13-2.01), a weaker association...

  17. Parallel motif extraction from very long sequences

    KAUST Repository

    Sahli, Majed

    2013-01-01

    Motifs are frequent patterns used to identify biological functionality in genomic sequences, periodicity in time series, or user trends in web logs. In contrast to a lot of existing work that focuses on collections of many short sequences, modern applications require mining of motifs in one very long sequence (i.e., in the order of several gigabytes). For this case, there exist statistical approaches that are fast but inaccurate; or combinatorial methods that are sound and complete. Unfortunately, existing combinatorial methods are serial and very slow. Consequently, they are limited to very short sequences (i.e., a few megabytes), small alphabets (typically 4 symbols for DNA sequences), and restricted types of motifs. This paper presents ACME, a combinatorial method for extracting motifs from a single very long sequence. ACME arranges the search space in contiguous blocks that take advantage of the cache hierarchy in modern architectures, and achieves almost an order of magnitude performance gain in serial execution. It also decomposes the search space in a smart way that allows scalability to thousands of processors with more than 90% speedup. ACME is the only method that: (i) scales to gigabyte-long sequences; (ii) handles large alphabets; (iii) supports interesting types of motifs with minimal additional cost; and (iv) is optimized for a variety of architectures such as multi-core systems, clusters in the cloud, and supercomputers. ACME reduces the extraction time for an exact-length query from 4 hours to 7 minutes on a typical workstation; handles 3 orders of magnitude longer sequences; and scales up to 16, 384 cores on a supercomputer. Copyright is held by the owner/author(s).

  18. Unified Sequence-Based Association Tests Allowing for Multiple Functional Annotations and Meta-analysis of Noncoding Variation in Metabochip Data.

    Science.gov (United States)

    He, Zihuai; Xu, Bin; Lee, Seunggeun; Ionita-Laza, Iuliana

    2017-09-07

    Substantial progress has been made in the functional annotation of genetic variation in the human genome. Integrative analysis that incorporates such functional annotations into sequencing studies can aid the discovery of disease-associated genetic variants, especially those with unknown function and located outside protein-coding regions. Direct incorporation of one functional annotation as weight in existing dispersion and burden tests can suffer substantial loss of power when the functional annotation is not predictive of the risk status of a variant. Here, we have developed unified tests that can utilize multiple functional annotations simultaneously for integrative association analysis with efficient computational techniques. We show that the proposed tests significantly improve power when variant risk status can be predicted by functional annotations. Importantly, when functional annotations are not predictive of risk status, the proposed tests incur only minimal loss of power in relation to existing dispersion and burden tests, and under certain circumstances they can even have improved power by learning a weight that better approximates the underlying disease model in a data-adaptive manner. The tests can be constructed with summary statistics of existing dispersion and burden tests for sequencing data, therefore allowing meta-analysis of multiple studies without sharing individual-level data. We applied the proposed tests to a meta-analysis of noncoding rare variants in Metabochip data on 12,281 individuals from eight studies for lipid traits. By incorporating the Eigen functional score, we detected significant associations between noncoding rare variants in SLC22A3 and low-density lipoprotein and total cholesterol, associations that are missed by standard dispersion and burden tests. Copyright © 2017 American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

  19. Six Reasons why hours of service regulations for truck drivers are violated

    DEFF Research Database (Denmark)

    Grøn, Sisse

    2008-01-01

      ABSTRACT Two decades of research has established a correlation between tiredness and fatigue, and traffic accident involving truck drivers.  Regulations limiting the driving hours of truck drivers thus are necessary precautions. But compliance is a problem. The answer from authorities tend to b...... independency ideal among truck drivers. The last reason is that the drivers and their employers share an interest in long work hours.......  ABSTRACT Two decades of research has established a correlation between tiredness and fatigue, and traffic accident involving truck drivers.  Regulations limiting the driving hours of truck drivers thus are necessary precautions. But compliance is a problem. The answer from authorities tend...... is that the regulation seems to be designed to long distance driving, and has some short-comings when applied to short distance drivers. The third reason is that the regulation deprives the drivers of means to control their tiredness. The fourth reason is that the regulation limits room for planning ahead generally...

