Analysis of accident sequences and source terms at waste treatment and storage facilities for waste generated by U.S. Department of Energy Waste Management Operations, Volume 3: Appendixes C-H

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

Mueller, C.; Nabelssi, B.; Roglans-Ribas, J.

1995-04-01

This report contains the Appendices for the Analysis of Accident Sequences and Source Terms at Waste Treatment and Storage Facilities for Waste Generated by the U.S. Department of Energy Waste Management Operations. The main report documents the methodology, computational framework, and results of facility accident analyses performed as a part of the U.S. Department of Energy (DOE) Waste Management Programmatic Environmental Impact Statement (WM PEIS). The accident sequences potentially important to human health risk are specified, their frequencies are assessed, and the resultant radiological and chemical source terms are evaluated. A personal computer-based computational framework and database have been developedmore » that provide these results as input to the WM PEIS for calculation of human health risk impacts. This report summarizes the accident analyses and aggregates the key results for each of the waste streams. Source terms are estimated and results are presented for each of the major DOE sites and facilities by WM PEIS alternative for each waste stream. The appendices identify the potential atmospheric release of each toxic chemical or radionuclide for each accident scenario studied. They also provide discussion of specific accident analysis data and guidance used or consulted in this report.« less

Comparative analysis of the countermeasures taken to mitigate exposure of the public to radioiodine following the Chernobyl and Fukushima accidents: lessons from both accidents.

PubMed

Uyba, Vladimir; Samoylov, Alexander; Shinkarev, Sergey

2018-04-01

In the case of a severe radiation accident at a nuclear power station, the most important radiation hazard for the public is internal exposure of the thyroid to radioiodine. The purposes of this paper were (i) to compare countermeasures conducted (following the Chernobyl and Fukushima accidents) aimed at mitigation of exposure to the thyroid for the public, (ii) to present comparative estimates of doses to the thyroid and (iii) to derive lessons from the two accidents. The scale and time of countermeasures applied in the early phase of the accidents (sheltering, evacuation, and intake of stable iodine to block the thyroid) and at a later time (control of 131I concentration in foodstuffs) have been described. After the Chernobyl accident, the estimation of the thyroid doses for the public was mainly based on direct thyroid measurements of ~400 000 residents carried out within the first 2 months. The highest estimates of thyroid doses to children reached 50 Gy. After the Fukushima accident, the estimation of thyroid doses was based on radioecological models due to a lack of direct thyroid measurements (only slightly more than 1000 residents were measured). The highest estimates of thyroid doses to children were a few hundred mGy. Following the Chernobyl accident, ingestion of 131I through cows' milk was the dominant pathway. Following the Fukushima accident, it appears that inhalation of contaminated air was the dominant pathway. Some lessons learned following the Chernobyl and Fukushima accidents have been presented in this paper.

Comparative analysis of the countermeasures taken to mitigate exposure of the public to radioiodine following the Chernobyl and Fukushima accidents: lessons from both accidents

PubMed Central

Uyba, Vladimir; Samoylov, Alexander; Shinkarev, Sergey

2018-01-01

Abstract In the case of a severe radiation accident at a nuclear power station, the most important radiation hazard for the public is internal exposure of the thyroid to radioiodine. The purposes of this paper were (i) to compare countermeasures conducted (following the Chernobyl and Fukushima accidents) aimed at mitigation of exposure to the thyroid for the public, (ii) to present comparative estimates of doses to the thyroid and (iii) to derive lessons from the two accidents. The scale and time of countermeasures applied in the early phase of the accidents (sheltering, evacuation, and intake of stable iodine to block the thyroid) and at a later time (control of 131I concentration in foodstuffs) have been described. After the Chernobyl accident, the estimation of the thyroid doses for the public was mainly based on direct thyroid measurements of ~400 000 residents carried out within the first 2 months. The highest estimates of thyroid doses to children reached 50 Gy. After the Fukushima accident, the estimation of thyroid doses was based on radioecological models due to a lack of direct thyroid measurements (only slightly more than 1000 residents were measured). The highest estimates of thyroid doses to children were a few hundred mGy. Following the Chernobyl accident, ingestion of 131I through cows’ milk was the dominant pathway. Following the Fukushima accident, it appears that inhalation of contaminated air was the dominant pathway. Some lessons learned following the Chernobyl and Fukushima accidents have been presented in this paper. PMID:29415268

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

Muhlheim, M.D.; Belles, R.J.; Cletcher, J.W.

The Accident Sequence Precursor (ASP) Program involves the systematic review and evaluation of operational events that have occurred at light-water reactors to identify and categorize precursors to potential severe core damage accident sequences. The results of the ASP Program are published in an annual report. The most recent report, which contains the precursors for 1995, is NUREG/CR-4674, Volume 23, Precursors to Potential Severe Core Damage Accidents: 1995, A Status Report, published in April 1997. This article provides an overview of the ASP review and evaluation process and a summary of the results for 1995.

SBLOCA outside containment at Browns Ferry Unit One: accident sequence analysis. [Small break

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

Condon, W.A.; Harrington, R.M.; Greene, S.R.

1982-11-01

This study describes the predicted response of Unit 1 at the Browns Ferry Nuclear Plant to a postulated small-break loss-of-coolant accident outside of the primary containment. The break has been assumed to occur in the scram discharge volume piping immediately following a reactor scram that cannot be reset. The events before core uncovering are discussed for both the worst-case accident sequence without operator action and for the more likely sequences with operator action. Without operator action, the events after core uncovering would include core meltdown and subsequent containment failure, and this event sequence has been determined through use of themore » MARCH code. An estimate of the magnitude and timing of the concomitant release of the noble gas, cesium, and iodine-based fission products to the environment is provided in Volume 2 of this report.« less

Manned space flight nuclear system safety. Volume 3: Reactor system preliminary nuclear safety analysis. Part 2: Accident Model Document (AMD)

NASA Technical Reports Server (NTRS)

1972-01-01

The Accident Model Document is one of three documents of the Preliminary Safety Analysis Report (PSAR) - Reactor System as applied to a Space Base Program. Potential terrestrial nuclear hazards involving the zirconium hydride reactor-Brayton power module are identified for all phases of the Space Base program. The accidents/events that give rise to the hazards are defined and abort sequence trees are developed to determine the sequence of events leading to the hazard and the associated probabilities of occurence. Source terms are calculated to determine the magnitude of the hazards. The above data is used in the mission accident analysis to determine the most probable and significant accidents/events in each mission phase. The only significant hazards during the prelaunch and launch ascent phases of the mission are those which arise form criticality accidents. Fission product inventories during this time period were found to be very low due to very limited low power acceptance testing.

Accident sequence precursor events with age-related contributors

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

Murphy, G.A.; Kohn, W.E.

1995-12-31

The Accident Sequence Precursor (ASP) Program at ORNL analyzed about 14.000 Licensee Event Reports (LERs) filed by US nuclear power plants 1987--1993. There were 193 events identified as precursors to potential severe core accident sequences. These are reported in G/CR-4674. Volumes 7 through 20. Under the NRC Nuclear Plant Aging Research program, the authors evaluated these events to determine the extent to which component aging played a role. Events were selected that involved age-related equipment degradation that initiated an event or contributed to an event sequence. For the 7-year period, ORNL identified 36 events that involved aging degradation as amore » contributor to an ASP event. Except for 1992, the percentage of age-related events within the total number of ASP events over the 7-year period ({approximately}19%) appears fairly consistent up to 1991. No correlation between plant ape and number of precursor events was found. A summary list of the age-related events is presented in the report.« less

Aircraft Loss-of-Control: Analysis and Requirements for Future Safety-Critical Systems and Their Validation

NASA Technical Reports Server (NTRS)

Belcastro, Christine M.

2011-01-01

Loss of control remains one of the largest contributors to fatal aircraft accidents worldwide. Aircraft loss-of-control accidents are complex, resulting from numerous causal and contributing factors acting alone or more often in combination. Hence, there is no single intervention strategy to prevent these accidents. This paper summarizes recent analysis results in identifying worst-case combinations of loss-of-control accident precursors and their time sequences, a holistic approach to preventing loss-of-control accidents in the future, and key requirements for validating the associated technologies.

Application of MELCOR Code to a French PWR 900 MWe Severe Accident Sequence and Evaluation of Models Performance Focusing on In-Vessel Thermal Hydraulic Results

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

De Rosa, Felice

2006-07-01

In the ambit of the Severe Accident Network of Excellence Project (SARNET), funded by the European Union, 6. FISA (Fission Safety) Programme, one of the main tasks is the development and validation of the European Accident Source Term Evaluation Code (ASTEC Code). One of the reference codes used to compare ASTEC results, coming from experimental and Reactor Plant applications, is MELCOR. ENEA is a SARNET member and also an ASTEC and MELCOR user. During the first 18 months of this project, we performed a series of MELCOR and ASTEC calculations referring to a French PWR 900 MWe and to themore » accident sequence of 'Loss of Steam Generator (SG) Feedwater' (known as H2 sequence in the French classification). H2 is an accident sequence substantially equivalent to a Station Blackout scenario, like a TMLB accident, with the only difference that in H2 sequence the scram is forced to occur with a delay of 28 seconds. The main events during the accident sequence are a loss of normal and auxiliary SG feedwater (0 s), followed by a scram when the water level in SG is equal or less than 0.7 m (after 28 seconds). There is also a main coolant pumps trip when {delta}Tsat < 10 deg. C, a total opening of the three relief valves when Tric (core maximal outlet temperature) is above 603 K (330 deg. C) and accumulators isolation when primary pressure goes below 1.5 MPa (15 bar). Among many other points, it is worth noting that this was the first time that a MELCOR 1.8.5 input deck was available for a French PWR 900. The main ENEA effort in this period was devoted to prepare the MELCOR input deck using the code version v.1.8.5 (build QZ Oct 2000 with the latest patch 185003 Oct 2001). The input deck, completely new, was prepared taking into account structure, data and same conditions as those found inside ASTEC input decks. The main goal of the work presented in this paper is to put in evidence where and when MELCOR provides good enough results and why, in some cases mainly referring to its specific models (candling, corium pool behaviour, etc.) they were less good. A future work will be the preparation of an input deck for the new MELCOR 1.8.6. and to perform a code-to-code comparison with ASTEC v1.2 rev. 1. (author)« less

Bilateral cerebrovascular accidents in incontinentia pigmenti.

PubMed

Fiorillo, Loretta; Sinclair, D Barry; O'Byrne, Mary L; Krol, Alfons L

2003-07-01

Incontinentia Pigmenti is an X-linked dominant neurocutaneous disorder with central nervous system manifestations in 30% of cases, including seizures and mental retardation. Ischemic or hemorrhagic cerebrovascular accidents have been reported rarely in incontinentia pigmenti. Chart review and literature search was performed following identification of the index case. We describe a patient with incontinentia pigmenti who developed bilateral cerebrovascular accidents in the neonatal period, with resultant severe neurologic sequelae. This is the second reported case of bilateral cerebrovascular accidents in a patient with incontinentia pigmenti. This finding may be secondary to cerebrovascular anomalies, similar to those observed in the retina. Recognition of cerebrovascular accidents as a complication of incontinentia pigmenti will hopefully lead to earlier recognition and treatment.

Fission product transport analysis in a loss of decay heat removal accident at Browns Ferry

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

Wichner, R.P.; Weber, C.F.; Hodge, S.A.

1984-01-01

This paper summarizes an analysis of the movement of noble gases, iodine, and cesium fission products within the Mark-I containment BWR reactor system represented by Browns Ferry Unit 1 during a postulated accident sequence initiated by a loss of decay heat removal (DHR) capability following a scram. The event analysis showed that this accident could be brought under control by various means, but the sequence with no operator action ultimately leads to containment (drywell) failure followed by loss of water from the reactor vessel, core degradation due to overheating, and reactor vessel failure with attendant movement of core debris ontomore » the drywell floor.« less

The effectiveness of using pictures in teaching young children about burn injury accidents.

PubMed

Liu, Hsueh-Fen; Lin, Fang-Suey; Chang, Chien-Ju

2015-11-01

This study utilized the "story grammar" approach (Stein and Glenn, 1979) to analyze the within-corpus differences in recounting of sixty 6- and 7-year-old children, specifically whether illustrations (5-factor accident sequence) were or were not resorted to as a means to assist their narration of a home accident in which a child received a burn injury from hot soup. Our investigation revealed that the message presentation strategy "combining oral and pictures" better helped young children to memorize the story content (sequence of events leading to the burn injury) than "oral only." Specifically, the content of "the dangerous objects that caused the injury", "the unsafe actions that people involved took", and "how the people involved felt about the severity of the accident" differed significantly between the two groups. Copyright © 2015 Elsevier Ltd and The Ergonomics Society. All rights reserved.

Interface requirements to couple thermal hydraulics codes to severe accident codes: ICARE/CATHARE

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

Camous, F.; Jacq, F.; Chatelard, P.

1997-07-01

In order to describe with the same code the whole sequence of severe LWR accidents, up to the vessel failure, the Institute of Protection and Nuclear Safety has performed a coupling of the severe accident code ICARE2 to the thermalhydraulics code CATHARE2. The resulting code, ICARE/CATHARE, is designed to be as pertinent as possible in all the phases of the accident. This paper is mainly devoted to the description of the ICARE2-CATHARE2 coupling.

Noble gas, iodine, and cesium transport in a postulated loss of decay heat removal accident at Browns Ferry

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

Wichner, R.P.; Hodge, S.A.; Weber, C.F.

1984-08-01

This report presents an analysis of the movement of noble gas, iodine, and cesium fission products within the Mark-I containment BWR reactor system represented by Browns Ferry Unit 1 during a postulated accident sequence initiated by a loss of decay heat removal capability following a scram. The event analysis showed that this accident could be brought under control by various means, but the sequence with no operator action ultimately leads to containment (drywell) failure followed by loss of water from the reactor vessel, core degradation due to overheating, and reactor vessel failure with attendant movement of core debris onto themore » drywell floor. The analysis of fission product transport presented in this report is based on the no-operator-action sequence and provides an estimate of fission product inventories, as a function of time, within 14 control volumes outside the core, with the atmosphere considered as the final control volume in the transport sequence. As in the case of accident sequences previously studied, we find small barrier for noble gas ejection to air, these gases being effectively purged from the drywell and reactor building by steam and concrete degradation gases. However, significant decay of krypton isotopes occurs during the long delay times involved in this sequence. In contrast, large degrees of holdup for iodine and cesium are projected due to the chemical reactivity of these elements. Only about 2 x 10/sup -4/% of the initial iodine and cesium activity are predicted to be released to the atmosphere. Principal barriers for release are deposition on reactor vessel and containment walls. A significant amount of iodine is captured in the water pool formed in the reactor building basement after actuation of the fire protection system.« less

Aircraft Loss-of-Control Accident Analysis

NASA Technical Reports Server (NTRS)

Belcastro, Christine M.; Foster, John V.

2010-01-01

Loss of control remains one of the largest contributors to fatal aircraft accidents worldwide. Aircraft loss-of-control accidents are complex in that they can result from numerous causal and contributing factors acting alone or (more often) in combination. Hence, there is no single intervention strategy to prevent these accidents. To gain a better understanding into aircraft loss-of-control events and possible intervention strategies, this paper presents a detailed analysis of loss-of-control accident data (predominantly from Part 121), including worst case combinations of causal and contributing factors and their sequencing. Future potential risks are also considered.

[Accidents with venomous and poisonous animals in Central Europe].

PubMed

Bodio, Mauro; Junghanss, Thomas

2009-05-01

Central Europe is largely safe from accidents with venomous and poisonous animals. The regions where European vipers are regularly found are shrinking. Today accidents with jellyfish and stings of venomous fish afflicted during leisure activities at the sea side play the dominant role. Life threatening accidents in Europe are mainly due to exotic snakes held in captivity. A system useful in daily medical practice is explained to classify and stage accidents due to poisonous and venomous animals. The important poisonous and venomous animals of Central Europe and the specific therapeutics, the antivenoms, are covered. The antivenom depot "Antivenin-CH" of the Swiss Toxicology Information Centre in Zurich and the MRITox in Munich with the antivenom registry Munich AntiVenom INdex (MAVIN) are presented.

Motor vehicle seat belt restraint system analysis during rollover.

PubMed

Meyer, Steven E; Hock, Davis; Forrest, Stephen; Herbst, Brian; Sances, Anthony; Kumaresan, Srirangam

2003-01-01

The multi-planar and multiple impact long duration accident sequence of a real world rollover results in multidirectional vehicle acceleration pulses and multiplanar occupant motions not typically seen in a planar crash sequence. Various researchers have documented that, while contemporary production emergency locking seatbelt retractors (ELRs) have been found to be extremely effective in the planar crashes in which they are extensively evaluated, when subjected to multi-planar acceleration environments their response may be different than expected. Specifically, accelerations in the vertical plane have been shown to substantially affect the timeliness of the retractors inertial sensor moving out of its neutral position and locking the seat belt. An analysis of the vehicle occupant motions relative to the acceleration pulses sensed at the retractor location indicates a time phase shift that, under certain circumstances, can result in unexpected seat belt spool out and occupant excursions in these multi-planar, multiple impact crash sequences. This paper will review the various previous studies focusing on the retractors response to these multidirectional, including vertical, acceleration environments and review statistical studies based upon U.S. government collected data indicating a significant difference in belt usage rates in rollover accidents as compared to all other planar accident modes. A significant number of real world accident case studies will be reviewed wherein the performance of ELR equipped seatbelt systems spooled out. Finally, the typical occupant injury and the associated mechanism due to belt spool out in real world accidents will be delineated.

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

Kastenberg, W.E.; Apostolakis, G.; Dhir, V.K.

Severe accident management can be defined as the use of existing and/or altemative resources, systems and actors to prevent or mitigate a core-melt accident. For each accident sequence and each combination of severe accident management strategies, there may be several options available to the operator, and each involves phenomenological and operational considerations regarding uncertainty. Operational uncertainties include operator, system and instrumentation behavior during an accident. A framework based on decision trees and influence diagrams has been developed which incorporates such criteria as feasibility, effectiveness, and adverse effects, for evaluating potential severe accident management strategies. The framework is also capable ofmore » propagating both data and model uncertainty. It is applied to several potential strategies including PWR cavity flooding, BWR drywell flooding, PWR depressurization and PWR feed and bleed.« less

Psychophysiological and other factors affecting human performance in accident prevention and investigation. [Comparison of aviation with other industries

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

Klinestiver, L.R.

Psychophysiological factors are not uncommon terms in the aviation incident/accident investigation sequence where human error is involved. It is highly suspect that the same psychophysiological factors may also exist in the industrial arena where operator personnel function; but, there is little evidence in literature indicating how management and subordinates cope with these factors to prevent or reduce accidents. It is apparent that human factors psychophysological training is quite evident in the aviation industry. However, while the industrial arena appears to analyze psychophysiological factors in accident investigations, there is little evidence that established training programs exist for supervisors and operator personnel.

A classification on human factor accident/incident of China civil aviation in recent twelve years.

PubMed

Luo, Xiao-li

2004-10-01

To study human factor accident/incident occurred during 1990-2001 using new classification standard. The human factor accident/incident classification standard is developed on the basis of Reason's Model, combining with CAAC's traditional classifying method, and applied to the classified statistical analysis for 361 flying incidents and 35 flight accidents of China civil aviation, which is induced by human factors and occurred from 1990 to 2001. 1) the incident percentage of taxi and cruise is higher than that of takeoff, climb and descent. 2) The dominating type of flight incidents is diverging of runway, overrunning, near-miss, tail/wingtip/engine strike and ground obstacle impacting. 3) The top three accidents are out of control caused by crew, mountain collision and over runway. 4) Crew's basic operating skill is lower than what we imagined, the mostly representation is poor correcting ability when flight error happened. 5) Crew errors can be represented by incorrect control, regulation and procedure violation, disorientation and diverging percentage of correct flight level. The poor CRM skill is the dominant factor impacting China civil aviation safety, this result has a coincidence with previous study, but there is much difference and distinct characteristic in top incident phase, the type of crew error and behavior performance compared with that of advanced countries. We should strengthen CRM training for all of pilots aiming at the Chinese pilot behavior characteristic in order to improve the safety level of China civil aviation.

Investigations on optimization of accident management measures following a station blackout accident in a VVER-1000 pressurized water reactor

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

Tusheva, P.; Schaefer, F.; Kliem, S.

2012-07-01

The reactor safety issues are of primary importance for preserving the health of the population and ensuring no release of radioactivity and fission products into the environment. A part of the nuclear research focuses on improvement of the safety of existing nuclear power plants. Studies, research and efforts are a continuing process at improving the safety and reliability of existing and newly developed nuclear power plants at prevention of a core melt accident. Station blackout (loss of AC power supply) is one of the dominant accidents taken into consideration at performing accident analysis. In case of multiple failures of safetymore » systems it leads to a severe accident. To prevent an accident to turn into a severe one or to mitigate the consequences, accident management measures must be performed. The present paper outlines possibilities for application and optimization of accident management measures following a station blackout accident. Assessed is the behaviour of the nuclear power plant during a station blackout accident without accident management measures and with application of primary/secondary side oriented accident management measures. Discussed are the possibilities for operators ' intervention and the influence of the performed accident management measures on the course of the accident. Special attention has been paid to the effectiveness of the passive feeding and physical phenomena having an influence on the system behaviour. The performed simulations show that the effectiveness of the secondary side feeding procedure can be limited due to an early evaporation or flashing effects in the feed water system. The analyzed cases show that the effectiveness of the accident management measures strongly depends on the initiation criteria applied for depressurization of the reactor coolant system. (authors)« less

A Qualitative Study on Organizational Factors Affecting Occupational Accidents

PubMed Central

ESKANDARI, Davood; JAFARI, Mohammad Javad; MEHRABI, Yadollah; KIAN, Mostafa Pouya; CHARKHAND, Hossein; MIRGHOTBI, Mostafa

2017-01-01

Background: Technical, human, operational and organizational factors have been influencing the sequence of occupational accidents. Among them, organizational factors play a major role in causing occupational accidents. The aim of this research was to understand the Iranian safety experts’ experiences and perception of organizational factors. Methods: This qualitative study was conducted in 2015 by using the content analysis technique. Data were collected through semi-structured interviews with 17 safety experts working in Iranian universities and industries and analyzed with a conventional qualitative content analysis method using the MAXQDA software. Results: Eleven organizational factors’ sub-themes were identified: management commitment, management participation, employee involvement, communication, blame culture, education and training, job satisfaction, interpersonal relationship, supervision, continuous improvement, and reward system. The participants considered these factors as effective on occupational accidents. Conclusion: The mentioned 11 organizational factors are probably involved in occupational accidents in Iran. Naturally, improving organizational factors can increase the safety performance and reduce occupational accidents. PMID:28435824

A Qualitative Study on Organizational Factors Affecting Occupational Accidents.

PubMed

Eskandari, Davood; Jafari, Mohammad Javad; Mehrabi, Yadollah; Kian, Mostafa Pouya; Charkhand, Hossein; Mirghotbi, Mostafa

2017-03-01

Technical, human, operational and organizational factors have been influencing the sequence of occupational accidents. Among them, organizational factors play a major role in causing occupational accidents. The aim of this research was to understand the Iranian safety experts' experiences and perception of organizational factors. This qualitative study was conducted in 2015 by using the content analysis technique. Data were collected through semi-structured interviews with 17 safety experts working in Iranian universities and industries and analyzed with a conventional qualitative content analysis method using the MAXQDA software. Eleven organizational factors' sub-themes were identified: management commitment, management participation, employee involvement, communication, blame culture, education and training, job satisfaction, interpersonal relationship, supervision, continuous improvement, and reward system. The participants considered these factors as effective on occupational accidents. The mentioned 11 organizational factors are probably involved in occupational accidents in Iran. Naturally, improving organizational factors can increase the safety performance and reduce occupational accidents.

Preliminary Analysis of Aircraft Loss of Control Accidents: Worst Case Precursor Combinations and Temporal Sequencing

NASA Technical Reports Server (NTRS)

Belcastro, Christine M.; Groff, Loren; Newman, Richard L.; Foster, John V.; Crider, Dennis H.; Klyde, David H.; Huston, A. McCall

2014-01-01

Aircraft loss of control (LOC) is a leading cause of fatal accidents across all transport airplane and operational classes, and can result from a wide spectrum of hazards, often occurring in combination. Technologies developed for LOC prevention and recovery must therefore be effective under a wide variety of conditions and uncertainties, including multiple hazards, and their validation must provide a means of assessing system effectiveness and coverage of these hazards. This requires the definition of a comprehensive set of LOC test scenarios based on accident and incident data as well as future risks. This paper defines a comprehensive set of accidents and incidents over a recent 15 year period, and presents preliminary analysis results to identify worst-case combinations of causal and contributing factors (i.e., accident precursors) and how they sequence in time. Such analyses can provide insight in developing effective solutions for LOC, and form the basis for developing test scenarios that can be used in evaluating them. Preliminary findings based on the results of this paper indicate that system failures or malfunctions, crew actions or inactions, vehicle impairment conditions, and vehicle upsets contributed the most to accidents and fatalities, followed by inclement weather or atmospheric disturbances and poor visibility. Follow-on research will include finalizing the analysis through a team consensus process, defining future risks, and developing a comprehensive set of test scenarios with correlation to the accidents, incidents, and future risks. Since enhanced engineering simulations are required for batch and piloted evaluations under realistic LOC precursor conditions, these test scenarios can also serve as a high-level requirement for defining the engineering simulation enhancements needed for generating them.

Hemispheric asymmetries of a motor memory in a recognition test after learning a movement sequence.

PubMed

Leinen, Peter; Panzer, Stefan; Shea, Charles H

2016-11-01

Two experiments utilizing a spatial-temporal movement sequence were designed to determine if the memory of the sequence is lateralized in the left or right hemisphere. In Experiment 1, dominant right-handers were randomly assigned to one of two acquisition groups: a left-hand starter and a right-hand starter group. After an acquisition phase, reaction time (RT) was measured in a recognition test by providing the learned sequential pattern in the left or right visual half-field for 150ms. In a retention test and two transfer tests the dominant coordinate system for sequence production was evaluated. In Experiment 2 dominant left-handers and dominant right-handers had to acquire the sequence with their dominant limb. The results of Experiment 1 indicated that RT was significantly shorter when the acquired sequence was provided in the right visual field during the recognition test. The same results occurred in Experiment 2 for dominant right-handers and left-handers. These results indicated a right visual field left hemisphere advantage in the recognition test for the practiced stimulus for dominant left and right-handers, when the task was practiced with the dominant limb. Copyright © 2016 Elsevier B.V. All rights reserved.

Severe Accident Sequence Analysis Program: Anticipated transient without scram simulations for Browns Ferry Nuclear Plant Unit 1

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

Dallman, R J; Gottula, R C; Holcomb, E E

1987-05-01

An analysis of five anticipated transients without scram (ATWS) was conducted at the Idaho National Engineering Laboratory (INEL). The five detailed deterministic simulations of postulated ATWS sequences were initiated from a main steamline isolation valve (MSIV) closure. The subject of the analysis was the Browns Ferry Nuclear Plant Unit 1, a boiling water reactor (BWR) of the BWR/4 product line with a Mark I containment. The simulations yielded insights to the possible consequences resulting from a MSIV closure ATWS. An evaluation of the effects of plant safety systems and operator actions on accident progression and mitigation is presented.

Fatty acid-oxidizing consortia along a nutrient gradient in the Florida Everglades.

PubMed

Chauhan, Ashvini; Ogram, Andrew

2006-04-01

The Florida Everglades is one of the largest freshwater marshes in North America and has been subject to eutrophication for decades. A gradient in P concentrations extends for several kilometers into the interior of the northern regions of the marsh, and the structure and function of soil microbial communities vary along the gradient. In this study, stable isotope probing was employed to investigate the fate of carbon from the fermentation products propionate and butyrate in soils from three sites along the nutrient gradient. For propionate microcosms, 16S rRNA gene clone libraries from eutrophic and transition sites were dominated by sequences related to previously described propionate oxidizers, such as Pelotomaculum spp. and Syntrophobacter spp. Significant representation was also observed for sequences related to Smithella propionica, which dismutates propionate to butyrate. Sequences of dominant phylotypes from oligotrophic samples did not cluster with known syntrophs but with sulfate-reducing prokaryotes (SRP) and Pelobacter spp. In butyrate microcosms, sequences clustering with Syntrophospora spp. and Syntrophomonas spp. dominated eutrophic microcosms, and sequences related to Pelospora dominated the transition microcosm. Sequences related to Pelospora spp. and SRP dominated clone libraries from oligotrophic microcosms. Sequences from diverse bacterial phyla and primary fermenters were also present in most libraries. Archaeal sequences from eutrophic microcosms included sequences characteristic of Methanomicrobiaceae, Methanospirillaceae, and Methanosaetaceae. Oligotrophic microcosms were dominated by acetotrophs, including sequences related to Methanosarcina, suggesting accumulation of acetate.

The impact of traffic sign deficit on road traffic accidents in Nigeria.

PubMed

Ezeibe, Christian; Ilo, Chukwudi; Oguonu, Chika; Ali, Alphonsus; Abada, Ifeanyi; Ezeibe, Ezinwanne; Oguonu, Chukwunonso; Abada, Felicia; Izueke, Edwin; Agbo, Humphrey

2018-04-04

This study assesses the impact of traffic sign deficit on road traffic accidents in Nigeria. The participants were 720 commercial vehicle drivers. While simple random sampling was used to select 6 out of 137 federal highways, stratified random sampling was used to select six categories of commercial vehicle drivers. The study used qual-dominant mixed methods approach comprising key informant interviews; group interviews; field observation; policy appraisal and secondary literature on traffic signs. Result shows that the failure of government to provide and maintain traffic signs in order to guide road users through the numerous accident black spots on the highways is the major cause of road accidents in Nigeria. The study argues that provision and maintenance of traffic signs present opportunity to promoting safety on the highways and achieving the sustainable development goals.

Loss of DHR sequences at Browns Ferry Unit One - accident-sequence analysis

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

Cook, D.H.; Grene, S.R.; Harrington, R.M.

1983-05-01

This study describes the predicted response of Unit One at the Browns Ferry Nuclear Plant to a postulated loss of decay heat removal (DHR) capability following scram from full power with the power conversion system unavailable. In accident sequences without DHR capability, the residual heat removal (RHR) system functions of pressure suppression pool cooling and reactor vessel shutdown cooling are unavailable. Consequently, all decay heat energy is stored in the pressure suppression pool with a concomitant increase in pool temperature and primary containment pressure. With the assumption that DHR capability is not regained during the lengthy course of this accidentmore » sequence, the containment ultimately fails by overpressurization. Although unlikely, this catastrophic failure might lead to loss of the ability to inject cooling water into the reactor vessel, causing subsequent core uncovery and meltdown. The timing of these events and the effective mitigating actions that might be taken by the operator are discussed in this report.« less

Systemic accident analysis: examining the gap between research and practice.

PubMed

Underwood, Peter; Waterson, Patrick

2013-06-01

The systems approach is arguably the dominant concept within accident analysis research. Viewing accidents as a result of uncontrolled system interactions, it forms the theoretical basis of various systemic accident analysis (SAA) models and methods. Despite the proposed benefits of SAA, such as an improved description of accident causation, evidence within the scientific literature suggests that these techniques are not being used in practice and that a research-practice gap exists. The aim of this study was to explore the issues stemming from research and practice which could hinder the awareness, adoption and usage of SAA. To achieve this, semi-structured interviews were conducted with 42 safety experts from ten countries and a variety of industries, including rail, aviation and maritime. This study suggests that the research-practice gap should be closed and efforts to bridge the gap should focus on ensuring that systemic methods meet the needs of practitioners and improving the communication of SAA research. Copyright © 2013 Elsevier Ltd. All rights reserved.

Chemistry, the Central Science? The History of the High School Science Sequence

ERIC Educational Resources Information Center

Sheppard, Keith; Robbins, Dennis M.

2005-01-01

Chemistry became the ''central science'' not by design but by accident in the US high schools. The three important factors, which had their influence on the high school science, are sequenced and their impact on the development of US science education, are mentioned.

Expert systems for fault diagnosis in nuclear reactor control

NASA Astrophysics Data System (ADS)

Jalel, N. A.; Nicholson, H.

1990-11-01

An expert system for accident analysis and fault diagnosis for the Loss Of Fluid Test (LOFT) reactor, a small scale pressurized water reactor, was developed for a personal computer. The knowledge of the system is presented using a production rule approach with a backward chaining inference engine. The data base of the system includes simulated dependent state variables of the LOFT reactor model. Another system is designed to assist the operator in choosing the appropriate cooling mode and to diagnose the fault in the selected cooling system. The response tree, which is used to provide the link between a list of very specific accident sequences and a set of generic emergency procedures which help the operator in monitoring system status, and to differentiate between different accident sequences and select the correct procedures, is used to build the system knowledge base. Both systems are written in TURBO PROLOG language and can be run on an IBM PC compatible with 640k RAM, 40 Mbyte hard disk and color graphics.

A smart phone-based pocket fall accident detection, positioning, and rescue system.

PubMed

Kau, Lih-Jen; Chen, Chih-Sheng

2015-01-01

We propose in this paper a novel algorithm as well as architecture for the fall accident detection and corresponding wide area rescue system based on a smart phone and the third generation (3G) networks. To realize the fall detection algorithm, the angles acquired by the electronic compass (ecompass) and the waveform sequence of the triaxial accelerometer on the smart phone are used as the system inputs. The acquired signals are then used to generate an ordered feature sequence and then examined in a sequential manner by the proposed cascade classifier for recognition purpose. Once the corresponding feature is verified by the classifier at current state, it can proceed to next state; otherwise, the system will reset to the initial state and wait for the appearance of another feature sequence. Once a fall accident event is detected, the user's position can be acquired by the global positioning system (GPS) or the assisted GPS, and sent to the rescue center via the 3G communication network so that the user can get medical help immediately. With the proposed cascaded classification architecture, the computational burden and power consumption issue on the smart phone system can be alleviated. Moreover, as we will see in the experiment that a distinguished fall accident detection accuracy up to 92% on the sensitivity and 99.75% on the specificity can be obtained when a set of 450 test actions in nine different kinds of activities are estimated by using the proposed cascaded classifier, which justifies the superiority of the proposed algorithm.

Scaling and design analyses of a scaled-down, high-temperature test facility for experimental investigation of the initial stages of a VHTR air-ingress accident

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

Arcilesi, David J.; Ham, Tae Kyu; Kim, In Hun

2015-07-01

A critical event in the safety analysis of the very high-temperature gas-cooled reactor (VHTR) is an air-ingress accident. This accident is initiated, in its worst case scenario, by a double-ended guillotine break of the coaxial cross vessel, which leads to a rapid reactor vessel depressurization. In a VHTR, the reactor vessel is located within a reactor cavity that is filled with air during normal operating conditions. Following the vessel depressurization, the dominant mode of ingress of an air–helium mixture into the reactor vessel will either be molecular diffusion or density-driven stratified flow. The mode of ingress is hypothesized to dependmore » largely on the break conditions of the cross vessel. Since the time scales of these two ingress phenomena differ by orders of magnitude, it is imperative to understand under which conditions each of these mechanisms will dominate in the air ingress process. Computer models have been developed to analyze this type of accident scenario. There are, however, limited experimental data available to understand the phenomenology of the air-ingress accident and to validate these models. Therefore, there is a need to design and construct a scaled-down experimental test facility to simulate the air-ingress accident scenarios and to collect experimental data. The current paper focuses on the analyses performed for the design and operation of a 1/8th geometric scale (by height and diameter), high-temperature test facility. A geometric scaling analysis for the VHTR, a time scale analysis of the air-ingress phenomenon, a transient depressurization analysis of the reactor vessel, a hydraulic similarity analysis of the test facility, a heat transfer characterization of the hot plenum, a power scaling analysis for the reactor system, and a design analysis of the containment vessel are discussed.« less

Association between Daily Hospital Outpatient Visits for Accidents and Daily Ambient Air Temperatures in an Industrial City.

PubMed

Chau, Tang-Tat; Wang, Kuo-Ying

2016-01-01

An accident is an unwanted hazard to a person. However, accidents occur. In this work, we search for correlations between daily accident rates and environmental factors. To study daily hospital outpatients who were admitted for accidents during a 5-year period, 2007-2011, we analyzed data regarding 168,366 outpatients using univariate regression models; we also used multivariable regression models to account for confounding factors. Our analysis indicates that the number of male outpatients admitted for accidents was approximately 1.31 to 1.47 times the number of female outpatients (P < 0.0001). Of the 12 parameters (regarding air pollution and meteorology) considered, only daily temperature exhibited consistent and significant correlations with the daily number of hospital outpatient visits for accidents throughout the 5-year analysis period. The univariate regression models indicate that older people (greater than 66 years old) had the fewest accidents per 1-degree increase in temperature, followed by young people (0-15 years old). Middle-aged people (16-65 years old) were the group of outpatients that were more prone to accidents, with an increase in accident rates of 0.8-1.2 accidents per degree increase in temperature. The multivariable regression models also reveal that the temperature variation was the dominant factor in determining the daily number of outpatient visits for accidents. Our further multivariable model analysis of temperature with respect to air pollution variables show that, through the increases in emissions and concentrations of CO, photochemical O3 production and NO2 loss in the ambient air, increases in vehicular emissions are associated with increases in temperatures. As such, increases in hospital visits for accidents are related to vehicular emissions and usage. This finding is consistent with clinical experience which shows about 60% to 80% of accidents are related to traffic, followed by accidents occurred in work place.

Association between Daily Hospital Outpatient Visits for Accidents and Daily Ambient Air Temperatures in an Industrial City

PubMed Central

Chau, Tang-Tat; Wang, Kuo-Ying

2016-01-01

An accident is an unwanted hazard to a person. However, accidents occur. In this work, we search for correlations between daily accident rates and environmental factors. To study daily hospital outpatients who were admitted for accidents during a 5-year period, 2007–2011, we analyzed data regarding 168,366 outpatients using univariate regression models; we also used multivariable regression models to account for confounding factors. Our analysis indicates that the number of male outpatients admitted for accidents was approximately 1.31 to 1.47 times the number of female outpatients (P < 0.0001). Of the 12 parameters (regarding air pollution and meteorology) considered, only daily temperature exhibited consistent and significant correlations with the daily number of hospital outpatient visits for accidents throughout the 5-year analysis period. The univariate regression models indicate that older people (greater than 66 years old) had the fewest accidents per 1-degree increase in temperature, followed by young people (0–15 years old). Middle-aged people (16–65 years old) were the group of outpatients that were more prone to accidents, with an increase in accident rates of 0.8–1.2 accidents per degree increase in temperature. The multivariable regression models also reveal that the temperature variation was the dominant factor in determining the daily number of outpatient visits for accidents. Our further multivariable model analysis of temperature with respect to air pollution variables show that, through the increases in emissions and concentrations of CO, photochemical O3 production and NO2 loss in the ambient air, increases in vehicular emissions are associated with increases in temperatures. As such, increases in hospital visits for accidents are related to vehicular emissions and usage. This finding is consistent with clinical experience which shows about 60% to 80% of accidents are related to traffic, followed by accidents occurred in work place. PMID:26815039

Scoping Study Investigating PWR Instrumentation during a Severe Accident Scenario

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

Rempe, J. L.; Knudson, D. L.; Lutz, R. J.

The accidents at the Three Mile Island Unit 2 (TMI-2) and Fukushima Daiichi Units 1, 2, and 3 nuclear power plants demonstrate the critical importance of accurate, relevant, and timely information on the status of reactor systems during a severe accident. These events also highlight the critical importance of understanding and focusing on the key elements of system status information in an environment where operators may be overwhelmed with superfluous and sometimes conflicting data. While progress in these areas has been made since TMI-2, the events at Fukushima suggests that there may still be a potential need to ensure thatmore » critical plant information is available to plant operators. Recognizing the significant technical and economic challenges associated with plant modifications, it is important to focus on instrumentation that can address these information critical needs. As part of a program initiated by the Department of Energy, Office of Nuclear Energy (DOE-NE), a scoping effort was initiated to assess critical information needs identified for severe accident management and mitigation in commercial Light Water Reactors (LWRs), to quantify the environment instruments monitoring this data would have to survive, and to identify gaps where predicted environments exceed instrumentation qualification envelop (QE) limits. Results from the Pressurized Water Reactor (PWR) scoping evaluations are documented in this report. The PWR evaluations were limited in this scoping evaluation to quantifying the environmental conditions for an unmitigated Short-Term Station BlackOut (STSBO) sequence in one unit at the Surry nuclear power station. Results were obtained using the MELCOR models developed for the US Nuclear Regulatory Commission (NRC)-sponsored State of the Art Consequence Assessment (SOARCA) program project. Results from this scoping evaluation indicate that some instrumentation identified to provide critical information would be exposed to conditions that significantly exceeded QE limits for extended time periods for the low frequency STSBO sequence evaluated in this study. It is recognized that the core damage frequency (CDF) of the sequence evaluated in this scoping effort would be considerably lower if evaluations considered new FLEX equipment being installed by industry. Nevertheless, because of uncertainties in instrumentation response when exposed to conditions beyond QE limits and alternate challenges associated with different sequences that may impact sensor performance, it is recommended that additional evaluations of instrumentation performance be completed to provide confidence that operators have access to accurate, relevant, and timely information on the status of reactor systems for a broad range of challenges associated with risk important severe accident sequences.« less

A comprehensive review of rollover accidents involving vehicles equipped with Electronic Stability Control (ESC) systems.

PubMed

Padmanaban, Jeya; Shields, Leland E; Scheibe, Robert R; Eyges, Vitaly E

2008-10-01

This study investigated 478 police accident reports from 9 states to examine and characterize rollover crashes involving ESC-equipped vehicles. The focus was on the sequence of critical events leading to loss of control and rollover, and the interactions between the accident, driver, and environment. Results show that, while ESC is effective in reducing loss of control leading to certain rollover crashes, its effectiveness is diminished in others, particularly when the vehicle departs the roadway or when environmental factors such as slick road conditions or driver factors such as speeding, distraction, fatigue, impairment, or overcorrection are present.

A Comprehensive Review of Rollover Accidents Involving Vehicles Equipped with Electronic Stability Control (ESC) Systems

PubMed Central

Padmanaban, Jeya; Shields, Leland E.; Scheibe, Robert R.; Eyges, Vitaly E.

2008-01-01

This study investigated 478 police accident reports from 9 states to examine and characterize rollover crashes involving ESC-equipped vehicles. The focus was on the sequence of critical events leading to loss of control and rollover, and the interactions between the accident, driver, and environment. Results show that, while ESC is effective in reducing loss of control leading to certain rollover crashes, its effectiveness is diminished in others, particularly when the vehicle departs the roadway or when environmental factors such as slick road conditions or driver factors such as speeding, distraction, fatigue, impairment, or overcorrection are present. PMID:19026219

10 CFR 50.43 - Additional standards and provisions affecting class 103 licenses and certifications for...

Code of Federal Regulations, 2010 CFR

2010-01-01

... licensed before 1997, or use simplified, inherent, passive, or other innovative means to accomplish their... sequences, including equilibrium core conditions; or (2) There has been acceptable testing of a prototype... accident sequences, including equilibrium core conditions. If a prototype plant is used to comply with the...

Low-Probability High-Consequence (LPHC) Failure Events in Geologic Carbon Sequestration Pipelines and Wells: Framework for LPHC Risk Assessment Incorporating Spatial Variability of Risk

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

Oldenburg, Curtis M.; Budnitz, Robert J.

If Carbon dioxide Capture and Storage (CCS) is to be effective in mitigating climate change, it will need to be carried out on a very large scale. This will involve many thousands of miles of dedicated high-pressure pipelines in order to transport many millions of tonnes of CO 2 annually, with the CO 2 delivered to many thousands of wells that will inject the CO 2 underground. The new CCS infrastructure could rival in size the current U.S. upstream natural gas pipeline and well infrastructure. This new infrastructure entails hazards for life, health, animals, the environment, and natural resources. Pipelinesmore » are known to rupture due to corrosion, from external forces such as impacts by vehicles or digging equipment, by defects in construction, or from the failure of valves and seals. Similarly, wells are vulnerable to catastrophic failure due to corrosion, cement degradation, or operational mistakes. While most accidents involving pipelines and wells will be minor, there is the inevitable possibility of accidents with very high consequences, especially to public health. The most important consequence of concern is CO 2 release to the environment in concentrations sufficient to cause death by asphyxiation to nearby populations. Such accidents are thought to be very unlikely, but of course they cannot be excluded, even if major engineering effort is devoted (as it will be) to keeping their probability low and their consequences minimized. This project has developed a methodology for analyzing the risks of these rare but high-consequence accidents, using a step-by-step probabilistic methodology. A key difference between risks for pipelines and wells is that the former are spatially distributed along the pipe whereas the latter are confined to the vicinity of the well. Otherwise, the methodology we develop for risk assessment of pipeline and well failures is similar and provides an analysis both of the annual probabilities of accident sequences of concern and of their consequences, and crucially the methodology provides insights into what measures might be taken to mitigate those accident sequences identified as of concern. Mitigating strategies could address reducing the likelihood of an accident sequence of concern, or reducing the consequences, or some combination. The methodology elucidates both local and integrated risks along the pipeline or at the well providing information useful to decision makers at various levels including local (e.g., property owners and town councils), regional (e.g., county and state representatives), and national levels (federal regulators and corporate proponents).« less

Application of forensic image analysis in accident investigations.

PubMed

Verolme, Ellen; Mieremet, Arjan

2017-09-01

Forensic investigations are primarily meant to obtain objective answers that can be used for criminal prosecution. Accident analyses are usually performed to learn from incidents and to prevent similar events from occurring in the future. Although the primary goal may be different, the steps in which information is gathered, interpreted and weighed are similar in both types of investigations, implying that forensic techniques can be of use in accident investigations as well. The use in accident investigations usually means that more information can be obtained from the available information than when used in criminal investigations, since the latter require a higher evidence level. In this paper, we demonstrate the applicability of forensic techniques for accident investigations by presenting a number of cases from one specific field of expertise: image analysis. With the rapid spread of digital devices and new media, a wealth of image material and other digital information has become available for accident investigators. We show that much information can be distilled from footage by using forensic image analysis techniques. These applications show that image analysis provides information that is crucial for obtaining the sequence of events and the two- and three-dimensional geometry of an accident. Since accident investigation focuses primarily on learning from accidents and prevention of future accidents, and less on the blame that is crucial for criminal investigations, the field of application of these forensic tools may be broader than would be the case in purely legal sense. This is an important notion for future accident investigations. Copyright © 2017 Elsevier B.V. All rights reserved.

Locomotive crashworthiness research

DOT National Transportation Integrated Search

2015-04-01

conducts research on locomotive crashworthiness. The research approach includes four phases: : 1. Accident investigations to assemble sequences of events leading to injury and fatality. : 2. Locomotive performance is analyzed, and potential improveme...

Injury protection and accident causation parameters for vulnerable road users based on German In-Depth Accident Study GIDAS.

PubMed

Otte, Dietmar; Jänsch, Michael; Haasper, Carl

2012-01-01

Within a study of accident data from GIDAS (German In-Depth Accident Study), vulnerable road users are investigated regarding injury risk in traffic accidents. GIDAS is the largest in-depth accident study in Germany. Due to a well-defined sampling plan, representativeness with respect to the federal statistics is also guaranteed. A hierarchical system ACASS (Accident Causation Analysis with Seven Steps) was developed in GIDAS, describing the human causation factors in a chronological sequence. The accordingly classified causation factors - derived from the systematic of the analysis of human accident causes ("7 steps") - can be used to describe the influence of accident causes on the injury outcome. The bases of the study are accident documentations over ten years from 1999 to 2008 with 8204 vulnerable road users (VRU), of which 3 different groups were selected as pedestrians n=2041, motorcyclists n=2199 and bicyclists n=3964, and analyzed on collisions with cars and trucks as well as vulnerable road users alone. The paper will give a description of the injury pattern and injury mechanisms of accidents. The injury frequencies and severities are pointed out considering different types of VRU and protective measures of helmet and clothes of the human body. The impact points are demonstrated on the car, following to conclusion of protective measures on the vehicle. Existing standards of protection devices as well as interdisciplinary research, including accident and injury statistics, are described. With this paper, a summarization of the existing possibilities on protective measures for pedestrians, bicyclists and motorcyclists is given and discussed by comparison of all three groups of vulnerable road users. Also the relevance of special impact situations and accident causes mainly responsible for severe injuries are pointed out, given the new orientation of research for the avoidance and reduction of accident patterns. 2010 Elsevier Ltd. All rights reserved.

Final safety analysis report for the Galileo Mission: Volume 2, Book 2: Accident model document: Appendices

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

Not Available

1988-12-15

This section of the Accident Model Document (AMD) presents the appendices which describe the various analyses that have been conducted for use in the Galileo Final Safety Analysis Report II, Volume II. Included in these appendices are the approaches, techniques, conditions and assumptions used in the development of the analytical models plus the detailed results of the analyses. Also included in these appendices are summaries of the accidents and their associated probabilities and environment models taken from the Shuttle Data Book (NSTS-08116), plus summaries of the several segments of the recent GPHS safety test program. The information presented in thesemore » appendices is used in Section 3.0 of the AMD to develop the Failure/Abort Sequence Trees (FASTs) and to determine the fuel releases (source terms) resulting from the potential Space Shuttle/IUS accidents throughout the missions.« less

Upon the reconstruction of accidents triggered by tire explosion. Analytical model and case study

NASA Astrophysics Data System (ADS)

Gaiginschi, L.; Agape, I.; Talif, S.

2017-10-01

Accident Reconstruction is important in the general context of increasing road traffic safety. In the casuistry of traffic accidents, those caused by tire explosions are critical under the severity of consequences, because they are usually happening at high speeds. Consequently, the knowledge of the running speed of the vehicle involved at the time of the tire explosion is essential to elucidate the circumstances of the accident. The paper presents an analytical model for the kinematics of a vehicle which, after the explosion of one of its tires, begins to skid, overturns and rolls. The model consists of two concurent approaches built as applications of the momentum conservation and energy conservation principles, and allows determination of the initial speed of the vehicle involved, by running backwards the sequences of the road event. The authors also aimed to both validate the two distinct analytical approaches by calibrating the calculation algorithms on a case study

Investigating accident causation through information network modelling.

PubMed

Griffin, T G C; Young, M S; Stanton, N A

2010-02-01

Management of risk in complex domains such as aviation relies heavily on post-event investigations, requiring complex approaches to fully understand the integration of multi-causal, multi-agent and multi-linear accident sequences. The Event Analysis of Systemic Teamwork methodology (EAST; Stanton et al. 2008) offers such an approach based on network models. In this paper, we apply EAST to a well-known aviation accident case study, highlighting communication between agents as a central theme and investigating the potential for finding agents who were key to the accident. Ultimately, this work aims to develop a new model based on distributed situation awareness (DSA) to demonstrate that the risk inherent in a complex system is dependent on the information flowing within it. By identifying key agents and information elements, we can propose proactive design strategies to optimize the flow of information and help work towards avoiding aviation accidents. Statement of Relevance: This paper introduces a novel application of an holistic methodology for understanding aviation accidents. Furthermore, it introduces an ongoing project developing a nonlinear and prospective method that centralises distributed situation awareness and communication as themes. The relevance of findings are discussed in the context of current ergonomic and aviation issues of design, training and human-system interaction.

[Effect of post-traumatic disorders of the victims and causes of traffic accidents in the early stages of treatment].

PubMed

Scigała, Dawid Konrad; Ziołek, Jakub; Kwiatkowski, Krzysztof

2013-12-01

Poland is a country in which every year there is a lot of motor vehicle accidents, number of victims is one of the highest in European union. Helping patients after motor vehicle accidents should base on cooperation of doctors and psychologists because holistic approach to patient enables rapid and effective rehabilitation. To show connection between physical damage cause in motor vehicle accident with mental trauma, which increase on process of full recovery. There were 31 victims who were involved in motor vehicle accidents not more than one month ago. In the second group there were people who was never involved in motor vehicle accident. The procedure consisted on filling demographic questionnaire, state traite anxety inventory and aqute stress disorder questionnare. In the second part of the research was to accomplish the emotional Stroop task, which based on selecting the name of the color of a word, which was on the screen. There were two types of the words: negative related to motor vehicle accident and neutral. Participants from the research group had higher level of anxiety than participants from control group and they had significantly longer reaction time in particular on words associated to accident, which could be the signal of problems with cognitive processes because of the anxiety. Furthermore participants with head injuries and upper limbs (whitout dominant limb) have had longer reaction times in Stroop test than participants with leg injuries, it indicating on higher level of anxiety and feeling of insecurity. It should be noted that looking on a character an range of a injuries, role that participant attend in accident (victims have more emotional disturbance), because it could determinate rate of recovery and the way communication with the patient.

BNL severe-accident sequence experiments and analysis program. [PWR; BWR

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

Greene, G.A.; Ginsberg, T.; Tutu, N.K.

1983-01-01

In the analysis of degraded core accidents, the two major sources of pressure loading on light water reactor containments are: steam generation from core debris-water thermal interactions; and molten core-concrete interactions. Experiments are in progress at BNL in support of analytical model development related to aspects of the above containment loading mechanisms. The work supports development and evaluation of the CORCON (Muir, 1981) and MARCH (Wooton, 1980) computer codes. Progress in the two programs is described.

The association between car accident fatalities and children’s fears: A study in seven EU countries

PubMed Central

Kovess-Masfety, Viviane; Sowa, David; Keyes, Katherine; Fermanian, Christophe; Bitfoi, Adina; Carta, Mauro Giovanni; Koç, Ceren; Goelitz, Dietmar; Lesinskiene, Sigita; Mihova, Zlatka; Otten, Roy; Pez, Ondine

2017-01-01

Children’s fear of a car accident occurring to parents or themselves has been used as a concrete example to illustrate one of the symptoms of anxiety disorders such as separation anxiety and generalized anxiety. However, its usage across countries may be questionable where the prevalence of this specific type of injury differs. This cross-sectional study compares samples from seven diverse European countries (Bulgaria, Germany, Italy, Lithuania, Netherlands, Romania, Turkey) to see if an environmental exposure, car accident death rate per 100,000 people (country-wide from WHO data), is associated with children’s self-report of car accident fears. In this study, 6–11 year-old children were surveyed by a diagnostic instrument (Dominic Interactive) about several situations and asked if they believed they were similar to a fictional child depicted in said situations. Mothers were surveyed for additional sociodemographic information. Multivariable logistic regression was used to adjust for covariates including mother’s age, mother’s education, single parenting, and mother’s professional inactivity. We report a monotonic relationship between higher car accident death rates and the prevalence of children reporting fear of parent’s or own accident. Relative to a reference of 3.9 deaths per 100,000 people, children’s odds of reporting fear of parent’s accident ranged from 1.99 (95% CI 1.51–2.61) times to 4.84 (95% CI 3.68–6.37) times as the risk of death by car accident increased across countries. A similar result arose from fear of child’s own accident, with significant ORs ranging from 1.91 (95% CI 1.53–2.40) to 2.68 (95% CI 2.07–3.47) alongside increased death rates. Given that reporting of these fears accompanies correspondingly high accident death rates, the pertinence of using fear of car accidents as an illustration for some diagnostic item for mental disorders cross-nationally appears to be an issue. PMID:28771500

The association between car accident fatalities and children's fears: A study in seven EU countries.

PubMed

Kovess-Masfety, Viviane; Sowa, David; Keyes, Katherine; Husky, Mathilde; Fermanian, Christophe; Bitfoi, Adina; Carta, Mauro Giovanni; Koç, Ceren; Goelitz, Dietmar; Lesinskiene, Sigita; Mihova, Zlatka; Otten, Roy; Pez, Ondine

2017-01-01

Children's fear of a car accident occurring to parents or themselves has been used as a concrete example to illustrate one of the symptoms of anxiety disorders such as separation anxiety and generalized anxiety. However, its usage across countries may be questionable where the prevalence of this specific type of injury differs. This cross-sectional study compares samples from seven diverse European countries (Bulgaria, Germany, Italy, Lithuania, Netherlands, Romania, Turkey) to see if an environmental exposure, car accident death rate per 100,000 people (country-wide from WHO data), is associated with children's self-report of car accident fears. In this study, 6-11 year-old children were surveyed by a diagnostic instrument (Dominic Interactive) about several situations and asked if they believed they were similar to a fictional child depicted in said situations. Mothers were surveyed for additional sociodemographic information. Multivariable logistic regression was used to adjust for covariates including mother's age, mother's education, single parenting, and mother's professional inactivity. We report a monotonic relationship between higher car accident death rates and the prevalence of children reporting fear of parent's or own accident. Relative to a reference of 3.9 deaths per 100,000 people, children's odds of reporting fear of parent's accident ranged from 1.99 (95% CI 1.51-2.61) times to 4.84 (95% CI 3.68-6.37) times as the risk of death by car accident increased across countries. A similar result arose from fear of child's own accident, with significant ORs ranging from 1.91 (95% CI 1.53-2.40) to 2.68 (95% CI 2.07-3.47) alongside increased death rates. Given that reporting of these fears accompanies correspondingly high accident death rates, the pertinence of using fear of car accidents as an illustration for some diagnostic item for mental disorders cross-nationally appears to be an issue.

Dominant Sequences of Human Major Histocompatibility Complex Conserved Extended Haplotypes from HLA-DQA2 to DAXX

PubMed Central

Larsen, Charles E.; Alford, Dennis R.; Trautwein, Michael R.; Jalloh, Yanoh K.; Tarnacki, Jennifer L.; Kunnenkeri, Sushruta K.; Fici, Dolores A.; Yunis, Edmond J.; Awdeh, Zuheir L.; Alper, Chester A.

2014-01-01

We resequenced and phased 27 kb of DNA within 580 kb of the MHC class II region in 158 population chromosomes, most of which were conserved extended haplotypes (CEHs) of European descent or contained their centromeric fragments. We determined the single nucleotide polymorphism and deletion-insertion polymorphism alleles of the dominant sequences from HLA-DQA2 to DAXX for these CEHs. Nine of 13 CEHs remained sufficiently intact to possess a dominant sequence extending at least to DAXX, 230 kb centromeric to HLA-DPB1. We identified the regions centromeric to HLA-DQB1 within which single instances of eight “common” European MHC haplotypes previously sequenced by the MHC Haplotype Project (MHP) were representative of those dominant CEH sequences. Only two MHP haplotypes had a dominant CEH sequence throughout the centromeric and extended class II region and one MHP haplotype did not represent a known European CEH anywhere in the region. We identified the centromeric recombination transition points of other MHP sequences from CEH representation to non-representation. Several CEH pairs or groups shared sequence identity in small blocks but had significantly different (although still conserved for each separate CEH) sequences in surrounding regions. These patterns partly explain strong calculated linkage disequilibrium over only short (tens to hundreds of kilobases) distances in the context of a finite number of observed megabase-length CEHs comprising half a population's haplotypes. Our results provide a clearer picture of European CEH class II allelic structure and population haplotype architecture, improved regional CEH markers, and raise questions concerning regional recombination hotspots. PMID:25299700

'It was a freak accident': an analysis of the labelling of injury events in the US press.

PubMed

Smith, Katherine C; Girasek, Deborah C; Baker, Susan P; Manganello, Jennifer A; Bowman, Stephen M; Samuels, Alicia; Gielen, Andrea C

2012-02-01

Given that the news media shape our understanding of health issues, a study was undertaken to examine the use by the US media of the expression 'freak accident' in relation to injury events. This analysis is intended to contribute to the ongoing consideration of lay conceptualisation of injuries as 'accidents'. LexisNexis Academic was used to search three purposively selected US news sources (Associated Press, New York Times and Philadelphia Inquirer) for the expression 'freak accident' over 5 years (2005-9). Textual analysis included both structured and open coding. Coding included measures for who used the expression within the story, the nature of the injury event and the injured person(s) being reported upon, incorporation of prevention information within the story and finally a phenomenological consideration of the uses and meanings of the expression within the story context. Results The search yielded a dataset of 250 human injury stories incorporating the term 'freak accident'. Injuries sustained by professional athletes dominated coverage (61%). Fewer than 10% of stories provided a clear and explicit injury prevention message. Stories in which journalists employed the expression 'freak accident' were less likely to include prevention information than stories in which the expression was used by people quoted in the story. Journalists who frame injury events as freak accidents may be an appropriate focus for advocacy efforts. Effective prevention messages should be developed and disseminated to accompany injury reporting in order to educate and protect the public.

10 CFR 963.13 - Preclosure suitability evaluation method.

Code of Federal Regulations, 2011 CFR

2011-01-01

... to evaluate whether the geologic repository is likely to comply with the applicable radiation... prevent or mitigate the effects of postulated Category 1 and 2 event sequences. The preclosure safety... prevent accidents. ...

A variational technique for smoothing flight-test and accident data

NASA Technical Reports Server (NTRS)

Bach, R. E., Jr.

1980-01-01

The problem of determining aircraft motions along a trajectory is solved using a variational algorithm that generates unmeasured states and forcing functions, and estimates instrument bias and scale-factor errors. The problem is formulated as a nonlinear fixed-interval smoothing problem, and is solved as a sequence of linear two-point boundary value problems, using a sweep method. The algorithm has been implemented for use in flight-test and accident analysis. Aircraft motions are assumed to be governed by a six-degree-of-freedom kinematic model; forcing functions consist of body accelerations and winds, and the measurement model includes aerodynamic and radar data. Examples of the determination of aircraft motions from typical flight-test and accident data are presented.

Qualification of safety-related electrical equipment in France. Methods, approach and test facilities

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

Raimondo, E.; Capman, J.L.; Herovard, M.

1985-05-01

Requirements for qualification of electrical equipment used in French-built nuclear power plants are stated in a national code, the RCC-E, or Regles de Construction et de Conception des Materiels Electriques. Under the RCC-E, safety related equipment is assigned to one of three different categories, according to location in the plant and anticipated normal, accident and post-accident behavior. Qualification tests differ for each category and procedures range in scope from the standard seismic test to the highly stringent VISA program, which specifies a predetermined sequence of aging, radiation, seismic and simulated accident testing. A network of official French test facilities wasmore » developed specifically to meet RCC-E requirements.« less

Assessment of an explosive LPG release accident: a case study.

PubMed

Bubbico, Roberto; Marchini, Mauro

2008-07-15

In the present paper, an accident occurred during a liquefied petroleum gas (LPG) tank filling activity has been taken into consideration. During the transfer of LPG from the source road tank car to the receiving fixed storage vessel, an accidental release of LPG gave rise to different final consequences ranging from a pool fire, to a fireball and to the catastrophic rupture of the tank with successive explosion of its contents. The sequence of events has been investigated by using some of the consequence calculation models most commonly adopted in risk analysis and accident investigation. On one hand, this allows to better understand the link between the various events of the accident. On the other hand, a comparison between the results of the calculations and the damages actually observed after the accident, allows to check the accuracy of the prediction models and to critically assess their validity. In particular, it was shown that the largest uncertainty is associated with the calculation of the energy involved in the physical expansion of the fluid (both liquid and vapor) after the catastrophic rupture of the tank.

[Scooter accidents in children at Aristide Le Dantec, Unversity Hospital of Dakar: a study of 74 cases].

PubMed

Mohamed, Azhar Salim; Ngom, Gabriel; Sow, Mamadou; Mbaye, Papa Alassane; Camara, Souleymane; Seck, Ndeye Fatou; Ndour, Oumar

2016-01-01

Scooter accidents are becoming more frequent in Dakar. The purpose of this study is to report the epidemiological and lesional aspects of these accidents on children in Dakar. A retrospective and descriptive study was conducted in Pediatric Surgery Unit of the Aristide Le Dantec Hospital in Dakar from January 1st, 2009 to December 31, 2011. Various parameters were studied. These parameters include: frequency, sociodemographic and lesional aspects. Scooter accidents represent 12% of highway accidents. They were more frequent in the day, from 12 am to 2 pm (27%) and in the night, from 6 pm to 8 pm (28.4%). They might occur every day but were more frequent during April (17.6%) and June (13.5%). They occurred mainly in the suburban district of Dakar (78%). The age group most affected was the one from 3 to 8 years (60.8%). Male gender was predominant (sex ratio 1.5). Pedestrians are the most vulnerable (93.2%). The fall was the dominant mechanism (98.7%). Lesions affected mainly the lower limb (51.1%) and were essentially constituted by fracture. The frequency of scooter accidents in children is related to the galloping urbanization and to the increase of the number of cars on the roads in the peninsula. Victims are essentially pedestrians and present most of the time fractures.

WHEN MODEL MEETS REALITY – A REVIEW OF SPAR LEVEL 2 MODEL AGAINST FUKUSHIMA ACCIDENT

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

Zhegang Ma

The Standardized Plant Analysis Risk (SPAR) models are a set of probabilistic risk assessment (PRA) models used by the Nuclear Regulatory Commission (NRC) to evaluate the risk of operations at U.S. nuclear power plants and provide inputs to risk informed regulatory process. A small number of SPAR Level 2 models have been developed mostly for feasibility study purpose. They extend the Level 1 models to include containment systems, group plant damage states, and model containment phenomenology and accident progression in containment event trees. A severe earthquake and tsunami hit the eastern coast of Japan in March 2011 and caused significantmore » damages on the reactors in Fukushima Daiichi site. Station blackout (SBO), core damage, containment damage, hydrogen explosion, and intensive radioactivity release, which have been previous analyzed and assumed as postulated accident progression in PRA models, now occurred with various degrees in the multi-units Fukushima Daiichi site. This paper reviews and compares a typical BWR SPAR Level 2 model with the “real” accident progressions and sequences occurred in Fukushima Daiichi Units 1, 2, and 3. It shows that the SPAR Level 2 model is a robust PRA model that could very reasonably describe the accident progression for a real and complicated nuclear accident in the world. On the other hand, the comparison shows that the SPAR model could be enhanced by incorporating some accident characteristics for better representation of severe accident progression.« less

Preliminary calculations related to the accident at Three Mile Island

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

Kirchner, W.L.; Stevenson, M.G.

This report discusses preliminary studies of the Three Mile Island Unit 2 (TMI-2) accident based on available methods and data. The work reported includes: (1) a TRAC base case calculation out to 3 hours into the accident sequence; (2) TRAC parametric calculations, these are the same as the base case except for a single hypothetical change in the system conditions, such as assuming the high pressure injection (HPI) system operated as designed rather than as in the accident; (3) fuel rod cladding failure, cladding oxidation due to zirconium metal-steam reactions, hydrogen release due to cladding oxidation, cladding ballooning, cladding embrittlement,more » and subsequent cladding breakup estimates based on TRAC calculated cladding temperatures and system pressures. Some conclusions of this work are: the TRAC base case accident calculation agrees very well with known system conditions to nearly 3 hours into the accident; the parametric calculations indicate that, loss-of-core cooling was most influenced by the throttling of High-Pressure Injection (HPI) flows, given the accident initiating events and the pressurizer electromagnetic-operated valve (EMOV) failing to close as designed; failure of nearly all the rods and gaseous fission product gas release from the failed rods is predicted to have occurred at about 2 hours and 30 minutes; cladding oxidation (zirconium-steam reaction) up to 3 hours resulted in the production of approximately 40 kilograms of hydrogen.« less

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

NASA Astrophysics Data System (ADS)

Ha, Taesung

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

United States Department of Energy severe accident research following the Fukushima Daiichi accidents

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

Farmer, M. T.; Corradini, M.; Rempe, J.

The U.S. Department of Energy (DOE) has played a major role in the U.S. response to the events at Fukushima Daiichi. During the first several weeks following the accident, U.S. assistance efforts were guided by results from a significant and diverse set of analyses. In the months that followed, a coordinated analysis activity aimed at gaining a more thorough understanding of the accident sequence was completed using laboratory-developed, system-level best-estimate accident analysis codes, while a parallel analysis was conducted by U.S. industry. A comparison of predictions for Unit 1 from these two studies indicated significant differences between MAAP and MELCORmore » results for key plant parameters, such as in-core hydrogen production. On that basis, a crosswalk was completed to determine the key modeling variations that led to these differences. In parallel with these activities, it became clear that there was a need to perform a technology gap evaluation on accident-tolerant components and severe accident analysis methodologies with the goal of identifying any data and/or knowledge gaps that may exist given the current state of light water reactor (LWR) severe accident research and augmented by insights from Fukushima. In addition, there is growing international recognition that data from Fukushima could significantly reduce uncertainties related to severe accident progression, particularly for boiling water reactors. On these bases, a group of U. S. experts in LWR safety and plant operations was convened by the DOE Office of Nuclear Energy (DOE-NE) to complete technology gap analysis and Fukushima forensics data needs identification activities. The results from these activities were used as the basis for refining DOE-NE's severe accident research and development (R&D) plan. Finally, this paper provides a high-level review of DOE-sponsored R&D efforts in these areas, including planned activities on accident-tolerant components and accident analysis methods.« less

United States Department of Energy severe accident research following the Fukushima Daiichi accidents

DOE PAGES

Farmer, M. T.; Corradini, M.; Rempe, J.; ...

2016-11-02

The U.S. Department of Energy (DOE) has played a major role in the U.S. response to the events at Fukushima Daiichi. During the first several weeks following the accident, U.S. assistance efforts were guided by results from a significant and diverse set of analyses. In the months that followed, a coordinated analysis activity aimed at gaining a more thorough understanding of the accident sequence was completed using laboratory-developed, system-level best-estimate accident analysis codes, while a parallel analysis was conducted by U.S. industry. A comparison of predictions for Unit 1 from these two studies indicated significant differences between MAAP and MELCORmore » results for key plant parameters, such as in-core hydrogen production. On that basis, a crosswalk was completed to determine the key modeling variations that led to these differences. In parallel with these activities, it became clear that there was a need to perform a technology gap evaluation on accident-tolerant components and severe accident analysis methodologies with the goal of identifying any data and/or knowledge gaps that may exist given the current state of light water reactor (LWR) severe accident research and augmented by insights from Fukushima. In addition, there is growing international recognition that data from Fukushima could significantly reduce uncertainties related to severe accident progression, particularly for boiling water reactors. On these bases, a group of U. S. experts in LWR safety and plant operations was convened by the DOE Office of Nuclear Energy (DOE-NE) to complete technology gap analysis and Fukushima forensics data needs identification activities. The results from these activities were used as the basis for refining DOE-NE's severe accident research and development (R&D) plan. Finally, this paper provides a high-level review of DOE-sponsored R&D efforts in these areas, including planned activities on accident-tolerant components and accident analysis methods.« less

A Multiplex PCR assay to differentiate between dog and red fox.

PubMed

Weissenberger, M; Reichert, W; Mattern, R

2011-11-01

Foxes are frequently the cause of car accidents in Baden-Württemberg (BW, Germany). The domestic dog (Canis familiaris) is in close relation to the red fox (Vulpes vulpes) and the silver fox which is a coat colour variant of the red fox. As insurance claims that involve accidents with animals require authentication, we analyzed frequency distribution and allele sizes in two canine microsatellite loci in 26 dogs (different breeds) and 19 red foxes of the region of BW, Germany. Moreover, sequencing analysis was performed. Red foxes exhibited only 1 allele at each microsatellite locus, whereas in dog 7 alleles at the CPH4 locus and 6 alleles at the CPH12 locus were detected. Sequences of PCR products from the two species revealed several differences between dogs and foxes. We established a sequenced allelic ladder and give population data from dogs and red foxes from the region of BW, Germany. Using microsatellite polymorphisms is efficient in differentiating between dogs and foxes in forensic casework. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

[Stones crushing lives: victims and their widows in the marble industry in Itaoca (ES)].

PubMed

Moulin, Maria das Graças Barbosa; Minayo-Gomez, Carlos

2008-01-01

This text based on an ethnographic survey presents the social impact on the families of victims of fatal work accidents in the ornamental stone industry in Itaoca, district of Cachoeiro de Itapemirim, Espírito Santo, Brazil. The following elements are analyzed: family culture; living with fatal accidents; experiences of family grief; the way the companies and the union deal with worker rights; material, symbolic, and emotional resources used by the families to face hardship caused by accidents. Authoritarian management appealing to masculinity and improvisation are factors that favor work accidents. The need to earn their living, the fact of valuing work as an attribute of honorableness and lack of options render the workers subject to domination. Most of the widows are highly religious and receive emotional, symbolic and material support from their families, the community and the union. There is a notable lack of concern and support for the families on the part of managers and public institutions. Advances in the organization of the union and improvement of the working conditions forced by the demands of export buyers have occurred recently.

[Epidemiological aspects of spinal traumas: about 139 cases].

PubMed

Bemora, Joseph Synèse; Rakotondraibe, Willy Francis; Ramarokoto, Mijoro; Ratovondrainy, Willy; Andriamamonjy, Clément

2017-01-01

Spinal trauma is one of the most common types of injuries among victims of traffic accidents, sports accidents, domestic accidents and workplace accidents. We conducted a 3-year retrospective study of 139 cases of spinal trauma hospitalized and treated in the Neurosurgery department of the CHUJRA, Madagascar. This study shows that 25.17% of injured patients were between 21 and 30 years of age, with a clear male predominance (69.78%; sex ratio 2.3). Falls were the dominating traumatic injury mechanism (33.09%) with risk factors including alcohol use (8.63%). Spinal injuries occurred in patients with polytrauma, of whom 34.63% had cranial trauma. Patients were admitted to the department within 1-5 hours after the trauma in 31.65% of cases, using private car as their means of transport 36.69% of cases. During the hospitalization 20 patients signed the discharge form and 6.34% of patients died. Spinal trauma is a public health problem requiring high intensity management, especially for patients with life-long disabilities. Any spine trauma requires a diligent search for cranial lesion.

Climate change and safety at work with ionizing radiations.

PubMed

Contessa, Gian Marco; Grandi, Carlo; Scognamiglio, Mario; Genovese, Elisabetta; Sandri, Sandro

2016-01-01

The accident at Tokyo Electric Power Company's (TEPCO's) Fukushima Daiichi nuclear power plant (NPP) has been one of the dominant topic in nuclear safety and it has brought new attention on the matter of accidents in NPPs due to external events related to natural causes. Climate change has risen new risks and the growing probability of extreme external events has increased exposure and vulnerability of workers in the nuclear sector. However extreme natural events are a threat not only to NPPs but to all facilities dealing with radioactive material and in an emergency scenario they can affect the effectiveness and implementation of safety devices and procedures and also prevent communications, causing delays in the readiness of response. It is clear that adaptation strategies are necessary to cope with emerging changes in climate and a new nuclear safety culture is growing, that addresses accidents initiated not only by internal but also by external events.

The Initial Atmospheric Transport (IAT) Code: Description and Validation

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

Morrow, Charles W.; Bartel, Timothy James

The Initial Atmospheric Transport (IAT) computer code was developed at Sandia National Laboratories as part of their nuclear launch accident consequences analysis suite of computer codes. The purpose of IAT is to predict the initial puff/plume rise resulting from either a solid rocket propellant or liquid rocket fuel fire. The code generates initial conditions for subsequent atmospheric transport calculations. The Initial Atmospheric Transfer (IAT) code has been compared to two data sets which are appropriate to the design space of space launch accident analyses. The primary model uncertainties are the entrainment coefficients for the extended Taylor model. The Titan 34Dmore » accident (1986) was used to calibrate these entrainment settings for a prototypic liquid propellant accident while the recent Johns Hopkins University Applied Physics Laboratory (JHU/APL, or simply APL) large propellant block tests (2012) were used to calibrate the entrainment settings for prototypic solid propellant accidents. North American Meteorology (NAM )formatted weather data profiles are used by IAT to determine the local buoyancy force balance. The IAT comparisons for the APL solid propellant tests illustrate the sensitivity of the plume elevation to the weather profiles; that is, the weather profile is a dominant factor in determining the plume elevation. The IAT code performed remarkably well and is considered validated for neutral weather conditions.« less

The burden of road traffic accidents in a French Departement: the description of the injuries and recent changes

PubMed Central

Lapostolle, Annabelle; Gadegbeku, Blandine; Ndiaye, Amina; Amoros, Emmanuelle; Chiron, Mireille; Spira, Alfred; Laumon, Bernard

2009-01-01

Background A significant reduction in road traffic accidents has been observed since prevention measures were introduced by the French public authorities in 2002. The goals of this study are to describe the burden of road traffic accidents in a French Departement, and to identify changes if any between the periods 1997-2001 and 2002-2006 on the basis of the disability adjusted life years (DALY). Methods Years of lost life (YLL) and years lived with disability (YLD) were calculated for two periods using the mortality and incidence data in the Rhone Departement Registry of Road Traffic Accident Casualties. Results YLD and YLL that are related to road traffic accidents are at their maximum value between 15 and 24 years of age. For men, intracranial fractures and intracranial injuries dominate, and for women it is spinal cord injuries that account for highest rates of YLD. A reduction in the rates of YLL and YLD has been observed for both genders and all age groups between 1997-2001 and 2002-2006. Conclusion The reduction in DALY between the two periods is explained both by the reduction in the number of fatalities and injuries but also by an increase in the age at which they occur. PMID:19825170

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

Sattison, M.B.; Schroeder, J.A.; Russell, K.D.

The Idaho National Engineering Laboratory (INEL) over the past year has created 75 plant-specific Accident Sequence Precursor (ASP) models using the SAPHIRE suite of PRA codes. Along with the new models, the INEL has also developed a new module for SAPHIRE which is tailored specifically to the unique needs of ASP evaluations. These models and software will be the next generation of risk tools for the evaluation of accident precursors by both NRR and AEOD. This paper presents an overview of the models and software. Key characteristics include: (1) classification of the plant models according to plant response with amore » unique set of event trees for each plant class, (2) plant-specific fault trees using supercomponents, (3) generation and retention of all system and sequence cutsets, (4) full flexibility in modifying logic, regenerating cutsets, and requantifying results, and (5) user interface for streamlined evaluation of ASP events.« less

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

Sattison, M.B.; Schroeder, J.A.; Russell, K.D.

The Idaho National Engineering Laboratory (INEL) over the past year has created 75 plant-specific Accident Sequence Precursor (ASP) models using the SAPHIRE suite of PRA codes. Along with the new models, the INEL has also developed a new module for SAPHIRE which is tailored specifically to the unique needs of conditional core damage probability (CCDP) evaluations. These models and software will be the next generation of risk tools for the evaluation of accident precursors by both NRR and AEOD. This paper presents an overview of the models and software. Key characteristics include: (1) classification of the plant models according tomore » plant response with a unique set of event trees for each plant class, (2) plant-specific fault trees using supercomponents, (3) generation and retention of all system and sequence cutsets, (4) full flexibility in modifying logic, regenerating cutsets, and requantifying results, and (5) user interface for streamlined evaluation of ASP events.« less

To Err is Human Case Reports of Two Military Aircraft Accidents

PubMed Central

Dikshit, Mohan B

2010-01-01

It has been postulated that pilot error or in-flight incapacitation may be the main contributory factors to 70–80% of aircraft accidents. Two fatal aircraft accidents are presented in which either of the above possibilities may have played a role. The first case report describes an erroneous decision by a fighter pilot to use a seat position adjustment of the ejection seat leading to fatal injuries when he had to eject from his aircraft. Injuries to the body of the pilot, and observations on the state of his flying clothing and the ejection seat were used to postulate the mechanism of fatal injury and establish the cause of the accident. The second case report describes the sequence of events which culminated in the incapacitation of a fighter pilot while executing a routine manouevre. This resulted in a fatal air crash. Possible contributions of environmental factors which may have resulted in failure of his physiological mechanisms are discussed. PMID:21509093

Deep Borehole Emplacement Mode Hazard Analysis Revision 0

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

Sevougian, S. David

This letter report outlines a methodology and provides resource information for the Deep Borehole Emplacement Mode Hazard Analysis (DBEMHA). The main purpose is identify the accident hazards and accident event sequences associated with the two emplacement mode options (wireline or drillstring), to outline a methodology for computing accident probabilities and frequencies, and to point to available databases on the nature and frequency of accidents typically associated with standard borehole drilling and nuclear handling operations. Risk mitigation and prevention measures, which have been incorporated into the two emplacement designs (see Cochran and Hardin 2015), are also discussed. A key intent ofmore » this report is to provide background information to brief subject matter experts involved in the Emplacement Mode Design Study. [Note: Revision 0 of this report is concentrated more on the wireline emplacement mode. It is expected that Revision 1 will contain further development of the preliminary fault and event trees for the drill string emplacement mode.]« less

The Viareggio LPG railway accident: event reconstruction and modeling.

PubMed

Brambilla, Sara; Manca, Davide

2010-10-15

This manuscript describes in detail the LPG accident occurred in Viareggio on June 2009 and its modeling. The accident investigation highlighted the uncertainty and complexity of assessing and modeling what happened in the congested environment close to the Viareggio railway station. Nonetheless, the analysis allowed comprehending the sequence of events, the way they influenced each other, and the different possible paths/evolutions. The paper describes suitable models for the quantitative assessment of the consequences of the most probable accidental dynamics and its outcomes. The main finding is that after about 80 s from the beginning of the release the dense-gas cloud reached the surrounding houses that were destroyed successively by internal explosions. This fact has two main implications. First, it shows that the adopted modeling framework can give a correct picture of what happened in Viareggio. Second, it confirms the need to develop effective mitigation measures because, in case of this kind of accidents, there is no time to apply any protective emergency plans/actions. 2010 Elsevier B.V. All rights reserved.