  20. Probabilistic Motor Sequence Yields Greater Offline and Less Online Learning than Fixed Sequence.

    Science.gov (United States)

    Du, Yue; Prashad, Shikha; Schoenbrun, Ilana; Clark, Jane E

    2016-01-01

    It is well acknowledged that motor sequences can be learned quickly through online learning. Subsequently, the initial acquisition of a motor sequence is boosted or consolidated by offline learning. However, little is known whether offline learning can drive the fast learning of motor sequences (i.e., initial sequence learning in the first training session). To examine offline learning in the fast learning stage, we asked four groups of young adults to perform the serial reaction time (SRT) task with either a fixed or probabilistic sequence and with or without preliminary knowledge (PK) of the presence of a sequence. The sequence and PK were manipulated to emphasize either procedural (probabilistic sequence; no preliminary knowledge (NPK)) or declarative (fixed sequence; with PK) memory that were found to either facilitate or inhibit offline learning. In the SRT task, there were six learning blocks with a 2 min break between each consecutive block. Throughout the session, stimuli followed the same fixed or probabilistic pattern except in Block 5, in which stimuli appeared in a random order. We found that PK facilitated the learning of a fixed sequence, but not a probabilistic sequence. In addition to overall learning measured by the mean reaction time (RT), we examined the progressive changes in RT within and between blocks (i.e., online and offline learning, respectively). It was found that the two groups who performed the fixed sequence, regardless of PK, showed greater online learning than the other two groups who performed the probabilistic sequence. The groups who performed the probabilistic sequence, regardless of PK, did not display online learning, as indicated by a decline in performance within the learning blocks. However, they did demonstrate remarkably greater offline improvement in RT, which suggests that they are learning the probabilistic sequence offline. These results suggest that in the SRT task, the fast acquisition of a motor sequence is driven

  1. Draft Genome Sequences of Two Extensively Drug-Resistant Strains of Mycobacterium tuberculosis Belonging to the Euro-American S Lineage

    NARCIS (Netherlands)

    Malinga, L.A.; Abeel, T.; Desjardins, C.A.; Dlamini, T.C.; Cassell, G.; Chapman, S.B.; Birren, B.W.; Earl, A.M.; Van der Walt, M.

    2016-01-01

    We report the whole-genome sequencing of two extensively drug-resistant tuberculosis strains belonging to the Euro-American S lineage. The RSA 114 strain showed single-nucleotide polymorphisms predicted to have drug efflux activity.

  2. Start with an Hour a Week: Enhancing Usability at Wayne State University Libraries

    Directory of Open Access Journals (Sweden)

    Maria Nuccilli

    2018-01-01

    Full Text Available Instead of pursuing traditional testing methods, Discovery and Innovation at Wayne State University Libraries settled on an alternate path to user-centered design when redesigning our library website: running hour-long “guerrilla” usability tests each week for two semesters. The team found immediate successes with this simple, cost-effective method of usability testing, leading to similar redesign projects for other online resources. Emphasizing the importance of iterative design and continuous improvement, this article will detail the authors’ experience conducting short weekly tests, suggestions for institutions looking to begin similar testing programs, and low-stakes testing as a pathway to improved design for the library as a whole. In spring 2016, the Discovery and Innovation web team at Wayne State University Libraries began a redesign of our main library homepage, making the first major updates to the site since 2013. After launching the initial design, we wanted to improve the new website with feedback from real users, following Jakob Nielsen’s decades-old assertion that redesigning websites based on user feedback “can substantially improve usability” (Nielsen, 1993. Instead of using remote and large-scale testing options, we chose a lean, iterative approach, and committed to two semesters of brief, weekly “guerrilla” usability sessions with student users. Not only did this method produce powerful results, but its attainable, iterative approach ultimately led to an increased user focus beyond the library homepage. If you have an hour a week, a laptop, and at least one other colleague willing to help, you can start usability testing, guerrilla-style. Though we found success with this method, using such a stripped-down approach wasn’t immediately obvious. At the beginning of this project, we didn’t know a whole lot about conducting user testing, having relied mostly on survey responses, search logs, and Piwik website

  3. Parents are interested in newborn genomic testing during the early postpartum period.

    Science.gov (United States)

    Waisbren, Susan E; Bäck, Danielle K; Liu, Christina; Kalia, Sarah S; Ringer, Steven A; Holm, Ingrid A; Green, Robert C

    2015-06-01

    We surveyed parents to ascertain interest in newborn genomic testing and determine whether these queries would provoke refusal of conventional state-mandated newborn screening. After a brief genetics orientation, parents rated their interest in receiving genomic testing for their healthy newborn on a 5-point Likert scale and answered questions about demographics and health history. We used logistic regression to explore factors associated with interest in genomic testing and tracked any subsequent rejection of newborn screening. We queried 514 parents within 48 hours after birth while still in hospital (mean age (SD) 32.7 (6.4) years, 65.2% female, 61.2% white, 79.3% married). Parents reported being not at all (6.4%), a little (10.9%), somewhat (36.6%), very (28.0%), or extremely (18.1%) interested in genomic testing for their newborns. None refused state-mandated newborn screening. Married participants and those with health concerns about their infant were less interested in newborn genomic testing (P = 0.012 and P = 0.030, respectively). Degree of interest for mothers and fathers was discordant (at least two categories different) for 24.4% of couples. Interest in newborn genomic testing was high among parents of healthy newborns, and the majority of couples had similar levels of interest. Surveying parents about genomic sequencing did not prompt rejection of newborn screening.Genet Med 17 6, 501-504.

  4. Axolotl hemoglobin: cDNA-derived amino acid sequences of two alpha globins and a beta globin from an adult Ambystoma mexicanum.

    Science.gov (United States)

    Shishikura, Fumio; Takeuchi, Hiro-aki; Nagai, Takatoshi

    2005-11-01

    Erythrocytes of the adult axolotl, Ambystoma mexicanum, have multiple hemoglobins. We separated and purified two kinds of hemoglobin, termed major hemoglobin (Hb M) and minor hemoglobin (Hb m), from a five-year-old male by hydrophobic interaction column chromatography on Alkyl Superose. The hemoglobins have two distinct alpha type globin polypeptides (alphaM and alpham) and a common beta globin polypeptide, all of which were purified in FPLC on a reversed-phase column after S-pyridylethylation. The complete amino acid sequences of the three globin chains were determined separately using nucleotide sequencing with the assistance of protein sequencing. The mature globin molecules were composed of 141 amino acid residues for alphaM globin, 143 for alpham globin and 146 for beta globin. Comparing primary structures of the five kinds of axolotl globins, including two previously established alpha type globins from the same species, with other known globins of amphibians and representatives of other vertebrates, we constructed phylogenetic trees for amphibian hemoglobins and tetrapod hemoglobins. The molecular trees indicated that alphaM, alpham, beta and the previously known alpha major globin were adult types of globins and the other known alpha globin was a larval type. The existence of two to four more globins in the axolotl erythrocyte is predicted.

  5. SU-F-T-475: An Evaluation of the Overlap Between the Acceptance Testing and Commissioning Processes for Conventional Medical Linear Accelerators

    International Nuclear Information System (INIS)

    Morrow, A; Rangaraj, D; Perez-Andujar, A; Krishnamurthy, N

    2016-01-01

    Purpose: This work’s objective is to determine the overlap of processes, in terms of sub-processes and time, between acceptance testing and commissioning of a conventional medical linear accelerator and to evaluate the time saved by consolidating the two processes. Method: A process map for acceptance testing for medical linear accelerators was created from vendor documentation (Varian and Elekta). Using AAPM TG-106 and inhouse commissioning procedures, a process map was created for commissioning of said accelerators. The time to complete each sub-process in each process map was evaluated. Redundancies in the processes were found and the time spent on each were calculated. Results: Mechanical testing significantly overlaps between the two processes - redundant work here amounts to 9.5 hours. Many beam non-scanning dosimetry tests overlap resulting in another 6 hours of overlap. Beam scanning overlaps somewhat - acceptance tests include evaluating PDDs and multiple profiles but for only one field size while commissioning beam scanning includes multiple field sizes and depths of profiles. This overlap results in another 6 hours of rework. Absolute dosimetry, field outputs, and end to end tests are not done at all in acceptance testing. Finally, all imaging tests done in acceptance are repeated in commissioning, resulting in about 8 hours of rework. The total time overlap between the two processes is about 30 hours. Conclusion: The process mapping done in this study shows that there are no tests done in acceptance testing that are not also recommended to do for commissioning. This results in about 30 hours of redundant work when preparing a conventional linear accelerator for clinical use. Considering these findings in the context of the 5000 linacs in the United states, consolidating acceptance testing and commissioning would have allowed for the treatment of an additional 25000 patients using no additional resources.