Is Racism in Education an Accident?

ERIC Educational Resources Information Center

Apple, Michael W.

2009-01-01

People live in a time where neoliberal positions, with their assumption that private is good and public is bad, are dominant. Yet, as the author and others have demonstrated, such positions consistently privilege particular and identifiable classed and raced groups. This is not accidental. Society, like many others throughout the world, is…

The Application of Next-Generation Sequencing for Mutation Detection in Autosomal-Dominant Hereditary Hearing Impairment.

PubMed

Gürtler, Nicolas; Röthlisberger, Benno; Ludin, Katja; Schlegel, Christoph; Lalwani, Anil K

2017-07-01

Identification of the causative mutation using next-generation sequencing in autosomal-dominant hereditary hearing impairment, as mutation analysis in hereditary hearing impairment by classic genetic methods, is hindered by the high heterogeneity of the disease. Two Swiss families with autosomal-dominant hereditary hearing impairment. Amplified DNA libraries for next-generation sequencing were constructed from extracted genomic DNA, derived from peripheral blood, and enriched by a custom-made sequence capture library. Validated, pooled libraries were sequenced on an Illumina MiSeq instrument, 300 cycles and paired-end sequencing. Technical data analysis was performed with SeqMonk, variant analysis with GeneTalk or VariantStudio. The detection of mutations in genes related to hearing loss by next-generation sequencing was subsequently confirmed using specific polymerase-chain-reaction and Sanger sequencing. Mutation detection in hearing-loss-related genes. The first family harbored the mutation c.5383+5delGTGA in the TECTA-gene. In the second family, a novel mutation c.2614-2625delCATGGCGCCGTG in the WFS1-gene and a second mutation TCOF1-c.1028G>A were identified. Next-generation sequencing successfully identified the causative mutation in families with autosomal-dominant hereditary hearing impairment. The results helped to clarify the pathogenic role of a known mutation and led to the detection of a novel one. NGS represents a feasible approach with great potential future in the diagnostics of hereditary hearing impairment, even in smaller labs.

How propeller suction is the dominant factor for ship accidents at shallow water conditions

NASA Astrophysics Data System (ADS)

Acar, Dursun; Alpar, Bedri; Ozeren, Sinan

2017-04-01

The laminar flow comes to the fore with the disappearance of the several other directions in the internal displacements in the water current. Due to the dominant speed direction during the straightforward motion of the ship, the underwater hull is associated with the continuous flow of laminar currents. The open marine environment acts as a compressible liquid medium because of the presence of many variables about water volume overflow boundaries where the ship is associated. Layers of water rising over the sea surface due to ship's body and the propeller's water push provides loss of liquid lifting force for the ship. These situations change the well-known sea-floor morphology and reliable depth limits, and lead to probable accidents. If the ship block coefficient for the front side is 0.7 or higher, the "squat" will be more on the bow, because the associated factor "displacement volume" causes to the low-pressure environment due to large and rapid turbulence. Thus, the bow sinks further, which faced with liquid's weaker lift force. The vessels Gerardus Mercator, Queen Elizabeth and Costa Concordia had accidents because of unified reasons of squat, fast water mass displacement by hull push and propeller suction interaction. In the case of water mass displacement from the bow side away, that accident occurred in 2005 by the vessel Gerardus Mercator with excessive longitudinal trim angularity in the shallow water. The vessel Costa Concordia (2012), voluminous water displaced from the rear left side was an important factor because of the sharp manoeuvre of that the captain made before the accident. Observations before the accident indicate that full-speed sharp turn provided listed position for the ship from left (port side) in the direction of travel before colliding and then strike a rock on the sloping side of the seabed. The reason why the ship drifted to the left depends mainly the water discharge occurred at the left side of the hull during left-hand rudder control. Additionally the second water drainage from the shallow ridge area by the propeller's left-directed suction created a shallower environment. Similar situation for example collision of two ships during their side by side forward motions; their positions will be approached and listed to each other more same as downslope movement because of the shared area's water level collapse occur more by two propeller's suction.

Station Blackout at Browns Ferry Unit One - accident sequence analysis. Volume 1

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

Cook, D.H.; Harrington, R.M.; Greene, S.R.

1981-11-01

This study describes the predicted response of Unit 1 at the Browns Ferry Nuclear Plant to Station Blackout, defined as a loss of offsite power combined with failure of all onsite emergency diesel-generators to start and load. Every effort has been made to employ the most realistic assumptions during the process of defining the sequence of events for this hypothetical accident. DC power is assumed to remain available from the unit batteries during the initial phase and the operator actions and corresponding events during this period are described using results provided by an analysis code developed specifically for this purpose.more » The Station Blackout is assumed to persist beyond the point of battery exhaustion and the events during this second phase of the accident in which dc power would be unavailable were determined through use of the MARCH code. Without dc power, cooling water could no longer be injected into the reactor vessel and the events of the second phase include core meltdown and subsequent containment failure. An estimate of the magnitude and timing of the concomitant release of the noble gas, cesium, and iodine-based fission products to the environment is provided in Volume 2 of this report. 58 refs., 75 figs., 8 tabs.« less

[Epidemiological, clinical and therapeutic aspects of blunt abdominal trauma in patients undergoing surgery at the General Hospital of National Reference of N'Djamena, Chad: about 49 cases].

PubMed

Choua, Ouchemi; Rimtebaye, Kimassoum; Yamingue, Ngueidjo; Moussa, Kalli; Kaboro, Mignagnal

2017-01-01

Blunt abdominal traumas are common. We retrospectively reviewed the medical records of 49 patients with blunt abdominal trauma who underwent surgery at the General Hospital of National Reference of N'Djamena, Chad over a period of 5 years. Epidemiological, clinical and therapeutic parameters of patients were studied. The study included 42 men and 7 women, mean age 21.3 years. The causes of blunt abdominal traumas were: road traffic accidents in 61.2% of cases; wall collapses (14.3%); assaults (8.2%). Blunt abdominal traumas were more frequent in August (14.28%) and October (16.32%). The waiting time for admission in hospital was 6-12h in 43% of cases. At discharge, wounded patients used private car in 85.7% of cases. Clinically, patients were often hemodynamically stable (55.1%). Medical imaging was dominated by direct radiography of the abdomen (57.1%). The most observed lesions were those located only in the small intestine (16.32%) or related to that of the bladder (8.16%) and spleen (2.04%). Laparotomy was negative in 6.12% of cases. Morbidity (12.2%) was dominated by abdominal wall abscess. Mortality rate was 6.1%. Road traffic accidents are the leading cause of blunt abdominal traumas. It is important to minimize delays in diagnosis, and treatment. Road safety measures should be implemented to prevent accidents.

Preliminary Investigation of Time Remaining Display on the Computer-based Emergency Operating Procedure

NASA Astrophysics Data System (ADS)

Suryono, T. J.; Gofuku, A.

2018-02-01

One of the important thing in the mitigation of accidents in nuclear power plant accidents is time management. The accidents should be resolved as soon as possible in order to prevent the core melting and the release of radioactive material to the environment. In this case, operators should follow the emergency operating procedure related with the accident, in step by step order and in allowable time. Nowadays, the advanced main control rooms are equipped with computer-based procedures (CBPs) which is make it easier for operators to do their tasks of monitoring and controlling the reactor. However, most of the CBPs do not include the time remaining display feature which informs operators of time available for them to execute procedure steps and warns them if the they reach the time limit. Furthermore, the feature will increase the awareness of operators about their current situation in the procedure. This paper investigates this issue. The simplified of emergency operating procedure (EOP) of steam generator tube rupture (SGTR) accident of PWR plant is applied. In addition, the sequence of actions on each step of the procedure is modelled using multilevel flow modelling (MFM) and influenced propagation rule. The prediction of action time on each step is acquired based on similar case accidents and the Support Vector Regression. The derived time will be processed and then displayed on a CBP user interface.

Control Characteristics of Alcohol-Impaired Operators

NASA Technical Reports Server (NTRS)

Jex, Henry R.; McRuer, Duane T.; Allen, R. Wade; Klein, Richard H.

1974-01-01

Although the operation of vehicles like airplanes, cars, and bicycles involves a complex array of perceptual, decision and control activities, most accident statistics clearly show that intoxicated operators are a dominant cause of accidents, and not the difficulty of the task itself. This paper summarizes some recent research on the nature of the impairment of operator control under blood alcohol concentrations (BAC) up to above 0.16 percent. Alcohol toxicity is shown to be quite specific with respect to visual-motor functions involved in control of a vehicle, and experiments with a generalized workload task and special driving simulator show how these are reflected in terms of changes in operator control parameters such as response latency, gains, stability margins, and coherency.

[Autoerotic fatalities in Greater Dusseldorf].

PubMed

Hartung, Benno; Hellen, Florence; Borchard, Nora; Huckenbeck, Wolfgang

2011-01-01

Autoerotic fatalities in the Greater Dusseldorf area correspond to the relevant medicolegal literature. Our results included exclusively young to middle-aged, usually single men who were found dead in their city apartments. Clothing and devices used showed a great variety. Women's or fetish clothing and complex shackling or hanging devices were disproportionately frequent. In most cases, death occurred due to hanging or ligature strangulation. There was no increased incidence of underlying psychiatric disorders. In most of the deceased no or at least no remarkable alcohol intoxication was found. Occasionally, it may be difficult to reliably differentiate autoerotic accidents, accidents occurring in connection with practices of bondage & discipline, dominance & submission (BDSM) from natural death, suicide or homicide.

Examination of Icing Induced Loss of Control and Its Mitigations

NASA Technical Reports Server (NTRS)

Reehorst, Andrew L.; Addy, Harold E., Jr.; Colantonio, Renato O.

2010-01-01

Factors external to the aircraft are often a significant causal factor in loss of control (LOC) accidents. In today s aviation world, very few accidents stem from a single cause and typically have a number of causal factors that culminate in a LOC accident. Very often the "trigger" that initiates an accident sequence is an external environment factor. In a recent NASA statistical analysis of LOC accidents, aircraft icing was shown to be the most common external environmental LOC causal factor for scheduled operations. When investigating LOC accident or incidents aircraft icing causal factors can be categorized into groups of 1) in-flight encounter with super-cooled liquid water clouds, 2) take-off with ice contamination, or 3) in-flight encounter with high concentrations of ice crystals. As with other flight hazards, icing induced LOC accidents can be prevented through avoidance, detection, and recovery mitigations. For icing hazards, avoidance can take the form of avoiding flight into icing conditions or avoiding the hazard of icing by making the aircraft tolerant to icing conditions. Icing detection mitigations can take the form of detecting icing conditions or detecting early performance degradation caused by icing. Recovery from icing induced LOC requires flight crew or automated systems capable of accounting for reduced aircraft performance and degraded control authority during the recovery maneuvers. In this report we review the icing induced LOC accident mitigations defined in a recent LOC study and for each mitigation describe a research topic required to enable or strengthen the mitigation. Many of these research topics are already included in ongoing or planned NASA icing research activities or are being addressed by members of the icing research community. These research activities are described and the status of the ongoing or planned research to address the technology needs is discussed

Impact of longer-term modest climate shifts on architecture of high-frequency sequences (Cyclothems), Pennsylvanian of midcontinent U.S.A

USGS Publications Warehouse

Feldman, H.R.; Franseen, E.K.; Joeckel, R.M.; Heckel, P.H.

2005-01-01

Pennsylvanian glacioeustatic cyclothems exposed in Kansas and adjacent areas provide a unique opportunity to test models of the impact of relative sea level and climate on stratal architecture. A succession of eight of these high-frequency sequences, traced along dip for 500 km, reveal that modest climate shifts from relatively dry-seasonal to relatively wet-seasonal with a duration of several sequences (???600,000 to 1 million years) had a dominant impact on facies, sediment dispersal patterns, and sequence architecture. The climate shifts documented herein are intermediate, both in magnitude and duration, between previously documented longer-term climate shifts throughout much of the Pennsylvanian and shorter-term shifts described within individual sequences. Climate indicators are best preserved at sequence boundaries and in incised-valley fills of the lowstand systems tracts (LST). Relatively drier climate indicators include high-chroma paleosols, typically with pedogenic carbonates, and plant assemblages that are dominated by gymnosperms, mostly xerophytic walchian conifers. The associated valleys are small (4 km wide and >20 m deep), and dominated by quartz sandstones derived from distant source areas, reflecting large drainage networks. Transgressive systems tracts (TST) in all eight sequences gen erally are characterized by thin, extensive limestones and thin marine shales, suggesting that the dominant control on TST facies distribution was the sequestration of siliciclastic sediment in updip positions. Highstand systems tracts (HST) were significantly impacted by the intermediate-scale climate cycle in that HSTs from relatively drier climates consist of thin marine shales overlain by extensive, thick regressive limestones, whereas HSTs from relatively wetter climates are dominated by thick marine shales. Previously documented relative sea-level changes do not track the climate cycles, indicating that climate played a role distinct from that of relative sea-level change. These intermediate-scale modest climate shifts had a dominant impact on sequence architecture. This independent measure of climate and relative sea level may allow the testing of models of climate and sediment supply based on modern systems. Copyright ?? 2005, SEPM.

Recent plant studies using Victoria 2.0

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

BIXLER,NATHAN E.; GASSER,RONALD D.

2000-03-08

VICTORIA 2.0 is a mechanistic computer code designed to analyze fission product behavior within the reactor coolant system (RCS) during a severe nuclear reactor accident. It provides detailed predictions of the release of radioactive and nonradioactive materials from the reactor core and transport and deposition of these materials within the RCS and secondary circuits. These predictions account for the chemical and aerosol processes that affect radionuclide behavior. VICTORIA 2.0 was released in early 1999; a new version VICTORIA 2.1, is now under development. The largest improvements in VICTORIA 2.1 are connected with the thermochemical database, which is being revised andmore » expanded following the recommendations of a peer review. Three risk-significant severe accident sequences have recently been investigated using the VICTORIA 2.0 code. The focus here is on how various chemistry options affect the predictions. Additionally, the VICTORIA predictions are compared with ones made using the MELCOR code. The three sequences are a station blackout in a GE BWR and steam generator tube rupture (SGTR) and pump-seal LOCA sequences in a 3-loop Westinghouse PWR. These sequences cover a range of system pressures, from fully depressurized to full system pressure. The chief results of this study are the fission product fractions that are retained in the core, RCS, secondary, and containment and the fractions that are released into the environment.« less

Nuclear Power Plant Cyber Security Discrete Dynamic Event Tree Analysis (LDRD 17-0958) FY17 Report

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

Wheeler, Timothy A.; Denman, Matthew R.; Williams, R. A.

Instrumentation and control of nuclear power is transforming from analog to modern digital assets. These control systems perform key safety and security functions. This transformation is occurring in new plant designs as well as in the existing fleet of plants as the operation of those plants is extended to 60 years. This transformation introduces new and unknown issues involving both digital asset induced safety issues and security issues. Traditional nuclear power risk assessment tools and cyber security assessment methods have not been modified or developed to address the unique nature of cyber failure modes and of cyber security threat vulnerabilities.more » iii This Lab-Directed Research and Development project has developed a dynamic cyber-risk in- formed tool to facilitate the analysis of unique cyber failure modes and the time sequencing of cyber faults, both malicious and non-malicious, and impose those cyber exploits and cyber faults onto a nuclear power plant accident sequence simulator code to assess how cyber exploits and cyber faults could interact with a plants digital instrumentation and control (DI&C) system and defeat or circumvent a plants cyber security controls. This was achieved by coupling an existing Sandia National Laboratories nuclear accident dynamic simulator code with a cyber emulytics code to demonstrate real-time simulation of cyber exploits and their impact on automatic DI&C responses. Studying such potential time-sequenced cyber-attacks and their risks (i.e., the associated impact and the associated degree of difficulty to achieve the attack vector) on accident management establishes a technical risk informed framework for developing effective cyber security controls for nuclear power.« less

Les accidents de la vie courante chez l’enfant à Dakar: à propos de 201 cas

PubMed Central

Mohamed, Azhar Salim; Sagna, Aloïse; Fall, Mbaye; Ndoye, Ndeye Aby; Mbaye, Papa Alassane; Fall, Aimé Lakh; Diaby, Alou; Ndour, Oumar; Ngom, Gabriel

2017-01-01

Les accidents de la vie courante (AcVC) sont fréquents chez l’enfant et peuvent être à l’origine de lésions handicapantes et de décès. L’objectif de notre travail était d’étudier les aspects épidémiologiques et lésionnels des AcVC à Dakar. C’est une étude transversale descriptive menée du 1er Janvier 2013 au 30 juin 2013. Les enfants victimes d’accidents domestiques, d’accidents de sport et de loisirs ou d’accidents scolaires ont été inclus. Nous avons étudié des paramètres généraux et des paramètres ayant trait à chaque type d’AcVC. Deux cent et un enfants ont été inclus, ce qui représentait 27% des consultations aux urgences. Il y avait 148 garçons et 53 filles. Les enfants de moins de 5 ans étaient les plus touchés (37,8%). Le football et le jeu de lutte étaient les grands pourvoyeurs d’AcVC. Les AcVC survenaient principalement à domicile (58,2%) et dans les aires de sport et de loisirs (31,8%). Les fractures prédominaient dans les différents types d’AcVC: 54,9% des accidents domestiques, 68,8% des accidents de sport et de loisirs et 40% des accidents scolaires. Au plan épidémiologique, nos résultats sont superposables à la littérature. Les fractures prédominent à l’opposé de la littérature où les contusions sont prépondérantes. Le jeu de lutte est le plus grand pourvoyeur de ces fractures après le football. La connaissance des aspects épidémiologiques et lésionnels permet de mener des campagnes de prévention des AcVC à Dakar. PMID:29187941

Control of Industrial Safety Based on Dynamic Characteristics of a Safety Budget-Industrial Accident Rate Model in Republic of Korea.

PubMed

Choi, Gi Heung; Loh, Byoung Gook

2017-06-01

Despite the recent efforts to prevent industrial accidents in the Republic of Korea, the industrial accident rate has not improved much. Industrial safety policies and safety management are also known to be inefficient. This study focused on dynamic characteristics of industrial safety systems and their effects on safety performance in the Republic of Korea. Such dynamic characteristics are particularly important for restructuring of the industrial safety system. The effects of damping and elastic characteristics of the industrial safety system model on safety performance were examined and feedback control performance was explained in view of cost and benefit. The implications on safety policies of restructuring the industrial safety system were also explored. A strong correlation between the safety budget and the industrial accident rate enabled modeling of an industrial safety system with these variables as the input and the output, respectively. A more effective and efficient industrial safety system could be realized by having weaker elastic characteristics and stronger damping characteristics in it. A substantial decrease in total social cost is expected as the industrial safety system is restructured accordingly. A simple feedback control with proportional-integral action is effective in prevention of industrial accidents. Securing a lower level of elastic industrial accident-driving energy appears to have dominant effects on the control performance compared with the damping effort to dissipate such energy. More attention needs to be directed towards physical and social feedbacks that have prolonged cumulative effects. Suggestions for further improvement of the safety system including physical and social feedbacks are also made.

DNA Shape Dominates Sequence Affinity in Nucleosome Formation

NASA Astrophysics Data System (ADS)

Freeman, Gordon S.; Lequieu, Joshua P.; Hinckley, Daniel M.; Whitmer, Jonathan K.; de Pablo, Juan J.

2014-10-01

Nucleosomes provide the basic unit of compaction in eukaryotic genomes, and the mechanisms that dictate their position at specific locations along a DNA sequence are of central importance to genetics. In this Letter, we employ molecular models of DNA and proteins to elucidate various aspects of nucleosome positioning. In particular, we show how DNA's histone affinity is encoded in its sequence-dependent shape, including subtle deviations from the ideal straight B-DNA form and local variations of minor groove width. By relying on high-precision simulations of the free energy of nucleosome complexes, we also demonstrate that, depending on DNA's intrinsic curvature, histone binding can be dominated by bending interactions or electrostatic interactions. More generally, the results presented here explain how sequence, manifested as the shape of the DNA molecule, dominates molecular recognition in the problem of nucleosome positioning.

Hybrid and electric low-noise cars cause an increase in traffic accidents involving vulnerable road users in urban areas.

PubMed

Brand, Stephan; Petri, Maximilian; Haas, Philipp; Krettek, Christian; Haasper, Carl

2013-01-01

Due to resource scarcity, the number of low-noise and electric cars is expected to increase rapidly. The frequent use of these cars will lead to a significant reduction of traffic related noise and pollution. On the other hand, due to the adaption and conditioning of vulnerable road users the number of traffic accidents involving pedestrians and bicyclists is postulated to increase as well. Children, older people with reduced eyesight and the blind are especially reliant on a combination of acoustic and visual warning signals with approaching or accelerating vehicles. This is even more evident in urban areas where the engine sound is the dominating sound up to 30 kph (kilometres per hour). Above this, tyre-road interaction is the main cause of traffic noise. With the missing typical engine sound a new sound design is necessary to prevent traffic accidents in urban areas. Drivers should not be able to switch the sound generator off.

Mortality in first generation white immigrants in California, 1989-1999.

PubMed

Nasseri, Kiumarss

2008-06-01

To identify mortality differentials in the first generation non-Hispanic White (NHW) immigrants in California for 1989 through 1999. First generation NHW immigrants (107,432) were identified in California Death Certificate files by place of birth outside the US and were grouped into Anglo-Saxon dominant, Northern, Western, Eastern, and Southern Europe, former USSR, Arabs and non-Arab Middle Eastern areas. US-born NHW (1,480,347) were used as standard to determine proportional mortality ratios (PMR) for major causes of death including: cancers, coronary heart disease, cerebrovascular accidents, chronic obstructive pulmonary disease (COPD), HIV/AIDS, accidents, diabetes, pneumonia, suicide, and homicide. All immigrants had significantly higher PMR for suicide and with few exceptions for cardiovascular diseases. Lower PMR was recorded for COPD and homicide. No difference was noticed for pneumonia and accidents. Cancer deaths were generally higher in European immigrants. Mortality patterns of NHW immigrants reflect the mixed impacts of acculturation, ethnic-specific characteristics, and psychological well being.

Analysis of unmitigated large break loss of coolant accidents using MELCOR code

NASA Astrophysics Data System (ADS)

Pescarini, M.; Mascari, F.; Mostacci, D.; De Rosa, F.; Lombardo, C.; Giannetti, F.

2017-11-01

In the framework of severe accident research activity developed by ENEA, a MELCOR nodalization of a generic Pressurized Water Reactor of 900 MWe has been developed. The aim of this paper is to present the analysis of MELCOR code calculations concerning two independent unmitigated large break loss of coolant accident transients, occurring in the cited type of reactor. In particular, the analysis and comparison between the transients initiated by an unmitigated double-ended cold leg rupture and an unmitigated double-ended hot leg rupture in the loop 1 of the primary cooling system is presented herein. This activity has been performed focusing specifically on the in-vessel phenomenology that characterizes this kind of accidents. The analysis of the thermal-hydraulic transient phenomena and the core degradation phenomena is therefore here presented. The analysis of the calculated data shows the capability of the code to reproduce the phenomena typical of these transients and permits their phenomenological study. A first sequence of main events is here presented and shows that the cold leg break transient results faster than the hot leg break transient because of the position of the break. Further analyses are in progress to quantitatively assess the results of the code nodalization for accident management strategy definition and fission product source term evaluation.

Acting, Accidents and Performativity: Challenging the Hegemonic Good Student in Secondary Schools

ERIC Educational Resources Information Center

Thompson, Greg

2010-01-01

Current educational practice tends to ascribe a limiting vision of the good student as one who is well behaved, performs well in assessments and demonstrates values in keeping with dominant expectations. This paper argues that this vision of the good student is antithetical to the lived experience of students as they negotiate their positionality…

Conceptual design study of Fusion Experimental Reactor (FY86 FER): Safety

NASA Astrophysics Data System (ADS)

Seki, Yasushi; Iida, Hiromasa; Honda, Tsutomu

1987-08-01

This report describes the study on safety for FER (Fusion Experimental Reactor) which has been designed as a next step machine to the JT-60. Though the final purpose of this study is to have an image of design base accident, maximum credible accident and to assess their risk or probability, etc., as FER plant system, the emphasis of this years study is placed on fuel-gas circulation system where the tritium inventory is maximum. The report consists of two chapters. The first chapter summarizes the FER system and describes FMEA (Failure Mode and Effect Analysis) and related accident progression sequence for FER plant system as a whole. The second chapter of this report is focused on fuel-gas circulation system including purification, isotope separation and storage. Probability of risk is assessed by the probabilistic risk analysis (PRA) procedure based on FMEA, ETA and FTA.

Fukushima Accident: Sequence of Events and Lessons Learned

NASA Astrophysics Data System (ADS)

Morse, Edward C.

2011-10-01

The Fukushima Dai-Ichi nuclear power station suffered a devastating Richter 9.0 earthquake followed by a 14.0 m tsunami on 11 March 2011. The subsequent loss of power for emergency core cooling systems resulted in damage to the fuel in the cores of three reactors. The relief of pressure from the containment in these three reactors led to sufficient hydrogen gas release to cause explosions in the buildings housing the reactors. There was probably subsequent damage to a spent fuel pool of a fourth reactor caused by debris from one of these explosions. Resultant releases of fission product isotopes in air were significant and have been estimated to be in the 3 . 7 --> 6 . 3 ×1017 Bq range (~10 MCi) for 131I and 137Cs combined, or approximately one tenth that of the Chernobyl accident. A synopsis of the sequence of events leading up to this large release of radioactivity will be presented, along with likely scenarios for stabilization and site cleanup in the future. Some aspects of the isotope monitoring programs, both locally and at large, will also be discussed. An assessment of radiological health risk for the plant workers as well as the general public will also be presented. Finally, the impact of this accident on design and deployment of nuclear generating stations in the future will be discussed.

Evaluation of potential severe accidents during low power and shutdown operations at Surry, Unit 1: Analysis of core damage frequency from internal events during mid-loop operations, Appendices E (Sections E.1--E.8). Volume 2, Part 3A

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

Chu, T.L.; Musicki, Z.; Kohut, P.

1994-06-01

During 1989, the Nuclear Regulatory Commission (NRC) initiated an extensive program to carefully examine the potential risks during low power and shutdown operations. The program includes two parallel projects being performed by Brookhaven National Laboratory (BNL) and Sandia National Laboratories (SNL). Two plants, Surry (pressurized water reactor) and Grand Gulf (boiling water reactor), were selected as the plants to be studied. The objectives of the program are to assess the risks of severe accidents initiated during plant operational states other than full power operation and to compare the estimated core damage frequencies, important accident sequences and other qualitative and quantitativemore » results with those accidents initiated during full power operation as assessed in NUREG-1150. The objective of this report is to document the approach utilized in the Surry plant and discuss the results obtained. A parallel report for the Grand Gulf plant is prepared by SNL. This study shows that the core-damage frequency during mid-loop operation at the Surry plant is comparable to that of power operation. The authors recognize that there is very large uncertainty in the human error probabilities in this study. This study identified that only a few procedures are available for mitigating accidents that may occur during shutdown. Procedures written specifically for shutdown accidents would be useful.« less

Massive dominance of Epsilonproteobacteria in formation waters from a Canadian oil sands reservoir containing severely biodegraded oil

PubMed Central

Hubert, Casey R J; Oldenburg, Thomas B P; Fustic, Milovan; Gray, Neil D; Larter, Stephen R; Penn, Kevin; Rowan, Arlene K; Seshadri, Rekha; Sherry, Angela; Swainsbury, Richard; Voordouw, Gerrit; Voordouw, Johanna K; Head, Ian M

2012-01-01

Summary The subsurface microbiology of an Athabasca oil sands reservoir in western Canada containing severely biodegraded oil was investigated by combining 16S rRNA gene- and polar lipid-based analyses of reservoir formation water with geochemical analyses of the crude oil and formation water. Biomass was filtered from formation water, DNA was extracted using two different methods, and 16S rRNA gene fragments were amplified with several different primer pairs prior to cloning and sequencing or community fingerprinting by denaturing gradient gel electrophoresis (DGGE). Similar results were obtained irrespective of the DNA extraction method or primers used. Archaeal libraries were dominated by Methanomicrobiales (410 of 414 total sequences formed a dominant phylotype affiliated with a Methanoregula sp.), consistent with the proposed dominant role of CO2-reducing methanogens in crude oil biodegradation. In two bacterial 16S rRNA clone libraries generated with different primer pairs, > 99% and 100% of the sequences were affiliated with Epsilonproteobacteria (n = 382 and 72 total clones respectively). This massive dominance of Epsilonproteobacteria sequences was again obtained in a third library (99% of sequences; n = 96 clones) using a third universal bacterial primer pair (inosine-341f and 1492r). Sequencing of bands from DGGE profiles and intact polar lipid analyses were in accordance with the bacterial clone library results. Epsilonproteobacterial OTUs were affiliated with Sulfuricurvum, Arcobacter and Sulfurospirillum spp. detected in other oil field habitats. The dominant organism revealed by the bacterial libraries (87% of all sequences) is a close relative of Sulfuricurvum kujiense – an organism capable of oxidizing reduced sulfur compounds in crude oil. Geochemical analysis of organic extracts from bitumen at different reservoir depths down to the oil water transition zone of these oil sands indicated active biodegradation of dibenzothiophenes, and stable sulfur isotope ratios for elemental sulfur and sulfate in formation waters were indicative of anaerobic oxidation of sulfur compounds. Microbial desulfurization of crude oil may be an important metabolism for Epsilonproteobacteria indigenous to oil reservoirs with elevated sulfur content and may explain their prevalence in formation waters from highly biodegraded petroleum systems. PMID:21824242

Dynamic Changes of Photosynthetic Picoeukaryotes Composition in the Northwestern Pacific Ocean Revealed by High-Throughput Tag Sequencing of Plastid 16S rRNA Gene

NASA Astrophysics Data System (ADS)

Choi, D. H.; Noh, J. H.; Selph, K. E.; Lee, C. M.

2016-02-01

Photosynthetic picoeukaryotes (PPEs) are major oceanic primary producers. However, the diversity of such communities remains poorly understood, especially in the northwestern (NW) Pacific. We investigated the abundance and diversity of PPEs, and recorded environmental variables, along a transect from the coast to the open Pacific Ocean. High-throughput tag sequencing (using the MiSeq system) revealed the diversity of plastid 16S rRNA genes. The dominant PPEs changed at the class level along the transect. Prymnesiophyceae were the only dominant PPEs in the warm pool of the NW Pacific, but Mamiellophyceae dominated in coastal waters of the East China Sea. Phylogenetically, most Prymnesiophyceae sequences could not be resolved at lower taxonomic levels because no close relatives have been cultured. Within the Mamiellophyceae, the genera Micromonas and Ostreococcus dominated in marginal coastal areas affected by open water, whereas Bathycoccus dominated in the lower euphotic depths of open oligotrophic waters. Cryptophyceae and Phaeocystis (of the Prymnesiophyceae) dominated in areas affected principally by coastal water. We also defined the biogeographical distributions of Chrysophyceae, Prasinophyceae, Bacillariophyceaea, and Pelagophyceae. These distributions were influenced by temperature, salinity, and chlorophyll a and nutrient concentrations.

Rontgen's Discovery of X Rays

ERIC Educational Resources Information Center

Thumm, Walter

1975-01-01

Relates the story of Wilhelm Conrad Rontgen and presents one view of the extent to which the discovery of the x-ray was an accident. Reconstructs the sequence of events that led to the discovery and includes photographs of the lab where he worked and replicas of apparatus used. (GS)

Diabetes insipidus--diagnosis and management.

PubMed

Di Iorgi, Natascia; Napoli, Flavia; Allegri, Anna Elsa Maria; Olivieri, Irene; Bertelli, Enrica; Gallizia, Annalisa; Rossi, Andrea; Maghnie, Mohamad

2012-01-01

Central diabetes insipidus (CDI) is the end result of a number of conditions that affect the hypothalamic-neurohypophyseal system. The known causes include germinoma/craniopharyngioma, Langerhans cell histiocytosis (LCH), local inflammatory, autoimmune or vascular diseases, trauma resulting from surgery or an accident, sarcoidosis, metastases and midline cerebral and cranial malformations. In rare cases, the underlying cause can be genetic defects in vasopressin synthesis that are inherited as autosomal dominant, autosomal recessive or X-linked recessive traits. The diagnosis of the underlying condition is challenging and raises several concerns for patients and parents as it requires long-term follow-up. Proper etiological diagnosis can be achieved via a series of steps that start with clinical observations and then progress to more sophisticated tools. Specifically, MRI identification of pituitary hyperintensity in the posterior part of the sella, now considered a clear marker of neurohypophyseal functional integrity, together with the careful analysis of pituitary stalk shape and size, have provided the most striking findings contributing to the diagnosis and understanding of some forms of 'idiopathic' CDI. MRI STIR (short-inversion-time inversion recovery sequencing) is a promising technology for the early identification of LCH-dependent CDI. Copyright © 2012 S. Karger AG, Basel.

Sequence polymorphism in an insect RNA virus field population: A snapshot from a single point in space and time reveals stochastic differences among and within individual hosts

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

Stenger, Drake C., E-mail: drake.stenger@ars.usda.

Population structure of Homalodisca coagulata Virus-1 (HoCV-1) among and within field-collected insects sampled from a single point in space and time was examined. Polymorphism in complete consensus sequences among single-insect isolates was dominated by synonymous substitutions. The mutant spectrum of the C2 helicase region within each single-insect isolate was unique and dominated by nonsynonymous singletons. Bootstrapping was used to correct the within-isolate nonsynonymous:synonymous arithmetic ratio (N:S) for RT-PCR error, yielding an N:S value ~one log-unit greater than that of consensus sequences. Probability of all possible single-base substitutions for the C2 region predicted N:S values within 95% confidence limits of themore » corrected within-isolate N:S when the only constraint imposed was viral polymerase error bias for transitions over transversions. These results indicate that bottlenecks coupled with strong negative/purifying selection drive consensus sequences toward neutral sequence space, and that most polymorphism within single-insect isolates is composed of newly-minted mutations sampled prior to selection. -- Highlights: •Sampling protocol minimized differential selection/history among isolates. •Polymorphism among consensus sequences dominated by negative/purifying selection. •Within-isolate N:S ratio corrected for RT-PCR error by bootstrapping. •Within-isolate mutant spectrum dominated by new mutations yet to undergo selection.« less

Epilithic Cyanobacterial Communities of a Marine Tropical Beach Rock (Heron Island, Great Barrier Reef): Diversity and Diazotrophy▿

PubMed Central

Díez, Beatriz; Bauer, Karolina; Bergman, Birgitta

2007-01-01

The diversity and nitrogenase activity of epilithic marine microbes in a Holocene beach rock (Heron Island, Great Barrier Reef, Australia) with a proposed biological calcification “microbialite” origin were examined. Partial 16S rRNA gene sequences from the dominant mat (a coherent and layered pink-pigmented community spread over the beach rock) and biofilms (nonstratified, differently pigmented microbial communities of small shallow depressions) were retrieved using denaturing gradient gel electrophoresis (DGGE), and a clone library was retrieved from the dominant mat. The 16S rRNA gene sequences and morphological analyses revealed heterogeneity in the cyanobacterial distribution patterns. The nonheterocystous filamentous genus Blennothrix sp., phylogenetically related to Lyngbya, dominated the mat together with unidentified nonheterocystous filaments of members of the Pseudanabaenaceae and the unicellular genus Chroococcidiopsis. The dominance and three-dimensional intertwined distribution of these organisms were confirmed by nonintrusive scanning microscopy. In contrast, the less pronounced biofilms were dominated by the heterocystous cyanobacterial genus Calothrix, two unicellular Entophysalis morphotypes, Lyngbya spp., and members of the Pseudanabaenaceae family. Cytophaga-Flavobacterium-Bacteroides and Alphaproteobacteria phylotypes were also retrieved from the beach rock. The microbial diversity of the dominant mat was accompanied by high nocturnal nitrogenase activities (as determined by in situ acetylene reduction assays). A new DGGE nifH gene optimization approach for cyanobacterial nitrogen fixers showed that the sequences retrieved from the dominant mat were related to nonheterocystous uncultured cyanobacterial phylotypes, only distantly related to sequences of nitrogen-fixing cultured cyanobacteria. These data stress the occurrence and importance of nonheterocystous epilithic cyanobacteria, and it is hypothesized that such epilithic cyanobacteria are the principal nitrogen fixers of the Heron Island beach rock. PMID:17416688

A complex dominance hierarchy is controlled by polymorphism of small RNAs and their targets.

PubMed

Yasuda, Shinsuke; Wada, Yuko; Kakizaki, Tomohiro; Tarutani, Yoshiaki; Miura-Uno, Eiko; Murase, Kohji; Fujii, Sota; Hioki, Tomoya; Shimoda, Taiki; Takada, Yoshinobu; Shiba, Hiroshi; Takasaki-Yasuda, Takeshi; Suzuki, Go; Watanabe, Masao; Takayama, Seiji

2016-12-22

In diploid organisms, phenotypic traits are often biased by effects known as Mendelian dominant-recessive interactions between inherited alleles. Phenotypic expression of SP11 alleles, which encodes the male determinants of self-incompatibility in Brassica rapa, is governed by a complex dominance hierarchy 1-3 . Here, we show that a single polymorphic 24 nucleotide small RNA, named SP11 methylation inducer 2 (Smi2), controls the linear dominance hierarchy of the four SP11 alleles (S 44 > S 60 > S 40 > S 29 ). In all dominant-recessive interactions, small RNA variants derived from the linked region of dominant SP11 alleles exhibited high sequence similarity to the promoter regions of recessive SP11 alleles and acted in trans to epigenetically silence their expression. Together with our previous study 4 , we propose a new model: sequence similarity between polymorphic small RNAs and their target regulates mono-allelic gene expression, which explains the entire five-phased linear dominance hierarchy of the SP11 phenotypic expression in Brassica.

Evaluation of potential severe accidents during low power and shutdown operations at Surry, Unit 1: Analysis of core damage frequency from internal events during mid-loop operations, Appendices A--D. Volume 2, Part 2

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

Chu, T.L.; Musicki, Z.; Kohut, P.

1994-06-01

During 1989, the Nuclear Regulatory Commission (NRC) initiated an extensive program to carefully examine the Potential risks during low Power and shutdown operations. The program includes two parallel projects being performed by Brookhaven National Laboratory (BNL) and Sandia National Laboratories (SNL). Two plants, Surry (pressurized water reactor) and Grand Gulf (boiling water reactor), were selected as the Plants to be studied. The objectives of the program are to assess the risks of severe accidents initiated during plant operational states other than full power operation and to compare the estimated core damage frequencies, important accident sequences and other qualitative and quantitativemore » results with those accidents initiated during full power operation as assessed in NUREG-1150. The objective of this report is to document the approach utilized in the Surry plant and discuss the results obtained. A parallel report for the Grand Gulf plant is prepared by SNL. This study shows that the core-damage frequency during mid-loop operation at the Surry plant is comparable to that of power operation. We recognize that there is very large uncertainty in the human error probabilities in this study. This study identified that only a few procedures are available for mitigating accidents that may occur during shutdown. Procedures written specifically for shutdown accidents would be useful. This document, Volume 2, Pt. 2 provides appendices A through D of this report.« less

Dynamic changes in the composition of photosynthetic picoeukaryotes in the northwestern Pacific Ocean revealed by high-throughput tag sequencing of plastid 16S rRNA genes.

PubMed

Choi, Dong H; An, Sung M; Chun, Sungjun; Yang, Eun C; Selph, Karen E; Lee, Charity M; Noh, Jae H

2016-02-01

Photosynthetic picoeukaryotes (PPEs) are major oceanic primary producers. However, the diversity of such communities remains poorly understood, especially in the northwestern (NW) Pacific. We investigated the abundance and diversity of PPEs, and recorded environmental variables, along a transect from the coast to the open Pacific Ocean. High-throughput tag sequencing (using the MiSeq system) revealed the diversity of plastid 16S rRNA genes. The dominant PPEs changed at the class level along the transect. Prymnesiophyceae were the only dominant PPEs in the warm pool of the NW Pacific, but Mamiellophyceae dominated in coastal waters of the East China Sea. Phylogenetically, most Prymnesiophyceae sequences could not be resolved at lower taxonomic levels because no close relatives have been cultured. Within the Mamiellophyceae, the genera Micromonas and Ostreococcus dominated in marginal coastal areas affected by open water, whereas Bathycoccus dominated in the lower euphotic depths of oligotrophic open waters. Cryptophyceae and Phaeocystis (of the Prymnesiophyceae) dominated in areas affected principally by coastal water. We also defined the biogeographical distributions of Chrysophyceae, prasinophytes, Bacillariophyceaea and Pelagophyceae. These distributions were influenced by temperature, salinity and chlorophyll a and nutrient concentrations. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Station blackout calculations for Browns Ferry

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

Ott, L.J.; Weber, C.F.; Hyman, C.R.

1985-01-01

This paper presents the results of calculations performed with the ORNL SASA code suite for the Station Blackout Severe Accident Sequence at Browns Ferry. The accident is initiated by a loss of offsite power combined with failure of all onsite emergency diesel generators to start and load. The Station Blackout is assumed to persist beyond the point of battery exhaustion (at six hours) and without DC power, cooling water could no longer be injected into the reactor vessel. Calculations are continued through the period of core degradation and melting, reactor vessel failure, and the subsequent containment failure. An estimate ofmore » the magnitude and timing of the concomitant fission product releases is also provided.« less

Manned space flight nuclear system safety. Volume 3: Reactor system preliminary nuclear safety analysis. Part 2A: Accident model document, appendix

NASA Technical Reports Server (NTRS)

1972-01-01

The detailed abort sequence trees for the reference zirconium hydride (ZrH) reactor power module that have been generated for each phase of the reference Space Base program mission are presented. The trees are graphical representations of causal sequences. Each tree begins with the phase identification and the dichotomy between success and failure. The success branch shows the mission phase objective as being achieved. The failure branch is subdivided, as conditions require, into various primary initiating abort conditions.

Timing, sequencing, and executive control in repetitive movement production.

PubMed

Krampe, Ralf Th; Mayr, Ulrich; Kliegl, Reinhold

2005-06-01

The authors demonstrate that the timing and sequencing of target durations require low-level timing and executive control. Sixteen young (M-sub(age) = 19 years) and 16 older (M-sub(age) = 70 years) adults participated in 2 experiments. In Experiment 1, individual mean-variance functions for low-level timing (isochronous tapping) and the sequencing of multiple targets (rhythm production) revealed (a) a dissociation of low-level timing and sequencing in both age groups, (b) negligible age differences for low-level timing, and (c) large age differences for sequencing. Experiment 2 supported the distinction between low-level timing and executive functions: Selection against a dominant rhythm and switching between rhythms impaired performances in both age groups and induced pronounced perseveration of the dominant pattern in older adults. ((c) 2005 APA, all rights reserved).

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

Sattison, M.B.

The Idaho National Engineering Laboratory (INEL) over the three years has created 75 plant-specific Accident Sequence Precursor (ASP) models using the SAPHIRE suite of PRA codes. Along with the new models, the INEL has also developed a new module for SAPHIRE which is tailored specifically to the unique needs of ASP evaluations. These models and software will be the next generation of risk tools for the evaluation of accident precursors by both the U.S. Nuclear Regulatory Commission`s (NRC`s) Office of Nuclear Reactor Regulation (NRR) and the Office for Analysis and Evaluation of Operational Data (AEOD). This paper presents an overviewmore » of the models and software. Key characteristics include: (1) classification of the plant models according to plant response with a unique set of event trees for each plant class, (2) plant-specific fault trees using supercomponents, (3) generation and retention of all system and sequence cutsets, (4) full flexibility in modifying logic, regenerating cutsets, and requantifying results, and (5) user interface for streamlined evaluation of ASP events. Future plans for the ASP models is also presented.« less

How life changes itself: the Read-Write (RW) genome.

PubMed

Shapiro, James A

2013-09-01

The genome has traditionally been treated as a Read-Only Memory (ROM) subject to change by copying errors and accidents. In this review, I propose that we need to change that perspective and understand the genome as an intricately formatted Read-Write (RW) data storage system constantly subject to cellular modifications and inscriptions. Cells operate under changing conditions and are continually modifying themselves by genome inscriptions. These inscriptions occur over three distinct time-scales (cell reproduction, multicellular development and evolutionary change) and involve a variety of different processes at each time scale (forming nucleoprotein complexes, epigenetic formatting and changes in DNA sequence structure). Research dating back to the 1930s has shown that genetic change is the result of cell-mediated processes, not simply accidents or damage to the DNA. This cell-active view of genome change applies to all scales of DNA sequence variation, from point mutations to large-scale genome rearrangements and whole genome duplications (WGDs). This conceptual change to active cell inscriptions controlling RW genome functions has profound implications for all areas of the life sciences. © 2013 Elsevier B.V. All rights reserved.

Phenotypic and genotypic expression of self-incompatibility haplotypes in Arabidopsis lyrata suggests unique origin of alleles in different dominance classes.

PubMed

Prigoda, Nadia L; Nassuth, Annette; Mable, Barbara K

2005-07-01

The highly divergent alleles of the SRK gene in outcrossing Arabidopsis lyrata have provided important insights into the evolutionary history of self-incompatibility (SI) alleles and serve as an ideal model for studies of the evolutionary and molecular interactions between alleles in cell-cell recognition systems in general. One tantalizing question is how new specificities arise in systems that require coordination between male and female components. Allelic recruitment via gene conversion has been proposed as one possibility, based on the division of DNA sequences at the SRK locus into two distinctive groups: (1) sequences whose relationships are not well resolved and display the long branch lengths expected for a gene under balancing selection (Class A); and (2) sequences falling into a well-supported group with shorter branch lengths (Class B) that are closely related to an unlinked paralogous locus. The purpose of this study was to determine if differences in phenotype (site of expression assayed using allele-specific reverse transcription-polymerase chain reaction) or function (dominance relationships assayed through controlled pollinations) accompany the sequence-based classification. Expression of Class A alleles was restricted to floral tissues, as predicted for genes involved in the SI response. In contrast, Class B alleles, despite being tightly linked to the SI phenotype, were unexpectedly expressed in both leaves and floral tissues; the same pattern found for a related unlinked paralogous sequence. Whereas Class A included haplotypes in three different dominance classes, all Class B haplotypes were found to be recessive to all except one Class A haplotype. In addition, mapping of expression and dominance patterns onto an S-domain-based genealogy suggested that allelic dominance may be determined more by evolutionary history than by frequency-dependent selection for lowered dominance as some theories suggest. The possibility that interlocus gene conversion might have contributed to allelic diversity is discussed.

Single-vehicle and Multi-vehicle Accidents Involving Motorcycles in a Small City in China: Characteristics and Injury Patterns

PubMed Central

Xiong, Lili; Li, Liping

2015-01-01

Introduction There is a gap that involves examining differences between patients in single-vehicle (SV) versus multi-vehicle (MV) accidents involving motorcycles in Shantou, China, regarding the injury patterns and mortality the patients sustained. This study aims to address this gap and provide a basis and reference for motorcycle injury prevention. Method Medical record data was collected between October 2002 and June 2012 on all motorcycle injury patients admitted to a hospital in the city of Shantou of the east Guangdong province in China. Comparative analysis was conducted between patients in SV accidents and patients in MV accidents regarding demographic and clinic characteristics, mortality, and injury patterns. Results Approximately 48% (n = 1977) of patients were involved in SV accidents and 52% (n = 2119) were involved in MV accidents. The average age was 34 years. Collision of a motorcycle with a heavy vehicle/bus (4%) was associated with a 34 times greater risk of death (RR: 34.32; 95% CI: 17.43–67.57). Compared to patients involved in MV accidents, those involved in SV accidents were more likely to sustain a skull fracture (RR: 1.47; 95% CI: 1.22–1.77), an open head wound (RR: 1.46; 95% CI: 1.23–1.74), an intracranial injury (RR: 1.39; 95% CI: 1.26–1.53), a superficial head injury (RR: 1.37; 95% CI: 1.01–1.86), an injury to an organ (RR: 2.01; 95% CI: 1.24–3.26), and a crushing injury (RR: 1.98; 95% CI: 1.06–3.70) to the thorax or abdomen. However, they were less likely to sustain a spinal fracture (RR: 0.58; 95% CI: 0.39–0.85), a pelvic fracture (RR: 0.22; 95% CI: 0.11–0.46), an upper extremity fracture (RR: 0.75; 95% CI: 0.59–0.96), or injuries to their lower extremities, except for a dislocation, sprain, or injury to a joint or ligament (RR: 0.82; 95% CI: 0.49–1.36). Conclusion The relative risk of death is higher for patients involved in multi-vehicle accidents than patients in single-vehicle accidents, especially when a collision involves mass vehicle(s). Injury to the head dominated motorcycle injuries. Single-vehicle accidents have a higher correlation with head injury or internal injuries to the thorax or abdomen. Multi-vehicle accidents are more correlated with extremity injuries, especially to the lower extremities or external trauma to the thorax or abdomen. PMID:29546097

The Miocene Sommières basin, SE France: Bioclastic carbonates in a tide-dominated depositional system

NASA Astrophysics Data System (ADS)

Reynaud, Jean-Yves; James, Noël P.

2012-12-01

The Miocene Sommières Basin in SE France is a semi-enclosed depression that was connected to the Mediterranean Sea by a flooded paleo-incised valley and then filled by a suite of sediments comprising carbonate grains coming from temperate factories that were largely deposited in tidal-dominated paleoenvironments. The strata are partitioned into two sequences that reflect repeated flooding of the incised valley system, one of several similar situations in this region of France. The carbonate grains are mostly bioclasts, namely from barnacles, bryozoans, coralline algae (encrusting, branching, and rhodoliths), echinoids, and benthic foraminifers (large and small) with ostracods, sponge spicules and planktic foraminifers prominent in muddy facies. Particles were produced by shallow water carbonate factories on hard substrates (valley walls in particular), associated with subaqueous dunes, and in deeper water basinal settings. Each depositional sequence is underlain by an eroded and bored hard surface that is progressively overlain by TST subaqueous tidal dunes or storm deposits that grade up, in one case, into HST marls (the HST of the upper sequence has been removed by erosion). The lower sequence is ebb tide dominated whereas the upper sequence is flood tide dominated. The succession is interpreted to represent a TST whose tidal currents were focused by the narrow valley and a HST that reflected flooding of the overbanks. This stratigraphic and depositional motif is comparable to that in other spatially separated Neogene paleovalleys that are filled with tide-dominated clastic carbonates in the region. Together with other recently documented similar systems, these limestones constitute an important new group of carbonate sand bodies in the carbonate depositional realm.

Autosomal-dominant Leber Congenital Amaurosis Caused by a Heterozygous CRX Mutation in a Father and Son.

PubMed

Arcot Sadagopan, Karthikeyan; Battista, Robert; Keep, Rosanne B; Capasso, Jenina E; Levin, Alex V

2015-06-01

Leber congenital amaurosis (LCA) is most often an autosomal recessive disorder. We report a father and son with autosomal dominant LCA due to a mutation in the CRX gene. DNA screening using an allele specific assay of 90 of the most common LCA-causing variations in the coding sequences of AIPL1, CEP290, CRB1, CRX, GUCY2D, RDH12 and RPE65 was performed on the father. Automated DNA sequencing of his son examining exon 3 of the CRX gene was subsequently performed. Both father and son have a heterozygous single base pair deletion of an adenine at codon 153 in the coding sequence of the CRX gene resulting in a frameshift mutation. Mutations involving the CRX gene may demonstrate an autosomal dominant inheritance pattern for LCA.

A base substitution in the donor site of intron 12 of KIT gene is responsible for the dominant white coat colour of blue fox (Alopex lagopus).

PubMed

Yan, S Q; Hou, J N; Bai, C Y; Jiang, Y; Zhang, X J; Ren, H L; Sun, B X; Zhao, Z H; Sun, J H

2014-04-01

The dominant white coat colour of farmed blue fox is inherited as a monogenic autosomal dominant trait and is suggested to be embryonic lethal in the homozygous state. In this study, the transcripts of KIT were identified by RT-PCR for a dominant white fox and a normal blue fox. Sequence analysis showed that the KIT transcript in normal blue fox contained the full-length coding sequence of 2919 bp (GenBank Acc. No KF530833), but in the dominant white individual, a truncated isoform lacking the entire exon 12 specifically co-expressed with the normal transcript. Genomic DNA sequencing revealed that a single nucleotide polymorphism (c.1867+1G>T) in intron 12 appeared only in the dominant white individuals and a 1-bp ins/del polymorphism in the same intron showed in individuals representing two different coat colours. Genotyping results of the SNP with PCR-RFLP in 185 individuals showed all 90 normal blue foxes were homozygous for the G allele, and all dominant white individuals were heterozygous. Due to the truncated protein with a deletion of 35 amino acids and an amino acid replacement (p.Pro623Ala) located in the conserved ATP binding domain, we propose that the mutant receptor had absent tyrosine kinase activity. These findings reveal that the base substitution at the first nucleotide of intron 12 of KIT gene, resulting in skipping of exon 12, is a causative mutation responsible for the dominant white phenotype of blue fox. © 2013 Stichting International Foundation for Animal Genetics.

Snowblower injuries to the hand.

PubMed

Jardin, E; Uhring, J; Rey, P-B; Ferrier, M; Obert, L

2014-09-01

The aim of this study was to describe the nature and incidence of hand injuries caused by snowblowers, as well as the accident conditions and accident prevention. We conducted a retrospective evaluation over ten consecutive winters. Nine patients were included. All were men with an average age of 49.7 years (17-71). The accidents occurred at home in seven out of nine patients. The machine was running in 50% of the injury events. In most cases, the injuries occurred when the patient tried to unclog snow from the lateral discharge chute. Only four out of the nine patients had read the instructions or received instructions from the salesperson. The dominant hand was injured in 7 out of 9 patients. An average of 2.7 fingers were injured. The longest fingers were most commonly injured: 8 middle fingers, 7 ring fingers, 4 little fingers, 2 indexes and 1 thumb. All the fractures were open. Three patients were operated on several times. In 7 out of 9 cases, the patients had sequelae such as amputation. The mean time off work was 11.4 weeks (3-24). All the patients were experienced snowblower users (9 years and 57th use on average). Snowblower accidents are very mutilating. Prevention must include protected access to blades and better verbal and written safety warnings. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

Comprehensive Analysis of Two Downburst-Related Aircraft Accidents

NASA Technical Reports Server (NTRS)

Shen, J.; Parks, E. K.; Bach, R. E.

1996-01-01

Although downbursts have been identified as the major cause of a number of aircraft takeoff and landing accidents, only the 1985 Dallas/Fort Worth (DFW) and the more recent (July 1994) Charlotte, North Carolina, landing accidents provided sufficient onboard recorded data to perform a comprehensive analysis of the downburst phenomenon. The first step in the present analysis was the determination of the downburst wind components. Once the wind components and their gradients were determined, the degrading effect of the wind environment on the airplane's performance was calculated. This wind-shear-induced aircraft performance degradation, sometimes called the F-factor, was broken down into two components F(sub 1) and F(sub 2), representing the effect of the horizontal wind gradient and the vertical wind velocity, respectively. In both the DFW and Charlotte cases, F(sub 1) was found to be the dominant causal factor of the accident. Next, the aircraft in the two cases were mathematically modeled using the longitudinal equations of motion and the appropriate aerodynamic parameters. Based on the aircraft model and the determined winds, the aircraft response to the recorded pilot inputs showed good agreement with the onboard recordings. Finally, various landing abort strategies were studied. It was concluded that the most acceptable landing abort strategy from both an analytical and pilot's standpoint was to hold constant nose-up pitch attitude while operating at maximum engine thrust.

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

Daling, P.M.; Marler, J.E.; Vo, T.V.

This study evaluates the values (benefits) and impacts (costs) associated with potential resolutions to Generic Issue 143, ``Availability of HVAC and Chilled Water Systems.`` The study identifies vulnerabilities related to failures of HVAC, chilled water, and room cooling systems; develops estimates of room heatup rates and safety-related equipment vulnerabilities following losses of HVAC/room cooler systems; develops estimates of the core damage frequencies and public risks associated with failures of these systems; develops three proposed resolution strategies to this generic issue; and performs a value/impact analysis of the proposed resolutions. Existing probabilistic risk assessments for four representative plants, including one plantmore » from each vendor, form the basis for the core damage frequency and public risk calculations. Both internal and external events were considered. It was concluded that all three proposed resolution strategies exceed the $1,000/person-rem cost-effectiveness ratio. Additional evaluations were performed to develop ``generic`` insights on potential design-related and configuration-related vulnerabilities and potential high-frequency ({approximately}1E-04/RY) accident sequences that involve failures of HVAC/room cooling functions. It was concluded that, although high-frequency accident sequences may exist at some plants, these high-frequency sequences are plant-specific in nature or have been resolved through hardware and/or operational changes. The plant-specific Individual Plant Examinations are an effective vehicle for identification and resolution of these plant-specific anomalies and hardware configurations.« less

Station blackout transient at the Browns Ferry Unit 1 Plant: a severe accident sequence analysis (SASA) program study

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

Schultz, R.R.

1982-01-01

Operating plant transients are of great interest for many reasons, not the least of which is the potential for a mild transient to degenerate to a severe transient yielding core damage. Using the Browns Ferry (BF) Unit-1 plant as a basis of study, the station blackout sequence was investigated by the Severe Accident Sequence Analysis (SASA) Program in support of the Nuclear Regulatory Commission's Unresolved Safety Issue A-44: Station Blackout. A station blackout transient occurs when the plant's AC power from a comemrcial power grid is lost and cannot be restored by the diesel generators. Under normal operating conditions, fmore » a loss of offsite power (LOSP) occurs (i.e., a complete severance of the BF plants from the Tennessee Valley Authority (TVA) power grid), the eight diesel generators at the three BF units would quickly start and power the emergency AC buses. Of the eight diesel generators, only six are needed to safely shut down all three units. Examination of BF-specific data show that LOSP frequency is low at Unit 1. The station blackout frequency is even lower (5.7 x 10/sup -4/ events per year) and hinges on whether the diesel generators start. The frequency of diesel generator failure is dictated in large measure by the emergency equipment cooling water (EECW) system that cools the diesel generators.« less

Perceived facial expressions of emotion as motivational incentives: evidence from a differential implicit learning paradigm.

PubMed

Schultheiss, Oliver C; Pang, Joyce S; Torges, Cynthia M; Wirth, Michelle M; Treynor, Wendy; Derryberry, Douglas

2005-03-01

Participants (N = 216) were administered a differential implicit learning task during which they were trained and tested on 3 maximally distinct 2nd-order visuomotor sequences, with sequence color serving as discriminative stimulus. During training, 1 sequence each was followed by an emotional face, a neutral face, and no face, using backward masking. Emotion (joy, surprise, anger), face gender, and exposure duration (12 ms, 209 ms) were varied between participants; implicit motives were assessed with a picture-story exercise. For power-motivated individuals, low-dominance facial expressions enhanced and high-dominance expressions impaired learning. For affiliation-motivated individuals, learning was impaired in the context of hostile faces. These findings did not depend on explicit learning of fixed sequences or on awareness of sequence-face contingencies. Copyright 2005 APA, all rights reserved.

The Lagerlunda collision and the introduction of color vision testing.

PubMed

Mollon, J D; Cavonius, L R

2012-01-01

In histories of vision testing, the origins of occupational screening for color blindness are often traced to a fatal railroad accident that occurred in Sweden on the night of 14-15 November 1875. The scene of the accident was the estate of Baron Lagerfelt in Östergötland, but the critical events were played out at Linköping (the normal passing place for the northbound and southbound expresses) and at Bankeberg (a small station to which the passing place was reassigned at a few minutes' notice). First to arrive at Bankeberg, the northbound express slowed almost to a halt, but then inexplicably accelerated forwards towards the Lagerlunda estate, despite a sequence of signals from the stationmaster, Uno Björkelund, and a lineman, Oskar Johansson. Soon after the accident, the ophthalmologist Frithiof Holmgren suggested that the engineer of the northbound express, Andersson, or his oiler, Larsson, had been color blind. Neither survived to be tested. Using the records of the subsequent trial and other archival materials, we have re-examined the role of color blindness in the Lagerlunda incident and conclude that the accident cannot be attributed to color blindness alone. Yet the accident undoubtedly had a central role in the introduction of color vision testing by European and North American railroads. To persuade the railroad management to introduce universal screening of employees for color blindness, Holmgren used a dramatic coup de theatre and some unashamed subterfuge. Copyright © 2012 Elsevier Inc. All rights reserved.

The Euratom-Rosatom ERCOSAM-SAMARA projects on containment thermal-hydraulics of current and future LWRs for severe accident management

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

Paladino, D.; Guentay, S.; Andreani, M.

2012-07-01

During a postulated severe accident with core degradation, hydrogen would form in the reactor pressure vessel mainly due to high temperatures zirconium-steam reaction and flow together with steam into the containment where it will mix with the containment atmosphere (steam-air). The hydrogen transport into the containment is a safety concern because it can lead to explosive mixtures through the associated phenomena of condensation, mixing and stratification. The ERCOSAM and SAMARA projects, co-financed by the European Union and the Russia, include various experiments addressing accident scenarios scaled down from existing plant calculations to different thermal-hydraulics facilities (TOSQAN, MISTRA, PANDA, SPOT). Themore » tests sequences aim to investigate hydrogen concentration build-up and stratification during a postulated accident and the effect of the activation of Severe Accident Management systems (SAMs), e.g. sprays, coolers and Passive Auto-catalytic Recombiners (PARs). Analytical activities, performed by the project participants, are an essential component of the projects, as they aim to improve and validate various computational methods. They accompany the projects in the various phases; plant calculations, scaling to generic containment and to the different facilities, planning pre-test and post-test simulations are performed. Code benchmark activities on the basis of conceptual near full scale HYMIX facility will finally provide a further opportunity to evaluate the applicability of the various methods to the study of scaling issues. (authors)« less

Potential effects of the fire protection system sprays at Browns Ferry on fission product transport

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

Niemczyk, S.J.

1983-01-01

The fire protection system (FPS) sprays within any nuclear plant are not intended to mitigate radioactive releases to the environment resulting from severe core-damage accidents. However, it has been shown here that during certain postulated severe accident scenarios at the Browns Ferry Nuclear Plant, the functioning of FPS sprays could have a significant impact on the radioactive releases. Thus the effects of those sprays need to be taken into account for realistic estimation of source terms for some accident scenarios. The effects would include direct ones such as cooling of the reactor building atmosphere and scrubbing of radioactivity from it,more » as well as indirect effects such as an altered likelihood of hydrogen burning and flooding of various safety-related pumps in the reactor building basement. Thus some of the impacts of the sprays would be beneficial with respect to mitigating releases to the environment but some others might not be. The effects of the FPS would be very scenario dependent with a wide range of potential effects often existing for a given accident sequence. Any generalization of the specific results presented here for Browns Ferry to other nuclear plants must be done cautiously, as it appears from a preliminary investigation that the relevant physical and operational characteristics of FPS spray systems differ widely among even otherwise apparently similar plants. Likewise the standby gas treatment systems, which substantially impact the effects of the FPS, differ significantly among plants. More work for both Mark I plants and other plants, BWRs and PWRs alike, is indicated so the potential effects of FPS spray systems during severe accidents can be at least ball-parked for more realistic accident analyses.« less

Anesthesia patient risk: a quantitative approach to organizational factors and risk management options.

PubMed

Paté-Cornell, M E; Lakats, L M; Murphy, D M; Gaba, D M

1997-08-01

The risk of death or brain damage to anesthesia patients is relatively low, particularly for healthy patients in modern hospitals. When an accident does occur, its cause is usually an error made by the anesthesiologist, either in triggering the accident sequence, or failing to take timely corrective measures. This paper presents a pilot study which explores the feasibility of extending probabilistic risk analysis (PRA) of anesthesia accidents to assess the effects of human and management components on the patient risk. We develop first a classic PRA model for the patient risk per operation. We then link the probabilities of the different accident types to their root causes using a probabilistic analysis of the performance shaping factors. These factors are described here as the "state of the anesthesiologist" characterized both in terms of alertness and competence. We then analyze the effects of different management factors that affect the state of the anesthesiologist and we compute the risk reduction benefits of several risk management policies. Our data sources include the published version of the Australian Incident Monitoring Study as well as expert opinions. We conclude that patient risk could be reduced substantially by closer supervision of residents, the use of anesthesia simulators both in training and for periodic recertification, and regular medical examinations for all anesthesiologists.

Bacterial inosine 5'-monophosphate dehydrogenase ("IMPDH") DNA as a dominant selectable marker in mammals and other eukaryotes

DOEpatents

Huberman, Eliezer [Chicago, IL; Baccam, Mekhine J [Woodridge, IL

2007-02-27

The present invention relates to a nucleic acid sequence and its corresponding protein sequence useful as a dominant selectable marker in eukaryotes. More specifically the invention relates to a nucleic acid encoding a bacterial IMPDH gene that has been engineered into a eukaryotic expression vectors, thereby permitting bacterial IMPDH expression in mammalian cells. Bacterial IMPDH expression confers resistance to MPA which can be used as dominant selectable marker in eukaryotes including mammals. The invention also relates to expression vectors and cells that express the bacterial IMPDH gene as well as gene therapies and protein synthesis.

[Memorization of Sequences of Movements of the Right and the Left Hand by Right- and Left-Handers].

PubMed

Bobrova, E V; Bogacheva, I N; Lyakhovetskii, V A; Fabinskaja, A A; Fomina, E V

2015-01-01

We analyzed the errors of right- and left-handers when performing memorized sequences by the left or the right hand during the task which activates positional coding: after 6-10 times the order of movements changed (the positions remained the same during all task). The task was first performed by one ("initial") hand, and then by another one ("continuing"); there were 2 groups of right-handers and 2 groups of left-handers. It was found that the pattern of errors during the task performance by the initial hand is similar in right- and left-handers both for the dominant and non-dominant hand. The information about the previous positions after changing the order of elements is used in the sequences for subdominant hands and not used in the sequences for dominant ones. After changing the hand, right- and left-handers show different patterns of errors ("non-symmetrical"). Thus, the errors of right- and left-handers are "symmetrical" at the early stages of task performance, while the transfer of this motor skill in right-and left-handers occurs in different ways.

Characterization of microbial compositions in a thermophilic chemostat of mixed culture fermentation.

PubMed

Zhang, Fang; Yang, Jing-Hua; Dai, Kun; Chen, Yun; Li, Qiu-Rong; Gao, Fa-Ming; Zeng, Raymond J

2016-02-01

The microbial community compositions of a chemostat enriched in a thermophilic (55 °C) mixed culture fermentation (MCF) for hydrogen production under different operational conditions were revealed in this work by integrating denaturing gradient gel electrophoresis (DGGE), Illumina Miseq high-throughput sequencing, and 16S rRNA clone library sequencing. The results showed that the community structure of the enriched cultures was relatively simple. Clones close to the genera of Thermoanaerobacter and/or Bacillus mainly dominated the bacteria. And homoacetogens and archaea were washed out and not detected even by Illumina Miseq high-throughput sequencing which supported the benefit for hydrogen production. On the other hand, the results revealed that the metabolic shift was clearly associated with the change of dominated bacterial groups. The effects of hydrogen partial pressure (PH2) and pH from 4.0 to 5.5 on the microbial compositions were not notable and Thermoanaerobacter was dominant, thus, the metabolites were also not changed. While Bacillus, Thermoanaerobacter and Propionispora hippei dominated the bacteria communities at neutral pH, or Bacillus and Thermoanaerobacter dominated at high influent glucose concentrations, consequently the main metabolites shifted to acetate, ethanol, propionate, or lactate. Thereby, the effect of microbial composition on the metabolite distribution and shift shall be considered when modeling thermophilic MCF in the future.

Late Pleistocene sequence architecture on the geostrophic current-dominated southwest margin of the Ulleung Basin, East Sea

NASA Astrophysics Data System (ADS)

Choi, Dong-Lim; Shin, Dong-Hyeok; Kum, Byung-Cheol; Jang, Seok; Cho, Jin-Hyung; Jou, Hyeong-Tae; Jang, Nam-Do

2018-06-01

High-resolution multichannel seismic data were collected to identify depositional sequences on the southwestern shelf of the Ulleung Basin, where a unidirectional ocean current is dominant at water depths exceeding 130 m. Four aggradational stratigraphic sequences with a 100,000-year cycle were recognized since marine isotope stage (MIS) 10. These sequences consist only of lowstand systems tracts (LSTs) and falling-stage systems tracts (FSSTs). Prograding wedge-shaped deposits are present in the LSTs near the shelf break. Oblique progradational clinoforms of forced regressive deposits are present in the FSSTs on the outer continental shelf. Each FSST has non-uniform forced regressional stratal geometries, reflecting that the origins of sediments in each depositional sequence changed when sea level was falling. Slump deposits are characteristically developed in the upper layer of the FSSTs, and this was used as evidence to distinguish the sequence boundaries. The subsidence rates around the shelf break reached as much as 0.6 mm/year since MIS 10, which contributed to the well-preserved depositional sequence. During the Quaternary sea-level change, the water depth in the Korea Strait declined and the intensity of the Tsushima Current flowing near the bottom of the inner continental shelf increased. This resulted in greater erosion of sediments that were delivered to the outer continental shelf, which was the main cause of sediment deposition on the deep, low-angled outer shelf. Therefore, a depositional sequence formation model that consists of only FSSTs and LSTs, excluding highstand systems tracts (HSTs) and transgressive systems tracts (TSTs), best explains the depositional sequence beneath this shelf margin dominated by a geostrophic current.

The female urinary microbiome in urgency urinary incontinence.

PubMed

Pearce, Meghan M; Zilliox, Michael J; Rosenfeld, Amy B; Thomas-White, Krystal J; Richter, Holly E; Nager, Charles W; Visco, Anthony G; Nygaard, Ingrid E; Barber, Matthew D; Schaffer, Joseph; Moalli, Pamela; Sung, Vivian W; Smith, Ariana L; Rogers, Rebecca; Nolen, Tracy L; Wallace, Dennis; Meikle, Susan F; Gai, Xiaowu; Wolfe, Alan J; Brubaker, Linda

2015-09-01

The purpose of this study was to characterize the urinary microbiota in women who are planning treatment for urgency urinary incontinence and to describe clinical associations with urinary symptoms, urinary tract infection, and treatment outcomes. Catheterized urine samples were collected from multisite randomized trial participants who had no clinical evidence of urinary tract infection; 16S ribosomal RNA gene sequencing was used to dichotomize participants as either DNA sequence-positive or sequence-negative. Associations with demographics, urinary symptoms, urinary tract infection risk, and treatment outcomes were determined. In sequence-positive samples, microbiotas were characterized on the basis of their dominant microorganisms. More than one-half (51.1%; 93/182) of the participants' urine samples were sequence-positive. Sequence-positive participants were younger (55.8 vs 61.3 years old; P = .0007), had a higher body mass index (33.7 vs 30.1 kg/m(2); P = .0009), had a higher mean baseline daily urgency urinary incontinence episodes (5.7 vs 4.2 episodes; P < .0001), responded better to treatment (decrease in urgency urinary incontinence episodes, -4.4 vs -3.3; P = .0013), and were less likely to experience urinary tract infection (9% vs 27%; P = .0011). In sequence-positive samples, 8 major bacterial clusters were identified; 7 clusters were dominated not only by a single genus, most commonly Lactobacillus (45%) or Gardnerella (17%), but also by other taxa (25%). The remaining cluster had no dominant genus (13%). DNA sequencing confirmed urinary bacterial DNA in many women with urgency urinary incontinence who had no signs of infection. Sequence status was associated with baseline urgency urinary incontinence episodes, treatment response, and posttreatment urinary tract infection risk. Copyright © 2015 Elsevier Inc. All rights reserved.

Late Pleistocene sequence architecture on the geostrophic current-dominated southwest margin of the Ulleung Basin, East Sea

NASA Astrophysics Data System (ADS)

Choi, Dong-Lim; Shin, Dong-Hyeok; Kum, Byung-Cheol; Jang, Seok; Cho, Jin-Hyung; Jou, Hyeong-Tae; Jang, Nam-Do

2017-11-01

High-resolution multichannel seismic data were collected to identify depositional sequences on the southwestern shelf of the Ulleung Basin, where a unidirectional ocean current is dominant at water depths exceeding 130 m. Four aggradational stratigraphic sequences with a 100,000-year cycle were recognized since marine isotope stage (MIS) 10. These sequences consist only of lowstand systems tracts (LSTs) and falling-stage systems tracts (FSSTs). Prograding wedge-shaped deposits are present in the LSTs near the shelf break. Oblique progradational clinoforms of forced regressive deposits are present in the FSSTs on the outer continental shelf. Each FSST has non-uniform forced regressional stratal geometries, reflecting that the origins of sediments in each depositional sequence changed when sea level was falling. Slump deposits are characteristically developed in the upper layer of the FSSTs, and this was used as evidence to distinguish the sequence boundaries. The subsidence rates around the shelf break reached as much as 0.6 mm/year since MIS 10, which contributed to the well-preserved depositional sequence. During the Quaternary sea-level change, the water depth in the Korea Strait declined and the intensity of the Tsushima Current flowing near the bottom of the inner continental shelf increased. This resulted in greater erosion of sediments that were delivered to the outer continental shelf, which was the main cause of sediment deposition on the deep, low-angled outer shelf. Therefore, a depositional sequence formation model that consists of only FSSTs and LSTs, excluding highstand systems tracts (HSTs) and transgressive systems tracts (TSTs), best explains the depositional sequence beneath this shelf margin dominated by a geostrophic current.

[CLAVICLE FRACTURES IN CHILDREN--CIRCUMSTANCES AND CAUSES OF INJURY].

PubMed

Antabak, Anko; Matković, Nikša; Papeš, Dino; Karlo, Robert; Romić, Ivan; Fuchs, Nino; Madarić, Miroslav; Stilinović, Marina; Stanić, Lana; Luetić, Tomislav

2015-01-01

Clavicle fractures in children occur twice as often as in adults. During a child's growth period they account for 10-15% of all fractures sustained. The questions which should be asked are how these fractures are sustained and under which circumstances are the children injured. In the study 256 children with clavicle fractures treated during the period 2008-2013 were analyzed. The underlying cause and place of injuries were classified using the ICD-10 classification system, using environmental causes of injury. The circumstances were in each case accidental injury. Environmental causes were traffic accidents (V01-V99) or mishaps/accidents (W00-X59). Fracture injuries were caused in traffic accidents in 24 (9.4%), and in mishaps/accidents in 232 (90.6%) children. Of the injuries caused by mishaps/accidents, in 204 children these were caused by falls (W00-W19). In 123 of them the injuries were caused by falls from a ground level, and in 81 were from a greater height. Direct blow injuries, caused by another person or a blunt instrument, weere the causes of fractures seen in 28 children. Place of fracture sustainment was dominantly at home. This was followed by injuries sustained outside in recreational areas, while least were suffered at school or kindergarden facilities. Bicycle riding was the cause of clavicle fractures in 48 children, which was 18.7% of all fractures seen. Sports related injuries and fractures were seen in 47 (18.4%) out of 256 children: 30 in football, 10 in defensive sports (wrestling, judo, karate), three in hockey, while basketball and gymnastics accounted for two each. Preschool children were injured more often while in the care of their parents while school aged children were adaquately protected, but in after-school activities they were often injured. The most common injuries after school were those suffered in traffic accidents and recreational sports activities. In the adolescent period, the most common injuries seen were again those in traffic accidents, bicycle riding, recreational sports activities and injuries sustained at home.

Why pilots are least likely to get good decision making precisely when they need it most

NASA Technical Reports Server (NTRS)

Maher, John W.

1991-01-01

Studies of commercial aircraft incidents and accidents indicate that, in flight conditions not covered by standard operating procedures, as well as when the environment is saturated with information or unmanaged stress, cognitive shortcuts dominate aircrews' decisionmaking processes. Multidisciplinary research on such situations with high-fidelity simulators becomes critically important, as do psychometric tools which examine vigilance, personality resiliency before stressful conditions, and decisional and interpersonal mind-sets.

The PSI Artist Project: Aerosol Retention and Accident Management Issues Following a Steam Generator Tube Rupture

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

Guntay, Salih; Dehbi, Abdel; Suckow, Detlef

2002-07-01

Steam generator tube rupture (SGTR) incidents, such as those, which occurred in various operating pressurized, water reactors in the past, are serious operational concerns and remain among the most risk-dominant events. Although considerable efforts have been spent to understand tube degradation processes, develop improved modes of operation, and take preventative and corrective measures, SGTR incidents cannot be completely ruled out. Under certain conditions, high releases of radionuclides to the environment are possible during design basis accidents (DBA) and severe accidents. The severe accident codes' models for aerosol retention in the secondary side of a steam generator (SG) have not beenmore » assessed against any experimental data, which means that the uncertainties in the source term following an un-isolated SGTR concurrent with a severe accident are not currently quantified. The accident management (AM) procedures aim at avoiding or minimizing the release of fission products from the SG. The enhanced retention of activity within the SG defines the effectiveness of the accident management actions for the specific hardware characteristics and accident conditions of concern. A sound database on aerosol retention due to natural processes in the SG is not available, nor is an assessment of the effect of management actions on these processes. Hence, the effectiveness of the AM in SGTR events is not presently known. To help reduce uncertainties relating to SGTR issues, an experimental project, ARTIST (Aerosol Trapping In a Steam generator), has been initiated at the Paul Scherrer Institut to address aerosol and droplet retention in the various parts of the SG. The test section is comprised of a scaled-down tube bundle, a full-size separator and a full-size dryer unit. The project will study phenomena at the separate effect and integral levels and address AM issues in seven distinct phases: Aerosol retention in 1) the broken tube under dry secondary side conditions, 2) the near field close to break under dry conditions, 3) the bundle far-field under dry conditions, 4) the separator and dryer under dry conditions, 5) the bundle section under wet conditions, 6) droplet retention in the separator and dryer sections and 7) the overall SG (integral tests). Prototypical test parameters are selected to cover the range of conditions expected in severe accident as well as DBA scenarios. This paper summarizes the relevant issues and introduces the ARTIST facility and the provisional test program which will run between 2003 and 2007. (authors)« less

An Exercise Health Simulation Method Based on Integrated Human Thermophysiological Model

PubMed Central

Chen, Xiaohui; Yu, Liang; Yang, Kaixing

2017-01-01

Research of healthy exercise has garnered a keen research for the past few years. It is known that participation in a regular exercise program can help improve various aspects of cardiovascular function and reduce the risk of suffering from illness. But some exercise accidents like dehydration, exertional heatstroke, and even sudden death need to be brought to attention. If these exercise accidents can be analyzed and predicted before they happened, it will be beneficial to alleviate or avoid disease or mortality. To achieve this objective, an exercise health simulation approach is proposed, in which an integrated human thermophysiological model consisting of human thermal regulation model and a nonlinear heart rate regulation model is reported. The human thermoregulatory mechanism as well as the heart rate response mechanism during exercise can be simulated. On the basis of the simulated physiological indicators, a fuzzy finite state machine is constructed to obtain the possible health transition sequence and predict the exercise health status. The experiment results show that our integrated exercise thermophysiological model can numerically simulate the thermal and physiological processes of the human body during exercise and the predicted exercise health transition sequence from finite state machine can be used in healthcare. PMID:28702074

MARTINS: A foam/film flow model for molten material relocation in HWRs with U-Al-fueled multi-tube assemblies

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

Kalimullah

1994-03-01

Some special purpose heavy-water reactors (EM) are made of assemblies consisting of a number of coaxial aluminum-clad U-Al alloy fuel tubes and an outer Al sleeve surrounding the fuel tubes. The heavy water coolant flows in the annular gaps between the circular tubes. Analysis of severe accidents in such reactors requires a model for predicting the behavior of the fuel tubes as they melt and disrupt. This paper describes a detailed, mechanistic model for fuel tube heatup, melting, freezing, and molten material relocation, called MARTINS (Melting and Relocation of Tubes in Nuclear subassembly). The paper presents the modeling of themore » phenomena in MARTINS, and an application of the model to analysis of a reactivity insertion accident. Some models are being developed to compute gradual downward relocation of molten material at decay-heat power levels via candling along intact tubes, neglecting coolant vapor hydrodynamic forces on molten material. These models are inadequate for high power accident sequences involving significant hydrodynamic forces. These forces are included in MARTINS.« less

Phenotypic Heterogeneity in a DFNA20/26 family segregating a novel ACTG1 mutation.

PubMed

Yuan, Yongyi; Gao, Xue; Huang, Bangqing; Lu, Jingqiao; Wang, Guojian; Lin, Xi; Qu, Yan; Dai, Pu

2016-02-01

Genetic factors play an important role in hearing loss, contributing to approximately 60% of cases of congenital hearing loss. Autosomal dominant deafness accounts for approximately 20% of cases of hereditary hearing loss. Diseases with autosomal dominant inheritance often show pleiotropy, different degrees of penetrance, and variable expressivity. A three-generation Chinese family with autosomal dominant nonsyndromic hearing impairment (ADNSHI) was enrolled in this study. Audiometric data and blood samples were collected from the family. In total, 129 known human deafness genes were sequenced using next-generation sequencing (NGS) to identify the responsible gene mutation in the family. Whole Exome Sequencing (WES) was performed to exclude any other variant that cosegregated with the phenotype. The age of onset of the affected family members was the second decade of life. The condition began with high-frequency hearing impairment in all family members excluding III:2. The novel ACTG1 c.638A > G (p.K213R) mutation was found in all affected family members and was not found in the unaffected family members. A heterozygous c.638A > G mutation in ACTG1 and homozygous c.109G > A (p.V37I) mutation in GJB2 were found in III:2, who was born with hearing loss. The WES result concurred with that of targeted sequencing of known deafness genes. The novel mutation p.K213R in ACTG1 was found to be co-segregated with hearing loss and the genetic cause of ADNSHI in this family. A homozygous mutation associated with recessive inheritance only rarely co-acts with a dominant mutation to result in hearing loss in a dominant family. In such cases, the mutations in the two genes, as in ACTG1 and GJB2 in the present study, may result in a more severe phenotype. Targeted sequencing of known deafness genes is one of the best choices to identify the genetic cause in hereditary hearing loss families.

Tetanus associated with road accidents in the infectious diseases department of Point G University Hospital, Bamako, Mali.

PubMed

Traoré, A M; Coulibaly, I; Dabo, G; Cissé, H; Diallo, K; Soukho-Kaya, A; Diango, M D; Cissé, T; Dembélé, M; Traoré, H A; Pichard, E; Minta, D K

2017-06-01

The aim of this study was to describe the epidemiological, clinical, and prognostic aspects of tetanus associated with road accidents and to make recommendations. This observational study collected retrospective clinical data over a 9-year period about adults admitted for trismus and/or generalized or localized paroxysm after a road accident. The study included 25 patients, accounting for 22.12 % of all tetanus cases. Men were massively overrepresented (sex-ratio M/F: 24/1). The median age was 34 ± 8 years. In all, vaccination status was unknown for 4 patients and known to be negative for 21. Immunoprophylaxis was nonexistent in all cases. The generalized clinical form was dominant (96 %). Severity reached level III for 12 % of patients. The points of entry included open leg fractures (4 cases), head wounds (2), mucocutaneous wounds (14), and muscle contusions (5). The mean time to referral for tetanus was 8 ± 7 days, and the median hospital stay 9.08 ± 11 days. Patients were mostly residents of urban (56 %) and suburban areas (28 %) [P = 0.04]. Two cases were complicated by severe malaria. The mortality rate was 60 %, and 52 % of the deaths occurred within the first 72 hours after hospitalization. It is essential to promote serum therapy and tetanus immunization for patients after road accidents. Increasing the awareness of traditional healers of these treatments deserves consideration.

The inheritance of fingerprint patterns.

PubMed

Slatis, H M; Katznelson, M B; Bonné-Tamir, B

1976-05-01

Analysis of the fingerprints of 571 members of the Habbanite isolate suggest inherited patterns and pattern sequences. A genetic theory has been developed; it assumes that the basic fingerprint pattern sequence is all ulnar loops and that a variety of genes cause deviations from this pattern sequence. Genes that have been proposed include: (1) a semidominant gene for whorls on the thumbs (one homozygote has whorls on both thumbs, the other has ulnar loops on both thumbs and the heterozygote usually has two ulnar loops or one ulnar loop and one whorl); (2) a semidominant gene for whorls on the ring fingers which acts like the gene for whorls on the thumbs; (3) a dominant gene for arches on the thumbs and often on other fingers; (4) one or more dominant genes for arches on the fingers; (5) a dominant gene for whorls on all fingers except for an ulnar loop on the middle finger; (6) a dominant gene for radial loops on the index fingers, frequently associated with an arch on the middle fingers; and (7) a recessive gene for radial loops on the ring and little fingers. These genes may act independently or may show epistasis.

The inheritance of fingerprint patterns.

PubMed Central

Slatis, H M; Katznelson, M B; Bonné-Tamir, B

1976-01-01

Analysis of the fingerprints of 571 members of the Habbanite isolate suggest inherited patterns and pattern sequences. A genetic theory has been developed; it assumes that the basic fingerprint pattern sequence is all ulnar loops and that a variety of genes cause deviations from this pattern sequence. Genes that have been proposed include: (1) a semidominant gene for whorls on the thumbs (one homozygote has whorls on both thumbs, the other has ulnar loops on both thumbs and the heterozygote usually has two ulnar loops or one ulnar loop and one whorl); (2) a semidominant gene for whorls on the ring fingers which acts like the gene for whorls on the thumbs; (3) a dominant gene for arches on the thumbs and often on other fingers; (4) one or more dominant genes for arches on the fingers; (5) a dominant gene for whorls on all fingers except for an ulnar loop on the middle finger; (6) a dominant gene for radial loops on the index fingers, frequently associated with an arch on the middle fingers; and (7) a recessive gene for radial loops on the ring and little fingers. These genes may act independently or may show epistasis. PMID:1266855

Development of accident tolerant FeCrAl-ODS steels utilizing Ce-oxide particles dispersion

NASA Astrophysics Data System (ADS)

Shibata, Hiroki; Ukai, Shigeharu; Oono, Naoko H.; Sakamoto, Kan; Hirai, Mutsumi

2018-04-01

FeCrAl-ODS ferritic steels with Ce-oxide dispersion instead of Y-oxide were produced for the accident tolerant fuel cladding of the light water reactor. Excess oxygen (Ex.O) was added to improve the mechanical property. The tensile strength at Ex.O = 0 is around 200 MPa at 700 °C, mainly owing to dispersed Ce2O3 particles in less than 10 nm size. The formation of the fine Ce2O3 particles is dominated by a coherent interface with ferritic matrix. With increasing Ex.O, an increased of number density of coarser Ce-Al type oxide particles over 10 nm size is responsible for the improvement of the tensile strength. Change of the type of oxide particle, CeO2, Ce2O3, CeAlO3, Al2O3, in FeCrAl-ODS steel was thermodynamically analyzed as a parameter of Ex.O.

Fear and Anger Responses to Local News Coverage of Alcohol-Related Crimes, Accidents, and Injuries: Explaining News Effects on Policy Support Using a Representative Sample of Messages and People

PubMed Central

Goodall, Catherine E.; Slater, Michael D.; Myers, Teresa A.

2013-01-01

An experiment investigated emotional reactions to news on policy support. Stimuli were selected from a nationally representative sample of local crime/accident news, and a nationally representative online panel of U.S. adults. Stories were manipulated to mention or not mention the role of alcohol. Anger elicited by stories increased blame of individuals, whereas fear increased consideration of contributing societal factors. Mention of alcohol increased likelihood of different emotional responses dominating--greater anger when alcohol was mentioned and greater fear when not mentioned. Such emotions influence policy support: enforcement of existing laws controlling individual behavior in addition to new laws when anger predominated, and, indirectly, support for new laws changing social context in which alcohol is promoted and sold when fear predominated. PMID:23729838

Parallel sequencing lives, or what makes large sequencing projects successful

PubMed Central

Cuartero, Yasmina; Stadhouders, Ralph; Graf, Thomas; Marti-Renom, Marc A; Beato, Miguel

2017-01-01

Abstract T47D_rep2 and b1913e6c1_51720e9cf were 2 Hi-C samples. They were born and processed at the same time, yet their fates were very different. The life of b1913e6c1_51720e9cf was simple and fruitful, while that of T47D_rep2 was full of accidents and sorrow. At the heart of these differences lies the fact that b1913e6c1_51720e9cf was born under a lab culture of Documentation, Automation, Traceability, and Autonomy and compliance with the FAIR Principles. Their lives are a lesson for those who wish to embark on the journey of managing high-throughput sequencing data. PMID:29048533

Sequence conservation predicts T cell reactivity against ragweed allergens.

PubMed

Pham, J; Oseroff, C; Hinz, D; Sidney, J; Paul, S; Greenbaum, J; Vita, R; Phillips, E; Mallal, S; Peters, B; Sette, A

2016-09-01

Ragweed is a major cause of seasonal allergy, affecting millions of people worldwide. Several allergens have been defined based on IgE reactivity, but their relative immunogenicity in terms of T cell responses has not been studied. We comprehensively characterized T cell responses from atopic, ragweed-allergic subjects to Amb a 1, Amb a 3, Amb a 4, Amb a 5, Amb a 6, Amb a 8, Amb a 9, Amb a 10, Amb a 11, and Amb p 5 and examined their correlation with serological reactivity and sequence conservation in other allergens. Peripheral blood mononuclear cells (PBMCs) from donors positive for IgE towards ragweed extracts after in vitro expansion for secretion of IL-5 (a representative Th2 cytokine) and IFN-γ (Th1) in response to a panel of overlapping peptides spanning the above-listed allergens were assessed. Three previously identified dominant T cell epitopes (Amb a 1 176-191, 200-215, and 344-359) were confirmed, and three novel dominant epitopes (Amb a 1 280-295, 304-319, and 320-335) were identified. Amb a 1, the dominant IgE allergen, was also the dominant T cell allergen, but dominance patterns for T cell and IgE responses for the other ragweed allergens did not correlate. Dominance for T cell responses correlated with conservation of ragweed epitopes with sequences of other well-known allergens. These results provide the first assessment of the hierarchy of T cell reactivity in ragweed allergens, which is distinct from that observed for IgE reactivity and influenced by T cell epitope sequence conservation. The results suggest that ragweed allergens associated with lesser IgE reactivity and significant T cell reactivity may be targeted for T cell immunotherapy, and further support the development of immunotherapies against epitopes conserved across species to generate broad reactivity against many common allergens. © 2016 John Wiley & Sons Ltd.

Phylogenetic and Functional Analysis of Metagenome Sequence from High-Temperature Archaeal Habitats Demonstrate Linkages between Metabolic Potential and Geochemistry

PubMed Central

Inskeep, William P.; Jay, Zackary J.; Herrgard, Markus J.; Kozubal, Mark A.; Rusch, Douglas B.; Tringe, Susannah G.; Macur, Richard E.; Jennings, Ryan deM.; Boyd, Eric S.; Spear, John R.; Roberto, Francisco F.

2013-01-01

Geothermal habitats in Yellowstone National Park (YNP) provide an unparalleled opportunity to understand the environmental factors that control the distribution of archaea in thermal habitats. Here we describe, analyze, and synthesize metagenomic and geochemical data collected from seven high-temperature sites that contain microbial communities dominated by archaea relative to bacteria. The specific objectives of the study were to use metagenome sequencing to determine the structure and functional capacity of thermophilic archaeal-dominated microbial communities across a pH range from 2.5 to 6.4 and to discuss specific examples where the metabolic potential correlated with measured environmental parameters and geochemical processes occurring in situ. Random shotgun metagenome sequence (∼40–45 Mb Sanger sequencing per site) was obtained from environmental DNA extracted from high-temperature sediments and/or microbial mats and subjected to numerous phylogenetic and functional analyses. Analysis of individual sequences (e.g., MEGAN and G + C content) and assemblies from each habitat type revealed the presence of dominant archaeal populations in all environments, 10 of whose genomes were largely reconstructed from the sequence data. Analysis of protein family occurrence, particularly of those involved in energy conservation, electron transport, and autotrophic metabolism, revealed significant differences in metabolic strategies across sites consistent with differences in major geochemical attributes (e.g., sulfide, oxygen, pH). These observations provide an ecological basis for understanding the distribution of indigenous archaeal lineages across high-temperature systems of YNP. PMID:23720654

Corruption of genomic databases with anomalous sequence.

PubMed

Lamperti, E D; Kittelberger, J M; Smith, T F; Villa-Komaroff, L

1992-06-11

We describe evidence that DNA sequences from vectors used for cloning and sequencing have been incorporated accidentally into eukaryotic entries in the GenBank database. These incorporations were not restricted to one type of vector or to a single mechanism. Many minor instances may have been the result of simple editing errors, but some entries contained large blocks of vector sequence that had been incorporated by contamination or other accidents during cloning. Some cases involved unusual rearrangements and areas of vector distant from the normal insertion sites. Matches to vector were found in 0.23% of 20,000 sequences analyzed in GenBank Release 63. Although the possibility of anomalous sequence incorporation has been recognized since the inception of GenBank and should be easy to avoid, recent evidence suggests that this problem is increasing more quickly than the database itself. The presence of anomalous sequence may have serious consequences for the interpretation and use of database entries, and will have an impact on issues of database management. The incorporated vector fragments described here may also be useful for a crude estimate of the fidelity of sequence information in the database. In alignments with well-defined ends, the matching sequences showed 96.8% identity to vector; when poorer matches with arbitrary limits were included, the aggregate identity to vector sequence was 94.8%.

Rate Theory Modeling and Simulation of Silicide Fuel at LWR Conditions

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

Miao, Yinbin; Ye, Bei; Hofman, Gerard

As a promising candidate for the accident tolerant fuel (ATF) used in light water reactors (LWRs), the fuel performance of uranium silicide (U 3Si 2) at LWR conditions needs to be well understood. In this report, rate theory model was developed based on existing experimental data and density functional theory (DFT) calculations so as to predict the fission gas behavior in U 3Si 2 at LWR conditions. The fission gas behavior of U 3Si 2 can be divided into three temperature regimes. During steady-state operation, the majority of the fission gas stays in intragranular bubbles, whereas the dominance of intergranularmore » bubbles and fission gas release only occurs beyond 1000 K. The steady-state rate theory model was also used as reference to establish a gaseous swelling correlation of U 3Si 2 for the BISON code. Meanwhile, the overpressurized bubble model was also developed so that the fission gas behavior at LOCA can be simulated. LOCA simulation showed that intragranular bubbles are still dominant after a 70 second LOCA, resulting in a controllable gaseous swelling. The fission gas behavior of U 3Si 2 at LWR conditions is benign according to the rate theory prediction at both steady-state and LOCA conditions, which provides important references to the qualification of U 3Si 2 as a LWR fuel material with excellent fuel performance and enhanced accident tolerance.« less

Sulfate Reducing Bacteria and Mycobacteria Dominate the Biofilm Communities in a Chloraminated Drinking Water Distribution System.

PubMed

Gomez-Smith, C Kimloi; LaPara, Timothy M; Hozalski, Raymond M

2015-07-21

The quantity and composition of bacterial biofilms growing on 10 water mains from a full-scale chloraminated water distribution system were analyzed using real-time PCR targeting the 16S rRNA gene and next-generation, high-throughput Illumina sequencing. Water mains with corrosion tubercles supported the greatest amount of bacterial biomass (n = 25; geometric mean = 2.5 × 10(7) copies cm(-2)), which was significantly higher (P = 0.04) than cement-lined cast-iron mains (n = 6; geometric mean = 2.0 × 10(6) copies cm(-2)). Despite spatial variation of community composition and bacterial abundance in water main biofilms, the communities on the interior main surfaces were surprisingly similar, containing a core group of operational taxonomic units (OTUs) assigned to only 17 different genera. Bacteria from the genus Mycobacterium dominated all communities at the main wall-bulk water interface (25-78% of the community), regardless of main age, estimated water age, main material, and the presence of corrosion products. Further sequencing of the mycobacterial heat shock protein gene (hsp65) provided species-level taxonomic resolution of mycobacteria. The two dominant Mycobacteria present, M. frederiksbergense (arithmetic mean = 85.7% of hsp65 sequences) and M. aurum (arithmetic mean = 6.5% of hsp65 sequences), are generally considered to be nonpathogenic. Two opportunistic pathogens, however, were detected at low numbers: M. hemophilum (arithmetic mean = 1.5% of hsp65 sequences) and M. abscessus (arithmetic mean = 0.006% of hsp65 sequences). Sulfate-reducing bacteria from the genus Desulfovibrio, which have been implicated in microbially influenced corrosion, dominated all communities located underneath corrosion tubercules (arithmetic mean = 67.5% of the community). This research provides novel insights into the quantity and composition of biofilms in full-scale drinking water distribution systems, which is critical for assessing the risks to public health and to the water supply infrastructure.

Genesis Failure Investigation Report

NASA Technical Reports Server (NTRS)

Klein, John

2004-01-01

The-Genesis mission to collect solar-wind samples and return them to Earth for detailed analysis proceeded successfully for 3.5 years. During reentry on September 8, 2004, a failure in the entry, descent and landing sequence resulted in a crash landing of the Genesis sample return capsule. This document describes the findings of the avionics sub-team that supported the accident investigation of the JPL Failure Review Board.

Memorization of Sequences of Movements of the Right or the Left Hand by Right- and Left-Handers: Vector Coding.

PubMed

Bobrova, E V; Bogacheva, I N; Lyakhovetskii, V A; Fabinskaja, A A; Fomina, E V

2017-01-01

In order to test the hypothesis of hemisphere specialization for different types of information coding (the right hemisphere, for positional coding; the left one, for vector coding), we analyzed the errors of right and left-handers during a task involving the memorization of sequences of movements by the left or the right hand, which activates vector coding by changing the order of movements in memorized sequences. The task was first performed by the right or the left hand, then by the opposite hand. It was found that both'right- and left-handers use the information about the previous movements of the dominant hand, but not of the non-dom" inant one. After changing the hand, right-handers use the information about previous movements of the second hand, while left-handers do not. We compared our results with the data of previous experiments, in which positional coding was activated, and concluded that both right- and left-handers use vector coding for memorizing the sequences of their dominant hands and positional coding for memorizing the sequences of non-dominant hand. No similar patterns of errors were found between right- and left-handers after changing the hand, which suggests that in right- and left-handersthe skills are transferred in different ways depending on the type of coding.

Deep sequencing of the viral phoH gene reveals temporal variation, depth-specific composition, and persistent dominance of the same viral phoH genes in the Sargasso Sea

PubMed Central

Goldsmith, Dawn B.; Parsons, Rachel J.; Beyene, Damitu; Salamon, Peter

2015-01-01

Deep sequencing of the viral phoH gene, a host-derived auxiliary metabolic gene, was used to track viral diversity throughout the water column at the Bermuda Atlantic Time-series Study (BATS) site in the summer (September) and winter (March) of three years. Viral phoH sequences reveal differences in the viral communities throughout a depth profile and between seasons in the same year. Variation was also detected between the same seasons in subsequent years, though these differences were not as great as the summer/winter distinctions. Over 3,600 phoH operational taxonomic units (OTUs; 97% sequence identity) were identified. Despite high richness, most phoH sequences belong to a few large, common OTUs whereas the majority of the OTUs are small and rare. While many OTUs make sporadic appearances at just a few times or depths, a small number of OTUs dominate the community throughout the seasons, depths, and years. PMID:26157645

ARTIST: An International Project Investigating Aerosol Retention in a Ruptured Steam Generator

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

Guentay, S.; Dehbi, A.; Suckow, D.

2002-07-01

Steam generator tube ruptures (SGTR) with a concurrent stuck open safety relief valve are counted among the risk dominant accident sequences because of the potential for radioactive products to bypass the containment. Owing to the absence of relevant empirical data and the complexity of the geometry and controlling processes, the aerosol removal in the steam generator (SG) tubes and in the secondary side is not well understood. Therefore, little or no credit is usually taken for aerosol retention due to natural processes in the various components of a SG. To help reduce the uncertainties associated with fission product release followingmore » an SGTR sequence, the Paul Scherrer Institut has initiated an international experimental project to be performed in the ARTIST (AeRosol Trapping In a Steam generaTor) facility in the time period from 2002 to 2007. The ARTIST test section is a scaled model of a real SG, and is comprised of a 264-tube bundle with a maximum height of 3.8 m, as well as one full-size droplet separator and one full-size steam dryer. The ARTIST facility is capable of producing soluble and insoluble aerosols and entrain them at sonic gas flow rates (up to 0.25 kg/s, thus matching comparable values predicted by the codes. In addition, aerosols can be generated at prototypical concentrations (up to 5 g/m{sup 3}) and sizes (0.2-5 mm AMMD). State of the art instrumentation is used (Low-pressure impactors, photometers, on-line particle sizer, online droplet sizer, etc.). The ARTIST project will simulate the flow and retention of aerosol-borne fission products in the SG, and provide a unique database to support safety assessments and analytical models. The project is foreseen in seven phases: 1) Aerosol retention in the tube under dry secondary side conditions, 2) Aerosol retention in the near field close to break under dry conditions, 3) Aerosol retention in the bundle far field under dry conditions, 4) Aerosol retention in the separator and dryer under dry conditions, 5) Aerosol retention in the bundle section under wet conditions, 6) Droplet retention in separator and dryer sections and 7) Integral tests to examine overall retention in the SG unit. The project will investigate phenomena at the separate effect and integral levels, and will also address selected accident management (AM) issues. The kick-off experiments are scheduled for the first half of 2002, and some early results will be summarized at the meeting. (authors)« less

Novel chytrid lineages dominate fungal sequences in diverse marine and freshwater habitats

NASA Astrophysics Data System (ADS)

Comeau, André M.; Vincent, Warwick F.; Bernier, Louis; Lovejoy, Connie

2016-07-01

In aquatic environments, fungal communities remain little studied despite their taxonomic and functional diversity. To extend the ecological coverage of this group, we conducted an in-depth analysis of fungal sequences within our collection of 3.6 million V4 18S rRNA pyrosequences originating from 319 individual marine (including sea-ice) and freshwater samples from libraries generated within diverse projects studying Arctic and temperate biomes in the past decade. Among the ~1.7 million post-filtered reads of highest taxonomic and phylogenetic quality, 23,263 fungal sequences were identified. The overall mean proportion was 1.35%, but with large variability; for example, from 0.01 to 59% of total sequences for Arctic seawater samples. Almost all sample types were dominated by Chytridiomycota-like sequences, followed by moderate-to-minor contributions of Ascomycota, Cryptomycota and Basidiomycota. Species and/or strain richness was high, with many novel sequences and high niche separation. The affinity of the most common reads to phytoplankton parasites suggests that aquatic fungi deserve renewed attention for their role in algal succession and carbon cycling.

Protein Sectors: Statistical Coupling Analysis versus Conservation

PubMed Central

Teşileanu, Tiberiu; Colwell, Lucy J.; Leibler, Stanislas

2015-01-01

Statistical coupling analysis (SCA) is a method for analyzing multiple sequence alignments that was used to identify groups of coevolving residues termed “sectors”. The method applies spectral analysis to a matrix obtained by combining correlation information with sequence conservation. It has been asserted that the protein sectors identified by SCA are functionally significant, with different sectors controlling different biochemical properties of the protein. Here we reconsider the available experimental data and note that it involves almost exclusively proteins with a single sector. We show that in this case sequence conservation is the dominating factor in SCA, and can alone be used to make statistically equivalent functional predictions. Therefore, we suggest shifting the experimental focus to proteins for which SCA identifies several sectors. Correlations in protein alignments, which have been shown to be informative in a number of independent studies, would then be less dominated by sequence conservation. PMID:25723535

The morphological transformation of red sequence galaxies in clusters since z ˜ 1

NASA Astrophysics Data System (ADS)

Cerulo, P.; Couch, W. J.; Lidman, C.; Demarco, R.; Huertas-Company, M.; Mei, S.; Sánchez-Janssen, R.; Barrientos, L. F.; Muñoz, R.

2017-11-01

The study of galaxy morphology is fundamental to understand the physical processes driving the structural evolution of galaxies. It has long been known that dense environments host high fractions of early-type galaxies and low fractions of late-type galaxies, indicating that the environment affects the structural evolution of galaxies. In this paper, we present an analysis of the morphological composition of red sequence galaxies in a sample of nine galaxy clusters at 0.8 < z < 1.5 drawn from the HAWK-I Cluster Survey (HCS), with the aim of investigating the evolutionary paths of galaxies with different morphologies. We classify galaxies according to their apparent bulge-to-total light ratio and compare with red sequence galaxies from the lower redshift WIde-field Nearby Galaxy-cluster Survey (WINGS) and ESO Distant Cluster Survey (EDisCS). We find that, while the HCS red sequence is dominated by elliptical galaxies at all luminosities and stellar masses, the WINGS red sequence is dominated by elliptical galaxies only at its bright end (MV < -21.0 mag), while S0s become the most frequent class at fainter luminosities. Disc-dominated galaxies comprise 10-14 per cent of the red sequence population in the low (WINGS) and high (HCS) redshift samples, although their fraction increases up to 40 per cent at 0.4 < z < 0.8 (EDisCS). We find a 20 per cent increase in the fraction of S0 galaxies from z ∼ 1.5 to 0.05 on the red sequence. These results suggest that elliptical and S0 galaxies follow different evolutionary histories and, in particular, that S0 galaxies result, at least at intermediate luminosities (-22.0 < MV < -20.0), from the morphological transformation of quiescent spiral galaxies.

Post-accidental riverine dispersion of sediments contaminated by radionuclides: confrontation of lessons learnt from Chernobyl and Fukushima case studies in catchments from Russia (1986-2009) and Japan (2011-2012)

NASA Astrophysics Data System (ADS)

Evrard, Olivier; Belyaev, Vladimir; Onda, Yuichi; Chartin, Caroline; Patin, Jeremy; Lefèvre, Irène; Ayrault, Sophie; Ivanova, Nadezda; Bonté, Philippe; Golosov, Valentin

2013-04-01

Chernobyl (1986) and Fukushima (2011) nuclear power plant accidents led to the release of important quantities of radionuclides (e.g., Cs-134; Cs-137) into the environment, and to the formation of severe contamination plumes (with initial Cs-137 activities exceeding typically 400 kBq m-2) on soils of the regions exposed to the radioactive fallout. This leads to important consequences for agriculture in strongly contaminated areas where the most affected fields should not be cultivated anymore during long periods of time, depending on the half life of the emitted radionuclides. Furthermore, sediment transfer in rivers can lead to the dispersion of radioactive contamination into larger areas over time. In this paper, we propose a methodology to trace and model radioactive contamination in river catchments over the short (2 yrs) and the longer term (25 yr) after major nuclear power plant accidents. This methodology is established and confronted to two case studies. The most recent study was conducted in the coastal catchments of the Rivers Nitta, Mano and Ota (ca. 600 km²) draining the main part of the radioactive pollution plume that deposited across Fukushima Prefecture. Three field campaigns were conducted to sample riverbed sediment along those rivers after the summer typhoons and the spring snowmelt (i.e., in Nov 2011, April 2012 and Nov 2012). Based on their analysis in gamma spectrometry, we show the rapid dispersion of the inland contamination and its progressive export by coastal rivers to the Pacific Ocean. This is confirmed by measurements of the Ag-110m: Cs-137 ratio. Analysis of sediment sequences that accumulated in reservoirs of the region provides additional information on the magnitude on sediment transfers in those areas. This rapid dispersion of radioactive contamination in Japan is confronted to lessons learnt from a case study conducted in the Plava River catchment (ca. 2000 km²) located in the so-called "Plavsk contamination hotspot", in western Russia. We used the Landsoil expert-based erosion model, 137Cs inventory profiles and alluvial sediment core analyses to understand and quantify contaminated sediment transfer across the cultivated catchment since 1986. Our results show that soil redistribution in the fields was dominant, and that sediment eroded from cropland mostly re-deposited in dry valleys during the heaviest storms. Overall, only 15 to 25% of material eroded from the hillslopes was delivered to the river valleys. Accumulation of contaminated sediment in dry valley systems therefore constitutes a major problem 25 years after Chernobyl accident. In conclusion, we show how the experience acquired after the Chernobyl accident contributed to facilitate the urgent analysis of sediment transfers across Fukushima Prefecture, where the possible measurement of relatively short-lived radionuclides (Ag-110m, Cs-134) provided a way to conduct a rapid quantitative assessment of contaminated sediment sources and exports.

SPATIALLY RESOLVED STAR FORMATION MAIN SEQUENCE OF GALAXIES IN THE CALIFA SURVEY

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

Cano-Díaz, M.; Sánchez, S. F.; Zibetti, S.

2016-04-20

The “main sequence of galaxies”–defined in terms of the total star formation rate ψ versus the total stellar mass M {sub *}—is a well-studied tight relation that has been observed at several wavelengths and at different redshifts. All earlier studies have derived this relation from integrated properties of galaxies. We recover the same relation from an analysis of spatially resolved properties, with integral field spectroscopic (IFS) observations of 306 galaxies from the CALIFA survey. We consider the SFR surface density in units of log( M {sub ⊙} yr{sup −1} Kpc{sup −2}) and the stellar mass surface density in units ofmore » log( M {sub ⊙} Kpc{sup −2}) in individual spaxels that probe spatial scales of 0.5–1.5 Kpc. This local relation exhibits a high degree of correlation with small scatter ( σ = 0.23 dex), irrespective of the dominant ionization source of the host galaxy or its integrated stellar mass. We highlight (i) the integrated star formation main sequence formed by galaxies whose dominant ionization process is related to star formation, for which we find a slope of 0.81 ± 0.02; (ii) for the spatially resolved relation obtained with the spaxel analysis, we find a slope of 0.72 ± 0.04; and (iii) for the integrated main sequence, we also identified a sequence formed by galaxies that are dominated by an old stellar population, which we have called the retired galaxies sequence.« less

Factors influencing biosafety level and LAI among the staff of medical laboratories.

PubMed

Kozajda, Anna; Bródka, Karolina; Szadkowska-Stańczyk, Irena

2013-01-01

The aim of the study was to assess the biological risks of medical laboratory employees with particular focus on laboratory acquired infection (LAI), activities having the greatest risk, accidents with biological material, post exposure procedure, preventive measures and workers' knowledge about biological exposure. The study involved 9 laboratories. A questionnaire survey was attended by 123 employees and 9 heads of these units with the use of two questionnaires for laboratory workers and the managers. 32.5% of the respondents (40 persons) had an accident at least once. Needlestick or a broken glass injury covered 18.7% respondents (23 persons), while splashing the skin, mucous membranes or conjunctivae related to 22.8% (28 persons). Among the employees who had an accident, only 45% of the respondents (18 persons) reported this to the manager. Microbes dominant in the biological material were known only to 57 respondents (46.3%), less than half could correctly give an example of a disease (57 persons, 46.3%). More than half of the respondents admitted that they do not know all of the possible routes of infection while working in the laboratory (68 persons, 55.3%). In the study population, a high incidence of accidents was observed, usually during blood sampling and transfer of biological material. Condition of the workers' equipment with personal protective measures and laboratory facilities in devices to reduce the risk of infection and procedures for handling the potentially infectious material should be considered as insufficient. Lack of basic knowledge of the employees about biohazards at workplaces was shown.

R/S analysis of reaction time in Neuron Type Test for human activity in civil aviation

NASA Astrophysics Data System (ADS)

Zhang, Hong-Yan; Kang, Ming-Cui; Li, Jing-Qiang; Liu, Hai-Tao

2017-03-01

Human factors become the most serious problem leading to accidents of civil aviation, which stimulates the design and analysis of Neuron Type Test (NTT) system to explore the intrinsic properties and patterns behind the behaviors of professionals and students in civil aviation. In the experiment, normal practitioners' reaction time sequences, collected from NTT, exhibit log-normal distribution approximately. We apply the χ2 test to compute the goodness-of-fit by transforming the time sequence with Box-Cox transformation to cluster practitioners. The long-term correlation of different individual practitioner's time sequence is represented by the Hurst exponent via Rescaled Range Analysis, also named by Range/Standard deviation (R/S) Analysis. The different Hurst exponent suggests the existence of different collective behavior and different intrinsic patterns of human factors in civil aviation.

Parallel sequencing lives, or what makes large sequencing projects successful.

PubMed

Quilez, Javier; Vidal, Enrique; Dily, François Le; Serra, François; Cuartero, Yasmina; Stadhouders, Ralph; Graf, Thomas; Marti-Renom, Marc A; Beato, Miguel; Filion, Guillaume

2017-11-01

T47D_rep2 and b1913e6c1_51720e9cf were 2 Hi-C samples. They were born and processed at the same time, yet their fates were very different. The life of b1913e6c1_51720e9cf was simple and fruitful, while that of T47D_rep2 was full of accidents and sorrow. At the heart of these differences lies the fact that b1913e6c1_51720e9cf was born under a lab culture of Documentation, Automation, Traceability, and Autonomy and compliance with the FAIR Principles. Their lives are a lesson for those who wish to embark on the journey of managing high-throughput sequencing data. © The Author 2017. Published by Oxford University Press.

Binomial test statistics using Psi functions

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

Bowman, Kimiko o

2007-01-01

For the negative binomial model (probability generating function (p + 1 - pt){sup -k}) a logarithmic derivative is the Psi function difference {psi}(k + x) - {psi}(k); this and its derivatives lead to a test statistic to decide on the validity of a specified model. The test statistic uses a data base so there exists a comparison available between theory and application. Note that the test function is not dominated by outliers. Applications to (i) Fisher's tick data, (ii) accidents data, (iii) Weldon's dice data are included.

Stressor Effects in Lab and Life: Correspondences between the Effects of the Accident at Three Mile Island and Stress Responses in the Laboratory.

DTIC Science & Technology

1982-09-01

data as well as administra- tion requirements are available. Video game task: a non-social, task-oriented setting in which the person is working...dominant arm and the subject was instructed to watch a video screen. After the experimenter left the room, videotaped instructions for a video game (similar...with video games to understand the task. The task itself was selected for its general interest across divergent groups of potential subjects and

Novel TMEM98 mutations in pedigrees with autosomal dominant nanophthalmos

PubMed Central

Khorram, David; Choi, Michael; Roos, Ben R.; Stone, Edwin M.; Kopel, Teresa; Allen, Richard; Alward, Wallace L.M.; Scheetz, Todd E.

2015-01-01

Purpose Autosomal dominant nanophthalmos is an inherited eye disorder characterized by a structurally normal but smaller eye. Patients with nanophthalmos have high hyperopia (far-sightedness), a greater incidence of angle-closure glaucoma, and increased risk of surgical complications. In this study, the clinical features and the genetic basis of nanophthalmos were investigated in two large autosomal dominant nanophthalmos pedigrees. Methods Fourteen members of a Caucasian pedigree from the United States and 15 members of a pedigree from the Mariana Islands enrolled in a genetic study of nanophthalmos and contributed DNA samples. Twenty of 29 family members underwent eye examinations that included measurement of axial eye length and/or refractive error. The genetic basis of nanophthalmos in the pedigrees was studied with linkage analysis, whole exome sequencing, and candidate gene (i.e., TMEM98) sequencing to identify the nanophthalmos-causing gene. Results Nine members of the pedigree from the United States and 11 members of the pedigree from the Mariana Islands were diagnosed with nanophthalmos that is transmitted as an autosomal dominant trait. The patients with nanophthalmos had abnormally short axial eye lengths, which ranged from 15.9 to 18.4 mm. Linkage analysis of the nanophthalmos pedigree from the United States identified nine large regions of the genome (greater than 10 Mbp) that were coinherited with disease in this family. Genes within these “linked regions” were examined for disease-causing mutations using exome sequencing, and a His196Pro mutation was detected in the TMEM98 gene, which was recently reported to be a nanophthalmos gene. Sanger sequencing subsequently showed that all other members of this pedigree with nanophthalmos also carry the His196Pro TMEM98 mutation. Testing the Mariana Islands pedigree for TMEM98 mutations identified a 34 bp heterozygous deletion that spans the 3′ end of exon 4 in all affected family members. Neither TMEM98 mutation was detected in public exome sequence databases. Conclusions A recent report identified a single TMEM98 missense mutation in a nanophthalmos pedigree. Our discovery of two additional TMEM98 mutations confirms the important role of the gene in the pathogenesis of autosomal dominant nanophthalmos. PMID:26392740

Novel TMEM98 mutations in pedigrees with autosomal dominant nanophthalmos.

PubMed

Khorram, David; Choi, Michael; Roos, Ben R; Stone, Edwin M; Kopel, Teresa; Allen, Richard; Alward, Wallace L M; Scheetz, Todd E; Fingert, John H

2015-01-01

Autosomal dominant nanophthalmos is an inherited eye disorder characterized by a structurally normal but smaller eye. Patients with nanophthalmos have high hyperopia (far-sightedness), a greater incidence of angle-closure glaucoma, and increased risk of surgical complications. In this study, the clinical features and the genetic basis of nanophthalmos were investigated in two large autosomal dominant nanophthalmos pedigrees. Fourteen members of a Caucasian pedigree from the United States and 15 members of a pedigree from the Mariana Islands enrolled in a genetic study of nanophthalmos and contributed DNA samples. Twenty of 29 family members underwent eye examinations that included measurement of axial eye length and/or refractive error. The genetic basis of nanophthalmos in the pedigrees was studied with linkage analysis, whole exome sequencing, and candidate gene (i.e., TMEM98) sequencing to identify the nanophthalmos-causing gene. Nine members of the pedigree from the United States and 11 members of the pedigree from the Mariana Islands were diagnosed with nanophthalmos that is transmitted as an autosomal dominant trait. The patients with nanophthalmos had abnormally short axial eye lengths, which ranged from 15.9 to 18.4 mm. Linkage analysis of the nanophthalmos pedigree from the United States identified nine large regions of the genome (greater than 10 Mbp) that were coinherited with disease in this family. Genes within these "linked regions" were examined for disease-causing mutations using exome sequencing, and a His196Pro mutation was detected in the TMEM98 gene, which was recently reported to be a nanophthalmos gene. Sanger sequencing subsequently showed that all other members of this pedigree with nanophthalmos also carry the His196Pro TMEM98 mutation. Testing the Mariana Islands pedigree for TMEM98 mutations identified a 34 bp heterozygous deletion that spans the 3' end of exon 4 in all affected family members. Neither TMEM98 mutation was detected in public exome sequence databases. A recent report identified a single TMEM98 missense mutation in a nanophthalmos pedigree. Our discovery of two additional TMEM98 mutations confirms the important role of the gene in the pathogenesis of autosomal dominant nanophthalmos.

Three distinct clades of cultured heterocystous cyanobacteria constitute the dominant N2-fixing members of biological soil crusts of the Colorado Plateau, USA

USGS Publications Warehouse

Yeager, C.M.; Kornosky, J.L.; Morgan, R.E.; Cain, E.C.; Garcia-Pichel, F.; Housman, D.C.; Belnap, J.; Kuske, C.R.

2007-01-01

The identity of the numerically dominant N2-fixing bacteria in biological soil crusts of the Colorado Plateau region and two outlying areas was determined using multiple approaches, to link the environmental diversity of nifH gene sequences to cultured bacterial isolates from the regions. Of the nifH sequence-types detected in soil crusts of the Colorado Plateau, 89% (421/473) were most closely related to nifH signature sequences from cyanobacteria of the order Nostocales. N2-fixing cyanobacterial strains were cultured from crusts and their morphotypes, 16S rRNA gene and nifH gene sequences were characterized. The numerically dominant diazotrophs in the Colorado Plateau crusts fell within three clades of heterocystous cyanobacteria. Two clades are well-represented by phylogenetically and morphologically coherent strains, corresponding to the descriptions of Nostoc commune and Scytonema hyalinum, which are widely recognized as important N2-fixing components of soil crusts. A third, previously-overlooked clade was represented by a phylogenetically coherent but morphologically diverse group of strains that encompass the morphogenera Tolypothrix and Spirirestis. Many of the strains in each of these groups contained at least two nifH copies that represent different clusters in the nifH environmental survey. ?? 2007 Federation of European Microbiological Societies.

Shallow-seated explosions in the construction of the Motukorea tuff ring (Auckland, New Zealand): Evidence from lithic and sedimentary characteristics

NASA Astrophysics Data System (ADS)

Agustín-Flores, Javier; Németh, Károly; Cronin, Shane J.; Lindsay, Jan M.; Kereszturi, Gábor

2015-10-01

At least 52 eruption centres are scattered within the 360 km2 Auckland Volcanic Field (AVF). Motukorea, now an island in the Waitemata Harbour, is one of 39 AVF volcanoes that experienced a phreatomagmatic explosive phase, before a magmatic phase. The volcano erupted through a 200-300 m-thick, consolidated, mudstone/sandstone sequence of the Miocene Waitemata Group, which overlies the Waipapa Terrane greywacke basement. Detailed field descriptions of the sedimentary characteristics of the early phreatomagmatic deposits were carried out, along with examination of lithics. The ejecta ring deposit comprises 55 to 60 vol.% lithics, of which Waitemata Group fragments constitute approximately 90 vol.%, whereas < 10 vol.% are Waipapa fragments, suggesting a dominance of shallow fragmentation. The sedimentary characteristics of the stratigraphic sequence at Motukorea suggest a dominance of wet surges at the beginning of the eruption with progression into drier sequences upwards. This is reflected in increasing inter-bedded juvenile-pyroclast-dominated fall deposits up-sequence. These characteristics are attributed to the changing hydrogeological conditions within the diatreme and the host rocks. These findings shed light on the eruption dynamics of phreatomagmatic eruptions through consolidated rocks in the AVF and enable the depiction of a scenario of future eruptions within the field in similar substrates.

Unlocking the Mystery of Columbia's Tragic Accident Through Materials Characterization

NASA Technical Reports Server (NTRS)

Shah, Sandeep; Jerman, Gregory; Coston, James

2003-01-01

The wing and underbelly reconstruction of Space Shuttle Columbia took place at the Shuttle Landing Facility Hangar after the accident which destroyed STS-107. Fragments were placed on a grid according to their original location on the orbiter. Some Reinforced Carbon-Carbon (RCC) panels of the left wing leading edge and other parts from both leading edges were recovered and incorporated into the reconstruction. The recovered parts were tracked on a database according to a number and also tracked on a map of the orbiter. This viewgraph presentation describes the process of failure analysis undertaken by the Materials and Processes (M&P) Problem Resolution Team. The team started with factual observations about the accident, and identified highest level questions for it to answer in order to understand where on the orbiter failure occured, what component(s) failed, and what was the sequence of events. The finding of Columbia's MADS/OEX data recorder shifted the focus of the team's analysis to the left wing leading edge damage. The team placed particular attention on slag deposits on some of the RCC panels. The presentation lists analysis techniques, and lower level questions for the team to answer.

[Necrotising fasciitis caused by Saksenaea vasiformis in an immunocompetent patient after a car accident].

PubMed

Mayayo, Emilio; Stchigel, Alberto M; Cano, José F; Bernal-Escoté, Xana; Guarro, Josep

2013-01-03

Cutaneous mucormycosis (zygomycosis), with subcutaneous spreading and dissemination, in immunocompetent patients is an uncommon disease caused by species belonging to the fungal genera Apophysomyces, Rhizopus and Saksenaea, among others. A case of necrotising fasciitis by Saksenaea vasiformis in an immunocompetent woman is described. The infection was acquired through a car accident resulting in multiple injuries affecting mainly her right arm. After the surgical reduction of fractures, skin lesions worsened and led to necrosis. The patient quickly developed a severe necrotising fasciitis with negative cultures at first. Despite the extensive surgical debridement and the aggressive antifungal treatment, the patient died. The histopathological study showed a fungal infection due to a fungus belonging to the Mucorales order, which was confirmed by culturing the clinical sample on Sabouraud agar, and identifying the species by cultures on Czapek-Dox agar, and sequencing of the ITS region of the ribosomal DNA. This case confirm the presence of this fungus in Spain, the value of histopathology for the mucormycosis diagnosis, as well as the need to perform special cultures to facilitate their isolation and identification to the species level by the combined use of Czapek-Dox agar and sequencing of the ITS region. Copyright © 2012 Revista Iberoamericana de Micología. Published by Elsevier España, S.L. All rights reserved.

Accident Source Terms for Pressurized Water Reactors with High-Burnup Cores Calculated using MELCOR 1.8.5.

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

Gauntt, Randall O.; Goldmann, Andrew; Kalinich, Donald A.

2016-12-01

In this study, risk-significant pressurized-water reactor severe accident sequences are examined using MELCOR 1.8.5 to explore the range of fission product releases to the reactor containment building. Advances in the understanding of fission product release and transport behavior and severe accident progression are used to render best estimate analyses of selected accident sequences. Particular emphasis is placed on estimating the effects of high fuel burnup in contrast with low burnup on fission product releases to the containment. Supporting this emphasis, recent data available on fission product release from high-burnup (HBU) fuel from the French VERCOR project are used in thismore » study. The results of these analyses are treated as samples from a population of accident sequences in order to employ approximate order statistics characterization of the results. These trends and tendencies are then compared to the NUREG-1465 alternative source term prescription used today for regulatory applications. In general, greater differences are observed between the state-of-the-art calculations for either HBU or low-burnup (LBU) fuel and the NUREG-1465 containment release fractions than exist between HBU and LBU release fractions. Current analyses suggest that retention of fission products within the vessel and the reactor coolant system (RCS) are greater than contemplated in the NUREG-1465 prescription, and that, overall, release fractions to the containment are therefore lower across the board in the present analyses than suggested in NUREG-1465. The decreased volatility of Cs 2 MoO 4 compared to CsI or CsOH increases the predicted RCS retention of cesium, and as a result, cesium and iodine do not follow identical behaviors with respect to distribution among vessel, RCS, and containment. With respect to the regulatory alternative source term, greater differences are observed between the NUREG-1465 prescription and both HBU and LBU predictions than exist between HBU and LBU analyses. Additionally, current analyses suggest that the NUREG-1465 release fractions are conservative by about a factor of 2 in terms of release fractions and that release durations for in-vessel and late in-vessel release periods are in fact longer than the NUREG-1465 durations. It is currently planned that a subsequent report will further characterize these results using more refined statistical methods, permitting a more precise reformulation of the NUREG-1465 alternative source term for both LBU and HBU fuels, with the most important finding being that the NUREG-1465 formula appears to embody significant conservatism compared to current best-estimate analyses. ACKNOWLEDGEMENTS This work was supported by the United States Nuclear Regulatory Commission, Office of Nuclear Regulatory Research. The authors would like to thank Dr. Ian Gauld and Dr. Germina Ilas, of Oak Ridge National Laboratory, for their contributions to this work. In addition to development of core fission product inventory and decay heat information for use in MELCOR models, their insights related to fuel management practices and resulting effects on spatial distribution of fission products in the core was instrumental in completion of our work.« less

Diversity and Structure of Diazotrophic Communities in Mangrove Rhizosphere, Revealed by High-Throughput Sequencing.

PubMed

Zhang, Yanying; Yang, Qingsong; Ling, Juan; Van Nostrand, Joy D; Shi, Zhou; Zhou, Jizhong; Dong, Junde

2017-01-01

Diazotrophic communities make an essential contribution to the productivity through providing new nitrogen. However, knowledge of the roles that both mangrove tree species and geochemical parameters play in shaping mangove rhizosphere diazotrophic communities is still elusive. Here, a comprehensive examination of the diversity and structure of microbial communities in the rhizospheres of three mangrove species, Rhizophora apiculata , Avicennia marina , and Ceriops tagal , was undertaken using high - throughput sequencing of the 16S rRNA and nifH genes. Our results revealed a great diversity of both the total microbial composition and the diazotrophic composition specifically in the mangrove rhizosphere. Deltaproteobacteria and Gammaproteobacteria were both ubiquitous and dominant, comprising an average of 45.87 and 86.66% of total microbial and diazotrophic communities, respectively. Sulfate-reducing bacteria belonging to the Desulfobacteraceae and Desulfovibrionaceae were the dominant diazotrophs. Community statistical analyses suggested that both mangrove tree species and additional environmental variables played important roles in shaping total microbial and potential diazotroph communities in mangrove rhizospheres. In contrast to the total microbial community investigated by analysis of 16S rRNA gene sequences, most of the dominant diazotrophic groups identified by nifH gene sequences were significantly different among mangrove species. The dominant diazotrophs of the family Desulfobacteraceae were positively correlated with total phosphorus, but negatively correlated with the nitrogen to phosphorus ratio. The Pseudomonadaceae were positively correlated with the concentration of available potassium, suggesting that diazotrophs potentially play an important role in biogeochemical cycles, such as those of nitrogen, phosphorus, sulfur, and potassium, in the mangrove ecosystem.

Diversity and Structure of Diazotrophic Communities in Mangrove Rhizosphere, Revealed by High-Throughput Sequencing

PubMed Central

Zhang, Yanying; Yang, Qingsong; Ling, Juan; Van Nostrand, Joy D.; Shi, Zhou; Zhou, Jizhong; Dong, Junde

2017-01-01

Diazotrophic communities make an essential contribution to the productivity through providing new nitrogen. However, knowledge of the roles that both mangrove tree species and geochemical parameters play in shaping mangove rhizosphere diazotrophic communities is still elusive. Here, a comprehensive examination of the diversity and structure of microbial communities in the rhizospheres of three mangrove species, Rhizophora apiculata, Avicennia marina, and Ceriops tagal, was undertaken using high-throughput sequencing of the 16S rRNA and nifH genes. Our results revealed a great diversity of both the total microbial composition and the diazotrophic composition specifically in the mangrove rhizosphere. Deltaproteobacteria and Gammaproteobacteria were both ubiquitous and dominant, comprising an average of 45.87 and 86.66% of total microbial and diazotrophic communities, respectively. Sulfate-reducing bacteria belonging to the Desulfobacteraceae and Desulfovibrionaceae were the dominant diazotrophs. Community statistical analyses suggested that both mangrove tree species and additional environmental variables played important roles in shaping total microbial and potential diazotroph communities in mangrove rhizospheres. In contrast to the total microbial community investigated by analysis of 16S rRNA gene sequences, most of the dominant diazotrophic groups identified by nifH gene sequences were significantly different among mangrove species. The dominant diazotrophs of the family Desulfobacteraceae were positively correlated with total phosphorus, but negatively correlated with the nitrogen to phosphorus ratio. The Pseudomonadaceae were positively correlated with the concentration of available potassium, suggesting that diazotrophs potentially play an important role in biogeochemical cycles, such as those of nitrogen, phosphorus, sulfur, and potassium, in the mangrove ecosystem. PMID:29093705

Surveillance of deaths on board Danish merchant ships, 1986-93: implications for prevention.

PubMed Central

Hansen, H L

1996-01-01

OBJECTIVE: To describe and analyse the types and circumstances of all natural and non-natural deaths among seamen on board Danish merchant ships. METHODS: Data on 147 cases were obtained from maritime authorities, an insurance company, shipping companies, hospitals, death registers, and death certificates in the period from 1986-93. RESULTS: The 53 natural deaths were dominated by cardiovascular diseases and infectious diseases. Insufficient treatment on board was identified as a contributing factor for death in some cases. Medical advice was not always sought and the advice given was in some cases insufficient. 73 fatal accidents were identified. The incidence of accidents of 5.29/10,000 person-years was 11.5 times higher than the incidence of 0.46/10,000 for the Danish male workforce ashore. 23 accidents (31%) were due to maritime casualties and 26 (36%) were occupational accidents. The remaining 24 (33%) were accidents during off duty hours including six self intoxications. Rough weather, inadequate awareness of safety, lack of use of personal protection devices, and inexperience were associated with many of the fatal injuries directly related to work. Alcohol played a major part in 12 out of 18 fatal injuries occurring during off duty hours. CONCLUSIONS: The maritime workplace was identified as a high risk workplace and in many aspects differs from the conditions ashore. Acute diseases and serious injuries pose special risks to seamen because of a lack of direct access to professional medical care at sea. Primary prevention of certain diseases is needed and possible. Improved training, improved systems of work, improved safety awareness, and greater use of personal protection devices are needed to prevent fatal injuries. Medical training of ships' officers providing medical care on board and specific training of doctors giving medical advise to ships should be improved to meet the needs. PMID:8664966

Evolution of multi-drug resistant HCV clones from pre-existing resistant-associated variants during direct-acting antiviral therapy determined by third-generation sequencing

NASA Astrophysics Data System (ADS)

Takeda, Haruhiko; Ueda, Yoshihide; Inuzuka, Tadashi; Yamashita, Yukitaka; Osaki, Yukio; Nasu, Akihiro; Umeda, Makoto; Takemura, Ryo; Seno, Hiroshi; Sekine, Akihiro; Marusawa, Hiroyuki

2017-03-01

Resistance-associated variant (RAV) is one of the most significant clinical challenges in treating HCV-infected patients with direct-acting antivirals (DAAs). We investigated the viral dynamics in patients receiving DAAs using third-generation sequencing technology. Among 283 patients with genotype-1b HCV receiving daclatasvir + asunaprevir (DCV/ASV), 32 (11.3%) failed to achieve sustained virological response (SVR). Conventional ultra-deep sequencing of HCV genome was performed in 104 patients (32 non-SVR, 72 SVR), and detected representative RAVs in all non-SVR patients at baseline, including Y93H in 28 (87.5%). Long contiguous sequences spanning NS3 to NS5A regions of each viral clone in 12 sera from 6 representative non-SVR patients were determined by third-generation sequencing, and showed the concurrent presence of several synonymous mutations linked to resistance-associated substitutions in a subpopulation of pre-existing RAVs and dominant isolates at treatment failure. Phylogenetic analyses revealed close genetic distances between pre-existing RAVs and dominant RAVs at treatment failure. In addition, multiple drug-resistant mutations developed on pre-existing RAVs after DCV/ASV in all non-SVR cases. In conclusion, multi-drug resistant viral clones at treatment failure certainly originated from a subpopulation of pre-existing RAVs in HCV-infected patients. Those RAVs were selected for and became dominant with the acquisition of multiple resistance-associated substitutions under DAA treatment pressure.

Holocene coastal development on the Florida peninsula

USGS Publications Warehouse

Davis, Richard; Hine, Albert C.; Shinn, Eugene A.

1992-01-01

The Florida peninsula contains five distinct coastal sections, each resulting from its own spectrum of coastal processes and sediment availability during a slowly rising, late Holocene sea level. The east coast barrier system is wave-dominated and has a large cuspate foreland (Cape Canaveral) near its middle. The Florida Keys and reef tract represent the only coastal carbonate system in the continental United States. An open-marine mangrove coast characterizes the low-energy, tide-dominated southwest part of the State. The central Gulf barrier system displays a mixed-energy morphology in a microtidal, low-energy setting. The open-coast marsh system of the Big Bend area that is north of the barrier system is also tide dominated, and is developed on a sediment-starved carbonate platform.The oldest preserved coastal Holocene section is the Florida Keys area where, at about 6 to 8 ka, sequences accumulated during the Holocene. Most of the remainder of the peninsular coast is characterized by terrigenous sequences less than 3 ka. The younger sequences accumulated almost exclusively from reworking of older strata without benefit of additional sediment supply from land.

Whole-exome sequencing, without prior linkage, identifies a mutation in LAMB3 as a cause of dominant hypoplastic amelogenesis imperfecta.

PubMed

Poulter, James A; El-Sayed, Walid; Shore, Roger C; Kirkham, Jennifer; Inglehearn, Chris F; Mighell, Alan J

2014-01-01

The conventional approach to identifying the defective gene in a family with an inherited disease is to find the disease locus through family studies. However, the rapid development and decreasing cost of next generation sequencing facilitates a more direct approach. Here, we report the identification of a frameshift mutation in LAMB3 as a cause of dominant hypoplastic amelogenesis imperfecta (AI). Whole-exome sequencing of three affected family members and subsequent filtering of shared variants, without prior genetic linkage, sufficed to identify the pathogenic variant. Simultaneous analysis of multiple family members confirms segregation, enhancing the power to filter the genetic variation found and leading to rapid identification of the pathogenic variant. LAMB3 encodes a subunit of Laminin-5, one of a family of basement membrane proteins with essential functions in cell growth, movement and adhesion. Homozygous LAMB3 mutations cause junctional epidermolysis bullosa (JEB) and enamel defects are seen in JEB cases. However, to our knowledge, this is the first report of dominant AI due to a LAMB3 mutation in the absence of JEB.

Genetic characterization of frameshift suppressors with new decoding properties.

PubMed Central

Hughes, D; Thompson, S; O'Connor, M; Tuohy, T; Nichols, B P; Atkins, J F

1989-01-01

Suppressor mutants that cause ribosomes to shift reading frame at specific and new sequences are described. Suppressors for trpE91, the only known suppressible -1 frameshift mutant, have been isolated in Escherichia coli and in Salmonella typhimurium. E. coli hopR acts on trpE91 within the 9-base-pair sequence GGA GUG UGA, is dominant, and is located at min 52 on the chromosome. Its Salmonella homolog maps at an equivalent position and arises as a rarer class in that organism as compared with E. coli. The Salmonella suppressor, hopE, believed to be in a duplicate copy of the same gene, maps at min 17. The +1 suppressor, sufT, acts at the nonmonotonous sequence CCGU, is dominant, and maps at min 59 on the Salmonella chromosome. PMID:2644219

Winnowing sequences from a database search.

PubMed

Berman, P; Zhang, Z; Wolf, Y I; Koonin, E V; Miller, W

2000-01-01

In database searches for sequence similarity, matches to a distinct sequence region (e.g., protein domain) are frequently obscured by numerous matches to another region of the same sequence. In order to cope with this problem, algorithms are developed to discard redundant matches. One model for this problem begins with a list of intervals, each with an associated score; each interval gives the range of positions in the query sequence that align to a database sequence, and the score is that of the alignment. If interval I is contained in interval J, and I's score is less than J's, then I is said to be dominated by J. The problem is then to identify each interval that is dominated by at least K other intervals, where K is a given level of "tolerable redundancy." An algorithm is developed to solve the problem in O(N log N) time and O(N*) space, where N is the number of intervals and N* is a precisely defined value that never exceeds N and is frequently much smaller. This criterion for discarding database hits has been implemented in the Blast program, as illustrated herein with examples. Several variations and extensions of this approach are also described.

Monitoring of microbial communities in anaerobic digestion sludge for biogas optimisation.

PubMed

Lim, Jun Wei; Ge, Tianshu; Tong, Yen Wah

2018-01-01

This study characterised and compared the microbial communities of anaerobic digestion (AD) sludge using three different methods - (1) Clone library; (2) Pyrosequencing; and (3) Terminal restriction fragment length polymorphism (T-RFLP). Although high-throughput sequencing techniques are becoming increasingly popular and affordable, the reliance of such techniques for frequent monitoring of microbial communities may be a financial burden for some. Furthermore, the depth of microbial analysis revealed by high-throughput sequencing may not be required for monitoring purposes. This study aims to develop a rapid, reliable and economical approach for the monitoring of microbial communities in AD sludge. A combined approach where genetic information of sequences from clone library was used to assign phylogeny to T-RFs determined experimentally was developed in this study. In order to assess the effectiveness of the combined approach, microbial communities determined by the combined approach was compared to that characterised by pyrosequencing. Results showed that both pyrosequencing and clone library methods determined the dominant bacteria phyla to be Proteobacteria, Firmicutes, Bacteroidetes, and Thermotogae. Both methods also found that sludge A and B were predominantly dominated by acetogenic methanogens followed by hydrogenotrophic methanogens. The number of OTUs detected by T-RFLP was significantly lesser than that detected by the clone library. In this study, T-RFLP analysis identified majority of the dominant species of the archaeal consortia. However, many of the more highly diverse bacteria consortia were missed. Nevertheless, the combined approach developed in this study where clone sequences from the clone library were used to assign phylogeny to T-RFs determined experimentally managed to accurately predict the same dominant microbial groups for both sludge A and sludge B, as compared to the pyrosequencing results. Results showed that the combined approach of clone library and T-RFLP accurately predicted the dominant microbial groups and thus is a reliable and more economical way to monitor the evolution of microbial systems in AD sludge. Copyright © 2017 Elsevier Ltd. All rights reserved.

Diversity of the small subunit ribosomal RNA gene of the arbuscular mycorrhizal fungi colonizing Clintonia borealis from a mixed-wood boreal forest.

PubMed

DeBellis, Tonia; Widden, Paul

2006-11-01

Arbuscular mycorrhizal fungi (AMF) communities in Clintonia borealis roots from a boreal mixed forests in northwestern Québec were investigated. Roots were sampled from 100 m2 plots whose overstory was dominated by either trembling aspen (Populus tremuloides Michx.), white birch (Betula papyrifera Marsh.), or mixed white spruce (Picea glauca (Moench) Voss) and balsam fir (Abies balsamea (L.) Mill.). Part of the 18S ribosomal gene of the AMF was amplified and the resulting PCR products were cloned. Restriction analysis of the 576 resulting clones yielded 92 different restriction patterns which were then sequenced. Fifty-two sequences closely matched other Glomus sequences from Genbank. Phylogenetic analysis revealed 10 different AMF sequence types, most of which clustered with other uncultured AM sequences from plant roots from various field sites. Compared with other AMF communities from comparable studies, richness and diversity were higher than observed in an arable field, but lower than seen in a tropical forest and a temperate wetland. The AMF communities from Clintonia roots under the different canopy types did not differ significantly and the dominant sequence type, which clustered with AM sequences from a variety of environments and hosts at distant geographical locations, represented 66.9% of all the clones analyzed.

A survey into process and worker's characteristics in the wood furniture industry in Songkhla Province, southern region of Thailand.

PubMed

Tuntiseranee, P; Chongsuvivatwong, V

1998-12-01

A cross-sectional survey of the wood furniture industry was conducted in southern Thailand in February 1993. The aim was to examine the manufacturing process, occupational hazards at the workplace, workers' demographic characteristics, period of employment, incidence rate of work related injury and some reproductive history of workers. Altogether 69 managers and 1,000 workers participated in the study. There are 2 main types of wood industry, rubberwood and hardwood. The rubberwood industry is semi-automated with advanced technology, has a female-dominated workforce of 200-300 workers per factory and overseas-market orientation. The hardwood industry is based in small-scale workplaces ranging from 20 to 60 workers, domestic-market orientation and has a male-dominated workforce. Most of the workers were young, single, of low education and were high turnover rate laborforce, with arduous work and long working hours per week. Solvent was the most frequent chemical exposure. The person-year incidence of chemical exposure in female workers was higher than in male workers for every group of chemicals. The incidence of accidents was twice as high as the official rate. The standardized fertility ratio of female wood workers was only 51.6% of that of the Thai female population. There was a high abortion rate among women who became pregnant inside the wood industry compared to that among pregnancies outside the wood factory. Wood industry workers were exposed to occupational hazards and accident-prone work conditions.

Population genetics of polymorphism and divergence for diploid selection models with arbitrary dominance.

PubMed

Williamson, Scott; Fledel-Alon, Adi; Bustamante, Carlos D

2004-09-01

We develop a Poisson random-field model of polymorphism and divergence that allows arbitrary dominance relations in a diploid context. This model provides a maximum-likelihood framework for estimating both selection and dominance parameters of new mutations using information on the frequency spectrum of sequence polymorphisms. This is the first DNA sequence-based estimator of the dominance parameter. Our model also leads to a likelihood-ratio test for distinguishing nongenic from genic selection; simulations indicate that this test is quite powerful when a large number of segregating sites are available. We also use simulations to explore the bias in selection parameter estimates caused by unacknowledged dominance relations. When inference is based on the frequency spectrum of polymorphisms, genic selection estimates of the selection parameter can be very strongly biased even for minor deviations from the genic selection model. Surprisingly, however, when inference is based on polymorphism and divergence (McDonald-Kreitman) data, genic selection estimates of the selection parameter are nearly unbiased, even for completely dominant or recessive mutations. Further, we find that weak overdominant selection can increase, rather than decrease, the substitution rate relative to levels of polymorphism. This nonintuitive result has major implications for the interpretation of several popular tests of neutrality.

Depletion of Unwanted Nucleic Acid Templates by Selective Cleavage: LNAzymes, Catalytically Active Oligonucleotides Containing Locked Nucleic Acids, Open a New Window for Detecting Rare Microbial Community Members

PubMed Central

Dolinšek, Jan; Dorninger, Christiane; Lagkouvardos, Ilias; Wagner, Michael

2013-01-01

Many studies of molecular microbial ecology rely on the characterization of microbial communities by PCR amplification, cloning, sequencing, and phylogenetic analysis of genes encoding rRNAs or functional marker enzymes. However, if the established clone libraries are dominated by one or a few sequence types, the cloned diversity is difficult to analyze by random clone sequencing. Here we present a novel approach to deplete unwanted sequence types from complex nucleic acid mixtures prior to cloning and downstream analyses. It employs catalytically active oligonucleotides containing locked nucleic acids (LNAzymes) for the specific cleavage of selected RNA targets. When combined with in vitro transcription and reverse transcriptase PCR, this LNAzyme-based technique can be used with DNA or RNA extracts from microbial communities. The simultaneous application of more than one specific LNAzyme allows the concurrent depletion of different sequence types from the same nucleic acid preparation. This new method was evaluated with defined mixtures of cloned 16S rRNA genes and then used to identify accompanying bacteria in an enrichment culture dominated by the nitrite oxidizer “Candidatus Nitrospira defluvii.” In silico analysis revealed that the majority of publicly deposited rRNA-targeted oligonucleotide probes may be used as specific LNAzymes with no or only minor sequence modifications. This efficient and cost-effective approach will greatly facilitate tasks such as the identification of microbial symbionts in nucleic acid preparations dominated by plastid or mitochondrial rRNA genes from eukaryotic hosts, the detection of contaminants in microbial cultures, and the analysis of rare organisms in microbial communities of highly uneven composition. PMID:23263968

Sequence-Based Genotyping for Marker Discovery and Co-Dominant Scoring in Germplasm and Populations

PubMed Central

Truong, Hoa T.; Ramos, A. Marcos; Yalcin, Feyruz; de Ruiter, Marjo; van der Poel, Hein J. A.; Huvenaars, Koen H. J.; Hogers, René C. J.; van Enckevort, Leonora. J. G.; Janssen, Antoine; van Orsouw, Nathalie J.; van Eijk, Michiel J. T.

2012-01-01

Conventional marker-based genotyping platforms are widely available, but not without their limitations. In this context, we developed Sequence-Based Genotyping (SBG), a technology for simultaneous marker discovery and co-dominant scoring, using next-generation sequencing. SBG offers users several advantages including a generic sample preparation method, a highly robust genome complexity reduction strategy to facilitate de novo marker discovery across entire genomes, and a uniform bioinformatics workflow strategy to achieve genotyping goals tailored to individual species, regardless of the availability of a reference sequence. The most distinguishing features of this technology are the ability to genotype any population structure, regardless whether parental data is included, and the ability to co-dominantly score SNP markers segregating in populations. To demonstrate the capabilities of SBG, we performed marker discovery and genotyping in Arabidopsis thaliana and lettuce, two plant species of diverse genetic complexity and backgrounds. Initially we obtained 1,409 SNPs for arabidopsis, and 5,583 SNPs for lettuce. Further filtering of the SNP dataset produced over 1,000 high quality SNP markers for each species. We obtained a genotyping rate of 201.2 genotypes/SNP and 58.3 genotypes/SNP for arabidopsis (n = 222 samples) and lettuce (n = 87 samples), respectively. Linkage mapping using these SNPs resulted in stable map configurations. We have therefore shown that the SBG approach presented provides users with the utmost flexibility in garnering high quality markers that can be directly used for genotyping and downstream applications. Until advances and costs will allow for routine whole-genome sequencing of populations, we expect that sequence-based genotyping technologies such as SBG will be essential for genotyping of model and non-model genomes alike. PMID:22662172

Diversity and Characterization of Sulfate-Reducing Bacteria in Groundwater at a Uranium Mill Tailings Site

PubMed Central

Chang, Yun-Juan; Peacock, Aaron D.; Long, Philip E.; Stephen, John R.; McKinley, James P.; Macnaughton, Sarah J.; Hussain, A. K. M. Anwar; Saxton, Arnold M.; White, David C.

2001-01-01

Microbially mediated reduction and immobilization of U(VI) to U(IV) plays a role in both natural attenuation and accelerated bioremediation of uranium-contaminated sites. To realize bioremediation potential and accurately predict natural attenuation, it is important to first understand the microbial diversity of such sites. In this paper, the distribution of sulfate-reducing bacteria (SRB) in contaminated groundwater associated with a uranium mill tailings disposal site at Shiprock, N.Mex., was investigated. Two culture-independent analyses were employed: sequencing of clone libraries of PCR-amplified dissimilatory sulfite reductase (DSR) gene fragments and phospholipid fatty acid (PLFA) biomarker analysis. A remarkable diversity among the DSR sequences was revealed, including sequences from δ-Proteobacteria, gram-positive organisms, and the Nitrospira division. PLFA analysis detected at least 52 different mid-chain-branched saturate PLFA and included a high proportion of 10me16:0. Desulfotomaculum and Desulfotomaculum-like sequences were the most dominant DSR genes detected. Those belonging to SRB within δ-Proteobacteria were mainly recovered from low-uranium (≤302 ppb) samples. One Desulfotomaculum-like sequence cluster overwhelmingly dominated high-U (>1,500 ppb) sites. Logistic regression showed a significant influence of uranium concentration over the dominance of this cluster of sequences (P = 0.0001). This strong association indicates that Desulfotomaculum has remarkable tolerance and adaptation to high levels of uranium and suggests the organism's possible involvement in natural attenuation of uranium. The in situ activity level of Desulfotomaculum in uranium-contaminated environments and its comparison to the activities of other SRB and other functional groups should be an important area for future research. PMID:11425735

Health impacts of productive conservation in urban transportation. Tapcut technical memorandum No. 27

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

Rowe, M.D.; Crowther, M.A.

1982-01-01

The literature on health effects of transportation-related pollutants is reviewed and assesses potential health risks of selected energy conservation policies for transportation systems in three representative cities. The conservation policies assessed are specified in other reports. The assessment includes health risks from pollutants emitted by vehicles, from pollutants emitted by industries involved in vehicle manufacturing, and from occupational accidents related to vehicle manufacturing throughout the economic system. Estimated health risk is dominated by ozone and hydrocarbon (benzo(a)pyrene) exposure. Results indicate that health risks from urban transportation systems will either remain constant or decline between 1980 and 2000 under all policiesmore » assessed. No significant change is projected for health risks from toxicants produced in vehicle manufacturing or from risks of occupational accidents throughout the economic system. In general, policies that reduce energy consumption also reduce projected health risks, even when they promote new technologies having potentially significant differences in emission characteristics and manufacturing requirements.« less

Commercial Aircraft Integrated Vehicle Health Management Study

NASA Technical Reports Server (NTRS)

Reveley, Mary S.; Briggs, Jeffrey L.; Evans, Joni K.; Jones, Sharon Monica; Kurtoglu, Tolga; Leone, Karen M.; Sandifer, Carl E.; Thomas, Megan A.

2010-01-01

Statistical data and literature from academia, industry, and other government agencies were reviewed and analyzed to establish requirements for fixture work in detection, diagnosis, prognosis, and mitigation for IVHM related hardware and software. Around 15 to 20 percent of commercial aircraft accidents between 1988 and 2003 involved inalftfnctions or failures of some aircraft system or component. Engine and landing gear failures/malfunctions dominate both accidents and incidents. The IVI vl Project research technologies were found to map to the Joint Planning and Development Office's National Research and Development Plan (RDP) as well as the Safety Working Group's National Aviation Safety Strategic. Plan (NASSP). Future directions in Aviation Technology as related to IVHlvl were identified by reviewing papers from three conferences across a five year time span. A total of twenty-one trend groups in propulsion, aeronautics and aircraft categories were compiled. Current and ftiture directions of IVHM related technologies were gathered and classified according to eight categories: measurement and inspection, sensors, sensor management, detection, component and subsystem monitoring, diagnosis, prognosis, and mitigation.

Analysis of bacterial and fungal communities in Marcha and Thiat, traditionally prepared amylolytic starters of India.

PubMed

Sha, Shankar Prasad; Jani, Kunal; Sharma, Avinash; Anupma, Anu; Pradhan, Pooja; Shouche, Yogesh; Tamang, Jyoti Prakash

2017-09-08

Marcha and thiat are traditionally prepared amylolytic starters use for production of various ethnic alcoholic beverages in Sikkim and Meghalaya states in India. In the present study we have tried to investigate the bacterial and fungal community composition of marcha and thiat by using high throughput sequencing. Characterization of bacterial community depicts phylum Proteobacteria is the most dominant in both marcha (91.4%) and thiat (53.8%), followed by Firmicutes, and Actinobacteria. Estimates of fungal community composition showed Ascomycota as the dominant phylum. Presence of Zygomycota in marcha distinguishes it from the thiat. The results of NGS analysis revealed dominance of yeasts in marcha whereas molds out numbers in case of thiat. This is the first report on microbial communities of traditionally prepared amylolytic starters of India using high throughput sequencing.

Fission products and nuclear fuel behaviour under severe accident conditions part 2: Fuel behaviour in the VERDON-1 sample

NASA Astrophysics Data System (ADS)

Geiger, E.; Le Gall, C.; Gallais-During, A.; Pontillon, Y.; Lamontagne, J.; Hanus, E.; Ducros, G.

2017-11-01

Within the framework of the International Source Term Programme (ISTP), the VERDON programme aims at quantifying the source term of radioactive materials in case of a hypothetical severe accident in a light water reactor (LWR). Tests were performed in a new experimental laboratory (VERDON) built in the LECA-STAR facility (CEA Cadarache). The VERDON-1 test was devoted to the study of a high burn-up UO2 fuel and FP releases at very high temperature (≈2873 K) in a reducing atmosphere. Post-test qualitative and quantitative characterisations of the VERDON-1 sample led to the proposal of a scenario explaining the phenomena occurring during the experimental sequence. Hence, the fuel and the cladding may have interacted which led to the melting of UO2-ZrO2 alloy. Although no relocation was observed during the test, it may have been imminent.

Radiant Heat Testing of the H1224A Shipping/Storage Container

DTIC Science & Technology

1994-05-01

re - entry vehicles caused by credible accidents during air and ground transportation. Radiant heat testing of the H1224A storage/shipping container is...inner container, and re - entry vehicle (RV) temperatures during radiant heat testing. Computer modelling can be used to predict weapon response throughout...Nomenclature RV Re - entry Vehicle midsection mass mock-up WR War Reserve STS Stockpile-to-Target Sequence NAWC Simulated H1224A container by Naval Air

Purification of Encephalitozoon Cultures Contaminated by Mycoplasmas by Murine Intraperitoneal Inoculation

PubMed Central

Ridoux, Olivier; Foucault, Cédric; Drancourt, Michel

1998-01-01

Encephalitozoon species are strict intracellular microsporidia. Cocultures with eukaryotic cell lines can become accidently contaminated by mycoplasmas. We propose a decontamination protocol based on differential cell targeting after intraperitoneal inoculation in mice. Mycoplasma-free microsporidia were isolated from the brains and spleens of inoculated mice 24 h postinoculation by using the centrifugation shell vial system. Identification was confirmed by direct sequencing of PCR-amplified 16S rRNA. PMID:9666031

Draft Genome Sequence of the Phytopathogenic Fungus Ganoderma boninense, the Causal Agent of Basal Stem Rot Disease on Oil Palm

PubMed Central

Tanjung, Zulfikar Achmad; Aditama, Redi; Buana, Rika Fithri Nurani; Pratomo, Antonius Dony Madu; Tryono, Reno; Liwang, Tony

2018-01-01

ABSTRACT Ganoderma boninense is the dominant fungal pathogen of basal stem rot (BSR) disease on Elaeis guineensis. We sequenced the nuclear genome of mycelia using both Illumina and Pacific Biosciences platforms for assembly of scaffolds. The draft genome comprised 79.24 Mb, 495 scaffolds, and 26,226 predicted coding sequences. PMID:29700132

Comparative genomic analysis reveals occurrence of genetic recombination in virulent Cryptosporidium hominis subtypes and telomeric gene duplications in Cryptosporidium parvum.

PubMed

Guo, Yaqiong; Tang, Kevin; Rowe, Lori A; Li, Na; Roellig, Dawn M; Knipe, Kristine; Frace, Michael; Yang, Chunfu; Feng, Yaoyu; Xiao, Lihua

2015-04-18

Cryptosporidium hominis is a dominant species for human cryptosporidiosis. Within the species, IbA10G2 is the most virulent subtype responsible for all C. hominis-associated outbreaks in Europe and Australia, and is a dominant outbreak subtype in the United States. In recent yearsIaA28R4 is becoming a major new subtype in the United States. In this study, we sequenced the genomes of two field specimens from each of the two subtypes and conducted a comparative genomic analysis of the obtained sequences with those from the only fully sequenced Cryptosporidium parvum genome. Altogether, 8.59-9.05 Mb of Cryptosporidium sequences in 45-767 assembled contigs were obtained from the four specimens, representing 94.36-99.47% coverage of the expected genome. These genomes had complete synteny in gene organization and 96.86-97.0% and 99.72-99.83% nucleotide sequence similarities to the published genomes of C. parvum and C. hominis, respectively. Several major insertions and deletions were seen between C. hominis and C. parvum genomes, involving mostly members of multicopy gene families near telomeres. The four C. hominis genomes were highly similar to each other and divergent from the reference IaA25R3 genome in some highly polymorphic regions. Major sequence differences among the four specimens sequenced in this study were in the 5' and 3' ends of chromosome 6 and the gp60 region, largely the result of genetic recombination. The sequence similarity among specimens of the two dominant outbreak subtypes and genetic recombination in chromosome 6, especially around the putative virulence determinant gp60 region, suggest that genetic recombination plays a potential role in the emergence of hyper-transmissible C. hominis subtypes. The high sequence conservation between C. parvum and C. hominis genomes and significant differences in copy numbers of MEDLE family secreted proteins and insulinase-like proteases indicate that telomeric gene duplications could potentially contribute to host expansion in C. parvum.

Emission, transport, deposition, and re-suspension of radionuclides from Fukushima Dai-ichi Nuclear Power Plant in the atmosphere - Overview of 2-year investigations in Japan

NASA Astrophysics Data System (ADS)

Kita, Kazuyuki; Igarashi, Yasuhiro; Yoshida, Naohiro; Nakajima, Teruyuki

2013-04-01

Following a huge earthquake and tsunami in Eastern Japan on 11 March, 2011, the accident in Fukushima Dai-ichi Nuclear Power Plant (FDNPP) occurred to emit a large amount of artificial radionuclides to the environment. Soon after the FDNPP accident, many Japanese researchers, as well as researchers in other countries, started monitoring radionuclides in various environmental fields and/or model calculations to understand extent and magnitude of radioactive pollution. In this presentation, we overview these activities for the atmospheric radionuclides in Japan as followings: 1. Investigations to evaluate radionuclide emissions by explosions at FNDPP in March 2011 and to estimate the respiration dose of the radiation at this stage. 2. Investigations to evaluate atmospheric transport and deposition processes of atmospheric radionuclide to determine the extent of radionuclide pollution. -- Based on results of the regular and urgent monitoring results, as well as the mapping of the distribution of radionuclide s accumulated by the deposition to the ground, restoration of their time-dependent emission rates has been tried, and processes determining atmospheric concentration and deposition to the ground have been investigated by using the model calculations. 3. Monitoring of the atmospheric concentrations of radionuclide after the initial, surge phase of FNDPP accident. 4. Investigations to evaluate re-suspension of radionuclide from the ground, including the soil and the vegetation. -- Intensive monitoring of the atmospheric concentrations and deposition amount of radionuclide after the initial, surge phase of the accident enable us to evaluate emission history from FNDPP, atmospheric transport and deposition processes, chemical and physical characteristics of atmospheric radionuclide especially of radio cesium, and re-suspension processes which has become dominant process to supply radio cesium to the atmosphere recently.

Sequence variations of the partially dominant DELLA gene Rht-B1c in wheat and their functional impacts

PubMed Central

Ma, Zhengqiang

2013-01-01

Rht-B1c, allelic to the DELLA protein-encoding gene Rht-B1a, is a natural mutation documented in common wheat (Triticum aestivum). It confers variation to a number of traits related to cell and plant morphology, seed dormancy, and photosynthesis. The present study was conducted to examine the sequence variations of Rht-B1c and their functional impacts. The results showed that Rht-B1c was partially dominant or co-dominant for plant height, and exhibited an increased dwarfing effect. At the sequence level, Rht-B1c differed from Rht-B1a by one 2kb Veju retrotransposon insertion, three coding region single nucleotide polymorphisms (SNPs), one 197bp insertion, and four SNPs in the 1kb upstream sequence. Haplotype investigations, association analyses, transient expression assays, and expression profiling showed that the Veju insertion was primarily responsible for the extreme dwarfing effect. It was found that the Veju insertion changed processing of the Rht-B1c transcripts and resulted in DELLA motif primary structure disruption. Expression assays showed that Rht-B1c caused reduction of total Rht-1 transcript levels, and up-regulation of GATA-like transcription factors and genes positively regulated by these factors, suggesting that one way in which Rht-1 proteins affect plant growth and development is through GATA-like transcription factor regulation. PMID:23918966

A novel variant of FGFR3 causes proportionate short stature.