  6. SU-F-T-475: An Evaluation of the Overlap Between the Acceptance Testing and Commissioning Processes for Conventional Medical Linear Accelerators

    Energy Technology Data Exchange (ETDEWEB)

    Morrow, A [Scott & White Hospital Temple, TX (United States); Rangaraj, D [Baylor Scott & White Health, Temple, TX (United States); Perez-Andujar, A [University of California San Francisco, San Francisco, CA (United States); Krishnamurthy, N [Baylor Scott & White Healthcare, Temple, TX (United States)

    2016-06-15

    Purpose: This work’s objective is to determine the overlap of processes, in terms of sub-processes and time, between acceptance testing and commissioning of a conventional medical linear accelerator and to evaluate the time saved by consolidating the two processes. Method: A process map for acceptance testing for medical linear accelerators was created from vendor documentation (Varian and Elekta). Using AAPM TG-106 and inhouse commissioning procedures, a process map was created for commissioning of said accelerators. The time to complete each sub-process in each process map was evaluated. Redundancies in the processes were found and the time spent on each were calculated. Results: Mechanical testing significantly overlaps between the two processes - redundant work here amounts to 9.5 hours. Many beam non-scanning dosimetry tests overlap resulting in another 6 hours of overlap. Beam scanning overlaps somewhat - acceptance tests include evaluating PDDs and multiple profiles but for only one field size while commissioning beam scanning includes multiple field sizes and depths of profiles. This overlap results in another 6 hours of rework. Absolute dosimetry, field outputs, and end to end tests are not done at all in acceptance testing. Finally, all imaging tests done in acceptance are repeated in commissioning, resulting in about 8 hours of rework. The total time overlap between the two processes is about 30 hours. Conclusion: The process mapping done in this study shows that there are no tests done in acceptance testing that are not also recommended to do for commissioning. This results in about 30 hours of redundant work when preparing a conventional linear accelerator for clinical use. Considering these findings in the context of the 5000 linacs in the United states, consolidating acceptance testing and commissioning would have allowed for the treatment of an additional 25000 patients using no additional resources.

  7. 75 FR 82170 - Hours of Service of Drivers

    Science.gov (United States)

    2010-12-29

    ... drivers to take breaks when needed and would reduce safety and health risks associated with long hours... long work hours, without significantly compromising their ability to do their jobs and earn a living... between hours 3.5 and 7 of an 11-hour driving period. Working beyond the 7th hour without a break is...

  8. Comparison of Paired ROC Curves through a Two-Stage Test.

    Science.gov (United States)

    Yu, Wenbao; Park, Eunsik; Chang, Yuan-Chin Ivan

    2015-01-01

    The area under the receiver operating characteristic (ROC) curve (AUC) is a popularly used index when comparing two ROC curves. Statistical tests based on it for analyzing the difference have been well developed. However, this index is less informative when two ROC curves cross and have similar AUCs. In order to detect differences between ROC curves in such situations, a two-stage nonparametric test that uses a shifted area under the ROC curve (sAUC), along with AUCs, is proposed for paired designs. The new procedure is shown, numerically, to be effective in terms of power under a wide range of scenarios; additionally, it outperforms two conventional ROC-type tests, especially when two ROC curves cross each other and have similar AUCs. Larger sAUC implies larger partial AUC at the range of low false-positive rates in this case. Because high specificity is important in many classification tasks, such as medical diagnosis, this is an appealing characteristic. The test also implicitly analyzes the equality of two commonly used binormal ROC curves at every operating point. We also apply the proposed method to synthesized data and two real examples to illustrate its usefulness in practice.

  9. Engineering fuel reloading sequence optimization for in-core shuffling system

    International Nuclear Information System (INIS)

    Jeong, Seo G.; Suh, Kune Y.