PubMed

Kant, Sarina G; Cervenkova, Iveta; Balek, Lukas; Trantirek, Lukas; Santen, Gijs W E; de Vries, Martine C; van Duyvenvoorde, Hermine A; van der Wielen, Michiel J R; Verkerk, Annemieke J M H; Uitterlinden, André G; Hannema, Sabine E; Wit, Jan M; Oostdijk, Wilma; Krejci, Pavel; Losekoot, Monique

2015-06-01

Mutations of the fibroblast growth factor receptor 3 (FGFR3) cause various forms of short stature, of which the least severe phenotype is hypochondroplasia, mainly characterized by disproportionate short stature. Testing for an FGFR3 mutation is currently not part of routine diagnostic testing in children with short stature without disproportion. A three-generation family A with dominantly transmitted proportionate short stature was studied by whole-exome sequencing to identify the causal gene mutation. Functional studies and protein modeling studies were performed to confirm the pathogenicity of the mutation found in FGFR3. We performed Sanger sequencing in a second family B with dominant proportionate short stature and identified a rare variant in FGFR3. Exome sequencing and/or Sanger sequencing was performed, followed by functional studies using transfection of the mutant FGFR3 into cultured cells; homology modeling was used to construct a three-dimensional model of the two FGFR3 variants. A novel p.M528I mutation in FGFR3 was detected in family A, which segregates with short stature and proved to be activating in vitro. In family B, a rare variant (p.F384L) was found in FGFR3, which did not segregate with short stature and showed normal functionality in vitro compared with WT. Proportionate short stature can be caused by a mutation in FGFR3. Sequencing of this gene can be considered in patients with short stature, especially when there is an autosomal dominant pattern of inheritance. However, functional studies and segregation studies should be performed before concluding that a variant is pathogenic. © 2015 European Society of Endocrinology.

Stratigraphic evolution of the Late Jurassic Hanifa Formation along the Tuwaiq Escarpment, Saudi Arabia: Evidence for a carbonate ramp system

NASA Astrophysics Data System (ADS)

Fallatah, Mohammed I.; Kerans, Charles

2018-01-01

A sequence stratigraphic framework of the Late Jurassic (Oxfordian) Hanifa Formation at its exposure in Central Arabia is presented for the first time. This study offers the first high-resolution stratigraphic framework of the Hanifa along the Tuwaiq Escarpment by measuring 15 sections ( 770 m total thickness) over an oblique-to-dip distance of 260 km and collecting 295 samples for petrographic analysis. On the basis of these data, the Hanifa Formation can be subdivided into eight facies; 1) tabular cross-bedded quartz-peloidal-skeletal grainstone, 2) cross-bedded skeletal-peloidal grainstone, 3) bioturbated foraminiferal wackestone/mud-dominated packstone, 4) oncolitic rudstone, 5) stromatoporoid-coral biostrome/bioherm, 6) peloidal/composite-grain grain-dominated packstone/grainstone, 7) bioturbated spiculitic wackestone/mud-dominated packstone, and 8) thinly-bedded argillaceous mudstone/wackestone. The vertical and lateral distributions of these facies along the exposure define their sequence setting using the principals of sequence stratigraphy. By recognizing erosional surfaces, facies offset, and changes in facies proportions, five third-order sequences, with an average duration of 1.1 Myr, are interpreted for the Hanifa Formation. The correlation of the sequences across the study area shows that only four sequences are preserved in the north where shallow-water deposits are well-developed. Facies trends within these sequences are further illustrated in depositional models representing the highstand systems tracts (HST) and the transgressive systems tracts (TST) of the Hanifa Formation. These proposed models represent depositional settings of a carbonate ramp with normal open-marine conditions. The HST depositional model is characterized by a high-energy shoreline and depicts the presence of an offshore, structurally controlled skeletal-peloidal shoal body described here for the first time at the Hanifa exposure in the Hozwa area. This work provides a predictive framework and outcrop analog for applications in hydrocarbon exploration and development. Furthermore, a basinal setting predicted to the south of the study area is a potential site for unconventional plays.

Attomole-level Genomics with Single-molecule Direct DNA, cDNA and RNA Sequencing Technologies.

PubMed

Ozsolak, Fatih

2016-01-01

With the introduction of next-generation sequencing (NGS) technologies in 2005, the domination of microarrays in genomics quickly came to an end due to NGS's superior technical performance and cost advantages. By enabling genetic analysis capabilities that were not possible previously, NGS technologies have started to play an integral role in all areas of biomedical research. This chapter outlines the low-quantity DNA and cDNA sequencing capabilities and applications developed with the Helicos single molecule DNA sequencing technology.

Health effects models for nuclear power plant accident consequence analysis. Part 1, Introduction, integration, and summary: Revision 2

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

Evans, J.S.; Abrahmson, S.; Bender, M.A.

1993-10-01

This report is a revision of NUREG/CR-4214, Rev. 1, Part 1 (1990), Health Effects Models for Nuclear Power Plant Accident Consequence Analysis. This revision has been made to incorporate changes to the Health Effects Models recommended in two addenda to the NUREG/CR-4214, Rev. 1, Part 11, 1989 report. The first of these addenda provided recommended changes to the health effects models for low-LET radiations based on recent reports from UNSCEAR, ICRP and NAS/NRC (BEIR V). The second addendum presented changes needed to incorporate alpha-emitting radionuclides into the accident exposure source term. As in the earlier version of this report, modelsmore » are provided for early and continuing effects, cancers and thyroid nodules, and genetic effects. Weibull dose-response functions are recommended for evaluating the risks of early and continuing health effects. Three potentially lethal early effects -- the hematopoietic, pulmonary, and gastrointestinal syndromes are considered. Linear and linear-quadratic models are recommended for estimating the risks of seven types of cancer in adults - leukemia, bone, lung, breast, gastrointestinal, thyroid, and ``other``. For most cancers, both incidence and mortality are addressed. Five classes of genetic diseases -- dominant, x-linked, aneuploidy, unbalanced translocations, and multifactorial diseases are also considered. Data are provided that should enable analysts to consider the timing and severity of each type of health risk.« less

Stratigraphic palaeobiology around the Pliocene-Pleistocene boundary at Altavilla Milicia (Sicily, Italy)

NASA Astrophysics Data System (ADS)

Dominici, Stefano; Benvenuti, Marco; Garilli, Vittorio; Uchman, Alfred; Pollina, Francesco

2017-04-01

The Pliocene-Pleistocene around Altavilla Milicia, near Palermo (Sicily), includes a thick siliciclastic succession rich with shell beds, dominated by molluscs, brachiopods and annelids in fine-grained, totally bioturbated sandstones. Taphonomy of fossil assemblages indicates the importance of taphonomic feedback and within-habitat time-averaging in proximity of maximum flooding intervals. The trace fossil suite is characterized by the abundance of Thalassinoides paradoxicus boxworks and by local occurence of Scalichnus, Piscichnus, ?Scolicia, ?Bichordites, Ophiomorpha, ?Gyrolithes, Palaeophycus, Diopatrichnus and ?Taenidium. These trace fossils are typical of the archetypal Cruziana ichnofacies, with local elements of the proximal Cruziana ichnofacies, which point to deposition mainly below the fairweather wave base. Three depositional sequences, characterized by geometries driven by the interplay of eustatism and regional tectonics, were recognized through sedimentary facies analysis. Biostratigraphic data frame the oldest sequence in the upper Pliocene, whereas the thickest part of the succession, occupied by the second sedimentary sequence, includes biozone NN16b/17 of calcareous nannoplankton stratigraphy, thereby comprising the base of the Pleistocene. Transgressive deposits of the third and uppermost sequence are marked by encrusted and bioeroded pebbles with sparse oyster shells. The whole time interval is characterized by glacio-eustatic fluctuations in the 50-100 m range and with 100 ky-periodicity. We performed a multivariate analysis of 22 samples yielding 92 species of mollusks collected in the first and second sequences. Clustering and ordination analysis allowed to recognize a gradient controlled by depth-related environmental variables. At one end of the continuum we have a very-shallow water assemblage dominated by the bivalve Loripes orbiculatus, indicating an organic-rich seagrass bottom. Opposite in the continuum is an offshore assemblage dominated by Corbula gibba and the extinct gastropod Petaloconchus intortus. Both the shallowest and the deepest assemblages are from the first (Piacenzian) sequence. The gradient at intermediate depths is better characterized by restricting the analysis to 17 collections from the second sequence (Piacenzian-Gelasian). The shallowest assemblage is here dominated by upper shoreface species, such as Tellina spp. and Spisula subtruncata, and the deepest by muddy bottom, offshore transition species, such as Venus nux, the extinct gastropod Nassarius semistriatus and deposit-feeding nuculanoid bivalves. Plotting samples along the composite section allows to recognize two deepening-upward trends and two intervals of maximum flooding, in accordance with the sequence-stratigraphic interpretation. Stratigraphic palaeobiology proves to be a powerful tool to understand factors that control the geologic record during an interval of intense climate change.

Nuclear energy: salvation or suicide. [Contains glossary

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

Collins, C.C.

A collection of 700 editorials and feature articles collected from 125 US newspapers addresses the dominant areas of concern about nuclear power: plant safety, radioactive wastes, proliferation, and cost. The editorial debates present the pros and cons of Three Mile Island and other accidents, ocean dumping, evacuation plans, radioactive waste transport and storage, nuclear fuel processing, the Karen Silkwood case, and breeder reactors. The appendix raises the question of the future for fission and the possibility of nuclear fusion as an alternative. There is a subject index and a glossary of basic terms.

Draft Genome Sequence of the Phytopathogenic Fungus Ganoderma boninense, the Causal Agent of Basal Stem Rot Disease on Oil Palm.

PubMed

Utomo, Condro; Tanjung, Zulfikar Achmad; Aditama, Redi; Buana, Rika Fithri Nurani; Pratomo, Antonius Dony Madu; Tryono, Reno; Liwang, Tony

2018-04-26

Ganoderma boninense is the dominant fungal pathogen of basal stem rot (BSR) disease on Elaeis guineensis We sequenced the nuclear genome of mycelia using both Illumina and Pacific Biosciences platforms for assembly of scaffolds. The draft genome comprised 79.24 Mb, 495 scaffolds, and 26,226 predicted coding sequences. Copyright © 2018 Utomo et al.

A qualitative study of the background and in-hospital medicolegal response to female burn injuries in India.

PubMed

Daruwalla, Nayreen; Belur, Jyoti; Kumar, Meena; Tiwari, Vinay; Sarabahi, Sujata; Tilley, Nick; Osrin, David

2014-11-30

Most burns happen in low- and middle-income countries. In India, deaths related to burns are more common in women than in men and occur against a complex background in which the cause - accidental or non-accidental, suicidal or homicidal - is often unclear. Our study aimed to understand the antecedents to burns and the problem of ascribing cause, the sequence of medicolegal events after a woman was admitted to hospital, and potential opportunities for improvement. We conducted semi-structured interviews with 33 women admitted to two major burns units, their families, and 26 key informant doctors, nurses, and police officers. We used framework analysis to examine the context in which burns occurred and the sequence of medicolegal action after admission to hospital. Interviewees described accidents, attempted suicide, and attempted homicide. Distinguishing between these was difficult because the underlying combination of poverty and cultural precedent was common to all and action was contingent on potentially conflicting narratives. Space constraint, problems with cooking equipment, and inflammable clothing increased the risk of accidental burns, but coexisted with household conflict, gender-based violence, and alcohol use. Most burns were initially ascribed to accidents. Clinicians adhered to medicolegal procedures, the police carried out their investigative requirements relatively rapidly, but both groups felt vulnerable in the face of the legal process. Women's understandable reticence to describe burns as non-accidental, the contested nature of statements, their perceived history of changeability, the limited quality and validity of forensic evidence, and the requirement for resilience on the part of clients underlay a general pessimism. The similarities between accident and intention cluster so tightly as to make them challenging to distinguish, especially given women's understandable reticence to describe burns as non-accidental. The contested status of forensic evidence and a reliance on testimony means that only a minority of cases lead to conviction. The emphasis should be on improving documentation, communication between service providers, and public understanding of the risks of burns.

Key findings and remaining questions in the areas of core-concrete interaction and debris coolability

DOE PAGES

Farmer, M. T.; Gerardi, C.; Bremer, N.; ...

2016-10-31

The reactor accidents at Fukushima-Dai-ichi have rekindled interest in late phase severe accident behavior involving reactor pressure vessel breach and discharge of molten core melt into the containment. Two technical issues of interest in this area include core-concrete interaction and the extent to which the core debris may be quenched and rendered coolable by top flooding. The OECD-sponsored Melt Coolability and Concrete Interaction (MCCI) programs at Argonne National Laboratory included the conduct of large scale reactor material experiments and associated analysis with the objectives of resolving the ex-vessel debris coolability issue, and to address remaining uncertainties related to long-term two-dimensionalmore » molten core-concrete interactions under both wet and dry cavity conditions. These tests provided a broad database to support accident management planning, as well as the development and validation of models and codes that can be used to extrapolate the experiment results to plant conditions. This paper provides a high level overview of the key experiment results obtained during the program. Finally, a discussion is also provided that describes technical gaps that remain in this area, several of which have arisen based on the sequence of events and operator actions during Fukushima.« less

Key findings and remaining questions in the areas of core-concrete interaction and debris coolability

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

Farmer, M. T.; Gerardi, C.; Bremer, N.

The reactor accidents at Fukushima-Dai-ichi have rekindled interest in late phase severe accident behavior involving reactor pressure vessel breach and discharge of molten core melt into the containment. Two technical issues of interest in this area include core-concrete interaction and the extent to which the core debris may be quenched and rendered coolable by top flooding. The OECD-sponsored Melt Coolability and Concrete Interaction (MCCI) programs at Argonne National Laboratory included the conduct of large scale reactor material experiments and associated analysis with the objectives of resolving the ex-vessel debris coolability issue, and to address remaining uncertainties related to long-term two-dimensionalmore » molten core-concrete interactions under both wet and dry cavity conditions. These tests provided a broad database to support accident management planning, as well as the development and validation of models and codes that can be used to extrapolate the experiment results to plant conditions. This paper provides a high level overview of the key experiment results obtained during the program. Finally, a discussion is also provided that describes technical gaps that remain in this area, several of which have arisen based on the sequence of events and operator actions during Fukushima.« less

Modeling of local steam condensation on walls in presence of non-condensable gases. Application to a loca calculation in reactor containment using the multidimensional geyser/tonus code

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

Benet, L.V.; Caroli, C.; Cornet, P.

1995-09-01

This paper reports part of a study of possible severe pressurized water reactor (PWR) accidents. The need for containment modeling, and in particular for a hydrogen risk study, was reinforced in France after 1990, with the requirement that severe accidents must be taken into account in the design of future plants. This new need of assessing the transient local hydrogen concentration led to the development, in the Mechanical Engineering and Technology Department of the French Atomic Energy Commission (CEA/DMT), of the multidimensional code GEYSER/TONUS for containment analysis. A detailed example of the use of this code is presented. The mixturemore » consisted of noncondensable gases (air or air plus hydrogen) and water vapor and liquid water. This is described by a compressible homogeneous two-phase flow model and wall condensation is based on the Chilton-Colburn formula and the analogy between heat and mass transfer. Results are given for a transient two-dimensional axially-symmetric computation for the first hour of a simplified accident sequence. In this there was an initial injection of a large amount of water vapor followed by a smaller amount and by hydrogen injection.« less

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

Farmer, M. T.

The overall objective of the current work is to carry out a scoping analysis to determine the impact of ATF on late phase accident progression; in particular, the molten core-concrete interaction portion of the sequence that occurs after the core debris fails the reactor vessel and relocates into containment. This additional study augments previous work by including kinetic effects that govern chemical reaction rates during core-concrete interaction. The specific ATF considered as part of this study is SiC-clad UO 2.

Ectomycorrhizal-dominated boreal and tropical forests have distinct fungal communities, but analogous spatial patterns across soil horizons.

PubMed

McGuire, Krista L; Allison, Steven D; Fierer, Noah; Treseder, Kathleen K

2013-01-01

Fungi regulate key nutrient cycling processes in many forest ecosystems, but their diversity and distribution within and across ecosystems are poorly understood. Here, we examine the spatial distribution of fungi across a boreal and tropical ecosystem, focusing on ectomycorrhizal fungi. We analyzed fungal community composition across litter (organic horizons) and underlying soil horizons (0-20 cm) using 454 pyrosequencing and clone library sequencing. In both forests, we found significant clustering of fungal communities by site and soil horizons with analogous patterns detected by both sequencing technologies. Free-living saprotrophic fungi dominated the recently-shed leaf litter and ectomycorrhizal fungi dominated the underlying soil horizons. This vertical pattern of fungal segregation has also been found in temperate and European boreal forests, suggesting that these results apply broadly to ectomycorrhizal-dominated systems, including tropical rain forests. Since ectomycorrhizal and free-living saprotrophic fungi have different influences on soil carbon and nitrogen dynamics, information on the spatial distribution of these functional groups will improve our understanding of forest nutrient cycling.

Myelin protein zero gene sequencing diagnoses Charcot-Marie-Tooth Type 1B disease

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

Su, Y.; Zhang, H.; Madrid, R.

1994-09-01

Charcot-Marie-Tooth disease (CMT), the most common genetic neuropathy, affects about 1 in 2600 people in Norway and is found worldwide. CMT Type 1 (CMT1) has slow nerve conduction with demyelinated Schwann cells. Autosomal dominant CMT Type 1B (CMT1B) results from mutations in the myelin protein zero gene which directs the synthesis of more than half of all Schwann cell protein. This gene was mapped to the chromosome 1q22-1q23.1 borderline by fluorescence in situ hybridization. The first 7 of 7 reported CMT1B mutations are unique. Thus the most effective means to identify CMT1B mutations in at-risk family members and fetuses ismore » to sequence the entire coding sequence in dominant or sporadic CMT patients without the CMT1A duplication. Of the 19 primers used in 16 pars to uniquely amplify the entire MPZ coding sequence, 6 primer pairs were used to amplify and sequence the 6 exons. The DyeDeoxy Terminator cycle sequencing method used with four different color fluorescent lables was superior to manual sequencing because it sequences more bases unambiguously from extracted genomic DNA samples within 24 hours. This protocol was used to test 28 CMT and Dejerine-Sottas patients without CMT1A gene duplication. Sequencing MPZ gene-specific amplified fragments identified 9 polymorphic sites within the 6 exons that encode the 248 amino acid MPZ protein. The large number of major CMT1B mutations identified by single strand sequencing are being verified by reverse strand sequencing and when possible, by restriction enzyme analysis. This protocol can be used to distringuish CMT1B patients from othre CMT phenotypes and to determine the CMT1B status of relatives both presymptomatically and prenatally.« less

Molecular cloning and structural modelling of gamma-phospholipase A2 inhibitors from Bothrops atrox and Micrurus lemniscatus snakes.

PubMed

Picelli, Carina G; Borges, Rafael J; Fernandes, Carlos A H; Matioli, Fabio M; Fernandes, Carla F C; Sobrinho, Juliana C; Holanda, Rudson J; Ozaki, Luiz S; Kayano, Anderson M; Calderon, Leonardo A; Fontes, Marcos R M; Stábeli, Rodrigo G; Soares, Andreimar M

2017-10-01

Phospholipases A 2 inhibitors (PLIs) produced by venomous and non-venomous snakes play essential role in this resistance. These endogenous inhibitors may be classified by their fold in PLIα, PLIβ and PLIγ. Phospholipases A 2 (PLA 2 s) develop myonecrosis in snake envenomation, a consequence that is not efficiently neutralized by antivenom treatment. This work aimed to identify and characterize two PLIs from Amazonian snake species, Bothrops atrox and Micrurus lemniscatus. Liver tissues RNA of specimens from each species were isolated and amplified by RT-PCR using PCR primers based on known PLIγ gene sequences, followed by cloning and sequencing of amplified fragments. Sequence similarity studies showed elevated identity with inhibitor PLIγ gene sequences from other snake species. Molecular models of translated inhibitors' gene sequences resemble canonical three finger fold from PLIγ and support the hypothesis that the decapeptide (residues 107-116) may be responsible for PLA 2 inhibition. Structural studies and action mechanism of these PLIs may provide necessary information to evaluate their potential as antivenom or as complement of the current ophidian accident treatment. Copyright © 2017 Elsevier B.V. All rights reserved.

Microbial diversity of culturable heterotrophs in the rhizosphere of salt marsh grass, Porteresia coarctata (Tateoka) in a mangrove ecosystem.

PubMed

Bharathkumar, Srinivasan; Paul, Diby; Nair, Sudha

2008-02-01

A study was conducted to understand the complexity of bacterial diversity of rhizosphere of Porteresia coarctata based on culture dependent method. A large number of bacteria were isolated on nutrient agar medium supplemented with 1% NaCl and the dominant ones were further analyzed with PCR-RFLP method. The sequence analyses of the dominant strains revealed that most of the sequences belonged to members of gamma proteobacteria, firmicutes, bacteroidetes and uncultured bacteria. The phylogenetic analysis of 16S rRNA gene sequences revealed close relationships to a wide range of clones or bacterial species of various divisions. These results afford an understanding of the role of rhizobacteria in alleviating salt stress in Porteresia coarctata expected to contribute towards long-term goal of improving plant-microbe interactions for salinity affected fields. (c) 2008 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Sequence stratigraphy and reservoir architecture of the J18/20 and J15 sequences in PM-9, Malay Basin

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

Rahman, R.A.; Said, Md.J.; Bedingfield, J.R.

1994-07-01

The group J stratigraphic interval is lower Miocene (18.5-21 Ma) in age and was deposited during the early sag phase of the Malay Basin structural development. Reduction in depositional relief and first evidence of widespread marine influence characterize the transition into this interval. Twelve group J sequences have been identified. Reservoirs consist of progradational to aggradational tidally-dominated paralic to shallow marine sands deposited in the lowstand systems tract. Transgressive and highstand deposits are dominantly offshore shales. In PM-9, the original lift-related depocenters, coupled with changes in relative sea level, have strongly influenced group J unit thickness and the distribution ofmore » reservoir and seal facies. Two important reservoir intervals in PM-9 are the J18/20 and J15 sands. The reservoirs in these intervals are contained within the lowstand systems tracts of fourth-order sequences. These fourth-order sequences stack to form sequence sets in response to a third-order change in relative sea level. The sequences of the J18/20 interval stack to form part of a lowstand sequence set, whereas the J15 interval forms part of the transgressive sequence set. Reservoir facies range from tidal bars and subtidal shoals in the J18/20 interval to lower shoreface sands in the J15. Reservoir quality and continuity in group J reservoirs are dependent on depositional facies. An understanding of the controls on the distribution of facies types is crucial to the success of the current phase of field development and exploration programs in PM-9.« less

18S rDNA Sequences from Microeukaryotes Reveal Oil Indicators in Mangrove Sediment

PubMed Central

Santos, Henrique F.; Cury, Juliano C.; Carmo, Flavia L.; Rosado, Alexandre S.; Peixoto, Raquel S.

2010-01-01

Background Microeukaryotes are an effective indicator of the presence of environmental contaminants. However, the characterisation of these organisms by conventional tools is often inefficient, and recent molecular studies have revealed a great diversity of microeukaryotes. The full extent of this diversity is unknown, and therefore, the distribution, ecological role and responses to anthropogenic effects of microeukaryotes are rather obscure. The majority of oil from oceanic oil spills (e.g., the May 2010 accident in the Gulf of Mexico) converges on coastal ecosystems such as mangroves, which are threatened with worldwide disappearance, highlighting the need for efficient tools to indicate the presence of oil in these environments. However, no studies have used molecular methods to assess the effects of oil contamination in mangrove sediment on microeukaryotes as a group. Methodology/Principal Findings We evaluated the population dynamics and the prevailing 18S rDNA phylotypes of microeukaryotes in mangrove sediment microcosms with and without oil contamination, using PCR/DGGE and clone libraries. We found that microeukaryotes are useful for monitoring oil contamination in mangroves. Our clone library analysis revealed a decrease in both diversity and species richness after contamination. The phylogenetic group that showed the greatest sensitivity to oil was the Nematoda. After contamination, a large increase in the abundance of the groups Bacillariophyta (diatoms) and Biosoecida was detected. The oil-contaminated samples were almost entirely dominated by organisms related to Bacillariophyta sp. and Cafeteria minima, which indicates that these groups are possible targets for biomonitoring oil in mangroves. The DGGE fingerprints also indicated shifts in microeukaryote profiles; specific band sequencing indicated the appearance of Bacillariophyta sp. only in contaminated samples and Nematoda only in non-contaminated sediment. Conclusions/Significance We believe that the microeukaryotic targets indicated by our work will be of great applicability in biomonitoring hydrocarbons in mangroves under oil contamination risk or during recovery strategies. PMID:20865054

18S rDNA sequences from microeukaryotes reveal oil indicators in mangrove sediment.

PubMed

Santos, Henrique F; Cury, Juliano C; Carmo, Flavia L; Rosado, Alexandre S; Peixoto, Raquel S

2010-08-26

Microeukaryotes are an effective indicator of the presence of environmental contaminants. However, the characterisation of these organisms by conventional tools is often inefficient, and recent molecular studies have revealed a great diversity of microeukaryotes. The full extent of this diversity is unknown, and therefore, the distribution, ecological role and responses to anthropogenic effects of microeukaryotes are rather obscure. The majority of oil from oceanic oil spills (e.g., the May 2010 accident in the Gulf of Mexico) converges on coastal ecosystems such as mangroves, which are threatened with worldwide disappearance, highlighting the need for efficient tools to indicate the presence of oil in these environments. However, no studies have used molecular methods to assess the effects of oil contamination in mangrove sediment on microeukaryotes as a group. We evaluated the population dynamics and the prevailing 18S rDNA phylotypes of microeukaryotes in mangrove sediment microcosms with and without oil contamination, using PCR/DGGE and clone libraries. We found that microeukaryotes are useful for monitoring oil contamination in mangroves. Our clone library analysis revealed a decrease in both diversity and species richness after contamination. The phylogenetic group that showed the greatest sensitivity to oil was the Nematoda. After contamination, a large increase in the abundance of the groups Bacillariophyta (diatoms) and Biosoecida was detected. The oil-contaminated samples were almost entirely dominated by organisms related to Bacillariophyta sp. and Cafeteria minima, which indicates that these groups are possible targets for biomonitoring oil in mangroves. The DGGE fingerprints also indicated shifts in microeukaryote profiles; specific band sequencing indicated the appearance of Bacillariophyta sp. only in contaminated samples and Nematoda only in non-contaminated sediment. We believe that the microeukaryotic targets indicated by our work will be of great applicability in biomonitoring hydrocarbons in mangroves under oil contamination risk or during recovery strategies.

Aspects épidémiologiques des traumatismes du rachis: à propos de 139 cas

PubMed Central

Bemora, Joseph Synèse; Rakotondraibe, Willy Francis; Ramarokoto, Mijoro; Ratovondrainy, Willy; Andriamamonjy, Clément

2017-01-01

Les traumatismes du rachis représentent une des lésions les plus fréquemment observées, chez les victimes d’accidents de circulation, d’accident de sportifs, domestique et du travail. Il s’agissait d’une étude rétrospective de 3 ans portant sur 139 cas de traumatismes du rachis hospitalisés et pris en charge dans le service de neurochirurgie du CHUJRA Madagascar. A travers cette étude, 25,17% des traumatisés étaient entre 21 et 30 ans avec une nette prédominance masculine de 69,78% (sexe ratio 2,3). L’étiologie était dominéepar la chute dans 33,09% des cas avec des facteurs de risque dont prise d’alcool (8,63%). Le traumatisme entrait dans le cadre d’un polytraumatisme dont un traumatisme crânien dans 34,63%. Les patients étaient admis dans le service 1 à 5h après le traumatisme dans 31,65% en utilisant comme moyen de transport une voiture personnelle dans 36,69%. Pendant l’hospitalisation 20 patients ont signé une décharge et 6,34% des patients sont décédés. Les traumatismes du rachis posent un problème de santé publique avec une prise en charge lourde surtout pour les patients déficitaires à vie. Devant tout traumatisme du rachis, il faut rechercher systématiquement une lésion crânienne. PMID:28450995

A Report on Molecular Diagnostic Testing for Inherited Retinal Dystrophies by Targeted Genetic Analyses.

PubMed

Ramkumar, Hema L; Gudiseva, Harini V; Kishaba, Kameron T; Suk, John J; Verma, Rohan; Tadimeti, Keerti; Thorson, John A; Ayyagari, Radha

2017-02-01

To test the utility of targeted sequencing as a method of clinical molecular testing in patients diagnosed with inherited retinal degeneration (IRD). After genetic counseling, peripheral blood was drawn from 188 probands and 36 carriers of IRD. Single gene testing was performed on each patient in a Clinical Laboratory Improvement Amendment (CLIA) certified laboratory. DNA was isolated, and all exons in the gene of interest were analyzed along with 20 base pairs of flanking intronic sequence. Genetic testing was most often performed on ABCA4, CTRP5, ELOV4, BEST1, CRB1, and PRPH2. Pathogenicity of novel sequence changes was predicted by PolyPhen2 and sorting intolerant from tolerant (SIFT). Of the 225 genetic tests performed, 150 were for recessive IRD, and 75 were for dominant IRD. A positive molecular diagnosis was made in 70 (59%) of probands with recessive IRD and 19 (26%) probands with dominant IRD. Analysis confirmed 12 (34%) of individuals as carriers of familial mutations associated with IRD. Thirty-two novel variants were identified; among these, 17 sequence changes in four genes were predicted to be possibly or probably damaging including: ABCA4 (14), BEST1 (2), PRPH2 (1), and TIMP3 (1). Targeted analysis of clinically suspected genes in 225 subjects resulted in a positive molecular diagnosis in 26% of patients with dominant IRD and 59% of patients with recessive IRD. Novel damaging mutations were identified in four genes. Single gene screening is not an ideal method for diagnostic testing given the phenotypic and genetic heterogeneity among IRD cases. High-throughput sequencing of all genes associated with retinal degeneration may be more efficient for molecular diagnosis.

Molecular Detection, Isolation, and Physiological Characterization of Functionally Dominant Phenol-Degrading Bacteria in Activated Sludge

PubMed Central

Watanabe, Kazuya; Teramoto, Maki; Futamata, Hiroyuki; Harayama, Shigeaki

1998-01-01

DNA was isolated from phenol-digesting activated sludge, and partial fragments of the 16S ribosomal DNA (rDNA) and the gene encoding the largest subunit of multicomponent phenol hydroxylase (LmPH) were amplified by PCR. An analysis of the amplified fragments by temperature gradient gel electrophoresis (TGGE) demonstrated that two major 16S rDNA bands (bands R2 and R3) and two major LmPH gene bands (bands P2 and P3) appeared after the activated sludge became acclimated to phenol. The nucleotide sequences of these major bands were determined. In parallel, bacteria were isolated from the activated sludge by direct plating or by plating after enrichment either in batch cultures or in a chemostat culture. The bacteria isolated were classified into 27 distinct groups by a repetitive extragenic palindromic sequence PCR analysis. The partial nucleotide sequences of 16S rDNAs and LmPH genes of members of these 27 groups were then determined. A comparison of these nucleotide sequences with the sequences of the major TGGE bands indicated that the major bacterial populations, R2 and R3, possessed major LmPH genes P2 and P3, respectively. The dominant populations could be isolated either by direct plating or by chemostat culture enrichment but not by batch culture enrichment. One of the dominant strains (R3) which contained a novel type of LmPH (P3), was closely related to Valivorax paradoxus, and the result of a kinetic analysis of its phenol-oxygenating activity suggested that this strain was the principal phenol digester in the activated sludge. PMID:9797297

[Study on Microbial Diversity of Peri-implantitis Subgingival by High-throughput Sequencing].

PubMed

Li, Zhi-jie; Wang, Shao-guo; Li, Yue-hong; Tu, Dong-xiang; Liu, Shi-yun; Nie, Hong-bing; Li, Zhi-qiang; Zhang, Ju-mei

2015-07-01

To study microbial diversity of peri-implantitis subgingival with high-throughput sequencing, and investigate microbiological etiology of peri-implantitis. Subgingival plaques were sampled from the patients with peri-implantitis (D group) and non-peri-implantitis subjects (N group). The microbiological diversity of the subgingival plaques was detected by sequencing V4 region of 16S rRNA with Illumina Miseq platform. The diversity of the community structure was analyzed using Mothur software. A total of 156 507 gene sequences were detected in nine samples and 4 402 operational taxonomic units (OTUs) were found. Selenomonas, Pseudomonas, and Fusobacterium were dominant bacteria in D group, while Fusobacterium, Veillonella and Streptococcus were dominant bacteria in N group. Differences between peri-implantitis and non-peri-implantitis bacterial communities were observed at all phylogenetic levels by LEfSe, which was also found in PcoA test. The occurrence of peri-implantitis is not only related to periodontitis pathogenic microbe, but also related with the changes of oral microbial community structure. Treponema, Herbaspirillum, Butyricimonas and Phaeobacte may be closely related to the occurrence and development of peri-implantitis.

A unique chromatin complex occupies young α-satellite arrays of human centromeres

PubMed Central

Henikoff, Jorja G.; Thakur, Jitendra; Kasinathan, Sivakanthan; Henikoff, Steven

2015-01-01

The intractability of homogeneous α-satellite arrays has impeded understanding of human centromeres. Artificial centromeres are produced from higher-order repeats (HORs) present at centromere edges, although the exact sequences and chromatin conformations of centromere cores remain unknown. We use high-resolution chromatin immunoprecipitation (ChIP) of centromere components followed by clustering of sequence data as an unbiased approach to identify functional centromere sequences. We find that specific dimeric α-satellite units shared by multiple individuals dominate functional human centromeres. We identify two recently homogenized α-satellite dimers that are occupied by precisely positioned CENP-A (cenH3) nucleosomes with two ~100–base pair (bp) DNA wraps in tandem separated by a CENP-B/CENP-C–containing linker, whereas pericentromeric HORs show diffuse positioning. Precise positioning is largely maintained, whereas abundance decreases exponentially with divergence, which suggests that young α-satellite dimers with paired ~100-bp particles mediate evolution of functional human centromeres. Our unbiased strategy for identifying functional centromeric sequences should be generally applicable to tandem repeat arrays that dominate the centromeres of most eukaryotes. PMID:25927077

Children at risk of residual physical problems after public road traffic injuries--a 1-year follow-up study.

PubMed

Olofsson, Eva; Bunketorp, Olle; Andersson, Anna-Lena

2012-01-01

To describe the residual physical problems 1 year after traffic injuries in children with respect to age, gender, extraction (Swedish or foreign), type of care, type of accident and use of protective equipment, type of injury, and the impact on daily living activities. Hospital data were analysed for children, aged 15 or under, after road traffic accidents in the Gothenburg region in 2000. Age, gender, type of road user, counterpart, use of protective equipment, type and severity of each injury, and type of care were related to follow-up data obtained by a self-completed questionnaire answered 1 year after the accident. The AIS90 was used for injury classification. Residual physical problems were specified, graded, and mapped on anatomical pictures of the body by the respondents. Logistic regression was used to explore independent factors for residual problems. A total of 341 children (81%) fulfilled the study. Cyclists dominated, 60%, followed by moped users, car occupants and pedestrians. The mean age was 11 years, 61% were boys, 16% were of foreign extraction, 26% were treated as inpatients, and 11% had at least one serious (AIS3+) injury. Residual problems were reported for 16% of the study group (n=53), and of these 31% were located to the lower extremities (mostly knee problems), upper extremities in 20%, face in 14%, neck in 14%, upper trunk in 8%, lower trunk in 8%, and skull/brain in 3%. Significant permanent impairment was reported in one case. Cyclists reported problems significantly less frequently than others. Children reporting problems tended to be older and were most often injured as moped users. Problems to the neck and the upper trunk were reported to a higher rate than the injury rate in these regions. Children with residual problems reported limitations in daily living activities after the accident more often than those without residual physical problems. Residual physical problems were reported in about one sixth of the study group, few with serious problems. The risk of residual problems should be recognised in older children, especially after moped accidents, and also in children with neck problems. Copyright © 2010 Elsevier Ltd. All rights reserved.

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

Ritchie, L.T.; Johnson, J.D.; Blond, R.M.

The CRAC2 computer code is a revision of the Calculation of Reactor Accident Consequences computer code, CRAC, developed for the Reactor Safety Study. The CRAC2 computer code incorporates significant modeling improvements in the areas of weather sequence sampling and emergency response, and refinements to the plume rise, atmospheric dispersion, and wet deposition models. New output capabilities have also been added. This guide is to facilitate the informed and intelligent use of CRAC2. It includes descriptions of the input data, the output results, the file structures, control information, and five sample problems.

Population genomic analysis of strain variation in Leptospirillum group II bacteria involved in acid mine drainage formation.

PubMed

Simmons, Sheri L; Dibartolo, Genevieve; Denef, Vincent J; Goltsman, Daniela S Aliaga; Thelen, Michael P; Banfield, Jillian F

2008-07-22

Deeply sampled community genomic (metagenomic) datasets enable comprehensive analysis of heterogeneity in natural microbial populations. In this study, we used sequence data obtained from the dominant member of a low-diversity natural chemoautotrophic microbial community to determine how coexisting closely related individuals differ from each other in terms of gene sequence and gene content, and to uncover evidence of evolutionary processes that occur over short timescales. DNA sequence obtained from an acid mine drainage biofilm was reconstructed, taking into account the effects of strain variation, to generate a nearly complete genome tiling path for a Leptospirillum group II species closely related to L. ferriphilum (sampling depth approximately 20x). The population is dominated by one sequence type, yet we detected evidence for relatively abundant variants (>99.5% sequence identity to the dominant type) at multiple loci, and a few rare variants. Blocks of other Leptospirillum group II types ( approximately 94% sequence identity) have recombined into one or more variants. Variant blocks of both types are more numerous near the origin of replication. Heterogeneity in genetic potential within the population arises from localized variation in gene content, typically focused in integrated plasmid/phage-like regions. Some laterally transferred gene blocks encode physiologically important genes, including quorum-sensing genes of the LuxIR system. Overall, results suggest inter- and intrapopulation genetic exchange involving distinct parental genome types and implicate gain and loss of phage and plasmid genes in recent evolution of this Leptospirillum group II population. Population genetic analyses of single nucleotide polymorphisms indicate variation between closely related strains is not maintained by positive selection, suggesting that these regions do not represent adaptive differences between strains. Thus, the most likely explanation for the observed patterns of polymorphism is divergence of ancestral strains due to geographic isolation, followed by mixing and subsequent recombination.

Population Genomic Analysis of Strain Variation in Leptospirillum Group II Bacteria Involved in Acid Mine Drainage Formation

PubMed Central

Denef, Vincent J; Goltsman, Daniela S. Aliaga; Thelen, Michael P; Banfield, Jillian F

2008-01-01

Deeply sampled community genomic (metagenomic) datasets enable comprehensive analysis of heterogeneity in natural microbial populations. In this study, we used sequence data obtained from the dominant member of a low-diversity natural chemoautotrophic microbial community to determine how coexisting closely related individuals differ from each other in terms of gene sequence and gene content, and to uncover evidence of evolutionary processes that occur over short timescales. DNA sequence obtained from an acid mine drainage biofilm was reconstructed, taking into account the effects of strain variation, to generate a nearly complete genome tiling path for a Leptospirillum group II species closely related to L. ferriphilum (sampling depth ∼20×). The population is dominated by one sequence type, yet we detected evidence for relatively abundant variants (>99.5% sequence identity to the dominant type) at multiple loci, and a few rare variants. Blocks of other Leptospirillum group II types (∼94% sequence identity) have recombined into one or more variants. Variant blocks of both types are more numerous near the origin of replication. Heterogeneity in genetic potential within the population arises from localized variation in gene content, typically focused in integrated plasmid/phage-like regions. Some laterally transferred gene blocks encode physiologically important genes, including quorum-sensing genes of the LuxIR system. Overall, results suggest inter- and intrapopulation genetic exchange involving distinct parental genome types and implicate gain and loss of phage and plasmid genes in recent evolution of this Leptospirillum group II population. Population genetic analyses of single nucleotide polymorphisms indicate variation between closely related strains is not maintained by positive selection, suggesting that these regions do not represent adaptive differences between strains. Thus, the most likely explanation for the observed patterns of polymorphism is divergence of ancestral strains due to geographic isolation, followed by mixing and subsequent recombination. PMID:18651792

Sedimentology of the fluvial and fluvio-marine facies of the Bahariya Formation (Early Cenomanian), Bahariya Oasis, Western Desert, Egypt

NASA Astrophysics Data System (ADS)

Khalifa, M. A.; Catuneanu, O.

2008-05-01

The Lower Cenomanian Bahariya Formation in the Bahariya Oasis, Western Desert, Egypt, was deposited under two coeval environmental conditions. A fully fluvial system occurs in the southern portion of the Bahariya Oasis, including depositional products of meandering and braided streams, and a coeval fluvio-marine setting is dominant to the north. These deposits are organized into four unconformity-bounded depositional sequences, whose architecture is shaped by a complex system of incised valleys. The fluvial portion of the lower two depositional sequences is dominated by low-energy, meandering systems with a tabular geometry, dominated by overbank facies. The fluvial deposits of the upper two sequences represent the product of sedimentation within braided streams, and consist mainly of amalgamated channel-fills. The braided fluvial systems form the fill of incised valleys whose orientation follows a southeast-northwest trending direction, and which truncate the underlying sequences. Four sedimentary facies have been identified within the braided-channel systems, namely thin-laminated sandstones (Sh), cross-bedded sandstones (Sp, St), massive ferruginous sandstones (Sm) and variegated mudstones (Fm). The exposed off-channel overbank facies of the meandering systems include floodplain (Fm) and crevasse splay (Sl) facies. The fluvio-marine depositional systems consist of interbedded floodplain, coastal and shallow-marine deposits. The floodplain facies include fine-grained sandstones (Sf), laminated siltstones (Stf) and mudstones (Mf) that show fining-upward cycles. The coastal to shallow-marine facies consist primarily of mudstones (Mc) and glauconitic sandstones (Gc) organized vertically in coarsening-upward prograding cyclothems topped by thin crusts of ferricrete (Fc). The four depositional sequences are present across the Bahariya Oasis, albeit with varying degrees of preservation related to post-depositional erosion associated with the formation of sequence boundaries. These unconformities may be overlain by braided-stream channel sandstones at the base of incised valleys, or marked by ferricrete paleosols (lithofacies Fc) in the interfluve areas.

Whole Exome Sequencing in Dominant Cataract Identifies a New Causative Factor, CRYBA2, and a Variety of Novel Alleles in Known Genes

PubMed Central

Reis, Linda M.; Tyler, Rebecca C.; Muheisen, Sanaa; Raggio, Victor; Salviati, Leonardo; Han, Dennis P.; Costakos, Deborah; Yonath, Hagith; Hall, Sarah; Power, Patricia; Semina, Elena V.

2013-01-01

Pediatric cataracts are observed in 1–15 per 10,000 births with 10–25% of cases attributed to genetic causes; autosomal dominant inheritance is the most commonly observed pattern. Since the specific cataract phenotype is not sufficient to predict which gene is mutated, whole exome sequencing (WES) was utilized to concurrently screen all known cataract genes and to examine novel candidate factors for a disease-causing mutation in probands from 23 pedigrees affected with familial dominant cataract. Review of WES data for 36 known cataract genes identified causative mutations in nine pedigrees (39%) in CRYAA, CRYBB1, CRYBB3, CRYGC (2), CRYGD, GJA8 (2), and MIP and an additional likely causative mutation in EYA1; the CRYBB3 mutation represents the first dominant allele in this gene and demonstrates incomplete penetrance. Examination of crystallin genes not yet linked to human disease identified a novel cataract gene, CRYBA2, a member of the βγ-crystallin superfamily. The p.(Val50Met) mutation in CRYBA2 cosegregated with disease phenotype in a four-generation pedigree with autosomal dominant congenital cataracts with incomplete penetrance. Expression studies detected cryba2 transcripts during early lens development in zebrafish, supporting its role in congenital disease. Our data highlight the extreme genetic heterogeneity of dominant cataract as the eleven causative/likely causative mutations affected nine different genes and the majority of mutant alleles were novel. Furthermore, these data suggest that less than half of dominant cataract can be explained by mutations in currently known genes. PMID:23508780

Diversity and function in microbial mats from the Lucky Strike hydrothermal vent field.

PubMed

Crépeau, Valentin; Cambon Bonavita, Marie-Anne; Lesongeur, Françoise; Randrianalivelo, Henintsoa; Sarradin, Pierre-Marie; Sarrazin, Jozée; Godfroy, Anne

2011-06-01

Diversity and function in microbial mats from the Lucky Strike hydrothermal vent field (Mid-Atlantic Ridge) were investigated using molecular approaches. DNA and RNA were extracted from mat samples overlaying hydrothermal deposits and Bathymodiolus azoricus mussel assemblages. We constructed and analyzed libraries of 16S rRNA gene sequences and sequences of functional genes involved in autotrophic carbon fixation [forms I and II RuBisCO (cbbL/M), ATP-citrate lyase B (aclB)]; methane oxidation [particulate methane monooxygenase (pmoA)] and sulfur oxidation [adenosine-5'-phosphosulfate reductase (aprA) and soxB]. To gain new insights into the relationships between mats and mussels, we also used new domain-specific 16S rRNA gene primers targeting Bathymodiolus sp. symbionts. All identified archaeal sequences were affiliated with a single group: the marine group 1 Thaumarchaeota. In contrast, analyses of bacterial sequences revealed much higher diversity, although two phyla Proteobacteria and Bacteroidetes were largely dominant. The 16S rRNA gene sequence library revealed that species affiliated to Beggiatoa Gammaproteobacteria were the dominant active population. Analyses of DNA and RNA functional gene libraries revealed a diverse and active chemolithoautotrophic population. Most of these sequences were affiliated with Gammaproteobacteria, including hydrothermal fauna symbionts, Thiotrichales and Methylococcales. PCR and reverse transcription-PCR using 16S rRNA gene primers targeted to Bathymodiolus sp. symbionts revealed sequences affiliated with both methanotrophic and thiotrophic endosymbionts. © 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

[Security at work in terms of risk factors (author's transl)].

PubMed

Faverge, J M

1977-09-23

Accident epidemiology aims at determining those factors which are associated with an increased risk. Here accidents at work are considered in which any given situation involves: one or many individuals (I); one or many tasks (T); one or many machines or production tools (M); an environment (E). Eight factors are proposed for each of which one of the above components is dominant. Each factor is defined and examples are given. In addition, where applicable, the following are given: subfactors; references to studies which demonstrate the association between risk and factor; one or several possible action mechanisms; proposals enabling a quantitative evaluation to be made for statistical purposes; suggestions for prevention. The factors are: Individual disposition (I) or liability. Worker's inexperience (I). Stress (T) imposed on the worker. Recovery (T) (an exceptional task must be performed in order to regain normal work conditions). Catachresis (M) (a tool is used for an unusual purpose or a machine is required to exceed normal work load). Material wear (M) or damage. Interference (E) between partially independent processes. Insufficient information (E) concerning the state of the system.

Differences in the Composition of Archaeal Communities in Sediments from Contrasting Zones of Lake Taihu

PubMed Central

Fan, Xianfang; Xing, Peng

2016-01-01

In shallow lakes, different primary producers might impact the physiochemical characteristics of the sediment and the associated microbial communities. Until now, little was known about the features of sediment Archaea and their variation across different primary producer-dominated ecosystems. Lake Taihu provides a suitable study area with cyanobacteria- and macrophyte-dominated zones co-occurring in one ecosystem. The composition of the sediment archaeal community was assessed using 16S rRNA gene amplicon sequencing technology, based on which the potential variation with respect to the physiochemical characteristics of the sediment was analyzed. Euryarchaeota (30.19% of total archaeal sequences) and Bathyarchaeota (28.00%) were the two most abundant phyla, followed by Crenarchaeota (11.37%), Aigarchaeota (10.24%) and Thaumarchaeota (5.98%). The differences found in the composition of the archaeal communities between the two zones was significant (p = 0.005). Sediment from macrophyte-dominated zones had high TOC and TN content and an abundance of archaeal lineages potentially involved in the degradation of complex organic compounds, such as the order Thermoplasmatales. In the area dominated by Cyanobacteria, archaeal lineages related to sulfur metabolism, for example, Sulfolobales and Desulfurococcales, were significantly enriched. Among Bathyarchaeota, subgroups MCG-6 and MCG-15 were significantly accumulated in the sediment of areas dominated by macrophytes whereas MCG-4 was consistently dominant in both type of sediments. The present study contributes to the knowledge of sediment archaeal communities with different primary producers and their possible biogeochemical functions in sediment habitats. PMID:27708641

Anaerobic degradation of propane and butane by sulfate-reducing bacteria enriched from marine hydrocarbon cold seeps.

PubMed

Jaekel, Ulrike; Musat, Niculina; Adam, Birgit; Kuypers, Marcel; Grundmann, Olav; Musat, Florin

2013-05-01

The short-chain, non-methane hydrocarbons propane and butane can contribute significantly to the carbon and sulfur cycles in marine environments affected by oil or natural gas seepage. In the present study, we enriched and identified novel propane and butane-degrading sulfate reducers from marine oil and gas cold seeps in the Gulf of Mexico and Hydrate Ridge. The enrichment cultures obtained were able to degrade simultaneously propane and butane, but not other gaseous alkanes. They were cold-adapted, showing highest sulfate-reduction rates between 16 and 20 °C. Analysis of 16S rRNA gene libraries, followed by whole-cell hybridizations with sequence-specific oligonucleotide probes showed that each enrichment culture was dominated by a unique phylotype affiliated with the Desulfosarcina-Desulfococcus cluster within the Deltaproteobacteria. These phylotypes formed a distinct phylogenetic cluster of propane and butane degraders, including sequences from environments associated with hydrocarbon seeps. Incubations with (13)C-labeled substrates, hybridizations with sequence-specific probes and nanoSIMS analyses showed that cells of the dominant phylotypes were the first to become enriched in (13)C, demonstrating that they were directly involved in hydrocarbon degradation. Furthermore, using the nanoSIMS data, carbon assimilation rates were calculated for the dominant cells in each enrichment culture.

Perchlorate reduction by hydrogen autotrophic bacteria and microbial community analysis using high-throughput sequencing.

PubMed

Wan, Dongjin; Liu, Yongde; Niu, Zhenhua; Xiao, Shuhu; Li, Daorong

2016-02-01

Hydrogen autotrophic reduction of perchlorate have advantages of high removal efficiency and harmless to drinking water. But so far the reported information about the microbial community structure was comparatively limited, changes in the biodiversity and the dominant bacteria during acclimation process required detailed study. In this study, perchlorate-reducing hydrogen autotrophic bacteria were acclimated by hydrogen aeration from activated sludge. For the first time, high-throughput sequencing was applied to analyze changes in biodiversity and the dominant bacteria during acclimation process. The Michaelis-Menten model described the perchlorate reduction kinetics well. Model parameters q(max) and K(s) were 2.521-3.245 (mg ClO4(-)/gVSS h) and 5.44-8.23 (mg/l), respectively. Microbial perchlorate reduction occurred across at pH range 5.0-11.0; removal was highest at pH 9.0. The enriched mixed bacteria could use perchlorate, nitrate and sulfate as electron accepter, and the sequence of preference was: NO3(-) > ClO4(-) > SO4(2-). Compared to the feed culture, biodiversity decreased greatly during acclimation process, the microbial community structure gradually stabilized after 9 acclimation cycles. The Thauera genus related to Rhodocyclales was the dominated perchlorate reducing bacteria (PRB) in the mixed culture.

Investigation of the microbial communities colonizing prepainted steel used for roofing and walling.

PubMed

Huynh, Tran T; Jamil, Ili; Pianegonda, Nicole A; Blanksby, Stephen J; Barker, Philip J; Manefield, Mike; Rice, Scott A

2017-04-01

Microbial colonization of prepainted steel, commonly used in roofing applications, impacts their aesthetics, durability, and functionality. Understanding the relevant organisms and the mechanisms by which colonization occurs would provide valuable information that can be subsequently used to design fouling prevention strategies. Here, next-generation sequencing and microbial community finger printing (T-RFLP) were used to study the community composition of microbes colonizing prepainted steel roofing materials at Burrawang, Australia and Kapar, Malaysia over a 52-week period. Community diversity was low and was dominated by Bacillus spp., cyanobacteria, actinobacteria, Cladosporium sp., Epicoccum nigrum, and Teratosphaeriaceae sp. Cultivation-based methods isolated approximately 20 different fungi and bacteria, some of which, such as E. nigrum and Cladosporium sp., were represented in the community sequence data. Fluorescence in situ hybridization imaging showed that fungi were the most dominant organisms present. Analysis of the sequence and T-RFLP data indicated that the microbial communities differed significantly between locations and changed significantly over time. The study demonstrates the utility of molecular ecology tools to identify and characterize microbial communities associated with the fouling of painted steel surfaces and ultimately can enable the targeted development of control strategies based on the dominant species responsible for fouling. © 2016 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

Eurasian otters, Lutra lutra, have a dominant mtDNA haplotype from the Iberian Peninsula to Scandinavia.

PubMed

Ferrando, Ainhoa; Ponsà, Montserrat; Marmi, Josep; Domingo-Roura, Xavier

2004-01-01

The Eurasian otter, Lutra lutra, has a Palaearctic distribution and has suffered a severe decline throughout Europe during the last century. Previous studies in this and other mustelids have shown reduced levels of variability in mitochondrial DNA, although otter phylogeographic studies were restricted to central-western Europe. In this work we have sequenced 361 bp of the mtDNA control region in 73 individuals from eight countries and added our results to eight sequences available from GenBank and the literature. The range of distribution has been expanded in relation to previous works north towards Scandinavia, east to Russia and Belarus, and south to the Iberian Peninsula. We found a single dominant haplotype in 91.78% of the samples, and six more haplotypes deviating a maximum of two mutations from the dominant haplotype restricted to a single country. Variability was extremely low in western Europe but higher in eastern countries. This, together with the lack of phylogeographical structuring, supports the postglacial recolonization of Europe from a single refugium. The Eurasian otter mtDNA control region has a 220-bp variable minisatellite in Domain III that we sequenced in 29 otters. We found a total of 19 minisatellite haplotypes, but they showed no phylogenetic information.

Recovery of symbiotic nitrogen fixing acacia rhizobia from Merzouga Desert sand dunes in South East Morocco--Identification of a probable new species of Ensifer adapted to stressed environments.

PubMed

Sakrouhi, Ilham; Belfquih, Meryem; Sbabou, Laïla; Moulin, Patricia; Bena, Gilles; Filali-Maltouf, Abdelkarim; Le Quéré, Antoine

2016-03-01

Bacteria capable of nodulating Acacia tortilis and A. gummifera could be recovered from sand dunes collected in the Moroccan Merzouga desert. The trapping approach enabled the recovery of 17 desert rhizobia that all clustered within the Ensifer (Sinorhizobium) genus. Four isolates of the dominant genotype comprising 15 strains as well as 2 divergent strains were further characterized by MLSA. Phylogenetic analyzes indicated that the dominant genetic type was belonging to a new and yet undefined species within the Ensifer genus. Interestingly, housekeeping gene phylogenies showed that this possibly new species is also present in another desert but in India. Phylogenetic analyses of nifH and nodC sequences showed high sequence conservation among the Moroccan strains belonging to the dominant genotype but high divergence with sequences from Indian isolates suggesting acquisition of symbiotic genes through Horizontal Gene Transfer. These desert rhizobia were capable of growing in media containing high salt concentrations, under high pH and most of the strains showed growth at 45°C. Only recovered from desert type of Biome, yet, this new taxon appears particularly adapted to such harsh environment. Copyright © 2016 Elsevier GmbH. All rights reserved.

Application of Faecalibacterium 16S rDNA genetic marker for accurate identification of duck faeces.

PubMed

Sun, Da; Duan, Chuanren; Shang, Yaning; Ma, Yunxia; Tan, Lili; Zhai, Jun; Gao, Xu; Guo, Jingsong; Wang, Guixue

2016-04-01

The aim of this study was to judge the legal duty of pollution liabilities by assessing a duck faeces-specific marker, which can exclude distractions of residual bacteria from earlier contamination accidents. With the gene sequencing technology and bioinformatics method, we completed the comparative analysis of Faecalibacterium sequences, which were associated with ducks and other animal species, and found the sequences unique to duck faeces. Polymerase chain reaction (PCR) and agarose gel electrophoresis techniques were used to verify the reliability of both human and duck faeces-specific primers. The duck faeces-specific primers generated an amplicon of 141 bp from 43.3 % of duck faecal samples, 0 % of control samples and 100 % of sewage wastewater samples that contained duck faeces. We present here the initial evidence of Faecalibacterium-based applicability as human faeces-specificity in China. Meanwhile, this study represents the initial report of a Faecalibacterium marker for duck faeces and suggests an independent or supplementary environmental biotechnology of microbial source tracking (MST).

TRAC-P1: an advanced best estimate computer program for PWR LOCA analysis. I. Methods, models, user information, and programming details

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

Not Available

1978-05-01

The Transient Reactor Analysis Code (TRAC) is being developed at the Los Alamos Scientific Laboratory (LASL) to provide an advanced ''best estimate'' predictive capability for the analysis of postulated accidents in light water reactors (LWRs). TRAC-Pl provides this analysis capability for pressurized water reactors (PWRs) and for a wide variety of thermal-hydraulic experimental facilities. It features a three-dimensional treatment of the pressure vessel and associated internals; two-phase nonequilibrium hydrodynamics models; flow-regime-dependent constitutive equation treatment; reflood tracking capability for both bottom flood and falling film quench fronts; and consistent treatment of entire accident sequences including the generation of consistent initial conditions.more » The TRAC-Pl User's Manual is composed of two separate volumes. Volume I gives a description of the thermal-hydraulic models and numerical solution methods used in the code. Detailed programming and user information is also provided. Volume II presents the results of the developmental verification calculations.« less

Pretest aerosol code comparisons for LWR aerosol containment tests LA1 and LA2

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

Wright, A.L.; Wilson, J.H.; Arwood, P.C.

The Light-Water-Reactor (LWR) Aerosol Containment Experiments (LACE) are being performed in Richland, Washington, at the Hanford Engineering Development Laboratory (HEDL) under the leadership of an international project board and the Electric Power Research Institute. These tests have two objectives: (1) to investigate, at large scale, the inherent aerosol retention behavior in LWR containments under simulated severe accident conditions, and (2) to provide an experimental data base for validating aerosol behavior and thermal-hydraulic computer codes. Aerosol computer-code comparison activities are being coordinated at the Oak Ridge National Laboratory. For each of the six LACE tests, ''pretest'' calculations (for code-to-code comparisons) andmore » ''posttest'' calculations (for code-to-test data comparisons) are being performed. The overall goals of the comparison effort are (1) to provide code users with experience in applying their codes to LWR accident-sequence conditions and (2) to evaluate and improve the code models.« less

In-vessel melt retention as a severe accident management strategy for the Loviisa Nuclear Power Plant

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

Kymaelaeinen, O.; Tuomisto, H.; Theofanous, T.G.

1997-02-01

The concept of lower head coolability and in-vessel retention of corium has been approved as a basic element of the severe accident management strategy for IVO`s Loviisa Plant (VVER-440) in Finland. The selected approach takes advantage of the unique features of the plant such as low power density, reactor pressure vessel without penetrations at the bottom and ice-condenser containment which ensures flooded cavity in all risk significant sequences. The thermal analyses, which are supported by experimental program, demonstrate that in Loviisa the molten corium on the lower head of the reactor vessel is coolable externally with wide margins. This papermore » summarizes the approach and the plant modifications being implemented. During the approval process some technical concerns were raised, particularly with regard to thermal loadings caused by contact of cool cavity water and hot corium with the reactor vessel. Resolution of these concerns is also discussed.« less

[Characteristics of arthropod community in alpine cabbage fields].

PubMed

Wang, Xiang-ping; Zhang, Zhong-ning

2007-01-01

The study on the community structure of arthropod in the alpine cabbage fields of Hubei Province showed that the dominant pests were Brevicoryne brassicae, Mamestra brassicae and Plutella xylostella, while the dominant natural enemies were Diaeretiella rapae, Cotesia plutella, Erigonidum gramiaicolum and Syrphus corollae. The richness, diversity index, evenness index and dominance index of pest and natural enemy sub-communities all changed with time. The dominance index of pest sub-community was higher, while its diversity and evenness indices were lower than those of natural enemy sub-community. Based on fuzzy clustering analysis, the pest and natural enemy subcommunities of 14 time sequences were grouped into 4 and 3 sorts, respectively.

Beyond Bacteria: A Study of the Enteric Microbial Consortium in Extremely Low Birth Weight Infants

PubMed Central

Cotton, Charles Michael; Goldberg, Ronald N.; Wynn, James L.; Jackson, Robert B.; Seed, Patrick C.

2011-01-01

Extremely low birth weight (ELBW) infants have high morbidity and mortality, frequently due to invasive infections from bacteria, fungi, and viruses. The microbial communities present in the gastrointestinal tracts of preterm infants may serve as a reservoir for invasive organisms and remain poorly characterized. We used deep pyrosequencing to examine the gut-associated microbiome of 11 ELBW infants in the first postnatal month, with a first time determination of the eukaryote microbiota such as fungi and nematodes, including bacteria and viruses that have not been previously described. Among the fungi observed, Candida sp. and Clavispora sp. dominated the sequences, but a range of environmental molds were also observed. Surprisingly, seventy-one percent of the infant fecal samples tested contained ribosomal sequences corresponding to the parasitic organism Trichinella. Ribosomal DNA sequences for the roundworm symbiont Xenorhabdus accompanied these sequences in the infant with the greatest proportion of Trichinella sequences. When examining ribosomal DNA sequences in aggregate, Enterobacteriales, Pseudomonas, Staphylococcus, and Enterococcus were the most abundant bacterial taxa in a low diversity bacterial community (mean Shannon-Weaver Index of 1.02±0.69), with relatively little change within individual infants through time. To supplement the ribosomal sequence data, shotgun sequencing was performed on DNA from multiple displacement amplification (MDA) of total fecal genomic DNA from two infants. In addition to the organisms mentioned previously, the metagenome also revealed sequences for gram positive and gram negative bacteriophages, as well as human adenovirus C. Together, these data reveal surprising eukaryotic and viral microbial diversity in ELBW enteric microbiota dominated bytypes of bacteria known to cause invasive disease in these infants. PMID:22174751

Microbial metatranscriptomics in a permanent marine oxygen minimum zone.

PubMed

Stewart, Frank J; Ulloa, Osvaldo; DeLong, Edward F

2012-01-01

Simultaneous characterization of taxonomic composition, metabolic gene content and gene expression in marine oxygen minimum zones (OMZs) has potential to broaden perspectives on the microbial and biogeochemical dynamics in these environments. Here, we present a metatranscriptomic survey of microbial community metabolism in the Eastern Tropical South Pacific OMZ off northern Chile. Community RNA was sampled in late austral autumn from four depths (50, 85, 110, 200 m) extending across the oxycline and into the upper OMZ. Shotgun pyrosequencing of cDNA yielded 180,000 to 550,000 transcript sequences per depth. Based on functional gene representation, transcriptome samples clustered apart from corresponding metagenome samples from the same depth, highlighting the discrepancies between metabolic potential and actual transcription. BLAST-based characterizations of non-ribosomal RNA sequences revealed a dominance of genes involved with both oxidative (nitrification) and reductive (anammox, denitrification) components of the marine nitrogen cycle. Using annotations of protein-coding genes as proxies for taxonomic affiliation, we observed depth-specific changes in gene expression by key functional taxonomic groups. Notably, transcripts most closely matching the genome of the ammonia-oxidizing archaeon Nitrosopumilus maritimus dominated the transcriptome in the upper three depths, representing one in five protein-coding transcripts at 85 m. In contrast, transcripts matching the anammox bacterium Kuenenia stuttgartiensis dominated at the core of the OMZ (200 m; 1 in 12 protein-coding transcripts). The distribution of N. maritimus-like transcripts paralleled that of transcripts matching ammonia monooxygenase genes, which, despite being represented by both bacterial and archaeal sequences in the community DNA, were dominated (> 99%) by archaeal sequences in the RNA, suggesting a substantial role for archaeal nitrification in the upper OMZ. These data, as well as those describing other key OMZ metabolic processes (e.g. sulfur oxidation), highlight gene-specific expression patterns in the context of the entire community transcriptome, as well as identify key functional groups for taxon-specific genomic profiling. © 2011 Society for Applied Microbiology and Blackwell Publishing Ltd.

Genome Comparisons Reveal a Dominant Mechanism of Chromosome Number Reduction in Grasses and Accelerated Genome Evolution in Triticeae

USDA-ARS?s Scientific Manuscript database

Single nucleotide polymorphism was employed in the construction of a high-resolution, expressed sequence tag (EST) map of Aegilops tauschii, the diploid source of the wheat D genome. Comparison of the map with the rice and sorghum genome sequences revealed 50 inversions and translocations; 2, 8, and...

A novel dominant GJB2 (DFNA3) mutation in a Chinese family

NASA Astrophysics Data System (ADS)

Wang, Hongyang; Wu, Kaiwen; Yu, Lan; Xie, Linyi; Xiong, Wenping; Wang, Dayong; Guan, Jing; Wang, Qiuju

2017-01-01

To decipher the phenotype and genotype of a Chinese family with autosomal dominant non-syndromic hearing loss (ADNSHL) and a novel dominant missense mutation in the GJB2 gene (DFNA3), mutation screening of GJB2 was performed on the propositus from a five-generation ADNSHL family through polymerase chain reaction amplification and Sanger sequencing. The candidate variation and the co-segregation of the phenotype were verified in all ascertained family members. Targeted genes capture and next-generation sequencing (NGS) were performed to explore additional genetic variations. We identified the novel GJB2 mutation c.524C > A (p.P175H), which segregated with high frequency and was involved in progressive sensorineural hearing loss. One subject with an additional c.235delC mutation showed a more severe phenotype than did the other members with single GJB2 dominant variations. Four patients diagnosed with noise-induced hearing loss did not carry this mutation. No other pathogenic variations or modifier genes were identified by NGS. In conclusion, a novel missense mutation in GJB2 (DFNA3), affecting the second extracellular domain of the protein, was identified in a family with ADNSHL.

Microbial dynamics in mixed culture biofilms of bacteria surviving sanitation of conveyor belts in salmon-processing plants.

PubMed

Langsrud, S; Moen, B; Møretrø, T; Løype, M; Heir, E

2016-02-01

The microbiota surviving sanitation of salmon-processing conveyor belts was identified and its growth dynamics further investigated in a model mimicking processing surfaces in such plants. A diverse microbiota dominated by Gram-negative bacteria was isolated after regular sanitation in three salmon processing plants. A cocktail of 14 bacterial isolates representing all genera isolated from conveyor belts (Listeria, Pseudomonas, Stenotrophomonas, Brochothrix, Serratia, Acinetobacter, Rhodococcus and Chryseobacterium) formed stable biofilms on steel coupons (12°C, salmon broth) of about 10(9) CFU cm(-2) after 2 days. High-throughput sequencing showed that Listeria monocytogenes represented 0·1-0·01% of the biofilm population and that Pseudomonas spp dominated. Interestingly, both Brochothrix sp. and a Pseudomonas sp. dominated in the surrounding suspension. The microbiota surviving sanitation is dominated by Pseudomonas spp. The background microbiota in biofilms inhibit, but do not eliminate L. monocytogenes. The results highlights that sanitation procedures have to been improved in the salmon-processing industry, as high numbers of a diverse microbiota survived practical sanitation. High-throughput sequencing enables strain level studies of population dynamics in biofilm. © 2015 The Society for Applied Microbiology.

The Hidden Diversity of Flagellated Protists in Soil.

PubMed

Venter, Paul Christiaan; Nitsche, Frank; Arndt, Hartmut

2018-07-01

Protists are among the most diverse and abundant eukaryotes in soil. However, gaps between described and sequenced protist morphospecies still present a pending problem when surveying environmental samples for known species using molecular methods. The number of sequences in the molecular PR 2 database (∼130,000) is limited compared to the species richness expected (>1 million protist species) - limiting the recovery rate. This is important, since high throughput sequencing (HTS) methods are used to find associative patterns between functional traits, taxa and environmental parameters. We performed HTS to survey soil flagellates in 150 grasslands of central Europe, and tested the recovery rate of ten previously isolated and cultivated cercomonad species, among locally found diversity. We recovered sequences for reference soil flagellate species, but also a great number of their phylogenetically evaluated genetic variants, among rare and dominant taxa with presumably own biogeography. This was recorded among dominant (cercozoans, Sandona), rare (apusozoans) and a large hidden diversity of predominantly aquatic protists in soil (choanoflagellates, bicosoecids) often forming novel clades associated with uncultured environmental sequences. Evaluating the reads, instead of the OTUs that individual reads are usually clustered into, we discovered that much of this hidden diversity may be lost due to clustering. Copyright © 2018 Elsevier GmbH. All rights reserved.

Expanding pedestrian injury risk to the body region level: how to model passive safety systems in pedestrian injury risk functions.

PubMed

Niebuhr, Tobias; Junge, Mirko; Achmus, Stefanie

2015-01-01

Assessment of the effectiveness of advanced driver assistance systems (ADAS) plays a crucial role in accident research. A common way to evaluate the effectiveness of new systems is to determine the potentials for injury severity reduction. Because injury risk functions describe the probability of an injury of a given severity conditional on a technical accident severity (closing speed, delta V, barrier equivalent speed, etc.), they are predestined for such evaluations. Recent work has stated an approach on how to model the pedestrian injury risk in pedestrian-to-passenger car accidents as a family of functions. This approach gave explicit and easily interpretable formulae for the injury risk conditional on the closing speed of the car. These results are extended to injury risk functions for pedestrian body regions. Starting with a double-checked German In-depth Accident Study (GIDAS) pedestrian-to-car accident data set (N = 444) and a functional-anatomical definition of the body regions, investigations on the influence of specific body regions on the overall injury severity will be presented. As the measure of injury severity, the ISSx, a rescaled version of the well-known Injury Severity Score (ISS), was used. Though traditional ISS is computed by summation of the squares of the 3 most severe injured body regions, ISSx is computed by the summation of the exponentials of the Abbreviated Injury Scale (AIS) severities of the 3 most severely injured body regions. The exponentials used are scaled to fit the ISS range of values between 0 and 75. Three body regions (head/face/neck, thorax, hip/legs) clearly dominated abdominal and upper extremity injuries; that is, the latter 2 body regions had no influence at all on the overall injury risk over the range of technical accident severities. Thus, the ISSx is well described by use of the injury codes from the same body regions for any pedestrian injury severity. As a mathematical consequence, the ISSx becomes explicitly decomposable into the 3 body regions and so are the risk functions as body region-specific risk functions. The risk functions for each body region are stated explicitly for different injury severity levels and compared to the real-world accident data. The body region-specific risk functions can then be used to model the effect of improved passive safety systems. These modified body region-specific injury risk functions are aggregated to a new pedestrian injury risk function. Passive safety systems can therefore be modeled in injury risk functions for the first time. A short example on how the results can be used for assessing the effectiveness of new driver assistance systems concludes the article.

Identification of IFRD1 variant in a Han Chinese family with autosomal dominant hereditary spastic paraplegia associated with peripheral neuropathy and ataxia.

PubMed

Lin, Pengfei; Zhang, Dong; Xu, Guangrun; Yan, Chuanzhu

2018-04-01

Spinocerebellar ataxias (SCAs) are a group of autosomal dominant, clinically heterogeneous neurodegenerative disorders. SCA18 is a rare autosomal dominant sensory/motor neuropathy with ataxia (OMIM#607458) associated with a single missense variant c.514 A>G in the interferon related developmental regulator 1 (IFRD1) gene previously reported in a five-generation American family of Irish origin. However, to date, there have been no other reports of the IFRD1 mutation to confirm its role in SCA. Here, we report a Han Chinese family with SCA18; the family members presented with a slowly progressing gait ataxia, pyramidal tract signs, and peripheral neuropathy. We identified a missense variant (c.514 A>G, p.I172V) in IFRD1 gene in the family using targeted next-generation sequencing and Sanger direct sequencing with specific primers. Our results suggest that the IFRD1 gene may be the causative allele for SCA18.

Risk-Based Fire Safety Experiment Definition for Manned Spacecraft

NASA Technical Reports Server (NTRS)

Apostolakis, G. E.; Ho, V. S.; Marcus, E.; Perry, A. T.; Thompson, S. L.

1989-01-01

Risk methodology is used to define experiments to be conducted in space which will help to construct and test the models required for accident sequence identification. The development of accident scenarios is based on the realization that whether damage occurs depends on the time competition of two processes: the ignition and creation of an adverse environment, and the detection and suppression activities. If the fire grows and causes damage faster than it is detected and suppressed, then an accident occurred. The proposed integrated experiments will provide information on individual models that apply to each of the above processes, as well as previously unidentified interactions and processes, if any. Initially, models that are used in terrestrial fire risk assessments are considered. These include heat and smoke release models, detection and suppression models, as well as damage models. In cases where the absence of gravity substantially invalidates a model, alternate models will be developed. Models that depend on buoyancy effects, such as the multizone compartment fire models, are included in these cases. The experiments will be performed in a variety of geometries simulating habitable areas, racks, and other spaces. These simulations will necessitate theoretical studies of scaling effects. Sensitivity studies will also be carried out including the effects of varying oxygen concentrations, pressures, fuel orientation and geometry, and air flow rates. The experimental apparatus described herein includes three major modules: the combustion, the fluids, and the command and power modules.

Fukushima-derived fission nuclides monitored around Taiwan: Free tropospheric versus boundary layer transport

NASA Astrophysics Data System (ADS)

Huh, Chih-An; Hsu, Shih-Chieh; Lin, Chuan-Yao

2012-02-01

The 2011 Fukushima nuclear accident in Japan was the worst nuclear disaster following the 1986 Chernobyl accident. Fission products (nuclides) released from the Fukushima plant site since March 12, 2011 had been detected around the northern hemisphere in about two weeks and also in the southern hemisphere about one month later. We report here detailed time series of radioiodine and radiocesium isotopes monitored in a regional network around Taiwan, including one high-mountain and three ground-level sites. Our results show several pulses of emission from a sequence of accidents in the Fukushima facility, with the more volatile 131I released preferentially over 134Cs and 137Cs at the beginning. In the middle of the time series, there was a pronounced peak of radiocesium observed in northern Taiwan, with activity concentrations of 134Cs and 137Cs far exceeding that of 131I during that episode. From the first arrival time of these fission nuclides and their spatial and temporal variations at our sampling sites and elsewhere, we suggest that Fukushima-derived radioactive nuclides were transported to Taiwan and its vicinity via two pathways at different altitudes. One was transported in the free troposphere by the prevailing westerly winds around the globe; the other was transported in the planetary boundary layer by the northeast monsoon wind directly toward Taiwan.

Biogeochemical cycles of Chernobyl-born radionuclides in the contaminated forest ecosystems: long-term dynamics of the migration processes

NASA Astrophysics Data System (ADS)

Shcheglov, Alexey; Tsvetnova, Ol'ga; Klyashtorin, Alexey

2013-04-01

Biogeochemical migration is a dominant factor of the radionuclide transport through the biosphere. In the early XX century, V.I. Vernadskii, a Russian scientist known, noted about a special role living things play in transport and accumulation of natural radionuclide in various environments. The role of biogeochemical processes in migration and redistribution of technogenic radionuclides is not less important. In Russia, V. M. Klechkovskii and N.V. Timofeev-Ressovskii showed some important biogeochemical aspects of radionuclide migration by the example of global fallout and Kyshtym accident. Their followers, R.M. Alexakhin, M.A. Naryshkin, N.V. Kulikov, F.A. Tikhomirov, E.B. Tyuryukanova, and others also contributed a lot to biogeochemistry of radionuclides. In the post-Chernobyl period, this area of knowledge received a lot of data that allowed building the radioactive element balance and flux estimation in various biogeochemical cycles [Shcheglov et al., 1999]. Regrettably, many of recent radioecological studies are only focused on specific radionuclide fluxes or pursue some applied tasks, missing the holistic approach. Most of the studies consider biogeochemical fluxes of radioactive isotopes in terms of either dose estimation or radionuclide migration rates in various food chains. However, to get a comprehensive picture and develop a reliable forecast of environmental, ecological, and social consequences of radioactive pollution in a vast contaminated area, it is necessary to investigate all the radionuclide fluxes associated with the biogeochemical cycles in affected ecosystems. We believe such an integrated approach would be useful to study long-term environmental consequences of the Fukushima accident as well. In our long-term research, we tried to characterize the flux dynamics of the Chernobyl-born radionuclides in the contaminated forest ecosystems and landscapes as a part of the integrated biogeochemical process. Our field studies were started in June of 1986 (less than two months after the accident) and have been continued up to now, focused on the most common forest ecosystems scattered over the contaminated areas of Russian Federation and Ukraine. A comprehensive analysis of the 137Cs and 90Sr biogeochemical fluxes shows that downward radionuclide fluxes (those directed from tree crowns to the soil) dominated over the upward fluxes (from the soil to forest vegetation) in the first years after the accident. Currently, the biological cycle in the contaminated ecosystems is a main factor impeding further vertical migration of long-lived radionuclides from upper soil layers to the ground water. The role of biota as a retardation factor depends on landscape type as well. In accumulative landscapes (with positive material balance), biota plays leading role in radionuclide retardation, while in eluvial landscapes (with the negative balance) soil absorbing complex serves as the dominant barrier for radionuclides leaching down the soil profile. The manifestation of both soil- and biota-driven factors depends on the radionuclide chemical speciation in the initial fallout. The latter factor is most important for 137Cs, yet less manifested for 90Sr. Among the biota components, fungi and forest vegetation are of particular importance for 137Cs and 90Sr accumulation, respectively. In summary, biogeochemical cycles of 137Cs and 90Sr in the investigated forest ecosystems serve as main factors impeding the radionuclide migration from the fallout to ground water. Larger-scale landscape factors determine the radionuclide flux intensity in the biogeochemical cycles and affect the radionuclide spatial variability in the contaminated biota components.

Hybrid selection for sequencing pathogen genomes from clinical samples

PubMed Central

2011-01-01

We have adapted a solution hybrid selection protocol to enrich pathogen DNA in clinical samples dominated by human genetic material. Using mock mixtures of human and Plasmodium falciparum malaria parasite DNA as well as clinical samples from infected patients, we demonstrate an average of approximately 40-fold enrichment of parasite DNA after hybrid selection. This approach will enable efficient genome sequencing of pathogens from clinical samples, as well as sequencing of endosymbiotic organisms such as Wolbachia that live inside diverse metazoan phyla. PMID:21835008

Macroscopic biofilms in fracture-dominated sediment that anaerobically oxidize methane

USGS Publications Warehouse

Briggs, B.R.; Pohlman, J.W.; Torres, M.; Riedel, M.; Brodie, E.L.; Colwell, F.S.

2011-01-01

Methane release from seafloor sediments is moderated, in part, by the anaerobic oxidation of methane (AOM) performed by consortia of archaea and bacteria. These consortia occur as isolated cells and aggregates within the sulfate-methane transition (SMT) of diffusion and seep-dominant environments. Here we report on a new SMT setting where the AOM consortium occurs as macroscopic pink to orange biofilms within subseafloor fractures. Biofilm samples recovered from the Indian and northeast Pacific Oceans had a cellular abundance of 10 7 to 10 8 cells cm -3. This cell density is 2 to 3 orders of magnitude greater than that in the surrounding sediments. Sequencing of bacterial 16S rRNA genes indicated that the bacterial component is dominated by Deltaproteobacteria, candidate division WS3, and Chloroflexi, representing 46%, 15%, and 10% of clones, respectively. In addition, major archaeal taxa found in the biofilm were related to the ANME-1 clade, Thermoplasmatales, and Desulfurococcales, representing 73%, 11%, and 10% of archaeal clones, respectively. The sequences of all major taxa were similar to sequences previously reported from cold seep environments. PhyloChip microarray analysis detected all bacterial phyla identified by the clone library plus an additional 44 phyla. However, sequencing detected more archaea than the PhyloChip within the phyla of Methanosarcinales and Desulfurococcales. The stable carbon isotope composition of the biofilm from the SMT (-35 to-43%) suggests that the production of the biofilm is associated with AOM. These biofilms are a novel, but apparently widespread, aggregation of cells represented by the ANME-1 clade that occur in methane-rich marine sediments. ?? 2011, American Society for Microbiology.

Application of denaturing gradient gel electrophoresis (DGGE) to the analysis of microbial communities of subgingival plaque.