    2008-01-01

    Optimizing the nuclear fuel reloading process is central to enhancing the economics of nuclear power plant (NPP). There are two kinds of reloading method: in-core shuffling and ex-core shuffling. In-core shuffling has an advantage of reloading time when compared with ex-core shuffling. It is, however, not easy to adopt an in-core shuffling because of additional facilities required and regulations involved at the moment. The in-core shuffling necessitates minimizing the movement of refueling machine because reloading paths can be varied according to differing reloading sequences. In the past, the reloading process depended on the expert's knowledge and experience. Recent advances in computer technology have apparently facilitated the heuristic approach to nuclear fuel reloading sequence optimization. This work presents a first in its kind of in-core shuffling whereas all the Korean NPPs have so far adopted ex-core shuffling method. Several plants recently applied the in-core shuffling strategy, thereby saving approximately 24 to 48 hours of outage time. In case of in-core shuffling one need minimize the movement of refueling machine because reloading path can be varied according to different reloading sequences. Advances in computer technology have enabled optimizing the in-core shuffling by solving a traveling salesman problem. To solve this problem, heuristic algorithm is used, such as ant colony algorithm and genetic algorithm. The Systemic Engineering Reload Analysis (SERA) program is written to optimize shuffling sequence based on heuristic algorithms. SERA is applied to the Optimized Power Reactor 1000 MWe (OPR1000) on the assumption that the NPP adopts the in-core shuffling in the foreseeable future. It is shown that the optimized shuffling sequence resulted in reduced reloading time. (author)

  10. Time Separation Between Events in a Sequence: a Regional Property?

    Science.gov (United States)

    Muirwood, R.; Fitzenz, D. D.

    2013-12-01

    Earthquake sequences are loosely defined as events occurring too closely in time and space to appear unrelated. Depending on the declustering method, several, all, or no event(s) after the first large event might be recognized as independent mainshocks. It can therefore be argued that a probabilistic seismic hazard assessment (PSHA, traditionally dealing with mainshocks only) might already include the ground shaking effects of such sequences. Alternatively all but the largest event could be classified as an ';aftershock' and removed from the earthquake catalog. While in PSHA the question is only whether to keep or remove the events from the catalog, for Risk Management purposes, the community response to the earthquakes, as well as insurance risk transfer mechanisms, can be profoundly affected by the actual timing of events in such a sequence. In particular the repetition of damaging earthquakes over a period of weeks to months can lead to businesses closing and families evacuating from the region (as happened in Christchurch, New Zealand in 2011). Buildings that are damaged in the first earthquake may go on to be damaged again, even while they are being repaired. Insurance also functions around a set of critical timeframes - including the definition of a single 'event loss' for reinsurance recoveries within the 192 hour ';hours clause', the 6-18 month pace at which insurance claims are settled, and the annual renewal of insurance and reinsurance contracts. We show how temporal aspects of earthquake sequences need to be taken into account within models for Risk Management, and what time separation between events are most sensitive, both in terms of the modeled disruptions to lifelines and business activity as well as in the losses to different parties (such as insureds, insurers and reinsurers). We also explore the time separation between all events and between loss causing events for a collection of sequences from across the world and we point to the need to

  11. Long Work Hours: Volunteers and Conscripts

    OpenAIRE

    Robert Drago; Mark Wooden; David Black

    2006-01-01

    Panel data from Australia are used to study the prevalence of work hours mismatch among long hours workers and, more importantly, how that mismatch persists and changes over time, and what factors are associated with these changes. Particular attention is paid to the roles played by household debt, ideal worker characteristics and gender. Both static and dynamic multinomial logit models are estimated, with the dependent variable distinguishing long hours workers from other workers, and within...

  12. Working Hours, Promotion and the Gender Gap in the Workplace

    DEFF Research Database (Denmark)

    Kato, Takao; Owan, Hideo; Ogawa, Hiromasa

    thereof. The firm's decision to provide training also depends on its private information about the worker's OJT ability, which affects his/her future productivity if and when the worker gets promoted. Upon completion of training, the firm then promotes the worker. The model illuminates under what......This paper presents a novel model of promotion within the firm which sheds new light on the interplay between working hours and the odds of subsequent promotion. The model's key feature is the coexistence of two different sources of asymmetric information: (i) the worker's cost of long working....../her on the job. Long working hours signal the worker's commitment to the firm, which determines the surplus produced when the worker is promoted. Thus, the firm provides the worker with managerial training only after observing the employee's hours worked, a signal of his/her commitment to the firm or lack...

  13. DNA sequence of 15 base pairs is sufficient to mediate both glucocorticoid and progesterone induction of gene expression

    International Nuclear Information System (INIS)

    Straehle, U.; Klock, G.; Schuetz, G.