PubMed

Fujimoto, C; Maeda, H; Kokeguchi, S; Takashiba, S; Nishimura, F; Arai, H; Fukui, K; Murayama, Y

2003-08-01

Denaturing gradient gel electrophoresis (DGGE) was applied to the microbiologic examination of subgingival plaque. The PCR primers were designed from conserved nucleotide sequences on 16S ribosomal RNA gene (16SrDNA) with GC rich clamp at the 5'-end. Polymerase chain reaction (PCR) was performed using the primers and genomic DNAs of typical periodontal bacteria. The generated 16SrDNA fragments were separated by denaturing gel. Although the sizes of the amplified DNA fragments were almost the same among the species, 16SrDNAs of the periodontal bacteria were distinguished according to their specific sequences. The microflora of clinical plaque samples were profiled by the PCR-DGGE method, and the dominant 16SrDNA bands were cloned and sequenced. Simultaneously, Actinobacillus actinomycetemcomitans, Porphyromonas gingivalis and Prevotella intermedia were detected by an ordinary PCR method. In the deep periodontal pockets, the bacterial community structures were complicated and P. gingivalis was the most dominant species, whereas the DGGE profiles were simple and Streptococcus or Neisseria species were dominant in the shallow pockets. The species-specific PCR method revealed the presence of A. actinomycetemcomitans, P. gingivalis and P. intermedia in the clinical samples. However, corresponding bands were not always observed in the DGGE profiles, indicating a lower sensitivity of the DGGE method. Although the DGGE method may have a lower sensitivity than the ordinary PCR methods, it could visualize the bacterial qualitative compositions and reveal the major species of the plaque. The DGGE analysis and following sequencing may have the potential to be a promising bacterial examination procedure in periodontal diseases.

Next generation sequencing to identify novel genetic variants causative of autosomal dominant familial hypercholesterolemia associated with increased risk of coronary heart disease.

PubMed

Al-Allaf, Faisal A; Athar, Mohammad; Abduljaleel, Zainularifeen; Taher, Mohiuddin M; Khan, Wajahatullah; Ba-Hammam, Faisal A; Abalkhail, Hala; Alashwal, Abdullah

2015-07-01

Familial hypercholesterolemia (FH) is an autosomal dominant inherited disease characterized by elevated plasma low-density lipoprotein cholesterol (LDL-C). It is an autosomal dominant disease, caused by variants in Ldlr, ApoB or Pcsk9, which results in high levels of LDL-cholesterol (LDL-C) leading to early coronary heart disease. Sequencing whole genome for screening variants for FH are not suitable due to high cost. Hence, in this study we performed targeted customized sequencing of FH 12 genes (Ldlr, ApoB, Pcsk9, Abca1, Apoa2, Apoc3, Apon2, Arh, Ldlrap1, Apoc2, ApoE, and Lpl) that have been implicated in the homozygous phenotype of a proband pedigree to identify candidate variants by NGS Ion torrent PGM. Only three genes (Ldlr, ApoB, and Pcsk9) were found to be highly associated with FH based on the variant rate. The results showed that seven deleterious variants in Ldlr, ApoB, and Pcsk9 genes were pathological and were clinically significant based on predictions identified by SIFT and PolyPhen. Targeted customized sequencing is an efficient technique for screening variants among targeted FH genes. Final validation of seven deleterious variants conducted by capillary resulted to only one novel variant in Ldlr gene that was found in exon 14 (c.2026delG, p. Gly676fs). The variant found in Ldlr gene was a novel heterozygous variant derived from a male in the proband. Copyright © 2015 Elsevier B.V. All rights reserved.

Dramatic Differences in Gut Bacterial Densities Correlate with Diet and Habitat in Rainforest Ants.

PubMed

Sanders, Jon G; Lukasik, Piotr; Frederickson, Megan E; Russell, Jacob A; Koga, Ryuichi; Knight, Rob; Pierce, Naomi E

2017-10-01

Abundance is a key parameter in microbial ecology, and important to estimates of potential metabolite flux, impacts of dispersal, and sensitivity of samples to technical biases such as laboratory contamination. However, modern amplicon-based sequencing techniques by themselves typically provide no information about the absolute abundance of microbes. Here, we use fluorescence microscopy and quantitative polymerase chain reaction as independent estimates of microbial abundance to test the hypothesis that microbial symbionts have enabled ants to dominate tropical rainforest canopies by facilitating herbivorous diets, and compare these methods to microbial diversity profiles from 16S rRNA amplicon sequencing. Through a systematic survey of ants from a lowland tropical forest, we show that the density of gut microbiota varies across several orders of magnitude among ant lineages, with median individuals from many genera only marginally above detection limits. Supporting the hypothesis that microbial symbiosis is important to dominance in the canopy, we find that the abundance of gut bacteria is positively correlated with stable isotope proxies of herbivory among canopy-dwelling ants, but not among ground-dwelling ants. Notably, these broad findings are much more evident in the quantitative data than in the 16S rRNA sequencing data. Our results provide quantitative context to the potential role of bacteria in facilitating the ants' dominance of the tropical rainforest canopy, and have broad implications for the interpretation of sequence-based surveys of microbial diversity. © The Author 2017. Published by Oxford University Press on behalf of the Society for Integrative and Comparative Biology. All rights reserved. For permissions please email: journals.permissions@oup.com.

Novel Single-Base Deletional Mutation in Major Intrinsic Protein (MIP) in Autosomal Dominant Cataract

PubMed Central

Geyer, David D.; Spence, M. Anne; Johannes, Meriam; Flodman, Pamela; Clancy, Kevin P.; Berry, Rebecca; Sparkes, Robert S.; Jonsen, Matthew D.; Isenberg, Sherwin J.; Bateman, J. Bronwyn

2006-01-01

PURPOSE To further elucidate the cataract phenotype, and identify the gene and mutation for autosomal dominant cataract (ADC) in an American family of European descent (ADC2) by sequencing the major intrinsic protein gene (MIP), a candidate based on linkage to chromosome 12q13. DESIGN Observational case series and laboratory experimental study. METHODS We examined two at-risk individuals in ADC2. We PCR-amplified and sequenced all four exons and all intron-exon boundaries of the MIP gene from genomic and cloned DNA in affected members to confirm one variant as the putative mutation. RESULTS We found a novel single deletion of nucleotide (nt) 3223 (within codon 235) in exon four, causing a frameshift that alters 41 of 45 subsequent amino acids and creates a premature stop codon. CONCLUSIONS We identified a novel single base pair deletion in the MIP gene and conclude that it is a pathogenic sequence alteration. PMID:16564824

Spatial and vertical distribution of bacterial community in the northern South China Sea.

PubMed

Sun, Fu-Lin; Wang, You-Shao; Wu, Mei-Lin; Sun, Cui-Ci; Cheng, Hao

2015-10-01

Microbial communities are highly diverse in coastal oceans and response rapidly with changing environments. Learning about this will help us understand the ecology of microbial populations in marine ecosystems. This study aimed to assess the spatial and vertical distributions of the bacterial community in the northern South China Sea. Multi-dimensional scaling analyses revealed structural differences of the bacterial community among sampling sites and vertical depth. Result also indicated that bacterial community in most sites had higher diversity in 0-75 m depths than those in 100-200 m depths. Bacterial community of samples was positively correlation with salinity and depth, whereas was negatively correlation with temperature. Proteobacteria and Cyanobacteria were the dominant groups, which accounted for the majority of sequences. The α-Proteobacteria was highly diverse, and sequences belonged to Rhodobacterales bacteria were dominant in all characterized sequences. The current data indicate that the Rhodobacterales bacteria, especially Roseobacter clade are the diverse group in the tropical waters.

Altitudinal characteristics of atmospheric deposition of aerosols in mountainous regions: Lessons from the Fukushima Daiichi Nuclear Power Station accident.

PubMed

Sanada, Yukihisa; Katata, Genki; Kaneyasu, Naoki; Nakanishi, Chika; Urabe, Yoshimi; Nishizawa, Yukiyasu

2018-03-15

To understand the formation process of radiologically contaminated areas in eastern Japan caused by the Fukushima Daiichi Nuclear Power Station (FDNPS) accident, the deposition mechanisms over complex topography are the key factors to be investigated. To characterize the atmospheric deposition processes of radionuclides over complex mountainous topography, we investigated the altitudinal distributions of the radiocesium deposited during the accident. In five selected areas, altitudinal characteristics of the air dose rates observed using airborne surveys were analyzed. To examine the deposition mechanisms, we supplementarily used vertical profiles of radiocesium deposition in each area calculated in the latest atmospheric dispersion model. In southern Iwate, the vertical profile of the observed air dose rate was uniform regardless of altitude. In western Tochigi, the areas with the highest levels of contamination were characteristically distributed in the middle of the mountains, while in southern Fukushima, the areas with the highest contamination levels were enhanced near the summits of mountains. In central Fukushima, high air dose rates were limited to the bottoms of basin-like valley. In the region northwest of FDNPS, the air dose rate was the highest at the bottom of valley topography and decreased gradually with altitude. The simulation results showed that calculated wet deposition and observed vertical profiles of total deposition were similar in areas of southern Iwate and northwest of FDNPS qualitatively, suggesting that the dominant deposition mechanism was wet deposition. In contrast, the atmospheric dispersion model failed to reproduce either the timing of precipitation events or vertical profiles of radiocesium deposition in three other areas. Although it was difficult to elucidate the deposition mechanisms in these areas due to uncertainties of the present model results, potential mechanisms such as cloud water deposition were still proposed based on circumstantial evidences of limited meteorological data during the early stage of the accident. Copyright © 2017 Elsevier B.V. All rights reserved.

Metagenomic Evaluation of Bacterial and Archaeal Diversity in the Geothermal Hot Springs of Manikaran, India

PubMed Central

Pathak, Ashish; Green, Stefan J.; Joshi, Amit; Chauhan, Ashvini

2015-01-01

Bacterial and archaeal diversity in geothermal spring water were investigated using 16S rRNA gene amplicon metagenomic sequencing. This revealed the dominance of Firmicutes, Aquificae, and the Deinococcus-Thermus group in this thermophilic environment. A number of sequences remained taxonomically unresolved, indicating the presence of potentially novel microbes in this unique habitat. PMID:25700403

Architecture of a Species: Phylogenomics of Staphylococcus aureus.

PubMed

Planet, Paul J; Narechania, Apurva; Chen, Liang; Mathema, Barun; Boundy, Sam; Archer, Gordon; Kreiswirth, Barry

2017-02-01

A deluge of whole-genome sequencing has begun to give insights into the patterns and processes of microbial evolution, but genome sequences have accrued in a haphazard manner, with biased sampling of natural variation that is driven largely by medical and epidemiological priorities. For instance, there is a strong bias for sequencing epidemic lineages of methicillin-resistant Staphylococcus aureus (MRSA) over sensitive isolates (methicillin-sensitive S. aureus: MSSA). As more diverse genomes are sequenced the emerging picture is of a highly subdivided species with a handful of relatively clonal groups (complexes) that, at any given moment, dominate in particular geographical regions. The establishment of hegemony of particular clones appears to be a dynamic process of successive waves of replacement of the previously dominant clone. Here we review the phylogenomic structure of a diverse range of S. aureus, including both MRSA and MSSA. We consider the utility of the concept of the 'core' genome and the impact of recombination and horizontal transfer. We argue that whole-genome surveillance of S. aureus populations could lead to better forecasting of antibiotic resistance and virulence of emerging clones, and a better understanding of the elusive biological factors that determine repeated strain replacement. Copyright © 2016. Published by Elsevier Ltd.

Interpretation of the results of the CORA-33 dry core BWR test

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

Ott, L.J.; Hagen, S.

All BWR degraded core experiments performed prior to CORA-33 were conducted under ``wet`` core degradation conditions for which water remains within the core and continuous steaming feeds metal/steam oxidation reactions on the in-core metallic surfaces. However, one dominant set of accident scenarios would occur with reduced metal oxidation under ``dry`` core degradation conditions and, prior to CORA-33, this set had been neglected experimentally. The CORA-33 experiment was designed specifically to address this dominant set of BWR ``dry`` core severe accident scenarios and to partially resolve phenomenological uncertainties concerning the behavior of relocating metallic melts draining into the lower regions ofmore » a ``dry`` BWR core. CORA-33 was conducted on October 1, 1992, in the CORA tests facility at KfK. Review of the CORA-33 data indicates that the test objectives were achieved; that is, core degradation occurred at a core heatup rate and a test section axial temperature profile that are prototypic of full-core nuclear power plant (NPP) simulations at ``dry`` core conditions. Simulations of the CORA-33 test at ORNL have required modification of existing control blade/canister materials interaction models to include the eutectic melting of the stainless steel/Zircaloy interaction products and the heat of mixing of stainless steel and Zircaloy. The timing and location of canister failure and melt intrusion into the fuel assembly appear to be adequately simulated by the ORNL models. This paper will present the results of the posttest analyses carried out at ORNL based upon the experimental data and the posttest examination of the test bundle at KfK. The implications of these results with respect to degraded core modeling and the associated safety issues are also discussed.« less

A novel mutation in PRPF31, causative of autosomal dominant retinitis pigmentosa, using the BGISEQ-500 sequencer.

PubMed

Zheng, Yu; Wang, Hai-Lin; Li, Jian-Kang; Xu, Li; Tellier, Laurent; Li, Xiao-Lin; Huang, Xiao-Yan; Li, Wei; Niu, Tong-Tong; Yang, Huan-Ming; Zhang, Jian-Guo; Liu, Dong-Ning

2018-01-01

To study the genes responsible for retinitis pigmentosa. A total of 15 Chinese families with retinitis pigmentosa, containing 94 sporadically afflicted cases, were recruited. The targeted sequences were captured using the Target_Eye_365_V3 chip and sequenced using the BGISEQ-500 sequencer, according to the manufacturer's instructions. Data were aligned to UCSC Genome Browser build hg19, using the Burroughs Wheeler Aligner MEM algorithm. Local realignment was performed with the Genome Analysis Toolkit (GATK v.3.3.0) IndelRealigner, and variants were called with the Genome Analysis Toolkit Haplotypecaller, without any use of imputation. Variants were filtered against a panel derived from 1000 Genomes Project, 1000G_ASN, ESP6500, ExAC and dbSNP138. In all members of Family ONE and Family TWO with available DNA samples, the genetic variant was validated using Sanger sequencing. A novel, pathogenic variant of retinitis pigmentosa, c.357_358delAA (p.Ser119SerfsX5) was identified in PRPF31 in 2 of 15 autosomal-dominant retinitis pigmentosa (ADRP) families, as well as in one, sporadic case. Sanger sequencing was performed upon probands, as well as upon other family members. This novel, pathogenic genotype co-segregated with retinitis pigmentosa phenotype in these two families. ADRP is a subtype of retinitis pigmentosa, defined by its genotype, which accounts for 20%-40% of the retinitis pigmentosa patients. Our study thus expands the spectrum of PRPF31 mutations known to occur in ADRP, and provides further demonstration of the applicability of the BGISEQ500 sequencer for genomics research.

Spatial dynamics of the bacterial community structure in the gastrointestinal tract of red kangaroo (Macropus rufus).

PubMed

Li, Meirong; Jin, Wei; Li, Yuanfei; Zhao, Lingling; Cheng, Yanfen; Zhu, Weiyun

2016-06-01

The quantification and community of bacteria in the gastrointestinal (GI) tract (stomach, jejunum, ileum, cecum, colon and rectum) of red kangaroos (Macropus rufus) were examined by using real-time PCR and paired-end Illumina sequencing. The quantification of bacteria showed that the number of bacteria in jejunum and rectum was significantly lower than that in colon and cecum (P < 0.05). A total of 1,872,590 sequences was remained after quality-filtering and 50,948 OTUs were identified at the 97 % similarity level. The dominant phyla in the GI tract of red kangaroos were identified as Actinobacteria, Bacteroidetes and Firmicutes. At the level of genus, the samples from different parts of GI tract clustered into three groups: stomach, small intestine (jejunum and ileum) and large intestine (cecum and rectum). Prevotella (29.81 %) was the most dominant genus in the stomach and significantly (P < 0.05) higher than that in other parts of GI tract. In the small intestine, Bifidobacterium (33.04, 12.14 %) and Streptococcus (22.90, 19.16 %) were dominant genera. Unclassified Ruminococcaceae was the most dominant family in large intestine and the total relative abundance of unclassified bacteria was above 50 %. In identified genera, Dorea was the most important variable to discriminate large intestine and it was significantly higher in cecum than in stomach, small intestine and colon (P < 0.05). Bifidobacterium (21.89 %) was the only dominant genus in colon. Future work on culture in vitro and genome sequencing of those unidentified bacteria might give us insight into the function of these microorganisms in the GI tract. In addition, the comparison of the bacterial community in the foregut of kangaroos and other herbivores and the rumen might give us insight into the mechanism of fiber degradation and help us exploit approaches to improve the feed efficiency and subsequently, reduce the methane emission from herbivores.

Analysis of the distal gut bacterial community by 454-pyrosequencing in captive giraffes (Giraffa camelopardalis).

PubMed

AlZahal, Ousama; Valdes, Eduardo V; McBride, Brian W

2016-01-01

The objective of this study was to characterize the structure of the fecal bacterial community of five giraffes (Giraffa camelopardalis) at Disney's Animal Kingdom, FL. Fecal genomic DNA was extracted and variable regions 1-3 of the 16S rRNA gene was PCR-amplified and then sequenced. The MOTHUR software-program was used for sequence processing, diversity analysis, and classification. A total of 181,689 non-chimeric bacterial sequences were obtained, and average number of sequences per sample was 36,338 -± 8,818. Sequences were assigned to 8,284 operational taxonomic units (OTU) with 95% of genetic similarity, which included 2,942 singletons (36%). Number of OTUs per sample was 2,554 ± 264. Samples were normalized and alpha (intra-sample) diversity indices; Chao1, Inverse Simpson, Shannon, and coverage were estimated as 3,712 ± 430, 116 -± 70, 6.1 ± 0.4, and 96 ± 1%, respectively. Thirteen phyla were detected and Firmicutes, Bacteroidetes, and Spirochaetes were the most dominant phyla (more than 2% of total sequences), and constituted 92% of the classified sequences, 66% of total sequences, and 43% of total OTUs. Our computation predicted that three OTUs were likely to be present in at least three of the five samples at greater than 1% dominance rate. These OTUs were Treponema, an unidentified OTU belonging to the order Bacteroidales, and Ruminococcus. This report was the first to characterize the bacterial community of the distal gut in giraffes utilizing fecal samples, and it demonstrated that the distal gut of giraffes is likely a potential reservoir for a number of undocumented species of bacteria. © 2015 Wiley Periodicals, Inc.

Detection of novel mutations that cause autosomal dominant retinitis pigmentosa in candidate genes by long-range PCR amplification and next-generation sequencing

PubMed Central

Dias, Miguel de Sousa; Hernan, Imma; Pascual, Beatriz; Borràs, Emma; Mañé, Begoña; Gamundi, Maria José

2013-01-01

Purpose To devise an effective method for detecting mutations in 12 genes (CA4, CRX, IMPDH1, NR2E3, RP9, PRPF3, PRPF8, PRPF31, PRPH2, RHO, RP1, and TOPORS) commonly associated with autosomal dominant retinitis pigmentosa (adRP) that account for more than 95% of known mutations. Methods We used long-range PCR (LR-PCR) amplification and next-generation sequencing (NGS) performed in a GS Junior 454 benchtop sequencing platform. Twenty LR-PCR fragments, between 3,000 and 10,000 bp, containing all coding exons and flanking regions of the 12 genes, were obtained from DNA samples of patients with adRP. Sequencing libraries were prepared with an enzymatic (Fragmentase technology) method. Results Complete coverage of the coding and flanking sequences of the 12 genes assayed was obtained with NGS, with an average sequence depth of 380× (ranging from 128× to 1,077×). Five previous known mutations in the adRP genes were detected with a sequence variation percentage between 35% and 65%. We also performed a parallel sequence analysis of four samples, three of them new patients with index adRP, in which two novel mutations were detected in RHO (p.Asn73del) and PRPF31 (p.Ile109del). Conclusions The results demonstrate that genomic LR-PCR amplification together with NGS is an effective method for analyzing individual patient samples for mutations in a monogenic heterogeneous disease such as adRP. This approach proved effective for the parallel analysis of adRP and has been introduced as routine. Additionally, this approach could be extended to other heterogeneous genetic diseases. PMID:23559859

Mitochondrial recessive ataxia syndrome mimicking dominant spinocerebellar ataxia.

PubMed

Palin, Eino J H; Hakonen, Anna H; Korpela, Mari; Paetau, Anders; Suomalainen, Anu

2012-04-15

We studied the genetic background of a family with SCA, showing dominant inheritance and anticipation. Muscle histology, POLG1 gene sequence, neuropathology and mitochondrial DNA analyses in a mother and a son showed typical findings for a mitochondrial disorder, and both were shown to be homozygous for a recessive POLG1 mutation, underlying mitochondrial recessive ataxia syndrome, MIRAS. The healthy father was a heterozygous carrier for the same mutation. Recessively inherited MIRAS mutations should be tested in dominantly inherited SCAs cases of unknown cause, as the high carrier frequency of MIRAS may result in two independent introductions of the mutant allele in the family and thereby mimic dominant inheritance. Copyright © 2011 Elsevier B.V. All rights reserved.

Chance, necessity and the origins of life: a physical sciences perspective

NASA Astrophysics Data System (ADS)

Hazen, Robert M.

2017-11-01

Earth's 4.5-billion-year history has witnessed a complex sequence of high-probability chemical and physical processes, as well as `frozen accidents'. Most models of life's origins similarly invoke a sequence of chemical reactions and molecular self-assemblies in which both necessity and chance play important roles. Recent research adds two important insights into this discussion. First, in the context of chemical reactions, chance versus necessity is an inherently false dichotomy-a range of probabilities exists for many natural events. Second, given the combinatorial richness of early Earth's chemical and physical environments, events in molecular evolution that are unlikely at limited laboratory scales of space and time may, nevertheless, be inevitable on an Earth-like planet at time scales of a billion years. This article is part of the themed issue 'Reconceptualizing the origins of life'.

Investigation of mixed ionospheric and fround scatter using high spectral content pulse sequences for SuperDARN radars

NASA Astrophysics Data System (ADS)

Spaleta, J.; Bristow, W. A.

2013-12-01

SuperDARN radars estimate plasma drift velocities from the Doppler shift observed on signals scattered from field-aligned density irregularities. These field-aligned density irregularities are embedded in the ionospheric plasma, and move at the same velocity as background plasma. As a result, the electromagnetic signals scattered from these irregularities are Doppler shifted. The SuperDARN radars routinely observe ionospheric scatter Doppler velocities ranging from zero to thousands of meters per second. The radars determine the Doppler shift of the ionospheric scatter by linear fitting the phase of an auto correlation function derived from the radar pulse sequence. The phase fitting technique employed assumes a single dominant velocity is present in the signal. In addition, the SuperDARN radars can also observe signals scattered from the ground. Once refracted by the ionospheric plasma and bent earthward, the radar pulses eventually reach the ground where they scatter, sending signal back to the radar. This ground-scatter signal is characterized as having a low Doppler shift and low spectral width. The SuperDARN radars are able to use these signal characteristics to discriminate the ground scatter signal from the ionospheric scatter, when regions of ground scatter are isolated from ionospheric scatter returns. The phase fitting assumption of a single dominate target can easily be violated at ranges where ground and ionospheric scatter mix together. Due to the wide elevation angle extent of the SuperDARN radar design, ground and ionospheric scatter from different propagation paths can mix together in the return signal. When this happens, the fitting algorithm attempts to fit to the dominant signal, and if ground scatter dominates, information about the ionospheric scatter at that range can be unresolved. One way to address the mix scatter situation is to use a high spectral content pulse sequence together with a spectral estimation technique. The high spectral content pulse sequence consists of twice as many pulses and five times as many distinct lags over which to calculate the auto correlation function. This additional spectral information makes it possible to use spectral estimator techniques, that are robust against aperiodic time series data, to calculate the existence of multiple scatter modes in the signal. A comparison of the operation of the traditional SuperDARN pulse sequence and high spectral content pulse sequence will be presented for both synthetic examples and real SuperDARN radar mixed scatter situation.

CRAC2 model description

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

Ritchie, L.T.; Alpert, D.J.; Burke, R.P.

1984-03-01

The CRAC2 computer code is a revised version of CRAC (Calculation of Reactor Accident Consequences) which was developed for the Reactor Safety Study. This document provides an overview of the CRAC2 code and a description of each of the models used. Significant improvements incorporated into CRAC2 include an improved weather sequence sampling technique, a new evacuation model, and new output capabilities. In addition, refinements have been made to the atmospheric transport and deposition model. Details of the modeling differences between CRAC2 and CRAC are emphasized in the model descriptions.

Role of susceptibility-weighted imaging in demonstration of cerebral fat embolism

PubMed Central

Yeap, Pheyming; Kanodia, Avinash Kumar; Main, Gavin; Yong, Aiwain

2015-01-01

Cerebral fat embolism (CFE) is a rare but potentially lethal complication of long bone fractures. Many cases of CFE occur as subclinical events and remain undiagnosed. We report a case of a 22-year-old man, with multiple long bone fractures from a road traffic accident, who subsequently developed hypoxia, neurological abnormality and petechial rash. CT of the head was normal. MRI of the head confirmed the diagnosis with lesions markedly conspicuous and most widespread on susceptibility-weighted imaging as compared to all other sequences including diffusion-weighted imaging. PMID:25572601

Previously unclassified bacteria dominate during thermophilic and mesophilic anaerobic pre-treatment of primary sludge.

PubMed

Pervin, Hasina M; Batstone, Damien J; Bond, Philip L

2013-06-01

Thermophilic biological pre-treatment enables enhanced anaerobic digestion for treatment of wastewater sludges but, at present, there is limited understanding of the hydrolytic-acidogenic microbial composition and its contribution to this process. In this study, the process was assessed by comparing the microbiology of thermophilic (50-65 °C) and mesophilic (35 °C) pre-treatment reactors treating primary sludge. A full-cycle approach for the 16S rRNA genes was applied in order to monitor the diversity of bacteria and their abundance in a thermophilic pre-treatment reactor treating primary sludge. For the thermophilic pre-treatment (TP), over 90% of the sequences were previously undetected and these had less than 97% sequence similarity to cultured organisms. During the first 83 days, members of the Betaproteobacteria dominated the community sequences and a newly designed probe was used to monitor a previously unknown bacterium affiliated with the genus Brachymonas. Between days 85 and 183, three phylotypes that affiliated with the genera Comamonas, Clostridium and Lysobacter were persistently dominant in the TP community, as revealed by terminal-restriction fragment length polymorphism (T-RFLP). Hydrolytic and fermentative functions have been speculated for these bacteria. Mesophilic pre-treatment (MP) and TP communities were different but they were both relatively dynamic. Statistical correlation analysis and the function of closely allied reference organisms indicated that previously unclassified bacteria dominated the TP community and may have been functionally involved in the enhanced hydrolytic performance of thermophilic anaerobic pre-treatment. This study is the first to reveal the diversity and dynamics of bacteria during anaerobic digestion of primary sludge. Copyright © 2013 Elsevier GmbH. All rights reserved.

The Fragility of Individual-Based Explanations of Social Hierarchies: A Test Using Animal Pecking Orders

PubMed Central

2016-01-01

The standard approach in accounting for hierarchical differentiation in biology and the social sciences considers a hierarchy as a static distribution of individuals possessing differing amounts of some valued commodity, assumes that the hierarchy is generated by micro-level processes involving individuals, and attempts to reverse engineer the processes that produced the hierarchy. However, sufficient experimental and analytical results are available to evaluate this standard approach in the case of animal dominance hierarchies (pecking orders). Our evaluation using evidence from hierarchy formation in small groups of both hens and cichlid fish reveals significant deficiencies in the three tenets of the standard approach in accounting for the organization of dominance hierarchies. In consequence, we suggest that a new approach is needed to explain the organization of pecking orders and, very possibly, by implication, for other kinds of social hierarchies. We develop an example of such an approach that considers dominance hierarchies to be dynamic networks, uses dynamic sequences of interaction (dynamic network motifs) to explain the organization of dominance hierarchies, and derives these dynamic sequences directly from observation of hierarchy formation. We test this dynamical explanation using computer simulation and find a good fit with actual dynamics of hierarchy formation in small groups of hens. We hypothesize that the same dynamic sequences are used in small groups of many other animal species forming pecking orders, and we discuss the data required to evaluate our hypothesis. Finally, we briefly consider how our dynamic approach may be generalized to other kinds of social hierarchies using the example of the distribution of empty gastropod (snail) shells occupied in populations of hermit crabs. PMID:27410230

[Kidney injuries. Apropos of 30 cases].

PubMed

Benchekroun, A; Lachkar, A; Soumana, A; Farih, M H; Belahnech, Z; Marzouk, M; Faik, M

1997-01-01

Renal trauma remains a topical subject due to its high incidence and the fact that it still raises therapeutic problems. The features of this disease were reviewed by means of a retrospective study of 30 cases of renal trauma observed over a 10-year period. The patients consisted of 27 males (90%) and 3 females (10%), with a mean age of 27 years (range: 20 to 60 years). The aetiology was largely dominated by road accidents (53%), falls (26%) and assaults (16%). Trauma was unilateral, predominantly affecting the left side (60%). The clinical features were dominated by haematuria (93%) and low back pain (90%). Trauma was associated with skeletal or visceral lesions in 46.6% of patients. Assessment of the lesions was based on IVU, ultrasonography and CT. Eight patients (26.6%) presented with moderate or minimal trauma (Chatelain stage 1 and 2) and were treated medically. Twenty-two patients (73%) were operated: 6 of them underwent total nephrectomy and 16 were treated conservatively. Seven of the operated patients subsequently developed complications.

Dynamic Energy Landscapes of Riboswitches Help Interpret Conformational Rearrangements and Function

PubMed Central

Quarta, Giulio; Sin, Ken; Schlick, Tamar

2012-01-01

Riboswitches are RNAs that modulate gene expression by ligand-induced conformational changes. However, the way in which sequence dictates alternative folding pathways of gene regulation remains unclear. In this study, we compute energy landscapes, which describe the accessible secondary structures for a range of sequence lengths, to analyze the transcriptional process as a given sequence elongates to full length. In line with experimental evidence, we find that most riboswitch landscapes can be characterized by three broad classes as a function of sequence length in terms of the distribution and barrier type of the conformational clusters: low-barrier landscape with an ensemble of different conformations in equilibrium before encountering a substrate; barrier-free landscape in which a direct, dominant “downhill” pathway to the minimum free energy structure is apparent; and a barrier-dominated landscape with two isolated conformational states, each associated with a different biological function. Sharing concepts with the “new view” of protein folding energy landscapes, we term the three sequence ranges above as the sensing, downhill folding, and functional windows, respectively. We find that these energy landscape patterns are conserved in various riboswitch classes, though the order of the windows may vary. In fact, the order of the three windows suggests either kinetic or thermodynamic control of ligand binding. These findings help understand riboswitch structure/function relationships and open new avenues to riboswitch design. PMID:22359488

Abundant Trimethylornithine Lipids and Specific Gene Sequences Are Indicative of Planctomycete Importance at the Oxic/Anoxic Interface in Sphagnum-Dominated Northern Wetlands.

PubMed

Moore, Eli K; Villanueva, Laura; Hopmans, Ellen C; Rijpstra, W Irene C; Mets, Anchelique; Dedysh, Svetlana N; Sinninghe Damsté, Jaap S

2015-09-01

Northern wetlands make up a substantial terrestrial carbon sink and are often dominated by decay-resistant Sphagnum mosses. Recent studies have shown that planctomycetes appear to be involved in degradation of Sphagnum-derived debris. Novel trimethylornithine (TMO) lipids have recently been characterized as abundant lipids in various Sphagnum wetland planctomycete isolates, but their occurrence in the environment has not yet been confirmed. We applied a combined intact polar lipid (IPL) and molecular analysis of peat cores collected from two northern wetlands (Saxnäs Mosse [Sweden] and Obukhovskoye [Russia]) in order to investigate the preferred niche and abundance of TMO-producing planctomycetes. TMOs were present throughout the profiles of Sphagnum bogs, but their concentration peaked at the oxic/anoxic interface, which coincided with a maximum abundance of planctomycete-specific 16S rRNA gene sequences. The sequences detected at the oxic/anoxic interface were affiliated with the Isosphaera group, while sequences present in the anoxic peat layers were related to an uncultured planctomycete group. Pyrosequencing-based analysis identified Planctomycetes as the major bacterial group at the oxic/anoxic interface at the Obukhovskoye peat (54% of total 16S rRNA gene sequence reads), followed by Acidobacteria (19% reads), while in the Saxnäs Mosse peat, Acidobacteria were dominant (46%), and Planctomycetes contributed to 6% of the total reads. The detection of abundant TMO lipids in planctomycetes isolated from peat bogs and the lack of TMO production by cultures of acidobacteria suggest that planctomycetes are the producers of TMOs in peat bogs. The higher accumulation of TMOs at the oxic/anoxic interface and the change in the planctomycete community with depth suggest that these IPLs could be synthesized as a response to changing redox conditions at the oxic/anoxic interface. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Abundant Trimethylornithine Lipids and Specific Gene Sequences Are Indicative of Planctomycete Importance at the Oxic/Anoxic Interface in Sphagnum-Dominated Northern Wetlands

PubMed Central

Villanueva, Laura; Hopmans, Ellen C.; Rijpstra, W. Irene C.; Mets, Anchelique; Dedysh, Svetlana N.

2015-01-01

Northern wetlands make up a substantial terrestrial carbon sink and are often dominated by decay-resistant Sphagnum mosses. Recent studies have shown that planctomycetes appear to be involved in degradation of Sphagnum-derived debris. Novel trimethylornithine (TMO) lipids have recently been characterized as abundant lipids in various Sphagnum wetland planctomycete isolates, but their occurrence in the environment has not yet been confirmed. We applied a combined intact polar lipid (IPL) and molecular analysis of peat cores collected from two northern wetlands (Saxnäs Mosse [Sweden] and Obukhovskoye [Russia]) in order to investigate the preferred niche and abundance of TMO-producing planctomycetes. TMOs were present throughout the profiles of Sphagnum bogs, but their concentration peaked at the oxic/anoxic interface, which coincided with a maximum abundance of planctomycete-specific 16S rRNA gene sequences. The sequences detected at the oxic/anoxic interface were affiliated with the Isosphaera group, while sequences present in the anoxic peat layers were related to an uncultured planctomycete group. Pyrosequencing-based analysis identified Planctomycetes as the major bacterial group at the oxic/anoxic interface at the Obukhovskoye peat (54% of total 16S rRNA gene sequence reads), followed by Acidobacteria (19% reads), while in the Saxnäs Mosse peat, Acidobacteria were dominant (46%), and Planctomycetes contributed to 6% of the total reads. The detection of abundant TMO lipids in planctomycetes isolated from peat bogs and the lack of TMO production by cultures of acidobacteria suggest that planctomycetes are the producers of TMOs in peat bogs. The higher accumulation of TMOs at the oxic/anoxic interface and the change in the planctomycete community with depth suggest that these IPLs could be synthesized as a response to changing redox conditions at the oxic/anoxic interface. PMID:26150465

Comparative and Joint Analysis of Two Metagenomic Datasets from a Biogas Fermenter Obtained by 454-Pyrosequencing

PubMed Central

Jaenicke, Sebastian; Ander, Christina; Bekel, Thomas; Bisdorf, Regina; Dröge, Marcus; Gartemann, Karl-Heinz; Jünemann, Sebastian; Kaiser, Olaf; Krause, Lutz; Tille, Felix; Zakrzewski, Martha; Pühler, Alfred

2011-01-01

Biogas production from renewable resources is attracting increased attention as an alternative energy source due to the limited availability of traditional fossil fuels. Many countries are promoting the use of alternative energy sources for sustainable energy production. In this study, a metagenome from a production-scale biogas fermenter was analysed employing Roche's GS FLX Titanium technology and compared to a previous dataset obtained from the same community DNA sample that was sequenced on the GS FLX platform. Taxonomic profiling based on 16S rRNA-specific sequences and an Environmental Gene Tag (EGT) analysis employing CARMA demonstrated that both approaches benefit from the longer read lengths obtained on the Titanium platform. Results confirmed Clostridia as the most prevalent taxonomic class, whereas species of the order Methanomicrobiales are dominant among methanogenic Archaea. However, the analyses also identified additional taxa that were missed by the previous study, including members of the genera Streptococcus, Acetivibrio, Garciella, Tissierella, and Gelria, which might also play a role in the fermentation process leading to the formation of methane. Taking advantage of the CARMA feature to correlate taxonomic information of sequences with their assigned functions, it appeared that Firmicutes, followed by Bacteroidetes and Proteobacteria, dominate within the functional context of polysaccharide degradation whereas Methanomicrobiales represent the most abundant taxonomic group responsible for methane production. Clostridia is the most important class involved in the reductive CoA pathway (Wood-Ljungdahl pathway) that is characteristic for acetogenesis. Based on binning of 16S rRNA-specific sequences allocated to the dominant genus Methanoculleus, it could be shown that this genus is represented by several different species. Phylogenetic analysis of these sequences placed them in close proximity to the hydrogenotrophic methanogen Methanoculleus bourgensis. While rarefaction analyses still indicate incomplete coverage, examination of the GS FLX Titanium dataset resulted in the identification of additional genera and functional elements, providing a far more complete coverage of the community involved in anaerobic fermentative pathways leading to methane formation. PMID:21297863

Naturally occurring dominant drug resistance mutations occur infrequently in the setting of recently acquired hepatitis C.

PubMed

Applegate, Tanya L; Gaudieri, Silvana; Plauzolles, Anne; Chopra, Abha; Grebely, Jason; Lucas, Michaela; Hellard, Margaret; Luciani, Fabio; Dore, Gregory J; Matthews, Gail V

2015-01-01

Direct-acting antivirals (DAAs) are predicted to transform hepatitis C therapy, yet little is known about the prevalence of naturally occurring resistance mutations in recently acquired HCV. This study aimed to determine the prevalence and frequency of drug resistance mutations in the viral quasispecies among HIV-positive and -negative individuals with recent HCV. The NS3 protease, NS5A and NS5B polymerase genes were amplified from 50 genotype 1a participants of the Australian Trial in Acute Hepatitis C. Amino acid variations at sites known to be associated with possible drug resistance were analysed by ultra-deep pyrosequencing. A total of 12% of individuals harboured dominant resistance mutations, while 36% demonstrated non-dominant resistant variants below that detectable by bulk sequencing (that is, <20%) but above a threshold of 1%. Resistance variants (<1%) were observed at most sites associated with DAA resistance from all classes, with the exception of sofosbuvir. Dominant resistant mutations were uncommonly observed in the setting of recent HCV. However, low-level mutations to all DAA classes were observed by deep sequencing at the majority of sites and in most individuals. The significance of these variants and impact on future treatment options remains to be determined. Clinicaltrials.gov NCT00192569.

Problems of standardizing and technical regulation in the electric power industry

NASA Astrophysics Data System (ADS)

Grabchak, E. P.

2016-12-01

A mandatory condition to ensure normal operation of a power system and efficiency in the sector is standardization and legal regulation of technological activities of electric power engineering entities and consumers. Compared to the times of USSR, the present-time technical guidance documents are not mandatory to follow in most cases, being of an advisory nature due to the lack of new ones. During the last five years, the industry has been showing a deterioration of the situation in terms of ensuring reliability and engineering controllability as a result of the dominant impact of short-term market stimuli and the differences in basic technological policies. In absence of clear requirements regarding the engineering aspects of such activities, production operation does not contribute to the preserving of technical integrity of the Russian power system, which leads to the loss of performance capability and controllability and causes disturbances in the power supply to consumers. The result of this problem is a high rate of accident incidence. The dynamics of accidents by the type of equipment is given, indicating a persisting trend of growth in the number of accidents, which are of a systematic nature. Several problematic aspects of engineering activities of electric power engineering entities, requiring standardization and legal regulation are pointed out: in the domestic power system, a large number of power electrotechnical and generating equipment operate along with systems of regulation, which do not comply with the principles and technical rules representing a framework where the Energy System of Russia is built and functioning

Analysis of microbial community variation during the mixed culture fermentation of agricultural peel wastes to produce lactic acid.

PubMed

Liang, Shaobo; Gliniewicz, Karol; Gerritsen, Alida T; McDonald, Armando G

2016-05-01

Mixed cultures fermentation can be used to convert organic wastes into various chemicals and fuels. This study examined the fermentation performance of four batch reactors fed with different agricultural (orange, banana, and potato (mechanical and steam)) peel wastes using mixed cultures, and monitored the interval variation of reactor microbial communities with 16S rRNA genes using Illumina sequencing. All four reactors produced similar chemical profile with lactic acid (LA) as dominant compound. Acetic acid and ethanol were also observed with small fractions. The Illumina sequencing results revealed the diversity of microbial community decreased during fermentation and a community of largely lactic acid producing bacteria dominated by species of Lactobacillus developed. Copyright © 2016 Elsevier Ltd. All rights reserved.

Toward a Mechanistic Source Term in Advanced Reactors: Characterization of Radionuclide Transport and Retention in a Sodium Cooled Fast Reactor

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

Brunett, Acacia J.; Bucknor, Matthew; Grabaskas, David

A vital component of the U.S. reactor licensing process is an integrated safety analysis in which a source term representing the release of radionuclides during normal operation and accident sequences is analyzed. Historically, source term analyses have utilized bounding, deterministic assumptions regarding radionuclide release. However, advancements in technical capabilities and the knowledge state have enabled the development of more realistic and best-estimate retention and release models such that a mechanistic source term assessment can be expected to be a required component of future licensing of advanced reactors. Recently, as part of a Regulatory Technology Development Plan effort for sodium cooledmore » fast reactors (SFRs), Argonne National Laboratory has investigated the current state of knowledge of potential source terms in an SFR via an extensive review of previous domestic experiments, accidents, and operation. As part of this work, the significant sources and transport processes of radionuclides in an SFR have been identified and characterized. This effort examines all stages of release and source term evolution, beginning with release from the fuel pin and ending with retention in containment. Radionuclide sources considered in this effort include releases originating both in-vessel (e.g. in-core fuel, primary sodium, cover gas cleanup system, etc.) and ex-vessel (e.g. spent fuel storage, handling, and movement). Releases resulting from a primary sodium fire are also considered as a potential source. For each release group, dominant transport phenomena are identified and qualitatively discussed. The key product of this effort was the development of concise, inclusive diagrams that illustrate the release and retention mechanisms at a high level, where unique schematics have been developed for in-vessel, ex-vessel and sodium fire releases. This review effort has also found that despite the substantial range of phenomena affecting radionuclide release, the current state of knowledge is extensive, and in most areas may be sufficient. Several knowledge gaps were identified, such as uncertainty in release from molten fuel and availability of thermodynamic data for lanthanides and actinides in liquid sodium. However, the overall findings suggest that high retention rates can be expected within the fuel and primary sodium for all radionuclides other than noble gases.« less

Dose and Dose Risk Caused by Natural Phenomena - Proposed Powder Metallurgy Core Manufacturing Facility

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

Holmes, W.G.

2001-08-16

The offsite radiological effects from high velocity straight winds, tornadoes, and earthquakes have been estimated for a proposed facility for manufacturing enriched uranium fuel cores by powder metallurgy. Projected doses range up to 30 mrem/event to the maximum offsite individual for high winds and up to 85 mrem/event for very severe earthquakes. Even under conservative assumptions on meteorological conditions, the maximum offsite dose would be about 20 per cent of the DOE limit for accidents involving enriched uranium storage facilities. The total dose risk is low and is dominated by the risk from earthquakes. This report discusses this test.

Autosomal dominant hypoparathyroidism caused by germline mutation in GNA11: phenotypic and molecular characterization.

PubMed

Li, Dong; Opas, Evan E; Tuluc, Florin; Metzger, Daniel L; Hou, Cuiping; Hakonarson, Hakon; Levine, Michael A

2014-09-01

Most cases of autosomal dominant hypoparathyroidism (ADH) are caused by gain-of-function mutations in CASR or dominant inhibitor mutations in GCM2 or PTH. Our objectives were to identify the genetic basis for ADH in a multigenerational family and define the underlying disease mechanism. Here we evaluated a multigenerational family with ADH in which affected subjects had normal sequences in these genes and were shorter than unaffected family members. We collected clinical and biochemical data from 6 of 11 affected subjects and performed whole-exome sequence analysis on DNA from two affected sisters and their affected father. Functional studies were performed after expression of wild-type and mutant Gα11 proteins in human embryonic kidney-293-CaR cells that stably express calcium-sensing receptors. Whole-exome-sequencing followed by Sanger sequencing revealed a heterozygous mutation, c.179G>T; p.R60L, in GNA11, which encodes the α-subunit of G11, the principal heterotrimeric G protein that couples calcium-sensing receptors to signal activation in parathyroid cells. Functional studies of Gα11 R60L showed increased accumulation of intracellular concentration of free calcium in response to extracellular concentration of free calcium with a significantly decreased EC50 compared with wild-type Gα11. By contrast, R60L was significantly less effective than the oncogenic Q209L form of Gα11 as an activator of the MAPK pathway. Compared to subjects with CASR mutations, patients with GNA11 mutations lacked hypercalciuria and had normal serum magnesium levels. Our findings indicate that the germline gain-of-function mutation of GNA11 is a cause of ADH and implicate a novel role for GNA11 in skeletal growth.

High-throughput sequencing reveals the core gut microbiome of Bar-headed goose (Anser indicus) in different wintering areas in Tibet.

PubMed

Wang, Wen; Cao, Jian; Yang, Fang; Wang, Xuelian; Zheng, Sisi; Sharshov, Kirill; Li, Laixing

2016-04-01

Elucidating the spatial dynamic and core gut microbiome related to wild bar-headed goose is of crucial importance for probiotics development that may meet the demands of bar-headed goose artificial breeding industries and accelerate the domestication of this species. However, the core microbial communities in the wild bar-headed geese remain totally unknown. Here, for the first time, we present a comprehensive survey of bar-headed geese gut microbial communities by Illumina high-throughput sequencing technology using nine individuals from three distinct wintering locations in Tibet. A total of 236,676 sequences were analyzed, and 607 OTUs were identified. We show that the gut microbial communities of bar-headed geese have representatives of 14 phyla and are dominated by Firmicutes, Proteobacteria, Actinobacteria, and Bacteroidetes. The additive abundance of these four most dominant phyla was above 96% across all the samples. At the genus level, the sequences represented 150 genera. A set of 19 genera were present in all samples and considered as core gut microbiome. The top seven most abundant core genera were distributed in that four dominant phyla. Among them, four genera (Lactococcus, Bacillus, Solibacillus, and Streptococcus) belonged to Firmicutes, while for other three phyla, each containing one genus, such as Proteobacteria (genus Pseudomonas), Actinobacteria (genus Arthrobacter), and Bacteroidetes (genus Bacteroides). This broad survey represents the most in-depth assessment, to date, of the gut microbes that associated with bar-headed geese. These data create a baseline for future bar-headed goose microbiology research, and make an original contribution to probiotics development for bar-headed goose artificial breeding industries. © 2015 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

Autosomal Dominant Hypoparathyroidism Caused by Germline Mutation in GNA11: Phenotypic and Molecular Characterization

PubMed Central

Li, Dong; Opas, Evan E.; Tuluc, Florin; Metzger, Daniel L.; Hou, Cuiping; Hakonarson, Hakon

2014-01-01

Context: Most cases of autosomal dominant hypoparathyroidism (ADH) are caused by gain-of-function mutations in CASR or dominant inhibitor mutations in GCM2 or PTH. Objective: Our objectives were to identify the genetic basis for ADH in a multigenerational family and define the underlying disease mechanism. Subjects: Here we evaluated a multigenerational family with ADH in which affected subjects had normal sequences in these genes and were shorter than unaffected family members. Methods: We collected clinical and biochemical data from 6 of 11 affected subjects and performed whole-exome sequence analysis on DNA from two affected sisters and their affected father. Functional studies were performed after expression of wild-type and mutant Gα11 proteins in human embryonic kidney-293-CaR cells that stably express calcium-sensing receptors. Results: Whole-exome-sequencing followed by Sanger sequencing revealed a heterozygous mutation, c.179G>T; p.R60L, in GNA11, which encodes the α-subunit of G11, the principal heterotrimeric G protein that couples calcium-sensing receptors to signal activation in parathyroid cells. Functional studies of Gα11 R60L showed increased accumulation of intracellular concentration of free calcium in response to extracellular concentration of free calcium with a significantly decreased EC50 compared with wild-type Gα11. By contrast, R60L was significantly less effective than the oncogenic Q209L form of Gα11 as an activator of the MAPK pathway. Compared to subjects with CASR mutations, patients with GNA11 mutations lacked hypercalciuria and had normal serum magnesium levels. Conclusions: Our findings indicate that the germline gain-of-function mutation of GNA11 is a cause of ADH and implicate a novel role for GNA11 in skeletal growth. PMID:24823460

The Intestinal Eukaryotic and Bacterial Biome of Spotted Hyenas: The Impact of Social Status and Age on Diversity and Composition.

PubMed

Heitlinger, Emanuel; Ferreira, Susana C M; Thierer, Dagmar; Hofer, Heribert; East, Marion L

2017-01-01

In mammals, two factors likely to affect the diversity and composition of intestinal bacteria (bacterial microbiome) and eukaryotes (eukaryome) are social status and age. In species in which social status determines access to resources, socially dominant animals maintain better immune processes and health status than subordinates. As high species diversity is an index of ecosystem health, the intestinal biome of healthier, socially dominant animals should be more diverse than those of subordinates. Gradual colonization of the juvenile intestine after birth predicts lower intestinal biome diversity in juveniles than adults. We tested these predictions on the effect of: (1) age (juvenile/adult) and (2) social status (low/high) on bacterial microbiome and eukaryome diversity and composition in the spotted hyena ( Crocuta crocuta ), a highly social, female-dominated carnivore in which social status determines access to resources. We comprehensively screened feces from 35 individually known adult females and 7 juveniles in the Serengeti ecosystem for bacteria and eukaryotes, using a set of 48 different amplicons (4 for bacterial 16S, 44 for eukaryote 18S) in a multi-amplicon sequencing approach. We compared sequence abundances to classical coprological egg or oocyst counts. For all parasite taxa detected in more than six samples, the number of sequence reads significantly predicted the number of eggs or oocysts counted, underscoring the value of an amplicon sequencing approach for quantitative measurements of parasite load. In line with our predictions, our results revealed a significantly less diverse microbiome in juveniles than adults and a significantly higher diversity of eukaryotes in high-ranking than low-ranking animals. We propose that free-ranging wildlife can provide an intriguing model system to assess the adaptive value of intestinal biome diversity for both bacteria and eukaryotes.

The Intestinal Eukaryotic and Bacterial Biome of Spotted Hyenas: The Impact of Social Status and Age on Diversity and Composition

PubMed Central

Heitlinger, Emanuel; Ferreira, Susana C. M.; Thierer, Dagmar; Hofer, Heribert; East, Marion L.

2017-01-01

In mammals, two factors likely to affect the diversity and composition of intestinal bacteria (bacterial microbiome) and eukaryotes (eukaryome) are social status and age. In species in which social status determines access to resources, socially dominant animals maintain better immune processes and health status than subordinates. As high species diversity is an index of ecosystem health, the intestinal biome of healthier, socially dominant animals should be more diverse than those of subordinates. Gradual colonization of the juvenile intestine after birth predicts lower intestinal biome diversity in juveniles than adults. We tested these predictions on the effect of: (1) age (juvenile/adult) and (2) social status (low/high) on bacterial microbiome and eukaryome diversity and composition in the spotted hyena (Crocuta crocuta), a highly social, female-dominated carnivore in which social status determines access to resources. We comprehensively screened feces from 35 individually known adult females and 7 juveniles in the Serengeti ecosystem for bacteria and eukaryotes, using a set of 48 different amplicons (4 for bacterial 16S, 44 for eukaryote 18S) in a multi-amplicon sequencing approach. We compared sequence abundances to classical coprological egg or oocyst counts. For all parasite taxa detected in more than six samples, the number of sequence reads significantly predicted the number of eggs or oocysts counted, underscoring the value of an amplicon sequencing approach for quantitative measurements of parasite load. In line with our predictions, our results revealed a significantly less diverse microbiome in juveniles than adults and a significantly higher diversity of eukaryotes in high-ranking than low-ranking animals. We propose that free-ranging wildlife can provide an intriguing model system to assess the adaptive value of intestinal biome diversity for both bacteria and eukaryotes. PMID:28670573

Biphasic Study to Characterize Agricultural Biogas Plants by High-Throughput 16S rRNA Gene Amplicon Sequencing and Microscopic Analysis.

PubMed

Maus, Irena; Kim, Yong Sung; Wibberg, Daniel; Stolze, Yvonne; Off, Sandra; Antonczyk, Sebastian; Pühler, Alfred; Scherer, Paul; Schlüter, Andreas

2017-02-28

Process surveillance within agricultural biogas plants (BGPs) was concurrently studied by high-throughput 16S rRNA gene amplicon sequencing and an optimized quantitative microscopic fingerprinting (QMF) technique. In contrast to 16S rRNA gene amplicons, digitalized microscopy is a rapid and cost-effective method that facilitates enumeration and morphological differentiation of the most significant groups of methanogens regarding their shape and characteristic autofluorescent factor 420. Moreover, the fluorescence signal mirrors cell vitality. In this study, four different BGPs were investigated. The results indicated stable process performance in the mesophilic BGPs and in the thermophilic reactor. Bacterial subcommunity characterization revealed significant differences between the four BGPs. Most remarkably, the genera Defluviitoga and Halocella dominated the thermophilic bacterial subcommunity, whereas members of another taxon, Syntrophaceticus , were found to be abundant in the mesophilic BGP. The domain Archaea was dominated by the genus Methanoculleus in all four BGPs, followed by Methanosaeta in BGP1 and BGP3. In contrast, Methanothermobacter members were highly abundant in the thermophilic BGP4. Furthermore, a high consistency between the sequencing approach and the QMF method was shown, especially for the thermophilic BGP. The differences elucidated that using this biphasic approach for mesophilic BGPs provided novel insights regarding disaggregated single cells of Methanosarcina and Methanosaeta species. Both dominated the archaeal subcommunity and replaced coccoid Methanoculleus members belonging to the same group of Methanomicrobiales that have been frequently observed in similar BGPs. This work demonstrates that combining QMF and 16S rRNA gene amplicon sequencing is a complementary strategy to describe archaeal community structures within biogas processes.

Recombination and Population Mosaic of a Multifunctional Viral Gene, Adeno-Associated Virus cap

PubMed Central

Takeuchi, Yasuhiro; Myers, Richard; Danos, Olivier

2008-01-01

Homologous recombination is a dominant force in evolution and results in genetic mosaics. To detect evidence of recombination events and assess the biological significance of genetic mosaics, genome sequences for various viral populations of reasonably large size are now available in the GenBank. We studied a multi-functional viral gene, the adeno-associated virus (AAV) cap gene, which codes for three capsid proteins, VP1, VP2 and VP3. VP1-3 share a common C-terminal domain corresponding to VP3, which forms the viral core structure, while the VP1 unique N-terminal part contains an enzymatic domain with phospholipase A2 activity. Our recombinant detection program (RecI) revealed five novel recombination events, four of which have their cross-over points in the N-terminal, VP1 and VP2 unique region. Comparison of phylogenetic trees for different cap gene regions confirmed discordant phylogenies for the recombinant sequences. Furthermore, differences in the phylogenetic tree structures for the VP1 unique (VP1u) region and the rest of cap highlighted the mosaic nature of cap gene in the AAV population: two dominant forms of VP1u sequences were identified and these forms are linked to diverse sequences in the rest of cap gene. This observation together with the finding of frequent recombination in the VP1 and 2 unique regions suggests that this region is a recombination hot spot. Recombination events in this region preserve protein blocks of distinctive functions and contribute to convergence in VP1u and divergence of the rest of cap. Additionally the possible biological significance of two dominant VP1u forms is inferred. PMID:18286191

Investigation of bacterial diversity in the feces of cattle fed different diets.

PubMed

Kim, M; Kim, J; Kuehn, L A; Bono, J L; Berry, E D; Kalchayanand, N; Freetly, H C; Benson, A K; Wells, J E

2014-02-01

The objective of this study is to investigate individual animal variation of bovine fecal microbiota including as affected by diets. Fecal samples were collected from 426 cattle fed 1 of 3 diets typically fed to feedlot cattle: 1) 143 steers fed finishing diet (83% dry-rolled corn, 13% corn silage, and 4% supplement), 2) 147 steers fed late growing diet (66% dry-rolled corn, 26% corn silage, and 8% supplement), and 3) 136 heifers fed early growing diet (70% corn silage and 30% alfalfa haylage). Bacterial 16S rRNA gene amplicons were determined from individual fecal samples using next-generation pyrosequencing technology. A total of 2,149,008 16S rRNA gene sequences from 333 cattle with at least 2,000 sequences were analyzed. Firmicutes and Bacteroidetes were dominant phyla in all fecal samples. At the genus level, Oscillibacter, Turicibacter, Roseburia, Fecalibacterium, Coprococcus, Clostridium, Prevotella, and Succinivibrio were represented by more than 1% of total sequences. However, numerous sequences could not be assigned to a known genus. Dominant unclassified groups were unclassified Ruminococcaceae and unclassified Lachnospiraceae that could be classified to a family but not to a genus. These dominant genera and unclassified groups differed (P < 0.001) with diets. A total of 176,692 operational taxonomic units (OTU) were identified in combination across all the 333 cattle. Only 2,359 OTU were shared across 3 diet groups. UniFrac analysis showed that bacterial communities in cattle feces were greatly affected by dietary differences. This study indicates that the community structure of fecal microbiota in cattle is greatly affected by diet, particularly between forage- and concentrate-based diets.

Recombinant Mip-PilE-FlaA dominant epitopes vaccine candidate against Legionella pneumophila.

PubMed

He, Jinlei; Huang, Fan; Chen, Han; Chen, Qiwei; Zhang, Junrong; Li, Jiao; Chen, Dali; Chen, Jianping

2017-06-01

Legionella pneumophila is the main causative agent of Legionnaires' disease, which is a severe multi-system disease with pneumonia as the primary manifestation. We designed a recombinant Mip-PilE-FlaA dominant epitopes vaccine against Legionella pneumophila to prevent the disease and evaluated its immunogenicity and protective immunity. The protein structures of Mip, PilE and FlaA were analyzed using a computer, and the gene sequences of the dominant epitopes of the three proteins were selected to construct and optimize the vaccine. The optimized mip, pilE, flaA and recombinant mip-pilE-flaA gene sequences were cloned, expressed and purified. The purified proteins were used as dominant epitopes vaccines to immunize BALB/c mice and determine the protective immunity and immunogenicity of these purified proteins. The identification confirmed that the recombinant mip-pilE-flaA was successfully cloned and expressed. ELISA revealed that the Mip-PilE-FlaA group produced the highest IgG response, and this protein may considerably improve the production of some cytokines in BALB/c mice. Histopathology analyses of lungs from mice immunized with Mip-PilE-FlaA revealed a certain protective effect. Our work demonstrated that the recombinant dominant epitopes of Mip-PilE-FlaA exhibited strong immunogenicity and immune protection, and this protein may be an efficient epitopes vaccine candidate against Legionella pneumophila. Copyright © 2017 European Federation of Immunological Societies. Published by Elsevier B.V. All rights reserved.

Ammonia-oxidizing bacteria dominate ammonia oxidation in a full-scale wastewater treatment plant revealed by DNA-based stable isotope probing.

PubMed

Pan, Kai-Ling; Gao, Jing-Feng; Li, Hong-Yu; Fan, Xiao-Yan; Li, Ding-Chang; Jiang, Hao

2018-05-01

A full-scale wastewater treatment plant (WWTP) with three separate treatment processes was selected to investigate the effects of seasonality and treatment process on the community structures of ammonia-oxidizing archaea (AOA) and bacteria (AOB). And then DNA-based stable isotope probing (DNA-SIP) was applied to explore the active ammonia oxidizers. The results of high-throughput sequencing indicated that treatment processes varied AOB communities rather than AOA communities. AOA slightly outnumbered AOB in most of the samples, whose abundance was significantly correlated with temperature. DNA-SIP results showed that the majority of AOB amoA gene was labeled by 13 C-substrate, while just a small amount of AOA amoA gene was labeled. As revealed by high-throughput sequencing of heavy DNA, Nitrosomonadaceae-like AOB, Nitrosomonas sp. NP1, Nitrosomonas oligotropha and Nitrosomonas marina were the active AOB, and Nitrososphaera viennensis dominated the active AOA. The results indicated that AOB, not AOA, dominated active ammonia oxidation in the test WWTP. Copyright © 2018 Elsevier Ltd. All rights reserved.

Small eukaryotic phytoplankton communities in tropical waters off Brazil are dominated by symbioses between Haptophyta and nitrogen-fixing cyanobacteria.

PubMed

Gérikas Ribeiro, Catherine; Lopes Dos Santos, Adriana; Marie, Dominique; Pereira Brandini, Frederico; Vaulot, Daniel

2018-05-01

Symbioses between eukaryotic algae and nitrogen-fixing cyanobacteria have been recognized in recent years as a key source of new nitrogen in the oceans. We investigated the composition of the small photosynthetic eukaryote communities associated with nitrogen-fixing cyanobacteria in the Brazilian South Atlantic Bight using a combination of flow cytometry sorting and high throughput sequencing of two genes: the V4 region of 18S rRNA and nifH. Two distinct eukaryotic communities were often encountered, one dominated by the Mamiellophyceae Bathycoccus and Ostreococcus, and one dominated by a prymnesiophyte known to live in symbiosis with the UCYN-A1 nitrogen-fixing cyanobacterium. Among nifH sequences, those from UCYN-A1 were most abundant but three other UCYN-A clades (A2, A3, A4) were also found. Network analysis confirmed the relation between A1 and A2 clades and their hypothesized hosts and pointed out to the potential association between novel clade A4 with Braarudosphaera bigelowii, previously hypothesized to host A2.

Analysis of the community compositions of rhizosphere fungi in soybeans continuous cropping fields.

PubMed

Bai, Li; Cui, Jiaqi; Jie, Weiguang; Cai, Baiyan

2015-11-01

We used rhizosphere soil sampled from one field during zero year and two years of continuous cropping of high-protein soybean to analyze the taxonomic community compositions of fungi during periods of high-incidence of root rot. Our objectives were to identify the dominant pathogens in order to provide a theoretical basis for the study of pathogenesis as well as control tactics for soybean root rot induced by continuous cropping. A total of 17,801 modified internal transcribed spacer (ITS) sequences were obtained from three different soybean rhizosphere soil samples after zero year and 1 or 2 years of continuous cropping using 454 high-throughput sequencing. The dominant eumycote fungal were identified to be Ascomycota and Basidiomycota in the three soil samples. Continuous cropping of soybean affected the diversity of fungi in rhizosphere soils and increased the abundance of Thelebolus and Mortierellales significantly. Thanatephorus, Fusarium, and Alternaria were identified to be the dominant pathogenic fungal genera in rhizosphere soil from continuously cropped soybean fields. Copyright © 2015 Elsevier GmbH. All rights reserved.

Characterization of microbial communities in heavy crude oil from Saudi Arabia.

PubMed

Albokari, Majed; Mashhour, Ibrahim; Alshehri, Mohammed; Boothman, Chris; Al-Enezi, Mousa

The complete mineralization of crude oil into carbon dioxide, water, inorganic compounds and cellular constituents can be carried out as part of a bioremediation strategy. This involves the transformation of complex organic contaminants into simpler organic compounds by microbial communities, mainly bacteria. A crude oil sample and an oil sludge sample were obtained from Saudi ARAMCO Oil Company and investigated to identify the microbial communities present using PCR-based culture-independent techniques. In total, analysis of 177 clones yielded 30 distinct bacterial sequences. Clone library analysis of the oil sample was found to contain Bacillus , Clostridia and Gammaproteobacteria species while the sludge sample revealed the presence of members of the Alphaproteobacteria , Betaproteobacteria , Gammaproteobacteria , Clostridia , Spingobacteria and Flavobacteria . The dominant bacterial class identified in oil and sludge samples was found to be Bacilli and Flavobacteria , respectively. Phylogenetic analysis showed that the dominant bacterium in the oil sample has the closest sequence identity to Enterococcus aquimarinus and the dominant bacterium in the sludge sample is most closely related to the uncultured Bacteroidetes bacterium designated AH.KK.

Investigation of Containment Flooding Strategy for Mark-III Nuclear Power Plant with MAAP4

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

Su Weinian; Wang, S.-J.; Chiang, S.-C

2005-06-15

Containment flooding is an important strategy for severe accident management of a conventional boiling water reactor (BWR) system. The purpose of this work is to investigate the containment flooding strategy of the Mark-III system after a reactor pressure vessel (RPV) breach. The Kuosheng Power Plant is a typical BWR-6 nuclear power plant (NPP) with Mark-III containment. The Severe Accident Management Guideline (SAMG) of the Kuosheng NPP has been developed based on the BWR Owners Group (BWROG) Emergency Procedure and Severe Accident Guidelines, Rev. 2. Therefore, the Kuosheng NPP is selected as the plant for study, and the MAAP4 code ismore » chosen as the tool for analysis. A postulated specific station blackout sequence for the Kuosheng NPP is cited as a reference case for this analysis. Because of the design features of Mark-III containment, the debris in the reactor cavity may not be submerged after an RPV breach when one follows the containment flooding strategy as suggested in the BWROG generic guideline, and the containment integrity could be challenged eventually. A more specific containment flooding strategy with drywell venting after an RPV breach is investigated, and a more stable plant condition is achieved with this strategy. Accordingly, the containment flooding strategy after an RPV breach will be modified for the Kuosheng SAMG, and these results are applicable to typical Mark-III plants with drywell vent path.« less

Environmental mobility of (110m)Ag: lessons learnt from Fukushima accident (Japan) and potential use for tracking the dispersion of contamination within coastal catchments.

PubMed

Lepage, Hugo; Evrard, Olivier; Onda, Yuichi; Patin, Jeremy; Chartin, Caroline; Lefèvre, Irène; Bonté, Philippe; Ayrault, Sophie

2014-04-01

Silver-110 metastable ((110m)Ag) has been far less investigated than other anthropogenic radionuclides, although it has the potential to accumulate in plants and animal tissues. It is continuously produced by nuclear power plants in normal conditions, but emitted in much larger quantities in accidental conditions facilitating its detection, which allows the investigation of its behaviour in the environment. We analysed (110m)Ag in soil and river drape sediment (i.e., mud drapes deposited on channel-bed sand) collected within coastal catchments contaminated in Fukushima Prefecture (Japan) after the Fukushima Dai-ichi Nuclear Power Plant accident that occurred on 11 March 2011. Several field experiments were conducted to document radiosilver behaviour in the terrestrial environment, with a systematic comparison to the more documented radiocesium behaviour. Results show a similar and low mobility for both elements in soils and a strong affinity with the clay fraction. Measurements conducted on sediment sequences accumulated in reservoirs tend to confirm a comparable deposition of those radionuclides even after their redistribution due to erosion and deposition processes. Therefore, as the (110m)Ag:(137)Cs initial activity ratio varied in soils across the area, we justified the relevance of using this tool to track the dispersion of contaminated sediment from the main inland radioactive pollution plume generated by FDNPP accident. Copyright © 2014 Elsevier Ltd. All rights reserved.

The role of PRA in the safety assessment of VVER Nuclear Power Plants in Ukraine.

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

Kot, C.

1999-05-10

Ukraine operates thirteen (13) Soviet-designed pressurized water reactors, VVERS. All Ukrainian plants are currently operating with annually renewable permits until they update their safety analysis reports (SARs), in accordance with new SAR content requirements issued in September 1995, by the Nuclear Regulatory Authority and the Government Nuclear Power Coordinating Committee of Ukraine. The requirements are in three major areas: design basis accident (DBA) analysis, probabilistic risk assessment (PRA), and beyond design-basis accident (BDBA) analysis. The last two requirements, on PRA and BDBA, are new, and the DBA requirements are an expanded version of the older SAR requirements. The US Departmentmore » of Energy (USDOE), as part of its Soviet-Designed Reactor Safety activities, is providing assistance and technology transfer to Ukraine to support their nuclear power plants (NPPs) in developing a Western-type technical basis for the new SARs. USDOE sponsored In-Depth Safety Assessments (ISAs) are in progress at three pilot nuclear reactor units in Ukraine, South Ukraine Unit 1, Zaporizhzhya Unit 5, and Rivne Unit 1, and a follow-on study has been initiated at Khmenytskyy Unit 1. The ISA projects encompass most areas of plant safety evaluation, but the initial emphasis is on performing a detailed, plant-specific Level 1 Internal Events PRA. This allows the early definition of the plant risk profile, the identification of risk significant accident sequences and plant vulnerabilities and provides guidance for the remainder of the safety assessments.« less

The Impact of Transformational Leadership on Safety Climate and Individual Safety Behavior on Construction Sites.

PubMed

Shen, Yuzhong; Ju, Chuanjing; Koh, Tas Yong; Rowlinson, Steve; Bridge, Adrian J

2017-01-05

Unsafe acts contribute dominantly to construction accidents, and increasing safety behavior is essential to reduce accidents. Previous research conceptualized safety behavior as an interaction between proximal individual differences (safety knowledge and safety motivation) and distal contextual factors (leadership and safety climate). However, relatively little empirical research has examined this conceptualization in the construction sector. Given the cultural background of the sample, this study makes a slight modification to the conceptualization and views transformational leadership as an antecedent of safety climate. Accordingly, this study establishes a multiple mediator model showing the mechanisms through which transformational leadership translates into safety behavior. The multiple mediator model is estimated by the structural equation modeling (SEM) technique, using individual questionnaire responses from a random sample of construction personnel based in Hong Kong. As hypothesized, transformational leadership has a significant impact on safety climate which is mediated by safety-specific leader-member exchange (LMX), and safety climate in turn impacts safety behavior through safety knowledge. The results suggest that future safety climate interventions should be more effective if supervisors exhibit transformational leadership, encourage construction personnel to voice safety concerns without fear of retaliation, and repeatedly remind them about safety on the job.

The Impact of Transformational Leadership on Safety Climate and Individual Safety Behavior on Construction Sites

PubMed Central

Shen, Yuzhong; Ju, Chuanjing; Koh, Tas Yong; Rowlinson, Steve; Bridge, Adrian J.

2017-01-01

Unsafe acts contribute dominantly to construction accidents, and increasing safety behavior is essential to reduce accidents. Previous research conceptualized safety behavior as an interaction between proximal individual differences (safety knowledge and safety motivation) and distal contextual factors (leadership and safety climate). However, relatively little empirical research has examined this conceptualization in the construction sector. Given the cultural background of the sample, this study makes a slight modification to the conceptualization and views transformational leadership as an antecedent of safety climate. Accordingly, this study establishes a multiple mediator model showing the mechanisms through which transformational leadership translates into safety behavior. The multiple mediator model is estimated by the structural equation modeling (SEM) technique, using individual questionnaire responses from a random sample of construction personnel based in Hong Kong. As hypothesized, transformational leadership has a significant impact on safety climate which is mediated by safety-specific leader–member exchange (LMX), and safety climate in turn impacts safety behavior through safety knowledge. The results suggest that future safety climate interventions should be more effective if supervisors exhibit transformational leadership, encourage construction personnel to voice safety concerns without fear of retaliation, and repeatedly remind them about safety on the job. PMID:28067775

An intelligent support system for automatic detection of cerebral vascular accidents from brain CT images.

PubMed

Hajimani, Elmira; Ruano, M G; Ruano, A E

2017-07-01

This paper presents a Radial Basis Functions Neural Network (RBFNN) based detection system, for automatic identification of Cerebral Vascular Accidents (CVA) through analysis of Computed Tomographic (CT) images. For the design of a neural network classifier, a Multi Objective Genetic Algorithm (MOGA) framework is used to determine the architecture of the classifier, its corresponding parameters and input features by maximizing the classification precision, while ensuring generalization. This approach considers a large number of input features, comprising first and second order pixel intensity statistics, as well as symmetry/asymmetry information with respect to the ideal mid-sagittal line. Values of specificity of 98% and sensitivity of 98% were obtained, at pixel level, by an ensemble of non-dominated models generated by MOGA, in a set of 150 CT slices (1,867,602pixels), marked by a NeuroRadiologist. This approach also compares favorably at a lesion level with three other published solutions, in terms of specificity (86% compared with 84%), degree of coincidence of marked lesions (89% compared with 77%) and classification accuracy rate (96% compared with 88%). Copyright © 2017. Published by Elsevier B.V.

Acoustical features of two Mayan monuments at Chichen Itza: Accident or design?

NASA Astrophysics Data System (ADS)

Lubman, David

2002-11-01

Chichen Itza dominated the early postclassic Maya world, ca. 900-1200 C.E. Two of its colossal monuments, the Great Ball Court and the temple of Kukulkan, reflect the sophisticated, hybrid culture of a Mexicanized Maya civilization. The architecture seems intended for ceremony and ritual drama. Deducing ritual practices will advance the understanding of a lost civilization, but what took place there is largely unknown. Perhaps acoustical science can add value. Unexpected and unusual acoustical features can be interpreted as intriguing clues or irrelevant accidents. Acoustical advocates believe that, when combined with an understanding of the Maya worldview, acoustical features can provide unique insights into how the Maya designed and used theater spaces. At Chichen Itza's monuments, sound reinforcement features improve rulers and priests ability to address large crowds, and Ball Court whispering galleries permit speech communication over unexpectedly large distances. Handclaps at Kukulkan stimulate chirps that mimic a revered bird (''Kukul''), thus reinforcing cultic beliefs. A ball striking playing field wall stimulates flutter echoes at the Great Ball Court; their strength and duration arguably had dramatic, mythic, and practical significance. Interpretations of the possible mythic, magic, and political significance of sound phenomena at these Maya monuments strongly suggests intentional design.

Content analysis to locate assistive technology in Queensland's motor injury insurance rehabilitation legislation and guidelines.

PubMed

Steel, Emily J

2018-06-08

Reforms to Australia's disability and rehabilitation sectors have espoused the potential of assistive technology as an enabler. As new insurance systems are being developed it is timely to examine the structure of existing systems. This exploratory study examined the policies guiding assistive technology provision in the motor accident insurance sector of one Australian state. Policy documents were analyzed iteratively with set of qualitative questions to understand the intent and interpretation of policies guiding assistive technology provision. Content analysis identified relevant sections and meaningful terminology, and context analysis explored the dominant perspectives informing policy. The concepts and language of assistive technology are not part of the policy frameworks guiding rehabilitation practice in Queensland's motor accident insurance sector. The definition of rehabilitation in the legislation is consistent contemporary international interpretations that focus on optimizing functioning in interaction with the environment. However, the supporting documents are focused on recovery from injuries where decisions are guided by clinical need and affordability. The policies frame rehabilitation in a medical model that assistive technology provision from the rehabilitation plan. The legislative framework provides opportunities to develop and improve assistive technology provision as part of an integrated approach to rehabilitation.

Microbial Communities in the Surface Mucopolysaccharide Layer and the Black Band Microbial Mat of Black Band-Diseased Siderastrea siderea

PubMed Central

Sekar, Raju; Mills, DeEtta K.; Remily, Elizabeth R.; Voss, Joshua D.; Richardson, Laurie L.

2006-01-01

Microbial community profiles and species composition associated with two black band-diseased colonies of the coral Siderastrea siderea were studied by 16S rRNA-targeted gene cloning, sequencing, and amplicon-length heterogeneity PCR (LH-PCR). Bacterial communities associated with the surface mucopolysaccharide layer (SML) of apparently healthy tissues of the infected colonies, together with samples of the black band disease (BBD) infections, were analyzed using the same techniques for comparison. Gene sequences, ranging from 424 to 1,537 bp, were retrieved from all positive clones (n = 43 to 48) in each of the four clone libraries generated and used for comparative sequence analysis. In addition to LH-PCR community profiling, all of the clone sequences were aligned with LH-PCR primer sequences, and the theoretical lengths of the amplicons were determined. Results revealed that the community profiles were significantly different between BBD and SML samples. The SML samples were dominated by γ-proteobacteria (53 to 64%), followed by β-proteobacteria (18 to 21%) and α-proteobacteria (5 to 11%). In contrast, both BBD clone libraries were dominated by α-proteobacteria (58 to 87%), followed by verrucomicrobia (2 to 10%) and 0 to 6% each of δ-proteobacteria, bacteroidetes, firmicutes, and cyanobacteria. Alphaproteobacterial sequence types related to the bacteria associated with toxin-producing dinoflagellates were observed in BBD clone libraries but were not found in the SML libraries. Similarly, sequences affiliated with the family Desulfobacteraceae and toxin-producing cyanobacteria, both believed to be involved in BBD pathogenesis, were found only in BBD libraries. These data provide evidence for an association of numerous toxin-producing heterotrophic microorganisms with BBD of corals. PMID:16957217

A novel mutation in PRPF31, causative of autosomal dominant retinitis pigmentosa, using the BGISEQ-500 sequencer

PubMed Central

Zheng, Yu; Wang, Hai-Lin; Li, Jian-Kang; Xu, Li; Tellier, Laurent; Li, Xiao-Lin; Huang, Xiao-Yan; Li, Wei; Niu, Tong-Tong; Yang, Huan-Ming; Zhang, Jian-Guo; Liu, Dong-Ning

2018-01-01

AIM To study the genes responsible for retinitis pigmentosa. METHODS A total of 15 Chinese families with retinitis pigmentosa, containing 94 sporadically afflicted cases, were recruited. The targeted sequences were captured using the Target_Eye_365_V3 chip and sequenced using the BGISEQ-500 sequencer, according to the manufacturer's instructions. Data were aligned to UCSC Genome Browser build hg19, using the Burroughs Wheeler Aligner MEM algorithm. Local realignment was performed with the Genome Analysis Toolkit (GATK v.3.3.0) IndelRealigner, and variants were called with the Genome Analysis Toolkit Haplotypecaller, without any use of imputation. Variants were filtered against a panel derived from 1000 Genomes Project, 1000G_ASN, ESP6500, ExAC and dbSNP138. In all members of Family ONE and Family TWO with available DNA samples, the genetic variant was validated using Sanger sequencing. RESULTS A novel, pathogenic variant of retinitis pigmentosa, c.357_358delAA (p.Ser119SerfsX5) was identified in PRPF31 in 2 of 15 autosomal-dominant retinitis pigmentosa (ADRP) families, as well as in one, sporadic case. Sanger sequencing was performed upon probands, as well as upon other family members. This novel, pathogenic genotype co-segregated with retinitis pigmentosa phenotype in these two families. CONCLUSION ADRP is a subtype of retinitis pigmentosa, defined by its genotype, which accounts for 20%-40% of the retinitis pigmentosa patients. Our study thus expands the spectrum of PRPF31 mutations known to occur in ADRP, and provides further demonstration of the applicability of the BGISEQ500 sequencer for genomics research. PMID:29375987

Development of Pineapple Microsatellite Markers and Germplasm Genetic Diversity Analysis

PubMed Central

Tong, Helin; Chen, You; Wang, Jingyi; Chen, Yeyuan; Sun, Guangming; He, Junhu; Wu, Yaoting

2013-01-01

Two methods were used to develop pineapple microsatellite markers. Genomic library-based SSR development: using selectively amplified microsatellite assay, 86 sequences were generated from pineapple genomic library. 91 (96.8%) of the 94 Simple Sequence Repeat (SSR) loci were dinucleotide repeats (39 AC/GT repeats and 52 GA/TC repeats, accounting for 42.9% and 57.1%, resp.), and the other three were mononucleotide repeats. Thirty-six pairs of SSR primers were designed; 24 of them generated clear bands of expected sizes, and 13 of them showed polymorphism. EST-based SSR development: 5659 pineapple EST sequences obtained from NCBI were analyzed; among 1397 nonredundant EST sequences, 843 were found containing 1110 SSR loci (217 of them contained more than one SSR locus). Frequency of SSRs in pineapple EST sequences is 1SSR/3.73 kb, and 44 types were found. Mononucleotide, dinucleotide, and trinucleotide repeats dominate, accounting for 95.6% in total. AG/CT and AGC/GCT were the dominant type of dinucleotide and trinucleotide repeats, accounting for 83.5% and 24.1%, respectively. Thirty pairs of primers were designed for each of randomly selected 30 sequences; 26 of them generated clear and reproducible bands, and 22 of them showed polymorphism. Eighteen pairs of primers obtained by the one or the other of the two methods above that showed polymorphism were selected to carry out germplasm genetic diversity analysis for 48 breeds of pineapple; similarity coefficients of these breeds were between 0.59 and 1.00, and they can be divided into four groups accordingly. Amplification products of five SSR markers were extracted and sequenced, corresponding repeat loci were found and locus mutations are mainly in copy number of repeats and base mutations in the flanking region. PMID:24024187

Elevated mitochondrial genome variation after 50 generations of radiation exposure in a wild rodent.

PubMed

Baker, Robert J; Dickins, Benjamin; Wickliffe, Jeffrey K; Khan, Faisal A A; Gaschak, Sergey; Makova, Kateryna D; Phillips, Caleb D

2017-09-01

Currently, the effects of chronic, continuous low dose environmental irradiation on the mitochondrial genome of resident small mammals are unknown. Using the bank vole ( Myodes glareolus ) as a model system, we tested the hypothesis that approximately 50 generations of exposure to the Chernobyl environment has significantly altered genetic diversity of the mitochondrial genome. Using deep sequencing, we compared mitochondrial genomes from 131 individuals from reference sites with radioactive contamination comparable to that present in northern Ukraine before the 26 April 1986 meltdown, to populations where substantial fallout was deposited following the nuclear accident. Population genetic variables revealed significant differences among populations from contaminated and uncontaminated localities. Therefore, we rejected the null hypothesis of no significant genetic effect from 50 generations of exposure to the environment created by the Chernobyl meltdown. Samples from contaminated localities exhibited significantly higher numbers of haplotypes and polymorphic loci, elevated genetic diversity, and a significantly higher average number of substitutions per site across mitochondrial gene regions. Observed genetic variation was dominated by synonymous mutations, which may indicate a history of purify selection against nonsynonymous or insertion/deletion mutations. These significant differences were not attributable to sample size artifacts. The observed increase in mitochondrial genomic diversity in voles from radioactive sites is consistent with the possibility that chronic, continuous irradiation resulting from the Chernobyl disaster has produced an accelerated mutation rate in this species over the last 25 years. Our results, being the first to demonstrate this phenomenon in a wild mammalian species, are important for understanding genetic consequences of exposure to low-dose radiation sources.

Novel CREB3L3 Nonsense Mutation in a Family With Dominant Hypertriglyceridemia.

PubMed

Cefalù, Angelo B; Spina, Rossella; Noto, Davide; Valenti, Vincenza; Ingrassia, Valeria; Giammanco, Antonina; Panno, Maria D; Ganci, Antonina; Barbagallo, Carlo M; Averna, Maurizio R

2015-12-01

Cyclic AMP responsive element-binding protein 3-like 3 (CREB3L3) is a novel candidate gene for dominant hypertriglyceridemia. To date, only 4 kindred with dominant hypertriglyceridemia have been found to be carriers of 2 nonsense mutations in CREB3L3 gene (245fs and W46X). We investigated a family in which hypertriglyceridemia displayed an autosomal dominant pattern of inheritance. The proband was a 49-year-old woman with high plasma triglycerides (≤1300 mg/dL; 14.68 mmol/L). Her father had a history of moderate hypertriglyceridemia, and her 51-year-old brother had triglycerides levels as high as 1600 mg/dL (18.06 mmol/L). To identify the causal mutation in this family, we analyzed the candidate genes of recessive and dominant forms of primary hypertriglyceridemia by direct sequencing. The sequencing of CREB3L3 gene led to the discovery of a novel minute frame shift mutation in exon 3 of CREB3L3 gene, predicted to result in the formation of a truncated protein devoid of function (c.359delG-p.K120fsX20). Heterozygosity for the c.359delG mutation resulted in a severe phenotype occurring later in life in the proband and her brother and a good response to diet and a hypotriglyceridemic treatment. The same mutation was detected in a 13-year-old daughter who to date is normotriglyceridemic. We have identified a novel pathogenic mutation in CREB3L3 gene in a family with dominant hypertriglyceridemia with a variable pattern of penetrance. © 2015 American Heart Association, Inc.

Metabolic characteristics of dominant microbes and key rare species from an acidic hot spring in Taiwan revealed by metagenomics

DOE PAGES

Lin, Kuei -Han; Liao, Ben -Yang; Chang, Hao -Wei; ...

2015-12-03

Microbial diversity and community structures in acidic hot springs have been characterized by 16S rRNA gene-based diversity surveys. However, our understanding regarding the interactions among microbes, or between microbes and environmental factors, remains limited. In the present study, a metagenomic approach, followed by bioinformatics analyses, were used to predict interactions within the microbial ecosystem in Shi-Huang-Ping (SHP), an acidic hot spring in northern Taiwan. Characterizing environmental parameters and potential metabolic pathways highlighted the importance of carbon assimilatory pathways. Four distinct carbon assimilatory pathways were identified in five dominant genera of bacteria. Of those dominant carbon fixers, Hydrogenobaculum bacteria outcompeted othermore » carbon assimilators and dominated the SHP, presumably due to their ability to metabolize hydrogen and to withstand an anaerobic environment with fluctuating temperatures. Furthermore, most dominant microbes were capable of metabolizing inorganic sulfur-related compounds (abundant in SHP). However, Acidithiobacillus ferrooxidans was the only species among key rare microbes with the capability to fix nitrogen, suggesting a key role in nitrogen cycling. In addition to potential metabolic interactions, based on the 16S rRNAs gene sequence of Nanoarchaeum-related and its potential host Ignicoccus-related archaea, as well as sequences of viruses and CRISPR arrays, we inferred that there were complex microbe-microbe interactions. In conclusion, our study provided evidence that there were numerous microbe-microbe and microbe-environment interactions within the microbial community in an acidic hot spring. We proposed that Hydrogenobaculum bacteria were the dominant microbial genus, as they were able to metabolize hydrogen, assimilate carbon and live in an anaerobic environment with fluctuating temperatures.« less

Metabolic characteristics of dominant microbes and key rare species from an acidic hot spring in Taiwan revealed by metagenomics

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

Lin, Kuei -Han; Liao, Ben -Yang; Chang, Hao -Wei

Microbial diversity and community structures in acidic hot springs have been characterized by 16S rRNA gene-based diversity surveys. However, our understanding regarding the interactions among microbes, or between microbes and environmental factors, remains limited. In the present study, a metagenomic approach, followed by bioinformatics analyses, were used to predict interactions within the microbial ecosystem in Shi-Huang-Ping (SHP), an acidic hot spring in northern Taiwan. Characterizing environmental parameters and potential metabolic pathways highlighted the importance of carbon assimilatory pathways. Four distinct carbon assimilatory pathways were identified in five dominant genera of bacteria. Of those dominant carbon fixers, Hydrogenobaculum bacteria outcompeted othermore » carbon assimilators and dominated the SHP, presumably due to their ability to metabolize hydrogen and to withstand an anaerobic environment with fluctuating temperatures. Furthermore, most dominant microbes were capable of metabolizing inorganic sulfur-related compounds (abundant in SHP). However, Acidithiobacillus ferrooxidans was the only species among key rare microbes with the capability to fix nitrogen, suggesting a key role in nitrogen cycling. In addition to potential metabolic interactions, based on the 16S rRNAs gene sequence of Nanoarchaeum-related and its potential host Ignicoccus-related archaea, as well as sequences of viruses and CRISPR arrays, we inferred that there were complex microbe-microbe interactions. In conclusion, our study provided evidence that there were numerous microbe-microbe and microbe-environment interactions within the microbial community in an acidic hot spring. We proposed that Hydrogenobaculum bacteria were the dominant microbial genus, as they were able to metabolize hydrogen, assimilate carbon and live in an anaerobic environment with fluctuating temperatures.« less

Accident diagnosis system based on real-time decision tree expert system

NASA Astrophysics Data System (ADS)

Nicolau, Andressa dos S.; Augusto, João P. da S. C.; Schirru, Roberto

2017-06-01

Safety is one of the most studied topics when referring to power stations. For that reason, sensors and alarms develop an important role in environmental and human protection. When abnormal event happens, it triggers a chain of alarms that must be, somehow, checked by the control room operators. In this case, diagnosis support system can help operators to accurately identify the possible root-cause of the problem in short time. In this article, we present a computational model of a generic diagnose support system based on artificial intelligence, that was applied on the dataset of two real power stations: Angra1 Nuclear Power Plant and Santo Antônio Hydroelectric Plant. The proposed system processes all the information logged in the sequence of events before a shutdown signal using the expert's knowledge inputted into an expert system indicating the chain of events, from the shutdown signal to its root-cause. The results of both applications showed that the support system is a potential tool to help the control room operators identify abnormal events, as accidents and consequently increase the safety.

Evaluation of the genetic diversity of Plum pox virus in a single plum tree.

PubMed

Predajňa, Lukáš; Šubr, Zdeno; Candresse, Thierry; Glasa, Miroslav

2012-07-01

Genetic diversity of Plum pox virus (PPV) and its distribution within a single perennial woody host (plum, Prunus domestica) has been evaluated. A plum tree was triply infected by chip-budding with PPV-M, PPV-D and PPV-Rec isolates in 2003 and left to develop untreated under open field conditions. In September 2010 leaf and fruit samples were collected from different parts of the tree canopy. A 745-bp NIb-CP fragment of PPV genome, containing the hypervariable region encoding the CP N-terminal end was amplified by RT-PCR from each sample and directly sequenced to determine the dominant sequence. In parallel, the PCR products were cloned and a total of 105 individual clones were sequenced. Sequence analysis revealed that after 7 years of infection, only PPV-M was still detectable in the tree and that the two other isolates (PPV-Rec and PPV-D) had been displaced. Despite the fact that the analysis targeted a relatively short portion of the genome, a substantial amount of intra-isolate variability was observed for PPV-M. A total of 51 different haplotypes could be identified from the 105 individual sequences, two of which were largely dominant. However, no clear-cut structuration of the viral population by the tree architecture could be highlighted although the results obtained suggest the possibility of intra-leaf/fruit differentiation of the viral population. Comparison of the consensus sequence with the original source isolate showed no difference, suggesting within-plant stability of this original isolate under open field conditions. Copyright © 2012 Elsevier B.V. All rights reserved.

Facies architecture and high resolution sequence stratigraphy of an aeolian, fluvial and shallow marine system in the Pennsylvanian Piauí Formation, Parnaíba Basin, Brazil

NASA Astrophysics Data System (ADS)

Vieira, Lucas Valadares; Scherer, Claiton Marlon dos Santos

2017-07-01

The Pennsylvanian Piauí Formation records the deposition of aeolian, fluvial and shallow marine systems accumulated in the cratonic sag Parnaíba basin. Characterization of the facies associations and sequence stratigraphic framework was done by detailed description and logging of outcrops. Six facies associations were recognized: aeolian dunes and interdunes, aeolian sandsheets, fluvial channels, tidally-influenced fluvial channels, shoreface and shoreface-shelf transition. Through correlation of stratigraphic surfaces, the facies associations were organized in system tracts, which formed eight high frequency depositional sequences, bounded by subaerial unconformities. These sequences are composed of a lowstand system tract (LST), that is aeolian-dominated or fluvial-dominated, a transgressive system tract (TST) that is formed by tidally-influenced fluvial channels and/or shoreface and shoreface-shelf transition deposits with retrogradational stacking, and a highstand system tract (HST), which is formed by shoreface-shelf transition and shoreface deposits with progradational stacking. Two low frequency cycles were determined by observing the stacking of the high frequency cycles. The Lower Sequence is characterized by aeolian deposits of the LST and an aggradational base followed by a progressive transgression, defining a general TST. The Upper Sequence is characterized by fluvial deposits and interfluve pedogenesis concurring with the aeolian deposits of the LST and records a subtle regression followed by transgression. The main control on sedimentation in the Piauí Formation was glacioeustasy, which was responsible for the changes in relative sea level. Even though, climate changes were associated with glacioeustatic phases and influenced the aeolian and fluvial deposition.

Hygromycin B phosphotransferase as a selectable marker for DNA transfer experiments with higher eucaryotic cells.

PubMed

Blochlinger, K; Diggelmann, H

1984-12-01

The DNA coding sequence for the hygromycin B phosphotransferase gene was placed under the control of the regulatory sequences of a cloned long terminal repeat of Moloney sarcoma virus. This construction allowed direct selection for hygromycin B resistance after transfection of eucaryotic cell lines not naturally resistant to this antibiotic, thus providing another dominant marker for DNA transfer in eucaryotic cells.

Hygromycin B phosphotransferase as a selectable marker for DNA transfer experiments with higher eucaryotic cells.

PubMed Central

Blochlinger, K; Diggelmann, H

1984-01-01

The DNA coding sequence for the hygromycin B phosphotransferase gene was placed under the control of the regulatory sequences of a cloned long terminal repeat of Moloney sarcoma virus. This construction allowed direct selection for hygromycin B resistance after transfection of eucaryotic cell lines not naturally resistant to this antibiotic, thus providing another dominant marker for DNA transfer in eucaryotic cells. Images PMID:6098829

Draft Genome Sequence of Cyanobacterium sp. Strain HL-69, Isolated from a Benthic Microbial Mat from a Magnesium Sulfate-Dominated Hypersaline Lake

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

Mobberley, J. M.; Romine, M. F.; Cole, J. K.

ABSTRACT The complete genome sequence ofCyanobacteriumsp. strain HL-69 consists of 3,155,247 bp and contains 2,897 predicted genes comprising a chromosome and two plasmids. The genome is consistent with a halophilic nondiazotrophic phototrophic lifestyle, and this organism is able to synthesize most B vitamins and produces several secondary metabolites.

Epitaxial Nucleation on Rationally Designed Peptide Functionalized Interface

DTIC Science & Technology

2011-07-19

of 17 amino acid peptides. In this report, we focus on the findings from several variants of these sequences, including the role of charge...separation and histidine-gold coordination. We find that these 17 amino acid peptide sequences behave robustly, where periodicity appears to dominate the...26,27 Secondary structure propensity refers to the intrinsic inclination of individual amino acids to a given secondary structure, where side-group

A recurrent deletion mutation in OPA1 causes autosomal dominant optic atrophy in a Chinese family

NASA Astrophysics Data System (ADS)

Zhang, Liping; Shi, Wei; Song, Liming; Zhang, Xiao; Cheng, Lulu; Wang, Yanfang; Ge, Xianglian; Li, Wei; Zhang, Wei; Min, Qingjie; Jin, Zi-Bing; Qu, Jia; Gu, Feng

2014-11-01

Autosomal dominant optic atrophy (ADOA) is the most frequent form of hereditary optic neuropathy and occurs due to the degeneration of the retinal ganglion cells. To identify the genetic defect in a family with putative ADOA, we performed capture next generation sequencing (CNGS) to screen known retinal disease genes. However, six exons failed to be sequenced by CNGS in optic atrophy 1 gene (OPA1). Sequencing of those exons identified a 4 bp deletion mutation (c.2983-1_2985del) in OPA1. Furthermore, we sequenced the transcripts of OPA1 from the patient skin fibroblasts and found there is six-nucleotide deletion (c.2984-c.2989, AGAAAG). Quantitative-PCR and Western blotting showed that OPA1 mRNA and its protein expression have no obvious difference between patient skin fibroblast and control. The analysis of protein structure by molecular modeling suggests that the mutation may change the structure of OPA1 by formation of an alpha helix protruding into an existing pocket. Taken together, we identified an OPA1 mutation in a family with ADOA by filling the missing CNGS data. We also showed that this mutation affects the structural intactness of OPA1. It provides molecular insights for clinical genetic diagnosis and treatment of optic atrophy.

A recurrent deletion mutation in OPA1 causes autosomal dominant optic atrophy in a Chinese family.

PubMed

Zhang, Liping; Shi, Wei; Song, Liming; Zhang, Xiao; Cheng, Lulu; Wang, Yanfang; Ge, Xianglian; Li, Wei; Zhang, Wei; Min, Qingjie; Jin, Zi-Bing; Qu, Jia; Gu, Feng

2014-11-06

Autosomal dominant optic atrophy (ADOA) is the most frequent form of hereditary optic neuropathy and occurs due to the degeneration of the retinal ganglion cells. To identify the genetic defect in a family with putative ADOA, we performed capture next generation sequencing (CNGS) to screen known retinal disease genes. However, six exons failed to be sequenced by CNGS in optic atrophy 1 gene (OPA1). Sequencing of those exons identified a 4 bp deletion mutation (c.2983-1_2985del) in OPA1. Furthermore, we sequenced the transcripts of OPA1 from the patient skin fibroblasts and found there is six-nucleotide deletion (c.2984-c.2989, AGAAAG). Quantitative-PCR and Western blotting showed that OPA1 mRNA and its protein expression have no obvious difference between patient skin fibroblast and control. The analysis of protein structure by molecular modeling suggests that the mutation may change the structure of OPA1 by formation of an alpha helix protruding into an existing pocket. Taken together, we identified an OPA1 mutation in a family with ADOA by filling the missing CNGS data. We also showed that this mutation affects the structural intactness of OPA1. It provides molecular insights for clinical genetic diagnosis and treatment of optic atrophy.

Genotyping microarray: Mutation screening in Spanish families with autosomal dominant retinitis pigmentosa

PubMed Central

García-Hoyos, María; Cortón, Marta; Ávila-Fernández, Almudena; Riveiro-Álvarez, Rosa; Giménez, Ascensión; Hernan, Inma; Carballo, Miguel; Ayuso, Carmen

2012-01-01

Purpose Presently, 22 genes have been described in association with autosomal dominant retinitis pigmentosa (adRP); however, they explain only 50% of all cases, making genetic diagnosis of this disease difficult and costly. The aim of this study was to evaluate a specific genotyping microarray for its application to the molecular diagnosis of adRP in Spanish patients. Methods We analyzed 139 unrelated Spanish families with adRP. Samples were studied by using a genotyping microarray (adRP). All mutations found were further confirmed with automatic sequencing. Rhodopsin (RHO) sequencing was performed in all negative samples for the genotyping microarray. Results The adRP genotyping microarray detected the mutation associated with the disease in 20 of the 139 families with adRP. As in other populations, RHO was found to be the most frequently mutated gene in these families (7.9% of the microarray genotyped families). The rate of false positives (microarray results not confirmed with sequencing) and false negatives (mutations in RHO detected with sequencing but not with the genotyping microarray) were established, and high levels of analytical sensitivity (95%) and specificity (100%) were found. Diagnostic accuracy was 15.1%. Conclusions The adRP genotyping microarray is a quick, cost-efficient first step in the molecular diagnosis of Spanish patients with adRP. PMID:22736939

Chance, necessity and the origins of life: a physical sciences perspective.

PubMed

Hazen, Robert M

2017-12-28

Earth's 4.5-billion-year history has witnessed a complex sequence of high-probability chemical and physical processes, as well as 'frozen accidents'. Most models of life's origins similarly invoke a sequence of chemical reactions and molecular self-assemblies in which both necessity and chance play important roles. Recent research adds two important insights into this discussion. First, in the context of chemical reactions, chance versus necessity is an inherently false dichotomy-a range of probabilities exists for many natural events. Second, given the combinatorial richness of early Earth's chemical and physical environments, events in molecular evolution that are unlikely at limited laboratory scales of space and time may, nevertheless, be inevitable on an Earth-like planet at time scales of a billion years.This article is part of the themed issue 'Reconceptualizing the origins of life'. © 2017 The Author(s).

High-throughput sequencing of microbial community diversity in soil, grapes, leaves, grape juice and wine of grapevine from China.

PubMed

Wei, Yu-Jie; Wu, Yun; Yan, Yin-Zhuo; Zou, Wan; Xue, Jie; Ma, Wen-Rui; Wang, Wei; Tian, Ge; Wang, Li-Ye

2018-01-01

In this study Illumina MiSeq was performed to investigate microbial diversity in soil, leaves, grape, grape juice and wine. A total of 1,043,102 fungal Internal Transcribed Spacer (ITS) reads and 2,422,188 high quality bacterial 16S rDNA sequences were used for taxonomic classification, revealed five fungal and eight bacterial phyla. At the genus level, the dominant fungi were Ascomycota, Sordariales, Tetracladium and Geomyces in soil, Aureobasidium and Pleosporaceae in grapes leaves, Aureobasidium in grape and grape juice. The dominant bacteria were Kaistobacter, Arthrobacter, Skermanella and Sphingomonas in soil, Pseudomonas, Acinetobacter and Kaistobacter in grape and grapes leaves, and Oenococcus in grape juice and wine. Principal coordinate analysis showed structural separation between the composition of fungi and bacteria in all samples. This is the first study to understand microbiome population in soil, grape, grapes leaves, grape juice and wine in Xinjiang through High-throughput Sequencing and identify microorganisms like Saccharomyces cerevisiae and Oenococcus spp. that may contribute to the quality and flavor of wine.

Type III Bartter-like syndrome in an infant boy with Gitelman syndrome and autosomal dominant familial neurohypophyseal diabetes insipidus.

PubMed

Brugnara, Milena; Gaudino, Rossella; Tedeschi, Silvana; Syrèn, Marie-Louise; Perrotta, Silverio; Maines, Evelina; Zaffanello, Marco

2014-09-01

We report the case of an infant boy with polyuria and a familial history of central diabetes insipidus. Laboratory blood tests disclosed hypokalemia, metabolic alkalosis, hyperreninemia, and hyperaldosteronism. Plasma magnesium concentration was slightly low. Urine analysis showed hypercalciuria, hyposthenuria, and high excretion of potassium. Such findings oriented toward type III Bartter syndrome (BSIII). Direct sequencing of the CLCNKB gene revealed no disease-causing mutations. The water deprivation test was positive. Magnetic resonance imaging showed a lack of posterior pituitary hyperintensity. Finally, direct sequencing of the AVP-NPII gene showed a point mutation (c.1884G>A) in a heterozygous state, confirming an autosomal dominant familial neurohypophyseal diabetes insipidus (adFNDI). This condition did not explain the patient's phenotype; thus, we investigated for Gitelman syndrome (GS). A direct sequencing of the SLC12A3 gene showed c.269A>C and c.1205C>A new mutations. In conclusion, the patient had a genetic combination of GS and adFNDI with a BSIII-like phenotype.

The gut microbiome of hooded cranes (Grus monacha) wintering at Shengjin Lake, China.

PubMed

Zhao, Guanghong; Zhou, Lizhi; Dong, Yuanqiu; Cheng, Yuanyuan; Song, Yunwei

2017-06-01

Gut microbes of animals play critical roles in processes such as digestion and immunity. Therefore, identifying gut microbes will shed light on understanding the annual life of animal species, particularly those that are threatened or endangered. In the present study, we conducted nucleotide sequence analyses of the 16S rRNA genes of gut microbiome of the hooded cranes (Grus monacha) wintering at Shengjin Lake, China, by Illumina high-throughput sequencing technology. We acquired 503,398 high-quality sequences and 785 operational taxonomic units (OTUs) from 15 fecal samples from different cranes, representing 22 phyla that were dominated by Firmicutes, Proteobacteria, and Actinobacteria. A total of 305 genera were identified that were dominated by Clostridium, Lysinibacillus, and Enterobacter. The core gut microbiome comprised 26 genera, including many probiotic species such as Clostridium, Bacillus, Cellulosilyticum, and Cellulomonas that could catabolize cellulose. The findings reported here contribute to our knowledge of the microbiology of hooded cranes and will likely advance efforts to protect waterbirds that inhabit Shengjin Lake Reserve during winter. © 2017 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

Computational design of RNAs with complex energy landscapes.

PubMed

Höner zu Siederdissen, Christian; Hammer, Stefan; Abfalter, Ingrid; Hofacker, Ivo L; Flamm, Christoph; Stadler, Peter F

2013-12-01

RNA has become an integral building material in synthetic biology. Dominated by their secondary structures, which can be computed efficiently, RNA molecules are amenable not only to in vitro and in vivo selection, but also to rational, computation-based design. While the inverse folding problem of constructing an RNA sequence with a prescribed ground-state structure has received considerable attention for nearly two decades, there have been few efforts to design RNAs that can switch between distinct prescribed conformations. We introduce a user-friendly tool for designing RNA sequences that fold into multiple target structures. The underlying algorithm makes use of a combination of graph coloring and heuristic local optimization to find sequences whose energy landscapes are dominated by the prescribed conformations. A flexible interface allows the specification of a wide range of design goals. We demonstrate that bi- and tri-stable "switches" can be designed easily with moderate computational effort for the vast majority of compatible combinations of desired target structures. RNAdesign is freely available under the GPL-v3 license. Copyright © 2013 Wiley Periodicals, Inc.

High-throughput sequencing of microbial community diversity in soil, grapes, leaves, grape juice and wine of grapevine from China

PubMed Central

Yan, Yin-zhuo; Zou, Wan; Ma, Wen-rui; Wang, Wei; Tian, Ge; Wang, Li-ye

2018-01-01

In this study Illumina MiSeq was performed to investigate microbial diversity in soil, leaves, grape, grape juice and wine. A total of 1,043,102 fungal Internal Transcribed Spacer (ITS) reads and 2,422,188 high quality bacterial 16S rDNA sequences were used for taxonomic classification, revealed five fungal and eight bacterial phyla. At the genus level, the dominant fungi were Ascomycota, Sordariales, Tetracladium and Geomyces in soil, Aureobasidium and Pleosporaceae in grapes leaves, Aureobasidium in grape and grape juice. The dominant bacteria were Kaistobacter, Arthrobacter, Skermanella and Sphingomonas in soil, Pseudomonas, Acinetobacter and Kaistobacter in grape and grapes leaves, and Oenococcus in grape juice and wine. Principal coordinate analysis showed structural separation between the composition of fungi and bacteria in all samples. This is the first study to understand microbiome population in soil, grape, grapes leaves, grape juice and wine in Xinjiang through High-throughput Sequencing and identify microorganisms like Saccharomyces cerevisiae and Oenococcus spp. that may contribute to the quality and flavor of wine. PMID:29565999

Depositional facies, environments and sequence stratigraphic interpretation of the Middle Triassic-Lower Cretaceous (pre-Late Albian) succession in Arif El-Naga anticline, northeast Sinai, Egypt

NASA Astrophysics Data System (ADS)

El-Azabi, M. H.; El-Araby, A.

2005-01-01

The Middle Triassic-Lower Cretaceous (pre-Late Albian) succession of Arif El-Naga anticline comprises various distinctive facies and environments that are connected with eustatic relative sea-level changes, local/regional tectonism, variable sediment influx and base-level changes. It displays six unconformity-bounded depositional sequences. The Triassic deposits are divided into a lower clastic facies (early Middle Triassic sequence) and an upper carbonate unit (late Middle- and latest Middle/early Late Triassic sequences). The early Middle Triassic sequence consists of sandstone with shale/mudstone interbeds that formed under variable regimes, ranging from braided fluvial, lower shoreface to beach foreshore. The marine part of this sequence marks retrogradational and progradational parasequences of transgressive- and highstand systems tract deposits respectively. Deposition has taken place under warm semi-arid climate and a steady supply of clastics. The late Middle- and latest Middle/early Late Triassic sequences are carbonate facies developed on an extensive shallow marine shelf under dry-warm climate. The late Middle Triassic sequence includes retrogradational shallow subtidal oyster rudstone and progradational lower intertidal lime-mudstone parasequences that define the transgressive- and highstand systems tracts respectively. It terminates with upper intertidal oncolitic packstone with bored upper surface. The next latest Middle/early Late Triassic sequence is marked by lime-mudstone, packstone/grainstone and algal stromatolitic bindstone with minor shale/mudstone. These lower intertidal/shallow subtidal deposits of a transgressive-systems tract are followed upward by progradational highstand lower intertidal lime-mudstone deposits. The overlying Jurassic deposits encompass two different sequences. The Lower Jurassic sequence is made up of intercalating lower intertidal lime-mudstone and wave-dominated beach foreshore sandstone which formed during a short period of rising sea-level with a relative increase in clastic supply. The Middle-Upper Jurassic sequence is represented by cycles of cross-bedded sandstone topped with thin mudstone that accumulated by northerly flowing braided-streams accompanying regional uplift of the Arabo-Nubian shield. It is succeeded by another regressive fluvial sequence of Early Cretaceous age due to a major eustatic sea-level fall. The Lower Cretaceous sequence is dominated by sandy braided-river deposits with minor overbank fines and basal debris flow conglomerate.

Parametric and experimentally informed BWR Severe Accident Analysis Utilizing FeCrAl - M3FT-17OR020205041

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

Ott, Larry J.; Howell, Michael; Robb, Kevin R.

Iron-chromium-aluminum (FeCrAl) alloys are being considered as advanced fuel cladding concepts with enhanced accident tolerance. At high temperatures, FeCrAl alloys have slower oxidation kinetics and higher strength compared with zirconium-based alloys. FeCrAl could be used for fuel cladding and spacer or mixing vane grids in light water reactors and/or as channel box material in boiling water reactors (BWRs). There is a need to assess the potential gains afforded by the FeCrAl accident-tolerant-fuel (ATF) concept over the existing zirconium-based materials employed today. To accurately assess the response of FeCrAl alloys under severe accident conditions, a number of FeCrAl properties and characteristicsmore » are required. These include thermophysical properties as well as burst characteristics, oxidation kinetics, possible eutectic interactions, and failure temperatures. These properties can vary among different FeCrAl alloys. Oak Ridge National Laboratory has pursued refined values for the oxidation kinetics of the B136Y FeCrAl alloy (Fe-13Cr-6Al wt %). This investigation included oxidation tests with varying heating rates and end-point temperatures in a steam environment. The rate constant for the low-temperature oxidation kinetics was found to be higher than that for the commercial APMT FeCrAl alloy (Fe-21Cr-5Al-3Mo wt %). Compared with APMT, a 5 times higher rate constant best predicted the entire dataset (root mean square deviation). Based on tests following heating rates comparable with those the cladding would experience during a station blackout, the transition to higher oxidation kinetics occurs at approximately 1,500°C. A parametric study varying the low-temperature FeCrAl oxidation kinetics was conducted for a BWR plant using FeCrAl fuel cladding and channel boxes using the MELCOR code. A range of station blackout severe accident scenarios were simulated for a BWR/4 reactor with Mark I containment. Increasing the FeCrAl low-temperature oxidation rate constant (3 times and 10 times that of the rate constant for APMT) had a negligible impact on the early stages of the accident and minor impacts on the accident progression after the first relocation of the fuel. At temperatures below 1,500°C, increasing the rate constant for APMT by a factor of 10 still resulted in only minor FeCrAl oxidation. In general, the gains afforded by the FeCrAl enhanced ATF concept with respect to accident sequence timing and combustible gas generation are consistent with previous efforts. Compared with the traditional Zircaloy-based cladding and channel box system, the FeCrAl concept could provide a few extra hours of time for operators to take mitigating actions and/or for evacuations to take place. A coolable core geometry is retained longer, enhancing the ability to stabilize an accident. For example, a station blackout was simulated in which cooling water injection was lost 36 hours after shutdown. The timing to first fuel relocation was delayed by approximately 5 h for the FeCrAl ATF concept compared with that of the traditional Zircaloy-based cladding and channel box system.« less

Metagenomic sequence of saline desert microbiota from wild ass sanctuary, Little Rann of Kutch, Gujarat, India.

PubMed

Patel, Rajesh; Mevada, Vishal; Prajapati, Dhaval; Dudhagara, Pravin; Koringa, Prakash; Joshi, C G

2015-03-01

We report Metagenome from the saline desert soil sample of Little Rann of Kutch, Gujarat State, India. Metagenome consisted of 633,760 sequences with size 141,307,202 bp and 56% G + C content. Metagenome sequence data are available at EBI under EBI Metagenomics database with accession no. ERP005612. Community metagenomics revealed total 1802 species belonged to 43 different phyla with dominating Marinobacter (48.7%) and Halobacterium (4.6%) genus in bacterial and archaeal domain respectively. Remarkably, 18.2% sequences in a poorly characterized group and 4% gene for various stress responses along with versatile presence of commercial enzyme were evident in a functional metagenome analysis.

Autosomal-dominant non-autoimmune hyperthyroidism presenting with neuromuscular symptoms.

PubMed

Elgadi, Aziz; Arvidsson, C-G; Janson, Annika; Marcus, Claude; Costagliola, Sabine; Norgren, Svante

2005-08-01

Neuromuscular presentations are common in thyroid disease, although the mechanism is unclear. In the present study, we investigated the pathogenesis in a boy with autosomal-dominant hyperthyroidism presenting with neuromuscular symptoms. The TSHr gene was investigated by direct sequencing. Functional properties of the mutant TSHr were investigated during transient expression in COS-7 cells. Family members were investigated by clinical and biochemical examinations. Sequence analysis revealed a previously reported heterozygous missense mutation Glycine 431 for Serine in the first transmembrane segment, leading to an increased specific constitutive activity. Three additional affected family members carried the same mutation. There was no indication of autoimmune disorder. All symptoms disappeared upon treatment with thacapzol and L-thyroxine and subsequent subtotal thyroidectomy. The data imply that neuromuscular symptoms can be caused by excessive thyroid hormone levels rather than by autoimmunity.

Macro and micro diversity of Clostridium difficile isolates from diverse sources and geographical locations.

PubMed

Stabler, Richard A; Dawson, Lisa F; Valiente, Esmeralda; Cairns, Michelle D; Martin, Melissa J; Donahue, Elizabeth H; Riley, Thomas V; Songer, J Glenn; Kuijper, Ed J; Dingle, Kate E; Wren, Brendan W

2012-01-01

Clostridium difficile has emerged rapidly as the leading cause of antibiotic-associated diarrheal disease, with the temporal and geographical appearance of dominant PCR ribotypes such as 017, 027 and 078. Despite this continued threat, we have a poor understanding of how or why particular variants emerge and the sources of strains that dominate different human populations. We have undertaken a breadth genotyping study using multilocus sequence typing (MLST) analysis of 385 C. difficile strains from diverse sources by host (human, animal and food), geographical locations (North America, Europe and Australia) and PCR ribotypes. Results identified 18 novel sequence types (STs) and 3 new allele sequences and confirmed the presence of five distinct clonal lineages generally associated with outbreaks of C. difficile infection in humans. Strains of animal and food origin were found of both ST-1 and ST-11 that are frequently associated with human disease. An in depth MLST analysis of the evolutionary distant ST-11/PCR ribotype 078 clonal lineage revealed that ST-11 can be found in alternative but closely related PCR ribotypes and PCR ribotype 078 alleles contain mutations generating novel STs. PCR ribotype 027 and 017 lineages may consist of two divergent subclades. Furthermore evidence of microdiversity was present within the heterogeneous clade 1. This study helps to define the evolutionary origin of dominant C. difficile lineages and demonstrates that C. difficile is continuing to evolve in concert with human activity.

Common and distinguishing features of the bacterial and fungal communities in biological soil crusts and shrub root zone soils

USGS Publications Warehouse

Steven, Blaire; Gallegos-Graves, La Verne; Yeager, Chris; Belnap, Jayne; Kuske, Cheryl R.

2013-01-01

Soil microbial communities in dryland ecosystems play important roles as root associates of the widely spaced plants and as the dominant members of biological soil crusts (biocrusts) colonizing the plant interspaces. We employed rRNA gene sequencing (bacterial 16S/fungal large subunit) and shotgun metagenomic sequencing to compare the microbial communities inhabiting the root zones of the dominant shrub, Larrea tridentata (creosote bush), and the interspace biocrusts in a Mojave desert shrubland within the Nevada Free Air CO2 Enrichment (FACE) experiment. Most of the numerically abundant bacteria and fungi were present in both the biocrusts and root zones, although the proportional abundance of those members differed significantly between habitats. Biocrust bacteria were predominantly Cyanobacteria while root zones harbored significantly more Actinobacteria and Proteobacteria. Pezizomycetes fungi dominated the biocrusts while Dothideomycetes were highest in root zones. Functional gene abundances in metagenome sequence datasets reflected the taxonomic differences noted in the 16S rRNA datasets. For example, functional categories related to photosynthesis, circadian clock proteins, and heterocyst-associated genes were enriched in the biocrusts, where populations of Cyanobacteria were larger. Genes related to potassium metabolism were also more abundant in the biocrusts, suggesting differences in nutrient cycling between biocrusts and root zones. Finally, ten years of elevated atmospheric CO2 did not result in large shifts in taxonomic composition of the bacterial or fungal communities or the functional gene inventories in the shotgun metagenomes.

Fungal communities in ancient peatlands developed from different periods in the Sanjiang Plain, China

PubMed Central

Tian, Lei; Ma, Lina; Luo, Shasha; Zhang, Jianfeng; Li, Xiujun

2017-01-01

Peatlands in the Sanjiang Plain could be more vulnerable to global warming because they are located at the southernmost boundary of northern peatlands. Unlike bacteria, fungi are often overlooked, even though they play important roles in substance circulation in the peatland ecosystems. Accordingly, it is imperative that we deepen our understanding of fungal community structure and diversity in the peatlands. In this study, high-throughput Illumina sequencing was used to study the fungal communities in three fens in the Sanjiang Plain, located at the southern edge of northern peatlands. Peat soil was collected from the three fens which developed during different periods. A total of 463,198 fungal ITS sequences were obtained, and these sequences were classified into at least six phyla, 21 classes, more than 60 orders and over 200 genera. The fungal community structures were distinct in the three sites and were dominated by Ascomycota and Basidiomycota. However, there were no significant differences between these three fens in any α-diversity index (p > 0.05). Soil age and the carbon (C) accumulation rate, as well as total carbon (TC), total nitrogen (TN), C/N ratio, and bulk density were found to be closely related to the abundance of several dominant fungal taxa. We captured a rich fungal community and confirmed that the dominant taxa were those which were frequently detected in other northern peatlands. Soil age and the C accumulation rate were found to play important roles in shaping the fungal community structure. PMID:29236715

Phylogenetic and functional diversity within toluene-degrading, sulphate-reducing consortia enriched from a contaminated aquifer.

PubMed

Kuppardt, Anke; Kleinsteuber, Sabine; Vogt, Carsten; Lüders, Tillmann; Harms, Hauke; Chatzinotas, Antonis

2014-08-01

Three toluene-degrading microbial consortia were enriched under sulphate-reducing conditions from different zones of a benzene, toluene, ethylbenzene and xylenes (BTEX) plume of two connected contaminated aquifers. Two cultures were obtained from a weakly contaminated zone of the lower aquifer, while one culture originated from the highly contaminated upper aquifer. We hypothesised that the different habitat characteristics are reflected by distinct degrader populations. Degradation of toluene with concomitant production of sulphide was demonstrated in laboratory microcosms and the enrichment cultures were phylogenetically characterised. The benzylsuccinate synthase alpha-subunit (bssA) marker gene, encoding the enzyme initiating anaerobic toluene degradation, was targeted to characterise the catabolic diversity within the enrichment cultures. It was shown that the hydrogeochemical parameters in the different zones of the plume determined the microbial composition of the enrichment cultures. Both enrichment cultures from the weakly contaminated zone were of a very similar composition, dominated by Deltaproteobacteria with the Desulfobulbaceae (a Desulfopila-related phylotype) as key players. Two different bssA sequence types were found, which were both affiliated to genes from sulphate-reducing Deltaproteobacteria. In contrast, the enrichment culture from the highly contaminated zone was dominated by Clostridia with a Desulfosporosinus-related phylotype as presumed key player. A distinct bssA sequence type with high similarity to other recently detected sequences from clostridial toluene degraders was dominant in this culture. This work contributes to our understanding of the niche partitioning between degrader populations in distinct compartments of BTEX-contaminated aquifers.

First report of bacterial community from a Bat Guano using Illumina next-generation sequencing.

PubMed

De Mandal, Surajit; Zothansanga; Panda, Amritha Kumari; Bisht, Satpal Singh; Senthil Kumar, Nachimuthu

2015-06-01

V4 hypervariable region of 16S rDNA was analyzed for identifying the bacterial communities present in Bat Guano from the unexplored cave - Pnahkyndeng, Meghalaya, Northeast India. Metagenome comprised of 585,434 raw Illumina sequences with a 59.59% G+C content. A total of 416,490 preprocessed reads were clustered into 1282 OTUs (operational taxonomical units) comprising of 18 bacterial phyla. The taxonomic profile showed that the guano bacterial community is dominated by Chloroflexi, Actinobacteria and Crenarchaeota which account for 70.73% of all sequence reads and 43.83% of all OTUs. Metagenome sequence data are available at NCBI under the accession no. SRP051094. This study is the first to characterize Bat Guano bacterial community using next-generation sequencing approach.

First report of bacterial community from a Bat Guano using Illumina next-generation sequencing

PubMed Central

De Mandal, Surajit; Zothansanga; Panda, Amritha Kumari; Bisht, Satpal Singh; Senthil Kumar, Nachimuthu

2015-01-01

V4 hypervariable region of 16S rDNA was analyzed for identifying the bacterial communities present in Bat Guano from the unexplored cave — Pnahkyndeng, Meghalaya, Northeast India. Metagenome comprised of 585,434 raw Illumina sequences with a 59.59% G+C content. A total of 416,490 preprocessed reads were clustered into 1282 OTUs (operational taxonomical units) comprising of 18 bacterial phyla. The taxonomic profile showed that the guano bacterial community is dominated by Chloroflexi, Actinobacteria and Crenarchaeota which account for 70.73% of all sequence reads and 43.83% of all OTUs. Metagenome sequence data are available at NCBI under the accession no. SRP051094. This study is the first to characterize Bat Guano bacterial community using next-generation sequencing approach. PMID:26484190

Exome Sequencing of 18 Chinese Families with Congenital Cataracts: A New Sight of the NHS Gene

PubMed Central

Sun, Wenmin; Xiao, Xueshan; Li, Shiqiang; Guo, Xiangming; Zhang, Qingjiong

2014-01-01

Purpose The aim of this study was to investigate the mutation spectrum and frequency of 34 known genes in 18 Chinese families with congenital cataracts. Methods Genomic DNA and clinical data was collected from 18 families with congenital cataracts. Variations in 34 cataract-associated genes were screened by whole exome sequencing and then validated by Sanger sequencing. Results Eleven candidate variants in seven of the 34 genes were detected by exome sequencing and then confirmed by Sanger sequencing, including two variants predicted to be benign and the other pathogenic mutations. The nine mutations were present in 9 of the 18 (50%) families with congenital cataracts. Of the four families with mutations in the X-linked NHS gene, no other abnormalities were recorded except for cataract, in which a pseudo-dominant inheritance form was suggested, as female carriers also had different forms of cataracts. Conclusion This study expands the mutation spectrum and frequency of genes responsible for congenital cataract. Mutation in NHS is a common cause of nonsyndromic congenital cataract with pseudo-autosomal dominant inheritance. Combined with our previous studies, a genetic basis could be identified in 67.6% of families with congenital cataracts in our case series, in which mutations in genes encoding crystallins, genes encoding connexins, and NHS are responsible for 29.4%, 14.7%, and 11.8% of families, respectively. Our results suggest that mutations in NHS are the common cause of congenital cataract, both syndromic and nonsyndromic. PMID:24968223

Formyltetrahydrofolate Synthetase Gene Diversity in the Guts of Higher Termites with Different Diets and Lifestyles ▿ †

PubMed Central

Ottesen, Elizabeth A.; Leadbetter, Jared R.

2011-01-01

In this study, we examine gene diversity for formyl-tetrahydrofolate synthetase (FTHFS), a key enzyme in homoacetogenesis, recovered from the gut microbiota of six species of higher termites. The “higher” termites (family Termitidae), which represent the majority of extant termite species and genera, engage in a broader diversity of feeding and nesting styles than the “lower” termites. Previous studies of termite gut homoacetogenesis have focused on wood-feeding lower termites, from which the preponderance of FTHFS sequences recovered were related to those from acetogenic treponemes. While sequences belonging to this group were present in the guts of all six higher termites examined, treponeme-like FTHFS sequences represented the majority of recovered sequences in only two species (a wood-feeding Nasutitermes sp. and a palm-feeding Microcerotermes sp.). The remaining four termite species analyzed (a Gnathamitermes sp. and two Amitermes spp. that were recovered from subterranean nests with indeterminate feeding strategies and a litter-feeding Rhynchotermes sp.) yielded novel FTHFS clades not observed in lower termites. These termites yielded two distinct clusters of probable purinolytic Firmicutes and a large group of potential homoacetogens related to sequences previously recovered from the guts of omnivorous cockroaches. These findings suggest that the gut environments of different higher termite species may select for different groups of homoacetogens, with some species hosting treponeme-dominated homoacetogen populations similar to those of wood-feeding, lower termites while others host Firmicutes-dominated communities more similar to those of omnivorous cockroaches. PMID:21441328

Identification of a novel splicing mutation within SLC17A8 in a Korean family with hearing loss by whole-exome sequencing.

PubMed

Ryu, Nari; Lee, Seokwon; Park, Hong-Joon; Lee, Byeonghyeon; Kwon, Tae-Jun; Bok, Jinwoong; Park, Chan Ik; Lee, Kyu-Yup; Baek, Jeong-In; Kim, Un-Kyung

2017-09-05

Hereditary hearing loss (HHL) is a common genetically heterogeneous disorder, which follows Mendelian inheritance in humans. Because of this heterogeneity, the identification of the causative gene of HHL by linkage analysis or Sanger sequencing have shown economic and temporal limitations. With recent advances in next-generation sequencing (NGS) techniques, rapid identification of a causative gene via massively parallel sequencing is now possible. We recruited a Korean family with three generations exhibiting autosomal dominant inheritance of hearing loss (HL), and the clinical information about this family revealed that there are no other symptoms accompanied with HL. To identify a causative mutation of HL in this family, we performed whole-exome sequencing of 4 family members, 3 affected and an unaffected. As the result, A novel splicing mutation, c.763+1G>T, in the solute carrier family 17, member 8 (SLC17A8) gene was identified in the patients, and the genotypes of the mutation were co-segregated with the phenotype of HL. Additionally, this mutation was not detected in 100 Koreans with normal hearing. Via NGS, we detected a novel splicing mutation that might influence the hearing ability within the patients with autosomal dominant non-syndromic HL. Our data suggests that this technique is a powerful tool to discover causative genetic factors of HL and facilitate diagnoses of the primary cause of HHL. Copyright © 2017 Elsevier B.V. All rights reserved.

Thysanophora penicillioides includes multiple genetically diverged groups that coexist respectively in Abies mariesii forests in Japan.

PubMed

Iwamoto, Susumu; Tokumasu, Seiji; Suyama, Yoshihisa; Kakishima, Makoto

2005-01-01

We investigated intraspecific diversity and genetic structures of a saprotrophic fungus--Thysanophora penicillioides--based on sequences of nuclear ribosomal internal transcribed spacer (ITS) in 15 discontinuous Abies mariesii forests of Japan. In such a well-defined morphological species, numerous unexpected ITS variations were revealed: 12 ITS sequence types detected in 254 isolates collected from 15 local populations were classified into five ITS sequence groups. Maximally, four ITS groups consisted of seven ITS types coexisting in one population. However, group 1 was dominant with approximately 65%; in particular, one haplotype, 1a, was most dominant with approximately 60% in respective populations. Therefore, few differences were recognized in genetic structure among local populations, implying that the gene flow of each lineage of the fungus occurs among local populations without geographic limitations. However, minor haplotypes in some ITS groups were found only in restricted areas, suggesting that they might expand steadily from their places of origin to neighboring A. mariesii forests. Aggregating sequence data of seven European strains and four North American strains from various substrates to those of Japanese strains, 18 ITS sequence types and 28 variable sites were recognized. They were clustered into nine lineages by phylogenetic analyses of the beta-tubulin and combined ITS and beta-tubulin datasets. According to phylogenetic species recognition by the concordance of genealogies, respective lineages correspond to phylogenetic species. Plural phylogenetic species coexist in a local population in an A. mariesii forest in Japan.

Geometric and Road Environmental Effects against Total Number of Traffic Accidents in Kendari

NASA Astrophysics Data System (ADS)

Kurdin, M. Akbar; Welendo, La; Annisa, Nur

2017-05-01

From the large number of traffic accidents that occurred, the carrying of Kendari as the biggest contributor to accidents in the Southeast. The number of accidents in Kendari row since 2011 was recorded at 18 accidents due to the influence of geometric road, in 2012 registered at 13 accident and in 2013 amounted to 6 accidents, with accident data because of the influence Geometric recorded for 3 consecutive years the biggest contributor to accidents because of the influence of geometric is Abeli districts. This study aimed to determine the road which common point of accident-prone (Black spot) in Kecamatan Abeli as accident-prone areas in Kendari, analyze the influence of geometric and road environment against accidents on roads in Kecamatan Abeli, provide alternative treatment based on the causes of accidents on the location of the accident-prone points (blackspot) to reduce the rate of traffic accidents. From the results of a study of 6 curve the accident-prone locations, that the curve I, II, and VI is the “Black Spot” influenced by the amount and condition of traffic accidents, while at the curve II, a traffic accident that occurred also be caused by unsafe geometric where the type of geometric should be changed from Spiral-Spiral type to Spiral-Circle-Spiral type. This indicates geometric effect on the number of accidents.

Composite pulses robust against charge noise and magnetic field noise for universal control of a singlet-triplet qubit

NASA Astrophysics Data System (ADS)

Wang, Xin; Barnes, Edwin; Kestner, Jason P.; Bishop, Lev S.; Das Sarma, Sankar

2013-03-01

We generalize our SUPCODE pulse sequences for singlet-triplet qubits to correct errors from imperfect control. This yields gates that are simultaneously corrected for both charge noise and magnetic field gradient fluctuations, addressing the two dominant T2* processes. By using this more efficient version of SUPCODE, we are able to introduce this capability while also substantially reducing the overall pulse time compared to the previous sequence. We show that our sequence remains realistic under experimental constraints such as finite bandwidth. This work is supported by LPS-NSA-CMTC, IARPA-MQCO and CNAM.

Th unnatural order of things: A history of the high school science sequence

NASA Astrophysics Data System (ADS)

Robbins, Dennis M.

Historical studies of US high school science education are rare. This study examines the historical origins of a unique characteristic of the secondary science curriculum, the Biology-Chemistry-Physics (B-C-P) order of courses. Statements from scientists, educators and the media claim that B-C-P has been the traditional curriculum sequence for over a century and can be traced back to the influential educational commission known as the Committee of Ten (CoT) of 1893. This study examines the history of the ordering of high school science subjects over the last 150 years. The reports and primary documents of important national educational commissions, such as the CoT, were searched for their recommendations on secondary science, particularly on course ordering. These recommendations were then compared to national, state and local statistical data on subject offerings and student enrollments to measure the effect of these national commissions on school policy. This study concludes that the Committee of Ten did not create B-P-C. The CoT made six recommendations, five placed Chemistry before Physics (P-C). One recommendation for C-P met with strong disagreement because it was thought an illogical order. Biology as a "uniform" course did not exist at this time and so the CoT made no recommendations for its grade placement. Statistical data shows that B-C-P evolved over many decades. From 1860 up to 1920 most schools used a P-C curriculum believing Physics was a foundational prerequisite of Chemistry. Biology was introduced in the early 1900s and it assumed a position before the physical sciences. Through the 1920s Chemistry and Physics were placed equally likely in 11th or 12 th grades and Biology was in the 10th grade. After World War II, B-C-P became the dominant pattern, exhibited in over 90% of schools. But up to this point in time no educational body or national commission had recommended B-C-P. The Biology-Chemistry-Physics order of courses is a product of many historical accidents and not the result of educational planning for the US high school curriculum.

Role of susceptibility-weighted imaging in demonstration of cerebral fat embolism.

PubMed

Yeap, Pheyming; Kanodia, Avinash Kumar; Main, Gavin; Yong, Aiwain

2015-01-08

Cerebral fat embolism (CFE) is a rare but potentially lethal complication of long bone fractures. Many cases of CFE occur as subclinical events and remain undiagnosed. We report a case of a 22-year-old man, with multiple long bone fractures from a road traffic accident, who subsequently developed hypoxia, neurological abnormality and petechial rash. CT of the head was normal. MRI of the head confirmed the diagnosis with lesions markedly conspicuous and most widespread on susceptibility-weighted imaging as compared to all other sequences including diffusion-weighted imaging. 2015 BMJ Publishing Group Ltd.

Diversity and dynamics of lactic acid bacteria in Atole agrio, a traditional maize-based fermented beverage from South-Eastern Mexico, analysed by high throughput sequencing and culturing.

PubMed

Pérez-Cataluña, Alba; Elizaquível, Patricia; Carrasco, Purificación; Espinosa, Judith; Reyes, Dolores; Wacher, Carmen; Aznar, Rosa

2018-03-01

The purpose of this work was to analyse the diversity and dynamics of lactic acid bacteria (LAB) throughout the fermentation process in Atole agrio, a traditional maize based food of Mexican origin. Samples of different fermentation times were analysed using culture-dependent and -independent approaches. Identification of LAB isolates revealed the presence of members of the genera Pediococcus, Weissella, Lactobacillus, Leuconostoc and Lactococcus, and the predominance of Pediococcus pentosaceus and Weissella confusa in liquid and solid batches, respectively. High-throughput sequencing (HTS) of the 16S rRNA gene confirmed the predominance of Lactobacillaceae and Leuconostocaceae at the beginning of the process. In liquid fermentation Acetobacteraceae dominate after 4 h as pH decreased. In contrast, Leuconostocaceae dominated the solid fermentation except at 12 h that were overgrown by Acetobacteraceae. Regarding LAB genera, Lactobacillus dominated the liquid fermentation except at 12 h when Weissella, Lactococcus and Streptococcus were the most abundant. In solid fermentation Weissella predominated all through the process. HTS determined that Lactobacillus plantarum and W. confusa dominated in the liquid and solid batches, respectively. Two oligotypes have been identified for L. plantarum and W. confusa populations, differing in a single nucleotide position each. Only one of the oligotypes was detected among the isolates obtained from each species, the biological significance of which remains unclear.

Freshwater ice as habitat: partitioning of phytoplankton and bacteria between ice and water in central European reservoirs.

PubMed

McKay, Robert M L; Prášil, Ondrej; Pechar, Libor; Lawrenz, Evelyn; Rozmarynowycz, Mark J; Bullerjahn, George S

2015-12-01

Abundant phytoplankton and bacteria were identified by high-throughput 16S rRNA tag Illumina sequencing of samples from water and ice phases collected during winter at commercial fish ponds and a sand pit lake within the UNESCO Třeboň Basin Biosphere Reserve, Czech Republic. Bacterial reads were dominated by Proteobacteria and Bacteroidetes. Despite dominance by members of just two phyla, UniFrac principal coordinates analysis of the bacterial community separated the water community of Klec fish pond, as well as the ice-associated community of Klec-Sand Pit from other samples. Both phytoplankton and cyanobacteria were represented with hundreds of sequence reads per sample, a finding corroborated by microscopy. In particular, ice from Klec-Sand Pit contained high contributions from photoautotrophs accounting for 25% of total reads with reads dominated by single operational taxonomic units (OTUs) of the cyanobacterium Planktothrix sp. and two filamentous diatoms. Dominant OTUs recovered from ice were largely absent (< 0.01%) from underlying water suggestive of low floristic similarity of phytoplankton partitioned between these phases. Photosynthetic characterization of phototrophs resident in water and ice analysed by variable chlorophyll a fluorescence showed that communities from both phases were photosynthetically active, thus supporting ice as viable habitat for phytoplankton in freshwater lakes and reservoirs. © 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.

Metagenomic insight of nitrogen metabolism in a tannery wastewater treatment plant bioaugmented with the microbial consortium BM-S-1.

PubMed

Sul, Woo-Jun; Kim, In-Soo; Ekpeghere, Kalu I; Song, Bongkeun; Kim, Bong-Soo; Kim, Hong-Gi; Kim, Jong-Tae; Koh, Sung-Cheol

2016-11-09

Nitrogen (N) removal in a tannery wastewater treatment plant was significantly enhanced by the bioaugmentation of the novel consortium BM-S-1. In order to identify dominant taxa responsible for N metabolisms in the different stages of the treatment process, Illumina MiSeq Sequencer was used to conduct metagenome sequencing of the microbial communities in the different stages of treatment system, including influent (I), buffering (B), primary aeration (PA), secondary aeration (SA) and sludge digestion (SD). Based on MG-RAST analysis, the dominant phyla were Proteobacteria, Bacteroidetes and Firmicutes in B, PA, SA and SD, whereas Firmicutes was the most dominant in I before augmentation. The augmentation increased the abundance of the denitrification genes found in the genera such as Ralstonia (nirS, norB and nosZ), Pseudomonas (narG, nirS and norB) and Escherichia (narG) in B and PA. In addition, Bacteroides, Geobacter, Porphyromonasand Wolinella carrying nrfA gene encoding dissimilatory nitrate reduction to ammonium were abundantly present in B and PA. This was corroborated with the higher total N removal in these two stages. Thus, metagenomic analysis was able to identify the dominant taxa responsible for dissimilatory N metabolisms in the tannery wastewater treatment system undergoing bioaugmentation. This metagenomic insight into the nitrogen metabolism will contribute to a successful monitoring and operation of the eco-friendly tannery wastewater treatment system.

Molecular Diagnostics in Autosomal Dominant Polycystic Kidney Disease: Utility and Limitations

PubMed Central

Zhao, Xiao; Paterson, Andrew D.; Zahirieh, Alireza; He, Ning; Wang, Kairong; Pei, York

2008-01-01

Background and objectives: Gene-based mutation screening is now available and has the potential to provide diagnostic confirmation or exclusion of autosomal dominant polycystic kidney disease. This study illustrates its utility and limitations in the clinical setting. Design, setting, participants, & measurements: Using a molecular diagnostic service, genomic DNA of one affected individual from each study family was screened for pathologic PKD1 and PKD2 mutations. Bidirectional sequencing was performed to identify sequence variants in all exons and splice junctions of both genes and to confirm the specific mutations in other family members. In two multiplex families, microsatellite markers were genotyped at both PDK1 and PKD2 loci, and pair-wise and multipoint linkage analysis was performed. Results: Three of five probands studied were referred for assessment of renal cystic disease without a family history of autosomal dominant polycystic kidney disease, and two others were younger at-risk members of families with autosomal dominant polycystic kidney disease being evaluated as living-related kidney donors. Gene-based mutation screening identified pathogenic mutations that provided confirmation or exclusion of disease in three probands, but in the other two, only unclassified variants were identified. In one proband in which mutation screening was indeterminate, DNA linkage studies provided strong evidence for disease exclusion. Conclusions: Gene-based mutation screening or DNA linkage analysis should be considered in individuals in whom the diagnosis of autosomal dominant polycystic kidney disease is uncertain because of a lack of family history or equivocal imaging results and in younger at-risk individuals who are being evaluated as living-related kidney donors. PMID:18077784

Origins of Protein Functions in Cells

NASA Technical Reports Server (NTRS)

Seelig, Burchard; Pohorille, Andrzej

2011-01-01

In modern organisms proteins perform a majority of cellular functions, such as chemical catalysis, energy transduction and transport of material across cell walls. Although great strides have been made towards understanding protein evolution, a meaningful extrapolation from contemporary proteins to their earliest ancestors is virtually impossible. In an alternative approach, the origin of water-soluble proteins was probed through the synthesis and in vitro evolution of very large libraries of random amino acid sequences. In combination with computer modeling and simulations, these experiments allow us to address a number of fundamental questions about the origins of proteins. Can functionality emerge from random sequences of proteins? How did the initial repertoire of functional proteins diversify to facilitate new functions? Did this diversification proceed primarily through drawing novel functionalities from random sequences or through evolution of already existing proto-enzymes? Did protein evolution start from a pool of proteins defined by a frozen accident and other collections of proteins could start a different evolutionary pathway? Although we do not have definitive answers to these questions yet, important clues have been uncovered. In one example (Keefe and Szostak, 2001), novel ATP binding proteins were identified that appear to be unrelated in both sequence and structure to any known ATP binding proteins. One of these proteins was subsequently redesigned computationally to bind GTP through introducing several mutations that introduce targeted structural changes to the protein, improve its binding to guanine and prevent water from accessing the active center. This study facilitates further investigations of individual evolutionary steps that lead to a change of function in primordial proteins. In a second study (Seelig and Szostak, 2007), novel enzymes were generated that can join two pieces of RNA in a reaction for which no natural enzymes are known. Recently it was found that, as in the previous case, the proteins have a structure unknown among modern enzymes. In this case, in vitro evolution started from a small, non-enzymatic protein. A similar selection process initiated from a library of random polypeptides is in progress. These results not only allow for estimating the occurrence of function in random protein assemblies but also provide evidence for the possibility of alternative protein worlds. Extant proteins might simply represent a frozen accident in the world of possible proteins. Alternative collections of proteins, even with similar functions, could originate alternative evolutionary paths.

Detection of Mixed Infection from Bacterial Whole Genome Sequence Data Allows Assessment of Its Role in Clostridium difficile Transmission

PubMed Central

Eyre, David W.; Cule, Madeleine L.; Griffiths, David; Crook, Derrick W.; Peto, Tim E. A.

2013-01-01

Bacterial whole genome sequencing offers the prospect of rapid and high precision investigation of infectious disease outbreaks. Close genetic relationships between microorganisms isolated from different infected cases suggest transmission is a strong possibility, whereas transmission between cases with genetically distinct bacterial isolates can be excluded. However, undetected mixed infections—infection with ≥2 unrelated strains of the same species where only one is sequenced—potentially impairs exclusion of transmission with certainty, and may therefore limit the utility of this technique. We investigated the problem by developing a computationally efficient method for detecting mixed infection without the need for resource-intensive independent sequencing of multiple bacterial colonies. Given the relatively low density of single nucleotide polymorphisms within bacterial sequence data, direct reconstruction of mixed infection haplotypes from current short-read sequence data is not consistently possible. We therefore use a two-step maximum likelihood-based approach, assuming each sample contains up to two infecting strains. We jointly estimate the proportion of the infection arising from the dominant and minor strains, and the sequence divergence between these strains. In cases where mixed infection is confirmed, the dominant and minor haplotypes are then matched to a database of previously sequenced local isolates. We demonstrate the performance of our algorithm with in silico and in vitro mixed infection experiments, and apply it to transmission of an important healthcare-associated pathogen, Clostridium difficile. Using hospital ward movement data in a previously described stochastic transmission model, 15 pairs of cases enriched for likely transmission events associated with mixed infection were selected. Our method identified four previously undetected mixed infections, and a previously undetected transmission event, but no direct transmission between the pairs of cases under investigation. These results demonstrate that mixed infections can be detected without additional sequencing effort, and this will be important in assessing the extent of cryptic transmission in our hospitals. PMID:23658511

Vulnerability assessment of chemical industry facilities in South Korea based on the chemical accident history

NASA Astrophysics Data System (ADS)

Heo, S.; Lee, W. K.; Jong-Ryeul, S.; Kim, M. I.

2016-12-01

The use of chemical compounds are keep increasing because of their use in manufacturing industry. Chemical accident is growing as the consequence of the chemical use increment. Devastating damages from chemical accidents are far enough to aware people's cautious about the risk of the chemical accident. In South Korea, Gumi Hydrofluoric acid leaking accident triggered the importance of risk management and emphasized the preventing the accident over the damage reducing process after the accident occurs. Gumi accident encouraged the government data base construction relate to the chemical accident. As the result of this effort Chemical Safety-Clearing-house (CSC) have started to record the chemical accident information and damages according to the Harmful Chemical Substance Control Act (HCSC). CSC provide details information about the chemical accidents from 2002 to present. The detail informations are including title of company, address, business type, accident dates, accident types, accident chemical compounds, human damages inside of the chemical industry facilities, human damage outside of the chemical industry facilities, financial damages inside of the chemical industry facilities, and financial damages outside of the chemical industry facilities, environmental damages and response to the chemical accident. Collected the chemical accident history of South Korea from 2002 to 2015 and provide the spatial information to the each accident records based on their address. With the spatial information, compute the data on ArcGIS for the spatial-temporal analysis. The spatial-temporal information of chemical accident is organized by the chemical accident types, damages, and damages on environment and conduct the spatial proximity with local community and environmental receptors. Find the chemical accident vulnerable area of South Korea from 2002 to 2015 and add the vulnerable area of total period to examine the historically vulnerable area from the chemical accident in South Korea.

Major Accidents (Gray Swans) Likelihood Modeling Using Accident Precursors and Approximate Reasoning.

PubMed

Khakzad, Nima; Khan, Faisal; Amyotte, Paul

2015-07-01

Compared to the remarkable progress in risk analysis of normal accidents, the risk analysis of major accidents has not been so well-established, partly due to the complexity of such accidents and partly due to low probabilities involved. The issue of low probabilities normally arises from the scarcity of major accidents' relevant data since such accidents are few and far between. In this work, knowing that major accidents are frequently preceded by accident precursors, a novel precursor-based methodology has been developed for likelihood modeling of major accidents in critical infrastructures based on a unique combination of accident precursor data, information theory, and approximate reasoning. For this purpose, we have introduced an innovative application of information analysis to identify the most informative near accident of a major accident. The observed data of the near accident were then used to establish predictive scenarios to foresee the occurrence of the major accident. We verified the methodology using offshore blowouts in the Gulf of Mexico, and then demonstrated its application to dam breaches in the United Sates. © 2015 Society for Risk Analysis.

An overview of Fukushima radionuclides measured in the northern hemisphere.

PubMed

Thakur, P; Ballard, S; Nelson, R

2013-08-01

The Great East Japan Earthquake and tsunami on March 11, 2011 resulted in the tragic accident at the Fukushima Nuclear Power Plant (NPP) and subsequently uncontrolled release of radioactive contaminants into the atmosphere. This review article attempts to compile and interpret data collected by various national and international monitoring networks in response to the Fukushima releases across the northern hemisphere. The majority of the releases occurred during the period March 12-22 with a maximum release phase from March 14-17, 2011. The radioactivity released was dominated by volatile fission products including isotopes of the noble gases (xenon and krypton), iodine, cesium, and tellurium. The radioactive gases and particles released in the accident were dispersed over the middle latitudes of the entire northern hemisphere and for the first time also measured in the southern Hemisphere. Isotopes of iodine and cesium were detected in air, water, milk and food samples collected across the entire northern hemisphere. Elevated levels of fission products were detected from March to May 2011 at many locations over the northern hemisphere. This article focuses on the most prevalent cesium and iodine isotopes, but other secondary isotopes are also discussed. Spatial and temporal patterns and differences are contrasted. The activity ratios of (131)I/(137)Cs and (134)Cs/(137)Cs measured at several locations are evaluated to gain an insight into the fuel burn-up, the inventory of radionuclides in the reactor and the isotopic signature of the accident. It is important to note that all of the radiation levels detected outside of Japan have been very low and are well below any level of public and environmental hazard. Published by Elsevier B.V.

Analysis of radiation safety for Small Modular Reactor (SMR) on PWR-100 MWe type

NASA Astrophysics Data System (ADS)

Udiyani, P. M.; Husnayani, I.; Deswandri; Sunaryo, G. R.

2018-02-01

Indonesia as an archipelago country, including big, medium and small islands is suitable to construction of Small Medium/Modular reactors. Preliminary technology assessment on various SMR has been started, indeed the SMR is grouped into Light Water Reactor, Gas Cooled Reactor, and Solid Cooled Reactor and from its site it is group into Land Based reactor and Water Based Reactor. Fukushima accident made people doubt about the safety of Nuclear Power Plant (NPP), which impact on the public perception of the safety of nuclear power plants. The paper will describe the assessment of safety and radiation consequences on site for normal operation and Design Basis Accident postulation of SMR based on PWR-100 MWe in Bangka Island. Consequences of radiation for normal operation simulated for 3 units SMR. The source term was generated from an inventory by using ORIGEN-2 software and the consequence of routine calculated by PC-Cream and accident by PC Cosyma. The adopted methodology used was based on site-specific meteorological and spatial data. According to calculation by PC-CREAM 08 computer code, the highest individual dose in site area for adults is 5.34E-02 mSv/y in ESE direction within 1 km distance from stack. The result of calculation is that doses on public for normal operation below 1mSv/y. The calculation result from PC Cosyma, the highest individual dose is 1.92.E+00 mSv in ESE direction within 1km distance from stack. The total collective dose (all pathway) is 3.39E-01 manSv, with dominant supporting from cloud pathway. Results show that there are no evacuation countermeasure will be taken based on the regulation of emergency.

An uncertainty analysis of the hydrogen source term for a station blackout accident in Sequoyah using MELCOR 1.8.5

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

Gauntt, Randall O.; Bixler, Nathan E.; Wagner, Kenneth Charles

2014-03-01

A methodology for using the MELCOR code with the Latin Hypercube Sampling method was developed to estimate uncertainty in various predicted quantities such as hydrogen generation or release of fission products under severe accident conditions. In this case, the emphasis was on estimating the range of hydrogen sources in station blackout conditions in the Sequoyah Ice Condenser plant, taking into account uncertainties in the modeled physics known to affect hydrogen generation. The method uses user-specified likelihood distributions for uncertain model parameters, which may include uncertainties of a stochastic nature, to produce a collection of code calculations, or realizations, characterizing themore » range of possible outcomes. Forty MELCOR code realizations of Sequoyah were conducted that included 10 uncertain parameters, producing a range of in-vessel hydrogen quantities. The range of total hydrogen produced was approximately 583kg 131kg. Sensitivity analyses revealed expected trends with respected to the parameters of greatest importance, however, considerable scatter in results when plotted against any of the uncertain parameters was observed, with no parameter manifesting dominant effects on hydrogen generation. It is concluded that, with respect to the physics parameters investigated, in order to further reduce predicted hydrogen uncertainty, it would be necessary to reduce all physics parameter uncertainties similarly, bearing in mind that some parameters are inherently uncertain within a range. It is suspected that some residual uncertainty associated with modeling complex, coupled and synergistic phenomena, is an inherent aspect of complex systems and cannot be reduced to point value estimates. The probabilistic analyses such as the one demonstrated in this work are important to properly characterize response of complex systems such as severe accident progression in nuclear power plants.« less

Status-Dependent Vasotocin Modulation of Dominance and Subordination in the Weakly Electric Fish Gymnotus omarorum.

PubMed

Perrone, Rossana; Silva, Ana C

2018-01-01

Dominant-subordinate status emerges from agonistic encounters. The weakly electric fish, Gymnotus omarorum , displays a clear-cut example of non-breeding territorial aggression. The asymmetry in the behavior of dominants and subordinates is outstanding. Dominants are highly aggressive and subordinates signal submission in a precise sequence of locomotor and electric traits: retreating, decreasing their electric organ discharge rate, and emitting transient electric signals. The hypothalamic neuropeptide arginine-vasotocin (AVT) and its mammalian homolog arginine-vasopressin, are key modulators of social behavior, known to adapt their actions to different contexts. By analyzing the effects of pharmacological manipulations of the AVT system in both dominants and subordinates, we show evidence of distinct status-dependent actions of AVT. We demonstrate an endogenous effect of AVT on dominants' aggression levels: blocking the V1a AVT receptor induced a significant decrease in dominants' attack rate. AVT administered to subordinates enhanced the expression of the electric signals of submission, without affecting subordinates' locomotor displays. This study contributes a clear example of status-dependent AVT modulation of agonistic behavior in teleosts, and reveals distinctive activation patterns of the AVT system between dominants and subordinates.

Diversity and Functional Analysis of Bacterial Communities Associated with Natural Hydrocarbon Seeps in Acidic Soils at Rainbow Springs, Yellowstone National Park

PubMed Central

Hamamura, Natsuko; Olson, Sarah H.; Ward, David M.; Inskeep, William P.

2005-01-01

In this paper we describe the bacterial communities associated with natural hydrocarbon seeps in nonthermal soils at Rainbow Springs, Yellowstone National Park. Soil chemical analysis revealed high sulfate concentrations and low pH values (pH 2.8 to 3.8), which are characteristic of acid-sulfate geothermal activity. The hydrocarbon composition of the seep soils consisted almost entirely of saturated, acyclic alkanes (e.g., n-alkanes with chain lengths of C15 to C30, as well as branched alkanes, predominately pristane and phytane). Bacterial populations present in the seep soils were phylogenetically characterized by 16S rRNA gene clone library analysis. The majority of the sequences recovered (>75%) were related to sequences of heterotrophic acidophilic bacteria, including Acidisphaera spp. and Acidiphilium spp. of the α-Proteobacteria. Clones related to the iron- and sulfur-oxidizing chemolithotroph Acidithiobacillus spp. were also recovered from one of the seep soils. Hydrocarbon-amended soil-sand mixtures were established to examine [14C]hexadecane mineralization and corresponding changes in the bacterial populations using denaturing gradient gel electrophoresis (DGGE) of 16S rRNA gene fragments. Approximately 50% of the [14C]hexadecane added was recovered as 14CO2 during an 80-day incubation, and this was accompanied by detection of heterotrophic acidophile-related sequences as dominant DGGE bands. An alkane-degrading isolate was cultivated, whose 16S rRNA gene sequence was identical to the sequence of a dominant DGGE band in the soil-sand mixture, as well as the clone sequence recovered most frequently from the original soil. This and the presence of an alkB gene homolog in this isolate confirmed the alkane degradation capability of one population indigenous to acidic hydrocarbon seep soils. PMID:16204508

Analysis of the Gull Fecal Microbial Community Reveals the Dominance of Catellicoccus marimammalium in Relation to Culturable Enterococci

PubMed Central

Koskey, Amber M.; Fisher, Jenny C.; Traudt, Mary F.; Newton, Ryan J.

2014-01-01

Gulls are prevalent in beach environments and can be a major source of fecal contamination. Gulls have been shown to harbor a high abundance of fecal indicator bacteria (FIB), such as Escherichia coli and enterococci, which can be readily detected as part of routine beach monitoring. Despite the ubiquitous presence of gull fecal material in beach environments, the associated microbial community is relatively poorly characterized. We generated comprehensive microbial community profiles of gull fecal samples using Roche 454 and Illumina MiSeq platforms to investigate the composition and variability of the gull fecal microbial community and to measure the proportion of FIB. Enterococcaceae and Enterobacteriaceae were the two most abundant families in our gull samples. Sequence comparisons between short-read data and nearly full-length 16S rRNA gene clones generated from the same samples revealed Catellicoccus marimammalium as the most numerous taxon among all samples. The identification of bacteria from gull fecal pellets cultured on membrane-Enterococcus indoxyl-β-d-glucoside (mEI) plates showed that the dominant sequences recovered in our sequence libraries did not represent organisms culturable on mEI. Based on 16S rRNA gene sequencing of gull fecal isolates cultured on mEI plates, 98.8% were identified as Enterococcus spp., 1.2% were identified as Streptococcus spp., and none were identified as C. marimammalium. Illumina deep sequencing indicated that gull fecal samples harbor significantly higher proportions of C. marimammalium 16S rRNA gene sequences (>50-fold) relative to typical mEI culturable Enterococcus spp. C. marimammalium therefore can be confidently utilized as a genetic marker to identify gull fecal pollution in the beach environment. PMID:24242244

Characterization and mapping of the human rhodopsin kinase gene and screening of the gene for mutations in patients with retinitis pigmentosa

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

Khani, S.C.; Lin, D.; Magovcevic, I.

1994-09-01

Rhodopsin kinase (RK) is a cytosolic enzyme in rod photoreceptors that initiates the deactivation of the phototransductions cascade by phosphorylating photoactivated rhodopsin. Although the cDNA sequence of bovine RK has been determined previously, no human cDNA or genomic sequence has thus far been available for genetic studies. In order to investigate the possible role of this candidate gene in retinitis pigmentosa (RP) and allied diseases, we have isolated and characterized human cDNA and genomic clones derived from the RK locus. The coding sequence of the human gene is 1692 nucleotides in length and is split into seven exons. The humanmore » and the bovine sequence show 84% identity at the nucleotide level and 92% identity at the amino acid level. Thus far, the intronic sequences flanking each exon except for one have been determined. We have also mapped the human RK gene to chromosome 13q34 using fluorescence in situ hybridization. To our knowledge, no RP gene has as yet been linked to this region. However, since the substrate for RK (rhodopsin) and other members of the phototransduction cascade have been implicated in the pathogenesis of RP, it is conceivable that defects in RK can also cause some forms of this disease. We are evaluating this possibility by screening DNA from 173 patients with autosomal recessive RP and 190 patients with autosomal dominant RP. So far, we have found 11 patients with variant bands. In one patient with autosomal dominant RP we discovered the missense change Ser536Leu. Cosegregation studies and further sequencing of the variant bands are currently underway.« less

Miocene and Pliocene lacustrine and fluvial sequences, Upper Ramparts and Canyon village, Porcupine river, east-central Alaska

USGS Publications Warehouse

Fouch, T.D.; Carter, L.D.; Kunk, Michael J.; Smith, C.A.S.; White, J.M.

1994-01-01

Cenozoic strata exposed along the Porcupine River between the Upper Ramparts and Canyon Village, Alaska, can be divided into five unconformity-bounded units (sequences) which are: lower and middle Miocene unit A, the white sandy fluvial sequence with peat beds; middle Miocene unit B, the basalt sequence-part B1 is basalt, and part B2 is organic-rich sedimentary beds; upper Miocene unit C, mudrock-dominated lake sequence; late Miocene or Pliocene to Pleistocene unit D, terrace gravels, detrital organic matter and associated sediments, and Holocene unit E, mixed sand and gravel-rich sediment and other sedimentary material including peat and eolian silt. The sequence (unit A) of lower and middle Miocene fluvial deposits formed in streams and on flood plains, just before the inception of local volanism. Fossil pollen from unit A suggests conifer-dominated regional forests and cool temperate climates. Peat beds and lake deposits from unit B contain pollen that indicates a warmer temperate climate coinciding with the middle Miocene thermal maximum. The lake deposits (unit C) downstream from the basalts accumulated in a small basin which resulted from a hydrologic system that was dammed in the late Miocene but breached soon thereafter. The lower part of the terrace gravels (unit D) expresses breaching of the dammed hydrologic system (of unit C). The Porcupine River became a major tributary of the Yukon River in late Pleistocene time when Laurentide ice blocked drainage from the Yukon interior basins causing meltwater to spill over the low divide separating it from the Porcupine River drainage initiating erosion and capture of the Yukon interior basins. ?? 1994.

Phylogenetic analysis of a spontaneous cocoa bean fermentation metagenome reveals new insights into its bacterial and fungal community diversity.

PubMed

Illeghems, Koen; De Vuyst, Luc; Papalexandratou, Zoi; Weckx, Stefan

2012-01-01

This is the first report on the phylogenetic analysis of the community diversity of a single spontaneous cocoa bean box fermentation sample through a metagenomic approach involving 454 pyrosequencing. Several sequence-based and composition-based taxonomic profiling tools were used and evaluated to avoid software-dependent results and their outcome was validated by comparison with previously obtained culture-dependent and culture-independent data. Overall, this approach revealed a wider bacterial (mainly γ-Proteobacteria) and fungal diversity than previously found. Further, the use of a combination of different classification methods, in a software-independent way, helped to understand the actual composition of the microbial ecosystem under study. In addition, bacteriophage-related sequences were found. The bacterial diversity depended partially on the methods used, as composition-based methods predicted a wider diversity than sequence-based methods, and as classification methods based solely on phylogenetic marker genes predicted a more restricted diversity compared with methods that took all reads into account. The metagenomic sequencing analysis identified Hanseniaspora uvarum, Hanseniaspora opuntiae, Saccharomyces cerevisiae, Lactobacillus fermentum, and Acetobacter pasteurianus as the prevailing species. Also, the presence of occasional members of the cocoa bean fermentation process was revealed (such as Erwinia tasmaniensis, Lactobacillus brevis, Lactobacillus casei, Lactobacillus rhamnosus, Lactococcus lactis, Leuconostoc mesenteroides, and Oenococcus oeni). Furthermore, the sequence reads associated with viral communities were of a restricted diversity, dominated by Myoviridae and Siphoviridae, and reflecting Lactobacillus as the dominant host. To conclude, an accurate overview of all members of a cocoa bean fermentation process sample was revealed, indicating the superiority of metagenomic sequencing over previously used techniques.

Whole exome sequencing frequently detects a monogenic cause in early onset nephrolithiasis and nephrocalcinosis.

PubMed

Daga, Ankana; Majmundar, Amar J; Braun, Daniela A; Gee, Heon Yung; Lawson, Jennifer A; Shril, Shirlee; Jobst-Schwan, Tilman; Vivante, Asaf; Schapiro, David; Tan, Weizhen; Warejko, Jillian K; Widmeier, Eugen; Nelson, Caleb P; Fathy, Hanan M; Gucev, Zoran; Soliman, Neveen A; Hashmi, Seema; Halbritter, Jan; Halty, Margarita; Kari, Jameela A; El-Desoky, Sherif; Ferguson, Michael A; Somers, Michael J G; Traum, Avram Z; Stein, Deborah R; Daouk, Ghaleb H; Rodig, Nancy M; Katz, Avi; Hanna, Christian; Schwaderer, Andrew L; Sayer, John A; Wassner, Ari J; Mane, Shrikant; Lifton, Richard P; Milosevic, Danko; Tasic, Velibor; Baum, Michelle A; Hildebrandt, Friedhelm

2018-01-01

The incidence of nephrolithiasis continues to rise. Previously, we showed that a monogenic cause could be detected in 11.4% of individuals with adult-onset nephrolithiasis or nephrocalcinosis and in 16.7-20.8% of individuals with onset before 18 years of age, using gene panel sequencing of 30 genes known to cause nephrolithiasis/nephrocalcinosis. To overcome the limitations of panel sequencing, we utilized whole exome sequencing in 51 families, who presented before age 25 years with at least one renal stone or with a renal ultrasound finding of nephrocalcinosis to identify the underlying molecular genetic cause of disease. In 15 of 51 families, we detected a monogenic causative mutation by whole exome sequencing. A mutation in seven recessive genes (AGXT, ATP6V1B1, CLDN16, CLDN19, GRHPR, SLC3A1, SLC12A1), in one dominant gene (SLC9A3R1), and in one gene (SLC34A1) with both recessive and dominant inheritance was detected. Seven of the 19 different mutations were not previously described as disease-causing. In one family, a causative mutation in one of 117 genes that may represent phenocopies of nephrolithiasis-causing genes was detected. In nine of 15 families, the genetic diagnosis may have specific implications for stone management and prevention. Several factors that correlated with the higher detection rate in our cohort were younger age at onset of nephrolithiasis/nephrocalcinosis, presence of multiple affected members in a family, and presence of consanguinity. Thus, we established whole exome sequencing as an efficient approach toward a molecular genetic diagnosis in individuals with nephrolithiasis/nephrocalcinosis who manifest before age 25 years. Copyright © 2017 International Society of Nephrology. Published by Elsevier Inc. All rights reserved.