    1987-01-01

    To define the recognition sequence of the glucocorticoid receptor and its relationship with that of the progesterone receptor, oligonucleotides derived from the glucocorticoid response element of the tyrosine aminotransferase gene were tested upstream of a heterologous promoter for their capacity to mediate effects of these two steroids. The authors show that a 15-base-pair sequence with partial symmetry is sufficient to confer glucocorticoid inducibility on the promoter of the herpes simplex virus thymidine kinase gene. The same 15-base-pair sequence mediates induction by progesterone. Point mutations in the recognition sequence affect inducibility by glucocorticoids and progesterone similarly. Together with the strong conservation of the sequence of the DNA-binding domain of the two receptors, these data suggest that both proteins recognize a sequence that is similar, if not the same

  14. Preferred vs Actual Working Hours in Couple Households

    OpenAIRE

    Yi-Ping Tseng; Mark Wooden

    2005-01-01

    Working hours in Australia are quite widely distributed around the population mean. That is, there are relatively many people working both relatively short hours and relatively long hours each week. From a welfare perspective, however, it is not the actual number of hours worked that is of importance, but whether the hours being worked are consistent with individual preferences. In this paper the question of how closely hours preferences are being met is examined using data collected in the f...

  15. Work Hours Constraints: Impacts and Policy Implications

    OpenAIRE

    Constant, Amelie F.; Otterbach, Steffen

    2011-01-01

    If individuals reveal their preference as consumers, then they are taken seriously. What happens if individuals, as employees, reveal their preferences in working hours? And what happens if there is a misalignment between actual hours worked and preferred hours, the so-called work hours constraints? How does this affect the productivity of workers, their health, and overall life satisfaction? Labor supply and corresponding demand are fundamental to production. Labor economists know for long t...

  16. Two new computational methods for universal DNA barcoding: a benchmark using barcode sequences of bacteria, archaea, animals, fungi, and land plants.

    Science.gov (United States)

    Tanabe, Akifumi S; Toju, Hirokazu

    2013-01-01

    Taxonomic identification of biological specimens based on DNA sequence information (a.k.a. DNA barcoding) is becoming increasingly common in biodiversity science. Although several methods have been proposed, many of them are not universally applicable due to the need for prerequisite phylogenetic/machine-learning analyses, the need for huge computational resources, or the lack of a firm theoretical background. Here, we propose two new computational methods of DNA barcoding and show a benchmark for bacterial/archeal 16S, animal COX1, fungal internal transcribed spacer, and three plant chloroplast (rbcL, matK, and trnH-psbA) barcode loci that can be used to compare the performance of existing and new methods. The benchmark was performed under two alternative situations: query sequences were available in the corresponding reference sequence databases in one, but were not available in the other. In the former situation, the commonly used "1-nearest-neighbor" (1-NN) method, which assigns the taxonomic information of the most similar sequences in a reference database (i.e., BLAST-top-hit reference sequence) to a query, displays the highest rate and highest precision of successful taxonomic identification. However, in the latter situation, the 1-NN method produced extremely high rates of misidentification for all the barcode loci examined. In contrast, one of our new methods, the query-centric auto-k-nearest-neighbor (QCauto) method, consistently produced low rates of misidentification for all the loci examined in both situations. These results indicate that the 1-NN method is most suitable if the reference sequences of all potentially observable species are available in databases; otherwise, the QCauto method returns the most reliable identification results. The benchmark results also indicated that the taxon coverage of reference sequences is far from complete for genus or species level identification in all the barcode loci examined. Therefore, we need to accelerate

  17. Breaking the Long Hours Culture.

    Science.gov (United States)

    Kodz, J.; Kersley, B.; Strebler, M. T.; O'Regan, S.

    Case studies of 12 leading British employers were driven by employers' interest in issues related to working long hours in light of introduction of the Working Time Directive, a European Community initiative enacted into British law that sets limits on working hours per week. Data showed over one-fourth of full-time employees worked over 48 hours…

  18. First experiment on LMJ facility: pointing and synchronisation qualification, sequences qualification

    Science.gov (United States)

    Henry, Olivier; Bretheau, Dominique; Luttmann, Michel; Graillot, Herve; Ferri, Michel; Seguineau, Frederic; Bar, Emmanuel; Patissou, Loic; Canal, Phillipe; Sautarel, Françoise; Tranquille Marques, Yves; Raffestin, Didier