Subsurface microbial diversity in deep-granitic-fracture water in Colorado

USGS Publications Warehouse

Sahl, J.W.; Schmidt, R.; Swanner, E.D.; Mandernack, K.W.; Templeton, A.S.; Kieft, Thomas L.; Smith, R.L.; Sanford, W.E.; Callaghan, R.L.; Mitton, J.B.; Spear, J.R.

2008-01-01

A microbial community analysis using 16S rRNA gene sequencing was performed on borehole water and a granite rock core from Henderson Mine, a >1,000-meter-deep molybdenum mine near Empire, CO. Chemical analysis of borehole water at two separate depths (1,044 m and 1,004 m below the mine entrance) suggests that a sharp chemical gradient exists, likely from the mixing of two distinct subsurface fluids, one metal rich and one relatively dilute; this has created unique niches for microorganisms. The microbial community analyzed from filtered, oxic borehole water indicated an abundance of sequences from iron-oxidizing bacteria (Gallionella spp.) and was compared to the community from the same borehole after 2 weeks of being plugged with an expandable packer. Statistical analyses with UniFrac revealed a significant shift in community structure following the addition of the packer. Phospholipid fatty acid (PLFA) analysis suggested that Nitrosomonadales dominated the oxic borehole, while PLFAs indicative of anaerobic bacteria were most abundant in the samples from the plugged borehole. Microbial sequences were represented primarily by Firmicutes, Proteobacteria, and a lineage of sequences which did not group with any identified bacterial division; phylogenetic analyses confirmed the presence of a novel candidate division. This "Henderson candidate division" dominated the clone libraries from the dilute anoxic fluids. Sequences obtained from the granitic rock core (1,740 m below the surface) were represented by the divisions Proteobacteria (primarily the family Ralstoniaceae) and Firmicutes. Sequences grouping within Ralstoniaceae were also found in the clone libraries from metal-rich fluids yet were absent in more dilute fluids. Lineage-specific comparisons, combined with phylogenetic statistical analyses, show that geochemical variance has an important effect on microbial community structure in deep, subsurface systems. Copyright ?? 2008, American Society for Microbiology. All Rights Reserved.

Subsurface Microbial Diversity in Deep-Granitic-Fracture Water in Colorado▿

PubMed Central

Sahl, Jason W.; Schmidt, Raleigh; Swanner, Elizabeth D.; Mandernack, Kevin W.; Templeton, Alexis S.; Kieft, Thomas L.; Smith, Richard L.; Sanford, William E.; Callaghan, Robert L.; Mitton, Jeffry B.; Spear, John R.

2008-01-01

A microbial community analysis using 16S rRNA gene sequencing was performed on borehole water and a granite rock core from Henderson Mine, a >1,000-meter-deep molybdenum mine near Empire, CO. Chemical analysis of borehole water at two separate depths (1,044 m and 1,004 m below the mine entrance) suggests that a sharp chemical gradient exists, likely from the mixing of two distinct subsurface fluids, one metal rich and one relatively dilute; this has created unique niches for microorganisms. The microbial community analyzed from filtered, oxic borehole water indicated an abundance of sequences from iron-oxidizing bacteria (Gallionella spp.) and was compared to the community from the same borehole after 2 weeks of being plugged with an expandable packer. Statistical analyses with UniFrac revealed a significant shift in community structure following the addition of the packer. Phospholipid fatty acid (PLFA) analysis suggested that Nitrosomonadales dominated the oxic borehole, while PLFAs indicative of anaerobic bacteria were most abundant in the samples from the plugged borehole. Microbial sequences were represented primarily by Firmicutes, Proteobacteria, and a lineage of sequences which did not group with any identified bacterial division; phylogenetic analyses confirmed the presence of a novel candidate division. This “Henderson candidate division” dominated the clone libraries from the dilute anoxic fluids. Sequences obtained from the granitic rock core (1,740 m below the surface) were represented by the divisions Proteobacteria (primarily the family Ralstoniaceae) and Firmicutes. Sequences grouping within Ralstoniaceae were also found in the clone libraries from metal-rich fluids yet were absent in more dilute fluids. Lineage-specific comparisons, combined with phylogenetic statistical analyses, show that geochemical variance has an important effect on microbial community structure in deep, subsurface systems. PMID:17981950

Diversity and functional analysis of bacterial communities associated with natural hydrocarbon seeps in acidic soils at Rainbow Springs, Yellowstone National Park.

PubMed

Hamamura, Natsuko; Olson, Sarah H; Ward, David M; Inskeep, William P

2005-10-01

In this paper we describe the bacterial communities associated with natural hydrocarbon seeps in nonthermal soils at Rainbow Springs, Yellowstone National Park. Soil chemical analysis revealed high sulfate concentrations and low pH values (pH 2.8 to 3.8), which are characteristic of acid-sulfate geothermal activity. The hydrocarbon composition of the seep soils consisted almost entirely of saturated, acyclic alkanes (e.g., n-alkanes with chain lengths of C15 to C30, as well as branched alkanes, predominately pristane and phytane). Bacterial populations present in the seep soils were phylogenetically characterized by 16S rRNA gene clone library analysis. The majority of the sequences recovered (>75%) were related to sequences of heterotrophic acidophilic bacteria, including Acidisphaera spp. and Acidiphilium spp. of the alpha-Proteobacteria. Clones related to the iron- and sulfur-oxidizing chemolithotroph Acidithiobacillus spp. were also recovered from one of the seep soils. Hydrocarbon-amended soil-sand mixtures were established to examine [14C]hexadecane mineralization and corresponding changes in the bacterial populations using denaturing gradient gel electrophoresis (DGGE) of 16S rRNA gene fragments. Approximately 50% of the [14C]hexadecane added was recovered as 14CO2 during an 80-day incubation, and this was accompanied by detection of heterotrophic acidophile-related sequences as dominant DGGE bands. An alkane-degrading isolate was cultivated, whose 16S rRNA gene sequence was identical to the sequence of a dominant DGGE band in the soil-sand mixture, as well as the clone sequence recovered most frequently from the original soil. This and the presence of an alkB gene homolog in this isolate confirmed the alkane degradation capability of one population indigenous to acidic hydrocarbon seep soils.

A novel deletion/insertion mutation in the mRNA transcribed from one {alpha}1(I) collagen allele in a family with dominant type III OI and germline mosaicism

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

Wang, O.; Masters, C.; Lewis, M.B.

1994-09-01

In an 8-year-old girl and her father, both of whom have severe type III OI, we have previously used RNA/RNA hybrid analysis to demonstrate a mismatch in the region of {alpha}1(I) mRNA coding for aa 558-861. We used SSCP to further localize the abnormality to a subregion coding for aa 579-679. This region was subcloned and sequenced. Each patient`s cDNA has a deletion of the sequences coding for the last residue of exon 34, and all of exons 35 and 36 (aa 604-639), followed by an insertion of 156 nt from the 3{prime}-end of intron 36. PCR amplification of leukocytemore » DNA from the patients and the clinically normal paternal grandmother yielded two fragments: a 1007 bp fragment predicted from normal genomic sequences and a 445 bp fragment. Subcloning and sequencing of the shorter genomic PCR product confirmed the presence of a 565 bp genomic deletion from the end of exon 34 to the middle of intron 36. The abnormal protein is apparently synthesized and incorporated into helix. The inserted nucleotides are in frame with the collagenous sequence and contain no stop codons. They encode a 52 aa non-collagenous region. The fibroblast procollagen of the patients has both normal and electrophoretically delayed pro{alpha}(I) bands. The electrophoretically delayed procollagen is very sensitive to pepsin or trypsin digestion, as predicted by its non-collagenous sequence, and cannot be visualized as collagen. This unique OI collagen mutation is an excellent candidate for molecular targeting to {open_quotes}turn off{close_quotes} a dominant mutant allele.« less

Tidal-bundle sequences in the Jordan Sandstone (Upper Cambrian), southeastern Minnesota, U.S.A.: Evidence for tides along inboard shorelines of the Sauk Epicontinental Sea

USGS Publications Warehouse

Tape, C.H.; Cowan, Clinton A.; Runkel, Anthony C.

2003-01-01

This study documents for the first time tidal bundling in a lower Paleozoic sheet sandstone from the cratonic interior of North America, providing insights into the hydrodynamics of ancient epicontinental seas. The Jordan Sandstone (Upper Cambrian) in the Upper Mississippi Valley contains large-scale planar tabular cross-sets with tidal-bundle sequences, which were analyzed in detail at an exceptional exposure. Tidal-bundle sequences (neap-spring-neap cycles) were delineated by foreset thickening-thinning patterns and composite shale drapes, the latter of which represent accumulations of mud during the neap tides of neap-spring-neap tidal cycles. Fourier analysis of the bundle thickness data from the 26 measurable bundle sequences revealed cycles ranging from 15 to 34 bundles per sequence, which suggests a semidiurnal or mixed tidal system along this part of the Late Cambrian shoreline. We extend the tidal interpretation to widespread occurrences of the same facies in outcrops of lesser quality, where the facies is recognizable but too few bundles are exposed for tidal cycles to be measured. By doing so, this study shows that tidally generated deposits have a significant geographic and temporal extent in Upper Cambrian strata of central mid-continent North America. The deposition and preservation of tidal facies was related to the intermittent development of shoreline embayments during transgressions. The tidally dominated deposits filled ravined topographies that were repeatedly developed on the updip parts of the shoreface. Resulting coastal geomorphologies, accompanied perhaps by larger-scale changes in basinal conditions and/or configuration, led to changes in depositional conditions from wave-dominated to tide-dominated. Outcrops of the Jordan Sandstone tidal facies in the Upper Mississippi Valley represent the farthest inboard recorded transmission of ocean-generated tides in the Laurentian epicontinental seas, demonstrating that tidal currents were significant agents in the transport of sand along the far cratonic interior shorelines of Cambrian North America. The results of this study improve the facies-level understanding of the genesis of sheet sandstones. Furthermore, tidalites documented here occur in a specific position within a sequence stratigraphic architecture for the Jordan Sandstone. This provides a framework to compare these ancient deposits and processes to younger (e.g., Carboniferous) epicontinental systems where stratal and sediment dynamics are better documented. ?? 2003, SEPM (Society for Sedimentary Geology).

Control of transcriptional pausing by biased thermal fluctuations on repetitive genomic sequences

PubMed Central

Imashimizu, Masahiko; Afek, Ariel; Takahashi, Hiroki; Lubkowska, Lucyna; Lukatsky, David B.

2016-01-01

In the process of transcription elongation, RNA polymerase (RNAP) pauses at highly nonrandom positions across genomic DNA, broadly regulating transcription; however, molecular mechanisms responsible for the recognition of such pausing positions remain poorly understood. Here, using a combination of statistical mechanical modeling and high-throughput sequencing and biochemical data, we evaluate the effect of thermal fluctuations on the regulation of RNAP pausing. We demonstrate that diffusive backtracking of RNAP, which is biased by repetitive DNA sequence elements, causes transcriptional pausing. This effect stems from the increased microscopic heterogeneity of an elongation complex, and thus is entropy-dominated. This report shows a linkage between repetitive sequence elements encoded in the genome and regulation of RNAP pausing driven by thermal fluctuations. PMID:27830653

A single determinant dominates the rate of yeast protein evolution.

PubMed

Drummond, D Allan; Raval, Alpan; Wilke, Claus O

2006-02-01

A gene's rate of sequence evolution is among the most fundamental evolutionary quantities in common use, but what determines evolutionary rates has remained unclear. Here, we carry out the first combined analysis of seven predictors (gene expression level, dispensability, protein abundance, codon adaptation index, gene length, number of protein-protein interactions, and the gene's centrality in the interaction network) previously reported to have independent influences on protein evolutionary rates. Strikingly, our analysis reveals a single dominant variable linked to the number of translation events which explains 40-fold more variation in evolutionary rate than any other, suggesting that protein evolutionary rate has a single major determinant among the seven predictors. The dominant variable explains nearly half the variation in the rate of synonymous and protein evolution. We show that the two most commonly used methods to disentangle the determinants of evolutionary rate, partial correlation analysis and ordinary multivariate regression, produce misleading or spurious results when applied to noisy biological data. We overcome these difficulties by employing principal component regression, a multivariate regression of evolutionary rate against the principal components of the predictor variables. Our results support the hypothesis that translational selection governs the rate of synonymous and protein sequence evolution in yeast.

Autosomal-dominant Meesmann epithelial corneal dystrophy without an exon mutation in the keratin-3 or keratin-12 gene in a Chinese family.

PubMed

Cao, Wei; Yan, Ming; Hao, QianYun; Wang, ShuLin; Wu, LiHua; Liu, Qing; Li, MingYan; Biddle, Fred G; Wu, Wei

2013-04-01

Meesmann epithelial corneal dystrophy (MECD) is a dominantly inherited disorder, characterized by fragility of the anterior corneal epithelium and formation of intraepithelial microcysts. It has been described in a number of different ancestral groups. To date, all reported cases of MECD have been associated with either a single mutation in one exon of the keratin-3 gene (KRT3) or a single mutation in one of two exons of the keratin-12 gene (KRT12). Each mutation leads to a predicted amino acid change in the respective keratin-3 or keratin-12 proteins that combine to form the corneal-specific heterodimeric intermediate filament protein. This case report describes a four-generation Chinese kindred with typical autosomal-dominant MECD. Exon sequencing of KRT3 and KRT12 in six affected and eight unaffected individuals (including two spouses) did not detect any mutations or nucleotide sequence variants. This kindred demonstrates that single mis-sense mutations may be sufficient but are not required in all individuals with the MECD phenotype. It provides a unique opportunity to investigate further genomic and functional heterogeneity in MECD.

49 CFR 837.3 - Published reports, material contained in the public accident investigation dockets, and accident...

Code of Federal Regulations, 2014 CFR

2014-10-01

... public accident investigation dockets, and accident database data. 837.3 Section 837.3 Transportation... investigation dockets, and accident database data. (a) Demands for material contained in the NTSB's official public docket files of its accident investigations, or its computerized accident database(s) shall be...

49 CFR 837.3 - Published reports, material contained in the public accident investigation dockets, and accident...

Code of Federal Regulations, 2012 CFR

2012-10-01

... public accident investigation dockets, and accident database data. 837.3 Section 837.3 Transportation... investigation dockets, and accident database data. (a) Demands for material contained in the NTSB's official public docket files of its accident investigations, or its computerized accident database(s) shall be...

49 CFR 837.3 - Published reports, material contained in the public accident investigation dockets, and accident...

Code of Federal Regulations, 2010 CFR

2010-10-01

... public accident investigation dockets, and accident database data. 837.3 Section 837.3 Transportation... investigation dockets, and accident database data. (a) Demands for material contained in the NTSB's official public docket files of its accident investigations, or its computerized accident database(s) shall be...

49 CFR 837.3 - Published reports, material contained in the public accident investigation dockets, and accident...

Code of Federal Regulations, 2013 CFR

2013-10-01

... public accident investigation dockets, and accident database data. 837.3 Section 837.3 Transportation... investigation dockets, and accident database data. (a) Demands for material contained in the NTSB's official public docket files of its accident investigations, or its computerized accident database(s) shall be...

49 CFR 837.3 - Published reports, material contained in the public accident investigation dockets, and accident...

Code of Federal Regulations, 2011 CFR

2011-10-01

... public accident investigation dockets, and accident database data. 837.3 Section 837.3 Transportation... investigation dockets, and accident database data. (a) Demands for material contained in the NTSB's official public docket files of its accident investigations, or its computerized accident database(s) shall be...

Comparative Genomics of Bacillus species and its Relevance in Industrial Microbiology.

PubMed

Sharma, Archana; Satyanarayana, T

2013-01-01

With the advent of high throughput sequencing platforms and relevant analytical tools, the rate of microbial genome sequencing has accelerated which has in turn led to better understanding of microbial molecular biology and genetics. The complete genome sequences of important industrial organisms provide opportunities for human health, industry, and the environment. Bacillus species are the dominant workhorses in industrial fermentations. Today, genome sequences of several Bacillus species are available, and comparative genomics of this genus helps in understanding their physiology, biochemistry, and genetics. The genomes of these bacterial species are the sources of many industrially important enzymes and antibiotics and, therefore, provide an opportunity to tailor enzymes with desired properties to suit a wide range of applications. A comparative account of strengths and weaknesses of the different sequencing platforms are also highlighted in the review.

[Occupational accidents in an oil refinery in Brazil].

PubMed

Souza, Carlos Augusto Vaz de; Freitas, Carlos Machado de

2002-10-01

Work in oil refineries involves the risk of minor to major accidents. National data show the impact of accidents on this industry. A study was carried out to describe accident profile and evaluate the adequacy of accident reporting system. Data on all accidents reported in an oil refinery in the state of Rio de Janeiro for the year 1997 were organized and analyzed. The study population consisted of 153 injury cases, 83 hired and 69 contracted workers. The variables were: type of accident, operation mode and position of the worker injured. Among hired workers, minor accidents predominated (54.2%) and they occurred during regular operation activities (62.9%). Among contracted workers, there also predominated minor accidents (75.5%) in a higher percentage, but they occurred mainly during maintenance activities (96.8%). The study results showed that there is a predominance of accidents in lower hierarchy workers, and these accidents occur mainly during maintenance activities. There is a need to improve the company's accident reporting system and accident investigation procedures.

Final safety analysis report for the Galileo Mission: Volume 2: Book 1, Accident model document

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

Not Available

The Accident Model Document (AMD) is the second volume of the three volume Final Safety Analysis Report (FSAR) for the Galileo outer planetary space science mission. This mission employs Radioisotope Thermoelectric Generators (RTGs) as the prime electrical power sources for the spacecraft. Galileo will be launched into Earth orbit using the Space Shuttle and will use the Inertial Upper Stage (IUS) booster to place the spacecraft into an Earth escape trajectory. The RTG's employ silicon-germanium thermoelectric couples to produce electricity from the heat energy that results from the decay of the radioisotope fuel, Plutonium-238, used in the RTG heat source.more » The heat source configuration used in the RTG's is termed General Purpose Heat Source (GPHS), and the RTG's are designated GPHS-RTGs. The use of radioactive material in these missions necessitates evaluations of the radiological risks that may be encountered by launch complex personnel as well as by the Earth's general population resulting from postulated malfunctions or failures occurring in the mission operations. The FSAR presents the results of a rigorous safety assessment, including substantial analyses and testing, of the launch and deployment of the RTGs for the Galileo mission. This AMD is a summary of the potential accident and failure sequences which might result in fuel release, the analysis and testing methods employed, and the predicted source terms. Each source term consists of a quantity of fuel released, the location of release and the physical characteristics of the fuel released. Each source term has an associated probability of occurrence. 27 figs., 11 tabs.« less

Methodology, status and plans for development and assessment of the code ATHLET

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

Teschendorff, V.; Austregesilo, H.; Lerchl, G.

1997-07-01

The thermal-hydraulic computer code ATHLET (Analysis of THermal-hydraulics of LEaks and Transients) is being developed by the Gesellschaft fuer Anlagen- und Reaktorsicherheit (GRS) for the analysis of anticipated and abnormal plant transients, small and intermediate leaks as well as large breaks in light water reactors. The aim of the code development is to cover the whole spectrum of design basis and beyond design basis accidents (without core degradation) for PWRs and BWRs with only one code. The main code features are: advanced thermal-hydraulics; modular code architecture; separation between physical models and numerical methods; pre- and post-processing tools; portability. The codemore » has features that are of special interest for applications to small leaks and transients with accident management, e.g. initialization by a steady-state calculation, full-range drift-flux model, dynamic mixture level tracking. The General Control Simulation Module of ATHLET is a flexible tool for the simulation of the balance-of-plant and control systems including the various operator actions in the course of accident sequences with AM measures. The code development is accompained by a systematic and comprehensive validation program. A large number of integral experiments and separate effect tests, including the major International Standard Problems, have been calculated by GRS and by independent organizations. The ATHLET validation matrix is a well balanced set of integral and separate effects tests derived from the CSNI proposal emphasizing, however, the German combined ECC injection system which was investigated in the UPTF, PKL and LOBI test facilities.« less

Microbial succession and the functional potential during the fermentation of Chinese soy sauce brine

PubMed Central

Sulaiman, Joanita; Gan, Han Ming; Yin, Wai-Fong; Chan, Kok-Gan

2014-01-01

The quality of traditional Chinese soy sauce is determined by microbial communities and their inter-related metabolic roles in the fermentation tank. In this study, traditional Chinese soy sauce brine samples were obtained periodically to monitor the transitions of the microbial population and functional properties during the 6 months of fermentation process. Whole genome shotgun method revealed that the fermentation brine was dominated by the bacterial genus Weissella and later dominated by the fungal genus Candida. Metabolic reconstruction of the metagenome sequences demonstrated a characteristic profile of heterotrophic fermentation of proteins and carbohydrates. This was supported by the detection of ethanol with stable decrease of pH values. To the best of our knowledge, this is the first study that explores the temporal changes in microbial successions over a period of 6 months, through metagenome shotgun sequencing in traditional Chinese soy sauce fermentation and the biological processes therein. PMID:25400624

Microbial succession and the functional potential during the fermentation of Chinese soy sauce brine.

PubMed

Sulaiman, Joanita; Gan, Han Ming; Yin, Wai-Fong; Chan, Kok-Gan

2014-01-01

The quality of traditional Chinese soy sauce is determined by microbial communities and their inter-related metabolic roles in the fermentation tank. In this study, traditional Chinese soy sauce brine samples were obtained periodically to monitor the transitions of the microbial population and functional properties during the 6 months of fermentation process. Whole genome shotgun method revealed that the fermentation brine was dominated by the bacterial genus Weissella and later dominated by the fungal genus Candida. Metabolic reconstruction of the metagenome sequences demonstrated a characteristic profile of heterotrophic fermentation of proteins and carbohydrates. This was supported by the detection of ethanol with stable decrease of pH values. To the best of our knowledge, this is the first study that explores the temporal changes in microbial successions over a period of 6 months, through metagenome shotgun sequencing in traditional Chinese soy sauce fermentation and the biological processes therein.

[Investigation of bacterial diversity in the biological desulfurization reactor for treating high salinity wastewater by the 16S rDNA cloning method].

PubMed

Liu, Wei-Guo; Liang, Cun-Zhen; Yang, Jin-Sheng; Wang, Gui-Ping; Liu, Miao-Miao

2013-02-01

The bacterial diversity in the biological desulfurization reactor operated continuously for 1 year was studied by the 16S rDNA cloning and sequencing method. Forty clones were randomly selected and their partial 16S rDNA genes (ca. 1,400 bp) were sequenced and blasted. The results indicated that there were dominant bacterias in the biological desulfurization reactor, where 33 clones belonged to 3 different published phyla, while 1 clone belonged to unknown phylum. The dominant bacterial community in the system was Proteobacteria, which accounted for 85.3%. The bacterial community succession was as follows: the gamma-Proteobacteria(55.9%), beta-Proteobacteria(17.6%), Actinobacteridae (8.8%), delta-Proteobacteria (5.9%) , alpha-Proteobacteria(5.9%), and Sphingobacteria (2.9%). Halothiobacillus sp. ST15 and Thiobacillus sp. UAM-I were the major desulfurization strains.

Sequential effects after practice with the dominant and non-dominant hand on the acquisition of a sliding task in schoolchildren.

PubMed

Senff, Oliver; Weigelt, Matthias

2011-03-01

This study was designed to investigate sequential effects after practice with the dominant and non-dominant hand on the acquisition of a new motor task. A total of 64 middle school children were asked to practise a cent-slide task, which required them to slide coins from one side of a cardboard into a circular target on the opposite side. Four groups practised this task within different practice schedules: (1) participants practised only with their dominant hand (right-only group); (2) participants used only their non-dominant hand (left-only group); (3) participants started to practise the skill with their dominant hand and then switched to their non-dominant hand (right-to-left group); or (4) participants started to practise the skill with their non-dominant hand and then switched to their dominant hand (left-to-right group). The acquisition of the task was facilitated after initial practice with the non-dominant hand. This was reflected in a better retention of the task and a stronger performance under a modified testing situation of the left-to-right group when compared to all other groups. Also, the left-only group showed larger interlimb transfer effects to the untrained hand than the right-only group. It is concluded that the sequence in which the dominant and non-dominant hands are used to practise influences the acquisition of new motor tasks.

Hydrochemical evolution and groundwater flow processes in the Galilee and Eromanga basins, Great Artesian Basin, Australia: a multivariate statistical approach.

PubMed

Moya, Claudio E; Raiber, Matthias; Taulis, Mauricio; Cox, Malcolm E

2015-03-01

The Galilee and Eromanga basins are sub-basins of the Great Artesian Basin (GAB). In this study, a multivariate statistical approach (hierarchical cluster analysis, principal component analysis and factor analysis) is carried out to identify hydrochemical patterns and assess the processes that control hydrochemical evolution within key aquifers of the GAB in these basins. The results of the hydrochemical assessment are integrated into a 3D geological model (previously developed) to support the analysis of spatial patterns of hydrochemistry, and to identify the hydrochemical and hydrological processes that control hydrochemical variability. In this area of the GAB, the hydrochemical evolution of groundwater is dominated by evapotranspiration near the recharge area resulting in a dominance of the Na-Cl water types. This is shown conceptually using two selected cross-sections which represent discrete groundwater flow paths from the recharge areas to the deeper parts of the basins. With increasing distance from the recharge area, a shift towards a dominance of carbonate (e.g. Na-HCO3 water type) has been observed. The assessment of hydrochemical changes along groundwater flow paths highlights how aquifers are separated in some areas, and how mixing between groundwater from different aquifers occurs elsewhere controlled by geological structures, including between GAB aquifers and coal bearing strata of the Galilee Basin. The results of this study suggest that distinct hydrochemical differences can be observed within the previously defined Early Cretaceous-Jurassic aquifer sequence of the GAB. A revision of the two previously recognised hydrochemical sequences is being proposed, resulting in three hydrochemical sequences based on systematic differences in hydrochemistry, salinity and dominant hydrochemical processes. The integrated approach presented in this study which combines different complementary multivariate statistical techniques with a detailed assessment of the geological framework of these sedimentary basins, can be adopted in other complex multi-aquifer systems to assess hydrochemical evolution and its geological controls. Copyright © 2014 Elsevier B.V. All rights reserved.

Microbial Communities on Seafloor Basalts at Dorado Outcrop Reflect Level of Alteration and Highlight Global Lithic Clades

PubMed Central

Lee, Michael D.; Walworth, Nathan G.; Sylvan, Jason B.; Edwards, Katrina J.; Orcutt, Beth N.

2015-01-01

Areas of exposed basalt along mid-ocean ridges and at seafloor outcrops serve as conduits of fluid flux into and out of a subsurface ocean, and microbe–mineral interactions can influence alteration reactions at the rock–water interface. Located on the eastern flank of the East Pacific Rise, Dorado Outcrop is a site of low-temperature (<20°C) hydrothermal venting and represents a new end-member in the current survey of seafloor basalt biomes. Consistent with prior studies, a survey of 16S rRNA gene sequence diversity using universal primers targeting the V4 hypervariable region revealed much greater richness and diversity on the seafloor rocks than in surrounding seawater. Overall, Gamma-, Alpha-, and Deltaproteobacteria, and Thaumarchaeota dominated the sequenced communities, together making up over half of the observed diversity, though bacterial sequences were more abundant than archaeal in all samples. The most abundant bacterial reads were closely related to the obligate chemolithoautotrophic, sulfur-oxidizing Thioprofundum lithotrophicum, suggesting carbon and sulfur cycling as dominant metabolic pathways in this system. Representatives of Thaumarchaeota were detected in relatively high abundance on the basalts in comparison to bottom water, possibly indicating ammonia oxidation. In comparison to other sequence datasets from globally distributed seafloor basalts, this study reveals many overlapping and cosmopolitan phylogenetic groups and also suggests that substrate age correlates with community structure. PMID:26779122

A dominant variant in the PDE1C gene is associated with nonsyndromic hearing loss.

PubMed

Wang, Li; Feng, Yong; Yan, Denise; Qin, Litao; Grati, M'hamed; Mittal, Rahul; Li, Tao; Sundhari, Abhiraami Kannan; Liu, Yalan; Chapagain, Prem; Blanton, Susan H; Liao, Shixiu; Liu, Xuezhong

2018-06-02

Identification of genes with variants causing non-syndromic hearing loss (NSHL) is challenging due to genetic heterogeneity. The difficulty is compounded by technical limitations that in the past prevented comprehensive gene identification. Recent advances in technology, using targeted capture and next-generation sequencing (NGS), is changing the face of gene identification and making it possible to rapidly and cost-effectively sequence the whole human exome. Here, we characterize a five-generation Chinese family with progressive, postlingual autosomal dominant nonsyndromic hearing loss (ADNSHL). By combining population-specific mutation arrays, targeted deafness genes panel, whole exome sequencing (WES), we identified PDE1C (Phosphodiesterase 1C) c.958G>T (p.A320S) as the disease-associated variant. Structural modeling insights into p.A320S strongly suggest that the sequence alteration will likely affect the substrate-binding pocket of PDE1C. By whole-mount immunofluorescence on postnatal day 3 mouse cochlea, we show its expression in outer (OHC) and inner (IHC) hair cells cytosol co-localizing with Lamp-1 in lysosomes. Furthermore, we provide evidence that the variant alters the PDE1C hydrolytic activity for both cyclic adenosine monophosphate (cAMP) and cyclic guanosine monophosphate (cGMP). Collectively, our findings indicate that the c.958G>T variant in PDE1C may disrupt the cross talk between cGMP-signaling and cAMP pathways in Ca 2+ homeostasis.

Exome Sequencing Identifies a Novel CEACAM16 Mutation Associated with Autosomal Dominant Nonsyndromic Hearing Loss DFNA4B in a Chinese Family

PubMed Central

He, Chufeng; Li, Haibo; Qing, Jie; Grati, Mhamed; Hu, Zhengmao; Li, Jiada; Hu, Yiqiao; Xia, Kun; Mei, Lingyun; Wang, Xingwei; Yu, Jianjun; Chen, Hongsheng; Jiang, Lu; Liu, Yalan; Men, Meichao; Zhang, Hailin; Guan, Liping; Xiao, Jingjing; Zhang, Jianguo; Liu, Xuezhong; Feng, Yong

2014-01-01

Autosomal dominant nonsyndromic hearing loss (ADNSHL/DFNA) is a highly genetically heterogeneous disorder. Hitherto only about 30 ADNSHL-causing genes have been identified and many unknown genes remain to be discovered. In this research, genome-wide linkage analysis mapped the disease locus to a 4.3 Mb region on chromosome 19q13 in SY-026, a five-generation nonconsanguineous Chinese family affected by late-onset and progressive ADNSHL. This linkage region showed partial overlap with the previously reported DFNA4. Simultaneously, probands were analyzed using exome capture followed by next generation sequencing. Encouragingly, a heterozygous missense mutation, c.505G>A (p.G169R) in exon 3 of the CEACAM16 gene (carcinoembryonic antigen-related cell adhesion molecule 16), was identified via this combined strategy. Sanger sequencing verified that the mutation co-segregated with hearing loss in the family and that it was not present in 200 unrelated control subjects with matched ancestry. This is the second report in the literature of a family with ADNSHL caused by CEACAM16 mutation. Immunofluorescence staining and Western blots also prove CEACAM16 to be a secreted protein. Furthermore, our studies in transfected HEK293T cells show that the secretion efficacy of the mutant CEACAM16 is much lower than that of the wild-type, suggesting a deleterious effect of the sequence variant. PMID:25589040

Exome sequencing identifies a novel CEACAM16 mutation associated with autosomal dominant nonsyndromic hearing loss DFNA4B in a Chinese family.

PubMed

Wang, Honghan; Wang, Xinwei; He, Chufeng; Li, Haibo; Qing, Jie; Grati, Mhamed; Hu, Zhengmao; Li, Jiada; Hu, Yiqiao; Xia, Kun; Mei, Lingyun; Wang, Xingwei; Yu, Jianjun; Chen, Hongsheng; Jiang, Lu; Liu, Yalan; Men, Meichao; Zhang, Hailin; Guan, Liping; Xiao, Jingjing; Zhang, Jianguo; Liu, Xuezhong; Feng, Yong

2015-03-01

Autosomal dominant nonsyndromic hearing loss (ADNSHL/DFNA) is a highly genetically heterogeneous disorder. Hitherto only about 30 ADNSHL-causing genes have been identified and many unknown genes remain to be discovered. In this research, genome-wide linkage analysis mapped the disease locus to a 4.3 Mb region on chromosome 19q13 in SY-026, a five-generation nonconsanguineous Chinese family affected by late-onset and progressive ADNSHL. This linkage region showed partial overlap with the previously reported DFNA4. Simultaneously, probands were analyzed using exome capture followed by next-generation sequencing. Encouragingly, a heterozygous missense mutation, c.505G>A (p.G169R) in exon 3 of the CEACAM16 gene (carcinoembryonic antigen-related cell adhesion molecule 16), was identified via this combined strategy. Sanger sequencing verified that the mutation co-segregated with hearing loss in the family and that it was not present in 200 unrelated control subjects with matched ancestry. This is the second report in the literature of a family with ADNSHL caused by CEACAM16 mutation. Immunofluorescence staining and western blots also prove CEACAM16 to be a secreted protein. Furthermore, our studies in transfected HEK293T cells show that the secretion efficacy of the mutant CEACAM16 is much lower than that of the wild type, suggesting a deleterious effect of the sequence variant.

Sequencing Bands of Ribosomal Intergenic Spacer Analysis Fingerprints for Characterization and Microscale Distribution of Soil Bacterium Populations Responding to Mercury Spiking

PubMed Central

Ranjard, Lionel; Brothier, Elisabeth; Nazaret, Sylvie

2000-01-01

Two major emerging bands (a 350-bp band and a 650-bp band) within the RISA (ribosomal intergenic spacer analysis) profile of a soil bacterial community spiked with Hg(II) were selected for further identification of the populations involved in the response of the community to the added metal. The bands were cut out from polyacrylamide gels, cloned, characterized by restriction analysis, and sequenced for phylogenetic affiliation of dominant clones. The sequences were the intergenic spacer between the rrs and rrl genes and the first 130 nucleotides of the rrl gene. Comparison of sequences derived from the 350-bp band to The GenBank database permitted us to identify the bacteria as being mostly close relatives to low G+C firmicutes (Clostridium-like genera), while the 650-bp band permitted us to identify the bacteria as being mostly close relatives to β-proteobacteria (Ralstonia-like genera). Oligonucleotide probes specific for the identified dominant bacteria were designed and hybridized with the RISA profiles derived from the control and spiked communities. These studies confirmed the contribution of these populations to the community response to the metal. Hybridization of the RISA profiles from subcommunities (bacterial pools associated with different soil microenvironments) also permitted to characterize the distribution and the dynamics of these populations at a microscale level following mercury spiking. PMID:11097911

Analysis of National Major Work Safety Accidents in China, 2003–2012

PubMed Central

YE, Yunfeng; ZHANG, Siheng; RAO, Jiaming; WANG, Haiqing; LI, Yang; WANG, Shengyong; DONG, Xiaomei

2016-01-01

Background: This study provides a national profile of major work safety accidents in China, which cause more than 10 fatalities per accident, intended to provide scientific basis for prevention measures and strategies to reduce major work safety accidents and deaths. Methods: Data from 2003–2012 Census of major work safety accidents were collected from State Administration of Work Safety System (SAWS). Published literature and statistical yearbook were also included to implement information. We analyzed the frequency of accidents and deaths, trend, geographic distribution and injury types. Additionally, we discussed the severity and urgency of emergency rescue by types of accidents. Results: A total of 877 major work safety accidents were reported, resulting in 16,795 deaths and 9,183 injuries. The numbers of accidents and deaths, mortality rate and incidence of major accidents have declined in recent years. The mortality rate and incidence was 0.71 and 1.20 per 106 populations in 2012, respectively. Transportation and mining contributed to the highest number of major accidents and deaths. Major aviation and railway accidents caused more casualties per incident, while collapse, machinery, electrical shock accidents and tailing dam accidents were the most severe situation that resulted in bigger proportion of death. Conclusion: Ten years’ major work safety accident data indicate that the frequency of accidents and number of eaths was declined and several safety concerns persist in some segments. PMID:27057515

Classification of circulation type sequences applied to snow avalanches over the eastern Pyrenees (Andorra and Catalonia)

NASA Astrophysics Data System (ADS)

Esteban, Pere; Beck, Christoph; Philipp, Andreas

2010-05-01

Using data associated with accidents or damages caused by snow avalanches over the eastern Pyrenees (Andorra and Catalonia) several atmospheric circulation type catalogues have been obtained. For this purpose, different circulation type classification methods based on Principal Component Analysis (T-mode and S-mode using the extreme scores) and on optimization procedures (Improved K-means and SANDRA) were applied . Considering the characteristics of the phenomena studied, not only single day circulation patterns were taken into account but also sequences of circulation types of varying length. Thus different classifications with different numbers of types and for different sequence lengths were obtained using the different classification methods. Simple between type variability, within type variability, and outlier detection procedures have been applied for selecting the best result concerning snow avalanches type classifications. Furthermore, days without occurrence of the hazards were also related to the avalanche centroids using pattern-correlations, facilitating the calculation of the anomalies between hazardous and no hazardous days, and also frequencies of occurrence of hazardous events for each circulation type. Finally, the catalogues statistically considered the best results are evaluated using the avalanche forecaster expert knowledge. Consistent explanation of snow avalanches occurrence by means of circulation sequences is obtained, but always considering results from classifications with different sequence length. This work has been developed in the framework of the COST Action 733 (Harmonisation and Applications of Weather Type Classifications for European regions).

Accident history, risk perception and traffic safe behaviour.

PubMed

Ngueutsa, Robert; Kouabenan, Dongo Rémi

2017-09-01

This study clarifies the associations between accident history, perception of the riskiness of road travel and traffic safety behaviours by taking into account the number and severity of accidents experienced. A sample of 525 road users in Cameroon answered a questionnaire comprising items on perception of risk, safe behaviour and personal accident history. Participants who reported involvement in more than three accidents or involvement in a severe accident perceived road travel as less risky and also reported behaving less safely compared with those involved in fewer, or less severe accidents. The results have practical implications for the prevention of traffic accidents. Practitioner Summary: The associations between accident history, perceived risk of road travel and safe behaviour were investigated using self-report questionnaire data. Participants involved in more than three accidents, or in severe accidents, perceived road travel as less risky and also reported more unsafe behaviour compared with those involved in fewer, or less severe accidents. Campaigns targeting people with a less serious, less extensive accident history should aim to increase awareness of hazards and the potential severity of their consequences, as well as emphasising how easy it is to take the recommended preventive actions. Campaigns targeting those involved in more frequent accidents, and survivors of serious accidents, should address feelings of invulnerability and helplessness.

Estimation of fatality and injury risk by means of in-depth fatal accident investigation data.

PubMed

Yannis, George; Papadimitriou, Eleonora; Dupont, Emmanuelle; Martensen, Heike

2010-10-01

In this article the factors affecting fatality and injury risk of road users involved in fatal accidents are analyzed by means of in-depth accident investigation data, with emphasis on parameters not extensively explored in previous research. A fatal accident investigation (FAI) database is used, which includes intermediate-level in-depth data for a harmonized representative sample of 1300 fatal accidents in 7 European countries. The FAI database offers improved potential for analysis, because it includes information on a number of variables that are seldom available, complete, or accurately recorded in road accident databases. However, the fact that only fatal accidents are examined requires for methodological adjustments, namely, the correction for two types of effects on a road user's baseline risk: "accident size" effects, and "relative vulnerability" effects. Fatality and injury risk can be then modeled through multilevel logistic regression models, which account for the hierarchical dependences of the road accident process. The results show that the baseline fatality risk of road users involved in fatal accidents decreases with accident size and increases with the vulnerability of the road user. On the contrary, accident size increases nonfatal injury risk of road users involved in fatal accidents. Other significant effects on fatality and injury risk in fatal accidents include road user age, vehicle type, speed limit, the chain of accident events, vehicle maneuver, and safety equipment. In particular, the presence and use of safety equipment such as seat belt, antilock braking system (ABS), and electronic stability program (ESP) are protection factors for car occupants, especially for those seated at the front seats. Although ABS and ESP systems are typically associated with positive effects on accident occurrence, the results of this research revealed significant related effects on accident severity as well. Moreover, accident consequences are more severe when the most harmful event of the accident occurs later within the accident chain.

Genome-wide characterization of differential transcript usage in Arabidopsis thaliana.

PubMed

Vaneechoutte, Dries; Estrada, April R; Lin, Ying-Chen; Loraine, Ann E; Vandepoele, Klaas

2017-12-01

Alternative splicing and the usage of alternate transcription start- or stop sites allows a single gene to produce multiple transcript isoforms. Most plant genes express certain isoforms at a significantly higher level than others, but under specific conditions this expression dominance can change, resulting in a different set of dominant isoforms. These events of differential transcript usage (DTU) have been observed for thousands of Arabidopsis thaliana, Zea mays and Vitis vinifera genes, and have been linked to development and stress response. However, neither the characteristics of these genes, nor the implications of DTU on their protein coding sequences or functions, are currently well understood. Here we present a dataset of isoform dominance and DTU for all genes in the AtRTD2 reference transcriptome based on a protocol that was benchmarked on simulated data and validated through comparison with a published reverse transciptase-polymerase chain reaction panel. We report DTU events for 8148 genes across 206 public RNA-Seq samples, and find that protein sequences are affected in 22% of the cases. The observed DTU events show high consistency across replicates, and reveal reproducible patterns in response to treatment and development. We also demonstrate that genes with different evolutionary ages, expression breadths and functions show large differences in the frequency at which they undergo DTU, and in the effect that these events have on their protein sequences. Finally, we showcase how the generated dataset can be used to explore DTU events for genes of interest or to find genes with specific DTU in samples of interest. © 2017 The Authors The Plant Journal © 2017 John Wiley & Sons Ltd.

Yeast diversity during the fermentation of Andean chicha: A comparison of high-throughput sequencing and culture-dependent approaches.

PubMed

Mendoza, Lucía M; Neef, Alexander; Vignolo, Graciela; Belloch, Carmela

2017-10-01

Diversity and dynamics of yeasts associated with the fermentation of Argentinian maize-based beverage chicha was investigated. Samples taken at different stages from two chicha productions were analyzed by culture-dependent and culture-independent methods. Five hundred and ninety six yeasts were isolated by classical microbiological methods and 16 species identified by RFLPs and sequencing of D1/D2 26S rRNA gene. Genetic typing of isolates from the dominant species, Saccharomyces cerevisiae, by PCR of delta elements revealed up to 42 different patterns. High-throughput sequencing (HTS) of D1/D2 26S rRNA gene amplicons from chicha samples detected more than one hundred yeast species and almost fifty filamentous fungi taxa. Analysis of the data revealed that yeasts dominated the fermentation, although, a significant percentage of filamentous fungi appeared in the first step of the process. Statistical analysis of results showed that very few taxa were represented by more than 1% of the reads per sample at any step of the process. S. cerevisiae represented more than 90% of the reads in the fermentative samples. Other yeast species dominated the pre-fermentative steps and abounded in fermented samples when S. cerevisiae was in percentages below 90%. Most yeasts species detected by pyrosequencing were not recovered by cultivation. In contrast, the cultivation-based methodology detected very few yeast taxa, and most of them corresponded with very few reads in the pyrosequencing analysis. Copyright © 2017 Elsevier Ltd. All rights reserved.

Litter Breakdown and Microbial Succession on Two Submerged Leaf Species in a Small Forested Stream

PubMed Central

Newman, Molli M.; Liles, Mark R.; Feminella, Jack W.

2015-01-01

Microbial succession during leaf breakdown was investigated in a small forested stream in west-central Georgia, USA, using multiple culture-independent techniques. Red maple (Acer rubrum) and water oak (Quercus nigra) leaf litter were incubated in situ for 128 days, and litter breakdown was quantified by ash-free dry mass (AFDM) method and microbial assemblage composition using phospholipid fatty acid analysis (PLFA), ribosomal intergenic spacer analysis (RISA), denaturing gradient gel electrophoresis (DGGE), and bar-coded next-generation sequencing of 16S rRNA gene amplicons. Leaf breakdown was faster for red maple than water oak. PLFA revealed a significant time effect on microbial lipid profiles for both leaf species. Microbial assemblages on maple contained a higher relative abundance of bacterial lipids than oak, and oak microbial assemblages contained higher relative abundance of fungal lipids than maple. RISA showed that incubation time was more important in structuring bacterial assemblages than leaf physicochemistry. DGGE profiles revealed high variability in bacterial assemblages over time, and sequencing of DGGE-resolved amplicons indicated several taxa present on degrading litter. Next-generation sequencing revealed temporal shifts in dominant taxa within the phylum Proteobacteria, whereas γ-Proteobacteria dominated pre-immersion and α- and β-Proteobacteria dominated after 1 month of instream incubation; the latter groups contain taxa that are predicted to be capable of using organic material to fuel further breakdown. Our results suggest that incubation time is more important than leaf species physicochemistry in influencing leaf litter microbial assemblage composition, and indicate the need for investigation into seasonal and temporal dynamics of leaf litter microbial assemblage succession. PMID:26098687

Characterizing Novel Archaeal Lineages in Salton Sea Sediments

NASA Astrophysics Data System (ADS)

Tarn, J.; Valentine, D. L.

2016-12-01

Biological communities in extreme environments are often dominated by microorganisms of the domain Archaea. Abundant microbial assemblages of this group are found in the hottest, saltiest, and most thermodynamically-limited ecosystems on earth. These taxing surroundings are thought to impose a state of chronic energy stress on resident organisms due to high costs of cellular maintenance relative to resource availability. Even in more temperate settings, Archaea are regularly associated with low-nutrient lifestyles, reflecting their adaptation to extreme, biologically-limiting conditions, which may be an ancestral, domain-wide trait. In this study, we seek to characterize the Archaeal community of the Salton Sea, where members of this domain are novel and highly abundant. Previous work by Swan et al. in 2010 showed that gradients in salinity, sulfate, carbon and nitrogen across sediment horizons of the Salton Sea are linked to changes in Archaeal dominance and community structure. In light of recent taxonomic revisions of the domain, I reclassified the 107 published small subunit rRNA Archaeal sequences from the 2010 study using updated reference databases. The majority of these Euryarchaeal sequences were reassigned to the so-called DPANN superphylum, with Pacearchaeota-related sequences being very abundant in shallow, organic-rich sediments. In deeper, energy-limited strata, several groups of Bathyarchaeota and one divergent DPANN clade were dominant. Ongoing metagenomic work on these sediment communities is being used to assemble genomes of these novel Archaeal groups. These results will help define genomic adaptations of Salton Sea Archaea to varying levels of energy stress as well as inform future cultivation efforts.

A novel nonsense mutation in CRYBB1 associated with autosomal dominant congenital cataract

PubMed Central

Yang, Juhua; Zhu, Yihua; Gu, Feng; He, Xiang; Cao, Zongfu; Li, Xuexi; Tong, Yi

2008-01-01

Purpose To identify the molecular defect underlying an autosomal dominant congenital nuclear cataract in a Chinese family. Methods Twenty-two members of a three-generation pedigree were recruited, clinical examinations were performed, and genomic DNA was extracted from peripheral blood leukocytes. All members were genotyped with polymorphic microsatellite markers adjacent to each of the known cataract-related genes. Linkage analysis was performed after genotyping. Candidate genes were screened for mutation using direct sequencing. Individuals were screened for presence of a mutation by restriction fragment length polymorphism (RFLP) analysis. Results Linkage analysis identified a maximum LOD score of 3.31 (recombination fraction [θ]=0.0) with marker D22S1167 on chromosome 22, which flanks the β-crystallin gene cluster (CRYBB3, CRYBB2, CRYBB1, and CRYBA4). Sequencing the coding regions and the flanking intronic sequences of these four candidate genes identified a novel, heterozygous C→T transition in exon 6 of CRYBB1 in the affected individuals of the family. This single nucleotide change introduced a novel BfaI site and was predicted to result in a nonsense mutation at codon 223 that changed a phylogenetically conserved amino acid to a stop codon (p.Q223X). RFLP analysis confirmed that this mutation co-segregated with the disease phenotype in all available family members and was not found in 100 normal unrelated individuals from the same ethnic background. Conclusions This study has identified a novel nonsense mutation in CRYBB1 (p.Q223X) associated with autosomal dominant congenital nuclear cataract. PMID:18432316

Influences of Plant Species, Season and Location on Leaf Endophytic Bacterial Communities of Non-Cultivated Plants

PubMed Central

Ding, Tao; Melcher, Ulrich

2016-01-01

Bacteria are known to be associated endophytically with plants. Research on endophytic bacteria has identified their importance in food safety, agricultural production and phytoremediation. However, the diversity of endophytic bacterial communities and the forces that shape their compositions in non-cultivated plants are largely uncharacterized. In this study, we explored the diversity, community structure, and dynamics of endophytic bacteria in different plant species in the Tallgrass Prairie Preserve of northern Oklahoma, USA. High throughput sequencing of amplified segments of bacterial rDNA from 81 samples collected at four sampling times from five plant species at four locations identified 335 distinct OTUs at 97% sequence similarity, representing 16 phyla. Proteobacteria was the dominant phylum in the communities, followed by the phyla Bacteriodetes and Actinobacteria. Bacteria from four classes of Proteobacteria were detected with Alphaproteobacteria as the dominant class. Analysis of molecular variance revealed that host plant species and collecting date had significant influences on the compositions of the leaf endophytic bacterial communities. The proportion of Alphaproteobacteria was much higher in the communities from Asclepias viridis than from other plant species and differed from month to month. The most dominant bacterial groups identified in LDA Effect Size analysis showed host-specific patterns, indicating mutual selection between host plants and endophytic bacteria and that leaf endophytic bacterial compositions were dynamic, varying with the host plant’s growing season in three distinct patterns. In summary, next generation sequencing has revealed variations in the taxonomic compositions of leaf endophytic bacterial communities dependent primarily on the nature of the plant host species. PMID:26974817

Influences of Plant Species, Season and Location on Leaf Endophytic Bacterial Communities of Non-Cultivated Plants.

PubMed

Ding, Tao; Melcher, Ulrich

2016-01-01

Bacteria are known to be associated endophytically with plants. Research on endophytic bacteria has identified their importance in food safety, agricultural production and phytoremediation. However, the diversity of endophytic bacterial communities and the forces that shape their compositions in non-cultivated plants are largely uncharacterized. In this study, we explored the diversity, community structure, and dynamics of endophytic bacteria in different plant species in the Tallgrass Prairie Preserve of northern Oklahoma, USA. High throughput sequencing of amplified segments of bacterial rDNA from 81 samples collected at four sampling times from five plant species at four locations identified 335 distinct OTUs at 97% sequence similarity, representing 16 phyla. Proteobacteria was the dominant phylum in the communities, followed by the phyla Bacteriodetes and Actinobacteria. Bacteria from four classes of Proteobacteria were detected with Alphaproteobacteria as the dominant class. Analysis of molecular variance revealed that host plant species and collecting date had significant influences on the compositions of the leaf endophytic bacterial communities. The proportion of Alphaproteobacteria was much higher in the communities from Asclepias viridis than from other plant species and differed from month to month. The most dominant bacterial groups identified in LDA Effect Size analysis showed host-specific patterns, indicating mutual selection between host plants and endophytic bacteria and that leaf endophytic bacterial compositions were dynamic, varying with the host plant's growing season in three distinct patterns. In summary, next generation sequencing has revealed variations in the taxonomic compositions of leaf endophytic bacterial communities dependent primarily on the nature of the plant host species.

Assessment of the microbial diversity of Brazilian kefir grains by PCR-DGGE and pyrosequencing analysis.

PubMed

Leite, A M O; Mayo, B; Rachid, C T C C; Peixoto, R S; Silva, J T; Paschoalin, V M F; Delgado, S

2012-09-01

The microbial diversity and community structure of three different kefir grains from different parts of Brazil were examined via the combination of two culture-independent methods: PCR-denaturing gradient gel electrophoresis (PCR-DGGE) and pyrosequencing. PCR-DGGE showed Lactobacillus kefiranofaciens and Lactobacillus kefiri to be the major bacterial populations in all three grains. The yeast community was dominated by Saccharomyces cerevisiae. Pyrosequencing produced a total of 14,314 partial 16S rDNA sequence reads from the three grains. Sequence analysis grouped the reads into three phyla, of which Firmicutes was dominant. Members of the genus Lactobacillus were the most abundant operational taxonomic units (OTUs) in all samples, accounting for up to 96% of the sequences. OTUs belonging to other lactic and acetic acid bacteria genera, such as Lactococcus, Leuconostoc, Streptococcus and Acetobacter, were also identified at low levels. Two of the grains showed identical DGGE profiles and a similar number of OTUs, while the third sample showed the highest diversity by both techniques. Pyrosequencing allowed the identification of bacteria that were present in small numbers and rarely associated with the microbial community of this complex ecosystem. Copyright © 2012 Elsevier Ltd. All rights reserved.

The Complete Plastome Sequence of an Antarctic Bryophyte Sanionia uncinata (Hedw.) Loeske

PubMed Central

Park, Mira; Park, Hyun; Lee, Hyoungseok; Lee, Byeong-ha

2018-01-01

Organellar genomes of bryophytes are poorly represented with chloroplast genomes of only four mosses, four liverworts and two hornworts having been sequenced and annotated. Moreover, while Antarctic vegetation is dominated by the bryophytes, there are few reports on the plastid genomes for the Antarctic bryophytes. Sanionia uncinata (Hedw.) Loeske is one of the most dominant moss species in the maritime Antarctic. It has been researched as an important marker for ecological studies and as an extremophile plant for studies on stress tolerance. Here, we report the complete plastome sequence of S. uncinata, which can be exploited in comparative studies to identify the lineage-specific divergence across different species. The complete plastome of S. uncinata is 124,374 bp in length with a typical quadripartite structure of 114 unique genes including 82 unique protein-coding genes, 37 tRNA genes and four rRNA genes. However, two genes encoding the α subunit of RNA polymerase (rpoA) and encoding the cytochrome b6/f complex subunit VIII (petN) were absent. We could identify nuclear genes homologous to those genes, which suggests that rpoA and petN might have been relocated from the chloroplast genome to the nuclear genome. PMID:29494552

Reservoir properties of submarine- fan facies: Great Valley sequence, California.

USGS Publications Warehouse

McLean, H.

1981-01-01

Submarine-fan sandstones of the Great Valley sequence west of the Sacramento Valley, California, have low porosities and permeabilities. However, petrography and scanning electron microscope studies indicate that most sands in almost all submarine-fan environments are originally porous and permeable. Thin turbidite sandstones deposited in areas dominated by shale in the outer-fan and basin-plain are cemented mainly by calcite; shale dewatering is inferred to contribute to rapid cementation early in the burial process. Sands deposited in inner- and middle-fan channels with only thin shale beds have small percentrages of intergranular cement. The original porosity is reduced mechanically at shallow depths and by pressure solution at deeperlevels. Permeability decreases with increasing age of the rocks, as a result of increasing burial depths. Computer-run stepwise regression analyses show that the porosity is inversely related to the percentage of calcite cement. The results reported here indicate original porosity and permeability can be high in deep-water submarine fans and that fan environments dominated by sand (with high sand/shale ratios) are more likely to retain higher porosity and permeability to greater depths than sand interbedded with thick shale sequences.-from Author

Viscoelastic lower crust and mantle relaxation following the 14-16 April 2016 Kumamoto, Japan, earthquake sequence

NASA Astrophysics Data System (ADS)

Pollitz, Fred F.; Kobayashi, Tomokazu; Yarai, Hiroshi; Shibazaki, Bunichiro; Matsumoto, Takumi

2017-09-01

The 2016 Kumamoto, Japan, earthquake sequence, culminating in the Mw=7.0 16 April 2016 main shock, occurred within an active tectonic belt of central Kyushu. GPS data from GEONET reveal transient crustal motions from several millimeters per year up to ˜3 cm/yr during the first 8.5 months following the sequence. The spatial pattern of horizontal postseismic motions is shaped by both shallow afterslip and viscoelastic relaxation of the lower crust and upper mantle. We construct a suite of 2-D regional viscoelastic structures in order to derive an optimal joint afterslip and viscoelastic relaxation model using forward modeling of the viscoelastic relaxation. We find that afterslip dominates the postseismic relaxation in the near field (within 30 km of the main shock epicenter), while viscoelastic relaxation dominates at greater distance. The viscoelastic modeling strongly favors a very weak lower crust below a ˜65 km wide zone coinciding with the Beppu-Shimabara graben and the locus of central Kyushu volcanism. Inferred uppermost mantle viscosity is relatively low beneath southern Kyushu, consistent with independent inferences of a hydrated mantle wedge within the Nankai trough fore -arc.

Viscoelastic lower crust and mantle relaxation following the 14–16 April 2016 Kumamoto, Japan, earthquake sequence

USGS Publications Warehouse

Pollitz, Fred; Kobayashi, Tomokazu; Yarai, Hiroshi; Shibazaki, Bunichiro; Matsumoto, Takumi

2017-01-01

The 2016 Kumamoto, Japan, earthquake sequence, culminating in the Mw=7.0 16 April 2016 main shock, occurred within an active tectonic belt of central Kyushu. GPS data from GEONET reveal transient crustal motions from several millimeters per year up to ∼3 cm/yr during the first 8.5 months following the sequence. The spatial pattern of horizontal postseismic motions is shaped by both shallow afterslip and viscoelastic relaxation of the lower crust and upper mantle. We construct a suite of 2-D regional viscoelastic structures in order to derive an optimal joint afterslip and viscoelastic relaxation model using forward modeling of the viscoelastic relaxation. We find that afterslip dominates the postseismic relaxation in the near field (within 30 km of the main shock epicenter), while viscoelastic relaxation dominates at greater distance. The viscoelastic modeling strongly favors a very weak lower crust below a ∼65 km wide zone coinciding with the Beppu-Shimabara graben and the locus of central Kyushu volcanism. Inferred uppermost mantle viscosity is relatively low beneath southern Kyushu, consistent with independent inferences of a hydrated mantle wedge within the Nankai trough fore -arc.

Developing techniques for cause-responsibility analysis of occupational accidents.

PubMed

Jabbari, Mousa; Ghorbani, Roghayeh

2016-11-01

The aim of this study was to specify the causes of occupational accidents, determine social responsibility and the role of groups involved in work-related accidents. This study develops occupational accidents causes tree, occupational accidents responsibility tree, and occupational accidents component-responsibility analysis worksheet; based on these methods, it develops cause-responsibility analysis (CRA) techniques, and for testing them, analyzes 100 fatal/disabling occupational accidents in the construction setting that were randomly selected from all the work-related accidents in Tehran, Iran, over a 5-year period (2010-2014). The main result of this study involves two techniques for CRA: occupational accidents tree analysis (OATA) and occupational accidents components analysis (OACA), used in parallel for determination of responsible groups and responsibilities rate. From the results, we find that the management group of construction projects has 74.65% responsibility of work-related accidents. The developed techniques are purposeful for occupational accidents investigation/analysis, especially for the determination of detailed list of tasks, responsibilities, and their rates. Therefore, it is useful for preventing work-related accidents by focusing on the responsible group's duties. Copyright © 2016 Elsevier Ltd. All rights reserved.

Diagnosis of autosomal dominant polycystic kidney disease using efficient PKD1 and PKD2 targeted next-generation sequencing.

PubMed

Trujillano, Daniel; Bullich, Gemma; Ossowski, Stephan; Ballarín, José; Torra, Roser; Estivill, Xavier; Ars, Elisabet

2014-09-01

Molecular diagnostics of autosomal dominant polycystic kidney disease (ADPKD) relies on mutation screening of PKD1 and PKD2, which is complicated by extensive allelic heterogeneity and the presence of six highly homologous sequences of PKD1. To date, specific sequencing of PKD1 requires laborious long-range amplifications. The high cost and long turnaround time of PKD1 and PKD2 mutation analysis using conventional techniques limits its widespread application in clinical settings. We performed targeted next-generation sequencing (NGS) of PKD1 and PKD2. Pooled barcoded DNA patient libraries were enriched by in-solution hybridization with PKD1 and PKD2 capture probes. Bioinformatics analysis was performed using an in-house developed pipeline. We validated the assay in a cohort of 36 patients with previously known PKD1 and PKD2 mutations and five control individuals. Then, we used the same assay and bioinformatics analysis in a discovery cohort of 12 uncharacterized patients. We detected 35 out of 36 known definitely, highly likely, and likely pathogenic mutations in the validation cohort, including two large deletions. In the discovery cohort, we detected 11 different pathogenic mutations in 10 out of 12 patients. This study demonstrates that laborious long-range PCRs of the repeated PKD1 region can be avoided by in-solution enrichment of PKD1 and PKD2 and NGS. This strategy significantly reduces the cost and time for simultaneous PKD1 and PKD2 sequence analysis, facilitating routine genetic diagnostics of ADPKD.

Distribution and diversity of Verrucomicrobia methanotrophs in geothermal and acidic environments.

PubMed

Sharp, Christine E; Smirnova, Angela V; Graham, Jaime M; Stott, Matthew B; Khadka, Roshan; Moore, Tim R; Grasby, Stephen E; Strack, Maria; Dunfield, Peter F

2014-06-01

Recently, methanotrophic members of the phylum Verrucomicrobia have been described, but little is known about their distribution in nature. We surveyed methanotrophic bacteria in geothermal springs and acidic wetlands via pyrosequencing of 16S rRNA gene amplicons. Putative methanotrophic Verrucomicrobia were found in samples covering a broad temperature range (22.5-81.6°C), but only in acidic conditions (pH 1.8-5.0) and only in geothermal environments, not in acidic bogs or fens. Phylogenetically, three 16S rRNA gene sequence clusters of putative methanotrophic Verrucomicrobia were observed. Those detected in high-temperature geothermal samples (44.1-81.6°C) grouped with known thermoacidiphilic 'Methylacidiphilum' isolates. A second group dominated in moderate-temperature geothermal samples (22.5-40.1°C) and a representative mesophilic methanotroph from this group was isolated (strain LP2A). Genome sequencing verified that strain LP2A possessed particulate methane monooxygenase, but its 16S rRNA gene sequence identity to 'Methylacidiphilum infernorum' strain V4 was only 90.6%. A third group clustered distantly with known methanotrophic Verrucomicrobia. Using pmoA-gene targeted quantitative polymerase chain reaction, two geothermal soil profiles showed a dominance of LP2A-like pmoA sequences in the cooler surface layers and 'Methylacidiphilum'-like pmoA sequences in deeper, hotter layers. Based on these results, there appears to be a thermophilic group and a mesophilic group of methanotrophic Verrucomicrobia. However, both were detected only in acidic geothermal environments. © 2014 Society for Applied Microbiology and John Wiley & Sons Ltd.

DNA barcoding of Bemisia tabaci complex (Hemiptera: Aleyrodidae) reveals southerly expansion of the dominant whitefly species on cotton in Pakistan.

PubMed

Ashfaq, Muhammad; Hebert, Paul D N; Mirza, M Sajjad; Khan, Arif M; Mansoor, Shahid; Shah, Ghulam S; Zafar, Yusuf

2014-01-01

Although whiteflies (Bemisia tabaci complex) are an important pest of cotton in Pakistan, its taxonomic diversity is poorly understood. As DNA barcoding is an effective tool for resolving species complexes and analyzing species distributions, we used this approach to analyze genetic diversity in the B. tabaci complex and map the distribution of B. tabaci lineages in cotton growing areas of Pakistan. Sequence diversity in the DNA barcode region (mtCOI-5') was examined in 593 whiteflies from Pakistan to determine the number of whitefly species and their distributions in the cotton-growing areas of Punjab and Sindh provinces. These new records were integrated with another 173 barcode sequences for B. tabaci, most from India, to better understand regional whitefly diversity. The Barcode Index Number (BIN) System assigned the 766 sequences to 15 BINs, including nine from Pakistan. Representative specimens of each Pakistan BIN were analyzed for mtCOI-3' to allow their assignment to one of the putative species in the B. tabaci complex recognized on the basis of sequence variation in this gene region. This analysis revealed the presence of Asia II 1, Middle East-Asia Minor 1, Asia 1, Asia II 5, Asia II 7, and a new lineage "Pakistan". The first two taxa were found in both Punjab and Sindh, but Asia 1 was only detected in Sindh, while Asia II 5, Asia II 7 and "Pakistan" were only present in Punjab. The haplotype networks showed that most haplotypes of Asia II 1, a species implicated in transmission of the cotton leaf curl virus, occurred in both India and Pakistan. DNA barcodes successfully discriminated cryptic species in B. tabaci complex. The dominant haplotypes in the B. tabaci complex were shared by India and Pakistan. Asia II 1 was previously restricted to Punjab, but is now the dominant lineage in southern Sindh; its southward spread may have serious implications for cotton plantations in this region.

Comparative genome analysis of the candidate functional starter culture strains Lactobacillus fermentum 222 and Lactobacillus plantarum 80 for controlled cocoa bean fermentation processes.

PubMed

Illeghems, Koen; De Vuyst, Luc; Weckx, Stefan

2015-10-12

Lactobacillus fermentum 222 and Lactobacillus plantarum 80, isolates from a spontaneous Ghanaian cocoa bean fermentation process, proved to be interesting functional starter culture strains for cocoa bean fermentations. Lactobacillus fermentum 222 is a thermotolerant strain, able to dominate the fermentation process, thereby converting citrate and producing mannitol. Lactobacillus plantarum 80 is an acid-tolerant and facultative heterofermentative strain that is competitive during cocoa bean fermentation processes. In this study, whole-genome sequencing and comparative genome analysis was used to investigate the mechanisms of these strains to dominate the cocoa bean fermentation process. Through functional annotation and analysis of the high-coverage contigs obtained through 454 pyrosequencing, plantaricin production was predicted for L. plantarum 80. For L. fermentum 222, genes encoding a complete arginine deiminase pathway were attributed. Further, in-depth functional analysis revealed the capacities of these strains associated with carbohydrate and amino acid metabolism, such as the ability to use alternative external electron acceptors, the presence of an extended pyruvate metabolism, and the occurrence of several amino acid conversion pathways. A comparative genome sequence analysis using publicly available genome sequences of strains of the species L. plantarum and L. fermentum revealed unique features of both strains studied. Indeed, L. fermentum 222 possessed genes encoding additional citrate transporters and enzymes involved in amino acid conversions, whereas L. plantarum 80 is the only member of this species that harboured a gene cluster involved in uptake and consumption of fructose and/or sorbose. In-depth genome sequence analysis of the candidate functional starter culture strains L. fermentum 222 and L. plantarum 80 revealed their metabolic capacities, niche adaptations and functionalities that enable them to dominate the cocoa bean fermentation process. Further, these results offered insights into the cocoa bean fermentation ecosystem as a whole and will facilitate the selection of appropriate starter culture strains for controlled cocoa bean fermentation processes.

What's gender got to do with it? Examining masculinities, health and safety and return to work in male dominated skilled trades.

PubMed

Stergiou-Kita, Mary; Mansfield, Elizabeth; Colantonio, Angela; Moody, Joel; Mantis, Steve

2016-06-16

Electrical injuries are a common cause of work-related injury in male dominated skilled trades. In this study we explored how issues of gender, masculinities and institutional workplace practices shape expectations of men and their choices when returning to work following a workplace electrical injury. Twelve workers, who suffered an electrical injury, and twelve employer representatives, completed semi-structured interviews. Using thematic analysis we identified key themes related to how masculinities influenced men's health and safety during the return to work process. Strong identification with worker roles can influence injured workers decisions to return to work 'too early'. A desire to be viewed as a strong, responsible, resilient worker may intersect with concerns about job loss, to influence participants' decisions to not report safety issues and workplace accidents, to not disclose post-injury work challenges, and to not request workplace supports. Institutionalized workplace beliefs regarding risk, de-legitimization of the severity of injuries, and the valorization of the "tough" worker can further re-enforce dominant masculine norms and influence return to work processes and health and safety practices. Workplaces are key sites where gender identities are constructed, affirmed and institutionalized. Further research is warranted to examine how established masculine norms and gendered workplace expectations can influence workplace health and safety in male dominated high risk occupations. Future research should also evaluate strategies that encourage men to discuss post-injury work challenges and request supports when work performance or health and safety issues arise during the return to work process.

Workplace accidents in materials transfer in Finland.

PubMed

Perttula, Pia; Salminen, Simo

2012-01-01

The aim of this study was to show the proportion of workplace accidents related to materials transfer and to decide whether they were more serious than other kinds of workplace accidents. The research material for this study were statistics and data, available in Finland, regarding workplace accidents and fatal accidents. Twenty-five percent of studied fatal accidents were related to materials transfer; 26.9-27.7% of all workplace accidents in Finland in 2003-2007 were workplace accidents related to materials transfer. Over half (54.7%) of workplace accidents related to materials transfer caused disabilities lasting over 3 days. Most accidents related to materials transfer occurred to men aged 20-49 years. The most common types of injuries were dislocations, sprains and strains.

Space Shuttle Columbia and Fukushima Nuclear Plant, Similarities and Differences in Organizational Accidents and Lessons Learned

NASA Astrophysics Data System (ADS)

Mitsui, Masami; Takeuchi, Nobuo; Kawada, Yasuhiro; Kobayashi, Royoji; Nogami, Manami; Miki, Masami

2013-09-01

When records of success are accumulating, we should be most alert to maintain the safety culture we labored to establish and nurture.Space Shuttle Columbia Accident in 2002 and Fukushima Nuclear Power Station Accident in 2011 are seemingly unrelated. But, by studying the accident reports issued after these accidents, the authors found that the organizational causes that led to the accidents were surprisingly similar. The causes of these accidents were rooted in the history and culture of the respective organizations.In this paper, the authors will discuss differences and similarities in these two accidents based on the reports submitted by the accident investigation boards of these two accidents. This will be followed by the lessons learned the authors derived.

Sleepy driver near-misses may predict accident risks.

PubMed

Powell, Nelson B; Schechtman, Kenneth B; Riley, Robert W; Guilleminault, Christian; Chiang, Rayleigh Ping-ying; Weaver, Edward M

2007-03-01

To quantify the prevalence of self-reported near-miss sleepy driving accidents and their association with self-reported actual driving accidents. A prospective cross-sectional internet-linked survey on driving behaviors. Dateline NBC News website. Results are given on 35,217 (88% of sample) individuals with a mean age of 37.2 +/- 13 years, 54.8% women, and 87% white. The risk of at least one accident increased monotonically from 23.2% if there were no near-miss sleepy accidents to 44.5% if there were > or = 4 near-miss sleepy accidents (P < 0.0001). After covariate adjustments, subjects who reported at least one near-miss sleepy accident were 1.13 (95% CI, 1.10 to 1.16) times as likely to have reported at least one actual accident as subjects reporting no near-miss sleepy accidents (P < 0.0001). The odds of reporting at least one actual accident in those reporting > or = 4 near-miss sleepy accidents as compared to those reporting no near-miss sleepy accidents was 1.87 (95% CI, 1.64 to 2.14). Furthermore, after adjustments, the summary Epworth Sleepiness Scale (ESS) score had an independent association with having a near-miss or actual accident. An increase of 1 unit of ESS was associated with a covariate adjusted 4.4% increase of having at least one accident (P < 0.0001). A statistically significant dose-response was seen between the numbers of self-reported sleepy near-miss accidents and an actual accident. These findings suggest that sleepy near-misses may be dangerous precursors to an actual accident.

Modeling secondary accidents identified by traffic shock waves.

PubMed

Junhua, Wang; Boya, Liu; Lanfang, Zhang; Ragland, David R

2016-02-01

The high potential for occurrence and the negative consequences of secondary accidents make them an issue of great concern affecting freeway safety. Using accident records from a three-year period together with California interstate freeway loop data, a dynamic method for more accurate classification based on the traffic shock wave detecting method was used to identify secondary accidents. Spatio-temporal gaps between the primary and secondary accident were proven be fit via a mixture of Weibull and normal distribution. A logistic regression model was developed to investigate major factors contributing to secondary accident occurrence. Traffic shock wave speed and volume at the occurrence of a primary accident were explicitly considered in the model, as a secondary accident is defined as an accident that occurs within the spatio-temporal impact scope of the primary accident. Results show that the shock waves originating in the wake of a primary accident have a more significant impact on the likelihood of a secondary accident occurrence than the effects of traffic volume. Primary accidents with long durations can significantly increase the possibility of secondary accidents. Unsafe speed and weather are other factors contributing to secondary crash occurrence. It is strongly suggested that when police or rescue personnel arrive at the scene of an accident, they should not suddenly block, decrease, or unblock the traffic flow, but instead endeavor to control traffic in a smooth and controlled manner. Also it is important to reduce accident processing time to reduce the risk of secondary accident. Copyright © 2015 Elsevier Ltd. All rights reserved.

Cesium distribution and phases in proxy experiments on the incineration of radioactively contaminated waste from the Fukushima area.

PubMed

Saffarzadeh, Amirhomayoun; Shimaoka, Takayuki; Kakuta, Yoshitada; Kawano, Takashi

2014-10-01

After the March 11, 2011 Tohoku earthquake and Fukushima I Nuclear Power Plant accident, incineration was initially adopted as an effective technique for the treatment of post-disaster wastes. Accordingly, considerable amounts of radioactively contaminated residues were immediately generated through incineration. The level of radioactivity associated with radiocesium in the incineration ash residues (bottom ash and fly ash) became significantly high (several thousand to 100,000 Bq/kg) as a result of this treatment. In order to understand the modes of occurrence of radiocesium, bottom ash products were synthesized through combusting of refuse-derived fuel (RDF) with stable Cs salts in a pilot incinerator. Microscopic and microanalytical (SEM-EDX) techniques were applied and the following Cs categories were identified: low and high concentrations in the matrix glass, low-level partitioning into some newly-formed silicate minerals, partitioning into metal-sulfide compounds, and occurring in newly-formed Cs-rich minerals. These categories that are essentially silicate-bound are the most dominant forms in large and medium size bottom ash particles. It is expected that these achievements provide solutions to the immobilization of radiocesium in the incineration ash products contaminated by Fukushima nuclear accident. Copyright © 2014 Elsevier Ltd. All rights reserved.

Test and Evaluation Metrics of Crew Decision-Making And Aircraft Attitude and Energy State Awareness

NASA Technical Reports Server (NTRS)

Bailey, Randall E.; Ellis, Kyle K. E.; Stephens, Chad L.

2013-01-01

NASA has established a technical challenge, under the Aviation Safety Program, Vehicle Systems Safety Technologies project, to improve crew decision-making and response in complex situations. The specific objective of this challenge is to develop data and technologies which may increase a pilot's (crew's) ability to avoid, detect, and recover from adverse events that could otherwise result in accidents/incidents. Within this technical challenge, a cooperative industry-government research program has been established to develop innovative flight deck-based counter-measures that can improve the crew's ability to avoid, detect, mitigate, and recover from unsafe loss-of-aircraft state awareness - specifically, the loss of attitude awareness (i.e., Spatial Disorientation, SD) or the loss-of-energy state awareness (LESA). A critical component of this research is to develop specific and quantifiable metrics which identify decision-making and the decision-making influences during simulation and flight testing. This paper reviews existing metrics and methods for SD testing and criteria for establishing visual dominance. The development of Crew State Monitoring technologies - eye tracking and other psychophysiological - are also discussed as well as emerging new metrics for identifying channelized attention and excessive pilot workload, both of which have been shown to contribute to SD/LESA accidents or incidents.

Comparisons of Traffic Collisions between Expressways and Rural Roads in Truck Drivers.

PubMed

Lee, Sangbok; Jeong, Byung Yong

2016-03-01

Truck driving is known as one of the occupations with the highest accident rate. This study investigates the characteristics of traffic collisions according to road types (expressway and rural road). Classifying 267 accidents into expressway and rural road, we analyzed them based on driver characteristics (age, working experience, size of employment), time characteristics (day of accident, time, weather), and accident characteristics (accident causes, accident locations, accident types, driving conditions). When we compared the accidents by road conditions, no differences were found between the driver characteristics. However, from the accident characteristics, the injured person distributions were different by the road conditions. In particular, driving while drowsy is shown to be highly related with the accident characteristics. This study can be used as a guideline and a base line to develop a plan of action to prevent traffic accidents. It can also help to prepare formal regulations about a truck driver's vehicle maintenance and driving attitude for a precaution on road accidents.

Accidents in Germany: evaluation of the german telephone health survey 2004.

PubMed

Saß, Anke-Christine

2008-09-01

In the year 2006 there were over 19 000 fatal accidents in Germany and estimates put the number of accidental injuries at more than 8 million. Detailed information on the pattern of accidents is indispensable for the definition of priorities in accident prevention. The German Telephone Health Survey 2004 provides representative cross-sectional data on the health of German residents from 18 years of age (n = 7341). Questions on the prevalence of accidents (13 items) were selected for analysis. Every tenth interviewee reported being injured in an accident in the previous 12 months. Men, particularly young men, are at greater risk of accidents than women. Almost one third of all accidents occurred at home. Social status had no influence on the probability of having an accident, but did affect where the accident happened. The survey yields information on the overall pattern of non-fatal accidents in Germany. The data point to target groups for accident prevention measures.

Occurrence and countermeasures of urban power grid accident

NASA Astrophysics Data System (ADS)

Wei, Wang; Tao, Zhang

2018-03-01

With the advance of technology, the development of network communication and the extensive use of power grids, people can get to know power grid accidents around the world through the network timely. Power grid accidents occur frequently. Large-scale power system blackout and casualty accidents caused by electric shock are also fairly commonplace. All of those accidents have seriously endangered the property and personal safety of the country and people, and the development of society and economy is severely affected by power grid accidents. Through the researches on several typical cases of power grid accidents at home and abroad in recent years and taking these accident cases as the research object, this paper will analyze the three major factors that cause power grid accidents at present. At the same time, combining with various factors and impacts caused by power grid accidents, the paper will put forward corresponding solutions and suggestions to prevent the occurrence of the accident and lower the impact of the accident.

Comparisons of Traffic Collisions between Expressways and Rural Roads in Truck Drivers

PubMed Central

Lee, Sangbok; Jeong, Byung Yong

2015-01-01

Background Truck driving is known as one of the occupations with the highest accident rate. This study investigates the characteristics of traffic collisions according to road types (expressway and rural road). Methods Classifying 267 accidents into expressway and rural road, we analyzed them based on driver characteristics (age, working experience, size of employment), time characteristics (day of accident, time, weather), and accident characteristics (accident causes, accident locations, accident types, driving conditions). Results When we compared the accidents by road conditions, no differences were found between the driver characteristics. However, from the accident characteristics, the injured person distributions were different by the road conditions. In particular, driving while drowsy is shown to be highly related with the accident characteristics. Conclusion This study can be used as a guideline and a base line to develop a plan of action to prevent traffic accidents. It can also help to prepare formal regulations about a truck driver's vehicle maintenance and driving attitude for a precaution on road accidents. PMID:27014489

Reconstruction of doses and deposition in the western trace from the Chernobyl accident.

PubMed

Sikkeland, T; Skuterud, L; Goltsova, N I; Lindmo, T

1997-05-01

A model is presented for the explosive cloud of particulates that produced the western trace of high radioactive ground contamination in the Chernobyl accident on 26 April 1986. The model was developed to reproduce measured dose rates and nuclide contamination and to relate estimated doses to observed changes in: (1) infrared emission from the foliage and (2) morphological and histological structures of individual pines. Dominant factors involved in ground contamination were initial cloud shape, particle size distribution, and rate of particle fallout. At time of formation, the cloud was assumed to be parabolical and to contain a homogeneous distribution of spherically shaped fuel particulates having a log-normal size distribution. The particulates were dispersed by steady winds and diffusion that produced a straight line deposition path. The analysis indicates that two clouds, denoted by Cloud I and Cloud II, were involved. Fallout from the former dominated the far field region and fallout from latter the region near the reactor. At formation they had a full width at half maximum of 1800 m and 500 m, respectively. For wind velocities of 5-10 m s(-1) the particulates' radial distribution at formation had a standard deviation and mode of 1.8 microm and 0.5 microm, respectively. This distribution corresponds to a release of 390 GJ in the runaway explosion. The clouds' height and mass are not uniquely determined but are coupled together. For an initial height of 3,600 m, Cloud I contained about 400 kg fuel. For Cloud II the values were, respectively, 1,500 m and 850 kg. Loss of activities from the clouds is found to be small. Values are obtained for the rate of radionuclide migration from the deposit. Various types of biological damage to pines, as reported in the literature, are shown to be mainly due to ionizing radiation from the deposit by Cloud II. A formula is presented for the particulate size distribution in the trace area.

Combined renin-angiotensin-aldosterone system blockade and statin therapy effectively reduces the risk of cerebrovascular accident in autosomal dominant polycystic kidney disease: a nationwide population-based cohort study

PubMed Central

Sung, Pei-Hsun; Chiang, Hsin-Ju; Lee, Mel S.; Chiang, John Y.; Yip, Hon-Kan; Yang, Yao-Hsu

2017-01-01

Fairly limited data reported the incidence and risk of cerebrovascular accident (CVA) in autosomal dominant polycystic kidney disease (ADPKD). Additionally, little is known regarding the therapeutic impact of renin-angiotensin-aldosterone system (RAAS) blockade and statin on reducing the occurrence of CVA in ADPKD. We utilized the data from Taiwan National Health Insurance Research Database (NHIRD) to perform a population-based cohort study (1997-2013). A total of 2,647 patients with ADPKD were selected from 1,000,000 general population after excluding patients with age<18, renal replacement therapy and concomitant diagnosis of CVA. Additionally, non-ADPKD subjects were assigned as comparison group by matching study cohort with age, gender, income and urbanization in 1:10 ratio (n=26,470). The results showed that ADPKD group had significantly higher frequency rate and cumulative incidence of CVA as compared with the non-ADPKD group (8.73% v.s. 3.93%, p<0.0001). Furthermore, the frequencies of both hemorrhagic and ischemic strokes were also significantly higher in the ADPKD than non-ADPKD group (all p-values <0.0001). After adjusting for age, gender and atherosclerotic risk factors with multivariate analysis, ADPKD independently carried 2.34- and 5.12-fold risk for occurrence of CVA and hemorrhagic stroke (95% CI: 2.02-2.72 and 4.01-6.54), respectively. Combination therapy [adjusted (a) HR=0.19, 95% CI: 0.11-0.31] was superior to either RAAS blockade (aHR=0.37, 95% CI, 0.28-0.5) or statin (aHR=0.44, 95% CI, 0.24-0.79) alone for reducing the CVA occurrence in the ADPKD population. In conclusion, ADPKD was associated with an increased risk of CVA occurrence. Combined RAAS blockade and statin therapy effectively reduces the risk of CVA in ADPKD. PMID:28977886

Analyzing Mosquito (Diptera: Culicidae) Diversity in Pakistan by DNA Barcoding

PubMed Central

Ashfaq, Muhammad; Hebert, Paul D. N.; Mirza, Jawwad H.; Khan, Arif M.; Zafar, Yusuf; Mirza, M. Sajjad

2014-01-01

Background Although they are important disease vectors mosquito biodiversity in Pakistan is poorly known. Recent epidemics of dengue fever have revealed the need for more detailed understanding of the diversity and distributions of mosquito species in this region. DNA barcoding improves the accuracy of mosquito inventories because morphological differences between many species are subtle, leading to misidentifications. Methodology/Principal Findings Sequence variation in the barcode region of the mitochondrial COI gene was used to identify mosquito species, reveal genetic diversity, and map the distribution of the dengue-vector species in Pakistan. Analysis of 1684 mosquitoes from 491 sites in Punjab and Khyber Pakhtunkhwa during 2010–2013 revealed 32 species with the assemblage dominated by Culex quinquefasciatus (61% of the collection). The genus Aedes (Stegomyia) comprised 15% of the specimens, and was represented by six taxa with the two dengue vector species, Ae. albopictus and Ae. aegypti, dominant and broadly distributed. Anopheles made up another 6% of the catch with An. subpictus dominating. Barcode sequence divergence in conspecific specimens ranged from 0–2.4%, while congeneric species showed from 2.3–17.8% divergence. A global haplotype analysis of disease-vectors showed the presence of multiple haplotypes, although a single haplotype of each dengue-vector species was dominant in most countries. Geographic distribution of Ae. aegypti and Ae. albopictus showed the later species was dominant and found in both rural and urban environments. Conclusions As the first DNA-based analysis of mosquitoes in Pakistan, this study has begun the construction of a barcode reference library for the mosquitoes of this region. Levels of genetic diversity varied among species. Because of its capacity to differentiate species, even those with subtle morphological differences, DNA barcoding aids accurate tracking of vector populations. PMID:24827460

Analyzing mosquito (Diptera: culicidae) diversity in Pakistan by DNA barcoding.

PubMed

Ashfaq, Muhammad; Hebert, Paul D N; Mirza, Jawwad H; Khan, Arif M; Zafar, Yusuf; Mirza, M Sajjad

2014-01-01

Although they are important disease vectors mosquito biodiversity in Pakistan is poorly known. Recent epidemics of dengue fever have revealed the need for more detailed understanding of the diversity and distributions of mosquito species in this region. DNA barcoding improves the accuracy of mosquito inventories because morphological differences between many species are subtle, leading to misidentifications. Sequence variation in the barcode region of the mitochondrial COI gene was used to identify mosquito species, reveal genetic diversity, and map the distribution of the dengue-vector species in Pakistan. Analysis of 1684 mosquitoes from 491 sites in Punjab and Khyber Pakhtunkhwa during 2010-2013 revealed 32 species with the assemblage dominated by Culex quinquefasciatus (61% of the collection). The genus Aedes (Stegomyia) comprised 15% of the specimens, and was represented by six taxa with the two dengue vector species, Ae. albopictus and Ae. aegypti, dominant and broadly distributed. Anopheles made up another 6% of the catch with An. subpictus dominating. Barcode sequence divergence in conspecific specimens ranged from 0-2.4%, while congeneric species showed from 2.3-17.8% divergence. A global haplotype analysis of disease-vectors showed the presence of multiple haplotypes, although a single haplotype of each dengue-vector species was dominant in most countries. Geographic distribution of Ae. aegypti and Ae. albopictus showed the later species was dominant and found in both rural and urban environments. As the first DNA-based analysis of mosquitoes in Pakistan, this study has begun the construction of a barcode reference library for the mosquitoes of this region. Levels of genetic diversity varied among species. Because of its capacity to differentiate species, even those with subtle morphological differences, DNA barcoding aids accurate tracking of vector populations.

Proximal dominant hereditary motor and sensory neuropathy with proximal dominance association with mutation in the TRK-fused gene.

PubMed

Lee, Sang-Soo; Lee, Hye Jin; Park, Jin-Mo; Hong, Young Bin; Park, Kee-Duk; Yoo, Jeong Hyun; Koo, Heasoo; Jung, Sung-Chul; Park, Hyung Soon; Lee, Ji Hyun; Lee, Min Goo; Hyun, Young Se; Nakhro, Khriezhanou; Chung, Ki Wha; Choi, Byung-Ok

2013-05-01

Hereditary motor and sensory neuropathy with proximal dominance (HMSN-P) has been reported as a rare type of autosomal dominant adult-onset Charcot-Marie-Tooth disease. HMSN-P has been described only in Japanese descendants since 1997, and the causative gene has not been found. To identify the genetic cause of HMSN-P in a Korean family and determine the pathogenic mechanism. Genetic and observational analysis. Translational research center for rare neurologic disease. Twenty-eight individuals (12 men and 16 women) from a Korean family with HMSN-P. Whole-exome sequencing, linkage analysis, and magnetic resonance imaging. Through whole-exome sequencing, we revealed that HMSN-P is caused by a mutation in the TRK-fused gene (TFG). Clinical heterogeneities were revealed in HMSN-P between Korean and Japanese patients. The patients in the present report showed faster progression of the disease compared with the Japanese patients, and sensory nerve action potentials of the sural nerve were lost in the early stages of the disease. Moreover, tremor and hyperlipidemia were frequently found. Magnetic resonance imaging of the lower extremity revealed a distinct proximal dominant and sequential pattern of muscular involvement with a clearly different pattern than patients with Charcot-Marie-Tooth disease type 1A. Particularly, endoneural blood vessels revealed marked narrowing of the lumen with swollen vesicular endothelial cells. The underlying cause of HMSN-P proves to be a mutation in TFG that lies on chromosome 3q13.2. This disease is not limited to Japanese descendants, and marked narrowing of endoneural blood vessels was noted in the present study. We believe that TFG can affect the peripheral nerve tissue.

Insight into Dominant Cellulolytic Bacteria from Two Biogas Digesters and Their Glycoside Hydrolase Genes

PubMed Central

Zhang, Jun; Zhang, Lei; Geng, Alei; Liu, Fanghua; Zhao, Guoping; Wang, Shengyue; Zhou, Zhihua; Yan, Xing

2015-01-01

Diverse cellulolytic bacteria are essential for maintaining high lignocellulose degradation ability in biogas digesters. However, little was known about functional genes and gene clusters of dominant cellulolytic bacteria in biogas digesters. This is the foundation to understand lignocellulose degradation mechanisms of biogas digesters and apply these gene resource for optimizing biofuel production. A combination of metagenomic and 16S rRNA gene clone library methods was used to investigate the dominant cellulolytic bacteria and their glycoside hydrolase (GH) genes in two biogas digesters. The 16S rRNA gene analysis revealed that the dominant cellulolytic bacteria were strains closely related to Clostridium straminisolvens and an uncultured cellulolytic bacterium designated BG-1. To recover GH genes from cellulolytic bacteria in general, and BG-1 in particular, a refined assembly approach developed in this study was used to assemble GH genes from metagenomic reads; 163 GH-containing contigs ≥ 1 kb in length were obtained. Six recovered GH5 genes that were expressed in E. coli demonstrated multiple lignocellulase activities and one had high mannanase activity (1255 U/mg). Eleven fosmid clones harboring the recovered GH-containing contigs were sequenced and assembled into 10 fosmid contigs. The composition of GH genes in the 163 assembled metagenomic contigs and 10 fosmid contigs indicated that diverse GHs and lignocellulose degradation mechanisms were present in the biogas digesters. In particular, a small portion of BG-1 genome information was recovered by PhyloPythiaS analysis. The lignocellulase gene clusters in BG-1 suggested that it might use a possible novel lignocellulose degradation mechanism to efficiently degrade lignocellulose. Dominant cellulolytic bacteria of biogas digester possess diverse GH genes, not only in sequences but also in their functions, which may be applied for production of biofuel in the future. PMID:26070087

An RNAi in silico approach to find an optimal shRNA cocktail against HIV-1

PubMed Central

2010-01-01

Background HIV-1 can be inhibited by RNA interference in vitro through the expression of short hairpin RNAs (shRNAs) that target conserved genome sequences. In silico shRNA design for HIV has lacked a detailed study of virus variability constituting a possible breaking point in a clinical setting. We designed shRNAs against HIV-1 considering the variability observed in naïve and drug-resistant isolates available at public databases. Methods A Bioperl-based algorithm was developed to automatically scan multiple sequence alignments of HIV, while evaluating the possibility of identifying dominant and subdominant viral variants that could be used as efficient silencing molecules. Student t-test and Bonferroni Dunn correction test were used to assess statistical significance of our findings. Results Our in silico approach identified the most common viral variants within highly conserved genome regions, with a calculated free energy of ≥ -6.6 kcal/mol. This is crucial for strand loading to RISC complex and for a predicted silencing efficiency score, which could be used in combination for achieving over 90% silencing. Resistant and naïve isolate variability revealed that the most frequent shRNA per region targets a maximum of 85% of viral sequences. Adding more divergent sequences maintained this percentage. Specific sequence features that have been found to be related with higher silencing efficiency were hardly accomplished in conserved regions, even when lower entropy values correlated with better scores. We identified a conserved region among most HIV-1 genomes, which meets as many sequence features for efficient silencing. Conclusions HIV-1 variability is an obstacle to achieving absolute silencing using shRNAs designed against a consensus sequence, mainly because there are many functional viral variants. Our shRNA cocktail could be truly effective at silencing dominant and subdominant naïve viral variants. Additionally, resistant isolates might be targeted under specific antiretroviral selective pressure, but in both cases these should be tested exhaustively prior to clinical use. PMID:21172023

Turbulent boundary layers subjected to multiple curvatures and pressure gradients

NASA Technical Reports Server (NTRS)

Bandyopadhyay, Promode R.; Ahmed, Anwar

1993-01-01

The effects of abruptly applied cycles of curvatures and pressure gradients on turbulent boundary layers are examined experimentally. Two two-dimensional curved test surfaces are considered: one has a sequence of concave and convex longitudinal surface curvatures and the other has a sequence of convex and concave curvatures. The choice of the curvature sequences were motivated by a desire to study the asymmetric response of turbulent boundary layers to convex and concave curvatures. The relaxation of a boundary layer from the effects of these two opposite sequences has been compared. The effect of the accompaying sequences of pressure gradient has also been examined but the effect of curvature dominates. The growth of internal layers at the curvature junctions have been studied. Measurements of the Gortler and corner vortex systems have been made. The boundary layer recovering from the sequence of concave to convex curvature has a sustained lower skin friction level than in that recovering from the sequence of convex to concave curvature. The amplification and suppression of turbulence due to the curvature sequences have also been studied.

Sequence and Structure Dependent DNA-DNA Interactions

NASA Astrophysics Data System (ADS)

Kopchick, Benjamin; Qiu, Xiangyun

Molecular forces between dsDNA strands are largely dominated by electrostatics and have been extensively studied. Quantitative knowledge has been accumulated on how DNA-DNA interactions are modulated by varied biological constituents such as ions, cationic ligands, and proteins. Despite its central role in biology, the sequence of DNA has not received substantial attention and ``random'' DNA sequences are typically used in biophysical studies. However, ~50% of human genome is composed of non-random-sequence DNAs, particularly repetitive sequences. Furthermore, covalent modifications of DNA such as methylation play key roles in gene functions. Such DNAs with specific sequences or modifications often take on structures other than the canonical B-form. Here we present series of quantitative measurements of the DNA-DNA forces with the osmotic stress method on different DNA sequences, from short repeats to the most frequent sequences in genome, and to modifications such as bromination and methylation. We observe peculiar behaviors that appear to be strongly correlated with the incurred structural changes. We speculate the causalities in terms of the differences in hydration shell and DNA surface structures.

Novel autosomal dominant TNNT1 mutation causing nemaline myopathy.

PubMed

Konersman, Chamindra G; Freyermuth, Fernande; Winder, Thomas L; Lawlor, Michael W; Lagier-Tourenne, Clotilde; Patel, Shailendra B

2017-11-01

Nemaline myopathy (NEM) is one of the three major forms of congenital myopathy and is characterized by diffuse muscle weakness, hypotonia, respiratory insufficiency, and the presence of nemaline rod structures on muscle biopsy. Mutations in troponin T1 (TNNT1) is 1 of 10 genes known to cause NEM. To date, only homozygous nonsense mutations or compound heterozygous truncating or internal deletion mutations in TNNT1 gene have been identified in NEM. This extended family is of historical importance as some members were reported in the 1960s as initial evidence that NEM is a hereditary disorder. Proband and extended family underwent Sanger sequencing for TNNT1. We performed RT-PCR and immunoblot on muscle to assess TNNT1 RNA expression and protein levels in proband and father. We report a novel heterozygous missense mutation of TNNT1 c.311A>T (p.E104V) that segregated in an autosomal dominant fashion in a large family residing in the United States. Extensive sequencing of the other known genes for NEM failed to identify any other mutant alleles. Muscle biopsies revealed a characteristic pattern of nemaline rods and severe myofiber hypotrophy that was almost entirely restricted to the type 1 fiber population. This novel mutation alters a residue that is highly conserved among vertebrates. This report highlights not only a family with autosomal dominant inheritance of NEM, but that this novel mutation likely acts via a dominant negative mechanism. © 2017 The Authors. Molecular Genetics & Genomic Medicine published by Wiley Periodicals, Inc.

Truncating SLC5A7 mutations underlie a spectrum of dominant hereditary motor neuropathies.

PubMed

Salter, Claire G; Beijer, Danique; Hardy, Holly; Barwick, Katy E S; Bower, Matthew; Mademan, Ines; De Jonghe, Peter; Deconinck, Tine; Russell, Mark A; McEntagart, Meriel M; Chioza, Barry A; Blakely, Randy D; Chilton, John K; De Bleecker, Jan; Baets, Jonathan; Baple, Emma L; Walk, David; Crosby, Andrew H

2018-04-01

To identify the genetic cause of disease in 2 previously unreported families with forms of distal hereditary motor neuropathies (dHMNs). The first family comprises individuals affected by dHMN type V, which lacks the cardinal clinical feature of vocal cord paralysis characteristic of dHMN-VII observed in the second family. Next-generation sequencing was performed on the proband of each family. Variants were annotated and filtered, initially focusing on genes associated with neuropathy. Candidate variants were further investigated and confirmed by dideoxy sequence analysis and cosegregation studies. Thorough patient phenotyping was completed, comprising clinical history, examination, and neurologic investigation. dHMNs are a heterogeneous group of peripheral motor neuron disorders characterized by length-dependent neuropathy and progressive distal limb muscle weakness and wasting. We previously reported a dominant-negative frameshift mutation located in the concluding exon of the SLC5A7 gene encoding the choline transporter (CHT), leading to protein truncation, as the likely cause of dominantly-inherited dHMN-VII in an extended UK family. In this study, our genetic studies identified distinct heterozygous frameshift mutations located in the last coding exon of SLC5A7 , predicted to result in the truncation of the CHT C-terminus, as the likely cause of the condition in each family. This study corroborates C-terminal CHT truncation as a cause of autosomal dominant dHMN, confirming upper limb predominating over lower limb involvement, and broadening the clinical spectrum arising from CHT malfunction.

Changes in the predominant human Lactobacillus flora during in vitro fertilisation

PubMed Central

Jakobsson, Tell; Forsum, Urban

2008-01-01

Background Signature matching of nucleotide sequences in the V1 and V3 regions 16S rRNA genes using pyrosequencing technology is a powerful tool for typing vaginal Lactobacilli to the species level and has been used for investigating the vaginal microbial niche. Methods This study has characterized the normal cultivable vaginal Lactobacillus flora at varying estradiol levels in plasma; the study comprised 17 patients undergoing ovarian stimulation for In Vitro Fertilization (IVF) treatment. The vaginal status of each participant was initially assessed as normal according to Amsel and Nugent criteria. Results L. crispatus, L. gasseri and/or L. jensenii were present in 10 of the patients throughout the study period, and little variation among these three species was encountered in individual patients. The flora of three women was dominated by L. delbrüeckii, L. rhamnosus or L. vaginalis. One woman exhibited a dominance of L. iners. The flora of the remaining three women were initially dominated by L. rhamnosus or L. reuteri, but as their estrogen levels rose, their flora composition altered, to become dominated by one of the three species most common in a normal, healthy vagina. Conclusion Signature matching of nucleotide sequences in the V1 and V3 regions of 16S rRNA genes is a discriminative tool for the study of vaginal Lactobacilli and can be used to track the Lactobacillus flora under a variety of physiological conditions. PMID:18590533

Utilization of 134Cs/137Cs in the environment to identify the reactor units that caused atmospheric releases during the Fukushima Daiichi accident

NASA Astrophysics Data System (ADS)

Chino, Masamichi; Terada, Hiroaki; Nagai, Haruyasu; Katata, Genki; Mikami, Satoshi; Torii, Tatsuo; Saito, Kimiaki; Nishizawa, Yukiyasu

2016-08-01

The Fukushima Daiichi nuclear power reactor units that generated large amounts of airborne discharges during the period of March 12-21, 2011 were identified individually by analyzing the combination of measured 134Cs/137Cs depositions on ground surfaces and atmospheric transport and deposition simulations. Because the values of 134Cs/137Cs are different in reactor units owing to fuel burnup differences, the 134Cs/137Cs ratio measured in the environment was used to determine which reactor unit ultimately contaminated a specific area. Atmospheric dispersion model simulations were used for predicting specific areas contaminated by each dominant release. Finally, by comparing the results from both sources, the specific reactor units that yielded the most dominant atmospheric release quantities could be determined. The major source reactor units were Unit 1 in the afternoon of March 12, 2011, Unit 2 during the period from the late night of March 14 to the morning of March 15, 2011. These results corresponded to those assumed in our previous source term estimation studies. Furthermore, new findings suggested that the major source reactors from the evening of March 15, 2011 were Units 2 and 3 and that the dominant source reactor on March 20, 2011 temporally changed from Unit 3 to Unit 2.

Utilization of (134)Cs/(137)Cs in the environment to identify the reactor units that caused atmospheric releases during the Fukushima Daiichi accident.

PubMed

Chino, Masamichi; Terada, Hiroaki; Nagai, Haruyasu; Katata, Genki; Mikami, Satoshi; Torii, Tatsuo; Saito, Kimiaki; Nishizawa, Yukiyasu

2016-08-22

The Fukushima Daiichi nuclear power reactor units that generated large amounts of airborne discharges during the period of March 12-21, 2011 were identified individually by analyzing the combination of measured (134)Cs/(137)Cs depositions on ground surfaces and atmospheric transport and deposition simulations. Because the values of (134)Cs/(137)Cs are different in reactor units owing to fuel burnup differences, the (134)Cs/(137)Cs ratio measured in the environment was used to determine which reactor unit ultimately contaminated a specific area. Atmospheric dispersion model simulations were used for predicting specific areas contaminated by each dominant release. Finally, by comparing the results from both sources, the specific reactor units that yielded the most dominant atmospheric release quantities could be determined. The major source reactor units were Unit 1 in the afternoon of March 12, 2011, Unit 2 during the period from the late night of March 14 to the morning of March 15, 2011. These results corresponded to those assumed in our previous source term estimation studies. Furthermore, new findings suggested that the major source reactors from the evening of March 15, 2011 were Units 2 and 3 and that the dominant source reactor on March 20, 2011 temporally changed from Unit 3 to Unit 2.

Utilization of 134Cs/137Cs in the environment to identify the reactor units that caused atmospheric releases during the Fukushima Daiichi accident

PubMed Central

Chino, Masamichi; Terada, Hiroaki; Nagai, Haruyasu; Katata, Genki; Mikami, Satoshi; Torii, Tatsuo; Saito, Kimiaki; Nishizawa, Yukiyasu

2016-01-01

The Fukushima Daiichi nuclear power reactor units that generated large amounts of airborne discharges during the period of March 12–21, 2011 were identified individually by analyzing the combination of measured 134Cs/137Cs depositions on ground surfaces and atmospheric transport and deposition simulations. Because the values of 134Cs/137Cs are different in reactor units owing to fuel burnup differences, the 134Cs/137Cs ratio measured in the environment was used to determine which reactor unit ultimately contaminated a specific area. Atmospheric dispersion model simulations were used for predicting specific areas contaminated by each dominant release. Finally, by comparing the results from both sources, the specific reactor units that yielded the most dominant atmospheric release quantities could be determined. The major source reactor units were Unit 1 in the afternoon of March 12, 2011, Unit 2 during the period from the late night of March 14 to the morning of March 15, 2011. These results corresponded to those assumed in our previous source term estimation studies. Furthermore, new findings suggested that the major source reactors from the evening of March 15, 2011 were Units 2 and 3 and that the dominant source reactor on March 20, 2011 temporally changed from Unit 3 to Unit 2. PMID:27546490

49 CFR 655.44 - Post-accident testing.

Code of Federal Regulations, 2011 CFR

2011-10-01

... the employer is unable to perform a post-accident test within the required period noted in paragraphs... 49 Transportation 7 2011-10-01 2011-10-01 false Post-accident testing. 655.44 Section 655.44... of Testing § 655.44 Post-accident testing. (a) Accidents. (1) Fatal accidents. (i) As soon as...

41 CFR 101-39.407 - Accident records.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 41 Public Contracts and Property Management 2 2011-07-01 2007-07-01 true Accident records. 101-39...-INTERAGENCY FLEET MANAGEMENT SYSTEMS 39.4-Accidents and Claims § 101-39.407 Accident records. If GSA's records of vehicle accidents indicate that a particular activity has had an unusually high accident frequency...

The relationship between safety climate and recent accidents: behavioral learning and cognitive attributions.

PubMed

Desai, Vinit M; Roberts, Karlene H; Ciavarelli, Anthony P

2006-01-01

The association between accidents and subsequent work unit safety perceptions was assessed to address cognitive and behavioral changes following accidents. Many studies attempt to predict accident rates using measures of work unit safety, but effects vary considerably. Conversely, this study examined whether recent accidents may be positively associated with work unit safety perceptions, as suggested by behavioral learning mechanisms (increases in safety investments following accidents) or cognitive mechanisms (defensive attributions regarding accident causality). Lagged squadron-level accident experience was correlated with work unit safety perceptions obtained through a 61-question safety climate survey administered to 6,361 individuals in U.S. Navy flight squadrons. Positive associations between minor or intermediately severe accidents and future safety climate scores were found, although no effect was found for major accidents. We suggest that accident history should be considered when examining work unit safety perceptions because recent accidents may be associated with higher safety climate scores. We did not find that this varies systematically with accident severity, and longitudinal research on additional samples is needed to further test this possibility. This research may be used to refine measurement of work unit safety and to examine impacts of accidents or safety violations on workers' cognitive processes and group behavioral changes.

[Analysis of work accidents during the years 1999-2006 in a hospital company in Lombardia].

PubMed

Melloni, P; Antoniazzi, E; Somenzi, V; Galli, L; Fazioli, R; Mottinelli, A; Franzosi, C; Cirla, A M; Gobba, E

2007-01-01

This study describe accidents occurred in the period between 1999 and 2006 in the Hospital of Cremona, in which about 2400 subjects operate. The analysis of Accident Register showed a reduction of about 30% of the total number of accidents during the examined period and a non homogeneous distribution of the various types of accidents. The most frequent accidents were prick (25.8%), trauma (22.9%) and "in itinere" accidents (7.8%). One type of accident has been little considered up to now: the aggressions. Professional nurses were the most frequently involved and the most affected units were those that belong to the Internal Medicine Department. "In itinere" accidents had the longest average prognosis (11.6 days). The repetition of accidents occurred to the same operator hasn't been analysed before now: a professional nurse had nine accidents (of various type) in the seven years considered. Probably the reduction of accident must be attributed to the effectiveness of the prevention activities undertaken during the reviewed period. Biological accidents, for which it was possible to implement prevention programs, have been markedly reduced; it was not the same for "In Itinere" accidents, that depend significantly on external factors that are not easily dismissed.

Secondary school accident reporting in one education authority.

PubMed

Williams, W R; Latif, A H A; Sibert, J

2002-01-01

Secondary schools appear to have very different accident rates when they are compared on the basis of accident report returns. The variation may be as a result of real differences in accident rates or different reporting procedures. This study investigates accident reporting from secondary schools and, in particular, the role of the school nurse. Accident form returns covering a 2-year period were collected for statistical analysis from 13 comprehensive schools in one local education authority in Wales. School sites were visited in the following school year to obtain information about accident records held on site and accident reporting procedures. The main factors determining the number of school accident reports submitted to the education authority relate to differences in recording and reporting procedures, such as the employment of a nurse and the policy of the head teacher/safety officer on submitting accident returns. Accident and emergency department referrals from similar schools may show significant differences in specific injuries and their causes. The level of school accident activity cannot be gauged from reports submitted to the education authority. Lack of incentives for collecting good accident data, in conjunction with the degree of complacency in the current system, suggest that future accident rates and reporting activity are unlikely to change.

Source Term Estimation of Radioxenon Released from the Fukushima Dai-ichi Nuclear Reactors Using Measured Air Concentrations and Atmospheric Transport Modeling

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

Eslinger, Paul W.; Biegalski, S.; Bowyer, Ted W.

2014-01-01

Systems designed to monitor airborne radionuclides released from underground nuclear explosions detected radioactive fallout from the Fukushima Daiichi nuclear accident in March 2011. Atmospheric transport modeling (ATM) of plumes of noble gases and particulates were performed soon after the accident to determine plausible detection locations of any radioactive releases to the atmosphere. We combine sampling data from multiple International Modeling System (IMS) locations in a new way to estimate the magnitude and time sequence of the releases. Dilution factors from the modeled plume at five different detection locations were combined with 57 atmospheric concentration measurements of 133-Xe taken from Marchmore » 18 to March 23 to estimate the source term. This approach estimates that 59% of the 1.24×1019 Bq of 133-Xe present in the reactors at the time of the earthquake was released to the atmosphere over a three day period. Source term estimates from combinations of detection sites have lower spread than estimates based on measurements at single detection sites. Sensitivity cases based on data from four or more detection locations bound the source term between 35% and 255% of available xenon inventory.« less

Level 1 Tornado PRA for the High Flux Beam Reactor

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

Bozoki, G.E.; Conrad, C.S.

This report describes a risk analysis primarily directed at providing an estimate for the frequency of tornado induced damage to the core of the High Flux Beam Reactor (HFBR), and thus it constitutes a Level 1 Probabilistic Risk Assessment (PRA) covering tornado induced accident sequences. The basic methodology of the risk analysis was to develop a ``tornado specific`` plant logic model that integrates the internal random hardware failures with failures caused externally by the tornado strike and includes operator errors worsened by the tornado modified environment. The tornado hazard frequency, as well as earlier prepared structural and equipment fragility data,more » were used as input data to the model. To keep modeling/calculational complexity as simple as reasonable a ``bounding`` type, slightly conservative, approach was applied. By a thorough screening process a single dominant initiating event was selected as a representative initiator, defined as: ``Tornado Induced Loss of Offsite Power.`` The frequency of this initiator was determined to be 6.37E-5/year. The safety response of the HFBR facility resulted in a total Conditional Core Damage Probability of .621. Thus, the point estimate of the HFBR`s Tornado Induced Core Damage Frequency (CDF) was found to be: (CDF){sub Tornado} = 3.96E-5/year. This value represents only 7.8% of the internal CDF and thus is considered to be a small contribution to the overall facility risk expressed in terms of total Core Damage Frequency. In addition to providing the estimate of (CDF){sub Tornado}, the report documents, the relative importance of various tornado induced system, component, and operator failures that contribute most to (CDF){sub Tornado}.« less

Integration of a radiation biomarker into modeling of thyroid carcinogenesis and post-Chernobyl risk assessment.

PubMed

Kaiser, Jan Christian; Meckbach, Reinhard; Eidemüller, Markus; Selmansberger, Martin; Unger, Kristian; Shpak, Viktor; Blettner, Maria; Zitzelsberger, Horst; Jacob, Peter

2016-12-01

Strong evidence for the statistical association between radiation exposure and disease has been produced for thyroid cancer by epidemiological studies after the Chernobyl accident. However, limitations of the epidemiological approach in order to explore health risks especially at low doses of radiation appear obvious. Statistical fluctuations due to small case numbers dominate the uncertainty of risk estimates. Molecular radiation markers have been searched extensively to separate radiation-induced cancer cases from sporadic cases. The overexpression of the CLIP2 gene is the most promising of these markers. It was found in the majority of papillary thyroid cancers (PTCs) from young patients included in the Chernobyl tissue bank. Motivated by the CLIP2 findings we propose a mechanistic model which describes PTC development as a sequence of rate-limiting events in two distinct paths of CLIP2-associated and multistage carcinogenesis. It integrates molecular measurements of the dichotomous CLIP2 marker from 141 patients into the epidemiological risk analysis for about 13 000 subjects from the Ukrainian-American cohort which were exposed below age 19 years and were put under enhanced medical surveillance since 1998. For the first time, a radiation risk has been estimated solely from marker measurements. Cross checking with epidemiological estimates and model validation suggests that CLIP2 is a marker of high precision. CLIP2 leaves an imprint in the epidemiological incidence data which is typical for a driver gene. With the mechanistic model, we explore the impact of radiation on the molecular landscape of PTC. The model constitutes a unique interface between molecular biology and radiation epidemiology. © The Author 2016. Published by Oxford University Press.

The tool in the brain: apraxia in ADL. Behavioral and neurological correlates of apraxia in daily living.

PubMed

Bieńkiewicz, Marta M N; Brandi, Marie-Luise; Goldenberg, Georg; Hughes, Charmayne M L; Hermsdörfer, Joachim

2014-01-01

Humans differ from other animals in the way they can skilfully and precisely operate or invent tools to facilitate their everyday life. Tools have dominated our home, travel and work environment, becoming an integral step for our motor skills development. What happens when the part of the brain responsible for tool use is damaged in our adult life due to a cerebrovascular accident? How does daily life change when we lose the previously mastered ability to make use of the objects around us? How do patients suffering from compromised tool use cope with food preparation, personal hygiene, grooming, housework, or use of home appliances? In this literature review we present a state of the art for single and multiple tool use research, with a focus on the impact that apraxia (impaired ability to perform tool-based actions) and action disorganization syndrome (ADS; impaired ability to carry out multi-step actions) have on activities of daily living (ADL). Firstly, we summarize the behavioral studies investigating the impact of apraxia and other comorbidity syndromes, such as neglect or visual extinction, on ADL. We discuss the hallmarks of the compromised tool use in terms of the sequencing of action steps, conceptual errors committed, spatial motor control, and temporal organization of the movement. In addition, we present an up-to-date overview of the neuroimaging and lesion analyses studies that provide an insight into neural correlates of tool use in the human brain and functional changes in the neural organization following a stroke, in the context of ADL. Finally we discuss the current practice in neurorehabilitation of ADL in apraxia and ADS aiming at increasing patients' independence.

Occupational accidents aboard merchant ships

PubMed Central

Hansen, H; Nielsen, D; Frydenberg, M

2002-01-01

Objectives: To investigate the frequency, circumstances, and causes of occupational accidents aboard merchant ships in international trade, and to identify risk factors for the occurrence of occupational accidents as well as dangerous working situations where possible preventive measures may be initiated. Methods: The study is a historical follow up on occupational accidents among crew aboard Danish merchant ships in the period 1993–7. Data were extracted from the Danish Maritime Authority and insurance data. Exact data on time at risk were available. Results: A total of 1993 accidents were identified during a total of 31 140 years at sea. Among these, 209 accidents resulted in permanent disability of 5% or more, and 27 were fatal. The mean risk of having an occupational accident was 6.4/100 years at sea and the risk of an accident causing a permanent disability of 5% or more was 0.67/100 years aboard. Relative risks for notified accidents and accidents causing permanent disability of 5% or more were calculated in a multivariate analysis including ship type, occupation, age, time on board, change of ship since last employment period, and nationality. Foreigners had a considerably lower recorded rate of accidents than Danish citizens. Age was a major risk factor for accidents causing permanent disability. Change of ship and the first period aboard a particular ship were identified as risk factors. Walking from one place to another aboard the ship caused serious accidents. The most serious accidents happened on deck. Conclusions: It was possible to clearly identify work situations and specific risk factors for accidents aboard merchant ships. Most accidents happened while performing daily routine duties. Preventive measures should focus on workplace instructions for all important functions aboard and also on the prevention of accidents caused by walking around aboard the ship. PMID:11850550

Whole-exome sequencing analysis of Waardenburg syndrome in a Chinese family.

PubMed

Chen, Dezhong; Zhao, Na; Wang, Jing; Li, Zhuoyu; Wu, Changxin; Fu, Jie; Xiao, Han

2017-01-01

Waardenburg syndrome (WS) is a dominantly inherited, genetically heterogeneous auditory-pigmentary syndrome characterized by non-progressive sensorineural hearing loss and iris discoloration. By whole-exome sequencing (WES), we identified a nonsense mutation (c.598C>T) in PAX3 gene, predicted to be disease causing by in silico analysis. This is the first report of genetically diagnosed case of WS PAX3 c.598C>T nonsense mutation in Chinese ethnic origin by WES and in silico functional prediction methods.

Genome Sequence of an Ammonia-Oxidizing Soil Archaeon, “Candidatus Nitrosoarchaeum koreensis” MY1

PubMed Central

Kim, Byung Kwon; Jung, Man-Young; Yu, Dong Su; Park, Soo-Je; Oh, Tae Kwang; Rhee, Sung-Keun; Kim, Jihyun F.

2011-01-01

Ammonia-oxidizing archaea are ubiquitous microorganisms which play important roles in global nitrogen and carbon cycle on earth. Here we present the high-quality draft genome sequence of an ammonia-oxidizing archaeon, “Candidatus Nitrosopumilus koreensis” MY1, that dominated an enrichment culture of a soil sample from the rhizosphere. Its genome contains genes for survival in the rhizosphere environment as well as those for carbon fixation and ammonium oxidation to nitrite. PMID:21914867

A novel frameshift mutation of CHD7 in a Japanese patient with CHARGE syndrome

PubMed Central

Kohmoto, Tomohiro; Shono, Miki; Naruto, Takuya; Watanabe, Miki; Suga, Ken-ichi; Nakagawa, Ryuji; Kagami, Shoji; Masuda, Kiyoshi; Imoto, Issei

2016-01-01

CHARGE syndrome is a rare autosomal dominant developmental disorder involving multiple organs. CHD7 is a major causative gene of CHARGE syndrome. We performed targeted-exome sequencing using a next-generation sequencer for molecular diagnosis of a 4-month-old male patient who was clinically suspected to have CHARGE syndrome, and report a novel monoallelic mutation in CHD7, NM_017780.3(CHD7_v001):c.2966del causing a reading frameshift [p.(Cys989Serfs*3)]. PMID:27081570

A novel frameshift mutation of CHD7 in a Japanese patient with CHARGE syndrome.

PubMed

Kohmoto, Tomohiro; Shono, Miki; Naruto, Takuya; Watanabe, Miki; Suga, Ken-Ichi; Nakagawa, Ryuji; Kagami, Shoji; Masuda, Kiyoshi; Imoto, Issei

2016-01-01

CHARGE syndrome is a rare autosomal dominant developmental disorder involving multiple organs. CHD7 is a major causative gene of CHARGE syndrome. We performed targeted-exome sequencing using a next-generation sequencer for molecular diagnosis of a 4-month-old male patient who was clinically suspected to have CHARGE syndrome, and report a novel monoallelic mutation in CHD7, NM_017780.3(CHD7_v001):c.2966del causing a reading frameshift [p.(Cys989Serfs*3)].

Whole-exome sequencing analysis of Waardenburg syndrome in a Chinese family

PubMed Central

Chen, Dezhong; Zhao, Na; Wang, Jing; Li, Zhuoyu; Wu, Changxin; Fu, Jie; Xiao, Han

2017-01-01

Waardenburg syndrome (WS) is a dominantly inherited, genetically heterogeneous auditory-pigmentary syndrome characterized by non-progressive sensorineural hearing loss and iris discoloration. By whole-exome sequencing (WES), we identified a nonsense mutation (c.598C>T) in PAX3 gene, predicted to be disease causing by in silico analysis. This is the first report of genetically diagnosed case of WS PAX3 c.598C>T nonsense mutation in Chinese ethnic origin by WES and in silico functional prediction methods. PMID:28690861

Review the number of accidents in Tehran over a two-year period and prediction of the number of events based on a time-series model

PubMed Central

Teymuri, Ghulam Heidar; Sadeghian, Marzieh; Kangavari, Mehdi; Asghari, Mehdi; Madrese, Elham; Abbasinia, Marzieh; Ahmadnezhad, Iman; Gholizadeh, Yavar

2013-01-01

Background: One of the significant dangers that threaten people’s lives is the increased risk of accidents. Annually, more than 1.3 million people die around the world as a result of accidents, and it has been estimated that approximately 300 deaths occur daily due to traffic accidents in the world with more than 50% of that number being people who were not even passengers in the cars. The aim of this study was to examine traffic accidents in Tehran and forecast the number of future accidents using a time-series model. Methods: The study was a cross-sectional study that was conducted in 2011. The sample population was all traffic accidents that caused death and physical injuries in Tehran in 2010 and 2011, as registered in the Tehran Emergency ward. The present study used Minitab 15 software to provide a description of accidents in Tehran for the specified time period as well as those that occurred during April 2012. Results: The results indicated that the average number of daily traffic accidents in Tehran in 2010 was 187 with a standard deviation of 83.6. In 2011, there was an average of 180 daily traffic accidents with a standard deviation of 39.5. One-way analysis of variance indicated that the average number of accidents in the city was different for different months of the year (P < 0.05). Most of the accidents occurred in March, July, August, and September. Thus, more accidents occurred in the summer than in the other seasons. The number of accidents was predicted based on an auto-regressive, moving average (ARMA) for April 2012. The number of accidents displayed a seasonal trend. The prediction of the number of accidents in the city during April of 2012 indicated that a total of 4,459 accidents would occur with mean of 149 accidents per day during these three months. Conclusion: The number of accidents in Tehran displayed a seasonal trend, and the number of accidents was different for different seasons of the year. PMID:26120405

Complete genome sequence of Pelosinus sp. strain UFO1 assembled using single-molecule real-time DNA sequencing technology

DOE PAGES

Brown, Steven D.; Utturkar, Sagar M.; Magnuson, Timothy S.; ...

2014-09-04

Pelosinus fermentans strain R7 was isolated from Russian kaolin clays as the type strain and it can reduce Fe(III) during fermentative growth (1). Draft genome sequences for P. fermentans R7 and four strains from Hanford, Washington, USA, have been published (2–4). The P. fermentans 16S rRNA sequence dominated the lactate-based enrichment cultures from three geochemically contrasting soils from the Melton Branch Watershed, Oak Ridge, Tennessee, USA (5) and also at another stimulated, uraniumcontaminated field site near Oak Ridge (6). For the current work, strain UFO1 was isolated from pristine sediments at a background field site in Oak Ridge and characterizedmore » as facilitating U(VI) reduction and precipitation with phosphate (7).« less

First Report of Echinococcus equinus in a Donkey in Turkey

PubMed Central

Simsek, Sami; Roinioti, Erifylli; Eroksuz, Hatice

2015-01-01

A 2-year-old female donkey (Equus asinus) was euthanized in the Pathology Department of Firat University, Elazig, Turkey. Necropsy disclosed the presence of 7 hydatid cysts distributed throughout the lung parenchyma. One of those cysts represented the parasite material of the present study and was molecularly identified through sequencing of a fragment of cytochrome c oxidase subunit 1 (CO1) and nicotinamide adenine dinucleotide dehydrogenase subunit 1 (NADH1) gene, as Echinococcus equinus. The generated CO1 sequence supports the presence of the dominant haplotype as has been described in Europe and Africa. The NADH1 sequence was found similar to sequences reported in equids in Egypt and the United Kingdom. The molecular identification of E. equinus in a donkey is being reported for the first time in Turkey. PMID:26797441

First Report of Echinococcus equinus in a Donkey in Turkey.

PubMed

Simsek, Sami; Roinioti, Erifylli; Eroksuz, Hatice

2015-12-01

A 2-year-old female donkey (Equus asinus) was euthanized in the Pathology Department of Firat University, Elazig, Turkey. Necropsy disclosed the presence of 7 hydatid cysts distributed throughout the lung parenchyma. One of those cysts represented the parasite material of the present study and was molecularly identified through sequencing of a fragment of cytochrome c oxidase subunit 1 (CO1) and nicotinamide adenine dinucleotide dehydrogenase subunit 1 (NADH1) gene, as Echinococcus equinus. The generated CO1 sequence supports the presence of the dominant haplotype as has been described in Europe and Africa. The NADH1 sequence was found similar to sequences reported in equids in Egypt and the United Kingdom. The molecular identification of E. equinus in a donkey is being reported for the first time in Turkey.

Microbial community analysis of the hypersaline water of the Dead Sea using high-throughput amplicon sequencing.

PubMed

Jacob, Jacob H; Hussein, Emad I; Shakhatreh, Muhamad Ali K; Cornelison, Christopher T

2017-10-01

Amplicon sequencing using next-generation technology (bTEFAP ® ) has been utilized in describing the diversity of Dead Sea microbiota. The investigated area is a well-known salt lake in the western part of Jordan found in the lowest geographical location in the world (more than 420 m below sea level) and characterized by extreme salinity (approximately, 34%) in addition to other extreme conditions (low pH, unique ionic composition different from sea water). DNA was extracted from Dead Sea water. A total of 314,310 small subunit RNA (SSU rRNA) sequences were parsed, and 288,452 sequences were then clustered. For alpha diversity analysis, sample was rarefied to 3,000 sequences. The Shannon-Wiener index curve plot reached a plateau at approximately 3,000 sequences indicating that sequencing depth was sufficient to capture the full scope of microbial diversity. Archaea was found to be dominating the sequences (52%), whereas Bacteria constitute 45% of the sequences. Altogether, prokaryotic sequences (which constitute 97% of all sequences) were found to predominate. The findings expand on previous studies by using high-throughput amplicon sequencing to describe the microbial community in an environment which in recent years has been shown to hide some interesting diversity. © 2017 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

Receptor homodimerization plays a critical role in a novel dominant negative P2RY12 variant identified in a family with severe bleeding.

PubMed

Mundell, S J; Rabbolini, D; Gabrielli, S; Chen, Q; Aungraheeta, R; Hutchinson, J L; Kilo, T; Mackay, J; Ward, C M; Stevenson, W; Morel-Kopp, M-C

2018-01-01

Essentials Three dominant variants for the autosomal recessive bleeding disorder type-8 have been described. To date, there has been no phenotype/genotype correlation explaining their dominant transmission. Proline plays an important role in P2Y12R ligand binding and signaling defects. P2Y12R homodimer formation is critical for the receptor function and signaling. Background Although inherited platelet disorders are still underdiagnosed worldwide, advances in molecular techniques are improving disease diagnosis and patient management. Objective To identify and characterize the mechanism underlying the bleeding phenotype in a Caucasian family with an autosomal dominant P2RY12 variant. Methods Full blood counts, platelet aggregometry, flow cytometry and western blotting were performed before next-generation sequencing (NGS). Detailed molecular analysis of the identified variant of the P2Y12 receptor (P2Y12R) was subsequently performed in mammalian cells overexpressing receptor constructs. Results All three referred individuals had markedly impaired ADP-induced platelet aggregation with primary wave only, despite normal total and surface P2Y12R expression. By NGS, a single P2RY12:c.G794C substitution (p.R265P) was identified in all affected individuals, and this was confirmed by Sanger sequencing. Mammalian cell experiments with the R265P-P2Y12R variant showed normal receptor surface expression versus wild-type (WT) P2Y12R. Agonist-stimulated R265P-P2Y12R function (both signaling and surface receptor loss) was reduced versus WT P2Y12R. Critically, R265P-P2Y12R acted in a dominant negative manner, with agonist-stimulated WT P2Y12R activity being reduced by variant coexpression, suggesting dramatic loss of WT homodimers. Importantly, platelet P2RY12 cDNA cloning and sequencing in two affected individuals also revealed three-fold mutant mRNA overexpression, decreasing even further the likelihood of WT homodimer formation. R265 located within extracellular loop 3 (EL3) is one of four residues that are important for receptor functional integrity, maintaining the binding pocket conformation and allowing rotation following ligand binding. Conclusion This novel dominant negative variant confirms the important role of R265 in EL3 in the functional integrity of P2Y12R, and suggests that pathologic heterodimer formation may underlie this family bleeding phenotype. © 2017 International Society on Thrombosis and Haemostasis.

49 CFR 655.44 - Post-accident testing.

Code of Federal Regulations, 2013 CFR

2013-10-01

... results may be used only when the employer is unable to perform a post-accident test within the required... 49 Transportation 7 2013-10-01 2013-10-01 false Post-accident testing. 655.44 Section 655.44... of Testing § 655.44 Post-accident testing. (a) Accidents. (1) Fatal accidents. (i) As soon as...

22 CFR 102.17 - Reports on accident.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 22 Foreign Relations 1 2010-04-01 2010-04-01 false Reports on accident. 102.17 Section 102.17... Accidents Abroad Foreign Aircraft Accidents Involving United States Persons Or Property § 102.17 Reports on accident. When an accident occurs to a foreign aircraft in the district of a Foreign Service post and...

22 CFR 102.17 - Reports on accident.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 22 Foreign Relations 1 2011-04-01 2011-04-01 false Reports on accident. 102.17 Section 102.17... Accidents Abroad Foreign Aircraft Accidents Involving United States Persons Or Property § 102.17 Reports on accident. When an accident occurs to a foreign aircraft in the district of a Foreign Service post and...

Efficient Identification of Murine M2 Macrophage Peptide Targeting Ligands by Phage Display and Next-Generation Sequencing.

PubMed

Liu, Gary W; Livesay, Brynn R; Kacherovsky, Nataly A; Cieslewicz, Maryelise; Lutz, Emi; Waalkes, Adam; Jensen, Michael C; Salipante, Stephen J; Pun, Suzie H

2015-08-19

Peptide ligands are used to increase the specificity of drug carriers to their target cells and to facilitate intracellular delivery. One method to identify such peptide ligands, phage display, enables high-throughput screening of peptide libraries for ligands binding to therapeutic targets of interest. However, conventional methods for identifying target binders in a library by Sanger sequencing are low-throughput, labor-intensive, and provide a limited perspective (<0.01%) of the complete sequence space. Moreover, the small sample space can be dominated by nonspecific, preferentially amplifying "parasitic sequences" and plastic-binding sequences, which may lead to the identification of false positives or exclude the identification of target-binding sequences. To overcome these challenges, we employed next-generation Illumina sequencing to couple high-throughput screening and high-throughput sequencing, enabling more comprehensive access to the phage display library sequence space. In this work, we define the hallmarks of binding sequences in next-generation sequencing data, and develop a method that identifies several target-binding phage clones for murine, alternatively activated M2 macrophages with a high (100%) success rate: sequences and binding motifs were reproducibly present across biological replicates; binding motifs were identified across multiple unique sequences; and an unselected, amplified library accurately filtered out parasitic sequences. In addition, we validate the Multiple Em for Motif Elicitation tool as an efficient and principled means of discovering binding sequences.

A-WINGS: an integrated genome database for Pleurocybella porrigens (Angel's wing oyster mushroom, Sugihiratake).

PubMed

Yamamoto, Naoki; Suzuki, Tomohiro; Kobayashi, Masaaki; Dohra, Hideo; Sasaki, Yohei; Hirai, Hirofumi; Yokoyama, Koji; Kawagishi, Hirokazu; Yano, Kentaro

2014-12-03

The angel's wing oyster mushroom (Pleurocybella porrigens, Sugihiratake) is a well-known delicacy. However, its potential risk in acute encephalopathy was recently revealed by a food poisoning incident. To disclose the genes underlying the accident and provide mechanistic insight, we seek to develop an information infrastructure containing omics data. In our previous work, we sequenced the genome and transcriptome using next-generation sequencing techniques. The next step in achieving our goal is to develop a web database to facilitate the efficient mining of large-scale omics data and identification of genes specifically expressed in the mushroom. This paper introduces a web database A-WINGS (http://bioinf.mind.meiji.ac.jp/a-wings/) that provides integrated genomic and transcriptomic information for the angel's wing oyster mushroom. The database contains structure and functional annotations of transcripts and gene expressions. Functional annotations contain information on homologous sequences from NCBI nr and UniProt, Gene Ontology, and KEGG Orthology. Digital gene expression profiles were derived from RNA sequencing (RNA-seq) analysis in the fruiting bodies and mycelia. The omics information stored in the database is freely accessible through interactive and graphical interfaces by search functions that include 'GO TREE VIEW' browsing, keyword searches, and BLAST searches. The A-WINGS database will accelerate omics studies on specific aspects of the angel's wing oyster mushroom and the family Tricholomataceae.

Containment Safety Of Super Phenix : Essai Mars

NASA Astrophysics Data System (ADS)

Falgayrettes, M. F.; Fiche, C.; Hamon, P.

1985-02-01

The protection of people and property must be assured by every situation around an industrial power plant. That is why the FRENCH Commissariat a l'Energie Atomique has defined the size of the confinement of Super Phenix to withstand the worst highly hypothetical accident. The study of the strength of the confinement has been carried out by two complementary means : - Calculation (Display poster # 491 188), - Experiment : reactor mock-up. The latter is presented in the film. The solution which have been adopted for the problems encountered are emphasied ; the work with high speed camera is presented. The film is illustrated with some fast movie sequences.

Source Term Experiments Project (STEP): Aerosol characterization system

NASA Astrophysics Data System (ADS)

Schlenger, B. J.; Dunn, P. F.

A series of four experiments is being conducted at Argonne National Laboratory's TREAT Reactor. They were designed to provide some of the necessary data regarding magnitude and release rates of fission products from degraded fuel pins, physical and chemical characteristics of released fission products, and aerosol formation and transport phenomena. These are in pile experiments, whereby the test fuel is heated by neutron induced fission and subsequent clad oxidation in steam environments that simulate as closely as practical predicted reactor accident conditions. The test sequences cover a range of pressure and fuel heatup rate, and include the effect of Aq/In/Cd control rod material.

Rough set approach for accident chains exploration.

PubMed

Wong, Jinn-Tsai; Chung, Yi-Shih

2007-05-01

This paper presents a novel non-parametric methodology--rough set theory--for accident occurrence exploration. The rough set theory allows researchers to analyze accidents in multiple dimensions and to model accident occurrence as factor chains. Factor chains are composed of driver characteristics, trip characteristics, driver behavior and environment factors that imply typical accident occurrence. A real-world database (2003 Taiwan single auto-vehicle accidents) is used as an example to demonstrate the proposed approach. The results show that although most accident patterns are unique, some accident patterns are significant and worth noting. Student drivers who are young and less experienced exhibit a relatively high possibility of being involved in off-road accidents on roads with a speed limit between 51 and 79 km/h under normal driving circumstances. Notably, for bump-into-facility accidents, wet surface is a distinctive environmental factor.

Road Traffic Accident Analysis of Ajmer City Using Remote Sensing and GIS Technology

NASA Astrophysics Data System (ADS)

Bhalla, P.; Tripathi, S.; Palria, S.

2014-12-01

With advancement in technology, new and sophisticated models of vehicle are available and their numbers are increasing day by day. A traffic accident has multi-facet characteristics associated with it. In India 93% of crashes occur due to Human induced factor (wholly or partly). For proper traffic accident analysis use of GIS technology has become an inevitable tool. The traditional accident database is a summary spreadsheet format using codes and mileposts to denote location, type and severity of accidents. Geo-referenced accident database is location-referenced. It incorporates a GIS graphical interface with the accident information to allow for query searches on various accident attributes. Ajmer city, headquarter of Ajmer district, Rajasthan has been selected as the study area. According to Police records, 1531 accidents occur during 2009-2013. Maximum accident occurs in 2009 and the maximum death in 2013. Cars, jeeps, auto, pickup and tempo are mostly responsible for accidents and that the occurrence of accidents is mostly concentrated between 4PM to 10PM. GIS has proved to be a good tool for analyzing multifaceted nature of accidents. While road safety is a critical issue, yet it is handled in an adhoc manner. This Study is a demonstration of application of GIS for developing an efficient database on road accidents taking Ajmer City as a study. If such type of database is developed for other cities, a proper analysis of accidents can be undertaken and suitable management strategies for traffic regulation can be successfully proposed.

[Sports accidents: 1963-1973 statistics].

PubMed

Fasler, S

1976-01-01

Every year, the Swiss Accident Insurance Administration is paying a considerable amount of money for sports accidents. From 1963 to 1973 the number of these accidents has increased more markedly than other types of accidents. Different tendencies can be observed in the different types of sports: skiing accidents have, after a long period of retrogression until 1973, shown a noticeable augmentation again. Football accidents and accidents in other types of sports have on the other hand increased year by year. Mountaineering and aquatic sports often result in fatal accidents. The numerous preventive measures in skiing accidents have obviously been successful. Not only the fractures have decreased, but also the average number of days where sickness benefit was paid. Next to the traffic accidents, the skiing accidents are the most expensive ones. The nature of the healing cost in sports accidents has changed during the period from 1967 to 1972, depending on the different types of sports. In particular, hospital costs have changed considerably. The number of medical consultations per accident has decreased. Payment of sickness benefit has followed the development of the salaries on the one hand and the modifications of the number of lost days on the other. Finally, the costs of the annuities show more or less the same tendency as the ones for sickness benefit. A very gross estimation on the economical losses through sports accidents in Switzerland makes us believe that the direct and indirect costs actually amount to more than one thousand millions of Swiss Francs per year.

[Minor and major work accidents in a Puglia business in the food sector: a 10-year study].

PubMed

Di Lorenzo, L; Zocchetti, C; Platania, A; De Francesco, G; De Metrio, R; Pirris, A; Gigante, M R

1998-01-01

At present no official data are available for those occupational accidents which, according to current law, are not subject to notification to the Italian National Institute for Insurance of Occupational Accidents (INAIL) and which are conventionally called "minor" accidents. They can be divided into accidents with prognosis from 1 to 3 days (franchises) and accidents which do not cause absence from work (medications). The already mentioned lack of data, which is not confined to Italy, is reflected in the small number of articles published in Italian and international journals. Also information regarding the possible relationships between "minor" accidents and the life habits of injured workers, are rare. The aim of this study was to provide detailed data on the characteristics of the different kinds of occupational accidents occurring in a food factory in Apulia, southern Italy, from 1985 to 1994, as well as to verify whether any relationship existed between the different types of occupational accidents and the consumption of cigarettes and alcohol by injured workers. The company's accident register yielded data on injuries which caused absence from work; the nursing service register provided information about accidents which did not determine absence from work; personal health documents gave details of worker life habits; and the company pay roll showed the amount of "worked hours". "Minor" accidents represented 70% of all accidents occurring during the ten year period studied. "Blue collars" had more frequent and serious occupational injuries, in comparison with "technical employees". "Minor" accidents, and especially "medications", occurred more frequently during one-shift work than during three-shift work. As work seniority increased, the number of "major" accidents decreased and number of accidents without absence from work rose. Contusions were the most frequent lesions and were responsible for the majority of the 3 kinds of accidents. "Medications" together with injuries notified to INAIL ("major" accidents), mostly involved upper limbs; "franchises" were mostly head interested. About 50% of all causes of occupational accidents were mainly associated with unsafe environmental and working situations, whereas the remaining 50% were mainly associated with unsafe behaviour by workers. Heavy smokers showed a higher frequency of "major" accidents. As alcohol consumption rose, she did number of accidents with absence from work. "Minor" accidents, particularly the "medicated" ones, represented the greatest part of occupational injuries. All the considered causes and circumstances contributed to determine the different kinds of accidents. Thereby, it appears necessary for prevention purposes to obtain information about any kind of injury in the different manufacturing sectors. Finally, it seems dutiful to inform workers about the relationships between life habits and occupational accidents.

Prediction accident triangle in maintenance of underground mine facilities using Poisson distribution analysis

NASA Astrophysics Data System (ADS)

Khuluqi, M. H.; Prapdito, R. R.; Sambodo, F. P.

2018-04-01

In Indonesia, mining is categorized as a hazardous industry. In recent years, a dramatic increase of mining equipment and technological complexities had resulted in higher maintenance expectations that accompanied by the changes in the working conditions, especially on safety. Ensuring safety during the process of conducting maintenance works in underground mine is important as an integral part of accident prevention programs. Accident triangle has provided a support to safety practitioner to draw a road map in preventing accidents. Poisson distribution is appropriate for the analysis of accidents at a specific site in a given time period. Based on the analysis of accident statistics in the underground mine maintenance of PT. Freeport Indonesia from 2011 through 2016, it is found that 12 minor accidents for 1 major accident and 66 equipment damages for 1 major accident as a new value of accident triangle. The result can be used for the future need for improving the accident prevention programs.

[Accidents in travellers - the hidden epidemic].

PubMed

Walz, Alexander; Hatz, Christoph

2013-06-01

The risk of malaria and other communicable diseases is well addressed in pre-travel advice. Accidents are usually less discussed. Thus, we aimed at assessing accident figures for the Swiss population, based on data of the register from 2004 to 2008 of the largest Swiss accident insurance organization (SUVA). More than 139'000 accidents over 5 years showed that 65 % of the accidents overseas are injuries, and 24 % are caused by poisoning or harm by cold, heat or air pressure. Most accidents happened during leisure activities or sports. More than one third of the non-lethal and more than 50 % of the fatal accidents happened in Asia. More than three-quarters of non-lethal accidents take place in people between 25 and 54 years. One out of 74 insured persons has an accident abroad per year. Despite of many analysis short-comings of the data set with regard to overseas travel, the figures document the underestimated burden of disease caused by accidents abroad and should affect the given pre-health advice.

A study on industrial accident rate forecasting and program development of estimated zero accident time in Korea.

PubMed

Kim, Tae-gu; Kang, Young-sig; Lee, Hyung-won

2011-01-01

To begin a zero accident campaign for industry, the first thing is to estimate the industrial accident rate and the zero accident time systematically. This paper considers the social and technical change of the business environment after beginning the zero accident campaign through quantitative time series analysis methods. These methods include sum of squared errors (SSE), regression analysis method (RAM), exponential smoothing method (ESM), double exponential smoothing method (DESM), auto-regressive integrated moving average (ARIMA) model, and the proposed analytic function method (AFM). The program is developed to estimate the accident rate, zero accident time and achievement probability of an efficient industrial environment. In this paper, MFC (Microsoft Foundation Class) software of Visual Studio 2008 was used to develop a zero accident program. The results of this paper will provide major information for industrial accident prevention and be an important part of stimulating the zero accident campaign within all industrial environments.

Emotional stress and traffic accidents: the impact of separation and divorce.

PubMed

Lagarde, Emmanuel; Chastang, Jean-François; Gueguen, Alice; Coeuret-Pellicer, Mireille; Chiron, Mireille; Lafont, Sylviane

2004-11-01

Personal responses to stressful life events are suspected of increasing the risk of serious traffic accidents. We analyzed data from a French cohort study (the GAZEL cohort), including a retrospective driving behavior questionnaire, from 13,915 participants (10,542 men age 52-62 years and 3373 women age 47-62 years in 2001). Follow-up data covered 1993-2000. Hazard ratios for serious accidents (n = 713) were computed by Cox's proportional hazard regression with time-dependent covariates. Separate analyses were also performed to consider only at-fault accidents. Marital separation or divorce was associated with an increased risk of a serious accident (all serious accidents: hazard ratio 2.9, 95% confidence interval = 1.7-5.0; at-fault accidents: 4.4, 2.3-8.3). The impact of separation and divorce did not differ according to alcohol consumption levels. Other life events associated with increased risk of serious accident were a child leaving home (all accidents: 1.2, 0.97-1.6; at-fault accidents: 1.5, 1.1-2.1), an important purchase (all accidents: 1.4, 1.1-1.7; at-fault accidents: 1.6, 1.2-2.1), and hospitalization of the partner (all accidents: 1.4, 1.1-2.0). This study suggests that recent separation and divorce are associated with an increase in serious traffic accidents.

Sequence Data for Clostridium autoethanogenum using Three Generations of Sequencing Technologies

DOE PAGES

Utturkar, Sagar M.; Klingeman, Dawn Marie; Bruno-Barcena, José M.; ...

2015-04-14

During the past decade, DNA sequencing output has been mostly dominated by the second generation sequencing platforms which are characterized by low cost, high throughput and shorter read lengths for example, Illumina. The emergence and development of so called third generation sequencing platforms such as PacBio has permitted exceptionally long reads (over 20 kb) to be generated. Due to read length increases, algorithm improvements and hybrid assembly approaches, the concept of one chromosome, one contig and automated finishing of microbial genomes is now a realistic and achievable task for many microbial laboratories. In this paper, we describe high quality sequencemore » datasets which span three generations of sequencing technologies, containing six types of data from four NGS platforms and originating from a single microorganism, Clostridium autoethanogenum. The dataset reported here will be useful for the scientific community to evaluate upcoming NGS platforms, enabling comparison of existing and novel bioinformatics approaches and will encourage interest in the development of innovative experimental and computational methods for NGS data.« less

An Assessment of the Suitability of Cone Penetration Testing in Identifying the Late Quaternary Successions Formed in Tide-dominated Tnvironments: A Case Study from the Eastern China Coastal Plain

NASA Astrophysics Data System (ADS)

Zhang, X.; Lin, C. M., Sr.; Dalrymple, R. W.; Gao, S., Sr.

2017-12-01

Cone penetration testing (CPT) has proved to be as an effective method for sedimentological purposes in wave-dominated coastal environments. This study, based upon interpretation of 500 CPTs, carried out in the late Quaternary Qiantang River incised-valley fill over the eastern China coastal plain, shows how CPTs can also be used for detailed facies characterization and identification of the key surfaces for sequence-stratigraphic interpretation in tide-dominated systems based upon estimation of three major parameters: cone-tip resistance (qc), sleeve friction (fs), and the ratio of fs and qc (FR). Plotting of qc versus FR, in combination with the CPT curve shape and the relative depth in profile, is adopted as the major tool. The lithologic character which is controlled mainly by sediment supply and dynamics, and post-depositional diagenesis is respected as the main factor affecting how well the CPT technique works. Within this particular tide-dominated environment, dominated by non-cohesive sand and silt, the accumulation of the materials from fluid muds is rare. As a result, the tidal-channel deposits exhibit the nature of coarse-grained deposits, different from that of the other mud-dominated facies associations. On the other hand, a distinct layer of fine-grained deposit at the base of the Holocene sequences was subjected to early diagenesis during the last glacial maximum and early transgression, to become uniformly hard and over-consolidated, geotechnically distinct from the overlying softer sediments. Besides, due to the different sediment dynamics, the tidal-flat and salt-marsh deposits exhibit a distinct geotechnical behavior with the offshore shallow marine muddy deposits. All the above mentioned situations provide the basis for the recognition of facies association and the correlated key surfaces, even for the mapping of the incised-valley boundary. As a consequence, the CPT method has a potential to be a very attractive alternative to economically less convenient methods for the geological mapping in the tide-dominated coastal plain areas.

Agonal sequences in 14 filmed hangings with comments on the role of the type of suspension, ischemic habituation, and ethanol intoxication on the timing of agonal responses.

PubMed

Sauvageau, Anny; Laharpe, Romano; King, David; Dowling, Graeme; Andrews, Sam; Kelly, Sean; Ambrosi, Corinne; Guay, Jean-Pierre; Geberth, Vernon J

2011-06-01

The Working Group on Human Asphyxia has analyzed 14 filmed hangings: 9 autoerotic accidents, 4 suicides, and 1 homicide. The following sequence of agonal responses was observed: rapid loss of consciousness in 10 ± 3 seconds, mild generalized convulsions in 14 ± 3 seconds, decerebrate rigidity in 19 ± 5 seconds, beginning of deep rhythmic abdominal respiratory movements in 19 ± 5 seconds, decorticate rigidity in 38 ± 15 seconds, loss of muscle tone in 1 minute 17 seconds ± 25 seconds, end of deep abdominal respiratory movements in 1 minute 51 seconds ± 30 seconds, and last muscle movement in 4 minutes 12 seconds ± 2 minutes 29 seconds. The type of suspension and ethanol intoxication does not seem to influence the timing of the agonal responses, whereas ischemic habituation in autoerotic practitioner might decelerate the late responses to hanging.

Loss-of-heterozygosity facilitates passage through Haldane's sieve for Saccharomyces cerevisiae undergoing adaptation.

PubMed

Gerstein, A C; Kuzmin, A; Otto, S P

2014-05-07

Haldane's sieve posits that the majority of beneficial mutations that contribute to adaptation should be dominant, as these are the mutations most likely to establish and spread when rare. It has been argued, however, that if the dominance of mutations in their current and previous environments are correlated, Haldane's sieve could be eliminated. We constructed heterozygous lines of Saccharomyces cerevisiae containing single adaptive mutations obtained during exposure to the fungicide nystatin. Here we show that no clear dominance relationship exists across environments: mutations exhibited a range of dominance levels in a rich medium, yet were exclusively recessive under nystatin stress. Surprisingly, heterozygous replicates exhibited variable-onset rapid growth when exposed to nystatin. Targeted Sanger sequencing demonstrated that loss-of-heterozygosity (LOH) accounted for these growth patterns. Our experiments demonstrate that recessive beneficial mutations can avoid Haldane's sieve in clonal organisms through rapid LOH and thus contribute to rapid evolutionary adaptation.

The relationship between shellbed type and sequence architecture: examples from Japan and New Zealand

NASA Astrophysics Data System (ADS)

Kondo, Yasuo; Abbott, Stephen T.; Kitamura, Akihisa; Kamp, Peter J. J.; Naish, Tim R.; Kamataki, Takanobu; Saul, Gordon S.

1998-12-01

Examples of lithology, fossil content and taphonomic features of shellbeds and intervening less fossiliferous intervals are presented from four Plio-Pleistocene successions (Shimosa Group, Boso Peninsula, Omma Formation, Hokuriku area, Japan, and Okehu, Kai-iwi, and Shakespeare groups in Wanganui, and the Rangitikei Group along the Rangitikei River in New Zealand). As for pre-Pliocene 3rd- and 4th-order depositional sequences, Plio-Pleistocene 5th- to 7th-order depositional sequences contain a variety of shellbeds which are often associated with surfaces or intervals that are characterized by sedimentary condensation, omission or erosion (e.g. sequence boundaries, ravinement surfaces, downlap surfaces and condensed sections). Stratigraphic patterns of shellbed type tend to be similar and repetitive within a basin and a locality. This demonstrates that a specific palaeogeography played an important role in determining the nature of shellbeds. For example, shellbeds formed in the context of toplap are common only in the Shimosa Group, which was deposited in a moderately sheltered sea, the palaeo-Tokyo Bay. Toplap shellbeds are rare in other sequences formed in more open conditions. Despite the variability resulting from such basin characteristics, common styles of shellbeds can be recognized that formed under conditions of marine onlap, backlap, downlap and toplap. Each type of shellbed has a characteristic fossil composition and taphonomy. Onlap and toplap shellbeds contain low-diversity macrobenthic associations including Glycymeris, Mercenaria, Paphies or other bivalves having robust shells, which are often abraded or fragmented. Backlap shellbeds, which are equivalent to the condensed section formed at the maximum transgression, are characterized by dominance of epifaunal macrobenthos such as bryozoa, brachiopoda, pectinid and ostreid bivalves, preserved in a slightly cemented, glauconitic muddy matrix. In contrast to fossils in such condensed sections, the shell density and species diversity of downlap shellbed associations are rather low, and in a few examples the macrobenthic association was buried rapidly in a lower unit of the highstand systems tract (HST) stratigraphically located above the condensed sections. Variations in the stratigraphic distribution of shellbed types are reflected in symmetrical and asymmetrical sequence architectures. Symmetrical sequences have roughly the same thickness of transgressive systems tracts (TST) and highstand systems tracts (HST), and have well segregated shellbeds that were formed during marine onlap and backlap. Asymmetrical cycles have very thin TSTs and much thicker HSTs, and are characterized by the amalgamation of condensed onlap and backlap shellbeds. Such contrasting cycle architectures are interpreted to reflect inner (symmetrical) and outer (asymmetrical) shelf palaeodepositional settings. The amalgamated onlap/backlap shellbeds appear to be common in Plio-Pleistocene sequences. Owing to the short duration of glacio-eustatic sea-level changes with dominant frequencies of 20,000, 40,000 or 100,000 years, shellbeds in the Plio-Pleistocene are relatively simple and thin compared to those formed in ordinary third-order depositional sequences. Infauna-dominated benthic associations are generally more common than in third-order cycles, and epifaunal associations facilitated by taphonomic feedback on sediment-starved shell-gravel substrates occur only in the condensed section corresponding to maximum transgression in most Plio-Pleistocene sequences.

Characteristics of worker accidents on NYSDOT construction projects.

PubMed

Mohan, Satish; Zech, Wesley C

2005-01-01

This paper aims at providing cost-effective safety measures to protect construction workers in highway work zones, based on real data. Two types of accidents that occur in work zones were: (a) construction work area accidents, and (b) traffic accidents involving construction worker(s). A detailed analysis of work zone accidents involving 36 fatalities and 3,055 severe injuries to construction workers on New York State Department of Transportation (NYSDOT) construction projects from 1990 to 2001 established that five accident types: (a) Struck/Pinned by Large Equipment, (b) Trip or Fall (elevated), (c) Contact w/Electrical or Gas Utility, (d) Struck-by Moving/Falling Load, and (e) Crane/Lift Device Failure accounted for nearly 96% of the fatal accidents, nearly 63% of the hospital-level injury accidents, and nearly 91% of the total costs. These construction work area accidents had a total cost of $133.8 million. Traffic accidents that involve contractors' employees were also examined. Statistical analyses of the traffic accidents established that five traffic accident types: (a) Work Space Intrusion, (b) Worker Struck-by Vehicle Inside Work Space, (c) Flagger Struck-by Vehicle, (d) Worker Struck-by Vehicle Entering/Exiting Work Space, and (e) Construction Equipment Struck-by Vehicle Inside Work Space accounted for nearly 86% of the fatal, nearly 70% of the hospital-level injury and minor injury traffic accidents, and $45.4 million (79.4%) of the total traffic accident costs. The results of this paper provide real statistics on construction worker related accidents reported on construction work zones. Potential preventions based on real statistics have also been suggested. The ranking of accident types, both within the work area as well as in traffic, will guide the heavy highway contractor and owner agencies in identifying the most cost effective safety preventions.

Insomnia and accidents: cross-sectional study (EQUINOX) on sleep-related home, work and car accidents in 5293 subjects with insomnia from 10 countries.

PubMed

Léger, Damien; Bayon, Virginie; Ohayon, Maurice M; Philip, Pierre; Ement, Philippe; Metlaine, Arnaud; Chennaoui, Mounir; Faraut, Brice

2014-04-01

The link between sleepiness and the risk of motor vehicle accidents is well known, but little is understood regarding the risk of home, work and car accidents of subjects with insomnia. An international cross-sectional survey was conducted across 10 countries in a population of subjects with sleep disturbances. Primary care physicians administered a questionnaire that included assessment of sociodemographic characteristics, sleep disturbance and accidents (motor vehicle, work and home) related to sleep problems to each subject. Insomnia was defined using the International Classification of Sleep Disorders (ICSD-10) criteria. A total of 5293 subjects were included in the study, of whom 20.9% reported having had at least one home accident within the past 12 months, 10.1% at least one work accident, 9% reported having fallen asleep while driving at least once and 4.1% reported having had at least one car accident related to their sleepiness. All types of accident were reported more commonly by subjects living in urban compared to other residential areas. Car accidents were reported more commonly by employed subjects, whereas home injuries were reported more frequently by the unemployed. Car accidents were reported more frequently by males than by females, whereas home accidents were reported more commonly by females. Patients with insomnia have high rates of home accidents, car accidents and work accidents related to sleep disturbances independently of any adverse effects of hypnotic treatments. Reduced total sleep time may be one factor explaining the high risk of accidents in individuals who complain of insomnia. © 2013 European Sleep Research Society.

World commercial aircraft accidents: 1st edition, 1946--1991

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

Kimura, C.Y.

1992-02-01

This report is a compilation of all accidents world-wide involving aircraft in commercial service which resulted in the loss of the airframe or one or more fatality, or both. This information has been gathered in order to present a complete inventory of commercial aircraft accidents. Events involving military action, sabotage, terrorist bombings, hijackings, suicides, and industrial ground accidents are included within this list. This report is organized into six chapters. The first chapter is the introduction. The second chapter contains the compilation of accidents involving world commercial jet aircraft from 1952 to 1991. The third chapter presents a compilation ofmore » accidents involving world commercial turboprop aircraft from 1952 to 1991. The fourth chapter presents a compilation of accidents involving world commercial pistonprop aircraft with four or more engines from 1946 to 1991. Each accident compilation or database in chapters two, three and four is presented in chronological order. Each accident is presented with information the following categories: date of accident, airline or operator and its flight number (if known), type of flight, type of aircraft and model, aircraft registration number, construction number/manufacturers serial number, aircraft damage resulting from accident, accident flight phase, accident location, number of fatalities, number of occupants, references used to compile the information, and finally cause, remarks, or description (brief) of the accident. The fifth chapter presents a list of all commercial aircraft accidents for all aircraft types with 100 or more fatalities in order of decreasing number of fatalities. Chapter six presents the commercial aircraft accidents for all aircraft types by flight phase. Future editions of this report will have additional follow-on chapters which will present other studies still in preparation at the time this edition was being prepared.« less

Resolution of aviation forensic toxicology findings with the aid of DNA profiling.

PubMed

Chaturvedi, Arvind K; Craft, Kristi J; Kupfer, Doris M; Burian, Dennis; Canfield, Dennis V

2011-03-20

Body components of aviation accident fatalities are often scattered, disintegrated, commingled, contaminated, and/or putrefied at accident scenes. These situations may impose difficulties in victim identification/tissue matching. The prevalence of misidentification in relation to aviation accident forensic toxicology has not been well established. Therefore, the Civil Aerospace Medical Institute (CAMI) toxicology database was searched for the 1998-2008 period for those cases wherein DNA profiling was performed to resolve identity issue of the samples submitted to CAMI for toxicological evaluation. During this period, biological samples from the casualties of a total of 3523 accidents were submitted to CAMI. The submitted samples were primarily from pilots. Out of the 3523 accidents, at least, one fatality had occurred in 3366 (≈ 96%) accidents; thus, these accidents were considered fatal accidents. Accordingly, biological samples from 3319 pilots (3319 of the 3366 accidents) were received at CAMI for toxicological testing. Of these 3319 pilots, 3275 (≈ 99%) were fatally injured. DNA profiling was performed in 15 (≈ 0.5%) of the 3319 accidents. The profiling was conducted upon the requests of families in two accidents, accident investigators in three, and pathologists in four. In six accidents, contradictory toxicological findings led CAMI to initiate DNA profiling. The requests made by families and investigators were primarily triggered by inconsistency between the toxicological results and the history of drug use of the victims, while by pathologists because of commingling of samples. In three (20%) of the 15 accidents, at least one submitted sample was misidentified or mislabeled. The present study demonstrated that the number of aviation accident cases requiring DNA profiling was small and this DNA approach was effectively applied in resolving aviation toxicology findings associated with those accidents. Published by Elsevier Ireland Ltd.

NASA Medical Response to Human Spacecraft Accidents

NASA Technical Reports Server (NTRS)

Patlach, Robert

2010-01-01

Manned space flight is risky business. Accidents have occurred and may occur in the future. NASA's manned space flight programs, with all their successes, have had three fatal accidents, one at the launch pad and two in flight. The Apollo fire and the Challenger and Columbia accidents resulted in a loss of seventeen crewmembers. Russia's manned space flight programs have had three fatal accidents, one ground-based and two in flight. These accidents resulted in the loss of five crewmembers. Additionally, manned spacecraft have encountered numerous close calls with potential for disaster. The NASA Johnson Space Center Flight Safety Office has documented more than 70 spacecraft incidents, many of which could have become serious accidents. At the Johnson Space Center (JSC), medical contingency personnel are assigned to a Mishap Investigation Team. The team deploys to the accident site to gather and preserve evidence for the Accident Investigation Board. The JSC Medical Operations Branch has developed a flight surgeon accident response training class to capture the lessons learned from the Columbia accident. This presentation will address the NASA Mishap Investigation Team's medical objectives, planned response, and potential issues that could arise subsequent to a manned spacecraft accident. Educational Objectives are to understand the medical objectives and issues confronting the Mishap Investigation Team medical personnel subsequent to a human space flight accident.

Work-Related Accidents and Sharp Injuries in Paramedics-Illustrated with an Example of a Multi-Specialist Hospital, Located in Central Poland.

PubMed

Garus-Pakowska, Anna; Szatko, Franciszek; Ulrichs, Magdalena

2017-08-10

(1) Background: An analysis of work-related accidents in paramedics in Poland by presenting the model and trend of accidents, accident rates and by identifying causes and results of accidents; (2) Methods: A retrospective analysis of medical documentation regarding work-related accidents in a multi-specialist hospital, located in central Poland, in the period 2005-2015. The study group included paramedics who had an accident while being on duty; (3) Results: According to hospital records, 88 paramedics were involved in 390 accidents and 265 injuries caused by sharp instruments. The annual accident rate was 5.34/100 employed paramedics. Most of the accidents occurred at night. The most common reason for the accident was careless behaviour of the paramedic, which resulted in joint sprains and dislocations. Injuries accounted for a huge portion of the total number of events. As many as 45% of injuries were not officially recorded; (4) Conclusion: High rates of work-related accidents and injuries caused by sharp instruments in paramedics are a serious public health problem. Further studies should be conducted in order to identify risk factors of accidents, particularly injuries, and to implement preventative programmes, aiming to minimise rates of occupational hazards for paramedics.