    2016-10-01

    The LMJ (Laser mega Joule) facility at the CESTA site (Aquitaine, France) is a tool designed to deliver up to 1.2 MJ at 351 nm for plasma experiments. The experiment system will include 11 diagnostics: UV and X energy balances, imagers (Streak and stripe camera, CCD), spectrometers, and a Visar/pyrometer. The facility must be able to deliver, within the hour following the shot, all the results of the plasma diagnostics, alignment images and laser diagnostic measurements. These results have to be guaranteed in terms of conformity to the request and quality of measurement. The end of 2014 was devoted to the qualification of system pointing on target and synchronization within and between beams. The shots made with one chain (divided in 2 quads - 8 laser beams) have achieved 50 µm of misalignment accuracy (chain and quad channel) and a synchronization accuracy in the order of 50 ps. The performances achieved for plasma diagnostic (in the order of less 100 µm of alignment and timing accuracy less than 150 ps) comply with expectations. At the same time the first automatic sequences were tested. They allowed a shot on target every 6h:30 and in some case twice a day by reducing preparation actions, leading to a sequence of 4h:00. These shooting sequences are managed by an operating team of 7 people helped by 3 people for security aspects.

  19. Long working hours and stroke among employees in the general workforce of Denmark.

    Science.gov (United States)

    Hannerz, Harald; Albertsen, Karen; Burr, Hermann; Nielsen, Martin Lindhardt; Garde, Anne Helene; Larsen, Ann Dyreborg; Pejtersen, Jan Hyld

    2018-05-01

    A systematic review and meta-analysis have found that long working hours were prospectively associated with an increased risk of overall stroke. The primary aim of the present study was to test if this finding could be reproduced in a sample that has been randomly selected from the general workforce of Denmark. A secondary aim was to estimate the association for haemorrhagic and ischaemic stroke separately. Individual participant data on 20- to 64-year-old employees were drawn from the Danish Labour Force Survey, 1999-2013, and linked to data on socio-economic status (SES), migrations, hospitalisations and deaths from national registers. The participants were followed from the time of the interview until the end of 2014. Poisson regression was used to estimate age-, sex- and SES-adjusted rate ratios for stroke as a function of weekly working hours. With 35-40 working hours per week as reference, the estimated rate ratios for overall stroke were 0.97 (95% confidence interval (CI) 0.83-1.13) for 41-48 working hours, 1.10 (95% CI 0.86-1.39) for 49-54 working hours and 0.89 (95% CI 0.69-1.16) for ≥55 working hours. The estimated rate ratios per one category increase in working hours were 0.99 (95% CI 0.93-1.06) for overall stroke, 0.96 (95% CI 0.88-1.05) for ischaemic stroke and 1.15 (95% CI 1.02-1.31) for haemorrhagic stroke. Our analysis does not support the hypothesis that long working hours are associated with increased rates of overall stroke. It suggests, however, that long working hours might be associated with increased rates of haemorrhagic stroke.

  20. Computational identification of MoRFs in protein sequences.

    Science.gov (United States)

    Malhis, Nawar; Gsponer, Jörg

    2015-06-01

    Intrinsically disordered regions of proteins play an essential role in the regulation of various biological processes. Key to their regulatory function is the binding of molecular recognition features (MoRFs) to globular protein domains in a process known as a disorder-to-order transition. Predicting the location of MoRFs in protein sequences with high accuracy remains an important computational challenge. In this study, we introduce MoRFCHiBi, a new computational approach for fast and accurate prediction of MoRFs in protein sequences. MoRFCHiBi combines the outcomes of two support vector machine (SVM) models that take advantage of two different kernels with high noise tolerance. The first, SVMS, is designed to extract maximal information from the general contrast in amino acid compositions between MoRFs, their surrounding regions (Flanks), and the remainders of the sequences. The second, SVMT, is used to identify similarities between regions in a query sequence and MoRFs of the training set. We evaluated the performance of our predictor by comparing its results with those of two currently available MoRF predictors, MoRFpred and ANCHOR. Using three test sets that have previously been collected and used to evaluate MoRFpred and ANCHOR, we demonstrate that MoRFCHiBi outperforms the other predictors with respect to different evaluation metrics. In addition, MoRFCHiBi is downloadable and fast, which makes it useful as a component in other computational prediction tools. http://www.chibi.ubc.ca/morf/. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.